Characterisation of the putative effector interaction site of the regulatory HbpR protein from Pseudomonas azelaica by site-directed mutagenesis.

Bacterial transcription activators of the XylR/DmpR subfamily exert their expression control via σ(54)-dependent RNA polymerase upon stimulation by a chemical effector, typically an aromatic compound. Where the chemical effector interacts with the transcription regulator protein to achieve activation is still largely unknown. Here we focus on the HbpR protein from Pseudomonas azelaica, which is a member of the XylR/DmpR subfamily and responds to biaromatic effectors such as 2-hydroxybiphenyl. We use protein structure modeling to predict folding of the effector recognition domain of HbpR and molecular docking to identify the region where 2-hydroxybiphenyl may interact with HbpR. A large number of site-directed HbpR mutants of residues in- and outside the predicted interaction area was created and their potential to induce reporter gene expression in Escherichia coli from the cognate P(C) promoter upon activation with 2-hydroxybiphenyl was studied. Mutant proteins were purified to study their conformation. Critical residues for effector stimulation indeed grouped near the predicted area, some of which are conserved among XylR/DmpR subfamily members in spite of displaying different effector specificities. This suggests that they are important for the process of effector activation, but not necessarily for effector specificity recognition.

Endothelial cells as key determinants of the tumor microenvironment: interaction with tumor cells, extracellular matrix and immune killer cells.

Besides tumor cells, the tumor microenvironment harbors a variety of host-derived cells, such as endothelial cells, fibroblasts, innate and adaptive immune cells. It is a complex and highly dynamic environment, providing very important cues to tumor development and progression. Tumor-associated endothelial cells play a key role in this process. On the one hand, they form tumor-associated (angiogenic) vessels through sprouting from locally preexisting vessels or recruitment of bone marrow-derived endothelial progenitor cells, to provide nutritional support to the growing tumor. On the other hand, they are the interface between circulating blood cells, tumor cells and the extracellular matrix, thereby playing a central role in controlling leukocyte recruitment, tumor cell behavior and metastasis formation. Hypoxia is a critical parameter modulating the tumor microenvironment and endothelial/tumor cell interactions. Under hypoxic stress, tumor cells produce factors that promote tumor angiogenesis, tumor cell motility and metastasis. Among these factors, VEGF, a main angiogenesis modulator, can also play a critical role in the control of immune tolerance. This review discusses some aspects of the role of endothelial cells within tumor microenvironment and emphasizes their interaction with tumor cells, the extracellular matrix and with immune killer cells. We will also address the role played by circulating endothelial progenitor cells and illustrate their features and mechanism of recruitment to the tumor microenvironment and their role in tumor angiogenesis.

TL1A-DR3 interaction regulates Th17 cell function and Th17-mediated autoimmune disease.

T helper type 17 (Th17) cells play an important pathogenic function in autoimmune diseases; their regulation, however, is not well understood. We show that the expression of a tumor necrosis factor receptor family member, death receptor 3 (DR3; also known as TNFRSF25), is selectively elevated in Th17 cells, and that TL1A, its cognate ligand, can promote the proliferation of effector Th17 cells. To further investigate the role of the TL1A-DR3 pathway in Th17 regulation, we generated a TL1A-deficient mouse and found that TL1A(-/-) dendritic cells exhibited a reduced capacity in supporting Th17 differentiation and proliferation. Consistent with these data, TL1A(-/-) animals displayed decreased clinical severity in experimental autoimmune encephalomyelitis (EAE). Finally, we demonstrated that during EAE disease progression, TL1A was required for the optimal differentiation as well as effector function of Th17 cells. These observations thus establish an important role of the TL1A-DR3 pathway in promoting Th17 cell function and Th17-mediated autoimmune disease.

Integrating life cycle costs and environmental impacts of composite rail car-bodies for a Korean train

