Myosin II-Mediated Focal Adhesion Maturation Is Tension Insensitive

Myosin II motors drive changes in focal adhesion morphology and composition in a “maturation process” that is crucial for regulating adhesion dynamics and signaling guiding cell adhesion, migration and fate. The underlying mechanisms of maturation, however, have been obscured by the intermingled effects of myosin II on lamellar actin architecture, dynamics and force transmission. Here, we show that focal adhesion growth rate stays constant even when cellular tension is reduced by 75%. Focal adhesion growth halts only when myosin stresses are sufficiently low to impair actin retrograde flow. Focal adhesion lifetime is reduced at low levels of cellular tension, but adhesion stability can be rescued at low levels of force by over-expression of α-actinin or constitutively active Dia1. Our work identifies a minimal myosin activity threshold that is necessary to drive lamellar actin retrograde flow is sufficient to permit focal adhesion elongation. Above this nominal threshold, myosin-mediated actin organization and dynamics regulate focal adhesion growth and stability in a force-insensitive fashion.     

Hydrodynamics and cell volume oscillations in the pollen tube apical region are integral components of the biomechanics of Nicotiana tabacum pollen tube growth

Pollen tube growth is localized at the apex and displays oscillatory dynamics. It is thought that a balance between intracellular turgor pressure (hydrostatic pressure, reflected by the cell volume) and cell wall loosening is a critical factor driving pollen tube growth. We previously demonstrated that water flows freely into and out of the pollen tube apical region dependent on the extracellular osmotic potential, that cell volume changes reflect changes in the intracellular pressure, and that cell volume changes differentially induce, increases or decreases in specific phospholipid signals. This article shows that manipulation of the extracellular osmotic potential rapidly induces modulations in pollen tube growth rate frequencies, demonstrating that changes in the intracellular pressure are sufficient to reset the pollen tube growth oscillator. This indicates a direct link between intracellular hydrostatic pressure and pollen tube growth. Altering hydrodynamic flow through the pollen tube by replacing extracellular H₂O with ²H₂O adversely affects both cell volume and growth rate oscillations and induces aberrant morphologies. Normal growth and cell morphology are rescued by replacing ²H₂O with H₂O. Further studies revealed that the cell volume oscillates in the pollen tube apical region. These cell volume oscillations were not from changes in cell shape at the tip and were detectable up to 30 μm distal to the tip (the longest length measured). Cell volume in the apical region oscillates with the same frequency as growth rate oscillations but surprisingly the cycles are phase-shifted by 180°. Raman microscopy yields evidence that hydrodynamic flow out of the apex may be part of the biomechanics that drive cellular expansion. The combined results suggest that hydrodynamic loading/unloading in the apical region induces cell volume oscillations and has a role in driving cell elongation and pollen tube growth.     

Mechanistic basis of otolith formation during teleost inner ear development

Otoliths, which are connected to stereociliary bundles in the inner ear, serve as inertial sensors for balance. In teleostei, otolith development is critically dependent on flow forces generated by beating cilia; however, the mechanism by which flow controls otolith formation remains unclear. Here, we have developed a noninvasive flow probe using optical tweezers and a viscous flow model in order to demonstrate how the observed hydrodynamics influence otolith assembly. We show that rotational flow stirs and suppresses precursor agglomeration in the core of the cilia-driven vortex. The velocity field correlates with the shape of the otolith and we provide evidence that hydrodynamics is actively involved in controlling otolith morphogenesis. An implication of this hydrodynamic effect is that otolith self-assembly is mediated by the balance between Brownian motion and cilia-driven flow. More generally, this flow feature highlights an alternative biological strategy for controlling particle localization in solution.     

