Influence of the sputtering flow regime on the structural properties and magnetic behavior of Fe-Ga thin films (Ga ∼ 30 at.%)

In this paper we analyze the structure of Fe-Ga layers with a Ga content of ∼30 at.% deposited by the sputtering technique under two different regimes. We also studied the correlation between the structure and magnetic behavior of the samples. Keeping the Ar pressure fixed, we modified the flow regime from ballistic to diffusive by increasing the distance between the target and the substrate. X-ray diffraction measurements have shown a lower structural quality when growing in the diffusive flow. We investigated the impact of the growth regime by means of x-ray absorption fine structure (XAFS) measurements and obtained signs of its influence on the local atomic order. Full multiple scattering and finite difference calculations based on XAFS measurements point to a more relevant presence of a disordered A2 phase and of orthorhombic Ga clusters on the Fe-Ga alloy deposited under a diffusive regime; however, in the ballistic sample, a higher presence of D0_3/B2 phases is evidenced. Structural characteristics, from local to long range, seem to determine the magnetic behavior of the layers. Whereas a clear in-plane magnetic anisotropy is observed in the film deposited under ballistic flow, the diffusive sample is magnetically isotropic. Therefore, our experimental results provide evidence of a correlation between flow regime and structural properties and its impact on the magnetic behavior of a rather unexplored compositional region of Fe-Ga compounds.

A Sting in the Tail : The N-Terminal Domain of the Androgen Receptor as a Drug Target

AEM was supported by a BBSRC-CASE studentship award. Research in the IJM laboratory is currently supported by the Chief Scientist's Office of the Scottish Government and the charity Friends of Anchor.

First-principles calculation of carrier-phonon scattering in n-type Si1−xGex alloys

First-principles electronic structure methods are used to find the rates of inelastic intravalley and intervalley n-type carrier scattering in Si1-xGex alloys. Scattering parameters for all relevant Delta and L intra- and intervalley scattering are calculated. The short-wavelength acoustic and the optical phonon modes in the alloy are computed using the random mass approximation, with interatomic forces calculated in the virtual crystal approximation using density functional perturbation theory. Optical phonon and intervalley scattering matrix elements are calculated from these modes of the disordered alloy. It is found that alloy disorder has only a small effect on the overall inelastic intervalley scattering rate at room temperature. Intravalley acoustic scattering rates are calculated within the deformation potential approximation. The acoustic deformation potentials are found directly and the range of validity of the deformation potential approximation verified in long-wavelength frozen phonon calculations. Details of the calculation of elastic alloy scattering rates presented in an earlier paper are also given. Elastic alloy disorder scattering is found to dominate over inelastic scattering, except for almost pure silicon (x approximate to 0) or almost pure germanium (x approximate to 1), where acoustic phonon scattering is predominant. The n-type carrier mobility, calculated from the total (elastic plus inelastic) scattering rate, using the Boltzmann transport equation in the relaxation time approximation, is in excellent agreement with experiments on bulk, unstrained alloys..

First-principles calculation of P-type alloy scattering in Si1-xGex

The p-type carrier scattering rate due to alloy disorder in Si1-xGex alloys is obtained from first principles. The required alloy scattering matrix elements are calculated from the energy splitting of the valence bands, which arise when one average host atom is replaced by a Ge or Si atom in supercells containing up to 128 atoms. Alloy scattering within the valence bands is found to be characterized by a single scattering parameter. The hole mobility is calculated from the scattering rate using the Boltzmann transport equation in the relaxation time approximation. The results are in good agreement with experiments on bulk, unstrained alloys..

Sortase as a Tool in Biotechnology and Medicine

We have harnessed two reactions catalyzed by the enzyme sortase A and applied them to generate new methods for the purification and site-selective modification of recombinant protein therapeutics.

