The (Un)Folding of Multidomain Proteins Through the Lens of Single-molecule Force-spectroscopy and Computer Simulation

Proteins are specialized molecules that catalyze most of the reactions that can sustain life, and they become functional by folding into a specific 3D structure. Despite their importance, the question, "how do proteins fold?" - first pondered in in the 1930's - is still listed as one of the top unanswered scientific questions as of 2005, according to the journal Science. Answering this question would provide a foundation for understanding protein function and would enable improved drug targeting, efficient biofuel production, and stronger biomaterials. Much of what we currently know about protein folding comes from studies on small, single-domain proteins, which may be quite different from the folding of large, multidomain proteins that predominate the proteomes of all organisms.

In this thesis I will discuss my work to fill this gap in understanding by studying the unfolding and refolding of large, multidomain proteins using the powerful combination of single-molecule force-spectroscopy experiments and molecular dynamic simulations.

The three model proteins studied - Luciferase, Protein S, and Streptavidin - lend insight into the inter-domain dependence for unfolding and the subdomain stabilization of binding ligands, and ultimately provide new insight into atomistic details of the intermediate states along the folding pathway.

Piezoelectric energy harvesting using blood-flow-like excitation for implantable devices

The goal of this research is to produce a system for powering medical implants to increase the lifetime of the implanted devices and reduce the battery size. The system consists of a number of elements – the piezoelectric material for generating power, the device design, the circuit for rectification and energy storage. The piezoelectric material is analysed and a process for producing a repeatable high quality piezoelectric material is described. A full width half maximum (FWHM) of the rocking curve X-Ray diffraction (XRD) scan of between ~1.5° to ~1.7° for test wafers was achieved. This is state of the art for AlN on silicon and means devices with good piezoelectric constants can be fabricated. Finite element modelling FEM) was used to design the structures for energy harvesting. The models developed in this work were established to have an accuracy better than 5% in terms of the difference between measured and modelled results. Devices made from this material were analysed for power harvesting ability as well as the effect that they have on the flow of liquid which is an important consideration for implantable devices. The FEM results are compared to experimental results from laser Doppler vibrometry (LDV), magnetic shaker and perfusion machine tests. The rectifying circuitry for the energy harvester was also investigated. The final solution uses multiple devices to provide the power to augment the battery and so this was a key feature to be considered. Many circuits were examined and a solution based on a fully autonomous circuit was advanced. This circuit was analysed for use with multiple low power inputs similar to the results from previous investigations into the energy harvesting devices. Polymer materials were also studied for use as a substitute for the piezoelectric material as well as the substrate because silicon is more brittle.

Two devices, each of which measure water velocity; on the right is an acoustic device that is permanently maintained at Gumbo Limbo by PI Rene Price; on the left is a 3D camera with a long fiberoptic lens, deployed for testing purposes by collaborator Evan Variano.

http://digitalcommons.fiu.edu/fce_lter_photos/1303/thumbnail.jpg

Africa through Chinese eyes: new frames or the same old lens? African news in English from China Central Television, compared with the BBC

[No abstract as this is a book chapter: the following represents the first 2 paragraphs.] The screen fills with close-ups of smiling African faces against a black-and-orange background: the carefree child, the gap-toothed man with smoke curling from his pipe. The faces retreat into an outline of a map of Africa as the saccharine background music dissolves into birdsong. The silhouette of an acacia tree appears. This is not the much-derided Western romantic stereotype of the continent: it is an extract from a promotional trailer on CCTV Africa, the embodiment of China’s “soft power” drive and a spearhead of Chinese state television’s overseas expansion. Yet this image is at variance with the English-language channel’s professed ambitions. The Chinese premier, Li Keqiang, himself declared that “CCTV embraces the vision of seeing Africa from an African perspective and reporting Africa from the viewpoint of Africa”. These contradictory messages prompt fundamental questions about CCTV’s expansion into Africa. Are the channel’s English-language news bulletins aimed at African or Chinese viewers? What kind of Africa – and indeed China – do they represent, and could the framing of African events by CCTV News provide an alternative to the perspective of international rivals? Is CCTV’s main mission in Africa to provide news or to act as mouthpiece of the Chinese Communist Party and state? This chapter addresses these questions by applying a cross-cultural variant of framing theory to the news content of CCTV’s Africa Live and that of its closest direct competitor, Focus on Africa from BBC World News TV.