Mesoscale Modeling of Amphiphilic Fluid Dynamics

Abstract

So-called “vector models”, in which surfactant molecules retain only translational and orientational degrees of freedom, have been used to study the equilibrium properties of amphiphilic fluids for nearly a decade now. We demonstrate that hydrodynamic lattice-gas automata provide an effective means of coupling the Hamiltonian of such vector models to hydrodynamic flow with conserved momentum, thereby providing a self-consistent treatment of the hydrodynamics of amphiphilic fluids. In this “talk”, we describe these hydrodynamic lattice-gas models in two and three dimensions, and present their application to problems of amphiphilic-fluid hydrodynamics, including the dynamics of phase separation and the shear-induced sponge-to-lamellar phase transition.     

A Computational Study of the Hydrodynamics in the Nasal Region of a Hammerhead Shark (Sphyrna tudes): Implications for Olfaction

The hammerhead shark possesses a unique head morphology that is thought to facilitate enhanced olfactory performance. The olfactory chambers, located at the distal ends of the cephalofoil, contain numerous lamellae that increase the surface area for olfaction. Functionally, for the shark to detect chemical stimuli, water-borne odors must reach the olfactory sensory epithelium that lines these lamellae. Thus, odorant transport from the aquatic environment to the sensory epithelium is the first critical step in olfaction. Here we investigate the hydrodynamics of olfaction in Sphyrna tudes based on an anatomically-accurate reconstruction of the head and olfactory chamber from high-resolution micro-CT and MRI scans of a cadaver specimen. Computational fluid dynamics simulations of water flow in the reconstructed model reveal the external and internal hydrodynamics of olfaction during swimming. Computed external flow patterns elucidate the occurrence of flow phenomena that result in high and low pressures at the incurrent and excurrent nostrils, respectively, which induces flow through the olfactory chamber. The major (prenarial) nasal groove along the cephalofoil is shown to facilitate sampling of a large spatial extent (i.e., an extended hydrodynamic “reach”) by directing oncoming flow towards the incurrent nostril. Further, both the major and minor nasal grooves redirect some flow away from the incurrent nostril, thereby limiting the amount of fluid that enters the olfactory chamber. Internal hydrodynamic flow patterns are also revealed, where we show that flow rates within the sensory channels between olfactory lamellae are passively regulated by the apical gap, which functions as a partial bypass for flow in the olfactory chamber. Consequently, the hammerhead shark appears to utilize external (major and minor nasal grooves) and internal (apical gap) flow regulation mechanisms to limit water flow between the olfactory lamellae, thus protecting these delicate structures from otherwise high flow rates incurred by sampling a larger area.     

Mesoscopic modeling of bacterial flagellar microhydrodynamics

A particle-based hybrid method of elastic network model and smooth-particle hydrodynamics has been employed to describe the propulsion of bacterial flagella in a viscous hydrodynamic environment. The method explicitly models the two aspects of bacterial propulsion that involve flagellar flexibility and long-range hydrodynamic interaction of low-Reynolds-number flow. The model further incorporates the molecular organization of the flagellar filament at a coarse-grained level in terms of the 11 protofilaments. Each of these protofilaments is represented by a collection of material points that represent the flagellin proteins. A computational model of a single flexible helical segment representing the filament of a bacterial flagellum is presented. The propulsive dynamics and the flow fields generated by the motion of the model filament are examined. The nature of flagellar deformation and the influence of hydrodynamics in determining the shape of deformations are examined based on the helical filament.     

Staining kinetics in single cells. Part I. Influence of convective diffusion on the staining rate

The staining kinetics of single cells have been investigated using a perfusion cuvette in combination with a computer controlled microscope spectrometer. The physicochemical hydrodynamics of staining are characterized. Using a steady-state laminar flow parallel to the cell surface a hydrodynamic and a diffusional boundary layer are observed which are determined by the flow rate. The thickness of the diffusional boundary layer revealed by experimental data is in agreement with theoretically calculated values. At certain well-defined hydrodynamic conditions convective diffusion has no further effect on the staining rate.     

