Lack of evidence to support the association of a single IL28B genotype SNP rs12979860 with the HTLV-1 clinical outcomes and proviral load

Background: The Interleukin 28B (IL28B) rs12979860 polymorphisms was recently reported to be associated with the human T-cell leukemia virus type 1 (HTLV-1) proviral load (PvL) and the development of the HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Methods: In an attempt to examine this hypothesis, we assessed the association of the rs12979860 genotypes with HTLV-1 PvL levels and clinical status in 112 unrelated Brazilian subjects (81 HTLV-1 asymptomatic carriers, 24 individuals with HAM/TSP and 7 with Adult T cell Leukemia/Lymphoma (ATLL)). Results: All 112 samples were successfully genotyped and their PvLs compared. Neither the homozygote TT nor the heterozygote CT mutations nor the combination genotypes (TT/CT) were associated with a greater PvL. We also observed no significant difference in allele distribution between asymptomatic carriers and patients with HTLV-1 associated HAM/TSP. Conclusions: Our study failed to support the previously reported positive association between the IL28B rs12979860 polymorphisms and an increased risk of developing HAM/TSP in the Brazilian population.

MSX2 copy number increase and craniosynostosis: copy number variation detected by array comparative genomic hybridization

Fleury Group

Microelectrode array in mixed alkanethiol self-assembled monolayers: Electrochemical studies

We report an efficient alternative to obtain recessed microelectrodes device on gold electrode surface, in which mixed self-assembled monolayer of long and short carbon alkanethiol chains was used for this purpose. Development of the modified electrodes included the chemical adsorption of 11-mercaptoundecanoic acid and 2-mercaptoethanol solution, as well as their mixtures, on gold surface, resulting in the final mixed self-assembled monolayer configuration. For comparison, the electrochemical performance of self-assembled monolayer of 11-mercaptoundecanoic acid. 3-mercaptopropionic acid, 4-mercapto-1-butanol and 6-mercapto-1-hexanol modified electrodes was also investigated. It was verified that, in the mixed self-assembled monolayer, the 11-mercaptoundecanoic acid acts as a barrier for electron transfer while the short alkanethiol chair is deposited in an island-like shape through which electrons can be freely transferred to ions in solution, allowing electrochemical reactions to occur. The performance of the modified electrodes toward microelectrode behavior was investigated via cyclic voltammetry and electrochemical impedance spectroscopy measurements using [Fe(CN)(6)](3-/4-) redox couple as a probe. In this case, sigmoidal voltammetric responses were obtained, very similar to those observed for microelectrodes. Such behavior reinforces the proposition of electron transfer through the short alkanethiol chain layer and surface blockage by the long chain one. Electrochemical impedance results allowed calculated the mean radius value of each microelectrode disks of 3.8 mu m with about 22 mu m interval between them. The microelectrode environment provided by the mixed self-assembled monolayer can be conveniently used to provide an efficient catalytic conversion in biosensing applications. (C) 2012 Elsevier Ltd. All rights reserved.

Development of an AMR-ACB Array for Gastrointestinal Motility Studies

The association between anisotropic magnetoresistive (AMR) sensor and AC biosusceptometry (ACB) to evaluate gastrointestinal motility is presented. The AMR-ACB system was successfully characterized in a bench-top study, and in vivo results were compared with those obtained by means of simultaneous manometry. Both AMR-ACB and manometry techniques presented high temporal cross correlation between the two periodicals signals (R = 0.9 +/- 0.1; P < 0.05). The contraction frequencies using AMR-ACB were 73.9 +/- 7.6 mHz and using manometry were 73.8 +/- 7.9 mHz during the baseline (r = 98, p < 0.05). The amplitude of contraction using AMR-ACB was 396 +/- 108 mu T.s and using manometry were 540 +/- 198 mmHg.s during the baseline. The amplitudes of signals for AMR-ACB and manometric recordings were similarly increased to 86.4% and 89.3% by neostigmine, and also decreased to 27.2% and 21.4% by hyoscine butylbromide in all animals, respectively. The AMR-ACB array is nonexpensive, portable, and has high-spatiotemporal resolution to provide helpful information about gastrointestinal tract.

Assessment of SNPs for linkage mapping in Eucalyptus: construction of a consensus SNP/microsatellite map from two unrelated pedigrees

Financial support. Brazilian Ministry of Science and Technology (CNPq Grant 577047-2008-6), FAP-DF NEXTREE Grant 193.000.570/2009 and EMBRAPA Macroprogram 2 project grant 02.07.01.004.

A complete CMOS UWB timed-array transmitter with a 3D Vivaldi antenna array for electronic high-resolution beam spatial scanning

We present a new Ultra Wide Band (UWB) Timed- Array Transmitter System with Beamforming capability for high-resolution remote acquisition of vital signals. The system consists of four identical channels, where each is formed of a serial topology with three modules: programmable delay circuit (PDC or τ), a novel UWB 5th Gaussian Derivative order pulse generator circuit (PG), and a planar Vivaldi antenna. The circuit was designed using 0.18μm CMOS standard process and the planar antenna array was designed with filmconductor on Rogers RO3206 substrate. Spice simulations results showed the pulse generation with 104 mVpp amplitude and 500 ps width. The power consumption is 543 μW, and energy consumption 0.27 pJ per pulse using a 2V power supply at a pulse repetition rate (PRR) of 100 MHz. Electromagnetic simulations results, using CST Microwave (MW) Studio 2011, showed the main lobe radiation with a gain maximum of 13.2 dB, 35.5º x 36.7º angular width, and a beam steering between 17º and -11º for azimuthal (θ) angles and 17º and -18º for elevation (φ) angles at the center frequency of 6 GHz

DNA-Array-Technologie

Es wurde ein genomischer DNA-Array der Modellpflanze Arabidopsis thaliana mit einer 13.800 EST-Klone umfassenden cDNA-Bibliothek entwickelt und in der Genexpressionsanalyse der pflanzlichen Pathogenabwehr eingesetzt. Mittels PCR-Amplifikation sind 13.000 PCR-Produkte der cDNA-Fragmente hergestellt worden, mit denen 66 genomische Arabidopsis-Arrays auf Nylon und Polypropylen als Trägermaterial hergestellt werden konnten. Die Validierung mit Fluoreszenz- und Radiaktivhybridisierung sowie der Vergleich von drei Normalisierungsmethoden führte zu reproduzierbaren Ergebnissen bei hohem Korrelationskoeffizienten. Die etablierte DNA-Array-Technologie wurde zur Genexpressionsanalyse der pathogeninduzierten Abwehrmechanismen der Pflanze Arabidopsis thaliana in den ersten 24 Stunden nach Infektion mit dem avirulenten Bakterium Pseudomonas syringae pv. tomato eingesetzt. In einer Auswahl von 75 Genen der Stoffwechselwege Glycolyse, Citrat-Cyclus, Pentosephosphat-Cyclus und Glyoxylatmetabolismus konnte für 25 % der Gene, im Shikimat-, Tryptophan- und Phenylpropanoidsyntheseweg für 60 % der Gene eine erhöhte Transkriptionsrate nachgewiesen werden. Die Ergebnisse dieser Arbeit stimmen mit experimentellen Daten verschiedener unabhängiger Studien zur pflanzlichen Pathogenantwort überein. Darüberhinaus sind erstmals Transkriptionsprofile von bisher auf Transkriptionsebene nicht untersuchten Genen erstellt worden. Diese Ergebnisse bestätigen die transkriptionelle Aktivierung ganzer Stoffwechselwege und gewähren erstmals einen Einblick in die koordinierte differentielle Transkription ganzer Stoffwechselwege während der Pathogenabwehr.

