Characterization and biological role of the O-polysaccharide gene cluster of Yersinia enterocolitica serotype O:9

Yersinia enterocolitica serotype O:9 is a gram-negative enteropathogen that infects animals and humans. The role of lipopolysaccharide (LPS) in Y. enterocolitica O:9 pathogenesis, however, remains unclear. The O:9 LPS consists of lipid A to which is linked the inner core oligosaccharide, serving as an attachment site for both the outer core (OC) hexasaccharide and the O-polysaccharide (OPS; a homopolymer of N-formylperosamine). In this work, we cloned the OPS gene cluster of O:9 and identified 12 genes organized into four operons upstream of the gnd gene. Ten genes were predicted to encode glycosyltransferases, the ATP-binding cassette polysaccharide translocators, or enzymes required for the biosynthesis of GDP-N-formylperosamine. The two remaining genes within the OPS gene cluster, galF and galU, were not ascribed a clear function in OPS biosynthesis; however, the latter gene appeared to be essential for O:9. The biological functions of O:9 OPS and OC were studied using isogenic mutants lacking one or both of these LPS parts. We showed that OPS and OC confer resistance to human complement and polymyxin B; the OPS effect on polymyxin B resistance could be observed only in the absence of OC.

Gelsolin induces colorectal tumor cell invasion via modulation of the urokinase-type plasminogen activator cascade

Gelsolin is a cytoskeletal protein which participates in actin filament dynamics and promotes cell motility and plasticity. Although initially regarded as a tumor suppressor, gelsolin expression in certain tumors correlates with poor prognosis and therapy-resistance. In vitro, gelsolin has anti-apoptotic and pro-migratory functions and is critical for invasion of some types of tumor cells. We found that gelsolin was highly expressed at tumor borders infiltrating into adjacent liver tissues, as examined by immunohistochemistry. Although gelsolin contributes to lamellipodia formation in migrating cells, the mechanisms by which it induces tumor invasion are unclear. Gelsolin's influence on the invasive activity of colorectal cancer cells was investigated using overexpression and small interfering RNA knockdown. We show that gelsolin is required for invasion of colorectal cancer cells through matrigel. Microarray analysis and quantitative PCR indicate that gelsolin overexpression induces the upregulation of invasion-promoting genes in colorectal cancer cells, including the matrix-degrading urokinase-type plasminogen activator (uPA). Conversely, gelsolin knockdown reduces uPA levels, as well as uPA secretion. The enhanced invasiveness of gelsolin-overexpressing cells was attenuated by treatment with function-blocking antibodies to either uPA or its receptor uPAR, indicating that uPA/uPAR activity is crucial for gelsolin-dependent invasion. In summary, our data reveals novel functions of gelsolin in colorectal tumor cell invasion through its modulation of the uPA/uPAR cascade, with potentially important roles in colorectal tumor dissemination to metastatic sites.

An anatomical study of the arterial and nerve supply of the infrahyoid muscles

A precise knowledge of the sources of the arterial and neural supply of the sternohyoid (SH), sternothyroid (STM), and superior belly of omohyoid (OM) is of value to surgeons using the infrahyoid muscles in reconstruction procedures of the head and neck. This study was designed to define the anatomical bases of the variable sources of the arterial and neural supply of these muscles. Fourteen cadavers were unilaterally dissected in the neck region, and the arterial pedicles of these muscles were followed and accurate measurements were taken. For the SH, two arterial pedicles (superior and inferior) originated from the superior thyroid artery ST and supplied the muscle in 57.1% of cases. The inferior pedicle was absent in 42.9% of cases. As regards the STM, one arterial pedicle from the ST supplied its upper end by multiple branches in 57.1% of cases. In 14.3% of cases, branches from the inferior thyroid artery (IT) supplied the STM in addition to its supply from the ST. As regards the OM, two arterial pedicles originated from the ST and supplied its upper and lower ends in 57.1% of cases. The main artery from the ST to the superior belly of OM entered at its superior portion. The ansa cervicalis (AC) innervated the infrahyoid muscles. SH usually had a double nerve supply. In 57.1% of cases, its superior part was innervated by the nerve to the superior belly of OM. Its inferior part received branches from the AC. In 35.7% of cases, its superior part received direct branches from the AC. As regards the STM, in (71.4%) of cases, a common trunk arose from the loop and supplied the inferior part of both the SH and STM. The nerve supply to the superior belly of OM originated from the AC below the loop in 64.3% of cases. These data will be useful for preserving the neuro-vascular supply of the infrahyoid muscles during flap preparation.

