A Model of Tracer Transport in Airway Surface Liquid

This study is concerned with reconciling theoretical modelling of the fluid flow in the airway surface liquid with experimental visualisation of tracer transport in human airway epithelial cultures. The airways are covered by a dense mat of cilia of length ∼ 6 μm beating in a watery periciliary liquid (PCL). Above this there is a layer of viscoelastic mucus which traps inhaled pathogens. Cilia propel mucus along the airway towards the trachea and mouth. Theoretical analyses of the beat cycle smithd, fulb predict small transport of PCL compared with mucus, based on the assumption that the epithelium is impermeable to fluid. However, an experimental study coord indicates nearly equal transport of PCL and mucus. Building on existing understanding of steady advection-diffusion in the ASL (Blake and Gaffney, 2001; Mitran,2004) numerical simulation of an advection-diffusion model of tracer transport is used to test several proposed flow profiles and to test the importance of oscillatory shearing caused by the beating cilia. A mechanically derived oscillatory flow with very low mean transport of PCL results in relatively little ‘smearing’ of the tracer pulses. Other effects such as mixing between the PCL and mucus, and significant transport in the upper part of the PCL above the cilia tips are tested and result in still closer transport, with separation between the tracer pulses in the two layers being less than 9%. Furthermore, experimental results may be replicated to a very high degree of accuracy if mean transport of PCL is only 50% of mucus transport, significantly less than the mean PCL transport first inferred on the basis of experimental results.     

Discrete Cilia Modelling with Singularity Distributions: Application to the Embryonic Node and the Airway Surface Liquid

We discuss in detail techniques for modelling flows due to finite and infinite arrays of beating cilia. An efficient technique, based on concepts from previous ‘singularity models’ is described, that is accurate in both near and far-fields. Cilia are modelled as curved slender ellipsoidal bodies by distributing Stokeslet and potential source dipole singularities along their centrelines, leading to an integral equation that can be solved using a simple and efficient discretisation. The computed velocity on the cilium surface is found to compare favourably with the boundary condition. We then present results for two topics of current interest in biology. 1) We present the first theoretical results showing the mechanism by which rotating embryonic nodal cilia produce a leftward flow by a ‘posterior tilt,’ and track particle motion in an array of three simulated nodal cilia. We find that, contrary to recent suggestions, there is no continuous layer of negative fluid transport close to the ciliated boundary. The mean leftward particle transport is found to be just over 1 μm/s, within experimentally measured ranges. We also discuss the accuracy of models that represent the action of cilia by steady rotlet arrays, in particular, confirming the importance of image systems in the boundary in establishing the far-field fluid transport. Future modelling may lead to understanding of the mechanisms by which morphogen gradients or mechanosensing cilia convert a directional flow to asymmetric gene expression. 2) We develop a more complex and detailed model of flow patterns in the periciliary layer of the airway surface liquid. Our results confirm that shear flow of the mucous layer drives a significant volume of periciliary liquid in the direction of mucus transport even during the recovery stroke of the cilia. Finally, we discuss the advantages and disadvantages of the singularity technique and outline future theoretical and experimental developments required to apply this technique to various other biological problems, particularly in the reproductive system.     

How to leave or stay on the substratum when you can’t swim? Evidence of the role of mucus thread secretion by postlarvae of Pectinaria koreni (Malmgren) in still water and flume experiments

Through an experimental approach we investigate the role of mucus secretion in postlarvae of Pectinaria koreni (tubicolous polychaete) on their ability to drift within the benthic boundary layer or to stay at the water–substratum interface. Fall velocity measurements were conducted with either living or dead postlarvae which were allowed to sink into a 2 m long Plexiglas cylindrical chamber. Five groups of increasing size-classes were tested ranging from the very first benthic stage (1 mm < Tube_length < 2 mm: membranous tube present accounting for more than 75% of the total tube length) to older stages (6 mm < Tube_length < 10 mm: membranous tube absent). We used these results to propose the first estimates of dispersal distances by several post-larval stages secreting mucus or sinking passively through the water column. Experiments were carried out in the HYCOBENTHOS flume to determine values of critical shear velocity (u _*c) inducing bedload transport and further resuspension of postlarvae of increasing sizes. The influence of mucus secretion by recruits on their ability to stay or quit a ‘suitable’ substratum was investigated by using either living or dead individuals. Results showed that: (a) the ability to secrete mucus rapidly is limited to the younger stages; (b) fall velocity of postlarvae is drastically lowered by mucus secretion (5 orders of magnitude) and is higher for the older stages; (c) dead recruits behave similarly to ‘passive’ recruits; (d) horizontal distances of drift dispersal may be considerable (up to 800 m for a single 22 min trip); (e) mucus secretion may be used by the postlarvae to anchor themselves to the substratum. Cost-benefit of using the mucus secretion as a tool for recruitment and the related spatial scales are discussed.     

