Diseño de celdas analógicas embebidas en sistemas en un chip (SOC)

La metodología actual de diseño de celdas analógicas embebidas se basa en una tecnología CMOS fija, no teniendo dichos módulos características de reutilización y de migración hacia otras tecnologías. Para avanzar a un mayor nivel de productividad en el diseño se necesita un cambio de paradigma. Este cambio en la metodología necesita reducir tiempo y esfuerzo en el desarrollo, incrementar la predictibilidad y reducir el riesgo involucrado en el diseño y la fabricación de complejos sistemas en un chip (SOC). Las celdas digitales embebidas se han aplicado al diseño VLSI digital debido a que la síntesis a través de lenguajes de descripción de hardware (HDL) permite mapear complejos algoritmos en una descripción sintáctica digital, la cual puede luego ser automáticamente colocada e interconectada (place&route). Sin embargo, dada la falta de automatización del diseño electrónico en el dominio analógico, como así también por factores como el ruido, el corrimiento y falta de apareamiento, el uso de los circuitos analógicos ha sido muy bajo en la medida de lo posible, por lo que las celdas analógicas embebidas son ahora un cuello de botella en el diseño de SOC. Por lo expuesto, en el proyecto que se propone se planea diseñar celdas analógicas embebidas con características de: bajo consumo, reutilización, bajo costo y alta performance para satisfacer el notable crecimiento del mercado de los sistemas portables alimentados por batería y el de sistemas de identificación remotamente energizados (RFID). Conjuntamente con el Área de Comunicaciones, se propone un generador de tensión de alimentación a partir de una señal de RF.

Análisis y optimización de redes inalámbricas de sensores remotos.

El proyecto inicialmente se denominó “Análisis y optimización del radio enlace en un sistema RFID”. A medida que el mismo fue avanzando, principalmente en el desarrollo de 2 planes de doctorado (Proyectos de Tesis Doctoral de Juan Castagnola y Agustín Laprovitta), los objetivos particulares fueron ajustándose a cada uno de estos trabajos. Así pues, los nuevos objetivos planteados para el proyecto son: a) Estudiar, generar modelos, simular e implementar nuevas configuraciones en la etapas de recepción de los transceptores, para lograr mayor alcance con menos potencia; b) Desarrollar metodologías de test para sistemas de redes inalámbricas de sensores, con énfasis en nodos activos y pasivos diseñados con circuitos analógicos y digitales configurables y componentes comerciales; c) Proponer estrategias de test de bajo consumo y alto desempeño focalizadas en las secciones analógicas, de conversión y digitales configurables del nodo. Además de la realización de los trabajos de tesis doctoral mencionados, en el grupo de investigación se encuentran alumnos de la carrera de Ingeniería Electrónica realizando sus trabajos finales de grado, los mismos se orientaron a trabajos de investigación e implementación en el área de las redes inalámbricas de sensores remotos. Los trabajos realizados en el invernadero y en el secadero de embutidos, están orientados también a esta misma temática. Por estos motivos se decidió el cambio en la denominación del proyecto, por: “Análisis y optimización de redes inalámbricas de sensores remotos”.

Perfil glicometabólico inicial em pacientes com síndrome coronariana aguda e síndrome metabólica

FUNDAMENTO: Pacientes com síndrome metabólica (SM) têm alto risco coronariano e a disfunção da célula beta ou resistência à insulina pode prever um risco adicional de eventos cardiovasculares precoces. OBJETIVO: Avaliar as alterações glicometabólicas precoces em pacientes com SM, mas sem diagnóstico de diabete tipo 2, após síndrome coronariana aguda. MÉTODOS: Um total de 114 pacientes foi submetido ao teste oral de tolerância à glicose (TOTG), 1-3 dias da alta hospitalar, após infarto agudo do miocárdio ou angina instável. Baseado no TOTG, definimos três grupos de pacientes: tolerância normal à glicose (TNG; n=26), tolerância alterada à glicose (TAG; n=39) ou diabetes mellitus (DM; n=49). O Modelo de Avaliação da Homeostase (HOMA-IR) foi usado para estimar a resistência à insulina; a responsividade da célula beta foi avaliada através do índice insulinogênico de 30 minutos (ΔI30/ΔG30). RESULTADOS: Baseado no HOMA-IR, os pacientes com DM eram mais insulino-resistentes do que aqueles com TNG ou TAG (p<0,001). De acordo com o índice insulinogênico, a responsividade da célula beta também estava alterada em indivíduos com DM (p<0,001 vs TNG ou TAG). CONCLUSÃO: Altas taxas de alterações glicometabólicas foram encontradas após síndrome coronariana aguda em pacientes com SM. Como essas anormalidades acentuadamente aumentam o risco de desfechos adversos, o TOTG precoce pode ser utilizado em pacientes com SM para identificar aqueles que apresentam maior risco coronariano.