Low pressure methane solubility in lithium-ion batteries based solvents and electrolytes as a function of temperature. Measurement and prediction

The methane solubility in five pure electrolyte solvents and one binary solvent mixture for lithium ion batteries – such as ethylene carbonate (EC), propylene carbonate (PC), dimethyl carbonate (DMC), ethyl methyl carbonate (EMC), diethyl carbonate (DEC) and the (50:50 wt%) mixture of EC:DMC was studied experimentally at pressures close to atmospheric and as a function of temperature between (280 and 343) K by using an isochoric saturation technique. The effect of the selected anions of a lithium salt LiX (X = hexafluorophosphate,

AaeAP1 and AaeAP2: Novel Antimicrobial Peptides from the Venom of the Scorpion, Androctonus aeneas: Structural Characterisation, Molecular Cloning of Biosynthetic Precursor-Encoding cDNAs and Engineering of Analogues with Enhanced Antimicrobial and Anticancer Activities

The main functions of the abundant polypeptide toxins present in scorpion venoms are the debilitation of arthropod prey or defence against predators. These effects are achieved mainly through the blocking of an array of ion channel types within the membranes of excitable cells. However, while these ion channel-blocking toxins are tightly-folded by multiple disulphide bridges between cysteine residues, there are additional groups of peptides in the venoms that are devoid of cysteine residues. These non-disulphide bridged peptides are the subject of much research interest, and among these are peptides that exhibit antimicrobial activity. Here, we describe two novel non-disulphide-bridged antimicrobial peptides that are present in the venom of the North African scorpion, Androctonus aeneas. The cDNAs encoding the biosynthetic precursors of both peptides were cloned from a venom-derived cDNA library using 3'- and 5'-RACE strategies. Both translated precursors contained open-reading frames of 74 amino acid residues, each encoding one copy of a putative novel nonadecapeptide, whose primary structures were FLFSLIPSVIAGLVSAIRN and FLFSLIPSAIAGLVSAIRN, respectively. Both peptides were C-terminally amidated. Synthetic versions of each natural peptide displayed broad-spectrum antimicrobial activities, but were devoid of antiproliferative activity against human cancer cell lines. However, synthetic analogues of each peptide, engineered for enhanced cationicity and amphipathicity, exhibited increases in antimicrobial potency and acquired antiproliferative activity against a range of human cancer cell lines. These data clearly illustrate the potential that natural peptide templates provide towards the design of synthetic analogues for therapeutic exploitation.

Tullis Rennie's Muscle Memory: Listening to the Act of Listening

This paper explores a recent, broadly 'electroacoustic', fixed medium composition by Tullis Rennie, which uses his background in ethnographic fieldwork to explore (in this case through auto-ethnography) modes of listening, and the role of technologies in mediating this listening. Muscle Memory: A conversation about jazz, with Graham South (trumpet) (2014) begins to answer questions about how one work can comment on and analyse or critique another through its own agency as music, bringing composition and ethnography together in fruitful collision, and illuminating the human capacity to manipulate and be manipulated by musical activity. The paper uses the piece to test the extent to which four functions, identified by Simon Frith (1987. Towards an aesthetic of popular music. In R. Leppert & S. McClary (Eds.), Music and society (pp. 133-49). Cambridge: Cambridge University Press) as crucial to the meaningfulness of popular music may, in the context of ubiquitously technologised music, have broader application than he originally intended.

Dublin 1916: theatre of revolt

At Easter 1916, Dublin city centre was one of a series of sites throughout Ireland where a rebellion was staged against British rule. It was a strategic failure, swiftly crushed by superior British forces. The event, however, subsequently took a central role in the mythology of modern Ireland.

The first visual representations were of the conflict’s aftermath: photographic journeys through landscapes of ruin. From the distance of the camera, we see none of the pockmarks of shell bursts, nor the etchings of machine guns. Instead, traces of life in the city seem to have been swept aside by an unseen hand: the passing of millennia or a violent action of nature. Architecture alone has witnessed and recorded its presence. Amongst the fragments, the shell of the General Post Office (G.P.O.) in Sackville Street is one of the few buildings still wholly recognizable. The remnants of its classical form, portico and pediment, columns and entablature seem to transcend its prosaic modern functions and allude to something more ancient. The bewilderment of city’s inhabitants is also recorded. Dubliners have become inquisitive tourists in streets which hitherto were the locus of everyday life. They wander around aimlessly in a landscape as alien and picturesque as Pompeii. This shift in perception was captured by the Irish poet W.B. Yeats who hinted that Dublin, purged of modern commercialism had transcended its petty inadequacies to revive a slumbering heroic past.

