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      Volume 36, Issue 1

      March 2011,   pages  1-200

    • Editorial: Coincidences: A tale of two genes, ami-1 and upr-1

      Durgadas P Kasbekar

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    • Clipboard: New paradigm for ATP synthesis and consumption

      C Channakeshava

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    • Commentary: Tone up your chromatin and stay young

      Navneet K Matharu Rakesh K Mishra

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    • Commentary: Michurin's legacy to biological science

      Yongsheng Liu Guangyin Wang Xiuju Li

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    • The charms of sex chromosomes in snakes

      Lalji Singh

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    • What history tells us XXIII. The genetic distance between humans and chimpanzees: What did Mary-Claire King and Allan Wilson really say in 1975?

      Michel Morange

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    • Lactam nonanic acid, a new substance from Cleome viscosa with allelopathic and antimicrobial properties

      Anirban Jana Suparna Mandal Biswas

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      Cleome viscosa L. (Capparidaceae) is well known for its medicinal properties. Lactam nonanoic acid (LNA) [2-amino-9-(4-oxoazetidin-2-yl)-nonanoic acid; C12H22N2O3, mol. wt. 242] has been isolated and purified from the root exudates of Cleome viscosa. The aqueous solution of this pure compound has been tested on bacteria (Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus) and fungi (Aspergillus fumigatus, A. niger and A. tamarii). At a dosage of 500 ppm and above, P. aeruginosa and S. aureus were totally inhibited while E. coli remained unaffected. On the other hand, growth of A. niger and A. tamarii was stimulated while there was no effect on A. fumigatus. This pure compound showed concentration-dependent inhibitory activity on rice, gram and mustard seeds.

    • Heat-inducible Cre-lox system for marker excision in transgenic rice

      Abhilasha Khattri Soumen Nandy Vibha Srivastava

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      The present study assessed the efficacy of a heat-inducible cre gene for conditional removal of the marker gene from a rice genome via Cre-lox recombination. A cre gene controlled by the soybean heat-shock promoter was introduced into the rice genome along with the recombination target (lox) construct. Cre-mediated recombination was expected to remove the marker gene and activate the promoter-less GUS gene. Six transgenic lines displayed well-regulated heat-inducible Cre activity in the callus. However, only one line that contained a single copy of the cre gene maintained this property in the regenerated plants and their progeny. Marker-free progeny were obtained from the plant that was heat-treated at the seedling stage, indicating the inheritance of the recombination `footprint’. The presence of the `footprint’ was verified by polymerase chain reaction and Southern analysis. Therefore, the cre gene controlled by the soybean heat-shock promoter is an effective tool for conditional removal of the marker gene in rice.

    • Effects of substitutions at position 180 in the Escherichia coli RNA polymerase 𝛼70 subunit

      Olga N Koroleva Stephen Jw Busby Valeriy L Drutsa

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      In order to investigate the role of His180 residue, located in the non-conserved region of the 𝜎70 subunit of Escherichia coli RNA polymerase, two mutant variants of the protein with substitutions for either alanine or glutamic acid were constructed and purified using the IMPACT system. The ability of mutant 𝜎70 subunits to interact with core RNA polymerase was investigated using native gel-electrophoresis. The properties of the corresponding reconstituted holoenzymes, as provided by gel shift analysis of their complexes with single- and double-stranded promoter-like DNA and by in vitro transcription experiments, allowed one to deduce that His180 influences several steps of transcription initiation, including core binding, promoter DNA recognition and open complex formation.

    • Antipathogenic potential of marine Bacillus sp. SS4 on N-acyl-homoserine-lactone-mediated virulence factors production in Pseudomonas aeruginosa (PAO1)

      K Syed Musthafa V Saroja S Karutha Pandian A Veera Ravi

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      Antipathogenic therapy is an outcome of the quorum-sensing inhibition (QSI) mechanism, which targets autoinducer-dependent virulent gene expression in bacterial pathogens. 𝑁-acyl homoserine lactone (AHL) acts as a key regulator in the production of virulence factors and biofilm formation in Pseudomonas aeruginosa PAO1 and violacein pigment production in Chromobacterium violaceum. In the present study, the marine bacterial strain SS4 showed potential QSI activity in a concentration-dependent manner (0.5–2 mg/ml) against the AHL-mediated violacein production in C. violaceum (33–86%) and biofilm formation (33–88%), total protease (20–65%), LasA protease (59–68%), LasB elastase (36–68%), pyocyanin (17–86%) and pyoverdin productions in PAO1. The light and confocal laser scanning microscopic analyses confirmed the reduction of the biofilm-forming ability of PAO1 when treated with SS4 extract. Furthermore, the antibiofilm potential was confirmed through static biofilm ring assay, in which ethyl acetate extract of SS4 showed concentration-dependent reduction in the biofilm-forming ability of PAO1. Thus, the result of this study clearly reveals the antipathogenic and antibiofilm properties of the bacterial isolate SS4. Through 16S rDNA analysis, the strain SS4 was identified as Bacillus sp. (GenBank Accession Number: GU471751).

    • Is endothelial-nitric-oxide-synthase-derived nitric oxide involved in cardiac hypoxia/reoxygenation-related damage?

      A Rus Ma Peinado S Blanco Ml Del Moral

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      Nitric oxide (NO) has been reported to act both as a destructive and a protective agent in the pathogenesis of the injuries that occur during hypoxia/reoxygenation (H/R). It has been suggested that this dual role of NO depends directly on the isoform of NO synthase (NOS) involved. In this work, we investigate the role that NO derived from endothelial NOS (eNOS) plays in cardiac H/R-induced injury.Wistar rats were submitted to H/R (hypoxia for 30 min; reoxygenation of 0 h, 12 h and 5 days), with or without prior treatment using the selective eNOS inhibitor L-NIO (20 mg/kg). Lipid peroxidation, apoptosis and protein nitration, as well as NO production (NOx), were analysed. The results showed that L-NIO administration lowered NOx levels in all the experimental groups. However, no change was found in the lipid peroxidation level, the percentage of apoptotic cells or nitrated protein expression, implying that eNOS-derived NO may not be involved in the injuries occurring during H/R in the heart. We conclude that L-NIO would not be useful in alleviating the adverse effects of cardiac H/R.

    • Requirements of Slm proteins for proper eisosome organization, endocytic trafficking and recycling in the yeast Saccharomyces cerevisiae

      Chitra Kamble Sandhya Jain Erin Murphy Kyoungtae Kim

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      Eisosomes are large immobile assemblies at the cortex of a cell under the membrane compartment of Can1 (MCC) in yeast. Slm1 has recently been identified as an MCC component that acts downstream of Mss4 in a pathway that regulates actin cytoskeleton organization in response to stress. In this study, we showed that inactivation of Slm proteins disrupts proper localization of the primary eisosome marker Pil1, providing evidence that Slm proteins play a role in eisosome organization. Furthermore, we found that slmts mutant cells exhibit actin defects in both the ability to polarize cortical F-actin and the formation of cytoplasmic actin cables even at the permissive temperature (30°C). We further demonstrated that the actin defect accounts for the slow traffic of FM4-64-labelled endosome in the cytoplasm, supporting the notion that intact actin is essential for endosome trafficking. However, our real-time microscopic analysis of Abp1-RFP revealed that the actin defect in slmts cells was not accompanied by a noticeable defect in actin patch internalization during receptor-mediated endocytosis. In addition, we found that slmts cells displayed impaired membrane recycling and that recycling occurred in an actin-independent manner. Our data provide evidence for the requirement of Slm proteins in eisosome organization and endosome trafficking and recycling.

    • In vivo NMR study of yeast fermentative metabolism in the presence of ferric irons

      Maso Ricci Silvia Martini Claudia Bonechi Daniela Braconi Annalisa Santucci Claudio Rossi

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      Mathematical modelling analysis of experimental data, obtained with in vivo NMR spectroscopy and 13C-labelled substrates, allowed us to describe how the fermentative metabolism in Saccharomyces cerevisiae, taken as eukaryotic cell model, is influenced by stress factors. Experiments on cellular cultures subject to increasing concentrations of ferric ions were conducted in order to study the effect of oxidative stress on the dynamics of the fermentative process. The developed mathematical model was able to simulate the cellular activity, the metabolic yield and the main metabolic fluxes occurring during fermentation and to describe how these are modulated by the presence of ferric ions.

    • Processing of abasic DNA clusters in hApeI-silenced primary fibroblasts exposed to low doses of X-irradiation

      Prolay Das Paula Bennett Betsy M Sutherland

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      Clustered damage in DNA includes two or more closely spaced oxidized bases, strand breaks or abasic sites that are induced by high- or low-linear-energy-transfer (LET) radiation, and these have been found to be repair-resistant and potentially mutagenic. In the present study we found that abasic clustered damages are also induced in primary human fibroblast cells by low-LET X-rays even at very low doses. In response to the induction of the abasic sites, primary fibroblasts irradiated by low doses of X-rays in the range 10–100 cGy showed dose-dependent up-regulation of the DNA repair enzyme, ApeI. We found that the abasic clusters in primary fibroblasts were more lethal to cells when hApeI enzyme expression was down-regulated by transfecting primary fibroblasts with hApeI siRNA as determined by clonogenic survival assay. Endonuclease activity of hApeI was found to be directly proportional to hApeI gene-silencing efficiency. The DNA repair profile showed that processing of abasic clusters was delayed in hApeI-siRNA-silenced fibroblasts, which challenges the survival of the cells even at very low doses of X-rays. Thus, the present study is the first to attempt to understand the induction of cluster DNA damage at very low doses of low-LET radiation in primary human fibroblasts and their processing by DNA repair enzyme ApeI and their relation with the survival of the cells.

    • Efficiency of wear and decalcification technique for estimating the age of estuarine dolphin Sotalia guianensis

      Nicolle V Sydney Emygdio La Monteiro-Filho

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      Most techniques used for estimating the age of Sotalia guianensis (van Bénéden, 1864) (Cetacea; Delphinidae) are very expensive, and require sophisticated equipment for preparing histological sections of teeth. The objective of this study was to test a more affordable and much simpler method, involving of the manual wear of teeth followed by decalcification and observation under a stereomicroscope. This technique has been employed successfully with larger species of Odontoceti. Twenty-six specimens were selected, and one tooth of each specimen was worn and demineralized for growth layers reading. Growth layers were evidenced in all specimens; however, in 4 of the 26 teeth, not all the layers could be clearly observed. In these teeth, there was a significant decrease of growth layer group thickness, thus hindering the layers count. The juxtaposition of layers hindered the reading of larger numbers of layers by the wear and decalcification technique. Analysis of more than 17 layers in a single tooth proved inconclusive. The method applied here proved to be efficient in estimating the age of Sotalia guianensis individuals younger than 18 years. This method could simplify the study of the age structure of the overall population, and allows the use of the more expensive methodologies to be confined to more specific studies of older specimens. It also enables the classification of the calf, young and adult classes, which is important for general population studies.

    • HrpNEa -induced deterrent effect on phloem feeding of the green peach aphid Myzus persicae requires AtGSL5 and AtMYB44 genes in Arabidopsis thaliana

      Beibei Lü Weiwei Sun Shuping Zhang Chunling Zhang Jun Qian Xiaomeng Wang Rong Gao Hansong Dong

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      In Arabidopsis thaliana (Arabidopsis) treated with the harpin protein HrpNEa, resistance to the green peach aphid Myzus persicae, a generalist phloem-feeding insect, develops with induced expression of the AtMYB44 gene. Special GLUCAN SYNTHESIS-LIKE (GSL) genes and 𝛽-1,3-glucan callose play an important role in plant defence responses to attacks by phloem-feeding insects. Here we report that AtGLS5 and AtMYB44 are both required for HrpNEa-induced repression of M. persicae feeding from the phloem of Arabidopsis leaves. In 24 h successive surveys on large-scale aphid populations, the proportion of feeding aphids was much smaller in HrpNEa-treated plants than in control plants, and aphids preferred to feed from the 37 tested atgsl mutants rather than the wild-type plant. The atgsl mutants were generated previously by mutagenesis in 12 identified AtGSL genes (AtGSL1 through AtGSL12); in the 24 h survey, both atgsl5 and atgsl6 tolerated aphid feeding, and atgsl5 was the most tolerant. Consistently, atgsl5 was also most inhibitive to the deterrent effect of HrpNEa on the phloem-feeding activity of aphids as monitored by the electrical penetration graph technique. These results suggested an important role of the AtGSL5 gene in the effect of HrpNEa. In response to HrpNEa, AtGSL5 expression and callose deposition were induced in the wild-type plant but not in atgsl5. In response to HrpNEa, moreover, the AtMYB44 gene known to be required for repression of aphid reproduction on the plant was also required for repression of the phloem-feeding activity. Small amounts of the AtGSL5 transcript and callose deposition were detected in the atmyb44 mutant, as in atgsl5. Both mutants performed similarly in tolerating the phloem-feeding activity and impairing the deterrent effect of HrpNEa, suggesting that AtGSL5 and AtMYB44 both contributed to the effect.