Novel tools for conservation genetics in marine fish: population structure and evolution of the European hake (Merluccius merluccius) inferred by SNP variation and applications to traceability

The research presented in my PhD thesis is part of a wider European project, FishPopTrace, focused on traceability of fish populations and products. My work was aimed at developing and analyzing novel genetic tools for a widely distributed marine fish species, the European hake (Merluccius merluccius), in order to investigate population genetic structure and explore potential applications to traceability scenarios. A total of 395 SNPs (Single Nucleotide Polymorphisms) were discovered from a massive collection of Expressed Sequence Tags, obtained by high-throughput sequencing, and validated on 19 geographic samples from Atlantic and Mediterranean. Genome-scan approaches were applied to identify polymorphisms on genes potentially under divergent selection (outlier SNPs), showing higher genetic differentiation among populations respect to the average observed across loci. Comparative analysis on population structure were carried out on putative neutral and outlier loci at wide (Atlantic and Mediterranean samples) and regional (samples within each basin) spatial scales, to disentangle the effects of demographic and adaptive evolutionary forces on European hake populations genetic structure. Results demonstrated the potential of outlier loci to unveil fine scale genetic structure, possibly identifying locally adapted populations, despite the weak signal showed from putative neutral SNPs. The application of outlier SNPs within the framework of fishery resources management was also explored. A minimum panel of SNP markers showing maximum discriminatory power was selected and applied to a traceability scenario aiming at identifying the basin (and hence the stock) of origin, Atlantic or Mediterranean, of individual fish. This case study illustrates how molecular analytical technologies have operational potential in real-world contexts, and more specifically, potential to support fisheries control and enforcement and fish and fish product traceability.

Mapping the elastic response of epithelial apical cell membranes suspended across porous array

As the elastic response of cell membranes to mechanical stimuli plays a key role in various cellular processes, novel biophysical strategies to quantify the elasticity of native membranes under physiological conditions at a nanometer scale are gaining interest. In order to investigate the elastic response of apical membranes, elasticity maps of native membrane sheets, isolated from MDCK II (Madine Darby Canine kidney strain II) epithelial cells, were recorded by local indentation with an Atomic Force Microscope (AFM). To exclude the underlying substrate effect on membrane indentation, a highly ordered gold coated porous array with a pore diameter of 1.2 μm was used to support apical membranes. Overlays of fluorescence and AFM images show that intact apical membrane sheets are attached to poly-D-lysine coated porous substrate. Force indentation measurements reveal an extremely soft elastic membrane response if it is indented at the center of the pore in comparison to a hard repulsion on the adjacent rim used to define the exact contact point. A linear dependency of force versus indentation (-dF/dh) up to 100 nm penetration depth enabled us to define an apparent membrane spring constant (kapp) as the slope of a linear fit with a stiffness value of for native apical membrane in PBS. A correlation between fluorescence intensity and kapp is also reported. Time dependent hysteresis observed with native membranes is explained by a viscoelastic solid model of a spring connected to a Kelvin-Voight solid with a time constant of 0.04 s. No hysteresis was reported with chemically fixated membranes. A combined linear and non linear elastic response is suggested to relate the experimental data of force indentation curves to the elastic modulus and the membrane thickness. Membrane bending is the dominant contributor to linear elastic indentation at low loads, whereas stretching is the dominant contributor for non linear elastic response at higher loads. The membrane elastic response was controlled either by stiffening with chemical fixatives or by softening with F-actin disrupters. Overall, the presented setup is ideally suitable to study the interactions of the apical membrane with the underlying cytoskeleton by means of force indentation elasticity maps combined with fluorescence imaging.

Caratterizzazione della superficie di array di nanofili di silicio

Nel primo capitolo viene introdotto lo studio eff�ettuato e descritto un metodo di misure successivo alla caratterizzazione della super�ficie. Nel secondo capitolo vengono descritti i campioni analizzati e, nello speci�fico, la crescita attraverso MaCE dei nanofi�li di silicio. Nel terzo capitolo viene descritto lo strumento AFM utilizzato e la teoria della caratterizzazione alla base dello studio condotto. Nella quarta sezione vengono descritti i risultati ottenuti mentre nelle conclusioni viene tratto il risultato dei valori ottenuti di RMS roughness e roughness exponent.

