An ecologically useful classification of mean and near-bed flows in streams and rivers

SUMMARY. 1. Mean motion and near-bed flows in streams and rivers can be described using a classification derived from fairly simple field measurements. Our proposed classification is ecologically useful because it incorporates the combined effects of velocity, depth and substrate roughness to provide a means of quantifying the flow regimes occurring within the microhabitats of stream benthos. 2. Mean motion is characterized by the Reynolds number and the Froude number. Both are easily calculated, and because they are dimensionless they provide a means of comparing flows at different sites. 3. Five categories of near-bed flows (i.e. the flow microenvironments of stream benthos) are recognized. Flow may be hydraulically smooth or hydraulically rough and the latter category is subdivided further into: chaotic flow, wake interference flow, isolated roughness flow and skimming flow. Hydraulically smooth flows occur in sections of a river bed with fine sediments (e.g. sands, muds and clays). over flat sheets of bedrock, or in association with the flat blades of submerged macrophytes. Hydraulically rough flows occur where the substrate elements are larger (e. g. pebbles, cobbles and boulders) and are a function of substrate roughness and the depth of flow relative to the height of the roughness elements. Chaotic flows and wake interference flows predominate in riffles whilst isolated roughness flows and skimming flows are more likely to be a feature of runs. 4. Conventional stream sampling methods (e.g. the Surber and box or cylinder samplers) may collect across several different flow microhabitats. Our classification should enable different flow microenvironments to be recognized and so sampled more appropriately which, in turn, may reduce apparent clumping and the wide confidence intervals of benthic population estimates. Because our classification identifies ‘patches’ within the flow regime associated with the stream bed it enables stream ecologists to generate testable hypotheses regarding the distribution and abundance of benthic species in response to flow. 5. Our classification identifies spatial patterns in the flow regimes associated with the stream bed. Temporal patterns have not been identified: however, predictable changes in spatial patterns will resuh from temporal changes in stream discharge.     

Calibration of FST-hemispheres against bottom shear stress in a laboratory flume*

SUMMARY.

• 1 Fliesswasserstammtisch (FST)-hemispheres of identical size but different densities were exposed on a horizontal plane on the pebble-covered bottom of a laboratory flume at streaming to shooting, turbulent and fully developed flow. The heaviest hemisphere moved was used as an indicator of shear stress, a flow force acting on the flume bottom.
• 2 The relationship between shear stress and hemisphere density was practically the same for three different sets of hemispheres, namely one prototype set newly prepared for the calibrations, one prototype set intensively used in the field prior to calibrations, and one randomly selected new set bought commercially.
• 3 Shear stress (y, dyn cm^?2) was related to hemisphere density (x, g cm^?3) by y= x^2.85 (n= 69; r²= 0.993). For lighter hemispheres this relationship was better explained by the linear model y= 7.32x– 6.60 (n= 35; r²=0.983).

     

Characterizing the fluid dynamics in the flow fields of cylindrical orbitally shaken bioreactors with different geometry sizes

Orbitally shaken bioreactors (OSRs) are commonly used for the cultivation of mammalian cells in suspension. To aid the geometry designing and optimizing of OSRs, we conducted a three‐dimensional computational fluid dynamics (CFD) simulation to characterize the flow fields in a 10 L cylindrical OSR with different vessel diameters. The liquid wave shape captured by a camera experimentally validated the CFD models established for the cylindrical OSR. The geometry size effect on volumetric mass transfer coefficient (k_La) and hydromechanical stress was analyzed by varying the ratio of vessel diameter (d) to liquid height at static (h_L), d/h_L. The highest value of k_La about 30 h^?1 was observed in the cylindrical vessel with the d/h_L of 6.35. Moreover, the magnitudes of shear stress and energy dissipation rate in all the vessels tested were below their minimum values causing cells damage separately, which indicated that the hydromechanical‐stress environment in OSRs is suitable for cells cultivation in suspension. Finally, the CFD results suggested that the d/h_L higher than 8.80 should not be adopted for the 10 L cylindrical OSR at the shaking speed of 180 rpm because the “out of phase” state probably will happen there.     

