Microscale mesoarrays created by dip-pen nanolithography for screening of protein-protein interactions

Using microarrays to probe protein-protein interactions is becoming increasingly attractive due to their compatibility with highly sensitive detection techniques, selectivity of interaction, robustness and capacity for examining multiple proteins simultaneously. The major drawback to using this approach is the relatively large volumes and high concentrations necessary. Reducing the protein array spot size should allow for smaller volumes and lower concentrations to be used as well as opening the way for combination with more sensitive detection technologies. Dip-Pen Nanolithography (DPN) is a recently developed technique for structure creation on the nano to microscale with the capacity to create biological architectures. Here we describe the creation of miniaturised microarrays, 'mesoarrays', using DPN with protein spots 400× smaller by area compared to conventional microarrays. The mesoarrays were then used to probe the ERK2-KSR binding event of the Ras/Raf/MEK/ERK signalling pathway at a physical scale below that previously reported. Whilst the overall assay efficiency was determined to be low, the mesoarrays could detect KSR binding to ERK2 repeatedly and with low non-specific binding. This study serves as a first step towards an approach that can be used for analysis of proteins at a concentration level comparable to that found in the cellular environment.

EDC-mediated oligonucleotide immobilization on a long period grating optical biosensor

We present the development and simplification of label-free fiber optic biosensors based on immobilization of oligonucleotides on dual-peak long period gratings (dLPGs). This improvement is the result of a simplification of biofunctionalization methodology. A one-step 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC)-mediated reaction has been developed for the straightforward immobilization of unmodified oligonucleotides on the glass fiber surface along the grating region, leading to covalent attachment of a 5´-phosphorylated probe oligonucleotide to the amino-derivatized fiber grating surface. Immobilization is achieved via a 5´phosphate-specific linkage, leaving the remainder of the oligonucleotide accessible for binding reactions. The dLPG has been tested in different external media to demonstrate its inherent ultrahigh sensitivity to the surrounding-medium refractive index (RI) achieving 50- fold improvement in RI sensitivity over the previously-published LPG sensor in media with RI’s relevant to biological assays. After functionalization, the dLPG biosensor was used to monitor the hybridization of complementary oligonucleotides showing a detectable oligonucleotide concentration of 4 nM. The proposed one-step EDC reaction approach can be further extended to develop fiber optic biosensors for disease analysis and medical diagnosis with the advances of label-free, real-time, multiplex, high sensitivity and specificity.

Label-free immunoassay for porcine circovirus type 2 based on excessively tilted fiber grating modified with staphylococcal protein A

Using excessively tilted fiber grating (Ex-TFG) inscribed in standard single mode fiber, we developed a novel label-free immunoassay for specific detection of porcine circovirus type 2 (PCV2), which is a minim animal virus. Staphylococcal protein A (SPA) was used to modify the silanized fiber surface thus forming a SPA layer, which would greatly enhance the proportion of anti-PCV2 monoclonal antibody (MAb) bioactivity, thus improving the effectiveness of specific adsorption and binding events between anti-PCV2 MAbs and PCV2 antigens. Immunoassay experiments were carried out by monitoring the resonance wavelength shift of the proposed sensor under different PCV2 titer levels. Anti-PCV2 MAbs were thoroughly dissociated from the SPA layer by treatment with urea, and recombined to the SPA layer on the sensor surface for repeated immunoassay of PCV2. The specificity of the immunosensor was inspected by detecting porcine reproductive and respiratory syndrome virus (PRRSV) first, and PCV2 subsequently. The results showed a limit of detection (LOD) for the PCV2 immunosensor of ~9.371TCID50/mL, for a saturation value of ~4.801×103TCID50/mL, with good repeatability and excellent specificity.

Estudo de um secador híbrido (solar-elétrico) para desidratação de frutas

The growing need for food is something that worries the world, which has a population that is growing at a geometric progression while their resources grows at an arithmetic progression. To alleviate this problem there are some proposals, including increased food production or reduce waste thereof. Many studies have been conducted in the world in order to reduce food waste that can reach 40% of production, depending on the region. For this purpose techniques are used to retard degradation of foods, including drying. This paper presents a design of a hybrid fruit dryer that uses solar energy and electric energy with automation of the process. To accomplish drying tests were chosen Typical fruits with good acceptability as processed fruits. During the experiments were measured temperature values at different points. Were also measured humidity values, solar radiation and mass. A data acquisition system was built using a Arduino for obtaining temperatures. The data were sent to a program named Secador de Frutas, done in this work, to plot the same. The volume of the drying chamber was 423 liters and despite the unusual size test using mirrors to increase the incidence of direct radiation, showed that the drier is competitive when compared with other solar dryers produced in Hydraulic Machines and Solar Energy Laboratory (LMHES ) UFRN. The drier has been built at a cost of 3 to 5 times smaller than industrial dryers that operate with the same load of fruit. And the energy cost to produce dried fruits was more feasible compared with such dryers that use LPG as an energy source. However, the drying time was longer.

Protótipo de rastreador solar de um eixo baseado em microcontrolador

The increase in the efficiency of photo-voltaic systems has been the object of various studies the past few years. One possible way to increase the power extracted by a photovoltaic panel is the solar tracking, performing its movement in order to follow the sun’s path. One way to activate the tracking system is using an electric induction motor, which should have sufficient torque and low speed, ensuring tracking accuracy. With the use of voltage source inverters and logic devices that generate the appropriate switching is possible to obtain the torque and speed required for the system to operate. This paper proposes the implementation of a angular position sensor and a driver to be applied in solar tracker built at a Power Electronics and Renewable Energies Laboratory, located in UFRN. The speed variation of the motor is performed via a voltage source inverter whose PWM command to actuate their keys will be implemented in an FPGA (Field Programmable Gate Array) device and a TM4C microcontroller. A platform test with an AC induction machine of 1.5 CV was assembled for the comparative testing. The angular position sensor of the panel is implemented in a ATMega328 microcontroller coupled to an accelerometer, commanded by an Arduino prototyping board. The solar position is also calculated by the microcontroller from the geographic coordinates of the site where it was placed, and the local time and date obtained from an RTC (Real-Time Clock) device. A prototype of a solar tracker polar axis moved by a DC motor was assembled to certify the operation of the sensor and to check the tracking efficiency.

Visualización de datos de comunidades colaborativas

Las comunidades colaborativas, donde grandes cantidades de personas colaboran para la producción de recursos compartidos (e.g. Github, Wikipedia, OpenStreetMap, Arduino, StackOverflow) están extendiéndose progresivamente a multitud de campos. No obstante, es complicado comprender cómo funcionan y evolucionan. ¿Qué tipos de usuarios son más activos en Wikia? ¿Cómo ha evolucionado el número de wikis activas en los últimos años? ¿Qué perfil de actividad presentan la mayor parte de colaboradores de Wikia? ¿Son más activos los hombres o las mujeres en la Wikipedia? En los proyectos de Github, ¿el esfuerzo de programación (y frecuencia de commits) se distribuye de forma homogénea a lo largo del tiempo o suele estar concentrado? Estas comunidades, típicamente online, dejan registrada su actividad en grandes bases de datos, muchas de ellas disponibles públicamente. Sin embargo, el ciudadano de a pie no tiene ni las herramientas ni el conocimiento necesario para sacar conclusiones de esos datos. En este TFG desarrollamos una herramienta de análisis exploratorio y visualización de datos de la plataforma Wikia, sitio web colaborativo que permite la creación, edición y modificación del contenido y estructura de miles de páginas web de tipo enciclopedia basadas en la tecnología wiki. Nuestro objetivo es que esta aplicación web sea usable por cualquiera y que no requiera que el usuario sea un experto en Big Data para poder visualizar las gráficas de evolución o distribuciones del comportamiento interno de la comunidad, pudiendo modificar algunos de sus parámetros y visualizando cómo cambian. Como resultado de este trabajo se ha desarrollado una primera versión de la aplicación disponible en GitHub1 y en http://chartsup.esy.es/

