Understanding the flow behavior around marine biofilms.

In vitro platforms capable of mimicking the hydrodynamic conditions prevailing in natural aquatic environments have been previously validated and used to predict the fouling behavior on different surfaces. Computational Fluid Dynamics (CFD) has been used to predict the shear forces occurring in these platforms. In general, these predictions are made for the initial stages of biofilm formation, where the amount of biofilm does not affect the flow behavior, enabling the estimation of the shear forces that initial adhering organisms have to withstand. In this work, we go a step further in understanding the flow behavior when a mature biofilm is present in such platforms to better understand the shear rate distribution affecting marine biofilms. Using 3D images obtained by Optical Coherence Tomography, a mesh was produced and used in CFD simulations. Biofilms of two different marine cyanobacteria were developed in agitated microtiter plates incubated at two different shaking frequencies for 7 weeks. The biofilm-flow interactions were characterized in terms of the velocity field and shear rate distribution. Results show that global hydrodynamics imposed by the different shaking frequencies affect biofilm architecture and also that this architecture affects local hydrodynamics, causing a large heterogeneity in the shear rate field. Biofilm cells located in the streamers of the biofilm are subjected to much higher shear values than those located on the bottom of the streamers and this dispersion in shear rate values increases at lower bulk fluid velocities. This heterogeneity in the shear force field may be a contributing factor for the heterogeneous behavior in metabolic activity, growth status, gene expression pattern, and antibiotic resistance often associated with nutrient availability within the biofilm.

Viscous Microcapsules as Microbioreactors to Study Mesenchymal Stem/Stromal Cells Osteolineage Commitment.

It is essential to design a multifunctional well-controlled platform to transfer mechanical cues to the cells in different magnitudes. This study introduces a platform, a miniaturized bioreactor, which enables to study the effect of shear stress in microsized compartmentalized structures. In this system, the well-established cell encapsulation system of liquefied capsules (LCs) is used as microbioreactors in which the encapsulated cells are exposed to variable core viscosities to experience different mechanical forces under a 3D dynamic culture. The LC technology is joined with electrospraying to produce such microbioreactors at high rates, thus allowing the application of microcapsules for high-throughput screening. Using this platform for osteogenic differentiation as an example, shows that microbioreactors with higher core viscosity which produce higher shear stress lead to significantly higher osteogenic characteristics. Moreover, in this system the forces experienced by cells in each LC are simulated by computational modeling. The maximum wall shear stress applied to the cells inside the bioreactor with low, and high core viscosity environment is estimated to be 297 and 1367 mPa, respectively, for the experimental setup employed. This work outlines the potential of LC microbioreactors as a reliable in vitro customizable platform with a wide range of applications.

Microfluidics combined with fluorescence in situ hybridization (FISH) for Candida spp. detection.

One of the most prevalent healthcare-associated infection is the urinary tract infection (UTI), caused by opportunistic pathogens such as Candida albicans or non-albicans Candida species (NACS). Urine culture methods are routinely used for UTI diagnostics due to their specificity, sensitivity and low-cost. However, these methods are also laborious, time- and reagent-consuming. Therefore, diagnostic methods relying on nucleic acids have been suggested as alternatives. Nucleic acid-based methods can provide results within 24 h and can be adapted to point-of-care (POC) detection. Here, we propose to combine fluorescence in situ hybridization (FISH) with a microfluidic platform for the detection of Candida spp. As a case study we used C. tropicalis, which is reported as the second most common NACS urine isolate obtained from patients suspected with UTI. The microfluidic platform proposed in this study relies on hydrodynamic trapping, and uses physical barriers (e.g., microposts) for the separation of target cells from the suspension. Using a specific peptide nucleic acid (PNA) probe, the FISH procedure was applied onto previously trapped C. tropicalis cells present inside the microfluidic platform. Fluorescence signal intensity of hybridized cells was captured directly under the epifluorescence microscope. Overall, the PNA probe successfully detected C. tropicalis in pure culture and artificial urine (AU) using FISH combined with the microfluidic platform. Our findings reveal that FISH using nucleic acid mimics (PNA) in combination with microfluidics is a reliable method for the detection of microorganisms such as C. tropicalis. As such, this work provides the basis for the development of a POC detection platform in the future.

Red blood cells tracking and cell-free layer formation in a microchannel with hyperbolic contraction: A CFD model validation.