Impact of diatomaceous biofilms on the frictional drag of fouling-release coatings

Skin-friction results are presented for fouling-release (FR) hull coatings in the unexposed, clean condition and after dynamic exposure to diatomaceous biofilms for 3 and 6 months. The experiments were conducted in a fully developed turbulent channel flow facility spanning a wide Reynolds number range. The results show that the clean FR coatings tested were hydraulically smooth over much of the Reynolds number range. Biofilms, however, resulted in an increase in skin-friction of up to 70%. The roughness functions for the biofilm-covered surfaces did not display universal behavior, but instead varied with the percentage coverage by the biofilm. The effect of the biofilm was observed to scale with its mean thickness and the square root of the percentage coverage. A new effective roughness length scale (k_eff) for biofilms based on these parameters is proposed. Boundary layer similarity-law scaling is used to predict the impact of these biofilms on the required shaft power for a mid-sized naval surface combatant at cruising speed. The increase in power is estimated to be between 1.5% and 10.1% depending on the biofilm thickness and percentage coverage.     

Shear inactivation of cellulase of Trichoderma reesei

Inactivation of the cellulase of Trichoderma reesei (EC 3.2.1.4) by shear, is of sufficient magnitude to merit consideration in the design of equipment for the enzymatic hydrolysis of cellulose. The inac inactivation constant, k_d, is a function of the flow rate of the enzyme solution through a fine capillary tube. k_d increased slowly at low shear stress, and much more rapidly when the shear stress was greater than 15 dynes cm^?2.     

Colonization of natural substrata of different roughness and colour by Ephemeroptera nymphs using retrieval and direct observation techniques

We investigated the colonization of stream substrata by Ephemeroptera nymphs in a Canadian Rocky Mountain stream. Stream substrata used in our study were different textures (smooth and rough) and colours (dark and light); the taxonomic groups studied were Drunella coloradensis Dodds (Ephemerellidae), Heptageniidae (Cinygmula and Epeorus) and a Baetis Ameletus group (Baetidae and Siphlonuridae). We tested the hypothesis that as D. coloradensis nymphs and other abundant Ephemeroptera nymphs increase in size they choose a dark substratum to remain cryptic and a substratum of greater texture to reduce the risk of being swept from the substratum by the water flow. Two approaches were used to test this hypothesis, a substratum basket experiment and direct observations.For the substratum basket experiment, there were no statistical differences in abundance of nymphs on the substratum types. But there was a general tendency that the D. coloradensis nymphs were least abundant on the rough dark-coloured substratum and developmental stage three nymphs were most abundant on the smooth white-coloured substratum.Colonization was investigated for other Ephemeroptera nymphs by making direct observations on the substratum baskets using a glass-bottomed box. For the taxonomic groups and two colonization periods, nymphs were statistically at greatest density on the smooth white-coloured substratum and lowest on the smooth black-coloured substratum. The Baetis-Ameletus groups were also found at greatest densities on the rough dark-coloured substratum.     

Seawater DMS in a perturbed coastal ecosystem

Intra- and interspecific niche overlap for two mayfly species with similar life cycle timing, Rhithrogena semicolorata and Ecdyonurus sp. gr. venosus, were investigated. The nymphs were classified into 5 classes according to size and spatial overlaps are measured along a substratum roughness gradient. Substratum roughness selection was investigated by defining utilisation curves, optimum and tolerance values of the nymphs in relation to larval growth. Differences between species and size classes within each species were observed. Ecdyonurus sp. gr. venosus dominated on rough substrates, whereas R. semicolorata was most abundant on smooth substrates. An intermediate value of total interspecific substratum roughness overlap (0.49) was found. Higher intraspecific than interspecific overlap values suggested a spatial niche segregation between the two species. The results suggested that the spatial niches measured, were closer to the `fundamental niches' than could be expected if competition was acting on the two studied populations.     