An Efficient Route to N-Monosubstituted Guanidino-Lactams

Date of Acceptance: 05/06/2015

An Efficient Route to N-Monosubstituted Guanidino-Lactams

Date of Acceptance: 05/06/2015

An Efficient Route to N-Monosubstituted Guanidino-Lactams

Date of Acceptance: 05/06/2015

C-MEMS Based Micro Enzymatic Biofuel Cells

Miniaturized, self-sufficient bioelectronics powered by unconventional micropower may lead to a new generation of implantable, wireless, minimally invasive medical devices, such as pacemakers, defibrillators, drug-delivering pumps, sensor transmitters, and neurostimulators. Studies have shown that micro-enzymatic biofuel cells (EBFCs) are among the most intuitive candidates for in vivo micropower. In the fisrt part of this thesis, the prototype design of an EBFC chip, having 3D intedigitated microelectrode arrays was proposed to obtain an optimum design of 3D microelectrode arrays for carbon microelectromechanical systems (C-MEMS) based EBFCs. A detailed modeling solving partial differential equations (PDEs) by finite element techniques has been developed on the effect of 1) dimensions of microelectrodes, 2) spatial arrangement of 3D microelectrode arrays, 3) geometry of microelectrode on the EBFC performance based on COMSOL Multiphysics. In the second part of this thesis, in order to investigate the performance of an EBFC, behavior of an EBFC chip performance inside an artery has been studied. COMSOL Multiphysics software has also been applied to analyze mass transport for different orientations of an EBFC chip inside a blood artery. Two orientations: horizontal position (HP) and vertical position (VP) have been analyzed. The third part of this thesis has been focused on experimental work towards high performance EBFC. This work has integrated graphene/enzyme onto three-dimensional (3D) micropillar arrays in order to obtain efficient enzyme immobilization, enhanced enzyme loading and facilitate direct electron transfer. The developed 3D graphene/enzyme network based EBFC generated a maximum power density of 136.3 μWcm-2 at 0.59 V, which is almost 7 times of the maximum power density of the bare 3D carbon micropillar arrays based EBFC. To further improve the EBFC performance, reduced graphene oxide (rGO)/carbon nanotubes (CNTs) has been integrated onto 3D mciropillar arrays to further increase EBFC performance in the fourth part of this thesisThe developed rGO/CNTs based EBFC generated twice the maximum power density of rGO based EBFC. Through a comparison of experimental and theoretical results, the cell performance efficiency is noted to be 67%.

Endonuclease Controlled Aggregation of Gold Nanoparticles for the Ultrasensitive Detection of Pathogenic Bacterial DNA

The development of an ultrasensitive biosensor for the low-cost and on-site detection of pathogenic DNA could transform detection capabilities within food safety, environmental monitoring and clinical diagnosis. Herein, we present an innovative approach exploiting endonuclease-controlled aggregation of plasmonic gold nanoparticles (AuNPs) for label-free and ultrasensitive detection of bacterial DNA. The method utilizes RNA-functionalized AuNPs which form DNA-RNA heteroduplex structures through specific hybridization with target DNA. Once formed, the DNA-RNA heteroduplex is susceptible to RNAse H enzymatic cleavage of the RNA probe, allowing the target DNA to liberate and hybridize with another RNA probe. This continuously happens until all of the RNA probes are cleaved, leaving the nanoparticles unprotected and thus aggregated upon exposure to a high electrolytic medium. The assay is ultrasensitive, allowing the detection of target DNA at femtomolar level by simple spectroscopic analysis (40.7 fM and 2.45 fM as measured by UV-vis and dynamic light scattering (DLS), respectively). The target DNA spiked food matrix (chicken meat) is also successfully detected at a concentration of 1.2 pM (by UV-vis) or 18.0 fM (by DLS). In addition to the ultra-high sensitivity, the total analysis time of the assay is less than 3 hours, thus demonstrating its practicality for food analysis.

Study of Tsunami-Induced Fluid and Debris Load on Bridges using the Material Point Method