Background, aim, and scope A coupled Life Cycle Costing and life cycle assessment has been performed for car-bodies of the Korean Tilting Train eXpress (TTX) project using European and Korean databases, with the objective of assessing environmental and cost performance to aid materials and process selection. More specifically, the potential of polymer composite car-body structures for the Korean Tilting Train eXpress (TTX) has been investigated. Materials and methods This assessment includes the cost of both carriage manufacturing and use phases, coupled with the life cycle environmental impacts of all stages from raw material production, through carriage manufacture and use, to end-of-life scenarios. Metallic carriages were compared with two composite options: hybrid steel-composite and full-composite carriages. The total planned production for this regional Korean train was 440 cars, with an annual production volume of 80 cars. Results and discussion The coupled analyses were used to generate plots of cost versus energy consumption and environmental impacts. The results show that the raw material and manufacturing phase costs are approximately half of the total life cycle costs, whilst their environmental impact is relatively insignificant (3-8%). The use phase of the car-body has the largest environmental impact for all scenarios, with near negligible contributions from the other phases. Since steel rail carriages weigh more (27-51%), the use phase cost is correspondingly higher, resulting in both the greatest environmental impact and the highest life cycle cost. Compared to the steel scenario, the hybrid composite variant has a lower life cycle cost (16%) and a lower environmental impact (26%). Though the full composite rail carriage may have the highest manufacturing cost, it results in the lowest total life cycle costs and lowest environmental impacts. Conclusions and recommendations This coupled cost and life cycle assessment showed that the full composite variant was the optimum solution. This case study showed that coupling of technical cost models with life cycle assessment offers an efficient route to accurately evaluate economic and environmental performance in a consistent way.

Weed or wheel! FMRI, behavioural, and toxicological investigations of how cannabis smoking affects skills necessary for driving.

Marijuana is the most widely used illicit drug, however its effects on cognitive functions underling safe driving remain mostly unexplored. Our goal was to evaluate the impact of cannabis on the driving ability of occasional smokers, by investigating changes in the brain network involved in a tracking task. The subject characteristics, the percentage of Δ(9)-Tetrahydrocannabinol in the joint, and the inhaled dose were in accordance with real-life conditions. Thirty-one male volunteers were enrolled in this study that includes clinical and toxicological aspects together with functional magnetic resonance imaging of the brain and measurements of psychomotor skills. The fMRI paradigm was based on a visuo-motor tracking task, alternating active tracking blocks with passive tracking viewing and rest condition. We show that cannabis smoking, even at low Δ(9)-Tetrahydrocannabinol blood concentrations, decreases psychomotor skills and alters the activity of the brain networks involved in cognition. The relative decrease of Blood Oxygen Level Dependent response (BOLD) after cannabis smoking in the anterior insula, dorsomedial thalamus, and striatum compared to placebo smoking suggests an alteration of the network involved in saliency detection. In addition, the decrease of BOLD response in the right superior parietal cortex and in the dorsolateral prefrontal cortex indicates the involvement of the Control Executive network known to operate once the saliencies are identified. Furthermore, cannabis increases activity in the rostral anterior cingulate cortex and ventromedial prefrontal cortices, suggesting an increase in self-oriented mental activity. Subjects are more attracted by intrapersonal stimuli ("self") and fail to attend to task performance, leading to an insufficient allocation of task-oriented resources and to sub-optimal performance. These effects correlate with the subjective feeling of confusion rather than with the blood level of Δ(9)-Tetrahydrocannabinol. These findings bolster the zero-tolerance policy adopted in several countries that prohibits the presence of any amount of drugs in blood while driving.

Vessel centerline tracking and boundary sgementation in coronary MRA with minimal manual interaction.

Magnetic resonance angiography (MRA) provides a noninvasive means to detect the presence, location and severity of atherosclerosis throughout the vascular system. In such studies, and especially those in the coronary arteries, the vessel luminal area is typically measured at multiple cross-sectional locations along the course of the artery. The advent of fast volumetric imaging techniques covering proximal to mid segments of coronary arteries necessitates automatic analysis tools requiring minimal manual interactions to robustly measure cross-sectional area along the three-dimensional track of the arteries in under-sampled and non-isotropic datasets. In this work, we present a modular approach based on level set methods to track the vessel centerline, segment the vessel boundaries, and measure transversal area using two user-selected endpoints in each coronary of interest. Arterial area and vessel length are measured using our method and compared to the standard Soap-Bubble reformatting and analysis tool in in-vivo non-contrast enhanced coronary MRA images.

