Bacterial accumulation in intestinal folds induced by physical and biological factors.

BACKGROUND: The gut microbiota, vital for host health, influences metabolism, immune function, and development. Understanding the dynamic processes of bacterial accumulation within the gut is crucial, as it is closely related to immune responses, antibiotic resistance, and colorectal cancer. We investigated Escherichia coli behavior and distribution in zebrafish larval intestines, focusing on the gut microenvironment. RESULTS: We discovered that E. coli spread was considerably suppressed within the intestinal folds, leading to a strong physical accumulation in the folds. Moreover, a higher concentration of E. coli on the dorsal side than on the ventral side was observed. Our in vitro microfluidic experiments and theoretical analysis revealed that the overall distribution of E. coli in the intestines was established by a combination of physical factor and bacterial taxis. CONCLUSIONS: Our findings provide valuable insight into how the intestinal microenvironment affects bacterial motility and accumulation, enhancing our understanding of the behavioral and ecological dynamics of the intestinal microbiota.

Glucose stockpile in the intestinal apical brush border in C. elegans.

Revealing the mechanisms of glucose transport is crucial for studying pathological diseases caused by glucose toxicities. Numerous studies have revealed molecular functions involved in glucose transport in the nematode Caenorhabditis elegans, a commonly used model organism. However, the behavior of glucose in the intestinal lumen-to-cell remains elusive. To address that, we evaluated the diffusion coefficient of glucose in the intestinal apical brush border of C. elegans by using fluorescent glucose and fluorescence recovery after photobleaching. Fluorescent glucose taken in the intestine of worms accumulates in the apical brush border, and its diffusion coefficient of ∼10-8 cm2/s is two orders of magnitude slower than that in bulk. This result indicates that the intestinal brush border is a viscous layer. ERM-1 point mutations at the phosphorylation site, which shorten the microvilli length, did not significantly affect the diffusion coefficient of fluorescent glucose in the brush border. Our findings imply that glucose enrichment is dominantly maintained by the viscous layer composed of the glycocalyx and molecular complexes on the apical surface.

Cilia and centrosomes: Ultrastructural and mechanical perspectives.

Cilia and centrosomes of eukaryotic cells play important roles in cell movement, fluid transport, extracellular sensing, and chromosome division. The physiological functions of cilia and centrosomes are generated by their dynamics, motions, and forces controlled by the physical, chemical, and biological environments. How an individual cilium achieves its beat pattern and induces fluid flow is governed by its ultrastructure as well as the coordination of associated molecular motors. Thus, a bottom-up understanding of the physiological functions of cilia and centrosomes from the molecular to tissue levels is required. Correlations between the structure and motion can be understood in terms of mechanics. This review first focuses on cilia and centrosomes at the molecular level, introducing their ultrastructure. We then shift to the organelle level and introduce the kinematics and mechanics of cilia and centrosomes. Next, at the tissue level, we introduce nodal ciliary dynamics and nodal flow, which play crucial roles in the organogenetic process of left-right asymmetry. We also introduce respiratory ciliary dynamics and mucous flow, which are critical for protecting the epithelium from drying and exposure to harmful particles and viruses, i.e., respiratory clearance function. Finally, we discuss the future research directions in this field.

Swimming, Feeding, and Inversion of Multicellular Choanoflagellate Sheets.

The recent discovery of the striking sheetlike multicellular choanoflagellate species Choanoeca flexa that dynamically interconverts between two hemispherical forms of opposite orientation raises fundamental questions in cell and evolutionary biology, as choanoflagellates are the closest living relatives of animals. It similarly motivates questions in fluid and solid mechanics concerning the differential swimming speeds in the two states and the mechanism of curvature inversion triggered by changes in the geometry of microvilli emanating from each cell. Here we develop fluid dynamical and mechanical models to address these observations and show that they capture the main features of the swimming, feeding, and inversion of C. flexa colonies, which can be viewed as active, shape-shifting polymerized membranes.

Swimming microorganisms acquire optimal efficiency with multiple cilia.

