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In this essay, we describe how rhetoric’s theories of temporality can inform ongoing urban development. We examine a transportation planning case to suggest that urban development must value contri...

This essay contributes to scholarship on precarity and rhetoric by exploring how participatory epideictic rhetorics, data, and infrastructure contribute to precarity. We concentrate on how shared d...

Optically active amines represent highly valuable building blocks for the synthesis of advanced pharmaceutical intermediates, drug molecules, and biologically active natural products. Hemoproteins have recently emerged as promising biocatalysts for the formation of C—N bonds via carbene transfer, but asymmetric N—H carbene insertion reactions using these or other enzymes have so far been elusive. Here, we report the successful development of a biocatalytic strategy for the asymmetric N—H carbene insertion of aromatic amines with 2-diazopropanoate esters using engineered variants of myoglobin. High activity and stereoinduction in this reaction could be achieved by tuning the chiral environment around the heme cofactor in the metalloprotein in combination with catalyst-matching and tailoring of the diazo reagent. Using this approach, an efficient biocatalytic protocol for the synthesis of a broad range of substituted aryl amines with up to 82% ee was obtained. In addition, a stereocomplementary catalyst useful to access the mirrorimage form of the N—H insertion products was identified. This work paves the way to asymmetric amine synthesis via biocatalytic carbene transfer, and the present strategy based on the synergistic combination of protein and diazo reagent engineering is expected to prove useful in the context of these as well as other challenging asymmetric carbene transfer reactions.

This article examines how sensation and affect make different kinds of resilience meaningful to communities. Through a case study, we analyze public deliberation about a proposal to expand interstates in Tampa, Florida. We describe how evidence introduced by opposing sides foregrounded conflicting sensory experiences. The resulting sensoriums upheld different aspects of the city’s identity as worth maintaining. Drawing from recent scholarship defining resilience as something that can always be done otherwise, we suggest that resilience is better understood as entangled with public affect. We argue that a key point for rhetorical intervention in city planning is considering which futures and visions of resilience are being imagined for publics.

Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large data set of published and newly generated sRNA sequencing data (1333 sRNA-seq libraries containing more than 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding more than 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24- and 21-nucleotide (nt) siRNAs, respectively. Most often, 24-nt-dominated siRNA loci occurred in intergenic regions, especially at the 5′-flanking regions of protein-coding genes. In contrast, 21-nt-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21-nt-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, whereas mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible.

Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but comprise only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large dataset of published and newly generated sRNA sequencing data (1,333 sRNA-seq libraries containing over 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding over 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24 nucleotide and 21 nucleotide siRNAs, respectively. 24 nucleotide-dominated siRNA loci usually occurred in intergenic regions, especially at the 5’-flanking regions of protein-coding genes. In contrast, 21 nucleotide-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21 nucleotide-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, while mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible at http://plantsmallrnagenes.science.psu.edu.

Plant small RNAs are subject to various modifications. Previous reports revealed widespread 3' modifications (truncations and non-templated tailing) of plant miRNAs when the 2'-C-methyltransferase HEN1 is absent. However, non-templated nucleotides in plant heterochromatic siRNAs have not been deeply studied, especially in wild-type plants. We systematically studied non-templated nucleotide patterns in plant small RNAs by analyzing small RNA sequencing libraries from Arabidopsis. tomato, Medicago, rice, maize, and Physcomitrella. Elevated rates of non-templated nucleotides were observed at the 3' ends of both miRNAs and endogenous siRNAs from wild-type specimens of all species. 'Off-sized' small RNAs, such as 25 and 23 nt siRNAs arising from loci dominated by 24 nt siRNAs, often had very high rates of 3'-non-templated nucleotides. The same pattern was observed in all species that we studied. Further analysis of 24 nt siRNA clusters in Arabidopsis revealed distinct patterns of 3'-non-templated nucleotides of 23 nt siRNAs arising from heterochromatic siRNA loci. This pattern of non-templated 3' nucleotides on 23 nt siRNAs is not affected by loss of known small RNA 3'-end modifying enzymes, and may result from modifications added to longer heterochromatic siRNA precursors.

Parasitic plants make direct contact with their host’s vasculature. In parasitism by Cuscuta, RNA and other macromolecules regularly move between host and parasite. Recently, trans-species microRNA from Cuscuta have been shown to functionally target host genes which have essential roles in host defense. Known pathways for the evolution of microRNAs, and the prevalence of horizontal gene transfer events in the Cuscuta lineage, hint that trans-species microRNAs could originate from captured host genes. It is unknown how the delivery of microRNAs from the parasite to the host takes place. One exciting possibility is through apoplastic export using extracellular vesicles, a process which has recently been shown to transport select small RNAs in plants and fungi. These discoveries represent the initial findings of what may be a widespread mechanism of interactions between species.

First paragraphDodders (Cuscutaspp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bi-directional movement of viruses, proteins, and mRNAs between host and parasite1, but the functional effects of these movements are not clear. Here we show thatC. campestrishaustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizingArabidopsis thalianahosts. Many of these miRNAs are 22 nts long, a usually rare size of plant miRNA associated with amplification of target silencing through secondary small interfering RNA (siRNA) production2. SeveralA. thalianamRNAs are targeted byC. campestris22 nt miRNAs during parasitism, resulting in mRNA cleavage, secondary siRNA production, and decreased mRNA accumulation levels. Hosts with mutations in two of the targets supported significantly higher growth ofC. campestris.Homologs of target mRNAs from diverse plants also have predicted target sites to inducedC. campestrismiRNAs, and the same miRNAs are expressed and active against host targets whenC. campestrisparasitizes a different host,Nicotiana benthamiana. These data show thatC. campestrismiRNAs act astrans-species regulators of host gene expression, and suggest that they may act as virulence factors during parasitism.

Enhancing the Epistemological Project in the Rhetoric of Science: Information Infrastructure as Tool for Identifying Epistemological Commitments in Scientific and Technical Communities. Article discusses how the STS concept of infrastructural provides a mesolayer approach to understand global issues in science with rhetorical methodology.

This article describes protocological rhetoric as a conceptual tool for exploring and changing institutions. Protocological rhetoric is an extension of two lines of thought: Porter, Sullivan, Blythe, Grabill, and Miles's institutional critique and Science & Technology Studies's (STS) concept of information infrastructure. As a result, protocological rhetoric imagines institutions as networked information infrastructures. This article describes the method and provides an example through historical case study. I suggest that the approach provides methods for actively transforming institutions.

The enzymatic mechanism that governs the synthesis of the xylan backbone polymer, a linear chain of xylose residues connected by β-1,4 glycosidic linkages, has remained elusive. Xylan is a major constituent of many kinds of plant cell walls, and genetic studies have identified multiple genes that affect xylan formation. In this study, we investigate several homologs of one of these previously identified xylan-related genes, IRX10 from Arabidopsis thaliana, by heterologous expression and in vitro xylan xylosyltransferase assay. We find that an IRX10 homolog from the moss Physcomitrella patens displays robust activity, and we show that the xylosidic linkage formed is a β-1,4 linkage, establishing this protein as a xylan β-1,4-xylosyltransferase. We also find lower but reproducible xylan xylosyltransferase activity with A. thaliana IRX10 and with a homolog from the dicot plant Plantago ovata, showing that xylan xylosyltransferase activity is conserved over large evolutionary distance for these proteins.

Dodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bidirectional movement of viruses, proteins and mRNAs between host and parasite, but the functional effects of these movements are not known. Here we show that Cuscuta campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana. Many of these miRNAs are 22 nucleotides in length. Plant miRNAs of this length are uncommon, and are associated with amplification of target silencing through secondary short interfering RNA (siRNA) production. Several A. thaliana mRNAs are targeted by 22-nucleotide C. campestris miRNAs during parasitism, resulting in mRNA cleavage, secondary siRNA production, and decreased mRNA accumulation. Hosts with mutations in two of the loci that encode target mRNAs supported significantly higher growth of C. campestris. The same miRNAs that are expressed and active when C. campestris parasitizes A. thaliana are also expressed and active when it infects Nicotiana benthamiana. Homologues of target mRNAs from many other plant species also contain the predicted target sites for the induced C. campestris miRNAs. These data show that C. campestris miRNAs act as trans-species regulators of host-gene expression, and suggest that they may act as virulence factors during parasitism.

This research argues that documents can become intermediaries which affect the relationships between disparate groups. Through a critical analysis of materials distributed during an online protest, the author traces the life of a single technical document, simultaneously describing how it was described during deliberation between several groups. Marcusean critical theory and rhetorical criticism framed the analysis. It is suggested that certain documents act as a locus between otherwise unaffiliated groups and that those documents become agents who can mediate deliberation. Further, it is suggested that document analysis can become an important aspect for interpreting group relationships. Future research examining the agency of documents is suggested.

This chapter examines how information infrastructure influences ethos in information labor. The primary text is discourse about ACID3, a web page created by members of the Web Standards Project. ACID3 tests the compliance of infrastructural standards for web browsers. In addition to analyzing ACID3 code, several other related conference presentations, job announcements, and web pages are analyzed to theorize ACID3 as a rhetorical text. This chapter argues that three rhetorical commonplaces (mastery, purity, infallibility) are central for the credibility of ACID3 as a text of legitimacy. This study provides a better understanding of rhetoric and infrastructure. To understand rhetorics of infrastructural standardization is to understand the power structures embedded within the modern world. ACID3 is a significant case because of its criticality for standards that enable publics to publish Web content. This chapter contributes to literature in information infrastructural studies, science and technology studies, and the rhetoric of science.

We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications. ©2008 by Cold Spring Harbor Laboratory Press. Fil: Rakyan, Vardhman K.. Barts And The London School Of Medicine And Dentistry; Fil: Down, Thomas A.. University of Cambridge; Estados Unidos Fil: Thorne, Natalie P.. University of Cambridge; Estados Unidos Fil: Flicek, Paul. European Bioinformatics Institute; Fil: Kulesha, Eugene. European Bioinformatics Institute; Fil: Gräf, Stefan. European Bioinformatics Institute; Fil: Tomazou, Eleni M.. Wellcome Trust Sanger Institute; Fil: Bäckdahl, Liselotte. Ucl Cancer Institute; Fil: Johnson, Nathan. European Bioinformatics Institute; Fil: Herberth, Marlis. University of Cambridge; Estados Unidos Fil: Howe, Kevin L.. University of Cambridge; Estados Unidos Fil: Jackson, David K.. Wellcome Trust Sanger Institute; Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina Fil: Fiegler, Heike. Roche Diagnostics Ltd.; . Wellcome Trust Sanger Institute; Fil: Marioni, John C.. University of Cambridge; Estados Unidos Fil: Birney, Ewan. European Bioinformatics Institute; Fil: Hubbard, Tim J. P.. Wellcome Trust Sanger Institute; Fil: Carter, Nigel P.. Wellcome Trust Sanger Institute; Fil: Tavaré, Simon. University of Cambridge; Estados Unidos Fil: Beck, Stephan G.. Ucl Cancer Institute