‘I have met them at the close of day
Coming with vivid faces
From counter or desk among grey
Eighteenth-century houses [.]’
All is changed, changed utterly:
A terrible beauty is born.’

His comments were prescient. Initially unpopular, the republican leaders, executed by the British, slowly became recast as heroic martyrs. Similarly, the spaces where their heroism was forged became venerated. The G.P.O. and Sackville Street, however, already had a republican history. It was originally conceived in the eighteenth century as part of a series of magnificent urban spaces to provide an arena of spectacle and self-celebration for the colonial Anglo-Irish and their vision of a Protestant republic. O’Connell/Sackville Street became the temporal, geographical and mythical hinge upon which two different versions of Irish republicanism waxed and waned. Its recasting after independence as a space of Catholic Nationalism bore testimony to its consistency in providing a backdrop for the production of ritual and myth. In the 1920s and 30s, as the nascent country, beset with economic stagnation and political tensions, turned to spectacle as a salve for it social problems, O’Connell Street and the G.P.O. provided its most sacred sites. Within the introduction of new myths, however, individual as well as national identities were created and consolidated. The emerging identity of modern Ireland became inextricably linked with that of one ambitious politician. His uses of the G.P.O. in particular revealed a perceptive understanding of the political uses of classical architecture and urban space.

Dublin 1916: theatre of revolt

In his essay, Anti-Object, Kengo Kuma proposes that architecture cannot and should not be understood as object alone but instead always as series of networks and connections, relationships within space and through form. Some of these relationships are tangible, others are invisible. Stan Allen and James Corner have also called for an architecture that is more performative and operative – ‘less concerned with what buildings look like and more concerned with what they do’ – as means of effecting a more intimate and promiscuous relationship between infrastructure, urbanism and buildings. According to Allen this expanding filed offers a reclamation of some of the areas ceded by architecture following disciplinary specialization:

‘Territory, communication and speed are properly infrastructural problems and architecture as a discipline has developed specific technical means to deal with these variables. Mapping, projection, calculation, notation and visualization are among architecture’s traditional tools for operating at the very large scale’.

The motorway may not look like it – partly because we are no longer accustomed to think about it as such – but it is a site for and of architecture, a territory where architecture can be critical and active. If the limits of the discipline have narrowed, then one of the functions of a school of architecture must be an attempt occupy those areas of the built environment where architecture is no longer, or has yet to reach. If this is a project about reclamation of a landscape, it is also a challenge to some of the boundaries that surround architecture and often confine it, as Kuma suggests, to the appreciation of isolated objects.

M:NI 2014-15
We tend to think of the motorway as a thing or an object, something that has a singular function. Historically this is how it has been seen, with engineers designing bridges and embankments and suchlike with zeal … These objects like the M3 Urban Motorway, Belfast’s own Westway, are beautiful of course, but they have caused considerable damage to the city they were inflicted upon.

Actually, it’s the fact that we have seen the motorway as a solid object that has caused this problem. The motorway actually is a fluid and dynamic thing, and it should be seen as such: in fact it’s not an organ at all but actually tissue – something that connects rather than is. Once we start to see the motorway as tissue, it opens up new propositions about what the motorway is, is used for and does. This new dynamic and connective view unlocks the stasis of the motorway as edifice, and allows adaptation to happen: adaptation to old contexts that were ignored by the planners, and adaptation to new contexts that have arisen because of or in spite of our best efforts.

Motorways as tissue are more than just infrastructures: they are landscapes. These landscapes can be seen as surfaces on which flows take place, not only of cars, buses and lorries, but also of the globalized goods carried and the lifestyles and mobilities enabled. Here the infinite speed of urban change of thought transcends the declared speed limit [70 mph] of the motorway, in that a consignment of bananas can cause soil erosion in Equador, or the delivery of a new iphone can unlock connections and ideas the world over.

So what is this new landscape to be like? It may be a parallax-shifting, cognitive looking glass; a drone scape of energy transformation; a collective farm, or maybe part of a hospital. But what’s for sure, is that it is never fixed nor static: it pulses like a heartbeat through that most bland of landscapes, the countryside. It transmits forces like a Caribbean hurricane creating surf on an Atlantic Storm Beach: alien forces that mutate and re-form these places screaming into new, unclear and unintended futures.

And this future is clear: the future is urban. In this small rural country, motorways as tissue have made the whole of it: countryside, mountain, sea and town, into one singular, homogenous and hyper-connected, generic city.

