Electron paramagnetic resonance studies of spin-labelled ethidium bromide DNA interactions

Spin-Labelled Ethidium Bromide (SLEB) was prepared in order to study its interactions with natural DNA in the form of fibres . The technique of electron paramagnetic resonance was used in this thesis. Knowledge of the conformational transition pathway of natural DNA for given counterion concentration as a function of relative humidity was utilised in the study of effect DNA confomation on the binding of SLEB. To aid interpretation of the results the relevant background material was reviewed. In order to attempt to extract geometric information on binding computer ERR lineshape simulations were used. To facilitate this a microcomputer spectrometer control system was designed and implemented. This allowed spectra to be acquired in digital form and transfered to the mainframe computer. Two schemes for magnetic field control were investigated, one based on a commercial NMR magnetometer, and a superior pulsed NMR field locking magnetometer developed in this laboratory. In order to obtain lineshapes undistorted by dipolar broadening it is advantageous to use fibres with a high phosphate to drug ratio (P/D), however spectrometer sensitivity becomes a limiting factor. A review of noise in spectrometer systems is included. The use of a microwave low-noise preamplifer to reduce the system noise figure was investigated. An attempt to construct a loop-gap resonator was made and justified theoretically. A 35GHz spectrometer was constructed and a cavity designed and built to allow the humidity to be varied. The system was made compatible with the control system. Spectra recorded and simulated at this frequency should help confirm those obtained at 9GHz. The results obtained from P/D«70 fibres with a 0.5mM NaCl concentration show the SLEB is in a disordered state from 33% to 75% relative humidity. Spectral changes occur in the range 75% to 98% consistant with intercalation. In this humidity range a transition to the B-form is expected

Control difuso en el contexto constitucional ecuatoriano, la certeza y la duda razonable y motivada en la Constitución de 2008.

This thesis has been developed based on the Judicial Review of constitutionality, from what doctrine says about key issues such as the Constitution, the principles of Constitutional Supremacy and the Normative Hierarchy related to this. Judicial Review is the stimulus for the various control mechanisms that guarantee the standards and conditions of the Supreme Law or Constitution. An analysis of the systems that control constitutionality has been done in order to be able to understand its nature, scope and functionality. This includes an assessment of the elements that allow us to argue that in Ecuador Judicial Review still exists.Esta tesina tiene como eje principal el control difuso de constitucionalidad. Para enfocar debidamente el tema, es necesario estudiar de lo que dice la doctrina en temas claves como la Constitución, los principios de supremacía constitucional y jerarquía normativa, inspiradores de los distintos mecanismos de control que garantizan su condición de norma suprema dentro del ordenamiento jurídico. De forma complementaria, este trabajo profundizará en cada uno de los sistemas de control de constitucionalidad para entender su naturaleza, alcance y funcionalidad. Así, será posible identificar los elementos que nos permiten sostener que en el Ecuador sigue existiendo el control difuso

Distinct conformational stability and functional activity of four highly homologous endonuclease colicins

The family of conserved colicin DNases E2, E7, E8, and E9 are microbial toxins that kill bacteria through random degradation of the chromosomal DNA. In the present work, we compare side by side the conformational stabilities of these four highly homologous colicin DNases. Our results indicate that the apo-forms of these colicins are at room temperature and neutral pH in a dynamic conformational equilibrium between at least two quite distinct conformers. We show that the thermal stabilities of the apo-proteins differ by up to 20degreesC. The observed differences correlate with the observed conformational behavior, that is, the tendency of the protein to form either an open, less stable or closed, more stable conformation in solution, as deduced by both tryptophan accessibility studies and electrospray ionization mass spectrometry. Given these surprising structural differences, we next probed the catalytic activity of the four DNases and also observed a significant variation in relative activities. However, no unequivocal link between the activity of the protein and its thermal and structural stability could easily be made. The observed differences in conformational and functional properties of the four colicin DNases are surprising given that they are a closely related ( greater than or equal to65% identity) family of enzymes containing a highly conserved (betabetaalpha-Me) active site motif. The different behavior of the apo-enzymes must therefore most likely depend on more subtle changes in amino acid sequences, most likely in the exosite region (residues 72-98) that is required for specific high-affinity binding of the cognate immunity protein

Evaluating and Optimizing Fish Health and Welfare During Experimental Procedures.

