Mycobacterium tuberculosis subverts innate immunity to evade specific effectors.

The macrophage is the niche of the intracellular pathogen Mycobacterium tuberculosis. Induction of macrophage apoptosis by CD4(+) or CD8(+) T cells is accompanied by reduced bacterial counts, potentially defining a host defense mechanism. We have already established that M. tuberculosis-infected primary human macrophages have a reduced susceptibility to Fas ligand (FasL)-induced apoptosis. To study the mechanisms by which M. tuberculosis prevents apoptotic signaling, we have generated a cell culture system based on PMA- and IFN-gamma-differentiated THP-1 cells recapitulating the properties of primary macrophages. In these cells, nucleotide-binding oligomerization domain 2 or TLR2 agonists and mycobacterial infection protected macrophages from apoptosis and resulted in NF-kappaB nuclear translocation associated with up-regulation of the antiapoptotic cellular FLIP. Transduction of a receptor-interacting protein-2 dominant-negative construct showed that nucleotide-binding oligomerization domain 2 is not involved in protection in the mycobacterial infection system. In contrast, both a dominant-negative construct of the MyD88 adaptor and an NF-kappaB inhibitor abrogated the protection against FasL-mediated apoptosis, showing the implication of TLR2-mediated activation of NF-kappaB in apoptosis protection in infected macrophages. The apoptosis resistance of infected macrophages might be considered as an immune escape mechanism, whereby M. tuberculosis subverts innate immunity signaling to protect its host cell against FasL(+)-specific cytotoxic lymphocytes.

Specific targeting of pro-death NMDA receptor signals with differing reliance on the NR2B PDZ ligand.

NMDA receptors (NMDARs) mediate ischemic brain damage, for which interactions between the C termini of NR2 subunits and PDZ domain proteins within the NMDAR signaling complex (NSC) are emerging therapeutic targets. However, expression of NMDARs in a non-neuronal context, lacking many NSC components, can still induce cell death. Moreover, it is unclear whether targeting the NSC will impair NMDAR-dependent prosurvival and plasticity signaling. We show that the NMDAR can promote death signaling independently of the NR2 PDZ ligand, when expressed in non-neuronal cells lacking PSD-95 and neuronal nitric oxide synthase (nNOS), key PDZ proteins that mediate neuronal NMDAR excitotoxicity. However, in a non-neuronal context, the NMDAR promotes cell death solely via c-Jun N-terminal protein kinase (JNK), whereas NMDAR-dependent cortical neuronal death is promoted by both JNK and p38. NMDAR-dependent pro-death signaling via p38 relies on neuronal context, although death signaling by JNK, triggered by mitochondrial reactive oxygen species production, does not. NMDAR-dependent p38 activation in neurons is triggered by submembranous Ca(2+), and is disrupted by NOS inhibitors and also a peptide mimicking the NR2B PDZ ligand (TAT-NR2B9c). TAT-NR2B9c reduced excitotoxic neuronal death and p38-mediated ischemic damage, without impairing an NMDAR-dependent plasticity model or prosurvival signaling to CREB or Akt. TAT-NR2B9c did not inhibit JNK activation, and synergized with JNK inhibitors to ameliorate severe excitotoxic neuronal loss in vitro and ischemic cortical damage in vivo. Thus, NMDAR-activated signals comprise pro-death pathways with differing requirements for PDZ protein interactions. These signals are amenable to selective inhibition, while sparing synaptic plasticity and prosurvival signaling.

Introducing Basic Systematic Requirements Engineering Practices in Small Organizations with an Easy to Adopt Method

Requirements-relatedissues have been found the third most important risk factor in software projects and as the biggest reason for software project failures. This is not a surprise since; requirements engineering (RE) practices have been reported deficient inmore than 75% of all; enterprises. A problem analysis on small and low maturitysoftware organizations revealed two; central reasons for not starting process improvement efforts: lack of resources and uncertainty; about process improvementeffort paybacks.; In the constructive part of the study a basic RE method, BaRE, was developed to provide an; easy to adopt way to introduce basic systematic RE practices in small and low maturity; organizations. Based on diffusion of innovations literature, thirteen desirable characteristics; were identified for the solution and the method was implemented in five key components:; requirements document template, requirements development practices, requirements; management practices, tool support for requirements management, and training.; The empirical evaluation of the BaRE method was conducted in three industrial case studies. In; this evaluation, two companies established a completely new RE infrastructure following the; suggested practices while the third company conducted continued requirements document; template development based on the provided template and used it extensively in practice. The; real benefits of the adoption of the method were visible in the companies in four to six months; from the start of the evaluation project, and the two small companies in the project completed; their improvement efforts with an input equal to about one person month. The collected dataon; the case studies indicates that the companies implemented new practices with little adaptations; and little effort. Thus it can be concluded that the constructed BaRE method is indeed easy to; adopt and it can help introduce basic systematic RE practices in small organizations.

Evolution based on domain combinations: the case of glutaredoxins

Background: Protein domains represent the basic units in the evolution of proteins. Domain duplication and shuffling by recombination and fusion, followed by divergence are the most common mechanisms in this process. Such domain fusion and recombination events are predicted to occur only once for a given multidomain architecture. However, other scenarios may be relevant in the evolution of specific proteins, such as convergent evolution of multidomain architectures. With this in mind, we study glutaredoxin (GRX) domains, because these domains of approximately one hundred amino acids are widespread in archaea, bacteria and eukaryotes and participate in fusion proteins. GRXs are responsible for the reduction of protein disulfides or glutathione-protein mixed disulfides and are involved in cellular redox regulation, although their specific roles and targets are often unclear. Results: In this work we analyze the distribution and evolution of GRX proteins in archaea,bacteria and eukaryotes. We study over one thousand GRX proteins, each containing at least one GRX domain, from hundreds of different organisms and trace the origin and evolution of the GRX domain within the tree of life. Conclusion: Our results suggest that single domain GRX proteins of the CGFS and CPYC classes have, each, evolved through duplication and divergence from one initial gene that was present in the last common ancestor of all organisms. Remarkably, we identify a case of convergent evolution in domain architecture that involves the GRX domain. Two independent recombination events of a TRX domain to a GRX domain are likely to have occurred, which is an exception to the dominant mechanism of domain architecture evolution.

Differential Dimerization of Variants Linked to Enhanced S-Cone Sensitivity Syndrome (ESCS) Located in the NR2E3 Ligand-Binding Domain.

NR2E3 encodes the photoreceptor-specific nuclear hormone receptor that acts as a repressor of cone-specific gene expression in rod photoreceptors, and as an activator of several rod-specific genes. Recessive variants located in the ligand-binding domain (LBD) of NR2E3 cause enhanced short wavelength sensitive- (S-) cone syndrome (ESCS), a retinal degeneration characterized by an excess of S-cones and non-functional rods. We analyzed the dimerization properties of NR2E3 and the effect of disease-causing LBD missense variants by bioluminescence resonance energy transfer (BRET(2) ) protein interaction assays. Homodimerization was not affected in presence of p.A256V, p.R039G, p.R311Q, and p.R334G variants, but abolished in presence of p.L263P, p.L336P, p.L353V, p.R385P, and p.M407K variants. Homology modeling predicted structural changes induced by NR2E3 LBD variants. NR2E3 LBD variants did not affect interaction with CRX, but with NRL and rev-erbα/NR1D1. CRX and NRL heterodimerized more efficiently together, than did either with NR2E3. NR2E3 did not heterodimerize with TLX/NR2E1 and RXRα/NR2C1. The identification of a new compound heterozygous patient with detectable rod function, who expressed solely the p.A256V variant protein, suggests a correlation between LBD variants able to form functional NR2E3 dimers and atypical mild forms of ESCS with residual rod function.