Characterization,Ecological Status and Type-specific Reference Conditions of Surface Water Bodies in Wallonia (Belgium) using Biocenotic Metrics based on Benthic Invertebrate Communities

The river types in Wallonia (Belgium) were defined according to the system B of the European Water Framework Directive (WFD) taking into account obligatory and optional factors synthesized in three criteria: ‘size’, ‘slope’ and ‘natural region’. Under the hypothesis that benthic invertebrate assemblages would be specialized according to river type, a set of 627 faunal samples originating from an 11-year sampling period was tested to characterize river types with faunal assemblages. A multivariate approach led to gather 23 river types into seven groups exhibiting similar faunal assemblages. Using biocenotic metrics based on benthic invertebrate assemblages (e.g., the French standard IBGN), type-specific reference conditions and ecological status class limits were defined for each ‘natural’ river type group. Ecological potential was defined for heavily modified and for artificial (i.e., man-made canals) types. An ‘ecological status’ evaluation strategy was therefore developed and applied in the southern – and more natural – part of Wallonia, where many reference sites were available. In the northern part of Wallonia (i.e., the ‘Loess region’) where no high quality site was available, the expert judgement took a larger part in the definition of the reference conditions and of the ecological status class limits, in addition to the calculations. Two independent distribution gradients of taxa assemblages resulted from multivariate ordination: a first ‘saprobity axis’, as the taxa-sensitivity to organic contamination was increasing from ‘very resistant’ taxa (mainly located in the ‘Loess region’) to ‘sensitive’ and ‘very sensitive’ taxa (from the river types belonging to the Condroz, the Famenne, the Arden and the Jurassic regions) and a second axis characterizing the Meuse-specific faunal assemblage, gathering exotic species and typical limnophilous taxa of large heavily modified rivers. The ecological status monitoring management system developed in this study – i.e., the definition of faunal river type groups, related reference conditions and ecological status class limits – represents a proposal to be integrated in the ecological status assessment of biological elements for the implementation of the WFD and was tested in Wallonia. For the period 2000–2002 involving 349 different sites, the element ‘benthic invertebrate fauna’ was in that way classified ‘high status’ for 31.5% of sites, ‘good status’ for 31.5% and below ‘good status’ for 37% of sites. The best ecological status (i.e., 100% ‘high’ and ‘good’ status) was found in river type ‘Arden’s xenotrophic brooks with strong slope’ and in river types 8large rivers with medium slope’. The worst status was found in river types ‘Loess brooks and rivers with medium slope’.     

Climate change and heat-related mortality in six cities Part 1: model construction and validation

Heat waves are expected to increase in frequency and magnitude with climate change. The first part of a study to produce projections of the effect of future climate change on heat-related mortality is presented. Separate city-specific empirical statistical models that quantify significant relationships between summer daily maximum temperature (T _max) and daily heat-related deaths are constructed from historical data for six cities: Boston, Budapest, Dallas, Lisbon, London, and Sydney. ‘Threshold temperatures’ above which heat-related deaths begin to occur are identified. The results demonstrate significantly lower thresholds in ‘cooler’ cities exhibiting lower mean summer temperatures than in ‘warmer’ cities exhibiting higher mean summer temperatures. Analysis of individual ‘heat waves’ illustrates that a greater proportion of mortality is due to mortality displacement in cities with less sensitive temperature–mortality relationships than in those with more sensitive relationships, and that mortality displacement is no longer a feature more than 12 days after the end of the heat wave. Validation techniques through residual and correlation analyses of modelled and observed values and comparisons with other studies indicate that the observed temperature–mortality relationships are represented well by each of the models. The models can therefore be used with confidence to examine future heat-related deaths under various climate change scenarios for the respective cities (presented in Part 2).     