The effect of substratum type on aspects of swimming performance and behaviour in shortnose sturgeon Acipenser brevirostrum

The swimming performance and associated swimming behaviour (i.e. substratum‐skimming, station‐holding and free swimming) were assessed in shortnose sturgeon Acipenser brevirostrum during critical swimming and endurance swimming tests over a rough and a smooth substratum. It was hypothesized that the addition of a rough substratum in the swimming flume may provide a surface for the A. brevirostrum to grip and offer an energetic advantage. Substratum type did not affect the critical swimming performance, but A. brevirostrum consistently performed more bottom behaviours (i.e. substratum‐skimming and station‐holding) while on a smooth substratum. Acipenser brevirostrum had little contact with the rough substratum until the velocity was >1 body length s^?1. Endurance swimming time was significantly lower for A. brevirostrum over the rough bottom at the highest velocity (30 cm s^?1) which may be attributed to the observed increase in free swimming and decrease in bottom behaviours. During endurance swimming, the rough substratum was mainly used at intermediate velocities, suggesting that there may be a stability cost associated with being in contact with the rough substratum at certain velocities.     

A New Model to Describe Flow Behaviour of Concentrated Orange Juice

The knowledge of rheological behaviour of juices and fruit derivatives is very useful both in the prediction of their stability and in process design, and it depends on the type of juice and on the raw material with which they are produced. Most of the equations that have been used to quantify flow behaviour describe the evolution of shear stress with the change of shear rate. Nevertheless, the essential variable in equipment design is viscosity. In this way, a mathematical model to easily describe the evolution of apparent viscosity of these non-Newtonian fluids with the shear rate would be very useful. In this work, a mathematical expression has been developed, fitted to experimental data and compared with the Herschel–Bulkley one. The obtained parameters with concentrated orange juice followed these trends: equilibrium apparent viscosity (η _∞) scarcely changed with temperature. Static apparent viscosity (η ₀) decreased with increasing temperature, contrary to what happened with the flow behaviour constant k.     

Darcian permeability constant as indicator for shear stresses in regular scaffold systems for tissue engineering

The shear stresses in printed scaffold systems for tissue engineering depend on the flow properties and void volume in the scaffold. In this work, computational fluid dynamics (CFD) is used to simulate flow fields within porous scaffolds used for cell growth. From these models the shear stresses acting on the scaffold fibres are calculated. The results led to the conclusion that the Darcian (k ₁) permeability constant is a good predictor for the shear stresses in scaffold systems for tissue engineering. This permeability constant is easy to calculate from the distance between and thickness of the fibres used in a 3D printed scaffold. As a consequence computational effort and specialists for CFD can be circumvented by using this permeability constant to predict the shear stresses. If the permeability constant is below a critical value, cell growth within the specific scaffold design may cause a significant increase in shear stress. Such a design should therefore be avoided when the shear stress experienced by the cells should remain in the same order of magnitude.     

Distribution of vessel size,vessel density and xylem conducting efficiency within a crown of silver birch (<Emphasis Type="Italic">Betula pendula</Emphasis>)

Spatial patterns in vessel diameter, vessel density and xylem conducting efficiency within a crown were examined in closed-canopy trees of silver birch (Betula pendula). The variation in anatomical and hydraulic characteristics of branches was considered from three perspectives: vertically within a crown (lower, middle and upper crown), radially along main branches (proximal, middle and distal part), and with respect to branch orders (first-, second- and third-order branches). Hydraulically weighted mean diameter of vessels (D _h) and theoretical specific conductivity of the xylem (k _t) exhibited no vertical trend within the tree crown, whereas leaf-specific conductivity of the xylem (LSC_t) decreased acropetally. Variation in LSC_t was governed by sapwood area to leaf area ratio (Huber value) rather than by changes in xylem anatomy. The acropetal increase in soil-to-leaf conductance (G _T) within the birch canopy is attributable to longer path length within the lower-crown branches and higher hydraulic resistance of the shade leaves. D _h, k _t and LSC_t decreased, while vessel density (VD) and relative area of vessel lumina (VA) increased distally along main branches. A strong negative relationship between vessel diameter and VD implies a trade-off between hydraulic efficiency and mechanical stability of xylem. D _h and VD combined explained 85.4% of the total variation of k _t in the regression model applied to the whole data set. Xylem in fast-growing branches (primary branches) had greater area of vessel lumina per unit cross-sectional area of sapwood, resulting in a positive relationship between branch radial growth rate and k _t. D _h, k _t and LSC_t decreased, whereas VD increased with increasing branch order. This pattern promotes the hydraulic dominance of primary branches over the secondary branches and their dominance over tertiary branches. In this way crown architecture contributes to preferential water flow along the main axes, potentially providing better water supply for the branch apical bud and foliage located in the outer, better-insolated part of the crown.     