    • Overexpression of the mitogen-activated protein kinase gene OsMAPK33 enhances sensitivity to salt stress in rice (Oryza sativa L.)

      Seong-Kon Lee Beom-Gi Kim Taek-Ryoun Kwon Mi-Jeong Jeong Sang-Ryeol Park Jung-Won Lee Myung-Ok Byun Hawk-Bin Kwon Benjamin F Matthews Choo-Bong Hong Soo-Chul Park

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      Mitogen-activated protein kinases (MAPK) signalling cascades are activated by extracellular stimuli such as environmental stresses and pathogens in higher eukaryotic plants. To know more about MAPK signalling in plants, a MAPK cDNA clone, OsMAPK33, was isolated from rice. The gene is mainly induced by drought stress. In phylogenetic analysis, OsMAPK33 (Os02g0148100) showed approximately 47–93% identity at the amino acid level with other plant MAPKs. It was found to exhibit organ-specific expression with relatively higher expression in leaves as compared with roots or stems, and to exist as a single copy in the rice genome. To investigate the biological functions of OsMAPK33 in rice MAPK signalling, transgenic rice plants that either overexpressed or suppressed OsMAPK33 were made. Under dehydration conditions, the suppressed lines showed lower osmotic potential compared with that of wild-type plants, suggesting a role of OsMAPK33 in osmotic homeostasis. Nonetheless, the suppressed lines did not display any significant difference in drought tolerance compared with their wild-type plants. With increased salinity, there was still no difference in salt tolerance between OsMAPK33-suppressed lines and their wild-type plants. However, the overexpressing lines showed greater reduction in biomass accumulation and higher sodium uptake into cells, resulting in a lower K+/Na+ ratio inside the cell than that in the wild-type plants and OsMAPK33-suppressed lines. These results suggest that OsMAPK33 could play a negative role in salt tolerance through unfavourable ion homeostasis. Gene expression profiling of OsMAPK33 transgenic lines through rice DNA chip analysis showed that OsMAPK33 altered expression of genes involved in ion transport. Further characterization of downstream components will elucidate various biological functions of this novel rice MAPK.

    • RNA interference for the control of whiteflies (Bemisia tabaci) by oral route

      Santosh Kumar Upadhyay K Chandrashekar Nidhi Thakur Praveen Chandra Verma J Francis Borgio Pradhyumna Kumar Rakesh Tuli

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      RNA interference (RNAi)-mediated gene silencing was explored for the control of sap-sucking pest Bemisia tabaci, commonly known as whitefly. dsRNAs and siRNAs were synthesized from five different genes – actin ortholog, ADP/ATP translocase, 𝛼-tubulin, ribosomal protein L9 (RPL9) and V-ATPase A subunit. A simplified insect bioassay method was developed for the delivery of ds/siRNA through the oral route, and efficacy was evaluated. ds/siRNA caused 29–97% mortality after 6 days of feeding. Each insect ingested nearly 150 nl of insect diet per day, which contained a maximum of 6 ng of RNA. Knocking down the expression of RPL9 and V-ATPase A caused higher mortality with LC50 11.21 and 3.08 𝜇g/ml, respectively, as compared to other genes. Semi-quantitative PCR of the treated insects showed significant decrease in the level of RPL9 and V-ATPase A transcripts. siRNAs were found stable in the insect diet for at least 7 days at the room temperature. Phloem-specific expression of dsRNAs of RPL9 and V-ATPase A in transgenic plants for the protection against whiteflies might be an interesting application of this technology.

    • Ascorbic acid is a key participant during the interactions between chloroplasts and mitochondria to optimize photosynthesis and protect against photoinhibition

      Saikrishna Talla Khateef Riazunnisa Lolla Padmavathi Pidakala Rajsheel Agepati S Raghavendra

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      The possible role of L-ascorbate (AsA) as a biochemical signal during the interactions between photosynthesis and respiration was examined in leaf discs of Arabidopsis thaliana. AsA content was either decreased as in AsA-deficient vtc1 mutants or increased by treatment with L-galactono-1, 4-lactone (L-GalL, a precursor of AsA; EC 1.3.2.3). In mutants, photosynthesis was extremely sensitive to both antimycin A (inhibitor of the cytochrome 𝑐 oxidase pathway [COX pathway]) and salicylhydroxamic acid (SHAM, inhibitor of the alternative pathway [AOX pathway]), particularly at high light conditions. Mitochondrial inhibitors lowered the ratio of reduced AsA to total AsA, at high light, indicating oxidative stress in leaf discs. Elevation of AsA by L-GalL decreased the sensitivity of photosynthesis at high light to antimycin A or SHAM, sustained photosynthesis at supraoptimal light and relieved the extent of photoinhibition. High ratios of reduced AsA to total AsA in L-GalL-treated leaf discs suggests that L-GalL lowers oxidative stress. The protection by L-GalL of photosynthesis against the mitochondrial inhibitors and photoinhibition was quite pronounced in vtc1 mutants. Our results suggest that the levels and redox state of AsA modify the pattern of modulation of photosynthesis by mitochondrial metabolism. The extent of the AOX pathway as a percentage of the total respiration in Arabidopsis mesophyll protoplasts was much higher in vtc1 than in wild type. We suggest that the role of AsA becomes pronounced at high light and/or when the AOX pathway is inhibited. While acknowledging the importance of the COX pathway, we hypothesize that AsA and the AOX pathway may complement each other to protect photosynthesis against photoinhibition.

    • Antibiotic resistance and pathogenicity factors in Staphylococcus aureus isolated from mastitic Sahiwal cattle

      Ravinder Kumar B R Yadav R S Singh

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      Methicillin-resistant Staphylococcus aureus (MRSA) poses a serious problem in dairy animals suffering from mastitis. In the present study, the distribution of mastitic MRSA and antibiotic resistance was studied in 107 strains of S. aureus isolated from milk samples from 195 infected udders. The characterizations pathogenic factors (adhesin and toxin genes) and antibiotic susceptibility of isolates were carried out using gene amplification and disc diffusion assays, respectively. A high prevalence of MRSA was observed in the tested isolates (13.1%). The isolates were also highly resistant to antibiotics, i.e. 36.4% were resistant to streptomycin, 33.6% to oxytetracycline, 29.9% to gentamicin and 26.2% each to chloramphenicol, pristinomycin and ciprofloxacin. A significant variation in the expression of pathogenic factors (Ig, coa and clf) was observed in these isolates. The overall distribution of adhesin genes ebp, fib, bbp, fnbB, cap5, cap8, map and cna in the isolates was found to be 69.1, 67.2, 6.5, 20.5, 60.7, 26.1, 81.3 and 8.4%, respectively. The presence of fib, fnbB, bbp and map genes was considerably greater in MRSA than in methicillin-susceptible S. aureus (MSSA) isolates. The proportions of toxin genes, namely, hlb, seb, sec, sed, seg and sei, in the isolates were found to be 94.3, 0.9, 8.4, 0.9, 10.2 and 49.5%, respectively. The proportions of agr genes I, II, III and IV were found to be 39.2, 27.1, 21.5 and 12.1%, respectively. A few isolates showed similar antibiotic-resistance patterns, which could be due to identical strains or the dissemination of the same strains among animals. These findings can be utilized in mastitis treatment programmes and antimicrobials strategies in organized herds.

    • P1 peptidase – a mysterious protein of family Potyviridae

      Jana Rohožková Milan Navrátil

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      The Potyviridae family, named after its type member, Potato virus Y (PVY), is the largest of the 65 plant virus groups and families currently recognized. The coding region for P1 peptidase is located at the very beginning of the viral genome of the family Potyviridae. Until recently P1 was thought of as serine peptidase with RNA-binding activity and with possible influence in cell-to-cell viral spreading. This N-terminal protein, among all of the potyviruses, is the most divergent protein: varying in length and in its amino acid sequence. Nevertheless, P1 peptidase in many ways is still a mysterious viral protein. In this review, we would like to offer a comprehensive overview, discussing the proteomic, biochemical and phylogenetic views of the P1 protein.

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