Shifts in drag and swimming potential during grayling ontogenesis: relations with habitat use

The drag coefficient (C_d) of grayling Thymallus thymallus was dependent on body surface conditions and rigidity. At comparable flow conditions, C_d values of a fish preserved in formalin (high body rigidity) were 15–30% lower than those obtained on a freshly-killed fish (medium rigidity); the presence of skin mucus on fish could reduce C_d by 10%. The hydrodynamic potential of grayling increased during ontogenesis, because C_d values decreased (except for yolk sac larvae, which had a particular morphology) and the swimming capacities (in terms of relative muscular mass) increased. Grayling morphology evolves towards hydrodynamically efficient shape at high velocities, and there is a relationship between these shifts in hydrodynamic abilities and the different habitats (in terms of current velocity) used by five morphological groups. Therefore, the concept of hydrodynamic potential (i.e. hydrodynamics of shape and swimming capacities) could be a useful tool in fish ecomorphology and predictions of habitat use.     

Growth kinetics of platelet thrombi

A model for the kinetics of a platelet thrombus growth is presented, which takes into account the principal hydrodynamic and cellular adhesion features of thrombus development. These consist of the rate at which platelets encounter the growing thrombus, their residence time near the surface of the thrombus, the rate of escape over the potential barrier between the free platelets and the surface of the thrombus, and the influence of ADP or related agents on the height of this potential barrier. The latter is explained in terms of the changes in the shape and surface potential of platelets, which are induced by exposure to ADP or related agents.In qualitative agreement with available experimental data, the model predicts an approximately exponential growth of the thrombus volume, a maximum in the growth rate with respect to the blood flow rate, and a plateau value which is reached by the thrombus volume with time. It is shown that at low flow rates the rate of provision of platelets by the blood stream is the determining factor, while at high flow rates the kinetics of adhesion to the surface of the thrombus are predominant. Under all circumstances, when the blood conduit becomes more than about half occluded, the resulting decrease in the blood flow rate decreases, in turn, the growth rate of the thrombus.     

Modelling three-dimensional flow over spur-and-groove morphology

Spur-and-groove (SAG) morphology characterizes the fore reef of many coral reefs worldwide. Although the existence and geometrical properties of SAG have been well documented, an understanding of the hydrodynamics over them is limited. Here, the three-dimensional flow patterns over SAG formations, and a sensitivity of those patterns to waves, currents, and SAG geometry were characterized using the physics-based Delft3D-FLOW and SWAN models. Shore-normal shoaling waves over SAG formations were shown to drive two circulation cells: a cell on the lower fore reef with offshore flow over the spurs and onshore flow over the grooves, except near the seabed where velocities were always onshore, and a cell on the upper fore reef with offshore surface velocities and onshore bottom currents, which result in depth-averaged onshore and offshore flow over the spurs and grooves, respectively. The mechanism driving this flow results from the net of the radiation stress gradients and pressure gradient, which is balanced by the Reynolds stress gradients and bottom friction that differ over the spur and over the groove. Waves were the primary driver of variations in modelled flow over SAG, with the flow strength increasing for increasing wave heights and periods. Spur height, SAG wavelength, and the water depth at peak spur height were the dominant influences on the hydrodynamics, with spur heights directly proportional to the strength of SAG circulation cells. SAG formations with shorter SAG wavelengths only presented one circulation cell on the shallower portion of the reef, as opposed to the two circulation cells for longer SAG wavelengths. SAG formations with peak spur heights occurring in shallower water had stronger circulation than those with peak spur heights occurring in deeper water. These hydrodynamic patterns also likely affect coral and reef development through sediment and nutrient fluxes.