Characterization of ‘Schizokinen’; a dihydroxamate-type siderophore produced by Rhizobium leguminosarum IARI 917

The Rhizobia comprise one of the most important groups of beneficial bacteria, which form nodules on the roots (rarely on the stems) of leguminous plants. They live within the nodules and reduce atmospheric nitrogen to ammonia, which is further assimilated by plants into required nitrogenous compounds. The Rhizobia in return obtain nutrition from the plant. Rhizobia are free-living soil bacteria and have to compete with other microorganisms for the limited available iron in the rhizosphere. In order to acquire iron Rhizobia have been shown to express siderophore-mediated iron transport systems. Rhizobium leguminosarum IARI 917 was investigated for its ability to produce siderophore. It was found to produce a dihydroxamate type siderophore under iron restricted conditions. The siderophore was purified and chemically characterized. The ESMS, MS/MS and NMR analysis indicate the dihydroxamate siderophore to be ‘schizokinen’, a siderophore reported to be produced by Bacillus megaterium that shares a similar structure to ‘rhizobactin 1021’ produced by Sinorhizobium meliloti 1021. This is the first report of production of schizokinen by a strain of R. leguminosarum, therefore it was carefully investigated to confirm that it is indeed ‘schizokinen’ and not a degradation product of ‘rhizobactin 1021’. Since ferric–siderophore complexes are transported across the outer membrane (OM) into the periplasm via an OM receptor protein, R. leguminosarum IARI 917 was investigated for the presence of an OM receptor for ‘ferric–schizokinen’. SDS PAGE analysis of whole cell pellet and extracted OM fractions indicate the presence of a possible iron-repressible OM receptor protein with the molecular weight (MW) of approximately 74 kDa.     

An approach to practical persistence

 A basic problem in community ecology is determining whether a community of interacting species will survive in the long term. A criterion ensuring this is that of permanence (or uniform persistence), which is based on the idea that species densities for large time are above minimum non-zero levels. There are various mathematical techniques for investigating permanence, but they do not yield an estimate for the minimum levels, and these may lie below minimum viability levels in the biological sense of ‘Practical Persistence’. Here we study a technique for obtaining explicit expressions for the minimum levels when one species is ‘slow’. This is illustrated for a predator–prey problem governed by difference equations, and we note that the technique is applicable even when the dynamics is chaotic.. Received: 7 April 1997 / Revised version: 25 March 1998     

Concentration polarization of atherogenic lipids in the arterial system

The transport of atherogenic lipids (LDL) in a straight segment of an artery with a semi-permeable wall was simulated numerically. The numerical analysis predicted that a mass transport phenomenon called ’concentration polarization’ of LDL might occur in the arterial system. Under normal physiological flow conditions, the luminal surface LDL concentration was 5%–14% greater than the bulk concentration in a straight segment of an artery. The luminal surface LDL concentration at the arterial wall was flow-dependent, varying linearly with the filtration rate across the arterial wall and inversely with wall shear rate. At low wall shear rate, the luminal surface LDL concentration was very sensitive to changes in flow conditions, decreasing sharply as wall shear rate increased. In order to verify the numerical analysis, the luminal surface concentration of bovine serum albumin (as a tracer macromolecule) in the canine carotid artery was measured in vitro by directly taking liquid samples from the luminal surface of the artery. The experimental result was in very good agreement with the numerical analysis. The authors believe that the mass transport phenomenon of ‘concentration polarization’ may indeed exist in the human circulation and play an important role in the localization of atherosclerosis.     