This is the final version of the article. It first appeared from Mary Ann Liebert, Inc. via http://dx.doi.org/10.1089/zeb.2015.1165Many facilities house fish in separate static containers post-procedure, for example, while awaiting genotyping results. This ensures fish can be easily identified, but it does not allow for provision of continuous filtered water or diet. At the Wellcome Trust Sanger Institute, concern over the housing conditions led to the development of an individual housing system (GeneS) enabling feeding and water filtration. Trials to compare the water quality measures between the various systems found that fish housed in static containers experienced rapid deterioration in water quality. By day 1, measures of ammonia were outside the Institute's prescribed values and continued to rise until it was 25-fold higher than recommended levels. Nitrite levels were also outside recommended levels for all fish by day 9 and were twofold higher by the end of the trial. The water quality measures for tanks held on the recirculating system were stable even though food was provided. These results indicate that for housing zebrafish, running water or appropriately timed water changes are a critical component to ensure that the ethical obligations are met.We thank the staff from the Sanger Institute's Research Support Facility, Zebrafish Mutation Project, and Jacqui White for their support. This work was supported by the Wellcome Trust grant number 098051

Prescribing Zonally Asymmetric Ozone Climatologies in Climate Models: Performance Compared to a Chemistry-Climate Model.

Three different methods of specifying ozone in an atmosphere-only version of the HadGEM3-A global circulation model are compared to the coupled chemistry configuration of this model. These methods include a specified zonal-mean ozone climatology, a specified 3-D ozone climatology, and a calculated-asymmetry scheme in which a specified zonal-mean ozone field is adapted online to be consistent with dynamically produced zonal asymmetries. These simulations all use identical boundary conditions and, by construction, have the same climatological zonal-mean ozone, that of the coupled chemistry configuration of the model. Prescribing ozone, regardless of scheme, results in a simulation which is 3-4 times faster than the coupled chemistry-climate model (CCM). Prescribing climatological zonal asymmetries leads to a vortex which is the correct intensity but which is systematically displaced over regions with lower prescribed ozone. When zonal asymmetries in ozone are free to evolve interactively with model dynamics, the modeled wintertime stratospheric vortex shape and mean sea level pressure patterns closely resemble that produced by the full CCM in both hemispheres, in terms of statistically significant differences. Further, we separate out the two distinct pathways by which zonal ozone asymmetries influence modeled dynamics. We present this interactive-ozone zonal-asymmetry scheme as an inexpensive tool for accurately modeling the impacts of dynamically consistent ozone fields as seen in a CCM which ultimately influence mean sea level pressure and tropospheric circulation (particularly during wintertime in the Northern Hemisphere, when ozone asymmetries are generally largest), without the computational burden of simulating interactive chemistry

Atmospheric composition and climate impacts of a future hydrogen economy

Hydrogen is expected to play a key role in the global energy transition to net zero emissions in many scenarios. However, fugitive emissions of hydrogen into the atmosphere during its production, storage, distribution and use could reduce the climate benefit and also have implications for air quality. Here we explore the atmospheric composition and climate impacts of increases in atmospheric hydrogen abundance using the UKESM1 chemistry-climate model. We find that increases in hydrogen result in increases in methane, tropospheric ozone and stratospheric water vapour, resulting in a positive radiative forcing. However, some of the impacts of hydrogen leakage are partially offset by potential reductions in emissions of methane, carbon monoxide, nitrogen oxides and volatile organic compounds from the consumption of fossil fuels. We derive a new methodology for determining indirect Global Warming Potentials from steady-state simulations which is applicable to both shorter-lived species and those with intermediate and longer lifetimes, such as hydrogen. Using this methodology, we determine a 100-year Global Warming Potential for hydrogen of 12 &plusmn; 6. To maximise the benefit of hydrogen as an energy source, emissions associated with hydrogen leakage and emissions of the ozone precursor gases need to be minimised.</p