Funktionelle Charakterisierung von mtch2 im Zebrafischmodell

Die steigende Zahl von Erkrankungen in Folge von Adipositas ist ein weltweites Gesundheitsproblem unserer Zeit. Genomweite Assoziationsstudien konnten single-nucleotide polymorphisms identifizieren, die in Zusammenhang mit Adipositas stehen könnten, darunter auch MTCH2. Weiterführende Untersuchungen konnten zeigen, dass MTCH2 eine regulatorische Rolle bei der Adipogenese einnimmt. Da mtch2 auch im Zebrafisch in verschiedenen Geweben und Organen wie Leber, Darm und Fettgewebe exprimiert wird, liegt die Vermutung nahe, dass es in diesen Organen und Geweben eine Funktion aufweist. Diese Funktion sollte über einen Morpholino-induzierten Knockdown des Gens und die Analyse des Phänotyps der Morpholino-injizierten Fische näher analysiert werden. Der Knockdown von mtch2 im Zebrafisch wurde mit Hilfe zweier Splice-Morpholinos induziert und über quantitative Real Time PCR identifiziert. Die Auswirkungen des Knockdowns auf die Entwicklung von Leber und Darm der Fische wurde über spezifische Marker mit der Methode der In situ Hybridisierung untersucht. Die Adipozytenbildung wurde durch Nilrotfärbung analysiert und über die Fütterung der Fische mit fluoreszierenden Beads mit dem Essverhalten in Zusammenhang gebracht. Bei beiden Morpholinos führte der Knockdown von mtch2 an Tag 4 der Entwicklung der Morpholino-injizierten Zebrafische zu Auffälligkeiten in der Ausbildung von Leber und Darm der Fische, die aber nicht mit einer generellen Störung der Entwicklung der Tiere einherging. An Tag 8 der Entwicklung der Zebrafische zeigte sich hingegen, dass die Tiere im Gegensatz zu den Kontroll-injizierten Fischen insgesamt kleiner beziehungsweise unterentwickelt waren, wobei dieser Umstand nicht mit ihrem Essverhalten in Zusammenhang gebracht werden konnte. Zudem konnte eine reduzierte Adipozytenbildung in den Morpholino-injizierten Zebrafischen festgestellt werden. (...)

