The collaborative research network: developing interdisciplinary student partnerships

An overview of the collaborative research undertaken by academics from the Lincoln School of Film and Media, and the formation of the co_LAB Research Network. co_LAB was designed to explore and develop new approaches to collaborative teaching and learning through the use of networked digital tools, and through the transferral of knowledge, skillsets and teaching styles. This talk outlines how the values of Student as Producer have recently been implemented by co_LAB, both at an institutional/curriculum level, and through a number of EU Erasmus funded projects in partnership with universities from across Europe

Sedimentary models and geomorphological classification of river-mouths on a subtropical, wave-dominated coast, Natal, South Africa.

Thesis (Ph.D.-Geology)-University of Natal, 1991Abstract available in PDF

Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

Population divergence and gene flow are key processes in evolution and ecology. Model‐based analysis of genome‐wide datasets allows discrimination between alternative scenarios for these processes even in non‐model taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum (bSFS), the second on the Pairwise Sequentially Markovian Coalescent (PSMC)) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia, and are separated into northern and southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of post divergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca . 196kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca . 57kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome‐level data for small population samples of tiny, non‐model organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.Output Status: Forthcoming/Available Onlin

co_LAB - Project 1

co_LAB is an interdisciplinary, educational project which houses intensive teaching programmes, the first of which took place between 12-16 May, 2014. co_LAB was designed to explore and develop new approaches to collaborative teaching and learning through the use of networked digital tools, and through the transferral of knowledge, skillsets and teaching styles. co_LAB aims to overcome the traditional barriers between individual course specialisms by bringing together students and colleagues from across academic disciplines to collaborate on transmedia design projects. co_LAB team: Martyn Thayne, James Field, Graham Cooper, Rob Coley, Richard Vickers, Adam Verity, Clive McCarthy (special thanks to Louise Lawlor, Mike Downing, Mark Aldridge, John Murray, Chris Heydra (The Hague University of Applied Sciences

Astrometry with the Keck-Interferometer: the ASTRA project and its science

The sensitivity and astrometry upgrade ASTRA of the Keck Interferometer is introduced. After a brief overview of the underlying interferometric principles, the technology and concepts of the upgrade are presented. The interferometric dual-field technology of ASTRA will provide the KI with the means to observe two objects simultaneously, and measure the distance between them with a precision eventually better than 100 uas. This astrometric functionality of ASTRA will add a unique observing tool to fields of astrophysical research as diverse as exo-planetary kinematics, binary astrometry, and the investigation of stars accelerated by the massive black hole in the center of the Milky Way as discussed in this contribution.Comment: 22 pages, 10 figures (low resolution), contribution to the summerschool "Astrometry and Imaging with the Very Large Telescope Interferometer", 2 - 13 June, 2008, Keszthely, Hungary, corrected authorlis

Novel octaketide macrolides related to 6-deoxyerythronolide B provide evidence for iterative operation of the erythromycin polyketide synthase

AbstractBackground: The macrolide antibiotic erythromycin A, like other complex aliphatic polyketides, is synthesised by a bacterial modular polyketide synthase (PKS). Such PKSs, in contrast to other fatty acid and polyketide synthases which work iteratively, contain a separate set or module of enzyme activities for each successive cycle of polyketide chain extension, and the number and type of modules together determine the structure of the polyketide product. Thus, the six extension modules of the erythromycin PKS (DEBS) together catalyse the production of the specific heptaketide 6-deoxyerythronolide B.Results: A mutant strain of the erythromycin producer Saccharopolyspora erythraea, which accumulates the aglycone intermediate erythronolide B, was found unexpectedly to produce two novel octaketides, both 16-membered macrolides. These compounds were detectable in fermentation broths of wild-type S. erythraea, but not in a strain from which the DEBS genes had been specifically deleted. From their structures, both of these octaketides appear to be aberrant products of DEBS in which module 4 has ‘stuttered’, that is, has catalysed two successive cycles of chain extension.Conclusions: The isolation of novel DEBS-derived octaketides provides the first evidence that an extension module in a modular PKS has the potential to catalyse iterative rounds of chain elongation like other type I FAS and PKS systems. The factors governing the extent of such ‘stuttering’ remain to be determined

A Sweet Killer: Mesoporous Polysaccharide Confined Silver Nanoparticles for Antibacterial Applications

Silver nanoparticles (AgNP) confined within porous starch have been prepared in a simple, green and efficient manner, utilising the nanoporous structure of predominantly mesoporous starch (MS) to act as nanoparticle stabiliser, support and reducing surface. MS/AgNP materials present high surface areas (SBET > 150 m2 g−1) and mesopore volumes (Vmeso > 0.45 cm3 g−1). The interaction of the AgNP precursor and forming nanoparticle nuclei with the mesoporous domains of the porous polysaccharide, direct porosity to increasingly narrower and more defined pore size distributions, indicative of a degree of cooperative assembly. Transmission electron microscopy images indicated the presence of spherical AgNP of a size reflective of the porous polysaccharide mesopore diameter (e.g., 5–25 nm), whilst XPS analysis confirmed the metallic Ag0 state. Materials were prepared at relatively low Ag loadings (<0.18 mmol g−1), demonstrating excellent antimicrobial activity in solid and liquid phase testing against Gram negative (E. coli) and positive (S. aureus) model bacteria. The resulting materials are biocompatible and present a useful solid porous carbohydrate-based polymer vehicle to control the AgNP size regime and facilitate transference to a biological environment

Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotopes

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode

Experimental investigation into the impact of a liquid droplet onto a granular bed using three-dimensional, time-resolved, particle tracking

This article was published in the journal, Physical Review E [ © American Physical Society] and the definitive version is available at: http://dx.doi.org/10.1103/PhysRevE.89.032201An experimental investigation into the interaction that occurs between an impacting water droplet and a granular bed of loose graded sand has been carried out. High-speed imaging, three-dimensional time-resolved particle tracking, and photogrammetric surface profiling have been used to examine individual impact events. The focus of the study is the quantification and trajectory analysis of the particles ejected from the sand bed, along with measurement of the change in bed morphology. The results from the experiments have detailed two distinct mechanisms of particle ejection: the ejection of water-encapsulated particles from the edge of the wetted region and the ejection of dry sand from the periphery of the impact crater. That the process occurs by these two distinct mechanisms has hitherto been unobserved. Presented in the paper are distributions of the particle ejection velocities, angles, and transport distances for both mechanisms. The ejected water-encapsulated particles, which are few in number, are characterized by low ejection angles and high ejection velocities, leading to large transport distances; the ejected dry particles, which are much greater in number, are characterized by high ejection angles and low velocities, leading to lower transport distances. From the particle ejection data, the momentum of the individual ballistic sand particles has been calculated; it was found that only 2% of the water-droplet momentum at impact is transferred to the ballistic sand particles. In addition to the particle tracking, surface profiling of the granular bed postimpact has provided detailed information on its morphology; these data have demonstrated the consistent nature of the craters produced by the impact and suggest that particle agglomerations released from their edges make up about twice the number of particles involved in ballistic ejection. It is estimated that, overall, about 4% of the water-droplet momentum is taken up in particle movement