The Devil and Views on the “Other” in Part One of Pedro Cieza de León’s "Crónica del Perú" (1553)

Many 16th century Spanish chroniclers and missionaries, arriving at what they interpreted as a New World, saw the Devil as a “hermeneutic wildcard” that allowed them to comprehend indigenous religions. Pedro Cieza de León, a soldier in the conquest of Peru, is a case in point. Cieza considers the Devil responsible for the most aberrant religious practices and customs of the Indians, although he views the natives in a positive light, as men susceptible to divine salvation. From a providentialist perspective of the history of the conquest, Cieza interprets that the evangelization and conversion of the Indians and the implantation of Christian civilization by the Spanish Crown, were able to defeat the Devil.

Effectiveness of early lens extraction for the treatment of primary angle-closure glaucoma (EAGLE): a randomised controlled trial

Background
Primary angle-closure glaucoma is a leading cause of irreversible blindness worldwide. In early-stage disease, intraocular pressure is raised without visual loss. Because the crystalline lens has a major mechanistic role, lens extraction might be a useful initial treatment.

Methods
From Jan 8, 2009, to Dec 28, 2011, we enrolled patients from 30 hospital eye services in five countries. Randomisation was done by a web-based application. Patients were assigned to undergo clear-lens extraction or receive standard care with laser peripheral iridotomy and topical medical treatment. Eligible patients were aged 50 years or older, did not have cataracts, and had newly diagnosed primary angle closure with intraocular pressure 30 mm Hg or greater or primary angle-closure glaucoma. The co-primary endpoints were patient-reported health status, intraocular pressure, and incremental cost-effectiveness ratio per quality-adjusted life-year gained 36 months after treatment. Analysis was by intention to treat. This study is registered, number ISRCTN44464607.

Findings
Of 419 participants enrolled, 155 had primary angle closure and 263 primary angle-closure glaucoma. 208 were assigned to clear-lens extraction and 211 to standard care, of whom 351 (84%) had complete data on health status and 366 (87%) on intraocular pressure. The mean health status score (0·87 [SD 0·12]), assessed with the European Quality of Life-5 Dimensions questionnaire, was 0·052 higher (95% CI 0·015–0·088, p=0·005) and mean intraocular pressure (16·6 [SD 3·5] mm Hg) 1·18 mm Hg lower (95% CI –1·99 to –0·38, p=0·004) after clear-lens extraction than after standard care. The incremental cost-effectiveness ratio was £14 284 for initial lens extraction versus standard care. Irreversible loss of vision occurred in one participant who underwent clear-lens extraction and three who received standard care. No patients had serious adverse events.

Interpretation
Clear-lens extraction showed greater efficacy and was more cost-effective than laser peripheral iridotomy, and should be considered as an option for first-line treatment.

Conceptualising cosmopolitanism and entrepreneurship through the lens of the three-dimensional theory of power

Purpose – The paper aims to conceptualise cosmopolitanism drivers from the third-level power perspective by drawing on Lukes’ (1974; 2005) theory of power. In addition, the paper aims to investigate the relationship between entrepreneurs’ cosmopolitan dispositions and habitus, i.e. a pattern of an individual’s demeanour, as understood by Bourdieu. Design/methodology/approach – This conceptual paper makes use of Bourdieu’s framework (habitus) by extending it to the urban cosmopolitan environment and linking habitus to the three-dimensional theory of power and, importantly, to the power’s third dimension – preference-shaping. Findings – Once cosmopolitanism is embedded in the urban area’s values, this creates multiple endless rounds of mutual influence (by power holders onto entrepreneurs via political and business elites, and by entrepreneurs onto power holders via the same channels), with mutual benefit. Therefore, mutually beneficial influence that transpires in continuous support of a cosmopolitan city’s environment may be viewed as one of the factors that enhances cosmopolitan cities’ resilience to changes in macroeconomic conditions. Originality/value – The paper offers a theoretical model that enriches the understanding of the power-cosmopolitanism-entrepreneurship link, by emphasising the preference-shaping capacity of power, which leads to the embedment of cosmopolitanism in societal values. As a value shared by political and business elites, cosmopolitanism is also actively promoted by entrepreneurs through their disposition and habitus. This ensures not only their willing compliance with power and the environment, but also their enhancement of favourable business conditions. Entrepreneurs depart from mere acquiescence (to power and its explicit dominance), and instead practice their cosmopolitan influence by active preference-shaping.

