Structure, function and intracellular dynamics of alphavirus replication complexes

Intracellular membrane alterations are hallmarks of positive-sense RNA (+RNA) virus replication. Strong evidence indicates that within these exotic compartments, viral replicase proteins engage in RNA genome replication and transcription. To date, fundamental questions such as the origin of altered membranes, mechanisms of membrane deformation and topological distribution and function of viral components, are still waiting for comprehensive answers. This study addressed some of the above mentioned questions for the membrane alterations induced during Semliki Forest virus (SFV) infection of mammalian cells. With the aid of electron and fluorescence microscopy coupled with radioactive labelling and immuno-cytochemistry techniques, our group and others showed that few hours after infection the four non structural proteins (nsP1-4) and newly synthesized RNAs of SFV colocalized in close proximity of small membrane invaginations, designated as spherules . These 50-70 nm structures were mainly detected in the perinuclear area, at the limiting membrane of modified endosomes and lysosomes, named CPV-I (cytopathic vacuoles type I). More rarely, spherules were also found at the plasma membrane (PM). In the first part of this study I present the first three-dimensional reconstruction of the CPV-I and the spherules, obtained by electron tomography after chemical or cryo-fixation. Different approaches for imaging these macromolecular assemblies to obtain better structure preservation and higher resolution are presented as unpublished data. This study provides insights into spherule organization and distribution of viral components. The results of this and other experiments presented in this thesis will challenge currently accepted models for virus replication complex formation and function. In a revisitation of our previous models, the second part of this work provides the first complete description of the biogenesis of the CPV-I. The results demonstrate that these virus-induced vacuoles, where hundreds of spherules accumulate at late stages during infection, represent the final phase of a journey initiated at the PM, which apparently serves as a platform for spherule formation. From the PM spherules were internalized by an endocytic event that required the activity of the class I PI3K, caveolin-1, cellular cholesterol and functional actin-myosin network. The resulting neutral endocytic carrier vesicle delivered the spherules to the membrane of pre-existing acidic endosomes via multiple fusion events. Microtubule based transport supported the vectorial transfer of these intermediates to the pericentriolar area where further fusions generated the CPV-I. A signal for spherule internalization was identified in one of the replicase proteins, nsP3. Infections of cells with viruses harbouring a deletion in a highly phosphorylated region of nsP3 did not result in the formation of CPV-Is. Instead, thousands of spherules remained at the PM throughout the infection cycle. Finally, the role of the replicase protein nsP2 during viral RNA replication and transcription was investigated. Three enzymatic activities, protease, NTPase and RNA-triphosphatase were studied with the aid of temperature sensitive mutants in vitro and, when possible, in vivo. The results highlighted the interplay of the different nsP2 functions during different steps of RNA replication and sub-genomic promoter regulation, and suggest that the protein could have different activities when participating in the replication complex or as a free enzyme.

Factors associated with medication adherence among tuberculosis patients in Timor-Leste

This thesis investigated medication adherence among people living with tuberculosis in Timor Leste. Suboptimal adherence was commonly reported, and was influenced by service inaccessibility, family poverty, patients' absence of disease symptoms and misperception of recovery, untreated depression and a popular cultural belief that luck or chance determines health outcomes. The study has implications for improving health literacy and counselling programs to achieve effective adherence to medication and good health outcomes.

Clathrin-independent carriers form a high capacity endocytic sorting system at the leading edge of migrating cells

Although the importance of clathrin- and caveolin-independent endocytic pathways has recently emerged, key aspects of these routes remain unknown. Using quantitative ultrastructural approaches, we show that clathrin-independent carriers (CLICs) account for approximately three times the volume internalized by the clathrin-mediated endocytic pathway, forming the major pathway involved in uptake of fluid and bulk membrane in fibroblasts. Electron tomographic analysis of the 3D morphology of the earliest carriers shows that they are multidomain organelles that form a complex sorting station as they mature. Proteomic analysis provides direct links between CLICs, cellular adhesion turnover, and migration. Consistent with this, CLIC-mediated endocytosis of key cargo proteins, CD44 and Thy-1, is polarized at the leading edge of migrating fibroblasts, while transient ablation of CLICs impairs their ability to migrate. These studies provide the first quantitative ultrastructural analysis and molecular characterization of the major endocytic pathway in fibroblasts, a pathway that provides rapid membrane turnover at the leading edge of migrating cells.