We utilized native peptide ligation —a well-known function of sortase A— to attach a small molecule drug specifically to the carboxy-terminus of a recombinant protein. By combining this reaction with the unique phase behavior of elastin-like polypeptides, we developed a protocol that produces homogenously-labeled protein-small molecule conjugates using only centrifugation. The same reaction can be used to produce unmodified therapeutic proteins simply by substituting a single reactant. The isolated proteins or protein-small molecule conjugates do not have any exogenous purification tags, eliminating the potential influence of these tags on bioactivity. Because both unmodified and modified proteins are produced by a general process that is the same for any protein of interest and does not require any chromatography, the time, effort, and cost associated with protein purification and modification is greatly reduced.

We also developed an innovative and unique method that attaches a tunable number of drug molecules to any recombinant protein of interest in a site-specific manner. Although the ability of sortase A to carry out native peptide ligation is widely used, we demonstrated that Sortase A is also capable of attaching small molecules to proteins through an isopeptide bond at lysine side chains within a unique amino acid sequence. This reaction —isopeptide ligation— is a new site-specific conjugation method that is orthogonal to all available protein-small conjugation technologies and is the first site-specific conjugation method that attaches the payload to lysine residues. We show that isopeptide ligation can be applied broadly to peptides, proteins, and antibodies using a variety of small molecule cargoes to efficiently generate stable conjugates. We thoroughly assessed the site-selectivity of this reaction using a variety of analytical methods and showed that in many cases the reaction is site-specific for lysines in flexible, disordered regions of the substrate proteins. Finally, we showed that isopeptide ligation can be used to create clinically-relevant antibody-drug conjugates that have potent cytotoxicity towards cancerous cells

Investigating the Structure of FtsZ to Understand its Functional Role in Bacterial Cell Division

FtsZ, a bacterial tubulin homologue, is a cytoskeleton protein that plays key roles in cytokinesis of almost all prokaryotes. FtsZ assembles into protofilaments (pfs), one subunit thick, and these pfs assemble further to form a “Z ring” at the center of prokaryotic cells. The Z ring generates a constriction force on the inner membrane, and also serves as a scaffold to recruit cell-wall remodeling proteins for complete cell division in vivo. FtsZ can be subdivided into 3 main functional regions: globular domain, C terminal (Ct) linker, and Ct peptide. The globular domain binds GTP to assembles the pfs. The extreme Ct peptide binds membrane proteins to allow cytoplasmic FtsZ to function at the inner membrane. The Ct linker connects the globular domain and Ct peptide. In the present studies, we used genetic and structural approaches to investigate the function of Escherichia coli (E. coli) FtsZ. We sought to examine three questions: (1) Are lateral bonds between pfs essential for the Z ring? (2) Can we improve direct visualization of FtsZ in vivo by engineering an FtsZ-FP fusion that can function as the sole source of FtsZ for cell division? (3) Is the divergent Ct linker of FtsZ an intrinsically disordered peptide (IDP)?

One model of the Z ring proposes that pfs associate via lateral bonds to form ribbons; however, lateral bonds are still only hypothetical. To explore potential lateral bonding sites, we probed the surface of E. coli FtsZ by inserting either small peptides or whole FPs. Of the four lateral surfaces on FtsZ pfs, we obtained inserts on the front and back surfaces that were functional for cell division. We concluded that these faces are not sites of essential interactions. Inserts at two sites, G124 and R174 located on the left and right surfaces, completely blocked function, and were identified as possible sites for essential lateral interactions. Another goal was to find a location within FtsZ that supported fusion of FP reporter proteins, while allowing the FtsZ-FP to function as the sole source of FtsZ. We discovered one internal site, G55-Q56, where several different FPs could be inserted without impairing function. These FtsZ-FPs may provide advances for imaging Z-ring structure by super-resolution techniques.