Protocol Specific Embedded Operating System

Sulautettujen järjestelmien määrä kuten niiden sisältämä älykkyyskin ovat viime vuosina kasvaneet merkittävästi. Sulautettujen ohjelmistojen yleistymistä ja monipuolistumista on edesauttanut sulautettujen laitteistojen prosessointitehon merkittävä kehittyminen, jonka myötä entistä vaativampien ohjelmistojen totetuttaminen sulautetusti on mahdollistunut. Seuraavana sulautettujen järjestelmien kehitysaskeleena on nähtävissä järjestelmien kommunikointikyvyn paraneminen ja siten uusien ja uudentyyppisten sulautettujen ratkaisujen toteuttaminen. VTT on päättänyt tutkia sulautettujen järjestelmien kommunikointia ja kehittää sulautettun protokolla-alustan. Tutkimuksen perusta on CVOPS protokollajärjestelmä, jota jatkokehittämällä pyritään toteuttamaan sulautettu protokollajärjestelmä, µCVOPS. Tässä diplomityössä esitetään kommunikaation sulautetulle järjestelmälle asettamia vaatimuksia, järjestelmän suunnittelu ja prototyypitys sulautetulla laitteistolla. Prototyypitykseen on käytetty sulautettua DragonBall mikrokontrolleria jonka käyttöjärjestelmänä käytettiin sulautettua Linux:a. Tälle alustalle on tehty CVOPS:sta modifioitu versio, jolla µCVOPS:ia pystytään simuloimaan.

A System-Level Simulation Model for a Protocol Processor

As the development of integrated circuit technology continues to follow Moore’s law the complexity of circuits increases exponentially. Traditional hardware description languages such as VHDL and Verilog are no longer powerful enough to cope with this level of complexity and do not provide facilities for hardware/software codesign. Languages such as SystemC are intended to solve these problems by combining the powerful expression of high level programming languages and hardware oriented facilities of hardware description languages. To fully replace older languages in the desing flow of digital systems SystemC should also be synthesizable. The devices required by modern high speed networks often share the same tight constraints for e.g. size, power consumption and price with embedded systems but have also very demanding real time and quality of service requirements that are difficult to satisfy with general purpose processors. Dedicated hardware blocks of an application specific instruction set processor are one way to combine fast processing speed, energy efficiency, flexibility and relatively low time-to-market. Common features can be identified in the network processing domain making it possible to develop specialized but configurable processor architectures. One such architecture is the TACO which is based on transport triggered architecture. The architecture offers a high degree of parallelism and modularity and greatly simplified instruction decoding. For this M.Sc.(Tech) thesis, a simulation environment for the TACO architecture was developed with SystemC 2.2 using an old version written with SystemC 1.0 as a starting point. The environment enables rapid design space exploration by providing facilities for hw/sw codesign and simulation and an extendable library of automatically configured reusable hardware blocks. Other topics that are covered are the differences between SystemC 1.0 and 2.2 from the viewpoint of hardware modeling, and compilation of a SystemC model into synthesizable VHDL with Celoxica Agility SystemC Compiler. A simulation model for a processor for TCP/IP packet validation was designed and tested as a test case for the environment.

Engineering Geology for Society and Territory: volume 2: landslide processes

This book is one out of 8 IAEG XII Congress volumes, and deals with Landslide processes, including: field data and monitoring techniques, prediction and forecasting of landslide occurrence, regional landslide inventories and dating studies, modeling of slope instabilities and secondary hazards (e.g. impulse waves and landslide-induced tsunamis, landslide dam failures and breaching), hazard and risk assessment, earthquake and rainfall induced landslides, instabilities of volcanic edifices, remedial works and mitigation measures, development of innovative stabilization techniques and applicability to specific engineering geological conditions, use of geophysical techniques for landslide characterization and investigation of triggering mechanisms. Focuses is given to innovative techniques, well documented case studies in different environments, critical components of engineering geological and geotechnical investigations, hydrological and hydrogeological investigations, remote sensing and geophysical techniques, modeling of triggering, collapse, runout and landslide reactivation, geotechnical design and construction procedures in landslide zones, interaction of landslides with structures and infrastructures and possibility of domino effects. The Engineering Geology for Society and Territory volumes of the IAEG XII Congress held in Torino from September 15-19, 2014, analyze the dynamic role of engineering geology in our changing world and build on the four main themes of the congress: environment, processes, issues, and approaches.