The re-birth of the "beat": A hyperlocal online newsgathering model

This is an Author's Accepted Manuscript of an article published in Journalism Practice, 6(5-6), 754 - 765, 2012, copyright Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/17512786.2012.667279.Scholars have long lamented the death of the 'beat' in news journalism. Today's journalists generate more copy than they used to, a deluge of PR releases often keeping them in the office, and away from their communities. Consolidation in industry has dislodged some journalists from their local sources. Yet hyperlocal online activity is thriving if journalists have the time and inclination to engage with it. This paper proposes an exploratory, normative schema intended to help local journalists systematically map and monitor their own hyperlocal online communities and contacts, with the aim of re-establishing local news beats online as networks. This model is, in part, technologically-independent. It encompasses proactive and reactive news-gathering and forward planning approaches. A schema is proposed, developed upon suggested news-gathering frameworks from the literature. These experiences were distilled into an iterative, replicable schema for local journalism. This model was then used to map out two real-world 'beats' for local news-gathering. Journalists working within these local beats were invited to trial the models created. It is hoped that this research will empower journalists by improving their information auditing, and could help re-define journalists' relationship with their online audiences

The cytotoxic domain of colicin E9 is a channel-forming endonuclease

Bacterial toxins commonly translocate cytotoxic enzymes into cells using dedicated channelforming subunits or domains as conduits. We demonstrate that the small cytotoxic endonuclease domain from the bacterial toxin colicin E9 (the E9 DNase) exhibits nonvoltage- gated, channel-forming activity in planar lipid bilayers and that this activity is linked to toxin translocation into cells. A disulfide bond engineered into the DNase abolished channel activity and colicin toxicity but left endonuclease activity unaffected, with NMR experiments suggesting decreased conformational flexibility as the likely reason for these alterations. Concomitant with the reduction of the disulfide bond was the restoration of conformational flexibility, DNase channel activity and colicin toxicity. Our data suggest that endonuclease domains of colicins may mediate their own translocation across the bacterial inner membrane through an intrinsic channel activity that is dependent on structural plasticity in the protein

Polar stratospheric clouds initiated by mountain waves in a global chemistry-climate model: A missing piece in fully modelling polar stratospheric ozone depletion

An important source of polar stratospheric clouds (PSCs), which play a crucial role in controlling polar stratospheric ozone depletion, is the temperature fluctuations induced by mountain waves. These enable stratospheric temperatures to fall below the threshold value for PSC formation in regions of negative temperature perturbations or cooling phases induced by the waves even if the synoptic-scale temperatures are too high. However, this formation mechanism is usually missing in global chemistry–climate models because these temperature fluctuations are neither resolved nor parameterised. Here, we investigate in detail the episodic and localised wintertime stratospheric cooling events produced over the Antarctic Peninsula by a parameterisation of mountain-wave-induced temperature fluctuations inserted into a 30-year run of the global chemistry–climate configuration of the UM-UKCA (Unified Model – United Kingdom Chemistry and Aerosol) model. Comparison of the probability distribution of the parameterised cooling phases with those derived from climatologies of satellite-derived AIRS brightness temperature measurements and high-resolution radiosonde temperature soundings from Rothera Research Station on the Antarctic Peninsula shows that they broadly agree with the AIRS observations and agree well with the radiosonde observations, particularly in both cases for the “cold tails” of the distributions. It is further shown that adding the parameterised cooling phase to the resolved and synoptic-scale temperatures in the UM-UKCA model results in a considerable increase in the number of instances when minimum temperatures fall below the formation temperature for PSCs made from ice water during late austral autumn and early austral winter and early austral spring, and without the additional cooling phase the temperature rarely falls below the ice frost point temperature above the Antarctic Peninsula in the model. Similarly, it was found that the formation potential for PSCs made from ice water was many times larger if the additional cooling is included. For PSCs made from nitric acid trihydrate (NAT) particles it was only during October that the additional cooling is required for temperatures to fall below the NAT formation temperature threshold (despite more NAT PSCs occurring during other months). The additional cooling phases also resulted in an increase in the surface area density of NAT particles throughout the winter and early spring, which is important for chlorine activation. The parameterisation scheme was finally shown to make substantial differences to the distribution of total column ozone during October, resulting from a shift in the position of the polar vortex