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Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants

Creator:: Carbonell, Alberto, Fahlgren, Noah, Garcia-Ruiz, Hernan, Gilbert, Kerrigan B., Montgomery, Taiowa A., Nguyen, Tammy, Cuperus, Josh T., and Carrington, James C.
Abstract:: In RNA-directed silencing pathways, ternary complexes result from small RNA-guided ARGONAUTE (AGO) associating with target transcripts. Target transcripts are often silenced through direct cleavage (slicing), destabilization through slicer-independent turnover mechanisms, and translational repression. Here, wild-type and active-site defective forms of several Arabidopsis thaliana AGO proteins involved in posttranscriptional silencing were...
Resource Type:: Article
Full Text:: Kerrigan B. Gilbert,a Taiowa A. Montgomery,b,1 Tammy Nguyen,b Josh T. Cuperus,b,2 and James C. Carringtona

Computational and analytical framework for small RNA profiling by high-throughput sequencing

Creator:: Fahlgren, Noah, Sullivan, Christopher M., Kasschau, Krisitin D., Chapman, Elisabeth J., Cumbie, Jason S., Montgomery, Taiowa A., Gilbert, Sunny D., Dasenko, Mark, Backman, Tyler W. H., Givan, Scott A., and Carrington, James C.
Abstract:: The advent of high-throughput sequencing (HTS) methods has enabled direct approaches to quantitatively profile small RNA populations. However, these methods have been limited by several factors, including representational artifacts and lack of established statistical methods of analysis. Furthermore, massive HTS data sets present new problems related to data processing and...
Resource Type:: Article
Full Text:: reads, BLAT required z78.8 h, which was judged to be unacceptably slow for SBS data sets. FIGURE 1

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Creator:: Manning, Viola A., Pandelova, Iovanna, Dhillon, Braham, Wilhelm, Larry J., Goodwin, Stephen B., Berlin, Aaron M., Figueroa, Melania, Freitag, Michael, Hane, James K., Henrissat, Bernard, Holman, Wade H., Kodira, Chinnappa D., Martin, Joel, Oliver, Richard P., Robbertse, Barbara, Schackwitz, Wendy, Schwartz, David C., Spatafora, Joseph W., Turgeon, B. Gillian, Yandava, Chandri, Young, Sarah, Zhou, Shiguo, Zeng, Qiandong, Grigoriev, Igor V., Ma, Li-Jun, and Ciuffetti, Lynda M.
Abstract:: Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins ( HST), which are recognized by their host in a genotype-specific...
Resource Type:: Article
Full Text:: ,‡‡,§§ James K. Hane,*** Bernard Henrissat,††† Wade H. Holman,* Chinnappa D. Kodira,**,‡‡‡ Joel Martin

Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly ‘Pseudomonas butanovora’

Creator:: Cooley, Richard B., Dubbels, Bradley L., Sayavedra-Soto, Luis A., Bottomley, Peter J., and Arp, Daniel J.
Abstract:: Soluble butane monooxygenase (sBMO), a three-component di-iron monooxygenase complex expressed by the C2–C9 alkane-utilizing bacterium Thauera butanivorans, was kinetically characterized by measuring substrate specificities for C1–C5 alkanes and product inhibition profiles. sBMO has high sequence homology with soluble methane monooxygenase (sMMO) and shares a similar substrate range, including gaseous and...
Resource Type:: Article
Full Text:: ., Zhu, M., Tso, L., Nguyen, H. H. T., Yip, J. H. K. & Chan, S. I. (1997). Regio- and stereoselectivity

Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis

Creator:: Lee, Hanna, Yoo, Seong Jeon, Lee, Jeong Hwan, Kim, Wanhui, Yoo, Seung Kwan, Fitzgerald, Heather, Carrington, James C., and Ahn, Ji Hoon
Abstract:: Flowering is the primary trait affected by ambient temperature changes. Plant microRNAs (miRNAs) are small non-coding RNAs playing an important regulatory role in plant development. In this study, to elucidate the mechanism of flowering-time regulation by small RNAs, we identified six ambient temperature-responsive miRNAs (miR156, miR163, miR169, miR172, miR398 and...
Resource Type:: Article
Full Text:: solidified Murashige and Skoog (MS) medium at 16 or 23�C under long day (LD; 16:8 h, light:dark) conditions

