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Search Results: 1 - 10 of 198815 matches for " Bishwo N. Adhikari "
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Desiccation survival in an Antarctic nematode: molecular analysis using expressed sequenced tags
Bishwo N Adhikari, Diana H Wall, Byron J Adams
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-69
Abstract: We obtained 2,486 expressed sequence tags (ESTs) from 2,586 clones derived from the cDNA library of desiccated P. murrayi. The 2,486 ESTs formed 1,387 putative unique transcripts of which 523 (38%) had matches in the model-nematode Caenorhabditis elegans, 107 (7%) in nematodes other than C. elegans, 153 (11%) in non-nematode organisms and 605 (44%) had no significant match to any sequences in the current databases. The 1,387 unique transcripts were functionally classified by using Gene Ontology (GO) hierarchy and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The results indicate that the transcriptome contains a group of transcripts from diverse functional areas. The subtractive library of desiccated nematodes showed 80 transcripts differentially expressed during desiccation stress, of which 28% were metabolism related, 19% were involved in environmental information processing, 28% involved in genetic information processing and 21% were novel transcripts. Expression profiling of 14 selected genes by quantitative Real-time PCR showed 9 genes significantly up-regulated, 3 down-regulated and 2 continuously expressed in response to desiccation.The establishment of a desiccation EST collection for Plectus murrayi, a useful model in assessing the structural, physiological, biochemical and genetic aspects of multiple stress tolerance, is an important step in understanding the genome level response of this nematode to desiccation stress. The type of transcript analysis performed in this study sets the foundation for more detailed functional and genome level analyses of the genes involved in desiccation tolerance in nematodes.The Dry Valleys of Antarctica are one of the most extreme terrestrial environments on Earth [1]. Soils in this cold desert ecosystem are subjected to freezing temperatures, desiccation and salt accumulation that affect biological water availability [2,3]. Soil communities in Antarctic Dry Valleys are simple; primary production is largely
mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection
Elizabeth A. Savory, Bishwo N. Adhikari, John P. Hamilton, Brieanne Vaillancourt, C. Robin Buell, Brad Day
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035796
Abstract: Pseudoperonospora cubensis, an oomycete, is the causal agent of cucurbit downy mildew, and is responsible for significant losses on cucurbit crops worldwide. While other oomycete plant pathogens have been extensively studied at the molecular level, Ps. cubensis and the molecular basis of its interaction with cucurbit hosts has not been well examined. Here, we present the first large-scale global gene expression analysis of Ps. cubensis infection of a susceptible Cucumis sativus cultivar, ‘Vlaspik’, and identification of genes with putative roles in infection, growth, and pathogenicity. Using high throughput whole transcriptome sequencing, we captured differential expression of 2383 Ps. cubensis genes in sporangia and at 1, 2, 3, 4, 6, and 8 days post-inoculation (dpi). Additionally, comparison of Ps. cubensis expression profiles with expression profiles from an infection time course of the oomycete pathogen Phytophthora infestans on Solanum tuberosum revealed similarities in expression patterns of 1,576–6,806 orthologous genes suggesting a substantial degree of overlap in molecular events in virulence between the biotrophic Ps. cubensis and the hemi-biotrophic P. infestans. Co-expression analyses identified distinct modules of Ps. cubensis genes that were representative of early, intermediate, and late infection stages. Collectively, these expression data have advanced our understanding of key molecular and genetic events in the virulence of Ps. cubensis and thus, provides a foundation for identifying mechanism(s) by which to engineer or effect resistance in the host.