The Ct linker is the most divergent region of FtsZ in both sequence and length. In E. coli FtsZ the Ct linker is 50 amino acids (aa), but for other FtsZ it can be as short as 37 aa or as long as 250 aa. The Ct linker has been hypothesized to be an IDP. In the present study, circular dichroism confirmed that isolated Ct linkers of E. coli (50 aa) and C. crescentus (175 aa) are IDPs. Limited trypsin proteolysis followed by mass spectrometry (LC-MS/MS) confirmed Ct linkers of E. coli (50 aa) and B. subtilis (47 aa) as IDPs even when still attached to the globular domain. In addition, we made chimeras, swapping the E. coli Ct linker for other peptides and proteins. Most chimeras allowed for normal cell division in E. coli, suggesting that IDPs with a length of 43 to 95 aa are tolerated, sequence has little importance, and electrostatic charge is unimportant. Several chimeras were purified to confirm the effect they had on pf assembly. We concluded that the Ct linker functions as a flexible tether allowing for force to be transferred from the FtsZ pf to the membrane to constrict the septum for division.

The extracellular matrix contributes to mechanotransduction in uterine fibroids.

The role of the extracellular matrix (ECM) and mechanotransduction as an important signaling factor in the human uterus is just beginning to be appreciated. The ECM is not only the substance that surrounds cells, but ECM stiffness will either compress cells or stretch them resulting in signals converted into chemical changes within the cell, depending on the amount of collagen, cross-linking, and hydration, as well as other ECM components. In this review we present evidence that the stiffness of fibroid tissue has a direct effect on the growth of the tumor through the induction of fibrosis. Fibrosis has two characteristics: (1) resistance to apoptosis leading to the persistence of cells and (2) secretion of collagen and other components of the ECM such a proteoglycans by those cells leading to abundant disposition of highly cross-linked, disoriented, and often widely dispersed collagen fibrils. Fibrosis affects cell growth by mechanotransduction, the dynamic signaling system whereby mechanical forces initiate chemical signaling in cells. Data indicate that the structurally disordered and abnormally formed ECM of uterine fibroids contributes to fibroid formation and growth. An appreciation of the critical role of ECM stiffness to fibroid growth may lead to new strategies for treatment of this common disease.

(Table 1) Lithology, mineralogy, and physical properties of Cretaceous cherts and porcellanites at DSDP Hole 56-436

Cretaceous chert and porcellanite recovered at Site 436, east of northern Honshu, Japan, are texturally and mineralogically similar to siliceous rocks of comparable age at Sites 303, 304, and 307 in the northwest Pacific. These rocks probably were formed by impregnation of the associated pelagic clay with locally derived silica from biogenic and perhaps some volcanic debris. Fine horizontal laminations are the only primary sedimentary structures, suggesting minimal reworking and transport. Collapse breccias and incipient chert nodules are diagenetic features related to silicification and compaction of the original sediment. Disordered opal-CT (d[101] = 4.09 Å) and microgranular quartz (crystallinity index < 1.0) are the two common silica minerals present. Some samples show quartz replacing this poorly ordered opal- CT, supporting the notion that opal-CT does not become completely ordered (i.e., d[101] = 4.04 Å) in some cases before being converted to quartz. The present temperature calculated for the depth of the shallowest chert and porcellanite at this site is 30 °C; this may represent the temperature of conversion of opal-CT to quartz. High reflection coefficients (0.29-0.65) calculated for the boundary between chert-porcellanite and clay-claystone support the common observation that chert is a strong seismic reflector in deep-sea sedimentary sections.

(Table II, page 668-669) Distribution of elements between minerals soluble in 1M Hydroxylamine hydrochloride (Reducible); in 1m HCL (Acid-soluble) and in the insoluble residue of manganese nodules

Attempts to classify pelagic sediments have been based either on appearance and composition, or on the ultimate origin of the components. In particular it appears feasible to distinguish minerals which crystallized in sea-water from those which formed in magmas, in hydrothermal solution, or by weathering under acidic conditions. It is the case of iron and manganese oxide mineral aggregates which constitute one of the major types of rock encountered on the ocean floor; according to Menard (unpublished) about 10% of the pelagic area of the Pacific is covered by such nodules. The nodules consist of intimately intergrown crystallites of different minerals among those identified, besides detrital minerals and organic matter, are opal, goethite, rutile, anatase, barite, nontronite, and at least three manganese oxide minerals of major importance. Arrhenius and Korkisch (1959) have attempted to separate from each other the different minerals constituting the nodules, in order to establish the details of their structure and the localization of the heavy metal ions. The results demonstrate (Table II) that copper and nickel are concentrated in the manganese oxide phases concentrated in the reducible fraction. Cobalt, part of the nickel and most of the chromium are distributed between these and the acid-soluble group of the non-manganese minerals, dominated by goethite and disordered FeOOH.

