Water temperature in a stream gravel bed and implications for salmonid incubation

SUMMARY. 1. Water temperatures were recorded at hourly intervals in the gravel of a trout spawning area in a small stony stream at depths of 0–20 cm in 1985–86 and 0– 40 cm in 1987.
2. As depth within gravel increased, the size of the daily fluctuations reduced and their time of occurrence was delayed by about 12 min cm⁻¹' in 1985–86 and about 6 min cm⁻¹ in 1987.
3. From October to February mean temperatures at 20 cm depth were, on average, 0.5°C higher than those at the gravel surface. This reflected elevated daily minima more than it reflected elevated daily maxima.
4. From March to July daily minima were lower and daily maxima were higher in the stream than in the gravel. Consequences were: (a) an appreciable increase in mean daily range at all depths in the gravel during the summer, (b) higher daily means (by an average of about 0.4°C) in the water than in the gravel in May to August.
5. Some implications for the early development of salmonid fish are considered.     

Analysis of a water mediated protein-protein interactions within RNase T1

Buried and well-ordered solvent molecules are an integral part of each folded protein. For a few individual water molecules, the exchange kinetics with solvent have been described in great detail. So far, little is known about the energetics of this exchange process. Here, we present an experimental approach to investigate water-mediated intramolecular protein-protein interactions by use of double mutant cycles. As a first example, we analyzed the interdependence of the contribution of two side chains (Asn9 and Thr93) to the conformational stability of RNase T1. In the folded state, both side chains are involved in the solvation of the same water molecule WAT1. The coupling of the contributions of Asn9 and Thr93 to the conformational stability of RNase T1 was measured by urea unfolding and differential scanning calorimetry. The structural integrity of each mutant was analyzed by X-ray crystallography. We find that the effects of the Asn9Ala and the Thr93Ala mutations on the conformational stability are additive in the corresponding double mutant. We conclude that the free energy of the WAT1 mediated intramolecular protein-protein interaction in the folded state is very similar to solvent mediated protein-protein interaction in the unfolded state.     

Calcium delivery and storage in plant leaves: exploring the link with water flow

Calcium (Ca) is a unique macronutrient with diverse but fundamental physiological roles in plant structure and signalling. In the majority of crops the largest proportion of long-distance calcium ion (Ca(2+)) transport through plant tissues has been demonstrated to follow apoplastic pathways, although this paradigm is being increasingly challenged. Similarly, under certain conditions, apoplastic pathways can dominate the proportion of water flow through plants. Therefore, tissue Ca supply is often found to be tightly linked to transpiration. Once Ca is deposited in vacuoles it is rarely redistributed, which results in highly transpiring organs amassing large concentrations of Ca ([Ca]). Meanwhile, the nutritional flow of Ca(2+) must be regulated so it does not interfere with signalling events. However, water flow through plants is itself regulated by Ca(2+), both in the apoplast via effects on cell wall structure and stomatal aperture, and within the symplast via Ca(2+)-mediated gating of aquaporins which regulates flow across membranes. In this review, an integrated model of water and Ca(2+) movement through plants is developed and how this affects [Ca] distribution and water flow within tissues is discussed, with particular emphasis on the role of aquaporins.     