Untersuchungen zum Einfluss von OLED Licht auf in vitro Zellkulturen

In der vorliegenden Arbeit werden Untersuchungen zum Einfluss von Licht auf humane in vitro-Zellkulturen beschrieben. Zunächst wird das Licht technisch erläutert und das Farbspektrum des Lichts betrachtet. Das natürliche Farbspektrum der Sonne ändert sich über den Tag, des Weiteren werden die Farben des Lichts in der Wissenschaft in verschiedenen Bereichen verwendet. Der Mensch hat einen geregelten Tagesablauf, der mit dem Tagesverlauf der Sonne parallel abläuft. Durch verschiedene Einflüsse kann diese Parallelität gestört werden. Für die Untersuchungen zum Einfluss des Lichts werden in vitro Modellsysteme verwendet, insbesondere Keratinozyten, die genauer beschrieben werden. Außerdem werden für die Untersuchungen organische Leuchtdioden (kurz: OLED) verwendet. Es wird eine Auswahl an Versuchs-OLEDs getroffen, welche für erste Versuche verwendet werden. In dieser Arbeit sollen erste Erkenntnisse über die Auswirkungen von Licht auf humane Zellen ermittelt werden, um aus der großen Auswahl von OLEDs Farbspektren zur genaueren Betrachtung herauszuziehen und später eine Anwendung in der Medizin zu ermöglichen. Hierzu werden das Wachstum und der Stoffwechselumsatz der Zellen betrachtet. Die Zellen werden mit Hilfe eines Versuchsaufbaus aus einer vorangegangenen Praktikumsarbeit beleuchtet. Als Lichtspektrum wurden 5 Farben ausgewählt: blau, grün, orange, warmweiß und kaltweiß. Als weitere Parameter werden eine feste Beleuchtungszeit, sowie eine identische Leuchtdichte bei allen Farben festgelegt. Aus den Versuchen können erste Erkenntnisse gezogen werden, jedoch müssen diese durch weitere Versuche bestätigt bzw. genauer betrachtet werden.

A novel gene expression signature in peripheral blood mononuclear cells for early detection of colorectal cancer.

BACKGROUND: Early detection and treatment of colorectal adenomatous polyps (AP) and colorectal cancer (CRC) is associated with decreased mortality for CRC. However, accurate, non-invasive and compliant tests to screen for AP and early stages of CRC are not yet available. A blood-based screening test is highly attractive due to limited invasiveness and high acceptance rate among patients. AIM: To demonstrate whether gene expression signatures in the peripheral blood mononuclear cells (PBMC) were able to detect the presence of AP and early stages CRC. METHODS: A total of 85 PBMC samples derived from colonoscopy-verified subjects without lesion (controls) (n = 41), with AP (n = 21) or with CRC (n = 23) were used as training sets. A 42-gene panel for CRC and AP discrimination, including genes identified by Digital Gene Expression-tag profiling of PBMC, and genes previously characterised and reported in the literature, was validated on the training set by qPCR. Logistic regression analysis followed by bootstrap validation determined CRC- and AP-specific classifiers, which discriminate patients with CRC and AP from controls. RESULTS: The CRC and AP classifiers were able to detect CRC with a sensitivity of 78% and AP with a sensitivity of 46% respectively. Both classifiers had a specificity of 92% with very low false-positive detection when applied on subjects with inflammatory bowel disease (n = 23) or tumours other than CRC (n = 14). CONCLUSION: This pilot study demonstrates the potential of developing a minimally invasive, accurate test to screen patients at average risk for colorectal cancer, based on gene expression analysis of peripheral blood mononuclear cells obtained from a simple blood sample.

Expression of Staphylococcus aureus clumping factor A in Lactococcus lactis subsp. cremoris using a new shuttle vector.

Staphylococcus aureus harbors redundant adhesins mediating tissue colonization and infection. To evaluate their intrinsic role outside of the staphylococcal background, a system was designed to express them in Lactococcus lactis subsp. cremoris 1363. This bacterium is devoid of virulence factors and has a known genetic background. A new Escherichia coli-L. lactis shuttle and expression vector was constructed for this purpose. First, the high-copy-number lactococcal plasmid pIL253 was equipped with the oriColE1 origin, generating pOri253 that could replicate in E. coli. Second, the lactococcal promoters P23 or P59 were inserted at one end of the pOri253 multicloning site. Gene expression was assessed by a luciferase reporter system. The plasmid carrying P23 (named pOri23) expressed luciferase constitutively at a level 10,000 times greater than did the P59-containing plasmid. Transcription was absent in E. coli. The staphylococcal clumping factor A (clfA) gene was cloned into pOri23 and used as a model system. Lactococci carrying pOri23-clfA produced an unaltered and functional 130-kDa ClfA protein attached to their cell walls. This was indicated both by the presence of the protein in Western blots of solubilized cell walls and by the ability of ClfA-positive lactococci to clump in the presence of plasma. ClfA-positive lactococci had clumping titers (titer of 4,112) similar to those of S. aureus Newman in soluble fibrinogen and bound equally well to solid-phase fibrinogen. These experiments provide a new way to study individual staphylococcal pathogenic factors and might complement both classical knockout mutagenesis and modern in vivo expression technology and signature tag mutagenesis.

