Manipulation of Microscale Fluid Using Laser-Irradiated Nanoparticle Arrays

The manipulation of microscale fluid has been widely used in biology, medicine, and chemistry. However, the traditional control systems are relatively large, complex, and costly. Optical driving micro- and nanofluid is a new trend of microfluidics, which combines the advantages of both optics and microfluidics in the micro-nano scale. In the present work, we investigated a method to drive microfluid by taking advantage of the localized surface plasmon resonance effect of gold nanoparticles, which can convert optical energy to fluid motion. First, numerical simulation was carried out to calculate the electromagnetic, temperature, and flow field around laser-irradiated gold nanoparticles. Then, the simplified heat source condition was verified. The nanoparticle array was regarded as heat source to induce convection flow. The influence of the spacing and number of nanoparticles in array was investigated. On this basis, the structural parameters of nanoparticle array that can be used to regulate the velocity of microfluidic were obtained.

     

A Model of Peritubular Capillary Control of Isotonic Fluid Reabsorption by the Renal Proximal Tubule

A mathematical model of peritubular transcapillary fluid exchange has been developed to investigate the role of the peritubular environment in the regulation of net isotonic fluid transport across the mammalian renal proximal tubule. The model, derived from conservation of mass and the Starling transcapillary driving forces, has been used to examine the quantitative effects on proximal reabsorption of changes in efferent arteriolar protein concentration and plasma flow rate. Under normal physiological conditions, relatively small perturbations in protein concentration are predicted to influence reabsorption more than even large variations in plasma flow, a prediction in close accord with recent experimental observations in the rat and dog. Changes either in protein concentration or plasma flow have their most pronounced effects when the opposing transcapillary hydrostatic and osmotic pressure differences are closest to equilibrium. Comparison of these theoretical results with variations in reabsorption observed in micropuncture studies makes it possible to place upper and lower bounds on the difference between interstitial oncotic and hydrostatic pressures in the renal cortex of the rat.     

Fluid Dynamics of Ventricular Filling in the Embryonic Heart

The vertebrate embryonic heart first forms as a valveless tube that pumps blood using waves of contraction. As the heart develops, the atrium and ventricle bulge out from the heart tube, and valves begin to form through the expansion of the endocardial cushions. As a result of changes in geometry, conduction velocities, and material properties of the heart wall, the fluid dynamics and resulting spatial patterns of shear stress and transmural pressure change dramatically. Recent work suggests that these transitions are significant because fluid forces acting on the cardiac walls, as well as the activity of myocardial cells that drive the flow, are necessary for correct chamber and valve morphogenesis. In this article, computational fluid dynamics was used to explore how spatial distributions of the normal forces acting on the heart wall change as the endocardial cushions grow and as the cardiac wall increases in stiffness. The immersed boundary method was used to simulate the fluid-moving boundary problem of the cardiac wall driving the motion of the blood in a simplified model of a two-dimensional heart. The normal forces acting on the heart walls increased during the period of one atrial contraction because inertial forces are negligible and the ventricular walls must be stretched during filling. Furthermore, the force required to fill the ventricle increased as the stiffness of the ventricular wall was increased. Increased endocardial cushion height also drastically increased the force necessary to contract the ventricle. Finally, flow in the moving boundary model was compared to flow through immobile rigid chambers, and the forces acting normal to the walls were substantially different.     

Spatial Ecology of Bacteria at the Microscale in Soil

Despite an exceptional number of bacterial cells and species in soils, bacterial diversity seems to have little effect on soil processes, such as respiration or nitrification, that can be affected by interactions between bacterial cells. The aim of this study is to understand how bacterial cells are distributed in soil to better understand the scaling between cell-to-cell interactions and what can be measured in a few milligrams, or more, of soil. Based on the analysis of 744 images of observed bacterial distributions in soil thin sections taken at different depths, we found that the inter-cell distance was, on average 12.46 µm and that these inter-cell distances were shorter near the soil surface (10.38 µm) than at depth (>18 µm), due to changes in cell densities. These images were also used to develop a spatial statistical model, based on Log Gaussian Cox Processes, to analyse the 2D distribution of cells and construct realistic 3D bacterial distributions. Our analyses suggest that despite the very high number of cells and species in soil, bacteria only interact with a few other individuals. For example, at bacterial densities commonly found in bulk soil (10⁸ cells g⁻¹ soil), the number of neighbours a single bacterium has within an interaction distance of ca. 20 µm is relatively limited (120 cells on average). Making conservative assumptions about the distribution of species, we show that such neighbourhoods contain less than 100 species. This value did not change appreciably as a function of the overall diversity in soil, suggesting that the diversity of soil bacterial communities may be species-saturated. All in all, this work provides precise data on bacterial distributions, a novel way to model them at the micrometer scale as well as some new insights on the degree of interactions between individual bacterial cells in soils.     