Planktonic microorganisms are ubiquitous in water, and their population dynamics are essential for forecasting the behavior of global aquatic ecosystems. Their population dynamics are strongly affected by these organisms' motility, which is generated by their hair-like organelles, called cilia or flagella. However, because of the complexity of ciliary dynamics, the precise role of ciliary flow in microbial life remains unclear. Here, we have used ciliary hydrodynamics to show that ciliates acquire the optimal propulsion efficiency. We found that ciliary flow highly resists an organism's propulsion and that the swimming velocity rapidly decreases with body size, proportional to the power of minus two. Accordingly, the propulsion efficiency decreases as the cube of body length. By increasing the number of cilia, however, efficiency can be significantly improved, up to 100-fold. We found that there exists an optimal number density of cilia, which provides the maximum propulsion efficiency for all ciliates. The propulsion efficiency in this case decreases inversely proportionally to body length. Our estimated optimal density of cilia corresponds to those of actual microorganisms, including species of ciliates and microalgae, which suggests that now-existing motile ciliates and microalgae have survived by acquiring the optimal propulsion efficiency. These conclusions are helpful for better understanding the ecology of microorganisms, such as the energetic costs and benefits of multicellularity in Volvocaceae, as well as for the optimal design of artificial microswimmers.

Effectiveness of substantial shortening of the endotracheal tube for decreasing airway resistance and increasing tidal volume during pressure-controlled ventilation in pediatric patients: a prospective observational study.

The endotracheal tubes (ETTs) used for children have a smaller inner diameter. Accordingly, the resistance across ETT (RETT) is higher. Theoretically, shortening the ETTs can decrease total airway resistance (Rtotal), because Rtotal is sum of RETT and patient's airway resistance. However, the effectiveness of ETT shortening for mechanical ventilation in the clinical setting has not been reported. We assessed the effectiveness of shortening a cuffed ETT for decreasing Rtotal, and increasing tidal volume (TV), and estimated the RETT/Rtotal ratio in children. In anesthetized children in a constant pressure-controlled ventilation setting, Rtotal and TV were measured with a pneumotachometer before and after shortening a cuffed ETT. In a laboratory experiment, the pressure gradient across the original length, shortened length, and the slip joint alone of the ETT were measured. We then determined the RETT/Rtotal ratio using the above results. The clinical study included 22 children. The median ETT percent shortening was 21.7%. Median Rtotal was decreased from 26 to 24 cmH2O/L/s, and median TV was increased by 6% after ETT shortening. The laboratory experiment showed that ETT length and the pressure gradient across ETT are linearly related under a certain flow rate, and approximately 40% of the pressure gradient across the ETT at its original length was generated by the slip joint. Median RETT/Rtotal ratio were calculated as 0.69. The effectiveness of ETT shortening on Rtotal and TV was very limited, because the resistance of the slip joint was very large.

Influence of Respiratory Gas Density on Tidal Volume during Mechanical Ventilation: A Laboratory Investigation and Observational Study in Children.

Fluid mechanics show that high-density gases need more energy while flowing through a tube. Thus, high-density anesthetic gases consume more energy to flow and less energy for lung inflation during general anesthesia. However, its impact has not been studied. Therefore, this study aimed to investigate the effects of high-density anesthetic gases on tidal volume in laboratory and clinical settings. In the laboratory study, a test lung was ventilated at the same pressure-controlled ventilation with 22 different gas compositions (density range, 1.22-2.27 kg/m3) using an anesthesia machine. A pneumotachometer was used to record the tidal volume of the test lung and the respiratory gas composition; it showed that the tidal volume of the test lung decreased as the respiratory gas density increased. In the clinical study, the change in tidal volume per body weight, accompanied by gas composition change (2% sevoflurane in oxygen and with 0-30-60% of N2O), was recorded in 30 pediatric patients. The median tidal volume per body weight decreased by 10% when the respiratory gas density increased from 1.41 kg/m3 to 1.70 kg/m3, indicating a significant between-group difference (P < 0.0001). In both settings, an increase in respiratory gas density decreased the tidal volume during pressure-controlled ventilation, which could be explained by the fluid dynamics theory. This study clarified the detailed mechanism of high-density anesthetic gas reduced the tidal volume during mechanical ventilation and revealed that this phenomenon occurs during pediatric anesthesia, which facilitates further understanding of the mechanics of ventilation during anesthesia practice and respiratory physiology.

Microbial Brazil nut effect.