Isotope analysis and heat flow measurements of Maria S. Merian cruise MSM21/4 on the western Svalbard margin

Methane hydrate is an ice-like substance that is stable at high-pressure and low temperature in continental margin sediments. Since the discovery of a large number of gas flares at the landward termination of the gas hydrate stability zone off Svalbard, there has been concern that warming bottom waters have started to dissociate large amounts of gas hydrate and that the resulting methane release may possibly accelerate global warming. Here, we can corroborate that hydrates play a role in the observed seepage of gas, but we present evidence that seepage off Svalbard has been ongoing for at least three thousand years and that seasonal fluctuations of 1-2°C in the bottom-water temperature cause periodic gas hydrate formation and dissociation, which focus seepage at the observed sites.

Unraveling the function of bacterial-type phosphoenolpyruvate carboxylase in vascular plants

Two distinct phosphoenolpyruvate carboxylase (PEPC) isozymes occur in vascular plants and green algae: plant-type PEPC (PTPC) and bacterial-type PEPC (BTPC). PTPC polypeptides typically form a tightly regulated cytosolic Class-1 PEPC homotetramer. BTPCs, however, appear to be less widely expressed and to exist only as catalytic and regulatory subunits that physically interact with co-expressed PTPC subunits to form hetero-octameric Class-2 PEPC complexes that are highly desensitized to Class-1 PEPC allosteric effectors. Yeast two-hybrid studies indicated that castor plant BTPC (RcPPC4) interacts with all three Arabidopsis thaliana PTPC isozymes, and that it forms stronger interactions with AtPPC2 and AtPPC3, suggesting that specific PTPCs are preferred for Class-2 PEPC formation. In contrast, Arabidopsis BTPC (AtPPC4) appeared to interact very weakly with AtPPC2 and AtPPC3, suggesting that BTPCs from different species may have different physical properties, hypothesized to be due to sequence dissimilarities within their ~10 kDa intrinsically disordered region. Recent RNA-seq and microarray data were analyzed to obtain a better understanding of BTPC expression patterns in different tissues of various monocot and dicot species. High levels of BTPC transcripts, polypeptides and Class-2 PEPC complexes were originally discovered in developing castor seeds, but the analysis revealed a broad range of diverse tissues where abundant BTPC transcripts are also expressed, such as the developing fruits of cucumber, grape, and tomato. Marked BTPC expression correlated well with the presence of ~116 kDa immunoreactive BTPC polypeptides, as well as Class-2 PEPC complexes in the immature fruit of cucumbers and tomatoes. It is therefore hypothesized that in vascular plants BTPC and thus Class-2 PEPC complexes maintain anaplerotic PEP flux in tissues with elevated malate levels that would potently inhibit ‘housekeeping’ Class-1 PEPCs. Elevated levels of malate can be used by biosynthetically active sink tissues such as immature tomatoes and cucumbers for rapid cell expansion, drought or salt stressed roots for osmoregulation, and developing seeds and pollen as a precursor for storage lipid and protein biosynthesis.

