The biochemical basis of changes in normal and mutant human skin fibroblasts during ageing in culture : an investigation into the free radical theory of ageing

From the pattern of inheritance of normal ageing, this process inevitably results from either abnormal aggregation of subunits of enzymes, abnormal feedback inhibition of enzymes, receptor mutations, membrane defects, or deposition of abnormal fibrillar proteins (Vogel and Motulsky, 1986). The process of ageing should, due to the principle of universality, occur at a site common to all cells : general metabolism, chromatin structure and function ( eg. DNA replication and gene expression) or the physiology of the membrane. The cell type to be studied should be fully functional as to these three sites, and the theories potentially able to explain the ageing process should all encompass changes at any of these aspects . of cellular function. The system to be used throughout this thesis is the cultured human skin fibroblast, which still expresses genes, replicates DNA, has a general metabolism and has functional membranes. This cell type alos undergoes a loss of proliferative potential both in vivo and in culture (Martin et al.,1970). Furthermore, any kind of a phenotype expressed in fibroblast-like cells can theoretically be used for prenatal diagnosis of human genotypes (eg. Werner's syndrome and Spielmeyer-Vogt syndrome). The following postulates can be derived now. First, free radicals should cause the accumulation of lipid peroxides or decay products, which should further yield to the accumulation of autofluorescence. Second, free radicals, or the reactive products resulting from them should impair cellular proliferation to the extent as to cause an irreversible growth arrest of initially dividing cells. Third, crosslinking of proteins by reactive breakdown products of lipid peroxides should occur. Fourth, the capacity of the systems implied in the detoxification of free radicals, or the reactive products thereof, should decrease in capacity during ageing of cultured cells

Identifying Human Disease Genes through Cross-Species Gene Mapping of Evolutionary Conserved Processes

Understanding complex networks that modulate development in humans is hampered by genetic and phenotypic heterogeneity within and between populations. Here we present a method that exploits natural variation in highly diverse mouse genetic reference panels in which genetic and environmental factors can be tightly controlled. The aim of our study is to test a cross-species genetic mapping strategy, which compares data of gene mapping in human patients with functional data obtained by QTL mapping in recombinant inbred mouse strains in order to prioritize human disease candidate genes.We exploit evolutionary conservation of developmental phenotypes to discover gene variants that influence brain development in humans. We studied corpus callosum volume in a recombinant inbred mouse panel (C57BL/6J×DBA/2J, BXD strains) using high-field strength MRI technology. We aligned mouse mapping results for this neuro-anatomical phenotype with genetic data from patients with abnormal corpus callosum (ACC) development.).This approach that exploits highly diverse mouse strains provides an efficient and effective translational bridge to study the etiology of human developmental disorders, such as autism and schizophrenia

Physical and functional interactions between Werner syndrome helicase and mismatch-repair initiation factors

Werner syndrome (WS) is a severe recessive disorder characterized by premature aging, cancer predisposition and genomic instability. The gene mutated in WS encodes a bi-functional enzyme called WRN that acts as a RecQ-type DNA helicase and a 3′-5′ exonuclease, but its exact role in DNA metabolism is poorly understood. Here we show that WRN physically interacts with the MSH2/MSH6 (MutSα), MSH2/MSH3 (MutSβ) and MLH1/PMS2 (MutLα) heterodimers that are involved in the initiation of mismatch repair (MMR) and the rejection of homeologous recombination. MutSα and MutSβ can strongly stimulate the helicase activity of WRN specifically on forked DNA structures with a 3′-single-stranded arm. The stimulatory effect of MutSα on WRN-mediated unwinding is enhanced by a G/T mismatch in the DNA duplex ahead of the fork. The MutLα protein known to bind to the MutS α–heteroduplex complexes has no effect on WRN-mediated DNA unwinding stimulated by MutSα, nor does it affect DNA unwinding by WRN alone. Our data are consistent with results of genetic experiments in yeast suggesting that MMR factors act in conjunction with a RecQ-type helicase to reject recombination between divergent sequences

Oil dispersal modelling: reanalysis of the Rena oil spill using open-source modelling tools

Oil spill forecast modelling is typically used immediately after a spill to predict oil dispersal and promote mobilisation of more effective response operations. The aim of this work was to map oil dispersal after the grounding of the MV Rena on Astrolabe Reef and to verify the results against observations. Model predictions were broadly consistent with observed distribution of oil contamination. However, some hot spots of oil accumulation, likely due to surf-zone and rip current circulation, were not well represented. Additionally, the model was run with 81 differing wind conditions to show that the events occurring during the grounding represented the typical likely behaviour of an oil spill on Astrolabe Reef. Oil dispersal was highly dependent on prevailing wind patterns; more accurate prediction would require better observations of local wind patterns. However, comparison of predictions with observations indicated that the GNOME model was an effective low-cost approach

Improving the Quality of Care in Care Homes Using the Quality Improvement Collaborative Approach: Lessons Learnt from Six Projects Conducted in the UK and The Netherlands.