Multiplex-Genotypisierung forensisch relevanter SNPs unter Verwendung von Microarrays auf chemisch aktivierten Glasflächen

Die Analyse tandem-repetitiver DNA-Sequenzen hat einen festen Platz als genetisches Typisierungsverfahren in den Breichen der stammesgeschichtlichen Untersuchung, der Verwandtschaftsanalyse und vor allem in der forensischen Spurenkunde, bei der es durch den Einsatz der Multiplex-PCR-Analyse von Short Tandem Repeat-Systemen (STR) zu einem Durchbruch bei der Aufklärung und sicheren Zuordnung von biologischen Tatortspuren kam. Bei der Sequenzierung des humanen Genoms liegt ein besonderes Augenmerk auf den genetisch polymorphen Sequenzvariationen im Genom, den SNPs (single nucleotide polymorphisms). Zwei ihrer Eigenschaften – das häufige Vorkommen innerhalb des humanen Genoms und ihre vergleichbar geringe Mutationsrate – machen sie zu besonders gut geeigneten Werkzeugen sowohl für die Forensik als auch für die Populationsgenetik.rnZum Ziel des EU-Projekts „SNPforID“, aus welchem die vorliegende Arbeit entstanden ist, wurde die Etablierung neuer Methoden zur validen Typisierung von SNPs in Multiplexverfahren erklärt. Die Berücksichtigung der Sensitivität bei der Untersuchung von Spuren sowie die statistische Aussagekraft in der forensischen Analyse standen dabei im Vordergrund. Hierfür wurden 52 autosomale SNPs ausgewählt und auf ihre maximale Individualisierungsstärke hin untersucht. Die Untersuchungen der ersten 23 selektierten Marker stellen den ersten Teil der vorliegenden Arbeit dar. Sie umfassen die Etablierung des Multiplexverfahrens und der SNaPshot™-Typisierungsmethode sowie ihre statistische Auswertung. Die Ergebnisse dieser Untersuchung sind ein Teil der darauf folgenden, in enger Zusammenarbeit der Partnerlaboratorien durchgeführten Studie der 52-SNP-Multiplexmethode. rnEbenfalls im Rahmen des Projekts und als Hauptziel der Dissertation erfolgten Etablierung und Evaluierung des auf der Microarray-Technologie basierenden Verfahrens der Einzelbasenverlängerung auf Glasobjektträgern. Ausgehend von einer begrenzten DNA-Menge wurde hierbei die Möglichkeit der simultanen Hybridisierung einer möglichst hohen Anzahl von SNP-Systemen untersucht. Die Auswahl der hierbei eingesetzten SNP-Marker erfolgte auf der Basis der Vorarbeiten, die für die Etablierung des 52-SNP-Multiplexes erfolgreich durchgeführt worden waren. rnAus einer Vielzahl von Methoden zur Genotypisierung von biallelischen Markern hebt sich das Assay in seiner Parallelität und der Einfachheit des experimentellen Ansatzes durch eine erhebliche Zeit- und Kostenersparnis ab. In der vorliegenden Arbeit wurde das „array of arrays“-Prinzip eingesetzt, um zur gleichen Zeit unter einheitlichen Versuchsbedingungen zwölf DNA-Proben auf einem Glasobjektträger zu typisieren. Auf der Basis von insgesamt 1419 typisierten Allelen von 33 Markern konnte die Validierung mit einem Typisierungserfolg von 86,75% abgeschlossen werden. Dabei wurden zusätzlich eine Reihe von Randbedingungen in Bezug auf das Sonden- und Primerdesign, die Hybridisierungsbedingungen sowie physikalische Parameter der laserinduzierten Fluoreszenzmessung der Signale ausgetestet und optimiert. rn

Hydrodynamic induced by an array of wave energy converters. Experimental and numerical analysis