BACKGROUND AND OBJECTIVE: In recent years, progress in microfabrication technologies has attracted the attention of researchers across disciplines. Microfluidic devices have the potential to be developed into powerful tools that can elucidate the biophysical behavior of blood flow in microvessels. Such devices can also be used to separate the suspended physiological fluid from whole in vitro blood, which includes cells. Therefore, it is essential to acquire a detailed description of the complex interaction between erythrocytes (red blood cells; RBCs) and plasma. RBCs tend to undergo axial migration caused by occurrence of the Fåhræus-Lindqvist effect. These dynamics result in a cell-free layer (CFL), or a low volume fraction of cells, near the vessel wall. The aim of the paper is to develop a numerical model capable of reproducing the behavior of multiphase flow in a microchannel obtained under laboratory conditions and to compare two multiphase modelling techniques Euler-Euler and Euler-Lagrange. METHODS: In this work, we employed a numerical Computational Fluid Dynamics (CFD) model of the blood flow within microchannels with two hyperbolic contraction shapes. The simulation was used to reproduce the blood flow behavior in a microchannel under laboratory conditions, where the CFL formation is visible downstream of the hyperbolic contraction. The multiphase numerical model was developed using Euler-Euler and hybrid Euler-Lagrange approaches. The hybrid CFD simulation of the RBC transport model was performed using a Discrete Phase Model. Blood was assumed to be a nonhomogeneous mixture of two components: dextran, whose properties are consistent with plasma, and RBCs, at a hematocrit of 5% (percent by volume of RBCs). RESULTS: The results show a 5 µm thick CFL in a microchannel with a broader contraction and a 35 µm thick CFL in a microchannel with a narrower contraction. The RBC volume fraction in the CFL is less than 2%, compared to 7-8% in the core flow. The results are consistent for both multiphase simulation techniques used. The simulation results were then validated against the experimentally-measured CFL in each of the studied microchannel geometries. CONCLUSIONS: Reasonable agreement between experiments and simulations was achieved. A validated model such as the one tested in this study can expedite the microchannel design process by minimizing the need to prefabricate prototypes and test them under laboratory conditions.

Predictive Models of Dairy Cow Thermal State: A Review from a Technological Perspective.

Dairy cattle are particularly sensitive to heat stress due to the higher metabolic rate needed for milk production. In recent decades, global warming and the increase in dairy production in warmer countries have stimulated the development of a wide range of environmental control systems for dairy farms. Despite their proven effectiveness, the associated energy and water consumption can compromise the viability of dairy farms in many regions, due to the cost and scarcity of these resources. To make these systems more efficient, they should be activated in time to prevent thermal stress and switched off when that risk no longer exists, which must consider environmental variables as well as the variables of the animals themselves. Nowadays, there is a wide range of sensors and equipment that support farm routine procedures, and it is possible to measure several variables that, with the aid of algorithms based on predictive models, would allow anticipating animals' thermal states. This review summarizes three types of approaches as predictive models: bioclimatic indexes, machine learning, and mechanistic models. It also focuses on the application of the current knowledge as algorithms to be used in the management of diverse types of environmental control systems.

Underwater Energy Harvesting to Extend Operation Time of Submersible Sensors.

A linear electromagnetic energy harvesting device for underwater applications, fabricated with a simple manufacturing process, was developed to operate with movement frequencies from 0.1 to 0.4 Hz. The generator has two coils, and the effect of the combination of the two coils was investigated. The experimental study has shown that the energy capture system was able to supply energy to several ocean sensors, producing 7.77 mJ per second with wave movements at 0.4 Hz. This study shows that this energy is enough to restore the energy used by the battery or the capacitor and continue supplying energy to the sensors used in the experimental work. For an ocean wave frequency of 0.4 Hz, the generator can supply power to 8 sensors or 48 sensors, depending on the energy consumed and its optimization.

Integration of FISH and Microfluidics.

Suitable molecular methods for a faster microbial identification in food and clinical samples have been explored and optimized during the last decades. However, most molecular methods still rely on time-consuming enrichment steps prior to detection, so that the microbial load can be increased and reach the detection limit of the techniques.In this chapter, we describe an integrated methodology that combines a microfluidic (lab-on-a-chip) platform, designed to concentrate cell suspensions and speed up the identification process in Saccharomyces cerevisiae , and a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) protocol optimized and adapted to microfluidics. Microfluidic devices with different geometries were designed, based on computational fluid dynamics simulations, and subsequently fabricated in polydimethylsiloxane by soft lithography. The microfluidic designs and PNA-FISH procedure described here are easily adaptable for the detection of other microorganisms of similar size.