     

湖泊水动力对水生植物分布的影响

水动力作为湖泊水生植物恢复的关键限制性因子,其对水生植物的影响机制是当前迫切需要关注的科学问题。从水动力作用下水生植物的分布、水生植物受力以及水生植物自身机械抗性3个方面系统梳理了当前的研究方法与结论。结果表明,水生植物在河流湖泊中的丰度、空间分布与水动力密切相关,各物种对水流胁迫表现出不同的响应;植物在水动力作用下的受力观测和研究主要依赖模拟试验,通过计算定量表征不同物理外型物种在水动力作用下的受力,明确了生物量和植物系数等影响受力的关键参数,为不同塑形物种受力的对比分析提供了研究方法;植物机械抗性主要基于测力装置观测,通过断裂应力、弯曲力等生物力学参数表征。在当前研究背景下,水生植物尤其是沉水植物在湖泊中的实际受力情况依然是研究难点,需要借助新的观测手段和研究方法来阐明植物在复杂的湖泊水动力环境下的实际受力特征。此外,还需要进一步开展水生植物在湖泊中的实际受力与植物自身机械抗性的耦合研究,这是开展水生植物响应湖泊水动力机理研究的关键。     

Novel aspects of cellular action of dipeptidyl peptidase IV/CD26

The cellular dipeptidyl peptidase IV (DPIV, E.C.3.4.14.5, CD26) is a type II membrane peptidase with various physio-logical functions. Our main knowledge on DPIV comes from studies of soluble DPIV which plays a role in regulation of glucose homeostasis by inactivation of the incretins glucagon-like peptide-1 and glucose-dependent insulinotropic poly-peptide. It has been reported that membrane-bound DPIV plays a crucial role in the immune system and in other tissues and cells, but the knowledge on the action of cellular DPIV and its regulation is limited. In this study, we show particularly for immune cells that DPIV and not DP8 or DP9 is the most potent member of the DPIV family in regulating cellular immune functions. Moreover, we provide evidence that soluble and cellular DPIV differ in functions and hand-ling of substrates and inhibitors owing to the different accessibility of peptide substrates to the two access paths of DPIV. The different functions are based on the favored access path of the central pore of cellular DPIV and a special central pore binding site which assists substrate access to the active site of the enzyme. The newly discovered central pore binding site mediates an autosterical regulation of cellular DPIV and is its most crucial target site to regulate cellular functions such as growth and cytokine production. Neuropeptide Y (NPY) processing by cellular DPIV was found to be inhibited by ligands which interact with the central pore binding site. This finding suggests a crucial role of the immunosuppressive cytokine NPY in the function of DPIV in growth regulation.     

Modeling the effects of the streamflow changes of Xinjiang Basin in future climate scenarios on the hydrodynamic conditions in Lake Poyang,China

The responses of lake hydrodynamics to the hydrological processes in watersheds have been associated with the ecological evolution of and the biochemical processes in aquatic ecosystems. This paper investigates how the changes in the streamflow of Xinjiang Basin in different future climate scenarios could affect the hydrodynamic conditions in Lake Poyang. First, the hydrodynamic processes in Lake Poyang (i.e., lake level and water velocity) were simulated based on the environmental fluid dynamics code (EFDC). Error statistics indicated that the hydrodynamic model reasonably reflected the hydrodynamics in Lake Poyang. Second, the future streamflow of Xinjiang Basin from 2016 to 2050, which was projected in two future climate scenarios (Sim_RCP4.5 and Sim_RCP8.5) based on the Xin’anjiang model, was applied to hydrodynamic modeling to investigate the relationship between future discharge and hydrodynamics. Results showed that the streamflow changes of Xinjiang Basin in future climate scenarios considerably affected the seasonal distribution of the flow field in Lake Poyang. The hydrodynamic change region that exceeded the threshold values under these two climate scenarios both demonstrated a fluctuating trend and nearly covered the entire lake until April. In Sim_RCP8.5 a slightly larger area was influenced than in Sim_RCP4.5, except in January, and the eastern channel was always significantly affected by streamflow change. These analyses can enhance the present understanding of the relationships between the hydrodynamics in lakes and the hydrological processes of sub-basins.     

