Momentum conserving defects in affine Toda field theory

This thesis expands previous work on defects appearing in classical integrable field theories, with a generalised form for momentum conserving defects being found. It is shown that the defect equations can always be augmented to give a Bäcklund transformation for the bulk theory, and new momentum conserving defects are found for the Br and Dr ATFTs. Momentum conservation is shown to be a necessary condition if the system is to have an infinite number of conserved quantities for all defects in ATFTs. The D4 defect in particular is investigated, with the system shown to have a zero curvature representation and soliton-defect interactions being investigated

Drug-responsive autism phenotypes in the 16p11.2 deletion mouse model: a central role for gene-environment interactions

There are no current treatments for autism, despite its high prevalence. Deletions of chromosome 16p11.2 dramatically increase risk for autism, suggesting that mice with an equivalent genetic rearrangement may offer a valuable model for the testing of novel classes of therapeutic drug. 16p11.2 deletion (16p11.2 DEL) mice and wild-type controls were assessed using an ethological approach, with 24 h monitoring of activity and social interaction of groups of mice in a home-cage environment. The ability of the excitation/inhibition modulator N-acetyl cysteine (NAC) and the 5-HT1B/1D/1F receptor agonist eletriptan to normalise the behavioural deficits observed was tested. 16p11.2 DEL mice exhibited largely normal behaviours, but, following the stress of an injection, showed hyperlocomotion, reduced sociability, and a strong anxiolytic phenotype. The hyperactivity and reduced sociability, but not the suppressed anxiety, were effectively attenuated by both NAC and eletriptan. The data suggest that 16p11.2 DEL mice show an autism-relevant phenotype that becomes overt after an acute stressor, emphasising the importance of gene-environmental interactions in phenotypic analysis. Further, they add to an emerging view that NAC, or 5-HT1B/1D/1F receptor agonist treatment, may be a promising strategy for further investigation as a future treatment

Characterizing replisome disassembly in human cells

To ensure timely duplication of the entire eukaryotic genome, thousands of replication machineries (replisomes) act on genomic DNA at any time during S phase. In the final stages of this process, replisomes are unloaded from chromatin. Unloading is driven by polyubiquitylation of MCM7, a subunit of the terminated replicative helicase, and processed by p97/VCP segregase. Most of our knowledge of replication termination comes from model organisms, and little is known about how this process is executed and regulated in human somatic cells. Here we show that replisome disassembly in this system requires CUL2LRR1-driven MCM7 ubiquitylation, p97, and UBXN7 for unloading and provide evidence for “backup” mitotic replisome disassembly, demonstrating conservation of such mechanisms. Finally, we find that small-molecule inhibitors against Cullin ubiquitin ligases (CULi) and p97 (p97i) affect replisome unloading but also lead to induction of replication stress in cells, which limits their usefulness to specifically target replisome disassembly processes

Trace Metal Chemistry in the Water Column of the Angola Basin - A Contribution to the International GEOTRACES Program - Cruise No. M121, November 22, – December 27, 2015, Walvis Bay (Namibia) – Walvis Bay (Namibia)

Meteor Cruise M121 was dedicated to the investigation of the distribution of dissolved and particulate trace metals and their isotopic compositions (TEIs) in the full water column of the Angola Basin and the northernmost Cape Basin. A key aim was to determine the driving factors for the observed distributions, which includes the main external inputs, as well as internal cycling and ocean circulation. The research program of the cruise is official part of the international GEOTRACES program (www.geotraces.org) and cruise M121 corresponds to GEOTRACES cruise GA11. Subject of the cruise was the trace metal clean and contamination-free sampling of waters and particulates for subsequent analyses of the TEIs in the home laboratories of the national and international participants. Besides a standard rosette for the less contaminant prone metals, trace metal clean sampling was realized by using for the first time a new dedicated, coated trace metal clean rosette equipped with Teflon-coated GO-FLO bottles operated via a plastic coated cable from a mobile winch of GEOMAR Kiel. The particulate samples were collected under trace metal clean conditions using established in-situ pump systems operated from Meteor’s Aramid line. The cruise track led from Walvis Bay northwards along the West African margin until 3°S, then turned west until the Zero Meridian, which was followed southwards until 30°S. Then the cruise track turned east again until the Namibian margin was reached and then completed the near shore track northwards until Walvis Bay. The track crossed areas of major external inputs including dust from the Namib Desert and exchange with the west African continental margin and with the oxygen depleted shelf sediments of the Benguela upwelling, as well as with the plume of the Congo outflow, that was followed from its mouth northwards. Our investigations of internal cycling included the extremely high productivity associated with the Benguela Upwelling and the elevated productivity of the Congo plume contrasting with the extremely oligotrophic waters of the southeastern Atlantic Gyre. The links between TEI biogeochemistry and the nitrogen cycle forms an important aspect of our study. The major water masses contributing the Atlantic Meridional Overturning Circulation were sampled in order to investigate if particular TEI signatures are suitable as water mass tracers, in particular near the ocean margin and in the restricted deep Angola Basin. A total of 51 full water column stations were sampled for the different dissolved TEIs, which were in most cases accompanied by sampling for particulates and radium isotopes using the in-situ pumps. In addition, surface waters were continuously sampled under trace metal clean conditions using a towed fish and aerosol and rain samples were continuously collected

Identification of functional elements and regulatory circuits by Drosophila modENCODE

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation

A Cis-Regulatory Map of the Drosophila Genome

Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide1, 2 has successfully identified specific subtypes of regulatory elements3. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements4, chromatin states5, transcription factor binding sites6, 7, 8, 9, RNA polymerase II regulation8 and insulator elements10; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships