New dynamic microreactor system to mimic biofilm formation and test anti-biofilm activity of nanoparticles

Microbial bioflms are composed of surface-adhered microorganisms enclosed in extracellular polymeric substances. The bioflm lifestyle is the intrinsic drug resistance imparted to bacterial cells protected by the matrix. So far, conventional drug susceptibility tests for bioflm are reagent and time-consuming, and most of them are in static conditions. Rapid and easyto-use methods for bioflm formation and antibiotic activity testing need to be developed to accelerate the discovery of new antibioflm strategies. Herein, a Lab-On-Chip (LOC) device is presented that provides optimal microenvironmental conditions closely mimicking real-life clinical bioflm status. This new device allows homogeneous attachment and immobilization of Pseudomonas aeruginosa PA01-EGFP cells, and the bioflms grown can be monitored by fuorescence microscopy. P. aeruginosa is an opportunistic pathogen known as a model for drug screening bioflm studies. The infuence of fow rates on bioflms growth was analyzed by fow simulations using COMSOL® 5.2. Signifcant cell adhesion to the substrate and bioflm formation inside the microchannels were observed at higher fow rates>100 µL/h. After bioflm formation, the efectiveness of silver nanoparticles (SNP), chitosan nanoparticles (CNP), and a complex of chitosan-coated silver nanoparticles (CSNP) to eradicate the bioflm under a continuous fow was explored. The most signifcant loss of bioflm was seen with CSNP with a 65.5% decrease in average live/dead cell signal in bioflm compared to the negative controls. Our results demonstrate that this system is a user-friendly tool for antibioflm drug screening that could be simply applied in clinical laboratories.Fil: Bourguignon, Natalia. Universidad Tecnológica Nacional; Argentina. Florida International University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kamat, Vivek. Florida International University; Estados UnidosFil: Perez, Maximiliano. Universidad Tecnológica Nacional; Argentina. Florida International University; Estados UnidosFil: Mathee, Kalai. Florida International University; Estados UnidosFil: Lerner, Betiana. Universidad Tecnológica Nacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Florida International University; Estados UnidosFil: Bhansali, Shekhar. Florida International University; Estados Unido

Evaluation of cell culture in microfluidic chips for application in monoclonal antibody production

Microfluidic chips are useful devices for cell culture that allow cell growth under highly controlled conditions, as is required for production of therapeutic recombinant proteins. To understand the optimal conditions for growth of cells amenable of recombinant protein expression in these devices,we culturedHEK-293T cells under different microfluidic experimental conditions. The cells were cultured in polymethyl methacrylate (PMMA) and polydi-methylsiloxane (PDMS)microdevices, in the absence or presence of the cell adhesion agent poly-D-lysine. Different microchannel geometries and thicknesses, as well as the influence of the flow rate have also been tested, showing their great influence in cell adhesion and growth. Results show that the presence of poly-D-lysine improves the adhesion and viability of the cells in continuous or discontinuous flow. Moreover, the optimal adhesion of cells was observed in the corners of themicrochannels, as well as in wide channels possibly due to the decrease in the flow rate in these areas. These studies provide insight into the optimal architecture of microchannels for long-term culture of adherent cells in order to use microfluidics devices as bioreactors for monoclonal antibodies production.Fil: Peñaherrera Pazmiño, Ana Belén. Universidad Tecnológica Nacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Payés, Cristian. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Sierra Rodero, Marina. Universidad Tecnológica Nacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vega, M.. Universidad Tecnológica Nacional; ArgentinaFil: Rosero, G.. Universidad Tecnológica Nacional; Argentina. Universidad de Buenos Aires; ArgentinaFil: Lerner, Betiana. Universidad Tecnológica Nacional; Argentina. Universidad de Buenos Aires; ArgentinaFil: Helguera, Gustavo Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Pérez, M. S.. Universidad Tecnológica Nacional; Argentina. Universidad de Buenos Aires; Argentin

Dynamic Bayesian networks for integrating multi-omics time-series microbiome data

. A key challenge in the analysis of longitudinal microbiomes data is to go beyond computing their compositional profiles and infer the complex web of interactions between the various microbial taxa, their genes, and the metabolites they consume and produce. To address this challenge, we developed a computational pipeline that first aligns multi-omics data and then uses dynamic Bayesian networks (DBNs) to integrate them into a unified model. We discuss how our approach handles the different sampling and progression rates between individuals, how we reduce the large number of different entities and parameters in the DBNs, and the construction and use of a validation set to model edges. Applying our method to data collected from Inflammatory Bowel Disease (IBD) patients, we show that it can accurately identify known and novel interactions between various entities and can improve on current methods for learning such interactions. Experimental validations support several predictions about novel metabolite-taxa interactions. The source code is freely available under the MIT Open Source license agreement and can be downloaded from https://github.com/DaniRuizPerez/longitudinal_multiomic_analysis_public

Dynamic bayesian networks for integrating multi-omics time series microbiome data