Design and analysis of ChIP-Seq experiments for nuclear factor I DNA-binding proteins

SUMMARY : Eukaryotic DNA interacts with the nuclear proteins using non-covalent ionic interactions. Proteins can recognize specific nucleotide sequences based on the sterical interactions with the DNA and these specific protein-DNA interactions are the basis for many nuclear processes, e.g. gene transcription, chromosomal replication, and recombination. New technology termed ChIP-Seq has been recently developed for the analysis of protein-DNA interactions on a whole genome scale and it is based on immunoprecipitation of chromatin and high-throughput DNA sequencing procedure. ChIP-Seq is a novel technique with a great potential to replace older techniques for mapping of protein-DNA interactions. In this thesis, we bring some new insights into the ChIP-Seq data analysis. First, we point out to some common and so far unknown artifacts of the method. Sequence tag distribution in the genome does not follow uniform distribution and we have found extreme hot-spots of tag accumulation over specific loci in the human and mouse genomes. These artifactual sequence tags accumulations will create false peaks in every ChIP-Seq dataset and we propose different filtering methods to reduce the number of false positives. Next, we propose random sampling as a powerful analytical tool in the ChIP-Seq data analysis that could be used to infer biological knowledge from the massive ChIP-Seq datasets. We created unbiased random sampling algorithm and we used this methodology to reveal some of the important biological properties of Nuclear Factor I DNA binding proteins. Finally, by analyzing the ChIP-Seq data in detail, we revealed that Nuclear Factor I transcription factors mainly act as activators of transcription, and that they are associated with specific chromatin modifications that are markers of open chromatin. We speculate that NFI factors only interact with the DNA wrapped around the nucleosome. We also found multiple loci that indicate possible chromatin barrier activity of NFI proteins, which could suggest the use of NFI binding sequences as chromatin insulators in biotechnology applications. RESUME : L'ADN des eucaryotes interagit avec les protéines nucléaires par des interactions noncovalentes ioniques. Les protéines peuvent reconnaître les séquences nucléotidiques spécifiques basées sur l'interaction stérique avec l'ADN, et des interactions spécifiques contrôlent de nombreux processus nucléaire, p.ex. transcription du gène, la réplication chromosomique, et la recombinaison. Une nouvelle technologie appelée ChIP-Seq a été récemment développée pour l'analyse des interactions protéine-ADN à l'échelle du génome entier et cette approche est basée sur l'immuno-précipitation de la chromatine et sur la procédure de séquençage de l'ADN à haut débit. La nouvelle approche ChIP-Seq a donc un fort potentiel pour remplacer les anciennes techniques de cartographie des interactions protéine-ADN. Dans cette thèse, nous apportons de nouvelles perspectives dans l'analyse des données ChIP-Seq. Tout d'abord, nous avons identifié des artefacts très communs associés à cette méthode qui étaient jusqu'à présent insoupçonnés. La distribution des séquences dans le génome ne suit pas une distribution uniforme et nous avons constaté des positions extrêmes d'accumulation de séquence à des régions spécifiques, des génomes humains et de la souris. Ces accumulations des séquences artéfactuelles créera de faux pics dans toutes les données ChIP-Seq, et nous proposons différentes méthodes de filtrage pour réduire le nombre de faux positifs. Ensuite, nous proposons un nouvel échantillonnage aléatoire comme un outil puissant d'analyse des données ChIP-Seq, ce qui pourraient augmenter l'acquisition de connaissances biologiques à partir des données ChIP-Seq. Nous avons créé un algorithme d'échantillonnage aléatoire et nous avons utilisé cette méthode pour révéler certaines des propriétés biologiques importantes de protéines liant à l'ADN nommés Facteur Nucléaire I (NFI). Enfin, en analysant en détail les données de ChIP-Seq pour la famille de facteurs de transcription nommés Facteur Nucléaire I, nous avons révélé que ces protéines agissent principalement comme des activateurs de transcription, et qu'elles sont associées à des modifications de la chromatine spécifiques qui sont des marqueurs de la chromatine ouverte. Nous pensons que lés facteurs NFI interagir uniquement avec l'ADN enroulé autour du nucléosome. Nous avons également constaté plusieurs régions génomiques qui indiquent une éventuelle activité de barrière chromatinienne des protéines NFI, ce qui pourrait suggérer l'utilisation de séquences de liaison NFI comme séquences isolatrices dans des applications de la biotechnologie.

trEST, trGEN and Hits: access to databases of predicted protein sequences.