Effects of trace element concentrations on culturing thermophiles

The majority of microorganisms in natural environments resist laboratory cultivation. Sometimes referred to as ‘unculturable’, many phylogenetic groups are known only by fragments of recovered DNA. As a result, the ecological significance of whole branches of the ‘tree of life’ remains a mystery; this is particularly true when regarding genetic material retrieved from extreme environments. Geochemically relevant media have been used to improve the success of culturing Archaea and Bacteria, but these efforts have focused primarily on optimizing pH, alkalinity, major ions, carbon sources, and electron acceptor–donor pairs. Here, we cultured thermophilic microorganisms from ‘Sylvan Spring’ (Yellowstone National Park, USA) on media employing different trace element solutions, including one that mimicked the source fluid of the inocula. The growth medium that best simulated trace elements found in ‘Sylvan Spring’ produced a more diverse and faster growing mixed culture than media containing highly elevated trace element concentrations. The elevated trace element medium produced fewer phylotypes and inhibited growth. Trace element concentrations appear to influence growth conditions in extreme environments. Incorporating geochemical data into cultivation attempts may improve culturing success.     

Evolution of early determinate tomato cultivars during the last three decades as a result of research conducted at Warsaw Agricultural University

Earliness is a crucial factor of tomato field production in Poland. A. Michalska and B. Kubicki (1978) conducted the first investigations on tomato earliness at the Department of Plant Genetics and Breeding. The main conclusions from these studies indicated that it was possible to obtain varieties earlier than ‘New Yorker’ as a result of transgression. The two new varieties (‘Alfa’ and ‘Akord F₁’) proved to be two weeks earlier than ‘New Yorker’. However, earliness was correlated with smaller fruit weight (30–40 g). At the next stage of experiment some improvement was achieved both in the size of fruit (45 g for ‘Beta’ up to 70 g for ‘Alka’) as well as colour intensity and good flavour. With the next few years fruit weight was still increased (up to 100 g for ‘Maskarena’) and a higher level of firmness was obtained (mid firm fruits for ‘Maskarena’ and ‘Delta’). At present, the Polish Research Centre for Cultivar Testing recommends our varieties ‘Betalux’, ‘Promyk’ and ‘Delta’ as standards.     

Bacterial assemblages differ between compartments within the coral holobiont

It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are organized within their hosts remains poorly understood. Previous sampling techniques (blasted coral tissues, coral swabs and milked mucus) may preferentially sample from different compartments such as mucus, tissue and skeleton, or amalgamate them, making comparisons and generalizations between studies difficult. This study characterized bacterial communities of corals with minimal mechanical disruption and contamination from water, air and sediments from three compartments: surface mucus layer (SML), coral tissue and coral skeleton. A novel apparatus (the ‘snot sucker’) was used to separate the SML from tissues and skeleton, and these three compartments were compared to swab samples and milked mucus along with adjacent environmental samples (water column and sediments). Bacterial 16S rRNA gene diversity was significantly different between the various coral compartments and environmental samples (PERMANOVA, F = 6.9, df = 8, P = 0.001), the only exceptions being the complete crushed coral samples and the coral skeleton, which were similar, because the skeleton represents a proportionally large volume and supports a relatively rich microflora. Milked mucus differed significantly from the SML collected with the ‘snot sucker’ and was contaminated with zooxanthellae, suggesting that it may originate at least partially from the gastrovascular cavity rather than the tissue surface. A common method of sampling the SML, surface swabs, produced a bacterial community profile distinct from the SML sampled using our novel apparatus and also showed contamination from coral tissues. Our results indicate that microbial communities are spatially structured within the coral holobiont, and methods used to describe these need to be standardized to allow comparisons between studies.     

Effects of NaCl stress on germination, antioxidant responses, and proline content in two rice cultivars