Bubbles Moving in Blood Flow in a Microchannel Network: The Effect on the Local Hematocrit.

Air inside of blood vessels is a phenomenon known as gas embolism. During the past years, studies have been performed to assess the influence of air bubbles in microcirculation. In this study, we investigated the flow of bubbles in a microchannel network with several bifurcations, mimicking part of a capillary system. Thus, two working fluids were used, composed by sheep red blood cells (RBCs) suspended in a Dextran 40 solution with different hematocrits (5% and 10%). The experiments were carried out in a polydimethylsiloxane (PDMS) microchannel network fabricated by a soft lithography. A high-speed video microscopy system was used to obtain the results for a blood flow rate of 10 µL/min. This system enables the visualization of bubble formation and flow along the network. The results showed that the passage of air bubbles strongly influences the cell's local concentration, since a higher concentration of cells was observed upstream of the bubble, whereas a lower local hematocrit was visualized at the region downstream of the bubble. In bifurcations, bubbles may split asymmetrically, leading to an uneven distribution of RBCs between the outflow branches.

Review on Microbubbles and Microdroplets Flowing through Microfluidic Geometrical Elements.

Two-phase flows are found in several industrial systems/applications, including boilers and condensers, which are used in power generation or refrigeration, steam generators, oil/gas extraction wells and refineries, flame stabilizers, safety valves, among many others. The structure of these flows is complex, and it is largely governed by the extent of interphase interactions. In the last two decades, due to a large development of microfabrication technologies, many microstructured devices involving several elements (constrictions, contractions, expansions, obstacles, or T-junctions) have been designed and manufactured. The pursuit for innovation in two-phase flows in these elements require an understanding and control of the behaviour of bubble/droplet flow. The need to systematize the most relevant studies that involve these issues constitutes the motivation for this review. In the present work, literature addressing gas-liquid and liquid-liquid flows, with Newtonian and non-Newtonian fluids, and covering theoretical, experimental, and numerical approaches, is reviewed. Particular focus is given to the deformation, coalescence, and breakup mechanisms when bubbles and droplets pass through the aforementioned microfluidic elements.

Biofilm formation behaviour of marine filamentous cyanobacterial strains in controlled hydrodynamic conditions.

Marine biofouling has severe economic impacts and cyanobacteria play a significant role as early surface colonizers. Despite this fact, cyanobacterial biofilm formation studies in controlled hydrodynamic conditions are scarce. In this work, computational fluid dynamics was used to determine the shear rate field on coupons that were placed inside the wells of agitated 12-well microtiter plates. Biofilm formation by three different cyanobacterial strains was assessed at two different shear rates (4 and 40 s-1 ) which can be found in natural ecosystems and using different surfaces (glass and perspex). Biofilm formation was higher under low shear conditions, and differences obtained between surfaces were not always statistically significant. The hydrodynamic effect was more noticeable during the biofilm maturation phase rather than during initial cell adhesion and optical coherence tomography showed that different shear rates can affect biofilm architecture. This study is particularly relevant given the cosmopolitan distribution of these cyanobacterial strains and the biofouling potential of these organisms.

Blood Cells Separation and Sorting Techniques of Passive Microfluidic Devices: From Fabrication to Applications.

Since the first microfluidic device was developed more than three decades ago, microfluidics is seen as a technology that exhibits unique features to provide a significant change in the way that modern biology is performed. Blood and blood cells are recognized as important biomarkers of many diseases. Taken advantage of microfluidics assets, changes on blood cell physicochemical properties can be used for fast and accurate clinical diagnosis. In this review, an overview of the microfabrication techniques is given, especially for biomedical applications, as well as a synopsis of some design considerations regarding microfluidic devices. The blood cells separation and sorting techniques were also reviewed, highlighting the main achievements and breakthroughs in the last decades.

Geometrical effects in the hemodynamics of stenotic and non-stenotic left coronary arteries-numerical and in vitro approaches.