International journal of engineering education

This work presents an analysis of the assessment tools used by professors at the Universitat Politécnica de Catalunya to assess the generic competencies introduced in the Bachelor’s Degrees in Engineering. In order to conduct this study, a survey was designed and administered anonymously to a sample of the professors most receptive to educational innovation at their own university. All total, 80 professors responded to this survey, of whom 26% turned out to be members of the university’s own evaluation innovation group (https://www.upc.edu/rima/grups/grapa), GRAPA. This percentage represents 47% of the total GRAPA membership, meaning that nearly half of the professors most concerned about evaluation at the university chose to participate. The analysis of the variables carried out using the statistical program SPSS v19 shows that for practically 49% of those surveyed, rubrics are the tools most commonly used to assess generic competencies integrated in more specific ones. Of those surveyed, 60% use them either frequently or always. The most frequently evaluated generic competencies were teamwork (28%), problem solving (26%), effective oral and written communication (24%) and autonomous learning (13%), all of which constitute commonly recognized competencies in the engineering profession. A two-dimensional crosstabs analysis with SPSS v19 shows a significant correlation (Asymp. Sig. 0.001) between the type of tool used and the competencies assessed. However, no significant correlation was found between the type of assessment tool used and the type of subject, type of evaluation (formative or summative), frequency of feedback given to the students or the degree of student satisfaction, and thus none of these variables can be considered to have an influence on the kind of assessment tool used. In addition, the results also indicate that there are no significant differences between the instructors belonging to GRAPA and the rest of those surveyed

The serine protease hepsin mediates urinary secretion and polymerisation of Zona Pellucida domain protein uromodulin.

Uromodulin is the most abundant protein in the urine. It is exclusively produced by renal epithelial cells and it plays key roles in kidney function and disease. Uromodulin mainly exerts its function as an extracellular matrix whose assembly depends on a conserved, specific proteolytic cleavage leading to conformational activation of a Zona Pellucida (ZP) polymerisation domain. Through a comprehensive approach, including extensive characterisation of uromodulin processing in cellular models and in specific knock-out mice, we demonstrate that the membrane-bound serine protease hepsin is the enzyme responsible for the physiological cleavage of uromodulin. Our findings define a key aspect of uromodulin biology and identify the first in vivo substrate of hepsin. The identification of hepsin as the first protease involved in the release of a ZP domain protein is likely relevant for other members of this protein family, including several extracellular proteins, as egg coat proteins and inner ear tectorins.

Molecular Interactions of Prodiginines with the BH3 Domain of Anti-Apoptotic Bcl-2 Family Members.

Prodigiosin and obatoclax, members of the prodiginines family, are small molecules with anti-cancer properties that are currently under preclinical and clinical trials. The molecular target(s) of these agents, however, is an open question. Combining experimental and computational techniques we find that prodigiosin binds to the BH3 domain in some BCL-2 protein families, which play an important role in the apoptotic programmed cell death. In particular, our results indicate a large affinity of prodigiosin for MCL-1, an anti-apoptotic member of the BCL-2 family. In melanoma cells, we demonstrate that prodigiosin activates the mitochondrial apoptotic pathway by disrupting MCL-1/BAK complexes. Computer simulations with the PELE software allow the description of the induced fit process, obtaining a detailed atomic view of the molecular interactions. These results provide new data to understand the mechanism of action of these molecules, and assist in the development of more specific inhibitors of anti-apoptotic BCL-2 proteins.

