Substrate-binding sites of UBR1, the ubiquitin ligase of the N-end rule pathway

Substrates of a ubiquitin-dependent proteolytic system called the N-end rule pathway include proteins with destabilizing N-terminal residues. N-recognins, the pathway’s ubiquitin ligases, contain three substrate-binding sites. The type-1 site is specific for basic N-terminal residues (Arg, Lys, His). The type-2 site is specific for bulky hydrophobic N-terminal residues (Trp, Phe, Tyr, Leu, Ile). We show here that the type-1/2 sites of UBR1, the sole N-recognin of the yeast Saccharomyces cerevisiae, are located in the first ~700 residues of the 1,950-residue UBR1. These sites are distinct in that they can be selectively inactivated by mutations, identified through a genetic screen. Mutations inactivating the type-1 site are in the previously delineated ~70 residue UBR motif characteristic of N-recognins. Fluorescence polarization and surface plasmon resonance were used to determine that UBR1 binds, with Kd of ~1 microM, to either type-1 or type-2 destabilizing N-terminal residues of reporter peptides, but does not bind to a stabilizing N-terminal residue such as Gly. A third substrate-binding site of UBR1 targets an internal degron of CUP9, a transcriptional repressor of peptide import. We show that the previously demonstrated in vivo dependence of CUP9 ubiquitylation on the binding of (cognate) dipeptides to the type-1/2 sites of UBR1 can be reconstituted in a completely defined in vitro system. We also found that purified UBR1 and CUP9 interact nonspecifically, and that specific binding (which involves, in particular, the binding by cognate dipeptides to the UBR1’s type-1/2 sites) can be restored either by a chaperone such as EF1A or through macromolecular crowding

Sistema de contagem de tráfego e classificação automática de veículos, em tempo real e sem fios

Esta tese tem por objectivo o desenho e avaliação de um sistema de contagem e classificação de veículos automóveis em tempo-real e sem fios. Pretende, também, ser uma alternativa aos actuais equipamentos, muito intrusivos nas vias rodoviárias. Esta tese inclui um estudo sobre as comunicações sem fios adequadas a uma rede de equipamentos sensores rodoviários, um estudo sobre a utilização do campo magnético como meio físico de detecção e contagem de veículos e um estudo sobre a autonomia energética dos equipamentos inseridos na via, com recurso, entre outros, à energia solar. O projecto realizado no âmbito desta tese incorpora, entre outros, a digitalização em tempo real da assinatura magnética deixada pela passagem de um veículo, no campo magnético da Terra, o respectivo envio para servidor via rádio e WAN, Wide Area Network, e o desenvolvimento de software tendo por base a pilha de protocolos ZigBee. Foram desenvolvidas aplicações para o equipamento sensor, para o coordenador, para o painel de controlo e para a biblioteca de Interface de um futuro servidor aplicacional. O software desenvolvido para o equipamento sensor incorpora ciclos de detecção e digitalização, com pausas de adormecimento de baixo consumo, e a activação das comunicações rádio durante a fase de envio, assegurando assim uma estratégia de poupança energética. Os resultados obtidos confirmam a viabilidade desta tecnologia para a detecção e contagem de veículos, assim como para a captura de assinatura usando magnetoresistências. Permitiram ainda verificar o alcance das comunicações sem fios com equipamento sensor embebido no asfalto e confirmar o modelo de cálculo da superfície do painel solar bem como o modelo de consumo energético do equipamento sensor.The aim of this thesis is the design and evaluation of a vehicle counting and classification system, in real-time and over wireless communications, thus resolving the current problems of nowadays intrusive road sensors. The thesis covers the study of the wireless communications suitable for a network of road sensors, the magnetic field as a physical mean of vehicle detection and classification, and the study of energy autonomy for the equipment placed on the road, using, among others, solar energy. It is also the subject of study the real-time scanning of the magnetic signature left by a passing vehicle in the Earth's magnetic field and its radio transmission to a server. The development focused on the software, the ZigBee protocol Stack and the system on a chip cc2530. Applications have been built for the road sensor, the coordinator, the control panel and an interface library designed for a future application server. The software developed for the road sensor incorporates duty cycles for detection and digitalization, followed by low energy pauses, and activation of the radio communications only during the data transfer, thus ensuring an energy saving strategy. The results obtained confirm the possibility using this technology for vehicle detection, counting and signature capture using magneto-resistance. Also allowed verification of the range of wireless communications for the road sensor embedded in asphalt and confirms the models for calculating the surface of the solar panel and for the energy consumption of the road sensor

SDI, NATO, and the Social Composition Function

International audienceThe strategic defense initiative (SDI) intends to renew the leadership of the USA on the western alliance. The initiative takes place in a period when a summation technology prevails for the aggregation of contributions of NATO allies. We investigate if SDI induces a shift in Hirshleifer's social composition function. Panel data tests over the period 1970-1990 do not confirm any break toward a best-shot aggregator. SDI does not alter the core of deterrence. It is indeed a public good at the US level but not at the NATO level, where, it is one of the joint products of the alliance. We also investigate the lessons to be drawn for the current debates on ballistic defense

Determination of strongly overlapping signaling activity from microarray data

BACKGROUND: As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease development or therapeutic intervention would assist in drug development, design of therapy, and target identification. Microarrays provide a global measure of cellular response, however linking these responses to signaling pathways requires an analytic approach tuned to the underlying biology. An ongoing issue in pattern recognition in microarrays has been how to determine the number of patterns (or clusters) to use for data interpretation, and this is a critical issue as measures of statistical significance in gene ontology or pathways rely on proper separation of genes into groups. RESULTS: Here we introduce a method relying on gene annotation coupled to decompositional analysis of global gene expression data that allows us to estimate specific activity on strongly coupled signaling pathways and, in some cases, activity of specific signaling proteins. We demonstrate the technique using the Rosetta yeast deletion mutant data set, decompositional analysis by Bayesian Decomposition, and annotation analysis using ClutrFree. We determined from measurements of gene persistence in patterns across multiple potential dimensionalities that 15 basis vectors provides the correct dimensionality for interpreting the data. Using gene ontology and data on gene regulation in the Saccharomyces Genome Database, we identified the transcriptional signatures of several cellular processes in yeast, including cell wall creation, ribosomal disruption, chemical blocking of protein synthesis, and, criticially, individual signatures of the strongly coupled mating and filamentation pathways. CONCLUSION: This works demonstrates that microarray data can provide downstream indicators of pathway activity either through use of gene ontology or transcription factor databases. This can be used to investigate the specificity and success of targeted therapeutics as well as to elucidate signaling activity in normal and disease processes

Simulation of Seasonal Snow Microwave TB Using Coupled Multi-Layered Snow Evolution and Microwave Emission Models

The accurate quantification of SWE has important societal benefits, including improving domestic and agricultural water planning, flood forecasting and electric power generation. However, passive-microwave SWE algorithms suffer from variations in TB due to snow metamorphism, difficult to distinguish from those due to SWE variations. Coupled snow evolution-emission models are able to predict snow metamorphism, allowing us to account for emissivity changes. They can also be used to identify weaknesses in the snow evolution model. Moreover, thoroughly evaluating coupled models is a contribution toward the assimilation of TB, which leads to a significant increase in the accuracy of SWE estimates

Secondary metabolites a potential improvement for the economy of second generation biofuel production

The decreasing prices of oil ($29.44US – feb.2016) and natural gas ($1.97US– feb.2016) have significantly restrained the opportunity for the development of the second-generation biofuel industry. Numerous investigations focus on improving processes in order to improve the yield of biofuels. However, the latter being a commodity submitted to a strong competition by the fossil fuel industry, there is strong necessity to find other approaches allowing getting more revenues per tonne of converted biomass. Furthermore, despite the fact that the price of fossil fuels is decreasing, biomass still requires to be transported over long distances to reach a centralized conversion facility, thus, it is of outmost importance to get the most of this renewable feedstock. Secondary metabolites may represent an interesting way to generate complementary value to biofuels production. Extraction of secondary metabolites can 1) improve processes by removing undesirable compounds thus purifying the raw material (as an example by removing fermentation inhibitors) and 2) add an increased value by recovering high value compounds that could represent additional values as pharmaceuticals, cosmetics or food additives. Please click Additional Files below to see the full abstract

Evaluation of facial changes in patients after maxillary transverse correction with MARPE: A systematic integrative review

Introdução: A Expansão Rápida Palatina Assistida por Mini-implante (MARPE) é uma técnica recente que permite a correção de deficiências maxilares enquanto limita os efeitos secundários da Expansão Rápida Palatina e da Expansão Rápida Palatina Assistida Cirurgicamente em jovem-adultos. Objetivos: O objetivo desta revisão sistemática é avaliar, através da literatura científica, as alterações das estruturas ósseas da face e as suas possíveis repercussões nos tecidos moles faciais após tratamento MARPE em jovem-adultos. Material e Métodos: Foi realizada uma pesquisa bibliográfica utilizando as seguintes bases de dados eletrónicas: MEDLINE/PubMed, EBSCO host e Cochrane Library. Os critérios de inclusão foram: artigos em inglês; ensaios clínicos aleatórios ou não aleatórios e estudos in-vivo em humanos. Resultados: De 137 artigos, 5 foram selecionados após uma leitura completa. Discussão: Os complexos zigomático-maxilares fazem um movimento circular de lateralizarão em torno de dois pontos de rotação: um em torno dos processos zigomáticos dos ossos frontais perto da sutura zigomático-frontal num plano coronal e outro em torno das partes proximais dos processos zigomáticos dos ossos temporais num plano axial. A maxila expande-se lateralmente, para cima e para a frente. O lábio superior, a região péri-nasal e as bochechas seguem a expansão descrita pela maxila. O nariz expande-se lateralmente, para baixo e para a frente. Conclusão: MARPE tem de facto um impacto nos ossos faciais que se reflete nos tecidos moles faciais.Introduction: Miniscrew-Assisted Rapid Palatal Expansion (MARPE) is a recent technique that allows the correction of maxillary deficiencies while limiting the side effects of Rapid Palatal Expansion and Surgically Assisted Rapid Palatal Expansion in young adults. Objectives: The objective of this systematic review is to evaluate, through the scientific literature, the alterations of the superficial bone structures of the face and their possible repercussions on the soft tissues of the face after MARPE treatment in young adults. Material and Methods: The documentary search was performed using the following electronic databases: MEDLINE/PubMed, EBSCO host and the Cochrane Library. The inclusion criteria were: articles in English; randomized or non-randomized clinical trials and in-vivo studies in humans. Results: Of 137 articles, 5 were selected after full reading. Discussion: The zygomatico-maxillary complexes make a circular lateralizing movement around two points of rotation: around the zygomatic processes of the frontal bones near the zygomatico-frontal suture in a coronal plane and around the proximal parts of the zygomatic processes of the temporal bones in an axial plane. The maxilla expands laterally, upward and forward. The upper lip, the peri-nasal region and the cheeks follow the expansion described by the maxilla. The nose expands laterally, downward and forward. Conclusion: MARPE does indeed have an impact on the facial bones reflected in the facial soft tissues

Effect of polymer architecture on Curcumin 1 encapsulation and release from PEGylated polymer nanoparticles: toward a drug delivery nano-platform to the CNS

We developed a nanoparticles (NPs) library from poly(ethylene glycol)–poly lactic acid comb-like polymers with variable amount of PEG. Curcumin was encapsulated in the NPs with a view to develop a delivery platform to treat diseases involving oxidative stress affecting the CNS. We observed a sharp decrease in size between 15 and 20% w/w of PEG which corresponds to a transition from a large solid particle structure to a “micelle-like” or “polymer nano-aggregate” structure. Drug loading, loading efficacy and release kinetics were determined. The diffusion coefficients of curcumin in NPs were determined using a mathematical modeling. The higher diffusion was observed for solid particles compared to “polymer nano-aggregate” particles. NPs did not present any significant toxicity when tested in vitro on a neuronal cell line. Moreover, the ability of NPs carrying curcumin to prevent oxidative stress was evidenced and linked to polymer architecture and NPs organization. Our study showed the intimate relationship between the polymer architecture and the biophysical properties of the resulting NPs and sheds light on new approaches to design efficient NP-based drug carriers