Goodbye, place. Hello, surface!

Deciphering the mechanisms underlying the loss of BDNF neuroprotection in an Alzheimer’s disease model

Tese de mestrado, Neurociências, Faculdade de Medicina, Universidade de Lisboa, 2016

Spectrum of Somatic Hypermutations and Implication on Antibody Function: Case of the anti HIV-1 antibody, b12

Thesis (Ph.D.)--University of Washington, 2015

The metamorphosis of authority: a case study of the Aga Khan Development Network and the Ismaili Imamate

This research is a study of modern developments of the institutions of the Nizārī Ismaili imamate during the time of the present Ismaili Imam, Shāh Karīm al-Ḥusaynī, Aga Khan IV, as the 49th hereditary living Imam of Shiʿi Nizārī Ismaili Muslims, particularly addressing the formation of the Aga Khan Development Network (AKDN) and the functions of the Community institutions. Using the case study of the Aga Khan Development Network and the Nizārī Ismaili imamate, this research demonstrates that the three ideal types of authority as proposed by Weber, namely the traditional, charismatic and legal-bureaucratic types, are not sufficient to explain the dynamics of authority among Muslims. This is partly due to Weber’s belief in the uniqueness of Western civilisation, which is a product of his thesis on Protestant Ethics and partly because his ideal typical system does not work in the case of the Muslim societies. The Ismaili imamate with its multifarious institutions in contemporary times is the most suitable counter-example by which to powerfully demonstrate that Weberian models of authority fail to explain this phenomenon and it would indeed appear as a paradoxical institution if viewed with Weberian theses. The Ismaili imamate in contemporary times represents a paradigm shift and a transmutation not only as regards the Weberian models but also when viewed from inside the tradition of Shiʿi Muslim history. This evolutionary leap forward, which has been crystallised over the course of the past half a century, in the Ismaili imamate suggests the development of a new form of authority which is unprecedented. There are clearly various elements in this form of authority which could be discerned as rooted in tradition and history; however the distinctive elements of this new form of authority give it a defining and exciting dimension. There are several qualities which are peculiar to the contemporary condition of the Ismaili imamate and its style of leadership which are distinctive. Most importantly, while some central features, like succession by way of designation (naṣṣ) has not changed, there is one overarching quality which can best capture all these elements and that is the transmutation of the Ismaili imamate from the person of the Imam into the office of imamate and thus we are now facing the institutionalisation of the imamate and the office being the embodiment of the authority of the Imam. I have described this new development as a metamorphosis of the authority because it gives an entirely new form and content to the previously familiar concept of authority in the Shiʿi Ismaili Muslim tradition.

Post-Transcriptional Regulation of BCL2 mRNA by the RNA-Binding Protein ZFP36L1 in Malignant B Cells

The human ZFP36 zinc finger protein family consists of ZFP36, ZFP36L1, and ZFP36L2. These proteins regulate various cellular processes, including cell apoptosis, by binding to adenine uridine rich elements in the 3′ untranslated regions of sets of target mRNAs to promote their degradation. The pro-apoptotic and other functions of ZFP36 family members have been implicated in the pathogenesis of lymphoid malignancies. To identify candidate mRNAs that are targeted in the pro-apoptotic response by ZFP36L1, we reverse-engineered a gene regulatory network for all three ZFP36 family members using the ‘maximum information coefficient’ (MIC) for target gene inference on a large microarray gene expression dataset representing cells of diverse histological origin. Of the three inferred ZFP36L1 mRNA targets that were identified, we focussed on experimental validation of mRNA for the pro-survival protein, BCL2, as a target for ZFP36L1. RNA electrophoretic mobility shift assay experiments revealed that ZFP36L1 interacted with the BCL2 adenine uridine rich element. In murine BCL1 leukemia cells stably transduced with a ZFP36L1 ShRNA lentiviral construct, BCL2 mRNA degradation was significantly delayed compared to control lentiviral expressing cells and ZFP36L1 knockdown in different cell types (BCL1, ACHN, Ramos), resulted in increased levels of BCL2 mRNA levels compared to control cells. 3′ untranslated region luciferase reporter assays in HEK293T cells showed that wild type but not zinc finger mutant ZFP36L1 protein was able to downregulate a BCL2 construct containing the BCL2 adenine uridine rich element and removal of the adenine uridine rich core from the BCL2 3′ untranslated region in the reporter construct significantly reduced the ability of ZFP36L1 to mediate this effect. Taken together, our data are consistent with ZFP36L1 interacting with and mediating degradation of BCL2 mRNA as an important target through which ZFP36L1 mediates its pro-apoptotic effects in malignant B-cells.