Gene functioning and storage within a folded genome

In mammals, genomic DNA that is roughly 2 m long is folded to fit the size of the cell nucleus that has a diameter of about 10 μm. The folding of genomic DNA is mediated via assembly of DNA-protein complex, chromatin. In addition to the reduction of genomic DNA linear dimensions, the assembly of chromatin allows to discriminate and to mark active (transcribed) and repressed (non-transcribed) genes. Consequently, epigenetic regulation of gene expression occurs at the level of DNA packaging in chromatin. Taking into account the increasing attention of scientific community toward epigenetic systems of gene regulation, it is very important to understand how DNA folding in chromatin is related to gene activity. For many years the hierarchical model of DNA folding was the most popular. It was assumed that nucleosome fiber (10-nm fiber) is folded into 30-nm fiber and further on into chromatin loops attached to a nuclear/chromosome scaffold. Recent studies have demonstrated that there is much less regularity in chromatin folding within the cell nucleus. The very existence of 30-nm chromatin fibers in living cells was questioned. On the other hand, it was found that chromosomes are partitioned into self-interacting spatial domains that restrict the area of enhancers action. Thus, TADs can be considered as structural-functional domains of the chromosomes. Here we discuss the modern view of DNA packaging within the cell nucleus in relation to the regulation of gene expression. Special attention is paid to the possible mechanisms of the chromatin fiber self-assembly into TADs. We discuss the model postulating that partitioning of the chromosome into TADs is determined by the distribution of active and inactive chromatin segments along the chromosome.This article was specially invited by the editors and represents work by leading researchers.     

Inferring network interactions within a cell

The continuing growth in high-throughput data acquisition has led to a proliferation of network models to represent and analyse biological systems. These networks involve distinct interaction types detected by a combination of methods, ranging from directly observed physical interactions based in biochemistry to interactions inferred from phenotype measurements, genomic expression and comparative genomics. The discovery of interactions increasingly requires a blend of experimental and computational methods. Considering yeast as a model system, recent analytical methods are reviewed here and specific aims are proposed to improve network interaction inference and facilitate predictive biological modelling.     

Nutrient transfer between parafluvial interstitial water and river water: influence of gravel bar heterogeneity

1. Nutrient concentrations in interstitial water springs at the downstream ends of two gravel bars in the River Rhône were measured in order to estimate the importance of nutrient inputs [nitrate, dissolved organic carbon (DOC), biodegradable and refractory fractions of DOC] from the parafluvial zone (saturated sediments adjacent to the wetted channel, i.e. interstitial habitats of gravel bars) to the river as well as seasonal variations in these inputs.
2. Compared with surface water, parafluvial water had lower concentrations of DOC (especially the refractory fraction) and generally higher concentrations of nitrate. These differences were at their lowest during winter.
3. The influence of gravel bar geomorphological heterogeneity (grain size and spatial distribution of fine sediments) on parafluvial inputs was studied in terms of nutrient content and biofilm characteristics along transects across the gravel bars.
4. A gravel bar located in a stable area of the river had low transversal heterogeneity and acted as a sink for DOC and as a source of nitrate. The low fine sediment content and the high oxygenation of interstitial water must have enabled aerobic processes such as mineralization of organic matter and nitrification to occur.
5. In contrast, gravel bars located in a degradation zone of the river had a spatially variable structure, acting as a sink for DOC and nitrate because localized accumulation of fine sediment and ensuing hypoxic conditions induced anaerobic processes such as denitrification.
6. This study highlights the important influence of geomorphological heterogeneity in gravel bars for nutrient transformations as well as nutrient exchanges between parafluvial interstitial systems and the adjacent river over a seasonal cycle.     

Nitrogen nutrition of beech forests in a changing climate: importance of plant-soil-microbe water,carbon, and nitrogen interactions

Background

For 15+ years, a beech (Fagus sylvatica L.) dominated forest on calcareous soil was studied on two opposing slopes with contrasting microclimate in Tuttlingen, Swabian Alb, Germany. The cool-humid NE aspect of these slopes represents the majority of beech forests under current climate, the warmer and drier SW aspect represents beech forests under future climate conditions. The field studies were supplemented by investigations under controlled conditions.

Scope

The research program aimed to provide a comprehensive understanding of plant-soil-microbe water, carbon and nitrogen feedbacks in a changing climate and a holistic view of the sensitivity of beech to climate change.

