Life Sciences

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Shiv Nadar University

The western margin of Australia is unique in being the only eastern boundary region undergoing no upwelling as the poleward flowing Leeuwin Current (LC) nullifies the equatorward-driven wind-induced circulation. The principal forcing mechanism of the Leeuwin Current is the alongshore pressure gradients and associated zonal geostrophic flows along the West Australian margin. Based on planktic foraminiferal census counts and stable isotopic analysis of a surface-dwelling planktic foraminifera, Globigerinoides sacculifer, we show that during the Quaternary there have been five intervals when this eastern boundary region behaved in an opposite manner and the margin experienced extensive upwelling due to weakening of the LC and dominance of equatorward wind-driven circulation, causing offshore Ekman transport. These events occurred at 2.22, 1.83, 0.68, 0.45 and 0.04 Ma and have been named here as PL-1 to PL-5 in ascending stratigraphic order. We demonstrate here that the previous two events, PL-1 and PL-2, occurred due to ENSO-induced changes in the Western Pacific Warm Pool, while the last three events, PL-3, PL-4, and PL-5, occurred due to reduced Indonesian throughflow as a result of lowered sea level caused by ice volume expansion. We envisage here that these periods must be those of reduced net heat input to the Indian Ocean from the Pacific via Indonesian Seaway and thus should have an effect on sea surface temperature of the Indian Ocean and Indian monsoon.

World University root node

(SoNS) School of Natural Sciences

Current Science

Palaeoceanographic and palaeoclimatic history of ODP site 763A (Exmouth Plateau), southeast Indian Ocean: 2.2 Ma record of planktic foraminifera

Auxin exerts pleiotropic effects on plant growth and development by regulating the expression of early auxin-responsive genes of auxin/ indoleacetic acid (Aux/IAA), small auxin-up RNA, and GH3 classes. These genes have been studied extensively in dicots like soybean and Arabidopsis. We had earlier characterized a cDNA of the first monocot member of Aux/IAA family from rice. The achievement of the large scale rice genome sequencing combined with the availability of full-length cDNA sequences from Knowledge-based Oryza Molecular Biological Encyclopedia provided us the opportunity to draw up the first comprehensive list of Aux/IAA genes in a monocot. By screening the available databases, we have identified 31 Aux/IAA genes having high sequence identity within the conserved domains I, II, III, and IV. The genomic organization as well as chromosomal location of all the Oryza sativa indoleacetic acid (OsIAA) genes is reported. The rice Aux/IAA proteins can be classified in two groups (A and B) on the basis of their phylogenetic relationship with Arabidopsis Aux/IAA proteins. An evolutionary pattern of the rice Aux/IAA genes has been discussed by analyzing their structure (exon/intron organization) and duplications. Interestingly, the duplication of rice Aux/IAA genes was found to be associated with chromosomal block duplication events in rice. The in-silico analysis has been complemented with real-time polymerase chain reaction analysis to quantify transcript levels of all Aux/IAA family members. OsIAA genes showed differential and overlapping organ-specific expression patterns in light- and dark-grown seedlings/plants. Although auxin enhanced the transcript abundance of most of the OsIAA genes, the effect was more pronounced on OsIAA9, 14, 19, 20, 24, and 31. These results provide a foundation for future studies on elucidating the precise role of rice Aux/IAA genes in early steps of auxin signal transduction. © Springer-Verlag 2005.

Functional and Integrative Genomics

Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa)

Aim: To evaluate the in vitro anti-HBV activity of recombinant human IFN-γ, alone and in combination with lamivudine. Methods: A recombinant baculovirus-HBV/HepG2 culture system was developed which could support productive HBV infection in vitro. Expression of HBsAg and HBeAg in infected HepG2 culture medium was detected by commercial enzyme immunoassays. HBV DNA replication intermediates were detected in infected cells by Southern hybridization and viral DNA load was determined by dot hybridization. Results: IFN-γ at 0.1 to 5 μg/L efficiently down regulated HBsAg expression in transduced HepG2 cells. At 5 μg/L, IFN-γ also suppressed HBV DNA replication in these cells. While treatment with a combination of lamivudine and IFN-γ showed no additive effect, sequential treatment first with lamivudine and then IFN-γ was found to be promising. In this culture system the best HBV suppression was observed with a pulse of 2 μmol/L lamivudine for two days, followed by 1 μg/L IFN-γ for another four days. Compared to treatment with lamivudine alone, the sequential use of 0.2 μmol/L lamivudine for two days, followed by 5 μg/L IFN-γ for six days showed a 72% reduction in HBV cccDNA pool. Conclusion: This in vitro study warrants further evaluation of a combination of IFN-γ and lamivudine, especially in IFN-α non-responder chronic hepatitis B patients. A reduced duration of lamivudine treatment would also restrict the emergence of drug-resistant HBV mutants. © 2006 The WIG Press. All rights reserved.