Atherosclerosis is a common cardiovascular disease found in the left coronary artery (LCA), closely linked to local hemodynamic, which, in turn, is highly influenced by the artery geometry. The hemodynamics in the LCA was studied in a patient-specific geometry without any sign of disease using both numerical and in vitro approaches. The influence of non-planarity was evaluated through two models of the patient-specific LCA that deviate from its original geometry in their planarity. Afterwards, in all models, irregular stenoses were created by a procedure in which the stenosis emerges by diffusion from low wall shear stress (WSS) areas. The WSS distribution and flow patterns were evaluated in all the models. The experimental results validate the numerical code developed to study the blood flow assuming a steady state Newtonian behavior. Comparison between the planar and non-planar idealized LCA revealed no significant differences in low WSS regions forming stenotic regions with identical shape. In the patient-specific LCA, the low WSS regions are not consistent with the idealized models leading to a different stenosis shape. The results revealed that the non-planarity has an unquestionable effect in helicity. It was also demonstrated that eccentricity of the vessels cross section and the position of the apex in relation to the axis of the parent branch contribute to the flow patterns observed. Numerical results of pulsatile blood flow assuming a non-Newtonian behavior, in the patient-specific LCA, reinforce the non-planarity effect in local hemodynamics.

Deformation of Red Blood Cells, Air Bubbles, and Droplets in Microfluidic Devices: Flow Visualizations and Measurements.

Techniques, such as micropipette aspiration and optical tweezers, are widely used to measure cell mechanical properties, but are generally labor-intensive and time-consuming, typically involving a difficult process of manipulation. In the past two decades, a large number of microfluidic devices have been developed due to the advantages they offer over other techniques, including transparency for direct optical access, lower cost, reduced space and labor, precise control, and easy manipulation of a small volume of blood samples. This review presents recent advances in the development of microfluidic devices to evaluate the mechanical response of individual red blood cells (RBCs) and microbubbles flowing in constriction microchannels. Visualizations and measurements of the deformation of RBCs flowing through hyperbolic, smooth, and sudden-contraction microchannels were evaluated and compared. In particular, we show the potential of using hyperbolic-shaped microchannels to precisely control and assess small changes in RBC deformability in both physiological and pathological situations. Moreover, deformations of air microbubbles and droplets flowing through a microfluidic constriction were also compared with RBCs deformability.

Yeasts identification in microfluidic devices using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH).

Peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) is a highly specific molecular method widely used for microbial identification. Nonetheless, and due to the detection limit of this technique, a time-consuming pre-enrichment step is typically required before identification. In here we have developed a lab-on-a-chip device to concentrate cell suspensions and speed up the identification process in yeasts. The PNA-FISH protocol was optimized to target Saccharomyces cerevisiae, a common yeast that is very relevant for several types of food industries. Then, several coin-sized microfluidic devices with different geometries were developed. Using Computational fluid dynamics (CFD), we modeled the hydrodynamics inside the microchannels and selected the most promising options. SU-8 structures were fabricated based on the selected designs and used to produce polydimethylsiloxane-based microchips by soft lithography. As a result, an integrated approach combining microfluidics and PNA-FISH for the rapid identification of S. cerevisiae was achieved. To improve fluid flow inside microchannels and the PNA-FISH labeling, oxygen plasma treatment was applied to the microfluidic devices and a new methodology to introduce the cell suspension and solutions into the microchannels was devised. A strong PNA-FISH signal was observed in cells trapped inside the microchannels, proving that the proposed methodology works as intended. The microfluidic designs and PNA-FISH procedure described in here should be easily adaptable for detection of other microorganisms of similar size.

Microbubble moving in blood flow in microchannels: effect on the cell-free layer and cell local concentration.

Gas embolisms can hinder blood flow and lead to occlusion of the vessels and ischemia. Bubbles in microvessels circulate as tubular bubbles (Taylor bubbles) and can be trapped, blocking the normal flow of blood. To understand how Taylor bubbles flow in microcirculation, in particular, how bubbles disturb the blood flow at the scale of blood cells, experiments were performed in microchannels at a low Capillary number. Bubbles moving with a stream of in vitro blood were filmed with the help of a high-speed camera. Cell-free layers (CFLs) were observed downstream of the bubble, near the microchannel walls and along the centerline, and their thicknesses were quantified. Upstream to the bubble, the cell concentration is higher and CFLs are less clear. While just upstream of the bubble the maximum RBC concentration happens at positions closest to the wall, downstream the maximum is in an intermediate region between the centerline and the wall. Bubbles within microchannels promote complex spatio-temporal variations of the CFL thickness along the microchannel with significant relevance for local rheology and transport processes. The phenomenon is explained by the flow pattern characteristic of low Capillary number flows. Spatio-temporal variations of blood rheology may have an important role in bubble trapping and dislodging.

A numerical and experimental study of acoustic micromixing in 3D microchannels for lab-on-a-chip devices.