De Invloed van Mentale Veerkracht op Copingstrategieën bij Eetproblematiek

Dit onderzoek bestudeerde het verband tussen probleemgerichte- en emotiegerichte coping en eetproblematiek en onderzocht daarnaast of mentale veerkracht de relaties tussen probleemgerichte en emotiegerichte coping enerzijds en eetproblematiek anderzijds beïnvloedt. Het doel van dit onderzoek was het verkrijgen van meer inzicht in de rol van mentale veerkracht als mogelijke moderator van de relatie tussen coping en eetproblematiek. Er is een eenmalige meting verricht bij jong volwassen vrouwen van 18 t/m 30 jaar uit de algemene populatie. Via e-mail en sociale media zijn online vragenlijsten verspreid die bruikbare gegevens opleverden van in totaal 188 vrouwen. Meetinstrumenten. Coping is gemeten middels de Utrechtse Coping Lijst (UCL) (Schreurs, Willige, van de Tellegen & Brosschot, 1988; Schreurs, Willige, van de Tellegen & Brosschot, 1993); mentale veerkracht is gemeten met behulp van de Resilience Scale-Nederlandse versie (RS-nl) (Portzky, 2008); en de mate van eetproblematiek is gemeten met de Eating Disorder Examination Questionnaire (EDE-Q) (Fairburn & Beglin, 1994). De resultaten hebben aangetoond dat er een significant negatief verband bestaat tussen probleemgerichte coping en mate van eetproblematiek en een significant positief verband tussen emotiegerichte coping en eetproblematiek. De negatieve samenhang tussen probleemgerichte coping en eetproblematiek bleek sterker bij een lagere mate van mentale veerkracht. De positieve samenhang tussen emotiegerichte coping en eetproblematiek bleek eveneens sterker bij een lagere mentale veerkracht. Personen met een lage mentale veerkracht en een ineffectieve (emotiegerichte of weinig probleemgerichte) copingstijl bleken de meeste eetproblemen te ervaren, bij een hoge mentale veerkracht werd de minste eetproblematiek gerapporteerd, ongeacht de gehanteerde copingstijl.

Crystallization on the Mesoscale : Self-Assembly of Iron Oxide Nanocubes into Mesocrystals

Self-assembly of nanoparticles is a promising route to form complex, nanostructured materials with functional properties. Nanoparticle assemblies characterized by a crystallographic alignment of the nanoparticles on the atomic scale, i.e. mesocrystals, are commonly found in nature with outstanding functional and mechanical properties. This thesis aims to investigate and understand the formation mechanisms of mesocrystals formed by self-assembling iron oxide nanocubes. We have used the thermal decomposition method to synthesize monodisperse, oleate-capped iron oxide nanocubes with average edge lengths between 7 nm and 12 nm and studied the evaporation-induced self-assembly in dilute toluene-based nanocube dispersions. The influence of packing constraints on the alignment of the nanocubes in nanofluidic containers has been investigated with small and wide angle X-ray scattering (SAXS and WAXS, respectively). We found that the nanocubes preferentially orient one of their {100} faces with the confining channel wall and display mesocrystalline alignment irrespective of the channel widths.  We manipulated the solvent evaporation rate of drop-cast dispersions on fluorosilane-functionalized silica substrates in a custom-designed cell. The growth stages of the assembly process were investigated using light microscopy and quartz crystal microbalance with dissipation monitoring (QCM-D). We found that particle transport phenomena, e.g. the coffee ring effect and Marangoni flow, result in complex-shaped arrays near the three-phase contact line of a drying colloidal drop when the nitrogen flow rate is high. Diffusion-driven nanoparticle assembly into large mesocrystals with a well-defined morphology dominates at much lower nitrogen flow rates. Analysis of the time-resolved video microscopy data was used to quantify the mesocrystal growth and establish a particle diffusion-based, three-dimensional growth model. The dissipation obtained from the QCM-D signal reached its maximum value when the microscopy-observed lateral growth of the mesocrystals ceased, which we address to the fluid-like behavior of the mesocrystals and their weak binding to the substrate. Analysis of electron microscopy images and diffraction patterns showed that the formed arrays display significant nanoparticle ordering, regardless of the distinctive formation process.  We followed the two-stage formation mechanism of mesocrystals in levitating colloidal drops with real-time SAXS. Modelling of the SAXS data with the square-well potential together with calculations of van der Waals interactions suggests that the nanocubes initially form disordered clusters, which quickly transform into an ordered phase.