Fabrication and Visualization of Capillary Bridges in Slit Pore Geometry

A procedure for creating and imaging capillary bridges in slit-pore geometry is presented. High aspect ratio hydrophobic pillars are fabricated and functionalized to render their top surfaces hydrophilic. The combination of a physical feature (the pillar) with a chemical boundary (the hydrophilic film on the top of the pillar) provides both a physical and chemical heterogeneity that pins the triple contact line, a necessary feature to create stable long but narrow capillary bridges. The substrates with the pillars are attached to glass slides and secured into custom holders. The holders are then mounted onto four axis microstages and positioned such that the pillars are parallel and facing each other. The capillary bridges are formed by introducing a fluid in the gap between the two substrates once the separation between the facing pillars has been reduced to a few hundred micrometers. The custom microstage is then employed to vary the height of the capillary bridge. A CCD camera is positioned to image either the length or the width of the capillary bridge to characterize the morphology of the fluid interface. Pillars with widths down to 250 µm and lengths up to 70 mm were fabricated with this method, leading to capillary bridges with aspect ratios (length/width) of over 100¹.     

Virio- and Bacterioplankton Microscale Distributions at the Sediment-Water Interface

The marine sediment-water interface is an important location for microbially controlled nutrient and gas exchange processes. While microbial distributions on the sediment side of the interface are well established in many locations, the distributions of microbes on the water side of the interface are less well known. Here, we measured that distribution for marine virio- and bacterioplankton with a new two-dimensional technique. Our results revealed higher heterogeneity in sediment-water interface biomass distributions than previously reported with a greater than 45– and 2500-fold change cm⁻¹ found within bacterial and viral subpopulations compared to previous maxima of 1.5- and 1.4-fold cm⁻¹ in bacteria and viruses in the same environments. The 45-fold and 2500-fold changes were due to patches of elevated and patches of reduced viral and bacterial abundance. The bacterial and viral hotspots were found over single and multiple sample points and the two groups often coincided whilst the coldspots only occurred over single sample points and the bacterial and viral abundances showed no correlation. The total mean abundances of viruses strongly correlated with bacteria (r = 0.90, p<0.0001, n = 12) for all three microplates (n = 1350). Spatial autocorrelation analysis via Moran’s I and Geary’s C revealed non-random distributions in bacterial subpopulations and random distributions in viral subpopulations. The variable distributions of viral and bacterial abundance over centimetre-scale distances suggest that competition and the likelihood of viral infection are higher in the small volumes important for individual cell encounters than bulk measurements indicate. We conclude that large scale measurements are not an accurate measurement of the conditions under which microbial dynamics exist. The high variability we report indicates that few microbes experience the ‘average’ concentrations that are frequently measured.     

Bioprocess Control in Microscale: Scalable Fermentations in Disposable and User-Friendly Microfluidic Systems

Background  

The efficiency of biotechnological production processes depends on selecting the best performing microbial strain and the optimal cultivation conditions. Thus, many experiments have to be conducted, which conflicts with the demand to speed up drug development processes. Consequently, there is a great need for high-throughput devices that allow rapid and reliable bioprocess development. This need is addressed, for example, by the fiber-optic online-monitoring system BioLector which utilizes the wells of shaken microtiter plates (MTPs) as small-scale fermenters. To further improve the application of MTPs as microbioreactors, in this paper, the BioLector technology is combined with microfluidic bioprocess control in MTPs. To realize a user-friendly system for routine laboratory work, disposable microfluidic MTPs are utilized which are actuated by a user-friendly pneumatic hardware.     

Potential for Microscale Bacterial Fe Redox Cycling at the Aerobic-Anaerobic Interface

Recent studies of bacterial Fe(II) oxidation at circumneutral pH by a newly-isolated lithotrophic β-Proteobacterium (strain TW2) are reviewed in relation to a conceptual model that accounts for the influence of biogenic Fe(III)-binding ligands on patterns of Fe(II) oxidation and Fe(III) oxide deposition in opposing gradients of Fe(II) and O₂. The conceptual model envisions complexation of Fe(III) by biogenic ligands as mechanism which alters the locus of Fe(III) oxide deposition relative to Fe(II) oxidation so as to delay/retard cell encrustation with Fe(III) oxides. Experiments examining the potential for bacterial Fe redox cycling in microcosms containing ferrihydrite-coated sand and a coculture of a lithotrophic Fe(II)-oxidizing bacterium (strain TW2) and a dissimilatory Fe(III)-reducing bacterium (Shewanella algae strain BrY) are described and interpreted in relation to an extended version of the conceptual model in which Fe(III)-binding ligands promote rapid microscale Fe redox cycling. The coculture systems showed minimal Fe(III) oxide accumulation at the sand-water interface, despite intensive O₂ input from the atmosphere and measurable dissolved O₂ to a depth of 2 mm below the sand-water interface. In contrast, a distinct layer of oxide precipitates formed in systems containing Fe(III)-reducing bacteria alone. Voltammetric microelectrode measurements revealed much lower concentrations of dissolved Fe(II) in the coculture systems. Examination of materials from the cocultures by fluorescence in situ hybridization indicated close physical juxtapositioning of Fe(II)-oxidizing and Fe(III)reducing bacteria in the upper few mm of sand. Together these results indicate that Fe(II)-oxidizing bacteria have the potential to enhance the coupling of Fe(II) oxidation and Fe(III) reduction at redox interfaces, thereby promoting rapid microscale cycling of Fe.     