Highly biocompatible and water-dispersible, amine functionalized magnetite nanoparticles, prepared by a low temperature, air-assisted polyol process: a new platform for bio-separation and diagnostics

A low temperature polyol process, based on glycolaldehyde mediated partial reduction of FeCl3 center dot 6H(2)O at 120 degrees C in the presence of sodium acetate as an alkali source and 2,2'-(ethylenedioxy)-bis-(ethylamine) as an electrostatic stabilizer has been used for the gram-scale preparation of biocompatible, water-dispersible, amine functionalized magnetite nanoparticles (MNPs) with an average diameter of 6 +/- 0.75 nm. With a reasonably high magnetization (37.8 e.m.u.) and amine groups on the outer surface of the nanoparticles, we demonstrated the magnetic separation and concentration implications of these ultrasmall particles in immunoassay. MRI studies indicated that these nanoparticles had the desired relaxivity for T-2 contrast enhancement in vivo. In vitro biocompatibility, cell uptake and MR imaging studies established that these nanoparticles were safe in clinical dosages and by virtue of their ultrasmall sizes and positively charged surfaces could be easily internalized by cancer cells. All these positive attributes make these functional nanoparticles a promising platform for further in vitro and in vivo evaluations.

Leskien ja orpojen muuttuva asema luo- ja kisii-yhteisöissä Länsi-Keniassa

Tutkielma käsittelee naisleskien ja orpojen elämää luo- ja kisii-yhteisöissä Länsi-Kenian maaseudulla. Tarkoituksena on selvittää, kuinka yhteiskunnassa tapahtuvat taloudelliset ja sosiaaliset muutokset ovat vaikuttaneet orpojen ja leskien asemaan patriarkaalisissa yhteisöissä. Tutkielma pyrkii osoittamaan paikallistason muutosten kulttuurisidonnaisuuden erilaisia muutosteemoja tarkastelemalla. Erityisesti on tarkasteltu aids-epidemian ja maapulan vaikutuksia leskien ja orpojen lähisuhteisiin, maankäyttöoikeuksiin ja luojen leviraattisuhteeseen. Tutkielman aineisto koostuu kahden kuukauden kenttätyöjakson aikana tehdyistä haastatteluista ja osallistuvasta havainnoinnista. Kenttätyö on tehty Suomen Luterilaisen Evankeliumiyhdistyksen ja Kenian Evangelic Lutheran Churchin orpotyöprojektin yhteydessä syksyllä 2007. Aids-epidemian myötä huollettavien määrä maaseutuyhteisöissä on kasvanut. Samanaikaisesti on havaittu, että sukulaisten muodostama turvaverkko on heikentynyt. Turvaverkon heikentyminen liittyy resurssipulaan ja arvojen muutokseen. Lesket ja orvot ovat vaarassa jäädä ilman tarvitsemaansa tukea ja apua. Kisiiden ja luojen sukulaisuusjärjestelmässä naisilla ei ole siskon tai tyttären rooliin liittyviä oikeuksia. Tutkielmasta käy ilmi, että leskien ja orpojen häätäminen kotitiloilta on yleistä, vaikka perinteisesti heidän asemansa maankäyttäjänä on ollut turvattu. Luo-leski saatetaan häätää myös hänen kieltäytyessään leviraattisuhteesta. Häätöjen keskeinen motiivi on saada lesken käytössä ollut maapala miesvainajan sukulaisten haltuun. Häädetyt lesket rinnastuvat Thomas Håkanssonin tutkimiin avoliitosta häädettyihin kisii-naisiin, joita hän nimittää suvuttomiksi naisiksi. Pekka Seppälän tutkimusta luhyoiden sukupolvenvaihdoksista käytetään maankäyttöoikeuksiin liittyvän analyysin pohjana. Luojen leviraattisuhteessa on tapahtunut merkittäviä muutoksia aids-epidemian aikana. Länsi-Kenian aids-tilanne on muuta maata huonompi. Alueen asukkailla on valistuskampanjoiden ansiosta hyvät tiedot sairaudesta, mutta he toimivat usein tämän tiedon vastaisesti. Tutkielman mukaan keskeisin syy näennäiselle välinpitämättömyydelle on leimautumisen pelko. Aidsiin liittyvä stigma on voimakasta ja sen vuoksi tauti pyritään salaamaan mahdollisimman pitkään. Sukulaismiehet kieltäytyvät usein leskenperijän roolista hiv-tartunnan pelossa. Tämä on luonut kysyntää ammattiperijöille, jotka suorittavat seksuaalisia rituaaleja leskille korvausta vastaan. Tutkielmassa esitellään rituaalisen seksin merkitystä luoille ja todetaan sen olevan tärkein syy leviraattikäytännön jatkumiselle. Luo-leskien perinteistä asemaa tarkastellaan Betty Potashin tutkimusten valossa.