Agricultural engineering at UNICAMP: undergraduate student dropout analysis

Nowadays, dropping out in B.Sc. courses practically occurs in all Universities of the contemporary world. Undergraduate student withdraw could means several losses as, to the student, not to graduate, to the teacher, for not accomplishing his goal as educator, to the university, for not attending its mission, to the society, economic and social losses and also to the family for unfulfilling the dreams. The objective of this research is to present a quantitative study on the dropping out rate in the Agricultural Engineering B.Sc. program (BSAGENG) at State University of Campinas (UNICAMP), seeking to contribute to the understanding of this issue. It has been determined the dropping out rate from 1995 to 2006 based on the university official data, by employing four different methods of calculation. Three of the methods revealed that dropping out rate is very close to the graduation index, i.e., close to 50%. Regardless of the adopted method for the dropping rate estimation and the statistics demonstrating that the agricultural engineering undergraduate course at UNICAMP figures falls within similar courses normality in Brazil, it should be recognized that a public institution of education should be concerned in presenting such figures. A detailed and deep analysis must be outlined in further studies seeking for specific actions aiming to reduce dropping out process.

Improving the competitiveness of electrolytic Zinc process by chemical reaction engineering approach

This doctoral thesis describes the development work performed on the leachand purification sections in the electrolytic zinc plant in Kokkola to increase the efficiency in these two stages, and thus the competitiveness of the plant. Since metallic zinc is a typical bulk product, the improvement of the competitiveness of a plant was mostly an issue of decreasing unit costs. The problems in the leaching were low recovery of valuable metals from raw materials, and that the available technology offered complicated and expensive processes to overcome this problem. In the purification, the main problem was consumption of zinc powder - up to four to six times the stoichiometric demand. This reduced the capacity of the plant as this zinc is re-circulated through the electrolysis, which is the absolute bottleneck in a zinc plant. Low selectivity gave low-grade and low-value precipitates for further processing to metallic copper, cadmium, cobalt and nickel. Knowledge of the underlying chemistry was poor and process interruptions causing losses of zinc production were frequent. Studies on leaching comprised the kinetics of ferrite leaching and jarosite precipitation, as well as the stability of jarosite in acidic plant solutions. A breakthrough came with the finding that jarosite could precipitate under conditions where ferrite would leach satisfactorily. Based on this discovery, a one-step process for the treatment of ferrite was developed. In the plant, the new process almost doubled the recovery of zinc from ferrite in the same equipment as the two-step jarosite process was operated in at that time. In a later expansion of the plant, investment savings were substantial compared to other technologies available. In the solution purification, the key finding was that Co, Ni, and Cu formed specific arsenides in the “hot arsenic zinc dust” step. This was utilized for the development of a three-step purification stage based on fluidized bed technology in all three steps, i.e. removal of Cu, Co and Cd. Both precipitation rates and selectivity increased, which strongly decreased the zinc powder consumption through a substantially suppressed hydrogen gas evolution. Better selectivity improved the value of the precipitates: cadmium, which caused environmental problems in the copper smelter, was reduced from 1-3% reported normally down to 0.05 %, and a cobalt cake with 15 % Co was easily produced in laboratory experiments in the cobalt removal. The zinc powder consumption in the plant for a solution containing Cu, Co, Ni and Cd (1000, 25, 30 and 350 mg/l, respectively), was around 1.8 g/l; i.e. only 1.4 times the stoichiometric demand – or, about 60% saving in powder consumption. Two processes for direct leaching of the concentrate under atmospheric conditions were developed, one of which was implemented in the Kokkola zinc plant. Compared to the existing pressure leach technology, savings were obtained mostly in investment. The scientific basis for the most important processes and process improvements is given in the doctoral thesis. This includes mathematical modeling and thermodynamic evaluation of experimental results and hypotheses developed. Five of the processes developed in this research and development program were implemented in the plant and are still operated. Even though these processes were developed with the focus on the plant in Kokkola, they can also be implemented at low cost in most of the zinc plants globally, and have thus a great significance in the development of the electrolytic zinc process in general.