Technology educational affordance: Bridging the gap between patterns of interaction and technology usage

Peer-reviewed

Mechanisms of interaction of therapeutic nanoparticles with cells

Nanoparticles (NPs) have gained a lot of interest in recent years due to their huge potential for applications in industry and medicine. Their unique properties offer a large number of attractive possibilities in the biomedical field, providing innovative tools for diagnosis of diseases and for novel therapies. Nevertheless, a deep understanding of their interactions with living tissues and the knowledge about their possible effects in the human body are necessary for the safe use of nanoparticulate formulations. The aim of this PhD project was to study in detail the interactions of therapeutic NPs with living cells, including cellular uptake and release, cellular localization and transport across the cell layers. Moreover, the effects of NPs on the cellular metabolic processes were determined using adapted in vitro assays. We evaluated the biological effect of several NPs potentially used in the biomedical field, including titanium dioxide (Ti02) NPs, 2-sized fluorescent silica NPs, ultrasmall superparamagnetic iron oxide (USPIO) NPs, either uncoated or coated with oleic acid or with polyvinylamine (aminoPVA) and poly(lactic-co-glycolic acid) - polyethylene-oxide (PLGA-PEO) NPs. We have found that the NPs were internalized by the cells, depending on their size, chemical composition, surface coating and also depending on the cell line considered. The uptake of aminoPVA-coated USPIO NPs by endothelial cells was enhanced in the presence of an external magnetic field. None of the tested USPIO NPs and silica NPs was transported across confluent kidney cell layers or brain endothelial cell layers, even in the presence of a magnetic field. However, in an original endothelium-glioblastoma barrier model which was developed, uncoated USPIO NPs were directly transferred from endothelial cells to glioblastoma cells. Following uptake, Ti02 NPs and uncoated USPIO NPs were released by the kidney cells, but not by the endothelial cells. Furthermore, these NPs induced an oxidative stress and autophagy in brain endothelial cells, possibly associated with their enhanced agglomeration in cell medium. A significant DNA damage was found in brain endothelial cells after their exposure to TiO2NPs. Altogether these results extend the existing knowledge about the effects of NPs on living cells with regard to their physicochemical characteristics and provide interesting tools for further investigation. The development of the in vitro toxicological assays with a special consideration for risk evaluation aims to reduce the use of animal experiments. -Les nanoparticules (NPs) présentent beaucoup d'intérêt dans le domaine biomédical et industriel. Leurs propriétés uniques offrent un grand nombre de possibilités de solutions innovantes pour le diagnostique et la thérapie. Cependant, pour un usage sûr des NPs il est nécessaire d'acquérir une connaissance approfondie des mécanismes d'interactions des NPs avec les tissus vivants et de leur effets sur le corps humain. Le but de ce projet de thèse était d'étudier en détail les mécanismes d'interactions de NPs thérapeutiques avec des cellules vivantes, en particulier les mécanismes d'internalisation cellulaire et leur subséquente sécrétion par les cellules, leur localisation cellulaire, leur transport à travers des couches cellulaires, et l'évaluation des effets de NPs sur le métabolisme cellulaire, en adaptant les méthodes existante d'évaluation cyto-toxico logique s in vitro. Pour ces expériences, les effets biologiques de nanoparticules d'intérêt thérapeutique, telles que des NPs d'oxyde de titane (TiO2), des NPs fluorescents de silicate de 2 tailles différentes, des NPs, d'oxyde de fer super-para-magnétiques ultra-petites (USPIO), soit non- enrobées soit enrobées d'acide oléique ou de polyvinylamine (aminoPVA), et des NPs d'acide poly(lactique-co-glycolique)-polyethylene-oxide (PLGA-PEO) ont été évalués. Les résultats ont démontré que les NPs sont internalisées par les cellules en fonction de leur taille, composition chimique, enrobage de surface, et également du type de cellules utilisées. L'internalisation cellulaire des USPIO NPs a été augmentée en présence d'un aimant externe. Aucune des NPs de fer et de silicate n'a été transportée à travers des couches de cellules épithéliales du rein ou endothéliales du cerveau, même en présence d'un aimant. Cependant, en développant un modèle original de barrière endothélium-glioblastome, un transfert direct de NPs d'oxyde de fer de cellule endothéliale à cellule de glioblastome a été démontré. A la suite de leur internalisation les NPs d'oxyde de fer et de titane sont relâchées par des cellules épithéliales du rein, mais pas des cellules endothéliales du cerveau. Dans les cellules endothéliales du cerveau ces NPs induisent en fonction de leur état d'agglomération un stress oxydatif et des mécanismes d'autophagie, ainsi que des dommages à l'ADN des cellules exposées aux NPs d'oxyde de titane. En conclusion, les résultats obtenus élargissent les connaissances sur les effets exercés par des NPs sur des cellules vivantes et ont permis de développer les outils expérimentaux pour étudier ces effets in vitro, réduisant ainsi le recours à des expériences sur animaux.

The barrel cortex as a model to study dynamic neuroglial interaction.