"Pitää kuitenkin lähentyä sitä vangin roolia, vaikka ite ois toista mieltä" : Diskurssianalyyttinen tutkimus toiseuden rakentumisesta vankilaopetuksessa

The focus of this discourse analytical study was to review the meanings which prison education and its participants are given in the formal educational policy and to find out whether these meanings are agreed by the prison students. The intrestes of this thesis were to examine what kind of social and individual promises are related to the prison education and what kind of subject positions are possible to the prison students. The thesis was also interested in the meanings of education in different contexts. The aim of this study was to examine prison education especially for women. This thesis was based on Michel Foucault s ideas of power and the view of this study was directly critical. The prison education was seen as normalizing governance which tends to prepare its subjects to the normal. In this process of differentiating the normal and the abnormal the subjects of prison education are reconstructed as the others . The three research questions of this thesis were: how and what kind of prison education is reconstructed firstly in the strategy of prison education and secondly in the interviews. Thirdly it was questioned how and what kind of meanings gender receive in the discourse of prison education. The main data was consisted by the Finnish Criminal Sanctions Agency s document The Strategy of the Prison education for years 2008 2012 and the three interviews of women who participated to prison education. The interviews were made for this thesis in Autumn 2010. Two other Finnish Criminal Sanctions Agency s documents Prisoners in education (2007) and Visible women (2008) - the report of the working group on female prisoners were also used as subtext materials. The methods of critical and realistic discourse analysis and rhetorical analysis were applied in the analysis. The results of the thesis support the outlook of prison education as a form of normalizing governance which reconstruct the others position for the prison students. Prison education was seen supportive for personal life control and for integrating to the society. The participants of prison education repeated the official discourses in their accounts which is a signal of internalized governance. The interviewees also used different types of anti-discourses when forming implications of prison education.

Domestic labour relations in India : Vulnerability and gendered life courses in Jaipur

This study explores labour relations between domestic workers and employers in India. It is based on interviews with both employers and workers, and ethnographically oriented field work in Jaipur, carried out in 2004-2007. Combining development studies with gender studies, labour studies, and childhood studies, it asks how labour relations between domestic workers and employers are formed in Jaipur, and how female domestic workers trajectories are created. Focusing on female part-time maids and live-in work arrangements, the study analyses children s work in the context of overall work force, not in isolation from it. Drawing on feminist Marxism, domestic labour relations are seen as an arena of struggle. The study takes an empirical approach, showing class through empiria and shows how paid domestic work is structured and stratified through intersecting hierarchies of class, caste, gender, age, ethnicity and religion. The importance of class in domestic labour relations is reiterated, but that of caste, so often downplayed by employers, is also emphasized. Domestic workers are crucial to the functioning of middle and upper middle class households, but their function is not just utilitarian. Through them working women and housewives are able to maintain purity and reproduce class disctinctions, both between poor and middle classes and lower and upper middle classes. Despite commodification of work relations, traditional elements of service relationships have been retained, particularly through maternalist practices such as gift giving, creating a peculiar blend of traditional and market practices. Whilst employers of part-time workers purchase services in a segmented market from a range of workers for specific, traditional live-in workers are also hired to serve employers round the clock. Employers and workers grudgingly acknowledged their dependence on one another, employers seeking various strategies to manage fear of servant crime, such as the hiring of children or not employing live-in workers in dual-earning households. Paid domestic work carries a heavy stigma and provide no entry to other jobs. It is transmitted from mothers to daughters and working girls were often the main income providers in their families. The diversity of working conditions is analysed through a continuum of vulnerability, generic live-in workers, particularly children and unmarried young women with no close family in Jaipur, being the most vulnerable and experienced part-time workers the least vulnerable. Whilst terms of employment are negotiated informally and individually, some informal standards regarding salary and days off existed for maids. However, employers maintain that workings conditions are a matter of individual, moral choice. Their reluctance to view their role as that of employers and the workers as their employees is one of the main stumbling blocks in the way of improved working conditions. Key words: paid domestic work, India, children s work, class, caste, gender, life course

