DIRECT METAGENOMIC DETECTION AND ANALYSIS OF PLANT VIRUSES USING AN UNBIASED HIGH-THROUGHPUT SEQUENCING APPROACH

It is well established that plants, along with other life forms, often are infected by viral parasites that require the host cellular machinery for replication. Since the overwhelming majority of these viruses have been from cultivated plants from laboratories and greenhouses, I investigated the viral populations from wild, uncultivated plants, hypothesizing that they would harbor new and novel viruses. To complete this study, an optimized method for the detection of plant viruses using a direct, unbiased metagenomic approach was developed and implemented from plants in the Tallgrass Prairie Preserve in Northeastern Oklahoma. Subsequently, their RNA viral genomes were isolated and converted to tagged cDNAs that were pyrosequenced on a Roche/454 GS-FLX, assembled and compared to other known gene sequences. A comprehensive relational mySQL-based web-accessible database also was implemented to facilitate analysis of the large amounts of metagenomic data generated. Of the 1254 sampled plants, 496 were infected with one or more viruses, that were represented by 1624 assembled cDNA sequences. Of the 19 viral families represented, the three most prevalent were Tymoviridae, Totiviridae, and Partitiviridae although the majority of observed virus sequences were new, previously un-described species, often representing new viral genera. Since Totiviridae and Partitiviridae, characteristically fungal viruses, also coincided with detection of fungi associated with the plants, it is very likely that the majority of the viruses observed represented viral infections of fungi that were interacting with the plants.Through these studies, a diverse number of new, previously undiscovered viral species were observed in the wild, uncultivated plants of the Tallgrass Prairie Preserve, that multiple infections of viruses in these plants are commonplace, at least one virus, a member of the family Tymoviridae, was widely distributed on a single species of plant, Asclepias viridis,a likely ecological viral niche, and that a majority of the classified viral species observed represented members of fungal associated virus familie

Mass Spectrometry in the Home and Garden

Identification of active components in a variety of chemical products used directly by consumers is described at both trace and bulk levels using mass spectrometry. The combination of external ambient ionization with a portable mass spectrometer capable of tandem mass spectrometry provides high chemical specificity and sensitivity as well as allowing on-site monitoring. These experiments were done using a custom-built portable ion trap mass spectrometer in combination with the ambient ionization methods of paper spray, leaf spray, and low temperature plasma ionization. Bactericides, garden chemicals, air fresheners, and other products were examined. Herbicide applied to suburban lawns was detected in situ on single leaves 5 d after application

Cloning, characterization and expression analysis of porcine microRNAs

Background: MicroRNAs (miRNAs) are small ~22-nt regulatory RNAs that can silence target genes, by blocking their protein production or degrading the mRNAs. Pig is an important animal in the agriculture industry because of its utility in the meat production. Besides, pig has tremendous biomedical importance as a model organism because of its closer proximity to humans than the mouse model. Several hundreds of miRNAs have been identified from mammals, humans, mice and rats, but little is known about the miRNA component in the pig genome. Here, we adopted an experimental approach to identify conserved and unique miRNAs and characterize their expression patterns in diverse tissues of pig.Results: By sequencing a small RNA library generated using pooled RNA from the pig heart, liver and thymus; we identified a total of 120 conserved miRNA homologs in pig. Expression analysis of conserved miRNAs in 14 different tissue types revealed heart-specific expression of miR-499 and miR-208 and liver-specific expression of miR-122. Additionally, miR-1 and miR-133 in the heart, miR-181a and miR-142-3p in the thymus, miR-194 in the liver, and miR-143 in the stomach showed the highest levels of expression. miR-22, miR-26b, miR-29c and miR-30c showed ubiquitous expression in diverse tissues. The expression patterns of pig-specific miRNAs also varied among the tissues examined.Conclusion: Identification of 120 miRNAs and determination of the spatial expression patterns of a sub-set of these in the pig is a valuable resource for molecular biologists, breeders, and biomedical investigators interested in post-transcriptional gene regulation in pig and in related mammals, including humans.Peer reviewedBiochemistry and Molecular BiologyAnimal Scienc

RBPJ Mutations Identified in Two Families Affected by Adams-Oliver Syndrome

Through exome resequencing, we identified two unique mutations in recombination signal binding protein for immunoglobulin kappa J (RBPJ) in two independent families affected by Adams-Oliver syndrome (AOS), a rare multiple-malformation disorder consisting primarily of aplasia cutis congenita of the vertex scalp and transverse terminal limb defects. These identified mutations link RBPJ, the primary transcriptional regulator for the Notch pathway, with AOS, a human genetic disorder. Functional assays confirmed impaired DNA binding of mutated RBPJ, placing it among other notch-pathway proteins altered in human genetic syndromes

Identification and replication of RNA-Seq gene network modules associated with depression severity

Genomic variation underlying major depressive disorder (MDD) likely involves the interaction and regulation of multiple genes in a network. Data-driven co-expression network module inference has the potential to account for variation within regulatory networks, reduce the dimensionality of RNA-Seq data, and detect significant geneexpression modules associated with depression severity. We performed an RNA-Seq gene co-expression network analysis of mRNA data obtained from the peripheral blood mononuclear cells of unmedicated MDD (n = 78) and healthy control (n = 79) subjects. Across the combined MDD and HC groups, we assigned genes into modules using hierarchical clustering with a dynamic tree cut method and projected the expression data onto a lower-dimensional module space by computing the single-sample gene set enrichment score of each module. We tested the singlesample scores of each module for association with levels of depression severity measured by the Montgomery-Åsberg Depression Scale (MADRS). Independent of MDD status, we identified 23 gene modules from the co-expression network. Two modules were significantly associated with the MADRS score after multiple comparison adjustment (adjusted p = 0.009, 0.028 at 0.05 FDR threshold), and one of these modules replicated in a previous RNA-Seq study of MDD (p = 0.03). The two MADRS-associated modules contain genes previously implicated in mood disorders and show enrichment of apoptosis and B cell receptor signaling. The genes in these modules show a correlation between network centrality and univariate association with depression, suggesting that intramodular hub genes are more likely to be related to MDD compared to other genes in a module

Sheep Updates 2003 - Pastures

This session covers seven papers from different authors: 1. Pastures for saline land, Ed Barrett-Lennard 1Department of Agriculture, Western Australia, Hayley Norman, Robyn Dynes and David Masters CSIRO Livestock Industries, Centre for Mediterranean Agricultural Research, Floreat Park, 2. Feeding value - the essential link between pastures and animals CSIRO Livestock Industries, Centre for Environmental and Life Sciences 3. ‘Pastures from space’ - how do we do it, how well do we do it and what do producers think about it? Stephen Gherardi Department of Agriculture Western Australia Graham Donald Asoka Edirisinghe Dave Henry CSIRO Livestock Industries Chris Oldham Department of Agriculture Western Australia Richard Smith Department of Land Information Joanne Sneddon University of Western Australia Mike Hyder Department of Agriculture Western Australia Andrew Thompson Department of Primary Industries, Hamilton Victoria Kazue Tanaka Roy Latta Department of Agriculture Western Australia Chris Matthews CRC for Plant-based Management of Dryland Salinity Brad Nutt Department of Agriculture Western Australia Angelo Loi, Centre for Legumes in Mediterranean Agriculture, UWA Tim Wiley, Department of Agriculture Western Australi

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

Abstract\ud \ud \ud \ud Background\ud \ud Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level.\ud \ud \ud \ud Results\ud \ud The microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons.\ud \ud \ud \ud Conclusions\ud \ud The sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.We acknowledge our colleagues at the University of Oklahomas Advanced Center for Genome Technology, Chunmei Qu and Ping Wang for their assistance with 454 GSFLX sequencing sample preparation and Steve Kenton for his help with deconvoluting the pooled BACs and their subsequent assembly. We also thank Eric Tang for assistance on sequencing two BACs using Sanger sequencers. This project is supported by startup funds from the University of Illinois to RM and a grant from the Energy Bioscience Institute (EBI) to SPM, MEH, RM, and DSR.We acknowledge our colleagues at the University of Oklahoma's Advanced Center for Genome Technology, Chunmei Qu and Ping Wang for their assistance with 454 GS-FLX sequencing sample preparation and Steve Kenton for his help with deconvoluting the pooled BACs and their subsequent assembly. We also thank Eric Tang for assistance on sequencing two BACs using Sanger sequencers. This project is supported by start-up funds from the University of Illinois to RM and a grant from the Energy Bioscience Institute (EBI) to SPM, MEH, RM, and DSR

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations

An improved assembly of the Ciona intestinalis genome reveals that it contains non-canonical introns and that about 20% of Ciona genes reside in operons

The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571

<p>Abstract</p> <p>Background</p> <p>Biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. <it>Azorhizobium caulinodans </it>ORS571 has the dual capacity to fix nitrogen both as free-living organism and in a symbiotic interaction with <it>Sesbania rostrata</it>. The host is a fast-growing, submergence-tolerant tropical legume on which <it>A. caulinodans </it>can efficiently induce nodule formation on the root system and on adventitious rootlets located on the stem.</p> <p>Results</p> <p>The 5.37-Mb genome consists of a single circular chromosome with an overall average GC of 67% and numerous islands with varying GC contents. Most nodulation functions as well as a putative type-IV secretion system are found in a distinct symbiosis region. The genome contains a plethora of regulatory and transporter genes and many functions possibly involved in contacting a host. It potentially encodes 4717 proteins of which 96.3% have homologs and 3.7% are unique for <it>A. caulinodans</it>. Phylogenetic analyses show that the diazotroph <it>Xanthobacter autotrophicus </it>is the closest relative among the sequenced genomes, but the synteny between both genomes is very poor.</p> <p>Conclusion</p> <p>The genome analysis reveals that <it>A. caulinodans </it>is a diazotroph that acquired the capacity to nodulate most probably through horizontal gene transfer of a complex symbiosis island. The genome contains numerous genes that reflect a strong adaptive and metabolic potential. These combined features and the availability of the annotated genome make <it>A. caulinodans </it>an attractive organism to explore symbiotic biological nitrogen fixation beyond leguminous plants.</p