Processo de planejamento estratégico em universidade pública: o caso da Universidade Federal do Pará

The goal of this research is to check if the strategic planning developed between 2001 and 2009 into the State University of Para (Universidade Federal do Pará - UFPA) was consolidated into its Academic Centers as a management practice. To this end, we identified the planning formalization degree of the Academic Centers, the conceived tools for the planning, the conception and the methodological process used in the tools elaboration, as also its implementation. The research used a qualitative approach: it is descriptive and it uses the case study technique. The data were gathered from primary and secondary sources, through bibliography, documents, and field researches through semi-structure interviews. The analysis and data interpretation were done by each investigated Academic Center from the analytics categories guided by the specifics goals. We used theoretic fundamental based principles and the university as a study empiric reference based on its structure analysis, organizational processes and institutional strategic plan. We inspected how the strategic planning process was developed throughout the fixed period and how the investigated Academic Centers are from the collected documents and interviews. The theoretical foundation was built from three axis: the Brazilian undergraduate and posgraduate education system; the university itself including its singularity and complexity as an organization; and the planning as a strategic management process. The main results show us that the UFPA has updated regulatory milestones, presenting organizational structure, laws, instructions, manuals and deployed management model that give the strategic planning development conditions beyond its administration, i. e., into its Academic Centers. The centers also present those established milestones and develop the basic planning processes of the institution. Those processes are conceived based on the institutional strategic planning and the managers mainly use the procedural orientation defined by the university management, from where the conceptual foundation is originated and propagated. According to the literature and to the research done in this work, we can conclude that the Academic Centers from the UFPA developed the strategic planning practice. This planning is organized and founded and guided the plans and decisions which avoided the disordered management and, according to the managers, allowed the advances and performance improvement. We can conclude that the UFPA built an important foundation with respect to the management professionalization. On the other hand, we can not conclude that the management practice is consolidated since there are weaknesses into the structuring of the technical teams and there is not any management tool for the implementation of the elaborated plans

A bio-coke for anode production and the manufacturing method thereof

Dans l’industrie de l’aluminium, le coke de pétrole calciné est considéré comme étant le composant principal de l’anode. Une diminution dans la qualité du coke de pétrole a été observée suite à une augmentation de sa concentration en impuretés. Cela est très important pour les alumineries car ces impuretés, en plus d’avoir un effet réducteur sur la performance des anodes, contaminent le métal produit. Le coke de pétrole est aussi une source de carbone fossile et, durant sa consommation, lors du processus d’électrolyse, il y a production de CO2. Ce dernier est considéré comme un gaz à effet de serre et il est bien connu pour son rôle dans le réchauffement planétaire et aussi dans les changements climatiques. Le charbon de bois est disponible et est produit mondialement en grande quantité. Il pourrait être une alternative attrayante pour le coke de pétrole dans la fabrication des anodes de carbone utilisées dans les cuves d’électrolyse pour la production de l’aluminium. Toutefois, puisqu’il ne répond pas aux critères de fabrication des anodes, son utilisation représente donc un grand défi. En effet, ses principaux désavantages connus sont sa grande porosité, sa structure désordonnée et son haut taux de minéraux. De plus, sa densité et sa conductivité électrique ont été rapportées comme étant inférieures à celles du coke de pétrole. L’objectif de ce travail est d’explorer l’effet du traitement de chaleur sur les propriétés du charbon de bois et cela, dans le but de trouver celles qui s’approchent le plus des spécifications requises pour la production des anodes. L’évolution de la structure du charbon de bois calciné à haute température a été suivie à l’aide de différentes techniques. La réduction de son contenu en minéraux a été obtenue suite à des traitements avec de l’acide chlorhydrique utilisé à différentes concentrations. Finalement, différentes combinaisons de ces deux traitements, calcination et lixiviation, ont été essayées dans le but de trouver les meilleures conditions de traitement.