We investigated the physiological and biochemical bases for salt tolerance in two rice (Oryza sativa L.) cultivars — relatively salt-tolerant ‘Dongjin’ and salt-sensitive ‘Kumnam’. Salinized hydroponic cultures were studied at the germination and seedling stages. NaCI inhibited germination more severely in ‘Kumnam’ than in ‘Dongjin’. Increasing the salt concentration also deterred growth to a larger extent in the former. Moreover, the leaves of ‘Kumnam’ exhibited greater increases in lipid peroxidation and Na⁺ accumulation than those of ‘Dongjin’ under stress. The activities of constitutive and salt-induced superoxide dismutase (SOD, EC 1.15.1.1) and ascorbate peroxidase (AP, EC 1.11.1.11) were also higher in ‘Kumnam’, while only catalase (CAT, EC 1.11.1.6) activity was slightly higher in stressed plants of ‘Dongjin’. The positive correlation between leaf proline levels and NaCI concentration was more evident in ‘Kumnam’. However, ‘Dongjin’ seeds, which had higher germinability in the presence of NaCI, also contained more proline. These results suggest that the higher salt tolerance in ‘Dongjin’ seedlings could be ascribed to their lower NaCI accumulations in the leaves. This presumably is due to reductions in the uptake or transport rates of saline ions to the shoots from the roots. Finally, we believe that the higher germination rate by ‘Dongjin’ is caused by its higher seed proline content.     

Steroidal glycoalkaloid content of potato,tomato and their somatic hybrids

Summary Analyses of leaves and ‘tubers’ from somatic hybrids of potato and tomato (‘pomato’ with plastids of potato, ‘topato’ with plastids of tomato) produced by fusion of protoplasts from liquid cultures of dihaploid potato and mesophyll of tomato revealed the presence of the two major potato glycoalkaloids (α-solanine and α-chaconine) as well as the tomato glycoalkaloid (αtomatine). The total alkaloid content of leaves was greater than that of ‘tubers’ and similar to levels in the foliage of parent plants. However, glycoalkaloids were more abundant in hybrid ‘tubers’ than in normal potato tubers by a factor of 5–15. In hybrid foliage, approximately 98% of the alkaloid present was of potato origin whereas in ‘tubers’ the reverse was the case, with tomatine comprising 60–70% of the total alkaloid. The similarities in alkaloid content and ratios between the pomato and the topato lines indicate that plastomes do not influence the biosynthesis and distribution of these alkaloids. The results indicate that major secondary metabolites may prove useful for assessing the hybrid nature of such plants.     

Where does heteroclisis come from? Evidence from Romanian dialects

This study examines some cases of heteroclisis in the history of Romanian dialects, and concludes that the data call for a reconsideration of Stump’s distinction (Language 82:279–322, 2006) between ‘cloven’ heteroclisis, where the intraparadigmatic ‘split’ is aligned with some morphosyntactic feature distinction, and ‘fractured’ heteroclisis, where this is not the case and the pattern of heteroclisis is purely morphological. Stump’s account creates the impression that the ‘cloven’ variety is universally predominant, and that the ‘fractured’ variety tends to follow very closely the available ‘cloven’ patterns of the language. I shall suggest, instead, that the ‘fractured-only’ situation may in fact underlie heteroclisis cross-linguistically, the phenomenon being in general sensitive not directly to morphosyntactic content, but rather to characteristic, and often purely ‘morphomic’, patterns of stem-allomorphy. Research for this paper was undertaken as part of the Arts and Humantities Research Council-funded project Autonomous Morphology in Diachrony: comparative evidence from the Romance Languages, currently being conducted at Oxford University.     

Seasonal studies on alginate and its composition II: Turbinaria conoides (J.Ag.) Kütz. (Fucales, Phaeophyceae)

The alginates extracted from ‘leaf’, ‘stem’ and entire thallus of Turbinaria conoides (J.Ag.) Kütz. were investigated for their viscosity and biochemical constituents namely, β-D-mannuronic acid (M-block}), α-L-guluronic acid (G-Block) and alternating sequences of β–D-mannuronic acid and α-L-guluronic acid (MG-block). Substantial seasonal variation was recorded with high yield of alginate during premonsoon. The yield of alginate was maximum in ‘leaf’ region. In contrast to this, viscosity and G-block were maximum in the ‘stem’ region. A significant positive correlation was observed between viscosity and G-block}. The ratio of guluronic: mannuronic acid was also assessed. Low levels of M/G ratio were recorded in the ‘stem’ region followed by ‘leaf’ and entire thallus.     