A key challenge in the analysis of longitudinal microbiome data is theinference of temporal interactions between microbial taxa, their genes, the metabolites that they consume and produce, and host genes. To address these challenges,we developed a computational pipeline, a pipeline for the analysis of longitudinalmulti-omics data (PALM), that first aligns multi-omics data and then uses dynamicBayesian networks (DBNs) to reconstruct a unified model. Our approach overcomesdifferences in sampling and progression rates, utilizes a biologically inspired multiomic framework, reduces the large number of entities and parameters in the DBNs,and validates the learned network. Applying PALM to data collected from inflammatory bowel disease patients, we show that it accurately identifies known and novelinteractions. Targeted experimental validations further support a number of the predicted novel metabolite-taxon interactionsFil: Ruiz Perez, Daniel. Florida International University; Estados UnidosFil: Lugo Martinez, Jose. University of Carnegie Mellon; Estados UnidosFil: Bourguignon, Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Florida International University; Estados Unidos. Universidad Tecnológica Nacional; ArgentinaFil: Mathee, Kalai. Florida International University; Estados UnidosFil: Lerner, Betiana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Tecnológica Nacional; ArgentinaFil: Bar Joseph, Ziv. University of Carnegie Mellon; Estados UnidosFil: Narasimhan, Giri. Florida International University; Estados Unido

Dynamic bayesian networks for integrating multi-omics time series microbiome data

A key challenge in the analysis of longitudinal microbiome data is the inference of temporal interactions between microbial taxa, their genes, the metabolites that they consume and produce, and host genes. To address these challenges, we developed a computational pipeline, a pipeline for the analysis of longitudinal multi-omics data (PALM), that first aligns multi-omics data and then uses dynamic Bayesian networks (DBNs) to reconstruct a unified model. Our approach overcomes differences in sampling and progression rates, utilizes a biologically inspired multiomic framework, reduces the large number of entities and parameters in the DBNs, and validates the learned network. Applying PALM to data collected from inflammatory bowel disease patients, we show that it accurately identifies known and novel interactions. Targeted experimental validations further support a number of the predicted novel metabolite-taxon interactions

Simple Microcontact Printing Technique to Obtain Cell Patterns by Lithography Using Grayscale, Photopolymer Flexographic Mold, and PDMS

Microcontact printing using PDMS embossing tools and its variations have aroused the interest of a wide spectrum of research fields, hence the feasibility of defining micro and nanoscale patterns. In this work, we have proposed and demonstrated a novel lithography method based on grayscale patterns printed in a flexographic photopolymer mold and transferred to epoxy resin and a single PDMS stamp to obtain different microprint pattern structures. The geometry of the patterns can be modified by adjusting the layout and grayscale of the stamp patterns. The functionality of this contact printing methodology was validated by generating human induced pluripotent stem cells (hiPSC) patterns. These specific micropatterns can be very useful for achieving complex differentiation in cell lines such as hiPSC. Microfabrication through the new technique provides a promising alternative to conventional lithography for constructing complex aligned surfaces; these structures could be used as components of biological patterns or microfluidic devices.Fil: Gimenez, Rocio. Universidad Tecnológica Nacional; ArgentinaFil: Pérez Sosa, Camilo José. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Tecnológica Nacional; ArgentinaFil: Bourguignon, Natalia. Universidad Tecnológica Nacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Miriuka, Santiago Gabriel. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bhansali, Shekhar. University of Florida; Estados UnidosFil: Arroyo, Carlos R.. Universidad de Las Fuerzas Armadas; EcuadorFil: Debut, Alexis. Universidad de Las Fuerzas Armadas; EcuadorFil: Lerner, Betiana. Universidad Tecnológica Nacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Perez, Maximiliano Sebastian. Universidad Tecnológica Nacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

A microfluidic study to investigate the effect of magnetic iron core-carbon shell nanoparticles on displacement mechanisms of crude oil for chemical enhanced oil recovery