Respiration and nitrogen assimilation: targeting mitochondria-associated metabolism as a means to enhance nitrogen use efficiency

Considerable advances in our understanding of the control of mitochondrial metabolism and its interactions with nitrogen metabolism and associated carbon/nitrogen interactions have occurred in recent years, particularly highlighting important roles in cellular redox homeostasis. The tricarboxylic acid (TCA) cycle is a central metabolic hub for the interacting pathways of respiration, nitrogen assimilation, and photorespiration, with components that show considerable flexibility in relation to adaptations to the different functions of mitochondria in photosynthetic and non-photosynthetic cells. By comparison, the operation of the oxidative pentose phosphate pathway appears to represent a significant limitation to nitrogen assimilation in non-photosynthetic tissues. Valuable new insights have been gained concerning the roles of the different enzymes involved in the production of 2-oxoglutarate (2-OG) for ammonia assimilation, yielding an improved understanding of the crucial role of cellular energy balance as a broker of co-ordinate regulation. Taken together with new information on the mechanisms that co-ordinate the expression of genes involved in organellar functions, including energy metabolism, and the potential for exploiting the existing flexibility for NAD(P)H utilization in the respiratory electron transport chain to drive nitrogen assimilation, the evidence that mitochondrial metabolism and machinery are potential novel targets for the enhancement of nitrogen use efficiency (NUE) is explored.     

Modeling methodology for defining a priori the hydrodynamics of a dynamic suspension bioreactor. Application to human induced pluripotent stem cell culture

Three-dimensional dynamic suspension is becoming an effective cell culture method for a wide range of bioprocesses, with an increasing number of bioreactors proposed for this purpose. The complex hydrodynamics establishing within these devices affects bioprocess outcomes and efficiency, and usually expensive in vitro trial-and-error experiments are needed to properly set the working parameters.Here we propose a methodology to define a priori the hydrodynamic working parameters of a dynamic suspension bioreactor, selected as a test case because of the complex hydrodynamics characterizing its operating condition. A combination of computational and analytical approaches was applied to generate operational guideline graphs for defining a priori specific working parameters. In detail, 43 simulations were performed under pulsed flow regime to characterize advective transport within the device depending on different operative conditions, i.e., culture medium flow rate and its duty cycle, cultured particle diameter, and initial particle suspension volume. The operational guideline graphs were then used to set specific hydrodynamic working parameters for an in vitro proof-of-principle test, where human induced pluripotent stem cell (hiPSC) aggregates were cultured for 24 h within the bioreactor. The in vitro findings showed that, under the selected pulsed flow regime, sedimentation was avoided, hiPSC aggregate circularity and viability were preserved, and culture heterogeneity was reduced, thus confirming the appropriateness of the a priori method. This methodology has the potential to be adaptable to other dynamic suspension devices to support experimental studies by providing in silico-based a priori knowledge, useful to limit costs and to optimize culture bioprocesses.     

Longitudinal Hydrodynamic Characteristics in Reservoir Tributary Embayments and Effects on Algal Blooms

Three Gorges Reservoir (TGR) is one of the largest man-made lakes in the world. Since the impoundment in 2003, however, algal blooms have been often observed in the tributary embayments. To control the algal blooms, a thorough understanding of the hydrodynamics (e.g., flow regime, velocity gradient, and velocity magnitude and direction) in the tributary embayments is particularly important. Using a calibrated three-dimensional hydrodynamic model, we carried out a hydrodynamic analysis of a typical tributary embayment (i.e., Xiangxi Bay) with emphasis on the longitudinal patterns. The results show distinct longitudinal gradients of hydrodynamics in the study area, which can be generally characterized as four zones: riverine, intermediate, lacustrine, and mainstream influenced zones. Compared with the typical longitudinal zonation for a pure reservoir, there is an additional mainstream influenced zone near the mouth due to the strong effects of TGR mainstream. The blooms are prone to occur in the intermediate and lacustrine zones; however, the hydrodynamic conditions of riverine and mainstream influence zones are not propitious for the formation of algal blooms. This finding helps to diagnose the sensitive areas for algal bloom occurrence.     