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits. isb-sib.ch).

Protection against Toxoplasmosis in Mice Immunized with Different Antigens of Toxoplasma gondii Incorporated into Liposomes

Different toxoplasma antigens were entrapped within liposomes and evaluated, in this form, for their ability to protect Swiss mice against toxoplasma infection: soluble tachyzoite antigen (L/TAg), tissue cyst (L/CAg), tachyzoite plus tissue cyst (L/TCAg) or purified antigen of tachyzoite (L/pTAg). The protein used in L/pTAg was purified from tachyzoites using a stage-specific monoclonal antibody which reacted at a molecular weight of 32 kD in SDS PAGE and silver stain using reduced condition. To compare the immuno-adjuvant action of liposomes and of Freund's Complete Adjuvant (FCA), another group of mice was immunized with soluble tachyzoite antigen (STAg) emulsified in FCA (FCA/TAg). Control groups were inoculated with (STAg) alone, phosphate-buffered saline (PBS), FCA with PBS (FCA/PBS) and empty liposomes (L/PBS). Mice were inoculated subcutaneously with these antigens six, four and two weeks before a challenge with 80 tissue cysts of the P strain of Toxoplasma gondii orally. All mice immunized with or without adjuvant showed a humoral response, as measured by Elisa. However, no correlation was found between antibody titer and protection against the challenge. All mice immunized with L/pTAg or L/TCAg survived (100), whereas 80% and 90% of mice from groups which received respectively PBS or FCA/PBS and L/PBS died. All mice immunized with antigens entrapped within liposomes (L/TAg, L/CAg, L/TCAg and L/pTAg) showed low numbers of intracerebral cysts.

Comparative genetic analyses point to HCP5 as susceptibility locus for HCV-associated hepatocellular carcinoma.

BACKGROUND & AIMS: Recently, genetic variations in MICA (lead single nucleotide polymorphism [SNP] rs2596542) were identified by a genome-wide association study (GWAS) to be associated with hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC) in Japanese patients. In the present study, we sought to determine whether this SNP is predictive of HCC development in the Caucasian population as well. METHODS: An extended region around rs2596542 was genotyped in 1924 HCV-infected patients from the Swiss Hepatitis C Cohort Study (SCCS). Pair-wise correlation between key SNPs was calculated both in the Japanese and European populations (HapMap3: CEU and JPT). RESULTS: To our surprise, the minor allele A of rs2596542 in proximity of MICA appeared to have a protective impact on HCC development in Caucasians, which represents an inverse association as compared to the one observed in the Japanese population. Detailed fine-mapping analyses revealed a new SNP in HCP5 (rs2244546) upstream of MICA as strong predictor of HCV-related HCC in the SCCS (univariable p=0.027; multivariable p=0.0002, odds ratio=3.96, 95% confidence interval=1.90-8.27). This newly identified SNP had a similarly directed effect on HCC in both Caucasian and Japanese populations, suggesting that rs2244546 may better tag a putative true variant than the originally identified SNPs. CONCLUSIONS: Our data confirms the MICA/HCP5 region as susceptibility locus for HCV-related HCC and identifies rs2244546 in HCP5 as a novel tagging SNP. In addition, our data exemplify the need for conducting meta-analyses of cohorts of different ethnicities in order to fine map GWAS signals.

Quantification, self-renewal, and genetic tracing of FL1+ tumor-initiating cells in a large cohort of human gliomas.