The Brazil nut effect (BNE) is a counter-intuitive process of segregation of a large object inside a vibrated granular medium (GM), which has been studied widely by subjecting GMs to various kinds of shears and vibrations. In this article, we report a new kind of BNE which occurs as a consequence of granular fluctuations induced by microbe-generated gas bubbles. We call it the 'microbial Brazil nut effect'. The paper demonstrates microbial BNE for a bidisperse granular mixture as well as for intruder segregation. Furthermore, using X-ray µCT and a simple scaling argument for segregation velocity, the paper clarifies the transport mechanics of an intruder inside a bubbly granular bed. We think the reported phenomenon should be ubiquitous in the microbe-populated wet sandy floors of waterbodies and may have some implication on the distribution of material near the floors.

Simple mechanosense and response of cilia motion reveal the intrinsic habits of ciliates.

An important habit of ciliates, namely, their behavioral preference for walls, is revealed through experiments and hydrodynamic simulations. A simple mechanical response of individual ciliary beating (i.e., the beating is stalled by the cilium contacting a wall) can solely determine the sliding motion of the ciliate along the wall and result in a wall-preferring behavior. Considering ciliate ethology, this mechanosensing system is likely an advantage in the single cell's ability to locate nutrition. In other words, ciliates can skillfully use both the sliding motion to feed on a surface and the traveling motion in bulk water to locate new surfaces according to the single "swimming" mission.

Mechanical roles of anterograde and retrograde intestinal peristalses after feeding in a larval fish (Danio rerio).

Transport in gut is important, not only for digestion, metabolism, and nutrient uptake, but also for microbiotic circumstance in the digestive tract; however, the effects of mixing and pumping in the intestine have not been fully clarified. Therefore, in this study, we quantitatively explored intestinal mixing and pumping, represented using a dispersion coefficient and pressure rise in zebrafish larvae, which is a model organism for vertebrate digestive studies, over time by measuring transport phenomena after feeding. Here we provide the first quantitative evidence of the roles of anterograde and retrograde intestinal peristalses in the larval fish of Danio rerio after feeding in terms of digestive pumping and mixing functions by an in vivo imaging of intestinal propagation waves in the larval intestine. Peristaltic velocities in the anterior and posterior intestines change considerably after feeding for 5 h, while the intervals and amplitudes remain almost constant. The intestinal transport is successively visualized after feeding to elimination. Moreover, the particle tracking velocimetry in the chyme leads our quantitative understanding of outstanding mixing and pumping functions in the anterior and posterior intestines by adopting physical parameters of diffusivity and pressure rise, respectively. From scaling analysis, we found that the anterior intestine maintains mixing for 5 h from feeding, whereas the posterior intestine activates gradually pumping up. These results suggest that time change of pumping and mixing functions of intestinal peristalsis could considerably influence the nutrient uptake and microbiotic circumstance in the larval fish intestine.NEW & NOTEWORTHY Transport in gut is important, not only for digestion, metabolism, and nutrient uptake, but also for microbiotic circumstance; however, hydrodynamic effects in the intestine have not been fully clarified. We provide the first quantitative evidence of the mechanical roles of anterograde and retrograde intestinal peristalses in the larval fish of Danio rerio by adopting physical parameters of diffusivity and pressure rise. The intestine transitionally regulates mixing and pumping functions by peristaltic propagations after feeding.

How do Caenorhabditis elegans worms survive in highly viscous habitats?

The nematode Caenorhabditis elegans is a filter feeder that lives in various viscous habitats such as soil, the intestines of slugs, and rotting materials such as fruits and stems. Caenorhabditis elegans draws in suspensions of bacteria and separates bacteria from water using the pharyngeal pump. Although these worms often live in highly viscous habitats, it is still unclear how they survive in these environments by eating bacteria. In this study, we investigated the effects of suspension viscosity on the survival rate of malnourished worms by combining live imaging and scaling analyses. We found that survival rate decreased with increases in viscosity because the high viscosity suppressed the amount of food ingested. The same tendency was found in two feeding-defective mutants, eat-6(ad467) and eat-6(ad997). We also found that the high viscosity weakened pump function, but the velocities in the pharynx were not zero, even in the most viscous suspensions. Finally, we estimated the amount of ingested food using scaling analyses, which provided a master curve of the experimental survival rates. These results illustrate that the survival rate of C. elegans worms is strongly dependent on the ingested bacteria per unit time associated with physical environments, such as the viscosity of food suspensions and the cell density of bacteria. The pump function of the C. elegans pharynx is not completely lost even in fluids that have 105 times higher viscosity than water, which may contribute to their ability to survive around the world in highly viscous environments.

The shape effect of flagella is more important than bottom-heaviness on passive gravitactic orientation in Chlamydomonas reinhardtii.

The way the unicellular, biflagellated, green alga Chlamydomonas orients upward has long been discussed in terms of both mechanics and physiology. In this study, we focus on the mechanics, i.e. the 'passive' mechanisms, of gravitaxis. To rotate the body upwards, cellular asymmetry is critical. Chlamydomonas can be depicted as a nearly spherical cell body with two anterior, symmetric flagella. The present study looks at the question of whether the existence of the flagella significantly affects torque generation in upward reorientation. The 'density asymmetry model' assumes that the cell is spherical and bottom-heavy and that the shape and weight of the flagella are negligible, while the 'shape asymmetry model' considers the shape of the flagella. Both our experimental and simulation results revealed a considerable contribution from shape asymmetry to the upward orientation of Chlamydomonas reinhardtii, which was several times larger than that of density asymmetry. From the experimental results, we also quantified the extent of bottom-heaviness, i.e. the distance between the centers of gravity and the figure when the cell body is assumed to be spherical. Our estimation was approximately 30 nm, only one-third of previous assumptions. These findings indicate the importance of the viscous drag of the flagella to the upward orientation, and thus negative gravitaxis, in Chlamydomonas.

Shear-Induced Migration of a Transmembrane Protein within a Vesicle.

Biomembranes feature phospholipid bilayers and serve as the interface between cells or organelles and the extracellular and/or cellular environment. Lipids can move freely throughout the membrane; the lipid bilayer behaves like a fluid. Such fluidity is important in terms of the actions of membrane transport proteins, which often mediate biological functions; membrane protein motion has attracted a great deal of attention. Because the proteins are small, diffusion phenomena are often in play, but flow-induced transport has rarely been addressed. Here, we used a dissipative particle dynamics approach to investigate flow-induced membrane protein transport. We analyzed the drift of a membrane protein located within a vesicle. Under the influence of shear flow, the protein gradually migrated toward the vorticity axis via a random walk, and the probability of retention around the axis was high. To understand the mechanism of protein migration, we varied both shear strength and protein size. Protein migration was induced by the balance between the drag and thermodynamic diffusion forces and could be represented by the Péclet number. These results improve our understanding of flow-induced membrane protein transport.

Biomechanics of Tetrahymena escaping from a dead end.

Understanding the behaviours of swimming microorganisms in various environments is important for understanding cell distribution and growth in nature and industry. However, cell behaviour in complex geometries is largely unknown. In this study, we used Tetrahymena thermophila as a model microorganism and experimentally investigated cell behaviour between two flat plates with a small angle. In this configuration, the geometry provided a 'dead end' line where the two flat plates made contact. The results showed that cells tended to escape from the dead end line more by hydrodynamics than by a biological reaction. In the case of hydrodynamic escape, the cell trajectories were symmetric as they swam to and from the dead end line. Near the dead end line, T. thermophila cells were compressed between the two flat plates while cilia kept beating with reduced frequency; those cells again showed symmetric trajectories, although the swimming velocity decreased. These behaviours were well reproduced by our computational model based on biomechanics. The mechanism of hydrodynamic escape can be understood in terms of the torque balance induced by lubrication flow. We therefore conclude that a cell's escape from the dead end was assisted by hydrodynamics. These findings pave the way for understanding cell behaviour and distribution in complex geometries.

What causes the spatial heterogeneity of bacterial flora in the intestine of zebrafish larvae?

Microbial flora in the intestine has been thoroughly investigated, as it plays an important role in the health of the host. Jemielita et al. (2014) showed experimentally that Aeromonas bacteria in the intestine of zebrafish larvae have a heterogeneous spatial distribution. Although bacterial aggregation is important biologically and clinically, there is no mathematical model describing the phenomenon and its mechanism remains largely unknown. In this study, we developed a computational model to describe the heterogeneous distribution of bacteria in the intestine of zebrafish larvae. The results showed that biological taxis could cause the bacterial aggregation. Intestinal peristalsis had the effect of reducing bacterial aggregation through mixing function. Using a scaling argument, we showed that the taxis velocity of bacteria must be larger than the sum of the diffusive velocity and background bulk flow velocity to induce bacterial aggregation. Our model and findings will be useful to further the scientific understanding of intestinal microbial flora.

Shear-induced platelet aggregation and distribution of thrombogenesis at stenotic vessels.