Design of Strain-Sensing Devices in Microscale by Using Surface Plasmon Polaritons

We have presented a strain-sensing device in microscale by using surface plasmon polaritons and multimode interference effects. The device is numerically investigated by the finite-difference time-domain method. Optimum depths and length of the structure are designed for sensing a strain. The size of the designed structure is several micrometers and is about a thousandth compared with a fiber Bragg grating strain sensor. The sensitivity of the designed structure is 11.34 pm/μ?? that is about ten times larger than that of a fiber Bragg grating strain sensor. The temperature sensitivity of the designed structure is 34.43 pm/ ^°C. This temperature sensitivity is three times larger than that of a fiber Bragg grating strain sensor. Therefore, temperature compensation techniques are needed for the structure. The presented structure has a simple design such as a plasmonic waveguide with a trench structure. The simple structural design device has a capability of being used in micro- and nano-electromechanical systems.     

Oligonucleotides Quality Control Analysis in Free Solution by Capillary Electrophoresis at Acidic pH

Abstract

A new method for fast, automated and inexpensive oligonucleotides analysis by capillary electrophoresis at low pH is presented. This method does not need any sieving media to resolve a mixture of polynucleotides which are analysed in free solution and separated on the base of composition and not length. This technique has been used to test a large set of standard and modified oligonucleotides thus to be applied in oligos routine quality control.     

Social Interactions and Distribution of Bacillus subtilis Pherotypes at Microscale