The Enlightenment Idea of History as a Legitimation Tool of Kemalism in Turkey

The study analyzes the effort to build political legitimacy in the Republic of Turkey by ex-ploring a group of influential texts produced by Kemalist writers. The study explores how the Kemalist regime reproduced certain long-lasting enlightenment meta-narrative in its effort to build political legitimacy. Central in this process was a hegemonic representation of history, namely the interpretation of the Anatolian Resistance Struggle of 1919 1922 as a Turkish Revolution executing the enlightenment in the Turkish nation-state. The method employed in the study is contextualizing narratological analysis. The Kemalist texts are analyzed with a repertoire of concepts originally developed in the theory of narra-tive. By bringing these concepts together with epistemological foundations of historical sciences, the study creates a theoretical frame inside of which it is possible to highlight how initially very controversial historical representations in the end manage to construct long-lasting, emotionally and intellectually convincing bases of national identity for the secular middle classes in Turkey. The two most important explanatory concepts in this sense are di-egesis and implied reader. The diegesis refers to the ability of narrative representation to create an inherently credible story-world that works as the basis of national community. The implied reader refers to the process where a certain hegemonic narrative creates a formula of identification and a position through which any individual real-world reader of a story can step inside the narrative story-world and identify oneself as one of us of the national narra-tive. The study demonstrates that the Kemalist enlightenment meta-narrative created a group of narrative accruals which enabled generations of secular middle classes to internalize Kemalist ideology. In this sense, the narrative in question has not only worked as a tool utilized by the so-called Kemalist state-elite to justify its leadership, but has been internalized by various groups in Turkey, working as their genuine world-view. It is shown in the study that secular-ism must be seen as the core ingredient of these groups national identity. The study proposes that the enlightenment narrative reproduced in the Kemalist ideology had its origin in a simi-lar totalizing cultural narrative created in and for Europe. Currently this enlightenment project is challenged in Turkey by those who are in an attempt to give religion a greater role in Turkish society. The study argues that the enduring practice of legitimizing political power through the enlightenment meta-narrative has not only become a major factor contributing to social polarization in Turkey, but has also, in contradiction to the very real potentials for crit-ical approaches inherent in the Enlightenment tradition, crucially restricted the development of critical and rational modes of thinking in the Republic of Turkey.

Differential reproductive success in Cassia fistula in different habitants-A case of pollinator limitations?

Differences in flower success patterns in two habitat types that differed drastically with respect to rainfall, tree density and species composition were studied at Mudumalai wildlife sanctuary, India. Observations on phenological patterns of two species, Cassia fistula and Gmelina arborea, were made from April 1988 through June 1990. Quantitative data on flower-fruit ratio, insect visitation rates, pollen grain per stigma and the number of fruits per tree were recorded. Data were also collected on the number of pollen deposited on the stigma after different types of bees visited the flower. The data suggested that only carpenter bees (Xylocopa spp) effect pollination in C. fistula. The differences in fruit-flower ratios were attributed to the differences in insect visitation rates to inflorescences between sites. The low pollen number per stigma and the resultant reduction in reproductive success in C. fistula are attributed to the competing species G. arborea receiving more visitations from pollinators in the wetter site. These results suggest that pollinator limitation is another constraint in reproductive success of plants.