The Breakthrough Series Quality Improvement Collaborative (QIC) initiative is a well-developed and widely used approach, but most of what we know about it has come from healthcare settings. In this article, those leading QICs to improve care in care homes provide detailed accounts of six QICs and share their learning of applying the QIC approach in the care home sector. Overall, five care home-specific lessons were learnt: (i) plan for the resources needed to support collaborative teams with collecting, processing, and interpreting data; (ii) create encouraging and safe working environments to help collaborative team members feel valued; (iii) recruit collaborative teams, QIC leads, and facilitators who have established relationships with care homes; (iv) regularly check project ideas are aligned with team members' job roles, responsibilities, and priorities; and (v) work flexibly and accept that planned activities may need adapting as the project progresses. These insights are targeted at teams delivering QICs in care homes. These insights demonstrate the need to consider the care home context when applying improvement tools and techniques in this setting

Compartmentalization of androgen receptors at endogenous genes in living cells

A wide range of nuclear proteins are involved in the spatio-temporal organization of the genome through diverse biological processes such as gene transcription and DNA replication. Upon stimulation by testosterone and translocation to the nucleus, multiple androgen receptors (ARs) accumulate in microscopically discernable foci which are irregularly distributed in the nucleus. Here, we investigated the formation and physical nature of these foci, by combining novel fluorescent labeling techniques to visualize a defined chromatin locus of AR-regulated genes-PTPRN2 or BANP-simultaneously with either AR foci or individual AR molecules. Quantitative colocalization analysis showed evidence of AR foci formation induced by R1881 at both PTPRN2 and BANP loci. Furthermore, single-particle tracking (SPT) revealed three distinct subdiffusive fractional Brownian motion (fBm) states: immobilized ARs were observed near the labeled genes likely as a consequence of DNA-binding, while the intermediate confined state showed a similar spatial behavior but with larger displacements, suggesting compartmentalization by liquid-liquid phase separation (LLPS), while freely mobile ARs were diffusing in the nuclear environment. All together, we show for the first time in living cells the presence of AR-regulated genes in AR foci.</p

Social responsiveness scale-aided analysis of the clinical impact of copy number variations in autism

Recent array-based studies have detected a wealth of copy number variations (CNVs) in patients with autism spectrum disorders (ASD). Since CNVs also occur in healthy individuals, their contributions to the patient’s phenotype remain largely unclear. In a cohort of children with symptoms of ASD, diagnosis of the index patient using ADOS-G and ADI-R was performed, and the Social Responsiveness Scale (SRS) was administered to the index patients, both parents, and all available siblings. CNVs were identified using SNP arrays and confirmed by FISH or array CGH. To evaluate the clinical significance of CNVs, we analyzed three families with multiple affected children (multiplex) and six families with a single affected child (simplex) in which at least one child carried a CNV with a brain-transcribed gene. CNVs containing genes that participate in pathways previously implicated in ASD, such as the phosphoinositol signaling pathway (PIK3CA, GIRDIN), contactin-based networks of cell communication (CNTN6), and microcephalin (MCPH1) were found not to co-segregate with ASD phenotypes. In one family, a loss of CNTN5 co-segregated with disease. This indicates that most CNVs may by themselves not be sufficient to cause ASD, but still may contribute to the phenotype by additive or epistatic interactions with inherited (transmitted) mutations or non-genetic factors. Our study extends the scope of genome-wide CNV profiling beyond de novo CNVs in sporadic patients and may aid in uncovering missing heritability in genome-wide screening studies of complex psychiatric disorders

Continuum elastic modeling of graphene resonators

Starting from an atomistic approach we have derived a hierarchy of successively more simplified continuum elasticity descriptions for modeling the mechanical properties of suspended graphene sheets. The descriptions are validated by applying them to square graphene-based resonators with clamped edges and studying numerically their mechanical responses. Both static and dynamic responses are treated. We find that already for deflections of the order of 0.5{\AA} a theory that correctly accounts for nonlinearities is necessary and that for many purposes a set of coupled Duffing-type equations may be used to accurately describe the dynamics of graphene membranes.Comment: 7 pages, 5 figure

Green function techniques in the treatment of quantum transport at the molecular scale

The theoretical investigation of charge (and spin) transport at nanometer length scales requires the use of advanced and powerful techniques able to deal with the dynamical properties of the relevant physical systems, to explicitly include out-of-equilibrium situations typical for electrical/heat transport as well as to take into account interaction effects in a systematic way. Equilibrium Green function techniques and their extension to non-equilibrium situations via the Keldysh formalism build one of the pillars of current state-of-the-art approaches to quantum transport which have been implemented in both model Hamiltonian formulations and first-principle methodologies. We offer a tutorial overview of the applications of Green functions to deal with some fundamental aspects of charge transport at the nanoscale, mainly focusing on applications to model Hamiltonian formulations.Comment: Tutorial review, LaTeX, 129 pages, 41 figures, 300 references, submitted to Springer series "Lecture Notes in Physics

Evidence for a hopping mechanism in metal|single molecule|metal junctions involving conjugated metal–terpyridyl complexes; potential-dependent conductances of complexes [M(pyterpy)₂] ²⁺ (M = Co and Fe; pyterpy = 4′-(pyridin-4-yl)-2,2′:6′,2′′-terpyridine) in ionic liquid

Extensive studies of various families of conjugated molecules in metal|molecule|metal junctions suggest that the mechanism of conductance is usually tunnelling for molecular lengths < ca. 4 nm, and that for longer molecules, coherence is lost as a hopping element becomes more significant. In this work we present evidence that, for a family of conjugated, redox-active metal complexes, hopping may be a significant factor for even the shortest molecule studied (ca. 1 nm between contact atoms). The length dependence of conductance for two series of such complexes which differ essentially in the number of conjugated 1,4-C₆H₄- rings in the structures has been studied, and it is found that the junction conductances vary linearly with molecular length, consistent with a hopping mechanism, whereas there is significant deviation from linearity in plots of log(conductance) vs. length that would be characteristic of tunnelling, and the slopes of the log(conductance)–length plots are much smaller than expected for an oligophenyl system. Moreover, the conductances of molecular junctions involving the redox–active molecules, [M(pyterpy)₂] ²⁺/³⁺ (M = Co, Fe) have been studied as a function of electrochemical potential in ionic liquid electrolyte, and the conductance–overpotential relationship is found to fit well with the Kuznetsov–Ulstrup relationship, which is essentially a hopping description