Paving the way for research findings: writers' rhetorical choices in education and applied linguistics

Notwithstanding the existence of previous investigations into how research results are presented in different academic disciplines, fewer studies have looked into how authors pave the way for their results, the interdisciplinary differences in ‘result pavements’, and the interconnections between their communicative functions and linguistic choices. Using the techniques of genre analysis, I have analyzed two corpora of research reports in applied linguistics and education in order to identify the possible ways in which experienced writers schematically pave the way for their findings. Using evidence based on authentic research articles, this study demonstrates how writers set the stage for their research results by (i) demonstrating their control of the structure and flow of result-related information, (ii) connecting past research with a current finding while furnishing pertinent background elements that lead the readership progressively to specific findings, (iii) regenerating readers’ interest in their initial research purposes, and (iv) deploying locatives to embed results in a ‘space-saving strategy’ aimed at presenting an abridged Results section. I have also analyzed interdisciplinary differences in the frequencies of these rhetorical steps and the range of intricate linguistic mechanisms employed by authors as communicative resources in each step to establish a smooth rhetorical transition that sets the stage for their research results

The expression of FHIT, PCNA and EGFR in benign and malignant breast lesions

Immunohistochemical staining for FHIT and PCNA proteins was carried out in 451 breast lesions showing nonproliferative benign breast disease (BBD) (n=263), proliferative BBD without atypia (n=128), proliferative BBD with atypia (n=11), carcinoma in situ (n=15) or invasive carcinoma (n=34) and for EGFR protein in a subset of 71 of these cases. FHIT underexpression was not detected in nonproliferative lesions, but occurred in 2% of proliferative BBD without atypia, 10% proliferative BBD with atypia, 27% of carcinoma in situ and 41% of invasive carcinoma, which suggests that it could be useful in assessing those carcinoma in situ lesions (ductal, DCIS and lobular, LCIS) that are more likely to progress to malignancy. Preliminary microarray comparisons on DCIS and invasive carcinoma samples dissected from formalin-fixed paraffin sections showed a consistent downregulation of two previously identified FHIT-related genes, caspase 1 and BRCA1 in lesions underexpressing FHIT

Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast

In eukaryotes, the conjugation of proteins to the small ubiquitin-like modifier (SUMO) regulates numerous cellular functions. A proportion of SUMO conjugates are targeted for degradation by SUMO-targeted ubiquitin ligases (STUbLs) and it has been proposed that the ubiquitin-selective chaperone Cdc48/p97-Ufd1-Npl4 facilitates this process. However, the extent to which the two pathways overlap, and how substrates are selected, remains unknown. Here we address these questions in fission yeast through proteome-wide analyses of SUMO modification sites. We identify over a thousand sumoylated lysines in a total of 468 proteins and quantify changes occurring in the SUMO modification status when the STUbL or Ufd1 pathways are compromised by mutations. The data suggest the coordinated processing of several classes of SUMO conjugates, many dynamically associated with centromeres or telomeres. They provide new insights into subnuclear organization and chromosome biology, and, altogether, constitute an extensive resource for the molecular characterization of SUMO function and dynamics

Uncovering Ubiquitin and Ubiquitin-like Signaling Networks

Microscopic imaging and technolog

The pragmatics of text facilitation : the study of academic English of native and non-native writers

In this paper I describe the discursive strategies related to the writer&ndash;reader textual reciprocity. I focus on one way of achieving such reciprocity -- the employment by the writer of facilitative schematic structures and metalanguage where one text segment signposts information conveyed in the segment that follows. I refer to these facilitative schematic structures as &quot;organising relational schemata&quot;. I see organising relations as the most explicit components of the rhetorical structure of texts: they illuminate the main message and aid the reader\u27s cognitive processes in the orientation of how information is conveyed by text.This paper discusses the way the choices of organising relations and associated metalanguage by the writers in different cultures and different discourse communities contribute to the communicative homeostasis in the world of text. It shows how the influence of a native culture and intellectual style together with the forces operating within the writer\u27s international disciplinary community interact in the authorial guidance in the scholarly prose.I introduce and exemplify three types of organising relational structures: Advance Organisers, Introducers and Enumerators. I trace the utilisation of these three types of relations in sociology research papers written in English and produced in &quot;Anglo&quot; and Polish academic discourse comunities by native English speaking and native Polish speaking scholars. The relational typology adopted is based on a study by Golebiowski (2002), which proposed a theoretical framework for the examination of discoursal structure of research papers, referred to as FARS &ndash; Framework for the Analysis of the Rhetorical Structure of Texts. FARS entails a relational taxonomy which displays a pattern of rhetorical relations utilised by the writer to achieve textual coherence.I describe intertextual differences in the frequency of occurrence of organising relations, their degree of explicitness and their positioning in the hierarchical structure of texts. Differences in the mode of employment of textual organisers suggest that the rhetorical structure of English research prose produced by non-native speakers cannot escape being shaped by the characteristics and conventions of the authors&rsquo; first language. They are also attributed to cultural norms and conventions as well as educational systems prevailing within the discourse communities which constitute the social contexts of texts.<br /

The distribution of discoursal salience in research papers: relational hypotaxis and parataxis

In this article I challenge the claim that nuclearity is a central principle in the organization of texts. I propose the Framework for the Relational Analysis of Texts (FARS) which accounts for the paratactic and hypotactic realization of coherence relations. Within this framework, the taxis of coherence relations is co-textually dictated. I consider the writer choices in the distribution of discoursal salience and the intertextual and intercultural variation of these choices. It is suggested that divergence between approaches that perceive text as exhibiting both hypotactic and paratactic organization and those that see nuclearity as a basic characteristic of text structure arises from differences in the linguistic corpora examined during the construction of respective theoretical frameworks.<br /

Solid-phase assembly and in situ screening of protein tyrosine phosphatase inhibitors

10.1021/ol8006875Organic Letters10112295-229

Mass spectrometric identification of SUMO substrates provides insights into heat stress-induced SUMOylation in plants

The covalent addition of Small Ubiquitin-Like Modifier (SUMO) to various intracellular proteins is an essential regulatory step in most eukaryotes. Due to its necessity and the large number of putative targets, SUMO is thought to be second only to ubiquitin (Ub) among Ub-fold proteins in terms of regulatory influence. Whereas, ubiquitylation (i.e., the attachment of Ub) is generally associated with protein degradation, SUMOylation appears to have more diverse consequences, including the regulation of transcription, chromatin structure/accessibility, nuclear import and various protein-protein interactions, and even appears to block the action of Ub by competing for the same binding sites on targets.1–3 Paramount to understanding SUMO function(s) is knowing the complete catalog of SUMO targets. In the following addendum we review our recent publication4 describing the proteomic identification of SUMO substrates in the model plant, Arabidopsis thaliana, and expand our analyses with regard to the changes in SUMOylation patterns that are induced by heat stress. Collectively, our data indicate that SUMOylation is highly dynamic with evidence that SUMO addition globally modifies transcription and chromatin accessibility, especially during stress

Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis

The covalent attachment of SUMO (small ubiquitin-like modifier) to other intracellular proteins affects a broad range of nuclear processes in yeast and animals, including chromatin maintenance, transcription, and transport across the nuclear envelope, as well as protects proteins from ubiquitin addition. Substantial increases in SUMOylated proteins upon various stresses have also implicated this modification in the general stress response. To help understand the role(s) of SUMOylation in plants, we developed a stringent method to isolate SUMO-protein conjugates from Arabidopsis thaliana that exploits a tagged SUMO1 variant that faithfully replaces the wild-type protein. Following purification under denaturing conditions, SUMOylated proteins were identified by tandem mass spectrometry from both nonstressed plants and those exposed to heat and oxidative stress. The list of targets is enriched for factors that direct SUMOylation and for nuclear proteins involved in chromatin remodeling/repair, transcription, RNA metabolism, and protein trafficking. Targets of particular interest include histone H2B, components in the LEUNIG/TOPLESS corepressor complexes, and proteins that control histone acetylation and DNA methylation, which affect genome-wide transcription. SUMO attachment site(s) were identified in a subset of targets, including SUMO1 itself to confirm the assembly of poly-SUMO chains. SUMO1 also becomes conjugated with ubiquitin during heat stress, thus connecting these two posttranslational modifications in plants. Taken together, we propose that SUMOylation represents a rapid and global mechanism for reversibly manipulating plant chromosomal functions, especially during environmental stress