Cytoplasmic calcium response to fluid shear stress in cultured vascular endothelial cells

Summary Vascular endothelial cells modulate their structure and functions in response to changes in hemodynamic forces such as fluid shear stress. We have studied how endothelial cells perceive the shearing force generated by blood flow and the substance(s) that may mediate such a response. We identify cytoplasmic-free calcium ion (Ca⁺⁺), a major component of an internal signaling system, as a mediator of the cellular response to fluid shear stress. Cultured monolayers of bovine aortic endothelial cells loaded with the highly fluorescent Ca⁺⁺-sensitive dye Fura 2 were exposed to different levels of fluid shear stress in a specially designed flow chamber, and simultaneous changes in fluorescence intensity, reflecting the intracellular-free calcium concentration ([Ca⁺⁺] _i ), were monitored by photometric fluorescence microscopy. Application of shear stress to cells by fluid perfusion led to an immediate severalfold increase in fluorescence within 1 min, followed by a rapid decline for about 5 min, and finally a plateau somewhat higher than control levels during the entire period of the stress application. Repeated application of the stress induced similar peak and plateau levels of [Ca⁺⁺] _i but at reduced magnitudes of response. These responses were observed even in Ca⁺⁺-free medium. Thus, a shear stress transducer might exist in endothelial cells, which perceives the shearing force on the membrane as a stimulus and mediates the signal to increase cytosolic free Ca⁺⁺. This work was partly supported by a grant-in-aid, for Special Project Research no. 61132008, from the Japanese Ministry of Education, Science and Culture and a research fund from the Atherosclerosis Study Association.     

On the relationships between absolute and allometric shell growth in unionid mussels (Bivalvia,Unionidae) from European Russia

The heuristic analysis of the relationship between the parameters of equations of linear (L. von Bertalanffy) and allometric shell growth was carried out on Unio pictorum (Linnaeus, 1758), U. tumidus Retzius, 1778, and U. crassus Retzius 1778 (Unionidae) from European Russia. Growth constants of the shell, k, were studied for length (k _L ), height (k _h ), and convexity (k _C ). It was shown that the ratios of growth constants (k _h /k _L , k _C /k _h , and k _C/k _L ) and parameter bfrom the allometric equations (h=aL ^b ;B=ah ^b ; C=aL ^b ) are connected by a strong negative correlation. If the b parameter is more than 1 (positive allometry), the growth constant relations are less than one, if b < 1 (negative allometry), the growth constant proportions are more than 1, and, in case when b is close to 1, (isometry), the growth constant proportions are also close to 1. All three types of allometric growth (isometry and both positive and negative allometry) are observed in the studied mussels.     

Xylitol Production from D‐Xylose at Different Oxygen Transfer Coefficients in a Batch Bioreactor