The effect of a selective CXCR2 antagonist (AZD5069) on human blood neutrophil count and innate immune functions.

Abstract AIMS: The aim of the present study was to investigate whether selective antagonism of the cysteine-X-cysteine chemokine receptor-2 (CXCR2) receptor has any adverse effects on the key innate effector functions of human neutrophils for defence against microbial pathogens. METHODS: In a double-blind, crossover study, 30 healthy volunteers were randomized to treatment with the CXCR2 antagonist AZD5069 (100 mg) or placebo, twice daily orally for 6 days. The peripheral blood neutrophil count was assessed at baseline, daily during treatment and in response to exercise challenge and subcutaneous injection of granulocyte-colony stimulating factor (G-CSF). Neutrophil function was evaluated by phagocytosis of Escherichia coli and by the oxidative burst response to E. coli. RESULTS: AZD5069 treatment reversibly reduced circulating neutrophil count from baseline by a mean [standard deviation (SD)] of -1.67 (0.67) ×10(9) l(-1) vs. 0.19 (0.78) ×10(9) l(-1) for placebo on day 2, returning to baseline by day 7 after the last dose. Despite low counts on day 4, a 10-min exercise challenge increased absolute blood neutrophil count, but the effect with AZD5069 was smaller and not sustained, compared with placebo treatment. Subcutaneous G-CSF on day 5 caused a substantial increase in blood neutrophil count in both placebo- and AZD5069-treated subjects. Superoxide anion production in E. coli-stimulated neutrophils and phagocytosis of E. coli were unaffected by AZD5069 (P = 0.375, P = 0.721, respectively vs. baseline, Day 4). AZD5069 was well tolerated. CONCLUSIONS: CXCR2 antagonism did not appear adversely to affect the mobilization of neutrophils from bone marrow into the peripheral circulation, phagocytosis or the oxidative burst response to bacterial pathogens. This supports the potential of CXCR2 antagonists as a treatment option for diseases in which neutrophils play a pathological role.

Design of New Materials for Passive Vibration Control

The aim of this contribution is to extend the techniques of composite materials design to non-linear material behaviour and apply it for design of new materials for passive vibration control. As a first step a computational tool allowing determination of macroscopic optimized one-dimensional isolator behaviour was developed. Voigt, Maxwell, standard and more complex material models can be implemented. Objective function considers minimization of the initial reaction and/or displacement peak as well as minimization of the steady-state amplitude of reaction and/or displacement. The complex stiffness approach is used to formulate the governing equations in an efficient way. Material stiffness parameters are assumed as non-linear functions of the displacement. The numerical solution is performed in the complex space. The steady-state solution in the complex space is obtained by an iterative process based on the shooting method which imposes the conditions of periodicity with respect to the known value of the period. Extension of the shooting method to the complex space is presented and verified. Non-linear behaviour of material parameters is then optimized by generic probabilistic meta-algorithm, simulated annealing. Dependence of the global optimum on several combinations of leading parameters of the simulated annealing procedure, like neighbourhood definition and annealing schedule, is also studied and analyzed. Procedure is programmed in MATLAB environment.

Distribution of the human intracellular serpin protease inhibitor 8 in human tissues.

Ovalbumin-like serine protease inhibitors are mainly localized intracellularly and their in vivo functions are largely unknown. To elucidate their physiological role(s), we studied the expression of one of these inhibitors, protease inhibitor 8 (PI-8), in normal human tissues by immunohistochemistry using a PI-8-specific monoclonal antibody. PI-8 was strongly expressed in the nuclei of squamous epithelium of mouth, pharynx, esophagus, and epidermis, and by the epithelial layer of skin appendages, particularly by more differentiated epithelial cells. PI-8 was also expressed by monocytes and by neuroendocrine cells in the pituitary gland, pancreas, and digestive tract. Monocytes showed nuclear and cytoplasmic localization of PI-8, whereas neuroendocrine cells showed only cytoplasmic staining. In vitro nuclear localization of PI-8 was confirmed by confocal analysis using serpin-transfected HeLa cells. Furthermore, mutation of the P(1) residue did not affect the subcellular distribution pattern of PI-8, indicating that its nuclear localization is independent of the interaction with its target protease. We conclude that PI-8 has a unique distribution pattern in human tissues compared to the distribution patterns of other intracellular serpins. Additional studies must be performed to elucidate its physiological role.