Alternative Splicing of a Multi-Drug Transporter from Pseudoperonospora cubensis Generates an RXLR Effector Protein That Elicits a Rapid Cell Death
Elizabeth A. Savory, Cheng Zou, Bishwo N. Adhikari, John P. Hamilton, C. Robin Buell, Shin-Han Shiu, Brad Day
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034701
Abstract: Pseudoperonospora cubensis, an obligate oomycete pathogen, is the causal agent of cucurbit downy mildew, a foliar disease of global economic importance. Similar to other oomycete plant pathogens, Ps. cubensis has a suite of RXLR and RXLR-like effector proteins, which likely function as virulence or avirulence determinants during the course of host infection. Using in silico analyses, we identified 271 candidate effector proteins within the Ps. cubensis genome with variable RXLR motifs. In extending this analysis, we present the functional characterization of one Ps. cubensis effector protein, RXLR protein 1 (PscRXLR1), and its closest Phytophthora infestans ortholog, PITG_17484, a member of the Drug/Metabolite Transporter (DMT) superfamily. To assess if such effector-non-effector pairs are common among oomycete plant pathogens, we examined the relationship(s) among putative ortholog pairs in Ps. cubensis and P. infestans. Of 271 predicted Ps. cubensis effector proteins, only 109 (41%) had a putative ortholog in P. infestans and evolutionary rate analysis of these orthologs shows that they are evolving significantly faster than most other genes. We found that PscRXLR1 was up-regulated during the early stages of infection of plants, and, moreover, that heterologous expression of PscRXLR1 in Nicotiana benthamiana elicits a rapid necrosis. More interestingly, we also demonstrate that PscRXLR1 arises as a product of alternative splicing, making this the first example of an alternative splicing event in plant pathogenic oomycetes transforming a non-effector gene to a functional effector protein. Taken together, these data suggest a role for PscRXLR1 in pathogenicity, and, in total, our data provide a basis for comparative analysis of candidate effector proteins and their non-effector orthologs as a means of understanding function and evolutionary history of pathogen effectors.
Expression Profiling of Cucumis sativus in Response to Infection by Pseudoperonospora cubensis
Bishwo N. Adhikari, Elizabeth A. Savory, Brieanne Vaillancourt, Kevin L. Childs, John P. Hamilton, Brad Day, C. Robin Buell
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034954
Abstract: The oomycete pathogen, Pseudoperonospora cubensis, is the causal agent of downy mildew on cucurbits, and at present, no effective resistance to this pathogen is available in cultivated cucumber (Cucumis sativus). To better understand the host response to a virulent pathogen, we performed expression profiling throughout a time course of a compatible interaction using whole transcriptome sequencing. As described herein, we were able to detect the expression of 15,286 cucumber genes, of which 14,476 were expressed throughout the infection process from 1 day post-inoculation (dpi) to 8 dpi. A large number of genes, 1,612 to 3,286, were differentially expressed in pair-wise comparisons between time points. We observed the rapid induction of key defense related genes, including catalases, chitinases, lipoxygenases, peroxidases, and protease inhibitors within 1 dpi, suggesting detection of the pathogen by the host. Co-expression network analyses revealed transcriptional networks with distinct patterns of expression including down-regulation at 2 dpi of known defense response genes suggesting coordinated suppression of host responses by the pathogen. Comparative analyses of cucumber gene expression patterns with that of orthologous Arabidopsis thaliana genes following challenge with Hyaloperonospora arabidopsidis revealed correlated expression patterns of single copy orthologs suggesting that these two dicot hosts have similar transcriptional responses to related pathogens. In total, the work described herein presents an in-depth analysis of the interplay between host susceptibility and pathogen virulence in an agriculturally important pathosystem.
Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes
Bishwo N. Adhikari, John P. Hamilton, Marcelo M. Zerillo, Ned Tisserat, C. André Lévesque, C. Robin Buell
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0075072
Abstract: The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as Phytophthora species, Hyaloperonospora arabidopsidis, and Pythium ultimum var. ultimum. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in Phytophthora species and an over-representation of genes involved in proteolytic degradation and signal transduction in Pythium species. A complete lack of classical RxLR effectors was observed in the seven surveyed Pythium genomes along with an overall reduction of pathogenesis-related gene families in H. arabidopsidis. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in Pythium species and H. arabidopsidis as compared to Phytophthora species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven Pythium species with the closely related oomycetes, Phytophthora species and H. arabidopsidis, and distantly related diatoms provide insight into genes that underlie virulence.
Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation
Marcelo M. Zerillo, Bishwo N. Adhikari, John P. Hamilton, C. Robin Buell, C. André Lévesque, Ned Tisserat
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0072572
Abstract: Carbohydrate-active enzymes (CAZymes) are involved in the metabolism of glycoconjugates, oligosaccharides, and polysaccharides and, in the case of plant pathogens, in the degradation of the host cell wall and storage compounds. We performed an in silico analysis of CAZymes predicted from the genomes of seven Pythium species (Py. aphanidermatum, Py. arrhenomanes, Py. irregulare, Py. iwayamai, Py. ultimum var. ultimum, Py. ultimum var. sporangiiferum and Py. vexans) using the “CAZymes Analysis Toolkit” and “Database for Automated Carbohydrate-active Enzyme Annotation” and compared them to previously published oomycete genomes. Growth of Pythium spp. was assessed in a minimal medium containing selected carbon sources that are usually present in plants. The in silico analyses, coupled with our in vitro growth assays, suggest that most of the predicted CAZymes are involved in the metabolism of the oomycete cell wall with starch and sucrose serving as the main carbohydrate sources for growth of these plant pathogens. The genomes of Pythium spp. also encode pectinases and cellulases that facilitate degradation of the plant cell wall and are important in hyphal penetration; however, the species examined in this study lack the requisite genes for the complete saccharification of these carbohydrates for use as a carbon source. Genes encoding for xylan, xyloglucan, (galacto)(gluco)mannan and cutin degradation were absent or infrequent in Pythium spp.. Comparative analyses of predicted CAZymes in oomycetes indicated distinct evolutionary histories. Furthermore, CAZyme gene families among Pythium spp. were not uniformly distributed in the genomes, suggesting independent gene loss events, reflective of the polyphyletic relationships among some of the species.
Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora
Bishwo N Adhikari, Chin-Yo Lin, Xiaodong Bai, Todd A Ciche, Parwinder S Grewal, Adler R Dillman, John M Chaston, David I Shapiro-Ilan, Anwar L Bilgrami, Randy Gaugler, Paul W Sternberg, Byron J Adams
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-609
Abstract: An expression profiling study was performed between experimental lines L5M and OHB of Hb with probes for 15,220 ESTs from the Hb transcriptome. Microarray analysis showed 1,185 DEGs comprising of 469 down- and 716 up-regulated genes in trait deteriorated nematodes. Analysis of the DEGs showed that trait deterioration involves massive changes of the transcripts encoding enzymes involved in metabolism, signal transduction, virulence and longevity. We observed a pattern of reduced expression of enzymes related to primary metabolic processes and induced secondary metabolism. Expression of sixteen DEGs in trait deteriorated nematodes was validated by quantitative reverse transcription-PCR (qRT-PCR) which revealed similar expression kinetics for all the genes tested as shown by microarray.As the most closely related major entomopathogen to C. elegans, Hb provides an attractive near-term application for using a model organism to better understand interspecies interactions and to enhance our understanding of the mechanisms underlying trait deterioration in biological control agents. This information could also be used to improve the beneficial traits of biological control agents and better understand fundamental aspects of nematode parasitism and mutualism.Biological control using predators, parasitoids, or pathogens, can be an effective alternative for management of arthropod pests [1,2]. In contrast to chemical insecticides, biological control agents are generally not harmful to humans or the environment, and have minimal or negligible potential to cause resistance or harm to non-target organisms. The success of a biological control agent depends on key traits, particularly compatibility with the target pest, reproductive potential, host-finding ability, environmental tolerance, and ability to be cultured. These traits, however, can deteriorate rapidly, and substantially when a biological control agent is isolated from nature and reared in the laboratory, or mass-produced
An ethical reflection on doctor-patient relationship
N Adhikari
Journal of Kathmandu Medical College , 2013, DOI: 10.3126/jkmc.v2i1.10556
Abstract: Not available. DOI: http://dx.doi.org/10.3126/jkmc.v2i1.10556 Journal of Kathmandu Medical College , Vol. 2, No. 1, Issue 3, Jan.-Mar., 2013, page: 40
A brewing public health crisis: antibiotic resistance
N. Adhikari
Journal of Institute of Medicine , 2009, DOI: 10.3126/joim.v31i3.2971
Abstract: Not Available; Editorial DOI: 10.3126/joim.v31i3.2971 Journal of Institute of Medicine Vol. 31, Issue 3, 2009, December Page: 1-2
Haemorrhagic pneumonitis: A rare presentation of leptospirosis.
Pai N,Adhikari P
Journal of Postgraduate Medicine , 2001,
Abstract: Leptospirosis is an uncommon zoonosis. As a systemic disease, it presents itself by multisystem involvement. Pulmonary involvement with leptospirosis often is manifested by respiratory symptoms; but pneumonia commonly is not a prominent clinical manifestation of the illness. We report a case of leptospiral pneumonia in which pulmonary manifestations were primary clinical features of the illness. The prompt resolution of chest x-ray on institution of treatment is noteworthy.
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