Conversion of D‐xylose to xylitol by Candida boidinii NRRL Y‐17213 was studied under anaerobic and oxygen limited conditions by varying the oxygen transfer coefficient k_La. Shake flask experiments were used to provide the preliminary information required to perform experiments in a bioreactor. The yeast did not grow under fully anaerobic conditions, but anaerobic formations of xylitol, ethanol, ribitol, and glycerol were observed as well as D‐xylose assimilation of 11 %. In shake flasks, with an initial D‐xylose concentration of 50 g/L, an increase in k_La from 8 to 46 h^–1 resulted in a faster growth, higher rate of substrate uptake and lower yields of products. The highest xylitol productivity (0.052 g/L h) was attained at k_La = 8 h^–1. At k_La = 46 h^–1, 98.6 % of D‐xylose was consumed and mainly converted to biomass. Using 130 g/L D‐xylose, k_La was varied in the fermenter from 26 to 78 h^–1. The percentage of consumed D‐xylose increased from 31 % at k_La = 26 h^–1 to 93–94 % at all other aeration levels. Biomass yield increased with k_La, whereas ethanol, ribitol, and glycerol yields exhibited an opposite dependence on the oxygenation level. The most favorable oxygen transfer coefficient for xylitol formation, in the fermenter, was k_La = 47 h^–1 when its concentration (57.5 g/L) surpassed ethanol accumulation by 3.6‐fold, and the glycerol plus ribitol by 10‐fold. Concurrently, xylitol yield and productivity reached 0.45 g/g and 0.26 g/L h, respectively. The volumetric xylitol productivity was affected more by changes in the aeration than the corresponding yield.     

Some optical features of the eyes of stomatopods

The optics of a variety of stomatopod eyes has been investigated using goniometric eye-mapping techniques and anatomical measurements. The species examined come from 3 of the 4 existing superfamilies: the Gonodactyloidea, Lysiosquilloidea and Squilloidea. This paper examines acuity, optical axes and general features of eye shape. Stomatopod eyes are divided into 3 clearly distinct zones; the mid-band and two hemispheres. Each hemisphere consists of an edge region, a visual streak and a near mid-band region. The optical axes of many ommatidia from both hemispheres are skewed inwards towards the centrally placed mid-band and are rarely normal to the corneal surface. The large skew angle enables each hemisphere to examine an area which extensively overlaps that of the other hemisphere. As a result monocular distance judgement is possible. Most of the ommatidia in each hemisphere are part of a horizontally aligned but vertically acute visual streak area. There is one visual streak per hemisphere and both look into the same 5–10° strip. This narrow strip is also the area in space the mid-band ommatidia examine. An acute zone is present in the eyes of lysiosquilloid and gonodactyloid stomatopods and includes ommatidia, from both the hemispheres and the mid-band. Here inter-ommatidial angles, especially those in the horizontal direction, are reduced. Acute zone facets are enlarged to increase sensitivity rather than aid spatial resolution.Abbreviations and definitions AZ Acute Zone - MB Mid-band - D Corneal facet diameter, as MB facets are asymmetrical, values for width and height of each facet are given - DH dorsal hemisphere - f Focal length of each ommatidium, estimated from the centre of the corneal lens to the tip of the rhabdom - NeMB Near mid-band ommatidia - R Resolving power=1/2_average - R_h Horizontal resolving power=1/2_h - R_v Vertical resolving power=1/2_v - VH ventral hemisphere - Geometrical acceptance angle (a/f×57.3) of each ommatidium - _h Horizontal inter-ommatidial angle, between facets along a row - _v Vertical inter-ommatidial angle, between rows; Superfamily Gonodactyloidea - g.c. Gonodactylus chiragra - O.s. Odontodactylus scyllarus - H.e. Hemisquilla ensigera; Superfamily Lysiosquilloidea - L.t. Lysiosquilla tredecimdentata - C.s. Coronis scolopendra; Superfamily Squilloidea - O.o. Oratosquilla solicitans     

Impacts of hydrodynamic conditions and microscale surface roughness on the critical shear stress to develop and thickness of early-stage Pseudomonas putida biofilms