Coloured hailnets alter light transmission,spectra and phytochrome,as well as vegetative growth,leaf chlorophyll and photosynthesis and reduce flower induction of apple

In view of alleged positive effects of coloured (red) hailnets on phytochrome, photosynthesis, yield and fruit quality, the objective of the present work was to investigate a range of red and green hailnets using apple as a model crop with cvs. ‘Pinova’ and ‘Fuji Kiku 8’. Light transmission of green or red hailnets peaked between 500 and 570 nm (green) or above 570 nm (red–orange) and was reduced by 12% (white) or 14% (red–white), 18% (red–black) and 23% (green–black) hailnets; there were no effects on phytochrome. Leaf chlorophyll concentration increased under coloured hailnets by up to 46% under the green–black hailnet, while air temperature was reduced by 0.2°C. Under sunny conditions, photosynthesis of ca. 18 μmol CO₂ m⁻² s⁻¹ was not reduced under coloured hailnets, in contrast with a 21% reduction under cloudy conditions with a concomitant reduction in transpiration by 13%. Vegetative growth was affected in different ways: shaded trees showed smaller trunk diameter, but increased the number and length of their 1-year shoots under coloured hailnets, particularly with cv. ‘Fuji’ when grown under green–black hailnet. Hailnets reduced flower induction in June and return bloom in the next spring to the same extent as they reduced the light transmission. Overall, tree growth under coloured hailnets was genetically influenced, with cv. ‘Fuji’ being more prone and sensitive to adverse effects of coloured hailnets than cv. ‘Pinova’, but is also influenced by the environment. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

History of the word photosynthesis and evolution of its definition

In 1893, Charles Barnes (1858–1910) proposed that the biological process for ‘synthesis of complex carbon compounds out of carbonic acid, in the presence of chlorophyll, under the influence of light’ should be designated as either ‘photosyntax’ or ‘photosynthesis.’ He preferred the word ‘photosyntax,’ but ‘photosynthesis’ came into common usage as the term of choice. Later discovery of anoxygenic photosynthetic bacteria and photophosphorylation necessitated redefinition of the term. This essay examines the history of changes in the meaning of photosynthesis. This revised version was published online in June 2006 with corrections to the Cover Date.     

Triploid banana cell growth phases and the correlation of medium pH changes with somatic embryogenesis in embryogenic cell suspension culture

Embryogenic cell suspensions of Musa AAA and AAB genomic groups were cultured in a maintenance culture medium for 17 generations (lasting for 238 days). The cell growth phases and medium pH changes were also observed correspondingly. Three major growth phases of AAA genomic group have been focused, namely cell releasing, proliferation and globularization phases. During almost all the subculture generations the cell stocks of AAB ‘Raja’ were continuously characterized by proliferating cell aggregates while the globularization phase occurred only for short duration. The medium acidity levels of the cell stocks of AAA ‘Pei-Chiao’ and ‘Robusta’ were commonly scattered in a wider range of pH 3.3–5.3, while the AAB ‘Raja’ were deviated in a narrow range of pH 4.0–4.6. After subculture, culture medium showed biphasic pH changes, which were drastic pH falls followed by an auto-regulated steady-state level. The steady-state pH values in each of the three growth phases (i.e. cell releasing, proliferation and globularization phases) were of 3.3–4.0, 4.0–4.8 and 4.8–5.3 respectively. Morphological bipolarity and the efficiency in the formation of somatic embryos have been thoroughly discussed. Reported research indicates that the condition of pH below 4.6 may prevent the development of embryogenic cells towards polar growth.     

A preliminary survey of organic pollution of shellfish in Tolo Harbour,Hong Kong

A preliminary survey on the contamination of clams and sea-waters in various towns in Tolo Harbour was carried out using bacteriological tests. The ‘percentage clean’ method and the ‘most probably number’ method were employed. The pH, salinity and temperature of the seawater were also tested in the field. It was discovered that the number of coliform bacteria obtained by the ‘percentage clean’ was zero in both seawater and clams from all sites including the control. The ‘most probable number’ indicated that the water and the clam tissue collected in the three sites in Tolo Harbour ranged from 15–1,100/100 ml in the water and 825–11,000/g in the clams compared with 0/100 ml and 115/g of the control site. Due to the high level of organic pollution in Tolo Harbour, improvement of the sanitary situation is urged. Cultivation of clams collected in this area in clean and sterilized water for a few days before consumption is recommended.