Evidence has emerged that the initiation and growth of gliomas is sustained by a subpopulation of cancer-initiating cells (CICs). Because of the difficulty of using markers to tag CICs in gliomas, we have previously exploited more robust phenotypic characteristics, including a specific morphology and intrincic autofluorescence, to identify and isolate a subpopulation of glioma CICs, called FL1(+). The objective of this study was to further validate our method in a large cohort of human glioma and a mouse model of glioma. Seventy-four human gliomas of all grades and the GFAP-V(12)HA-ras B8 mouse model were analyzed for in vitro self-renewal capacity and their content of FL1(+). Nonneoplastic brain tissue and embryonic mouse brain were used as control. Genetic traceability along passages was assessed with microsatellite analysis. We found that FL1(+) cells from low-grade gliomas and from control nonneoplasic brain tissue show a lower level of autofluorescence and undergo a restricted number of cell divisions before dying in culture. In contrast, we found that FL1(+) cells derived from many but not all high-grade gliomas acquire high levels of autofluorescence and can be propagated in long-term cultures. Moreover, FL1(+) cells show a remarkable traceability over time in vitro and in vivo. Our results show that FL1(+) cells can be found in all specimens of a large cohort of human gliomas of different grades and in a model of genetically induced mouse glioma as well as nonneoplastic brain. However, their self-renewal capacity is variable and seems to be dependent on the tumor grade.

r-Sm14 - pRSETA efficacy in experimental animals

Previous studies carried out with Sm14 in experimental vaccination against Schistosoma mansoni or Fasciola hepatica infections were performed with recombinant Sm14 (rSm14) produced in Escherichia coli by the pGEMEX system (Promega). The rSm14 was expressed as a 40 kDa fusion protein with the major bacteriophage T7 capsid protein. Vaccination experiments with this rSm14 in animal models resulted in consistent high protective activity against S. mansoni cercariae challenge and enabled rSm14 to be included among the vaccine antigens endorsed by the World Health Organization for phase I/II clinical trials. Since the preparation of pGEMEX based rSm14 is time consuming and results in low yield for large scale production, we have tested other E. coli expression systems which would be more suitable for scale up and downstream processing. We expressed two different 6XHis-tagged Sm14 fusion proteins in a T7 promoter based plasmids. The 6XHis-tag fusions allowed rapid purification of the recombinant proteins through a Ni+2-charged resin. The resulted recombinant 18 and 16 kDa proteins were recognized by anti-Sm14 antibodies and also by antiserum against adult S. mansoni soluble secreted/excreted proteins in Western-Blot. Both proteins were also protective against S. mansoni cercariae infection to the same extent as the rSm14 expressed by the pGEMEX system.

Clustering of Schistosoma mansoni mRNA sequences and analysis of the most transcribed genes: implications in metabolism and biology of different developmental stages

The study of the Schistosoma mansoni genome, one of the etiologic agents of human schistosomiasis, is essential for a better understanding of the biology and development of this parasite. In order to get an overview of all S. mansoni catalogued gene sequences, we performed a clustering analysis of the parasite mRNA sequences available in public databases. This was made using softwares PHRAP and CAP3. The consensus sequences, generated after the alignment of cluster constituent sequences, allowed the identification by database homology searches of the most expressed genes in the worm. We analyzed these genes and looked for a correlation between their high expression and parasite metabolism and biology. We observed that the majority of these genes is related to the maintenance of basic cell functions, encoding genes whose products are related to the cytoskeleton, intracellular transport and energy metabolism. Evidences are presented here that genes for aerobic energy metabolism are expressed in all the developmental stages analyzed. Some of the most expressed genes could not be identified by homology searches and may have some specific functions in the parasite.

Disseny i implementació d'un Videoclub online amb J2EE i una llibreria de tags de suport per la capa de presentació

Disseny i implementació parcial d'un Videoclub online en J2EE. Es fa ús dels patrons de disseny i frameworks més adients les diferents capes de l'arquitectura justificant la seva elecció. Així mateix, es desenvolupa una llibreria de tags pròpia, que dóna suport en el desenvolupament de les vistes d'un model de negoci d'aquest tipus.