Bacillus subtilis strains communicate through the comQXPA quorum sensing (QS) system, which regulates genes expressed during early stationary phase. A high polymorphism of comQXP′ loci was found in closely related strains isolated from desert soil samples separated by distances ranging from meters to kilometers. The observed polymorphism comprised four communication groups (pherotypes), such that strains belonging to the same pherotype exchanged information efficiently but strains from different pherotypes failed to communicate. To determine whether the same level of polymorphism in the comQXP′ QS system could be detected at microscale, B. subtilis isolates were obtained from two separate 1-cm³ soil samples, which were progressively divided into smaller sections. Cross-activation studies using pherotype-responsive reporter strains indicated the same number of communication pherotypes at microscale as previously determined at macroscale. Sequencing of the housekeeping gene gyrA and the QS comQ gene confirmed different evolutionary rates of these genes. Furthermore, an asymmetric communication response was detected inside the two pherotype clusters, suggesting continuous evolution of the QS system and possible development of new languages. To our knowledge, this is the first microscale study demonstrating the presence of different QS languages among isolates of one species, and the implications of this microscale diversity for microbial interactions are discussed.Quorum sensing (QS), a widespread phenomenon in the bacterial world, controls a wide range of cell density-dependent behaviors. Bacillus subtilis uses QS to control production of antimicrobial peptides, bacteriocins, and antibiotics (20) but also to alternate between two cell types during stationary phase: competent cells, able to take in DNA from the environment, and dormant spores, able to survive harsh environmental conditions (9, 12, 24). Development of genetic competence in B. subtilis is controlled by a QS system encoded by the comQXPA operon (2, 53, 54). This involves the ComX pheromone that accumulates during exponential growth (25, 46, 47) and is initially synthesized as a 55-residue protein that is processed, modified, and released into the extracellular medium as a 5- to 10-amino-acid peptide. The isoprenoidal modification on the tryptophan residue of this peptide is catalyzed by the ComQ protein (2, 25, 34, 35, 42, 52). Upon reaching the threshold concentration, processed and modified ComX binds to the membrane-associated, histidine protein kinase ComP and triggers the QS response, linking autophosphorylation of ComP and transfer of phosphate to the response regulator ComA (59). The level of phosphorylated ComA is also controlled by dephosphorylation, which is dependent on a separate QS system involving competence sporulation factor (CSF) and the RapC phosphatase (3, 59). Phosphorylated ComA directly controls expression of various genes (6, 33), including the srfAB operon that contains the comS gene (15, 41), required for development of competence (55).Previous studies of environmental B. subtilis strains indicate a high polymorphism (approximately 56% identity at the nucleotide level) in the QS locus, which is restricted to comQ, comX, and the N-terminal region of the comP gene. Sequences surrounding this locus, downstream gene comA, a C-terminal region of comP, and the upstream degQ gene, are highly conserved (2, 53, 54). Sequence analysis of the comQXP loci of 13 strains indicated clustering into four distinct similarity groups (2). These groups were congruent for comQ, comX, and the N-terminal region of comP, indicating coevolution of the three genes. In addition, the similarity groups correlated with four pherotypes, able to communicate efficiently within but not between groups. Similar variation has been reported for the agr QS system in staphylococci (19, 56) and in the competence QS system of Streptococcus pneumoniae (17, 19, 37, 38, 60).B. subtilis is often referred to as a soil-dwelling organism, its spores persisting in soil until encountering conditions suitable for germination and growth (10). The basic structural unit of soil ecosystems is the soil aggregate, in which biogeochemical processes occur at scales relevant to microorganisms. Approximately 50% of the volume of a soil aggregate represents open pores, while the remainder consists of mineral particles (sand, silt, and clay) held together by organic material (48), with which B. subtilis may be preferentially associated (16, 43). Soil aggregates can be classified as macroaggregates (diameter, >250 μm) and microaggregates (diameter, 2 to 250 μm) (39), but little is known about the distribution of bacteria within aggregates. Structural organization of the soil creates a mosaic of microenvironments, within which water movement and diffusion of nutrients and other molecules play key roles in functioning of the soil microbiota (7, 13, 39). These roles may vary with the scale at which they operate. Tisdall and Oades (51) suggest that scales at which microorganisms are important in the soil aggregation process range between 2 and 2,000 μm, depending on the specific system being investigated (13). Although the microscale distribution of microorganisms and their associated functions have rarely been studied, it is becoming recognized that greater knowledge of spatial organization at the scale of a soil aggregate (microscale) is essential for a better understanding of soil ecosystem function and of the mechanisms that generate and maintain diversity, including speciation, extinction, dispersal, and interactions within and between species (7, 13, 26).The aim of this study was to assess the potential role of QS in generating and maintaining microscale diversity within the soil. This was achieved by determining the genomic and functional diversification of the B. subtilis QS system with regard to geographical distance and ecological characteristics. Isolates were obtained from two 1-cm³ sandy, riverbank soil samples separated by approximately 5 m, allowing assessment of macroscale diversity. In addition, each riverbank soil sample was treated as a separate macroaggregate that was progressively sectioned to obtain subsamples of different sizes, allowing assessment of microscale diversity. The riverbank soil B. subtilis isolates were compared with Bacillus isolates previously obtained from desert soil samples separated by distances of meters to kilometers (2, 40), representing macroscale distribution. The Bacillus isolates were used to (i) correlate geographical distance (microscale/macroscale) with genomic distance of the QS comQ gene and the housekeeping gyrA gene, (ii) investigate and compare the specificity of the QS response of microscale and macroscale isolates, and (iii) explore dominance of pherotypes inside soil aggregates. To our knowledge, this is the first investigation of a QS system that addresses the genomic and functional diversification of bacterial populations at microscale.     

Broadband Mid-infrared Dual-Band Double-Negative Metamaterial: Realized Using a Simple Geometry

We design and numerically demonstrate a novel metamaterial structure consisting of a dielectric layer sandwiched between two silver films and is perforated with two kinds of square-shaped holes at different angles, which is a dual-band double-negative (each band possesses simultaneously negative permittivity and permeability) metamaterial with broad NRI bands in mid-infrared region(3–30 μm). The broadband of NRI contributed to the strong magnetic resonance caused by the excitation of surface plasmon polaritons. The influence of the number of square-shaped holes on the properties of the designed structures are also investigated by analyzing and comparing the transmission, permeability, permittivity, refractive index, and figure of merit. Then, by optimizing the structural parameters, the proposed structure exhibits a negative band with a figure of merit of 3.3, which is to our knowledge larger than previously reported plasmonic metamaterial in mid-infrared region(M-IR). The value of negative refractive index(NRI) reaches −6 and the bandwidth of NRI can reach up to 4.2 THz in the low-frequency band of M-IR region, which is the widest NRI band in M-IR spectrum at present as far as we know. Moreover, the metamaterial structure is simple and easy to be manufactured with standard fabrication techniques. This work will be very meaningful in designing dual-band negative-index material with broad NRI band and low loss. Finally, the proposed metamaterial has huge potential applications in multiband or broadband devices.