Reframing the relationship between service design and operations: a service engineering approach

The significance of services as business and human activities has increased dramatically throughout the world in the last three decades. Becoming a more and more competitive and efficient service provider while still being able to provide unique value opportunities for customers requires new knowledge and ideas. Part of this knowledge is created and utilized in daily activities in every service organization, but not all of it, and therefore an emerging phenomenon in the service context is information awareness. Terms like big data and Internet of things are not only modern buzz-words but they are also describing urgent requirements for a new type of competences and solutions. When the amount of information increases and the systems processing information become more efficient and intelligent, it is the human understanding and objectives that may get separated from the automated processes and technological innovations. This is an important challenge and the core driver for this dissertation: What kind of information is created, possessed and utilized in the service context, and even more importantly, what information exists but is not acknowledged or used? In this dissertation the focus is on the relationship between service design and service operations. Reframing this relationship refers to viewing the service system from the architectural perspective. The selected perspective allows analysing the relationship between design activities and operational activities as an information system while maintaining the tight connection to existing service research contributions and approaches. This type of an innovative approach is supported by research methodology that relies on design science theory. The methodological process supports the construction of a new design artifact based on existing theoretical knowledge, creation of new innovations and testing the design artifact components in real service contexts. The relationship between design and operations is analysed in the health care and social care service systems. The existing contributions in service research tend to abstract services and service systems as value creation, working or interactive systems. This dissertation adds an important information processing system perspective to the research. The main contribution focuses on the following argument: Only part of the service information system is automated and computerized, whereas a significant part of information processing is embedded in human activities, communication and ad-hoc reactions. The results indicate that the relationship between service design and service operations is more complex and dynamic than the existing scientific and managerial models tend to view it. Both activities create, utilize, mix and share information, making service information management a necessary but relatively unknown managerial task. On the architectural level, service system -specific elements seem to disappear, but access to more general information elements and processes can be found. While this dissertation focuses on conceptual-level design artifact construction, the results provide also very practical implications for service providers. Personal, visual and hidden activities of service, and more importantly all changes that take place in any service system have also an information dimension. Making this information dimension visual and prioritizing the processed information based on service dimensions is likely to provide new opportunities to increase activities and provide a new type of service potential for customers.

Serotyping HIV-1 with V3 peptides: detection of high avidity antibodies presenting clade-specific reactivity

The main objective of the present study was to assess the specificity and sensitivity of a modified assay using short synthetic peptides of the V3 region of HIV-1 gp120, which is the main target for neutralizing antibodies. Results from an enzyme immunoassay (EIA) employing a panel of synthetic peptides of HIV-1 subtypes and using urea washes to detect high avidity antibodies (AAV3) were compared with those obtained by the heteroduplex mobility assay and DNA sequencing. The EIA correctly typed 100% of subtype B (sensitivity = 1.0; specificity = 0.95), 100% of HIV-1 E samples (sensitivity = 1.0; specificity = 1.0), and 95% of subtype C specimens (sensitivity = 0.95; specificity = 0.94). In contrast, only 50% of subtype A (sensitivity = 0.5; specificity = 0.95), 60% of subtype D (sensitivity = 0.6; specificity = 1.0), and 28% of subtype F samples (sensitivity = 0.28; specificity = 0.95) were correctly identified. This approach was also able to discriminate in a few samples antibodies from patients infected with B variants circulating in Brazil and Thailand that reacted specifically. The assays described in this study are relatively rapid and simple to perform compared to molecular approaches and can be used to screen large numbers of serum or plasma samples. Moreover, the classification in subtypes (genotypes) may overestimate HIV-1 diversity and a classification into serotypes, based on antigenic V3 diversity or another principal neutralization domain, may be more helpful for vaccine development and identification of variants.