There is increasing evidence that glial cells, in particular astrocytes, interact dynamically with neurons. The well-known anatomofunctional organization of neurons in the barrel cortex offers a suitable and promising model to study such neuroglial interaction. This review summarizes and discusses recent in vitro as well as in vivo works demonstrating that astrocytes receive, integrate, and respond to neuronal signals. In addition, they are active elements of brain metabolism and exhibit a certain degree of plasticity that affects neuronal activity. Altogether these findings indicate that the barrel cortex presents glial compartments overlapping and interacting with neuronal compartments and that these properties help define barrels as functional and independent units. Finally, this review outlines how the use of the barrel cortex as a model might in the future help to address important questions related to dynamic neuroglia interaction.

Physical interaction between bacterial heat shock protein (Hsp) 90 and Hsp70 chaperones mediates their cooperative action to refold denatured proteins.

In eukaryotes, heat shock protein 90 (Hsp90) is an essential ATP-dependent molecular chaperone that associates with numerous client proteins. HtpG, a prokaryotic homolog of Hsp90, is essential for thermotolerance in cyanobacteria, and in vitro it suppresses the aggregation of denatured proteins efficiently. Understanding how the non-native client proteins bound to HtpG refold is of central importance to comprehend the essential role of HtpG under stress. Here, we demonstrate by yeast two-hybrid method, immunoprecipitation assays, and surface plasmon resonance techniques that HtpG physically interacts with DnaJ2 and DnaK2. DnaJ2, which belongs to the type II J-protein family, bound DnaK2 or HtpG with submicromolar affinity, and HtpG bound DnaK2 with micromolar affinity. Not only DnaJ2 but also HtpG enhanced the ATP hydrolysis by DnaK2. Although assisted by the DnaK2 chaperone system, HtpG enhanced native refolding of urea-denatured lactate dehydrogenase and heat-denatured glucose-6-phosphate dehydrogenase. HtpG did not substitute for DnaJ2 or GrpE in the DnaK2-assisted refolding of the denatured substrates. The heat-denatured malate dehydrogenase that did not refold by the assistance of the DnaK2 chaperone system alone was trapped by HtpG first and then transferred to DnaK2 where it refolded. Dissociation of substrates from HtpG was either ATP-dependent or -independent depending on the substrate, indicating the presence of two mechanisms of cooperative action between the HtpG and the DnaK2 chaperone system.

Synergistic and antagonistic interaction between different branches of the immune system is related to melanin-based coloration in nestling tawny owls.

When exposed to parasites, hosts often mount energetically expensive immune responses, and this may alter resource allocation between competing life history traits including other components of the immune system. Here, we investigated whether a humoral immune challenge towards a vaccine reduces or enhances the cutaneous immune responses towards an injection of lipopolysaccharid (LPS, innate immunity) and phytohaemagglutinin (PHA, T-cell immunity) in nestling tawny owls in interaction with the degree of plumage melanin-based coloration. The humoral immune challenge enhanced the response to LPS similarly in differently coloured nestlings. In contrast, the same humoral immune challenge enhanced immune response to PHA in dark reddish melanic nestlings while reducing it in pale reddish melanic nestlings. Our results highlight that both antagonistic and synergistic interactions can take place among branches of immune system, and that the sign and magnitude of these interactions can vary with immune responses involved and the degree of melanin-based coloration.

Designing online interaction to address disciplinary competencies: A cross-country comparison of faculty perspectives

This study was conducted at colleges in three countries (United States, Venezuela, and Spain) and across three academic disciplines (engineering, education, and business), to examine how experienced faculty define competencies for their discipline, and design instructional interaction for online courses. A qualitative research design employing in-depth interviews was selected. Results show that disciplinary knowledge takes precedence when faculty members select competencies to be developed in online courses for their respective professions. In all three disciplines, the design of interaction to correspond with disciplinary competencies was often influenced by contextual factors that modify faculty intention. Therefore, instructional design will vary across countries in the same discipline to address the local context, such as the needs and expectations of the learners, faculty perspectives, beliefs and values, and the needs of the institution, the community, and country. The three disciplines from the three countries agreed on the importance of the following competencies: knowledge of the field, higher order cognitive processes such as critical thinking, analysis, problem solving, transfer of knowledge, oral and written communication skills, team work, decision making, leadership and management skills, indicating far more similarities in competencies than differences between the three different applied disciplines. We found a lack of correspondence between faculty¿s intent to develop collaborative learning skills and the actual development of them. Contextual factors such as faculty prior experience in design, student reluctance to engage in collaborative learning, and institutional assessment systems that focus on individual performance were some of these reasons.

Siltanosturin teräsrakenteen suunnittelun avuksi luodun ohjelman jatkokehitys

Diplomityössä tehdään jatkokehitystä KCI Konecranes yrityksen siltanosturin laskentaohjelmaan. Ohjelman tärkeimmät jatkokehityskohteet kartoitettiin käyttäjäkyselyn avulla ja niistä valittiin toivotuimmat, sekä diplomityön lujuusopilliseen aihepiiriin parhaiten soveltuvat. Työhön valitut kaksi aihetta ovat koteloprofiilin kaksiosaisen uuman lujuuslaskennan selvittäminen ja siltanosturin kahdeksanpyöräisenpäätykannattajan elementtimallin suunnittelu. Diplomityössä selvitetään jatkokehityskohteisiin liittyvä teoria, mutta varsinainen ohjelmointi jätetään työn ulkopuolelle. Kaksiosaisella uumalla varustetussa koteloprofiilissa nostovaunun kulkukiskon alla olevan uuman yläosa tehdään paksummaksi, jotta uuma kestäisi nostovaunun pyöräkuormasta aiheutuvan paikallisen jännityksen, eliniin sanotun rusennusjännityksen. Rusennusjännityksen määrittäminen uumalevyissä on kaksiosaisen uuman lujuuslaskennan tärkein tehtävä. Rusennuksen aiheuttamankalvojännityksen ja jännityskeskittymien määrittämiseen erilaisissa konstruktioissa etsittiin sopivimmat menetelmät kirjallisuudesta ja standardeista. Kalvojännitys voidaan määrittää luotettavasti käyttäen joko 45 asteen sääntöä tai standardin mukaista menetelmää ja jännityskonsentraatioiden suuruus saadaan kertomallakalvojännitys jännityskonsentraatiokertoimilla. Menetelmien toimivuus verifioitiin tekemällä kymmeniä uuman elementtimalleja erilaisin dimensioin ja reunaehdoin ja vertaamalla elementtimallien tuloksia käsin laskettuihin. Käsin lasketut jännitykset saatiin vastaamaan tarkasti elementtimallien tuloksia. Kaksiosaisen uuman lommahdus- ja väsymislaskentaa tutkittiin alustavasti. Kahdeksanpyöräisiä päätykannattajia käytetään suurissa siltanostureissa pienentämään pyöräkuormia ja radan rusennusjännityksiä. Kahdeksanpyöräiselle siltanosturin päätykannattajalle suunniteltiin elementtimallit molempiin rakenteesta käytettyihin konstruktioihin: nivelöityyn ja jäykkäkehäiseen malliin. Elementtimallien rakentamisessa hyödynnettiin jo olemassa olevia malleja, jolloin niiden lisääminen ohjelmakoodiin nopeutuu ja ne ovat varmasti yhteensopivia muiden laskentamoduuleiden kanssa. Elementtimallien värähtelyanalyysin reunaehtoja tarkasteltiin. Värähtelyanalyysin reunaehtoihin ei tutkimuksen perusteella tarvitse tehdä muutoksia, mutta staattisen analyysin reunaehdot kaipaavat vielä lisätutkimusta.

Characterization of Fas (Apo-1, CD95)-Fas ligand interaction.

The death-inducing receptor Fas is activated when cross-linked by the type II membrane protein Fas ligand (FasL). When human soluble FasL (sFasL, containing the extracellular portion) was expressed in human embryo kidney 293 cells, the three N-linked glycans of each FasL monomer were found to be essential for efficient secretion. Based on the structure of the closely related lymphotoxin alpha-tumor necrosis factor receptor I complex, a molecular model of the FasL homotrimer bound to three Fas molecules was generated using knowledge-based protein modeling methods. Point mutations of amino acid residues predicted to affect the receptor-ligand interaction were introduced at three sites. The F275L mutant, mimicking the loss of function murine gld mutation, exhibited a high propensity for aggregation and was unable to bind to Fas. Mutants P206R, P206D, and P206F displayed reduced cytotoxicity toward Fas-positive cells with a concomitant decrease in the binding affinity for the recombinant Fas-immunoglobulin Fc fusion proteins. Although the cytotoxic activity of mutant Y218D was unaltered, mutant Y218R was inactive, correlating with the prediction that Tyr-218 of FasL interacts with a cluster of three basic amino acid side chains of Fas. Interestingly, mutant Y218F could induce apoptosis in murine, but not human cells.