Thesis (Ph.D.)--University of Washington, 2016-08

Medição do transporte sólido por arrastamento através de sensores acústicos

A quantificação do material sólido transportado (transporte sólido) ao longo de um curso de água é extremamente importante nas mais variadas áreas da engenharia fluvial. O transporte sólido em rios de montanha dá-se maioritariamente por arrastamento no fundo, através de deslizamento, rolamento e saltação dos sedimentos. Ao longo dos tempos foram desenvolvidas várias fórmulas para estimar o transporte sólido por arrastamento, contudo, devido à complexidade dos processos de transporte de sedimentos, bem como a variabilidade espacial e temporal, a previsão de taxas de transporte não foi conseguida exclusivamente através de investigação teórica. Para obter um melhor conhecimento sobre os processos de transporte sólido por arrastamento em rios de montanha, torna-se necessário monitorizá-los com maior precisão possível. Com os avanços na electrónica, novos métodos tecnológicos foram desenvolvidos para resolver a problemática da quantificação do transporte sólido, em detrimento dos atuais métodos tradicionais, que se baseiam na recolha de amostras em campo, para posterior correlação. O objetivo principal da presente dissertação foi o desenvolvimento de um equipamento capaz de estimar/monitorizar continuamente o transporte sólido por arrastamento em rios de montanha, que utilizasse tecnologia de baixo custo. Este equipamento dispõe de um sensor piezolelétrico que realizará medições à vibração causada pelo embate dos sedimentos sobre uma chapa metálica. A energia do sinal resultante dos impactos reverterá em peso. A metodologia usada para a obtenção das medições foi a realização de ensaios laboratoriais, tendo sido dado especial destaque à influência da variação do caudal, bem como da forma dos sedimentos, na intensidade do sinal adquirido.

A Stationless Bikeshare Proof of Concept for College Campuses

Bikeshares promote healthy lifestyles and sustainability among commuters, casual riders, and tourists. However, the central pillar of modern systems, the bike station, cannot be easily integrated into a compact college campus. Fixed stations lack the flexibility to meet the needs of college students who make quick, short-distance trips. Additionally, the necessary cost of implementing and maintaining each station prohibits increasing the number of stations for user convenience. Therefore, the team developed a stationless bikeshare based on a smartlock permanently attached to bicycles in the system. The smartlock system design incorporates several innovative approaches to provide usability, security, and reliability that overcome the limitations of a station centered design. A focus group discussion allowed the team to receive feedback on the early lock, system, and website designs, identify improvements and craft a pleasant user experience. The team designed a unique, two-step lock system that is intuitive to operate while mitigating user error. To ensure security, user access is limited through near field ii communications (NFC) technology connected to a mechatronic release system. The said system relied on a NFC module and a servo working through an Arduino microcontroller coded in the Arduino IDE. To track rentals and maintain the system, each bike is fitted with an XBee module to communicate with a scalable ZigBee mesh network. The network allows for bidirectional, real-time communication with a Meteor.js web application, which enables user and administrator functions through an intuitive user interface available on mobile and desktop. The development of an independent smartlock to replace bike stations is essential to meet the needs of the modern college student. With the goal of creating a bikeshare that better serves college students, Team BIKES has laid the framework for a system that is affordable, easily adaptable, and implementable on any university expressing an interest in bringing a bikeshare to its campus.

Development of paper-based color test-strip for drug detection in aquatic environment: Application to oxytetracycline

The wide use of antibiotics in aquaculture has led to the emergence of resistant microbial species. It should be avoided/minimized by controlling the amount of drug employed in fish farming. For this purpose, the present work proposes test-strip papers aiming at the detection/semi-quantitative determination of organic drugs by visual comparison of color changes, in a similar analytical procedure to that of pH monitoring by universal pH paper. This is done by establishing suitable chemical changes upon cellulose, attributing the paper the ability to react with the organic drug and to produce a color change. Quantitative data is also enabled by taking a picture and applying a suitable mathematical treatment to the color coordinates given by the HSL system used by windows. As proof of concept, this approach was applied to oxytetracycline (OXY), one of the antibiotics frequently used in aquaculture. A bottom-up modification of paper was established, starting by the reaction of the glucose moieties on the paper with 3-triethoxysilylpropylamine (APTES). The so-formed amine layer allowed binding to a metal ion by coordination chemistry, while the metal ion reacted after with the drug to produce a colored compound. The most suitable metals to carry out such modification were selected by bulk studies, and the several stages of the paper modification were optimized to produce an intense color change against the concentration of the drug. The paper strips were applied to the analysis of spiked environmental water, allowing a quantitative determination for OXY concentrations as low as 30 ng/mL. In general, this work provided a simple, method to screen and discriminate tetracycline drugs, in aquaculture, being a promising tool for local, quick and cheap monitoring of drugs.