Conclusions

The results of comparative and experimental studies underpin the high vulnerability of adult beech and its natural regeneration on calcareous soil to both direct climate change effects on plant physiology and indirect effects mediated by soil biogeochemical cycles. Mechanisms contributing to this vulnerability at the ecosystem and organismic level indicate a high significance of competitive interactions of beech with other vegetation components and soil microbial communities. Obvious forest management practices such as selective felling did not necessarily counteract negative effects of climate change.

     

Suitable water temperature for seed storage of Zostera japonica for subtropical seagrass bed restoration

Restoration of Zostera japonica is needed. Laboratory culture experiments to know the germination characteristics might be helpful for implementation of actual restoration. As a part of germination experiments, we explored suitable water temperature for long-term storage of Z. japonica seeds. This work was based on earlier reports of Zostera marina, which presumably has similar physiological properties to Z. japonica. This study consisted of two experiments: (1) preservation experiments to investigate the fate of stored Z. japonica seeds and (2) germination experiments to investigate the germination potential of the stored seeds. The results of the preservation experiments suggested that seed condition, that is, germinated, degraded, unstable, stable, etc., showed variations between the seeds stored at 4 and 23 °C. The majority of the seeds stored at 4 °C were germinated, while those at 23 °C seemed to be degraded, presumably by bacteria and mold. The germination experiments suggested high germination potential of seeds stored at 4 °C even after 302 days had elapsed. In conclusion, including previously reported results on Z. marina, low temperature was suitable for the preservation of seeds to maintain germination potential.     

Trypanosoma rangeli interactions within the vector Rhodnius prolixus: a mini review

This article is an integrative mini review of the research on the interactions between Trypanosoma rangeli and the insect vector, Rhodnius prolixus. Special attention is given to the interactions of these parasites with the gut environment, gut walls, with hemolymph invasion, hemocytes, hemocyte microaggregations, prophenoloxidase-activating system, superoxide, and nitric acid generation and eicosanoid pathways. We described factors affecting vectorial capacity and suggested that T. rangeli may modulate the hemocoelic invasion and the survival of the parasites by overcoming the cellular and humoral defense reactions of the insect vector at different physiological events. The mechanisms of these interactions and their significance for parasite transmission are discussed.     

Random patch dynamics of larval Chironomidae (Diptera) in the bed sediments of a gravel stream

• 1 The larval chironomid community of the sediment surface and the hyporheic inters titial was investigated in two longitudinal transects of an alpine gravel stream between September 1984 and August 1985. Eighty larval species and species groups were identified, most of which belonged to the subfamily Orthocladiinae. Of all larval individuals 51.1% inhabited the first 10cm of the bed sediments, and 93.2% occurred between the surface and 40cm depth.
• 2 The spatial species turnover showed marked variations between horizontally adjacent sampling sites in each of the four sediment depth layers. In both transects the species composition showed a significantly lower turnover in the upper 10cm of the bed sediments than in the deeper layers.
• 3 Spatial community stability showed an oscillating pattern between all sampling sites due to density shifts of larvae between depth layers. Temporal differences in resilience (local stability) were significantly and positively related to changes in the cumulative discharge pattern in the gravel brook, thus indicating the apparent ability of the community to recover quickly following disturbances.
• 4 The five abundant species, Corynoneura lobata, Synorthocladius semivirens, Tvetenia calvescens, Micropsectra atrofasciata and Rheotanytarsus nigricauda, exhibited significant differences in their sediment depth distribution, with density maxima shifting between depth layers. Spatial autocorrelations suggest that these larvae form patches between neighbouring sampling sites with varying sizes and inter-patch distances in each of four sediment layers. A simulation test, in which individuals of each species were randomly permuted between microhabitats of each depth layer separately, indicated that the patches might have arisen by chance.
• 5 To evaluate the significance of observed spatial resource overlap values amongst these five chironomid species, neutral models were developed based on 300 randomizations of each possible species pair-wise association of individuals and patches of species. The spatial organization of a larval chironomid assemblage in the stream Oberer Seebach seemed to be governed by coexistence due to random patch formation and dispersal patterns within the interstitial habitats, which reduce the probability of strong competitive interactions.