The main objective of this work is to evaluate the effect of the simultaneous use of a surfactant mixture and magnetic iron core-carbon shell nanoparticles on oil recovery via a microfluidic study based on the rock-on-a-chip technology. The surfactant solution used for all experiments was prepared based on a field formulation and consisted of a mixture of a hydrophilic and a lipophilic surfactant. Magnetic iron core-carbon shell nanoparticles with a mean particle size of 60 nm and a surface area of 123 m2 g−1 were employed. The displacement experiments consisted of waterflooding, surfactant flooding and nanoparticle-surfactant flooding and were performed using PDMS (polydimethylsiloxane)-glass microdevices type random network. The characteristics and design of the microfluidic device allowed to emulate a mixed wettability of a porous medium. Then, the oil was displaced by injecting the solution at a constant injection rate, until steady-state conditions were obtained. Furthermore, the effect of three injection rates corresponding to 0.1 ft day−1, 1 ft day−1, and 10 ft day−1 was investigated. The increase in the injection rate favored the oil recovery percentage. In addition, for all injection rates, the oil recovery decreased in the following order: nanoparticle-surfactant flooding > surfactant flooding > waterflooding. The nanoparticle-surfactant system at the injection rate of 1.9 μL min−1 presented the highest oil recovery (i.e., 84%). Likewise, nanoparticle-surfactant flooding showed a more stable displacement front and consequently, the highest capillary number among the injection fluids. Oil recovery by waterflooding was the lowest among the evaluated systems due to the viscous fingering phenomena under different injection rates. In addition, it can be observed that for all injection rates, the presence of the surfactant mixture and nanoparticles reduce the viscous fingering effect. The results can be used to visually and quantitatively analyze the role of the simultaneous use of nanoparticles with surfactants in enhanced oil recovery processes.Fil: Betancur, Stefanía. Universidad Nacional de Colombia. Sede Medellín; Colombia. Universidad de Granada; EspañaFil: Olmos Carreno, Carol Maritza. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Colombia. Sede Medellín; Colombia. Universidad Tecnológica Nacional. Facultad Regional Haedo; ArgentinaFil: Perez, Maximiliano Sebastian. Universidad Tecnológica Nacional. Facultad Regional Haedo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires; ArgentinaFil: Lerner, Betiana. Universidad Tecnológica Nacional. Facultad Regional Haedo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires; ArgentinaFil: Franco, Camilo A.. Universidad Nacional de Colombia. Sede Medellin; ColombiaFil: Riazi, Masoud. Shiraz University; IránFil: Gallego, Jaime. Universidad Nacional de Colombia. Sede Medellin; Colombia. Universidad de Antioquia; ColombiaFil: Carrasco Marín, Francisco. Universidad de Granada; EspañaFil: Cortés, Farid B.. Universidad Nacional de Colombia. Sede Medellin; Colombi

Effect of butanol and salt concentration on solid-state nanopores resistance

The objective of this study was to demonstrate the possibility of using 1-butanol to detect in a reliable way the open pore current of pyramidal solid-state nanopores produced in silicon wafers. The nanopores were produced through controlled pore formation by neutralizing an etchant (KOH) with a strong acid (HCl). Since nanopores produced by this method have a larger depth than those made in nanometer thick membranes, they behave as nanochannels. As a consequence, the open pore current detection is more challenging. Thus, we report that low amounts of butanol considerably aid in the detection of the open pore current of nanopores.Fil: Vega, M.. Universidad Tecnológica Nacional. Facultad Regional Haedo; ArgentinaFil: Perez, Maximiliano Sebastian. Universidad Tecnológica Nacional. Facultad Regional Haedo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Granell, Pablo Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Golmar, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Wloka, C.. University of Groningen; Países BajosFil: Maglia, G.. University of Groningen; Países BajosFil: Dieguez, M.J.. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Del Valle, E.M.. Universidad de Salamanca; EspañaFil: Lasorsa, Carlos Alberto. Universidad Tecnológica Nacional. Facultad Regional Haedo; ArgentinaFil: Lerner, Betiana. Universidad Tecnológica Nacional. Facultad Regional Haedo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Design and analysis of different models of microfluidic devices evaluated in enhanced oil recovery (EOR) assays

Microfluidic devices are a new platform for Enhanced Oil Recovery (EOR) assays. A successful oil recoveryin a reservoir can be different in another, hence the importance of a methodology for assessment prior toinjection. In the current study, micro and nanotechnology techniques were applied to develop EOR assays.The EOR chips simulated the phenomena occurred in micro-nano scale reservoirs. In general, the first step ofthe experiments corresponded to fill the microchannels with oil, then was injected water at constant flow rateuntil oil recovery ceases and finally was injected polymer or CDG. The recovery behaviors of the fluids werestudied by digital image analysis. Results allowed obtaining oil recovery for each evaluated fluid. Theoptimum configuration of the microchannels showed 80% of oil residual saturation after water injection.Keywords: EOR, poral volume, microgels and polymers, microfuidic devices.Fil: Rosero Yánez, Gustavo Ivan. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Tecnológica Nacional. Facultad Regional Haedo. Grupo de Ingeniería de Recubrimientos Especiales y Nanotecnología; ArgentinaFil: Peñaherrera Pazmiño, Ana Belén. Universidad Tecnológica Nacional. Facultad Regional Haedo. Grupo de Ingeniería de Recubrimientos Especiales y Nanotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Olmos Carreno, Carol Maritza. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Tecnológica Nacional. Facultad Regional Haedo. Grupo de Ingeniería de Recubrimientos Especiales y Nanotecnología; ArgentinaFil: Boschan, Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ingeniería; ArgentinaFil: Granell, Pablo Nicolás. Instituto Nacional de Tecnología Industrial; ArgentinaFil: Golmar, Federico. Instituto Nacional de Tecnología Industrial; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Lasorsa, Carlos Alberto. Universidad Tecnológica Nacional. Facultad Regional Haedo. Grupo de Ingeniería de Recubrimientos Especiales y Nanotecnología; ArgentinaFil: Lerner, Betiana. Universidad Tecnológica Nacional. Facultad Regional Haedo. Grupo de Ingeniería de Recubrimientos Especiales y Nanotecnología; Argentina. Universidad de Buenos Aires. Facultad de Ingeniería; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Perez, Maximiliano Sebastian. Universidad Tecnológica Nacional. Facultad Regional Haedo. Grupo de Ingeniería de Recubrimientos Especiales y Nanotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ingeniería; Argentin