Fulltext

World Journal of Gastroenterology

Inhibition of hepatitis B virus DNA replicative intermediate forms by recombinant interferon-γ

Translation initiation of hepatitis C virus RNA occurs via ribosome binding to an 'internal ribosome entry site (IRES)' located in the 5′untranslated region of the viral RNA. The principle interaction between the 40S ribosomal subunit and the HCV IRES has been shown to be largely factor independent, which is followed by the joining of the 60S ribosomal subunit to form functional 80S complex. However several additional cellular proteins have been reported to bind to HCV IRES and enhance the initiation of translation. In order to identify novel factors involved in the ribosome assembly during internal initiation of HCV RNA, northwestern screening of a HeLa cDNA expression library was performed, using HCV IRES RNA as probe. We demonstrate here, that human ribosomal protein L18a, a constituent of 60S subunit, interacts with HCV IRES RNA. This interaction was further confirmed by using a recombinant protein similar to L18a (sL18a), cloned from human blood. Interestingly, addition of increasing concentration of the purified recombinant sL18a protein, showed moderate stimulation of HCV IRES activity in the in vitro translation assay. These observations suggest that the human L18a might influence the HCV IRES mediated translation. © Springer-Verlag 2005.

Archives of Virology

Human ribosomal protein L18a interacts with hepatitis C virus internal ribosome entry site

As one of the final steps in the bacterial growth cycle, daughter cells must be released from one another by cutting the shared peptidoglycan wall that separates them. In Escherichia coli, this delicate operation is performed by several peptidoglycan hydrolases, consisting of multiple amidases, lytic transglycosylases, and endopeptidases. The interactions among these enzymes and the molecular mechanics of how separation occurs without lysis are unknown. We show here that deleting the endopeptidase PBP 4 from strains lacking AmiC produces long chains of unseparated cells, indicating that PBP 4 collaborates with the major peptidoglycan amidases during cell separation. Another endopeptidase, PBP 7, fulfills a secondary role. These functions may be responsible for the contributions of PBPs 4 and 1 to the generation of regular cell shape and the production of normal biofilms. In addition, we find that the E. coli peptidoglycan amidases may have different substrate preferences. When the oo-carboxypeptidase PBP 5 was deleted, thereby producing cells with higher levels of pentapeptides, mutants carrying only AmiC produced a higher percentage of cells in chains, while mutants with active AmiA or AmiB were unaffected. The results suggest that AmiC prefers to remove tetrapeptides from peptidoglycan and that AmiA and AmiB either have no preference or prefer pentapeptides. Muropeptide compositions of the mutants corroborated this latter conclusion. Unexpectedly, amidase mutants lacking PBP 5 grew in long twisted chains instead of straight filaments, indicating that overall septal morphology was also defective in these strains. Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Journal of Bacteriology

Daughter cell separation by penicillin-binding proteins and peptidoglycan amidases in Escherichia coli

In order to understand the molecular mechanisms involved in the gene-for-gene type of pathogen resistance, high-resolution genetic and physical mapping of resistance loci is required to facilitate map-based cloning of resistance genes. Here, we report the molecular mapping and cloning of a dominant gene (Pi-kh) present in the rice line Tetep, which is associated with resistance to rice blast disease caused by Magnaporthe grisea. This gene is effective against M. grisea populations prevalent in the Northwestern Himalayan region of India. Using 178 sequence tagged microsatellite, sequence-tagged site, expressed sequence tag and simple sequence repeat (SSR) markers to genotype a population of 208 F2 individuals, we mapped the Pi-kh gene between two SSR markers (TRS26 and TRS33) which are 0.7 and 0.5 cM away, respectively, and can be used in marker-assisted-selection for blast-resistant rice cultivars. We used the markers to identify the homologous region in the genomic sequence of Oryza sativa cv. Nipponbare, and a physical map consisting of two overlapping bacterial artificial chromosome and P1 artificial chromosome clones was assembled, spanning a region of 143,537 bp on the long arm of chromosome 11. Using bioinformatic analyses, we then identified a candidate blast-resistance gene in the region, and cloned the homologous sequence from Tetep. The putative Pi-kh gene cloned from Tetep is 1.5 kbp long with a single ORF, and belongs to the nucleotide binding site-leucine rich repeat class of disease resistance genes. Structural and expression analysis of the Pi-kh gene revealed that its expression is pathogen inducible. © Springer-Verlag 2005.