     

Soil water status influences plant nitrogen use: a case study

We studied differences in nitrogen use efficiency (NUE) among six species [Calamagrostis epigejos (L.) Roth., Carex duriuscula C.A. Mey., Phragmites communis (L.) Trin., Salix gordejevii Y.L. Chang, Salix cheilophila Schneid., and Typha minima Funk.] growing in two contrasting habitat types, i.e., a riverine wetland with high water supply and a riparian zone with low water supply. The two sites were different in soil water supply, but not in nitrogen supply. Here, NUE was defined as the total net primary production per unit nitrogen absorbed. There was no significant difference in NUE between the species growing in the riverine wetland (Carex duriuscula, P. communis, S. cheilophila, T. minima) and the species growing in the river bank (Carex duriuscula, Calamagrostis epigejos, P. communis, S. gordejevii). We further analyzed NUE as the product of the nitrogen productivity (A, the rate of dry matter production per unit of nitrogen in the plant) and the mean residence time of nitrogen (MRT, the period of time a unit of nitrogen is present in the plant). The species growing in the riverine wetland had larger A but lower MRT than the species growing in the river bank. There was an inverse relationship between A and MRT. Consequently, NUE was similar among species and habitats. These results suggested that environmental factors, such as soil water supply, can influence N use by plants.     

Minimising biomass/adsorbent interactions in expanded bed adsorption processes: a methodological design approach

Expanded bed adsorption (EBA) is an integrated technology for the primary recovery of proteins from crude feedstock. Interactions between solid matter in the feed suspension and fluidised adsorbent particles influence bed stability and therefore have a significant impact on protein adsorption in expanded beds. In order to design efficient and reliable EBA processes a strategy is needed, which allows to find operating conditions, where these adverse events do not take place. In this paper a methodological approach is presented, which allows systematic characterisation and minimisation of cell/adsorbent interactions with as little experimental effort as possible. Adsorption of BSA to the anion exchanger Streamline Q XL from a suspension containing S. cerevisiae cells was chosen as a model system with a strong affinity of the biomass towards the stationary phase. Finite bath biomass adsorption experiments were developed as an initial screening method to estimate a potential interference. The adhesiveness of S. cerevisiae to the anion exchanger could be reduced significantly by increasing the conductivity of the feedstock. A biomass pulse response method was used to find optimal operation conditions showing no cell/adsorbent interactions. A good correlation was found between the finite bath test and the pulse experiment for a variety of suspensions (intact yeast cells, E. coli homogenate and hybridoma cells) and adsorbents (Streamline Q XL, DEAE and SP), which allows to predict cell/adsorbent interactions in expanded beds just from finite bath adsorption tests. Under the optimised operating conditions obtained using the prior methods, the stability of the expanded bed was investigated during fluidisation in biomass containing feedstock (up to 15% yeast on wet weight basis) employing residence time distribution analysis and evaluation by an advanced model. Based on these studies threshold values were defined for the individual experiments, which have to be achieved in order to obtain an efficient EBA process. Breakthrough experiments were conducted to characterise the efficiency of BSA adsorption from S. cerevisiae suspensions in EBA mode under varying operating conditions. This allowed to correlate the stability of the expanded bed with its sorption efficiency and therefore could be used to verify the threshold values defined. The approach presented in this work provides a fast and simple way to minimise cell/adsorbent interactions and to define a window of operation for protein purification using EBA.     

