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

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

Metronomic doses and drug schematic combination response tested within chambered coverslips for the treatment of breast cancer cells (JIMT-1)

Low-dose metronomic (LDM) chemotherapy is an alternative to conventional chemotherapy and is the most frequently used approach in low dose chemotherapy regimens. The selection of patients, drug dosages, and dosing intervals in LDM is empirical. In this study, we systematically examined the schedule-dependent interaction of drugs on a breast cancer cell line (BCC) cultured in chambered coverslips. The LDM studies were combined with cell staining in order to better characterize different cell states and cell death modes, including caspase-dependent apoptosis, caspase-independent cell death and autophagy-dependent cell death. Microscope images were examined using the Fiji Trainable Weka Segmentation plugin to analyse cell area in 7500 images showing different modes of cell death. Paclitaxel combined with LDM chemotherapy demonstrated a reduction in the area covered by live cells. In contrast, there was an induction of high levels of cell death due to caspase-dependent apoptosis.Fil: Rosero, Gustavo. Universidad Tecnológica Nacional; Argentina. Albert Ludwigs University of Freiburg; AlemaniaFil: Pattarone, Gisela. Albert Ludwigs University of Freiburg; AlemaniaFil: Peñaherrera Pazmiño, Ana Belén. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Tecnológica Nacional; Argentina. Albert Ludwigs University of Freiburg; AlemaniaFil: Pilz, Julia. Albert Ludwigs University of Freiburg; AlemaniaFil: Bödecker, Joschka. Albert Ludwigs University of Freiburg; AlemaniaFil: Perez, Maximiliano Sebastian. Universidad de Buenos Aires; Argentina. Universidad Tecnológica Nacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Mertelsmann, Roland. Albert Ludwigs University of Freiburg; AlemaniaFil: Lerner, Betiana. Universidad de Buenos Aires; Argentina. Universidad Tecnológica Nacional; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Follo, Marie. Universidad de Buenos Aires; Argentin

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

The effect of crop sequences on soil microbial, chemical and physical indicators and its relationship with soybean sudden death syndrome (complex of Fusarium species)

The effect of crop sequences on soil quality indicators and its relationship with sudden death syndrome (SDS, a complex of Fusarium species) was evaluated by physical, chemical, biochemical and molecular techniques. Regarding physical aspects, soybean/maize and maize monoculture exhibited the highest stable aggregate level, with values 41% and 43% higher than in soybean monoculture, respectively, and 133% higher than in bean monoculture. Bulk density (BD) was higher in soybean monoculture, being 4% higher than in bean monoculture. The chemical parameters organic matter, total N, P, K, Mg, Ca, and water holding capacity also indicated that soybean/maize and maize monoculture improved soil quality. Fungal and bacterial community fingerprints generated using Terminal Restriction Fragment Length Polymorphism analysis of intergenic transcribed spacer regions of rRNA genes and 16S rRNA genes, respectively, indicated a clear separation between the rotations. Fatty acid profiles evaluated by FAME showed that bean monoculture had higher biomass of Gram (+) bacteria and stress indicators than maize monoculture, while the soybean/maize system showed a significant increase in total microbial biomass (total FAMEs content) in comparison with soybean and bean monoculture. The incidence of SDS (Fusarium crassistipitatum) was markedly higher (15%) under soybean monoculture than when soybean was grown in rotation with maize. In the present work, soil microbial properties were improved under soybean/maize relative to continuous soybean. The improvement of soil health was one of the main causes for the reduction of disease pressure and crop yield improvement due to the benefits that crop rotation produces for soil quality.EEA SaltaFil: Perez Brandan, Carolina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Salta; ArgentinaFil: Arzeno, Jose Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Salta; ArgentinaFil: Huidobro, Dina Jorgelina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Salta; ArgentinaFil: Conforto, Erica Cinthia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Grumberg, Betiana Clarisa. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Hilton, Sally. University of Warwick. School of Life Sciences; Reino UnidoFil: Bending, Gary D. University of Warwick. School of Life Sciences; Reino UnidoFil: Meriles, Jose Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Vargas Gil, Silvina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentin