Locating and building knowledges outside of the academy : approaches to engaged teaching at the University of Sheffield

This article draws on three case studies, which illuminate a number of practical, ethical and intellectual issues that arise from engaged teaching activities within the curriculum. Projects from the disciplines of Architecture, English and Journalism Studies illustrate the possibilities offered by learning and teaching projects which emphasise public facing, co-produced knowledge as central components. It is argued that such approaches enable dynamic forms of learning to emerge, which work to expand the parameters of subject-specific knowledge while enabling the development of citizenship attributes and employability skills amongst students in ways that deepen, rather than dilute, intellectual rigour. The article locates these practical pedagogical reflections within theoretical frameworks offered by those working (largely in North America* on publicly engaged approaches to scholarship and seeks to draw connections with contemporary developments in learning and teaching in the UK. Keywords: civic university; engaged teaching; engaged scholarship; co-productio

Genome-Wide Functional Analysis of the Cotton Transcriptome by Creating an Integrated EST Database

A total of 28,432 unique contigs (25,371 in consensus contigs and 3,061 as singletons) were assembled from all 268,786 cotton ESTs currently available. Several in silico approaches [comparative genomics, Blast, Gene Ontology (GO) analysis, and pathway enrichment by Kyoto Encyclopedia of Genes and Genomes (KEGG)] were employed to investigate global functions of the cotton transcriptome. Cotton EST contigs were clustered into 5,461 groups with a maximum cluster size of 196 members. A total of 27,956 indel mutants and 149,616 single nucleotide polymorphisms (SNPs) were identified from consensus contigs. Interestingly, many contigs with significantly high frequencies of indels or SNPs encode transcription factors and protein kinases. In a comparison with six model plant species, cotton ESTs show the highest overall similarity to grape. A total of 87 cotton miRNAs were identified; 59 of these have not been reported previously from experimental or bioinformatics investigations. We also predicted 3,260 genes as miRNAs targets, which are associated with multiple biological functions, including stress response, metabolism, hormone signal transduction and fiber development. We identified 151 and 4,214 EST-simple sequence repeats (SSRs) from contigs and raw ESTs respectively. To make these data widely available, and to facilitate access to EST-related genetic information, we integrated our results into a comprehensive, fully downloadable web-based cotton EST database (www.leonxie.com)

How I See Me-A Meta-Analysis Investigating the Association Between Identities and Pro-environmental Behaviour

Prolific research suggests identity associates with pro-environmental behaviours (PEBs) that are individual and/or group focused. Individual PEB is personally driven, self-reliant, and are conducted on one’s own (e.g., home recycling). Group focused PEB is other people-reliant and completed as part of a group (e.g., attending meetings of an environmental organisation). A wide range of identities have been related to PEBs. For example, a recent systematic qualitative review revealed 99 different types of identities studied in a PEB context. Most studies were correlational, few had an experimental design. However, the relationships between all these identities and PEBs have so far not been tested quantitatively with meta-analytical techniques. As such, a clear overview of this field is currently lacking. Due to the diverse nature of the field, a priori hypotheses were not possible and relatively broad definitions of identity had to be used to encompass all types of identities and the diverse meanings of identity that have been included in PEB research. What prior theory did allow for was to assess the distinction between two main types of identity, namely how people label, describe, and recognise oneself individually (individual identity), or as part of a group (group identity). Our overall goal was thus to assess the current state of knowledge on identities and PEBs. In 104 studies using a meta-regression following the preferred reporting items for systematic reviews and meta-analyses guidelines, our random-effects meta-analysis showed that the overall concept of identity associated with PEB with a medium Pearson’s r (Aim 1). Furthermore, we found that individual identities associated more strongly with PEBs than group identities (Aim 2). The associations between individual and group identities were stronger when the identity and PEB were from the same category (e.g., when both were group-focused; Aim 3). Methodologically, the findings revealed that group identities and group PEBs were most strongly associated for self-reported rather than observed PEBs (Aim 4). Overall identity associated most strongly with group PEBs in the field rather than in the lab (Aim 5) and in student- rather than non-student samples (Aim 6). We discuss the theoretical and practical implications

Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp.

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community. (Résumé d'auteur

Development and mapping of SNP assays in allotetraploid cotton

A narrow germplasm base and a complex allotetraploid genome have made the discovery of single nucleotide polymorphism (SNP) markers difficult in cotton (Gossypiumhirsutum). To generate sequence for SNP discovery, we conducted a genome reduction experiment (EcoRI, BafI double digest, followed by adapter ligation, biotin–streptavidin purification, and agarose gel separation) on two accessions of G. hirsutum and two accessions of G. barbadense. From the genome reduction experiment, a total of 2.04 million genomic sequence reads were assembled into contigs with an N50 of 508 bp and analyzed for SNPs. A previously generated assembly of expressed sequence tags (ESTs) provided an additional source for SNP discovery. Using highly conservative parameters (minimum coverage of 8× at each SNP and 20% minor allele frequency), a total of 11,834 and 1,679 non-genic SNPs were identified between accessions of G. hirsutum and G. barbadense in genome reduction assemblies, respectively. An additional 4,327 genic SNPs were also identified between accessions of G. hirsutum in the EST assembly. KBioscience KASPar assays were designed for a portion of the intra-specific G. hirsutum SNPs. From 704 non-genic and 348 genic markers developed, a total of 367 (267 non-genic, 100 genic) mapped in a segregating F2 population (Acala Maxxa × TX2094) using the Fluidigm EP1 system. A G. hirsutum genetic linkage map of 1,688 cM was constructed based entirely on these new SNP markers. Of the genic-based SNPs, we were able to identify within which genome (‘A’ or ‘D’) each SNP resided using diploid species sequence data. Genetic maps generated by these newly identified markers are being used to locate quantitative, economically important regions within the cotton genome