This paper reports a numerical and experimental study of acoustic streaming and micromixing in polydimethylsiloxane microchannels. The mixing between two fluids flowing in microchannels was evaluated through the following conditions: (1) using a 28 µm thick ß-poly(vinylidene fluoride) (ß-PVDF) as a piezoelectric transducer actuated with a 24 Vpp and 40 MHz sinusoidal voltage; (2) using different flow rates. The results suggest that the mixing length increases as the flow rate increases and that the acoustic streaming phenomenon leads to a reduction on the mixing length. The good qualitative agreement between numerical and experimental results is a valuable indicator to predict the mixing performance of microfluidic devices, for improving biological fluid analysis in diagnosis lab-on-a-chip devices.

Morcegos (Mammalia: Chiroptera) da região do Médio Rio Teles Pires, Sul da Amazônia, Brasil / Bats (Mammalia: Chiroptera) from the Middle Teles Pires River region, Southern Amazonia, Brazil

Amazonia is the largest tropical rainforest in the world and at least 147 bat species occur in this environment. Despite its richness, the diversity of bat fauna is poorly known for this region and there are large gaps in its knowledge. This study aims to describe the bat assemblage of the Middle Teles Pires River (MTP) region, southern Amazonia. Furthermore, we evaluated the similarity of this assemblage in relation to 14 assemblages studied in other Amazonian localities, and correlations were found between the similarity values among the sites and their geographic distances. Thirty-three bat species were recorded, accounting for 71% of the estimated species richness (Jackknife2). The three species that had the higher relative abundance values were Carollia perspicillata, Pteronotus parnellii and Phyllostomus hastatus, which together accounted for more than 50% of the captures. The frugivore functional group had the highest number of recorded species. A negative correlation was found between the geographic distances and the similarities among the Amazonian bat assemblages (r = -0.22; p = 0.014). Geographic distance could explain only 6% of the similarities among the analyzed assemblages, even though, the similarity found allowed them to be grouped by their distances. Besides, the MTP bat fauna is different from other Amazonian areas, which gives it a special role in the Amazonian bat conservation.

A Amazônia é a maior floresta tropical do mundo e pelo menos 147 espécies de morcegos ocorrem neste ambiente. A despeito desta grande riqueza, a diversidade de morcegos da Amazônia é pobremente conhecida e existem grandes lacunas neste conhecimento. O objetivo do presente trabalho foi descrever a assembleia de morcegos ocorrentes na região do Médio Teles Pires (MTP), no sul da Amazônia. Além disso, avaliou-se a similaridade dessa assembleia em relação a 14 assembleias estudadas em outras localidades amazônicas e avaliou-se a correlação entre as similaridades destas localidades e suas distâncias. Trinta e três espécies de morcegos foram registradas, representando 71% das espécies estimadas (Jackknife2). As três espécies com maior abundância relativa foram:Carollia perspicillata, Pteronotus parnellii e Phyllostomus hastatus que somadas contam com mais de 50% das capturas. O grupo funcional dos frugívoros obteve o maior número de espécies capturadas. Foi encontrada uma correlação negativa entre as distâncias e as similaridades das assembleias de morcegos amazônicos (r = -0,22; p = 0,014). A distância geográfica pode explicar apenas 6% da similaridade entre as assembleias analisadas, ainda assim, as similaridades destas assembleias permitem que as mesmas sejam agrupadas por suas distâncias geográficas. Além disso, a fauna de morcegos do MTP é diferenciada de outras áreas da Amazônia o que lhe confere um papel especial na conservação dos morcegos amazônicos.

Sympatry between Alouatta caraya and Alouatta clamitans and the rediscovery of free-ranging potential hybrids in Southern Brazil.

Records of sympatry between Alouatta caraya and A. clamitans are rare despite their extensive range overlap. An example of their current sympatry and the rediscovery of free-ranging potential hybrids of A. caraya and A. clamitans in the forests of the Upper Paraná River, Southern Brazil, are reported in this paper. Eight groups were observed in the study area: five monospecific groups of A. caraya, two of A. clamitans, and a group containing two adult males and two adult females of A. caraya and a sub-adult male and two adult females identified as Alouatta sp. The color of the last three individuals was a mosaic between the two species; this is consistent with previously described variations in museum specimens collected in the Paraná River in the 1940s that had been identified as potential hybrids. The results from this study emphasize the need for scientific studies in the region of the Ilha Grande National Park, one of the few regions in the Paraná River that currently harbors both howler species.