The diatom genus Gomphonema Ehrenberg in India: Checklist and description of three new species

We have compiled a checklist of Gomphonema Ehrenberg taxa reported previously from India. From forty-nine references, over 100 Gomphonema taxa have been reported, including 39 new taxon descriptions. In addition to these previous reports of Gomphonema taxa, we describe three new species. G. gandhii Karthick & Kociolek, sp. nov., G. difformum Karthick & Kociolek, sp. nov. and G. diminutum Karthick & Kociolek, sp. nov., all from hill streams of Western Ghats, India. Frustule morphology, as studied in light and scanning electron microscopy, is compared with that of other recently described Gomphonema species from Africa and Asia. All three Indian species have distinctly dilated proximal raphe ends, in addition to differentiated apical pore fields, septa, pseudosepta and a round external stigma! opening. Gomphonema gandhii is linear-lanceolate-clavate, has a wide axial area, and is 19-51 mu m long, 3-7 mu m broad. Gomphonema difformum is smaller than G. gandhii, and has a hyaline area around the headpole. Gomphonema diminuta is much smaller and narrower than the other two species. These species are distinct from their closest congeners by their sizes, shape and structure of the head pole, and striae densities. All these species were described from low nutrient, neutral, low ionic content streams of Western Ghats. As most other species described from tropical region these three species appear to be endemic to India. Moreover, within India they have hitherto only been found in Western Ghats, one of the twelve biodiversity hotspots of the World.

CNT loading into cationic cholesterol suspensions show improved DNA binding and serum stability and ability to internalize into cancer cells

Methods which disperse single-walled carbon nanotubes (SWNTs) in water as `debundled', while maintaining their unique physical properties are highly useful. We present here a family of cationic cholesterol compounds (Chol(+)) {Cholest-5en-3 beta-oxyethyl pyridinium bromide (Chol-PB+), Cholest-5en-3 beta-oxyethyl N-methyl pyrrolidinium bromide (Chol-MPB+), Cholest-5en-3 beta-oxyethyl N-methyl morpholinium bromide (Chol-MMB+) and Cholest-5en-3 beta-oxyethyl diazabicyclo octanium bromide (Chol-DOB+)}. Each of these could be easily dispersed in water. The resulting cationic cholesterol (Chol(+)) suspensions solubilized single-walled carbon nanotubes (SWCNTs) by the non-specific physical adsorption of Chol(+) to form stable, transparent, dark aqueous suspensions at room temperature. Electron microscopy reveals the existence of highly segregated CNTs in these samples. Zeta potential measurements showed an increase in potential of cationic cholesterol aggregates on addition of CNTs. The CNT-Chol(+) suspensions were capable of forming stable complexes with genes (DNA) efficiently. The release of double-helical DNA from such CNT-Chol(+) complexes could be induced upon the addition of anionic micellar solution of SDS. Furthermore, the CNT-based DNA complexes containing cationic cholesterol aggregates showed higher stability in fetal bovine serum media at physiological conditions. Confocal studies confirm that CNT-Chol(+) formulations adhere to HeLa cell surfaces and get internalized more efficiently than the cationic cholesterol suspensions alone (devoid of any CNTs). These cationic cholesterol-CNT suspensions therefore appear to be a promising system for further use in biological applications.

Two new species of Gomphonema (Bacillariophyceae) from Doon Valley, Uttarakhand, India

This paper describes two new Gomphonema species from the lesser Himalayas, India, with their valve morphology using light and scanning electron microscopy. The two species, Gomphonema juettnerii sp. nov. and G. doonensis sp. nov., were found in Nalota stream in Doon Valley of Uttarakhand State. Main features of G. juettnerii are valve outline, shape of the areolae and striae pattern and presence of stigma. Main features of G. doonensis are rounded headpole, striae made by doubly punctate striae and features in central area. A detailed discussion on doubly punctate striae in members of gomphonemoid diatoms is presented.

Botulinum neurotoxin type-A enters a non-recycling pool of synaptic vesicles

Neuronal communication relies on synaptic vesicles undergoing regulated exocytosis and recycling for multiple rounds of fusion. Whether all synaptic vesicles have identical protein content has been challenged, suggesting that their recycling ability may differ greatly. Botulinum neurotoxin type-A (BoNT/A) is a highly potent neurotoxin that is internalized in synaptic vesicles at motor nerve terminals and induces flaccid paralysis. Recently, BoNT/A was also shown to undergo retrograde transport, suggesting it might enter a specific pool of synaptic vesicles with a retrograde trafficking fate. Using high-resolution microscopy techniques including electron microscopy and single molecule imaging, we found that the BoNT/A binding domain is internalized within a subset of vesicles that only partially co-localize with cholera toxin B-subunit and have markedly reduced VAMP2 immunoreactivity. Synaptic vesicles loaded with pHrodo-BoNT/A-Hc exhibited a significantly reduced ability to fuse with the plasma membrane in mouse hippocampal nerve terminals when compared with pHrodo-dextran-containing synaptic vesicles and pHrodo-labeled anti-GFP nanobodies bound to VAMP2-pHluorin or vGlut-pHluorin. Similar results were also obtained at the amphibian neuromuscular junction. These results reveal that BoNT/A is internalized in a subpopulation of synaptic vesicles that are not destined to recycle, highlighting the existence of significant molecular and functional heterogeneity between synaptic vesicles.

Regional research priorities in brain and nervous system disorders

The characteristics of neurological, psychiatric, developmental and substance-use disorders in low-and middle-income countries are unique and the burden that they have will be different from country to country. Many of the differences are explained by the wide variation in population demographics and size, poverty, conflict, culture, land area and quality, and genetics. Neurological, psychiatric, developmental and substance-use disorders that result from, or are worsened by, a lack of adequate nutrition and infectious disease still afflict much of sub-Saharan Africa, although disorders related to increasing longevity, such as stroke, are on the rise. In the Middle East and North Africa, major depressive disorders and post-traumatic stress disorder are a primary concern because of the conflict-ridden environment. Consanguinity is a serious concern that leads to the high prevalence of recessive disorders in the Middle East and North Africa and possibly other regions. The burden of these disorders in Latin American and Asian countries largely surrounds stroke and vascular disease, dementia and lifestyle factors that are influenced by genetics. Although much knowledge has been gained over the past 10 years, the epidemiology of the conditions in low-and middle-income countries still needs more research. Prevention and treatments could be better informed with more longitudinal studies of risk factors. Challenges and opportunities for ameliorating nervous-system disorders can benefit from both local and regional research collaborations. The lack of resources and infrastructure for health-care and related research, both in terms of personnel and equipment, along with the stigma associated with the physical or behavioural manifestations of some disorders have hampered progress in understanding the disease burden and improving brain health. Individual countries, and regions within countries, have specific needs in terms of research priorities.

Stimuli-responsive protamine-based biodegradable nanocapsules for enhanced bioavailability and intracellular delivery of anticancer agents

Enzyme-and pH-responsive polyelectrolyte nanocapsules having diameters in the range of 200 +/- 20 nm were fabricated by means of Layer-by-Layer assembly of biopolymers, protamine, and heparin, and then loaded with anticancer drug doxorubicin. The incorporation of the FDA-approved peptide drug protamine as a wall component rendered the capsules responsive to enzyme stimuli. The stimuli-responsive drug release from these nanocapsules was evaluated, and further modulation of capsule permeability to avoid premature release was demonstrated by crosslinking the wall components. The interaction of the nanocapsules with cancer cells was studied using MCF-7 breast cancer cells. These capsules were readily internalized and disintegrated inside the cells, culminating in the release of the loaded doxorubicin and subsequent cell death as observed by confocal microscopy and MTT Assay. The bioavailability studies performed using BALB/c mice revealed that the encapsulated doxorubicin exhibited enhanced bioavailability compared to free doxorubicin. Our results indicate that this stimuli-responsive system fabricated from clinically used FDA-approved molecules and exhibiting minimal premature release has great potential for drug-delivery applications.