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

Creator:: Padamsee, Mahajabeen, Kumar, T. K. Arun, Riley, Robert, Binder, Manfred, Boyd, Alex, Calvo, Ana M., Furukawa, Kentaro, Hesse, Cedar, Hohmann, Stefan, James, Tim Y., LaButti, Kurt, Lapidus, Alla, Lindquist, Erika, Lucas, Susan, Miller, Kari, Shantappa, Sourabha, Grigoriev, Igor V., Hibbett, David S., McLaughlin, David J., Spatafora, Joseph W., and Aime, M. Catherine
Abstract:: Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W....
Resource Type:: Article
Full Text:: , Kentaro Furukawa g, Cedar Hesse e, Stefan Hohmann g, Tim Y. James h, Kurt LaButti c, Alla Lapidus c,3

Within-population genetic structure differs between two sympatric sister-species of ectomycorrhizal fungi, Rhizopogon vinicolor and R. vesiculosus

Creator:: Dunham, Susie M., Mujic, Alija Bajro, Spatafora, Joseph W., and Kretzer, Annette M.
Abstract:: Using spatial autocorrelation analysis, we examined the within-population genetic structure of Rhizopogon vinicolor and R. vesiculosus, two hypogeous ectomycorrhizal (EM) species that are sympatric sister taxa known to differ in their clonal structure. We collected 121 sporocarps and 482 tuberculate EM of both species from a 20 ha forest stand...
Resource Type:: Article
Full Text:: on ice immediately after collection and dried at 35 C within 24 h. Before drying, we divided each

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

Creator:: Parks, Matthew, Cronn, Richard, and Liston, Aaron
Abstract:: Background: Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating ‘noisy’ data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and/or...
Resource Type:: Article
Full Text:: product using 0.4 N KOH, and then amplified and biotinylated in a single in- cubation of 18 h at 30°C in

Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci

Creator:: Syring, John, Willyard, Ann, Cronn, Richard, and Liston, Aaron
Abstract:: Sequence data from nrITS and cpDNA have failed to fully resolve phylogenetic relationships among Pinus species. Four low‐copy nuclear genes, developed from the screening of 73 mapped conifer anchor loci, were sequenced from 12 species representing all subsections. Individual loci do not uniformly support either the nrITS or cpDNA hypotheses...
Resource Type:: Article
Full Text:: ) 10.5 (7.0) subg. Strobus 365 201.7 (110–229)h 27.5 38 15 0.0759 (.017) 2.5 (11.3) IFG8612 exon A ) B

StPIP1, a PAMP-induced peptide in potato, elicits plant defenses and is associated with disease symptom severity in a compatible interaction with potato virus Y

Creator:: Combest, Max M., Moroz, Natalia, Tanaka, Kiwamu, Rogan, Conner J., Anderson, Jeffrey C., Thura, Lin, Rakotondrafara, Aurélie M., and Goyer, Aymeric
Abstract:: The role of small secreted peptides in plant defense responses to viruses has been seldom investigated. Here, we report a role for potato (Solanum tuberosum) PIP1, a gene predicted to encode a member of the PAMP-induced peptide (PIP) family, in the response of potato to potato virus Y infection (PVY)....
Resource Type:: Article

ScholarsArchive@OSU

Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants

Computational and analytical framework for small RNA profiling by high-throughput sequencing

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly ‘Pseudomonas butanovora’

Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

Within-population genetic structure differs between two sympatric sister-species of ectomycorrhizal fungi, Rhizopogon vinicolor and R. vesiculosus

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci

StPIP1, a PAMP-induced peptide in potato, elicits plant defenses and is associated with disease symptom severity in a compatible interaction with potato virus Y

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