Biofilms can increase pathogenic contamination of drinking water, cause biofilm-related diseases, alter the sediment erosion rate, and degrade contaminants in wastewater. Compared with mature biofilms, biofilms in the early-stage have been shown to be more susceptible to antimicrobials and easier to remove. Mechanistic understanding of physical factors controlling early-stage biofilm growth is critical to predict and control biofilm development, yet such understanding is currently incomplete. Here, we reveal the impacts of hydrodynamic conditions and microscale surface roughness on the development of early-stage Pseudomonas putida biofilm through a combination of microfluidic experiments, numerical simulations, and fluid mechanics theories. We demonstrate that early-stage biofilm growth is suppressed under high flow conditions and that the local velocity for early-stage P. putida biofilms (growth time < 14 h) to develop is about 50 μm/s, which is similar to P. putida's swimming speed. We further illustrate that microscale surface roughness promotes the growth of early-stage biofilms by increasing the area of the low-flow region. Furthermore, we show that the critical average shear stress, above which early-stage biofilms cease to form, is 0.9 Pa for rough surfaces, three times as large as the value for flat or smooth surfaces (0.3 Pa). The important control of flow conditions and microscale surface roughness on early-stage biofilm development, characterized in this study, will facilitate future predictions and managements of early-stage P. putida biofilm development on the surfaces of drinking water pipelines, bioreactors, and sediments in aquatic environments.     

The effect of surface roughness on claw and adhesive hair performance in the dock beetle Gastrophysa viridula

Abstract Natural adhesive systems are adapted to attach to rough surfaces, but the underlying mechanisms have not been fully clarified. Attachment forces for the beetle Gastrophysa viridula were recorded on epoxy casts of surfaces with different roughness using a centrifuge device. Replicas were made of standardized polishing paper with asperity sizes ranging from 0.05 to 30 μm and of dock leaves (Rumex obtusifolius). Beetles adhered with a safety factor of up to 36 times body weight on smooth substrates or on casts of leaves of their host plant. On the rough substrates, forces were much lower and a minimum at small scale roughness (0.05 μm asperity size, with a mean safety factor of 5) was observed. Removal of the claws led to a significant reduction in force for rough substrates with asperity sizes ≥ 12 μm. Attachment forces of the hairy adhesive system itself (without the claws) slightly increased from small‐scale to large‐scale surface roughness, but remained below the level seen on the smooth substrate. This is explained by the inability of setal tips to make full contact to the surface.     

Effect of shear stress on activity of cellular enzyme in animal cell

The effect of shear stress on the activity of cellular enzyme in an animal cell was discussed by using a flow channel. The activity of lactate dehydrogenase (LDH) in cells exposed to a shear stress of 0.5 Pa for 12 h was about 4-fold greater than in the cells without exposure to shear stress. The relative LDH activity was correlated with the dissipation energy density of the flowing medium. A good correlation was obtained and it was found that the dependency of cellular enzyme activity on the shear stress and the exposure time was related to the transmission of the energy from the flowing medium to attached cells.List of Symbols b m width of flow channel - E J/m² dissipation energy density - h m distance between two plates - Q m³/s volume flow rate - t s exposure time - u m/s velocity of medium - y m distance from wall attached cells - Pa s viscosity - Pa shear stress     

Potential use of beaver Castor fiber L., 1758 dams by the thick-shelled river mussel Unio crassus Philipsson, 1788

ABSTRACT

The objective of this paper is to draw attention to a previously unrecognised habitat for Unio crassus Philipsson, 1788 (Bivalvia: Unionidae), namely beaver dam-and-pond complexes. The construction of beaver ponds will allow the colonisation of high energy streams by providing flow refuges during periods of high near-bed shear stress. The absence of freshwater mussels (Unionidae) in mountain streams may result from steep slopes, shear stress during floods, lack of food suspended in the water column (seston), and unfavourable conditions for the settlement and growth of juvenile mussels. Transportation of parasitic larvae on host fish is the main dispersal mechanism for the mussels. A possible constraint on the colonisation of beaver complexes by freshwater mussels is that beaver dams may hinder the upstream movement of their minnow hosts. In the surveyed beaver ponds, the first specimens of U. crassus were found in 2008. Single mussels were also found in subsequent years. It is uncertain whether the occurrence of U. crassus depends on the periodic support of the population from the main river, but the presence of beaver ponds is certain to have given it the opportunity of colonising new areas.