Ion dynamics and hydrodynamics in the regulation of pollen tube growth

A coherent picture of pollen tube growth is beginning to emerge that couples ion dynamics with biochemical, biophysical and cytological processes in ordered and controlled feedback circuits that define the nature of polarized apical growth. It is a paradox, however, that complete understanding of the mechanical forces that drive cell elongation in this system still remains to be fully achieved. The results of our recent studies to characterize Cl^– ion dynamics during apical growth in tobacco pollen tubes led us to re-examine this question in the light of a possible force-generating role provided by hydrodynamic flow. Previously we found that oscillatory Cl^– efflux from the apex is closely coupled to oscillatory growth and the cell volume of the apical domain. Cl^– influx occurs in a region of the tube that is distal to the clear zone; hence, a vectorial flow of anion traverses the apical domain and fluxes out of the tip with oscillatory dynamics. Because of the effects that this could induce on charge and osmotic potentials, water could potentially flow through the apical domain, linked to the flux of Cl^–. This conjecture is consistent with studies in other plant cells that demonstrate a pivotal role for flux through anion channels in the control or normalization of osmotic status. In the current report, the relationship between Cl^– efflux oscillations and the physical characteristics of the apical dome during oscillatory growth is examined in closer detail. Evidence is presented that shows a cyclic deformation of the extreme apex occurs during the growth pulse and is correlated with cyclic Cl^– efflux. In addition, there is a dramatic increase in the number and density of clear thread-like zones traversing the apical plasma membrane during the process of tip elongation. Possible functional roles of Cl^– flux and hydrodynamics are discussed in the context of what drives tip elongation during cycles of pollen tube growth. Received: 23 November 2000 / Revision accepted: 19 June 2001     

Airlift column photobioreactors for Porphyridium sp. culturing: Part II. verification of dynamic growth rate model for reactor performance evaluation

Dynamic growth rate model has been developed to quantify the impact of hydrodynamics on the growth of photosynthetic microorganisms and to predict the photobioreactor performance. Rigorous verification of such reactor models, however, is rare in the literature. In this part of work, verification of a dynamic growth rate model developed in Luo and Al-Dahhan (2004) [Biotech Bioeng 85(4): 382-393] was attempted using the experimental results reported in Part I of this work and results from literature. The irradiance distribution inside the studied reactor was also measured at different optical densities and successfully correlated by the Lambert-Beer Law. When reliable hydrodynamic data were used, the dynamic growth rate model successfully predicted the algae's growth rate obtained in the experiments in both low and high irradiance regime indicating the robustness of this model. The simulation results also indicate the hydrodynamics is significantly different between the real algae culturing system and an air-water system that signifies the importance in using reliable data input for the growth rate model.     

Preface: Blasts from the past and back to the future

The invasion of dreissenid mussels into inland waters of the Northern Hemisphere has received considerable attention and, both zebra mussels and quagga mussels continue to spread westward. Despite studies aimed at understanding the biology of dreissenid mussels, relatively few studies have focused on water velocity and other hydrodynamic characteristics of water flow. The objective of this review was to identify, through a search of online databases, the papers that have been made available that directly have assessed the influence of hydrodynamic characteristics of water flow on dreissenid mussel biology. Using Thompson Reuters Web of Science, Google Scholar, and other resources, 46 papers were identified. These papers detailed that metrics associated with hydrodynamics of water flow, including current, wave action, velocity, flow rate, and discharge, can influence the biology of dreissenid mussels (primarily zebra mussel, which were studied far more than quagga mussel). Hydrodynamic characteristics influenced external fertilization, larval development and settlement, juvenile recruitment and attachment, and suspension feeding, growth and abundance of adults. In most cases, the impact of higher flow rates were locally negative and may present an opportunity for applications of water flow to control the spread or establishment of dreissenid mussels. Several knowledge gaps have been identified.