Sasakian quiver gauge theories and instantons on cones over lens 5-spaces

We consider SU(3)-equivariant dimensional reduction of Yang Mills theory over certain cyclic orbifolds of the 5-sphere which are Sasaki-Einstein manifolds. We obtain new quiver gauge theories extending those induced via reduction over the leaf spaces of the characteristic foliation of the Sasaki-Einstein structure, which are projective planes. We describe the Higgs branches of these quiver gauge theories as moduli spaces of spherically symmetric instantons which are SU(3)-equivariant solutions to the Hermitian Yang-Mills equations on the associated Calabi-Yau cones, and further compare them to moduli spaces of translationally-invariant instantons on the cones. We provide an explicit unified construction of these moduli spaces as Kahler quotients and show that they have the same cyclic orbifold singularities as the cones over the lens 5-spaces. (C) 2015 The Authors. Published by Elsevier B.V.

Building digital capability: Employability lens on the Six Elements of Digital Capability

This is a version of the Jisc ‘Six Elements of Digital Capabilities’ model, developed to support student-facing sta working in Careers and Employability roles and curriculum sta working to embed employability issues into the curriculum. It draws on the work of the Jisc Developing Student Employability project e.g. on the model of the ‘employable student’ produced by Peter Chatterton for that project.

Implantable cardioverter-defibrillators in the elderly: rationale and specific age-related considerations

Despite the increasingly high rate of implantation of cardioverter-defibrillators (ICD) in elderly patients, data supporting their clinical and cost-effectiveness in this age stratum are ambiguous and contradictory. We comprehensively reviewed the state-of-the-art data regarding the applicability, safety, clinical- and cost-effectiveness of the ICD in elderly patients, and analysed which patients in this age stratum are more likely to get a survival benefit from this therapy. Although peri-procedural risk may be slightly higher in the elderly, this procedure is still relatively safe in this age group. In terms of correcting potentially life-threatening arrhythmias, the effectiveness of ICD therapy is comparable in older and younger individuals. However, the assumption of persistent ICD benefit in the elderly population is questionable, as any advantage of the device on arrhythmic death may be largely attenuated by a higher total non-arrhythmic mortality. While septuagenarians and octogenarians have higher annual all-cause mortality rates, ICD therapy may remain effective in highly selected patients at high risk of arrhythmic death and with minimum comorbidities despite advanced age. ICD intervention among the elderly, as a group, may not be cost-effective, but the procedure may reach cost-effectiveness in those expected to live >5-7 years after implantation. Biological age rather than chronological age per se should be the decisive factor in making a decision on ICD selection for survival benefit.

Rapid hydrothermal cooling above the axial melt lens at fast-spreading mid-ocean ridge

Axial melt lenses sandwiched between the lower oceanic crust and the sheeted dike sequences at fast-spreading mid-ocean ridges are assumed to be the major magma source of oceanic crust accretion. According to the widely discussed "gabbro glacier'' model, the formation of the lower oceanic crust requires efficient cooling of the axial melt lens, leading to partial crystallization and crystal-melt mush subsiding down to lower crust. These processes are believed to be controlled by periodical magma replenishment and hydrothermal circulation above the melt lens. Here we quantify the cooling rate above melt lens using chemical zoning of plagioclase from hornfelsic recrystallized sheeted dikes drilled from the East Pacific at the Integrated Ocean Drilling Program Hole 1256D. Weestimate the cooling rate using a forward modelling approach based on CaAl-NaSi interdiffusion in plagioclase. The results show that cooling from the peak thermal overprint at 1000-10506 degrees C to 6006 degrees C are yielded within about 10-30 years as a result of hydrothermal circulation above melt lens during magma starvation. The estimated rapid hydrothermal cooling explains how the effective heat extraction from melt lens is achieved at fast-spreading mid-ocean ridges.

The outset of mental torture. Through the lens of the Ticking Time Bomb Scenario

No doubt shall be placed when qualifying torture as one of the cruellest crime offences against human beings. It is widely known that the first torture practices go back to the Middle Ages, where torture mechanisms and devices were used as a legitimate means of punishment, extraction of confessions or executions. Brutal techniques such as ‘Judas Cradle’, ‘The Rack’ or the ‘Rat Torture’ were indeed, the ones commonly used. Moreover, some centuries onwards, torture warrants were permitted and authorised by Privy Councils in legislations such as the English one. However, examples like that were the only ones which public accountability was given to, whereas off-the-book practices remained in silence in other countries for long lasting years. Nowadays, in the 21st century, there are innumerable enforced laws and provisions that prohibit the act of torture, to be precise, physical and psychological torture. Nonetheless, not only are these legislations necessary for fighting torture, but also ad hoc courts and specialised committees continuously report the existence of this crime offence.