The thesis analyses the hydrodynamic induced by an array of Wave energy Converters (WECs), under an experimental and numerical point of view. WECs can be considered an innovative solution able to contribute to the green energy supply and –at the same time– to protect the rear coastal area under marine spatial planning considerations. This research activity essentially rises due to this combined concept. The WEC under exam is a floating device belonging to the Wave Activated Bodies (WAB) class. Experimental data were performed at Aalborg University in different scales and layouts, and the performance of the models was analysed under a variety of irregular wave attacks. The numerical simulations performed with the codes MIKE 21 BW and ANSYS-AQWA. Experimental results were also used to calibrate the numerical parameters and/or to directly been compared to numerical results, in order to extend the experimental database. Results of the research activity are summarized in terms of device performance and guidelines for a future wave farm installation. The device length should be “tuned” based on the local climate conditions. The wave transmission behind the devices is pretty high, suggesting that the tested layout should be considered as a module of a wave farm installation. Indications on the minimum inter-distance among the devices are provided. Furthermore, a CALM mooring system leads to lower wave transmission and also larger power production than a spread mooring. The two numerical codes have different potentialities. The hydrodynamics around single and multiple devices is obtained with MIKE 21 BW, while wave loads and motions for a single moored device are derived from ANSYS-AQWA. Combining the experimental and numerical it is suggested –for both coastal protection and energy production– to adopt a staggered layout, which will maximise the devices density and minimize the marine space required for the installation.

Identification of CNV and QTL for productive and functional traits in dairy cattle using dense SNP chips

The thesis identify CNV structural variants as possible markers for genomic selection and identify QTL regions for Fatty Acid Content in the Italian Brown Swiss population. Additionally it maps the QTL for mastitis resistance in the Valdostana Red Pied cattle.

Observability of high density tracing molecular lines in lensed galaxies with the Atacama large millimeter array

Lo scopo di questo lavoro di tesi è indagare le capacità di ALMA di osservare il continuo e le righe molecolari di emissione di HCN, HCO+ e HNC, in galassie lensate ad alto z, nelle prime fasi della loro formazione. Per farlo vengono utilizzate osservazioni ALMA di righe di emissione molecolare, relative a dati pubblici di Ciclo 0. Queste osservazioni vengono utilizzate per simulare in modo realistico l’emissione da parte di galassie ad alto z e la risposta osservativa del telescopio, assumendo diverse possibili geometrie di lensing. Inoltre le recenti osservazioni ALMA sono state utilizzate per aggiornare le relazioni già esistenti tra la luminosità FIR e la luminosità delle righe molecolari. Queste recenti osservazioni con maggiore sensibilità e risoluzione angolare, sembrano essere in buon accordo con le precedenti osservazioni. Per realizzare questo progetto di tesi, sono stati scaricati dall’archivio ALMA i dati non calibrati relativi a due sorgenti ben studiate: NGC1614, rappresentativa delle galassie di tipo starburst ed IRAS 20551-4250, un AGN oscurato. Il processo di calibrazione è stato ripetuto per esaminare le proprietà dei cubi di dati utilizzando il pacchetto Common Astronomy Software Applications (CASA). Le righe spettrali osservate e l’emissione del continuo sono state successivamente estrapolate ad alto z riscalando adeguatamente le distanze, le dimensioni delle sorgenti e le frequenze di emissione. In seguito è stato applicato un modello di lensing gravitazionale basato su quello di Lapi et al. (2012). Sono state considerate diverse configurazioni tra lente e sorgente per ottenere diverse geometrie delle immagini e diversi fattori di amplificazione. Infine stato utilizzato il software CASA per simulare le osservazioni ALMA in modo da verificare le capacità osservative del telescopio al variare della geometria del sistema. Per ogni riga molecolare e per l’emissione del continuo sono state determinate la sensibilit e la risoluzione che possono essere raggiunte con le osservazioni ALMA e sono state analizzate alcune strategie osservative per effettuare survey di righe spettrali in oggetti lensati. Inoltre stata analizzata la possibilit di caratterizzare oggetti starburst ed AGN dai rapporti tra le righe di emissione delle molecole traccianti di alta densit. Le prestazioni di ALMA consentiranno di distinguere e stimare i contributi relativi di SB ed AGN in galassie lensate a z > 2.5, quindi vicine alla loro presunta epoca di formazione (Lapi et al. 2010), in meno di 5 minuti di osservazione per qualsiasi fattore di magnificazione. Nel presente lavoro sono state inoltre discusse alcune strategie osservative per condurre survey o followup per osservare le righe di HCN(4-3), HCO+(4-3) e HNC(4-3) in galassie lensate a redshift 2.5 < z < 3, dimostrando che sono possibili per campioni statisticamente significativi in tempi relativamente brevi.