OBJECTIVE: SIPA, which is mediated by vWF, is a key mechanism in arterial thrombosis under an abnormally high shear rate of blood flow. We investigated the influence of SIPA on thrombogenesis, focusing on alterations in blood flow at stenotic vessels. METHODS: We carried out a computer simulation of thrombogenesis in stenotic vessels at three different injury positions (ie, upstream, apex, and downstream of the stenosis) to evaluate the effect of SIPA. RESULTS: The results demonstrated that thrombus volume increased downstream of the stenosis. In particular, growth was enhanced significantly as blood flow velocity and severity of stenosis increased. The influence of SIPA was induced by continuous exposure to high shear rate; thus, SIPA had a greater effect from the apex to downstream of the stenosis along the vessel wall. The asymmetry of the impact of SIPA contributed to the distribution of the thrombus. Furthermore, we found that the degree of SIPA was prolonged in a stenotic vessel with a distal injury, whereas it was moderate with thrombus growth in a nonstenosed vessel. This occurred because platelets and vWF that underwent a high shear rate around the apex were transported to the region downstream of the stenosis. CONCLUSIONS: These results suggest that thrombus formation downstream of the stenosis is easily affected by SIPA and hemodynamics.

Mixing and pumping functions of the intestine of zebrafish larvae.

Due to its transparency, the intestine of zebrafish larvae has been widely used in studies of gastrointestinal diseases and the microbial flora of the gut. However, transport phenomena in the intestine of zebrafish larvae have not been fully clarified. In this study, therefore, transport caused by peristaltic motion in the intestine of zebrafish larvae was investigated by numerical simulation. An anatomically realistic three-dimensional geometric model of the intestine at various times after feeding was constructed based on the experimental data of Field et al. (2009). The flow of digested chyme was analyzed using the governing equations of fluid mechanics, together with peristaltic motion and long-term contraction of the intestinal wall. The results showed that retrograde peristaltic motion was the main contributor to the mixing function. The dispersion caused by peristalsis over 30min was in the order of 10-12m2/s, which is greater than the Brownian diffusion of a sphere of 0.4µm diameter. In contrast, anterograde peristaltic motion contributed mainly to the pumping function. The pressure decrease due to peristalsis was in the order of millipascals, which may reduce the activation and maintenance heat of intestinal muscle. These findings enhance our understanding of the mixing and pumping functions of the intestine of zebrafish larvae.

Relationship between gastric motility and liquid mixing in the stomach.

The relationship between gastric motility and the mixing of liquid food in the stomach was investigated with a numerical analysis. Three parameters of gastric motility were considered: the propagation velocity, frequency, and terminal acceleration of peristaltic contractions. We simulated gastric flow with an anatomically realistic geometric model of the stomach, considering free surface flow and moving boundaries. When a peristaltic contraction approaches the pylorus, retropulsive flow is generated in the antrum. Flow separation then occurs behind the contraction. The extent of flow separation depends on the Reynolds number (Re), which quantifies the inertial forces due to the peristaltic contractions relative to the viscous forces of the gastric contents; no separation is observed at low Re, while an increase in reattachment length is observed at high Re. While mixing efficiency is nearly constant for low Re, it increases with Re for high Re because of flow separation. Hence, the effect of the propagation velocity, frequency, or terminal acceleration of peristaltic contractions on mixing efficiency increases with Re.

Cell adhesion during bullet motion in capillaries.

A numerical analysis is presented of cell adhesion in capillaries whose diameter is comparable to or smaller than that of the cell. In contrast to a large number of previous efforts on leukocyte and tumor cell rolling, much is still unknown about cell motion in capillaries. The solid and fluid mechanics of a cell in flow was coupled with a slip bond model of ligand-receptor interactions. When the size of a capillary was reduced, the cell always transitioned to "bullet-like" motion, with a consequent decrease in the velocity of the cell. A state diagram was obtained for various values of capillary diameter and receptor density. We found that bullet motion enables firm adhesion of a cell to the capillary wall even for a weak ligand-receptor binding. We also quantified effects of various parameters, including the dissociation rate constant, the spring constant, and the reactive compliance on the characteristics of cell motion. Our results suggest that even under the interaction between P-selectin glycoprotein ligand-1 (PSGL-1) and P-selectin, which is mainly responsible for leukocyte rolling, a cell is able to show firm adhesion in a small capillary. These findings may help in understanding such phenomena as leukocyte plugging and cancer metastasis.