Molecular Genetics and Genomics

High-resolution mapping, cloning and molecular characterization of the Pi-kh gene of rice, which confers resistance to Magnaporthe grisea

In eukaryotes, the origin recognition complex (ORC) is essential for the initiation of DNA replication. The largest subunit of this complex (ORC1) has a regulatory role in origin activation. Here we report the cloning and functional characterization of Plasmodium falciparum ORC1 homolog. Using immunofluorescence and immunoelectron microscopy, we show here that PfORC1 is expressed in the nucleus during the late trophozoite and schizont stages where maximum amount of DNA replication takes place. Homology modelling of the carboxy terminal region of PfORC1 (781-1033) using Saccharomyces pombe Cdc6/Cdc18 homolog as a template reveals the presence of a similar AAA+ type nucleotide-binding fold. This region shows ATPase activity in vitro that is important for the origin activity. To our knowledge, this is the first evidence of an individual ORC subunit that shows ATPase activity. These observations strongly suggest that PfORC1 might be involved in DNA replication initiation during the blood stage of the parasitic life cycle. © 2005 Elsevier Inc. All rights reserved.

Biochemical and Biophysical Research Communications

Expression and characterization of human malaria parasite Plasmodium falciparum origin recognition complex subunit 1

Several 6-carboethoxy-(2-substituted)-1,3,4-thia/oxadiazolo[2,3-b] pyrimidin-5-ones 3 and 6 and 5-amino-(2-substituted)-1,3,4-thia/oxadiazolo[2,3- b]pyrimidin-7-ones 4 and 7 have been synthesised from the synthon 2-amino-(5-substituted)-1,3,4-thia/oxadiazoles 1 and diethyl ethoxymethylenemalonate and ethyl cyanoacetate respectively. The molluscicidal activity of few title compounds have been evaluated against snail Lymnaea accuminata.

Journal of the Indian Chemical Society

Synthesis and molluscicidal activity of 6-carboethoxy-(2-substituted)-1,3, 4-thia/oxadiazolo[2,3-b]pyrimidin-5-ones and 5-amino-(2-substituted)-1,3,4-thia/ oxadiazolo[2,3-b]pyrimidin-7-ones

A study was conducted during 2000-2003 to study segregation pattern of 4 pyramided resistance genes against bacterial blight caused by Xanthomonas oryzae pv oryzae in 'IRBB 60' in crosses involving 3 susceptible basmati quality genotypes ('Pusa Basmati 1', 'Pusa 1121' and 'Pusa 1387') of rice (Oryza sativa L.). All the basmati quality genotypes were found susceptible to bacterial blight. Three genes, Xa 4, xa 13 and Xa 21 were found resistant, while xa 5 showed susceptible reaction. Genetic analysis of 'IRBB 60' indicated 2 dominant and 1 recessive gene controlling resistance against bacterial blight in the cross 'Pusa Basmati 1' x 'IRBB 60' and 'Pusa 1121' x 'IRBB 60'. Deviation from expected segregation was observed in 'Pusa 1387' x 'IRBB 60' cross that may be owing to residual level of resistance or epistatic interaction. From the segregating generations, 32 high-quality, high resistance lines were identified that possessed high linear kernel elongation and length/ breadth ratio.

Indian Journal of Agricultural Sciences

Genetic analysis of pyramided genes for resistance to bacterial blight (Xanthomonas oryzae pv oryzae) and development of resistant lines of basmati rice (Oryza sativa)

Land races adapted to a variety of agro-ecological niches constitute a rich source of rice biodiversity. Large-scale cultivation of high-yielding varieties has resulted in the replacement of the land races, except a few that are still being cultivated by the resource-poor farmers practising subsistence farming. From the viewpoints of their conservation and utilization, it is important to understand the genetic structure of the present-day land races. The present study was designed to explore if the present-day land races of rice still retain a composite genetic structure that forms the basis of their stability. Two land races, which are being grown by the rural farmers in the coastal regions of Orissa over several generations, were characterized and compared with four commercial high-yielding varieties using sequence-tagged microsatellite site (STMS) markers. A high-resolution (3% Metaphor) agarose gel when compared with 6% denaturing PAGE was found useful for the differentiation of the STMS alleles. The DNA profiles based on forty-eight mapped STMS markers revealed a high degree of genetic diversity between the land races and the commercial varieties. Analysis of 18 individual plants of each land race and variety, using ten most informative markers detected a high degree of genetic uniformity in the commercial varieties. Residual heterozygosity for only one of the marker loci was evident in the case of the popular commercial cultivar, Lalat. In both the land races, heterozygosity and heterogeneity were clearly evident with the presence of additional marker locus genotypes carrying new STMS alleles at much lower frequency than the major allele. Of the two land races characterized, one (Galleiganthi) was more heterogeneous than the other (Bankosa).