Ephaptic interactions within a chemical synapse: hemichannel-mediated ephaptic inhibition in the retina

The two best-known types of cell-cell communication are chemical synapses and electrical synapses, which are formed by gap junctions. A third, less well known, form of communication is ephaptic transmission, in which electric fields generated by a specific neuron alter the excitability of neighboring neurons as a result of their anatomical and electrical proximity. Ephaptic communication can be present in a variety of forms, each with their specific features and functional implications. One of these is ephaptic modulation within a chemical synapse. This type of communication has recently been proposed for the cone-horizontal cell synapse in the vertebrate retina. Evidence indicates that the extracellular potential in the synaptic terminal of photoreceptors is modulated by current flowing through connexin hemichannels at the tips of the horizontal cell dendrites, mediating negative feedback from horizontal cells to cones. This example can be added to the growing list of cases of ephaptic communication in the central nervous system.     

Geographical patterns of adaptation within a species' range: interactions between drift and gene flow

We use individual-based stochastic simulations and analytical deterministic predictions to investigate the interaction between drift, natural selection and gene flow on the patterns of local adaptation across a fragmented species' range under clinally varying selection. Migration between populations follows a stepping-stone pattern and density decreases from the centre to the periphery of the range. Increased migration worsens gene swamping in small marginal populations but mitigates the effect of drift by replenishing genetic variance and helping purge deleterious mutations. Contrary to the deterministic prediction that increased connectivity within the range always inhibits local adaptation, simulations show that low intermediate migration rates improve fitness in marginal populations and attenuate fitness heterogeneity across the range. Such migration rates are optimal in that they maximize the total mean fitness at the scale of the range. Optimal migration rates increase with shallower environmental gradients, smaller marginal populations and higher mutation rates affecting fitness.     

Stem water storage capacity and efficiency of water transport: their functional significance in a Hawaiian dry forest

We investigated the contribution of internal water storage and efficiency of water transport to the maintenance of water balance in six evergreen tree species in a Hawaiian dry forest. Wood‐saturated water content, a surrogate for relative water storage capacity, ranged from 70 to 105%, and was inversely related to its morphological correlate, wood density, which ranged between 0·51 and 0·65 g cm^?3. Leaf‐specific conductivity (k_L) measured in stem segments from terminal branches ranged from 3 to 18 mmol m^?1 s^?1 MPa^?1, and whole‐plant hydraulic efficiency calculated as stomatal conductance (g) divided by the difference between predawn and midday leaf water potential (Ψ_L), ranged from 70 to 150 mmol m^?2 s^?1 MPa^?1. Hydraulic efficiency was positively correlated with k_L (r² = 0·86). Minimum annual Ψ_L ranged from ? 1·5 to ? 4·1 MPa among the six species. Seasonal and diurnal variation in Ψ_L were associated with differences among species in wood‐saturated water content, wood density and k_L. The species with higher wood‐saturated water content were more efficient in terms of long‐distance water transport, exhibited smaller diurnal variation in Ψ_L and higher maximum photosynthetic rates. Smaller diurnal variation in Ψ_L in species with higher wood‐saturated water content, k_L and hydraulic efficiency was not associated with stomatal restriction of transpiration when soil water deficit was moderate, but avoidance of low minimum seasonal Ψ_L in these species was associated with a substantial seasonal decline in g. Low seasonal minimum Ψ_L in species with low k_L, hydraulic efficiency, and wood‐saturated water content was associated with higher leaf solute content and corresponding lower leaf turgor loss point. Despite the species‐specific differences in leaf water relations characteristics, all six evergreen tree species shared a common functional relationship defined primarily by k_L and stem water storage capacity.     

Spatial interactions within modular organisms: genetic heterogeneity and organism fitness

Modular organisms are composed of iterated units of construction that vary in their spatial arrangement. This variation is expected to affect the fitness of modular organisms due to interactions among neighboring modules and the potential for such organisms to be genetically heterogeneous. We devise a spatially explicit model to investigate how spatial interactions among neighboring modules affect organism fitness. We show that fitness is strongly dependent on the spatial arrangement of modules in both genetically homogeneous and heterogeneous organisms, and that the magnitude of the variation is dependent on the strength of interactions among modules. Organism fitness is more variable with interactions among modules that are symmetrical (each affects each other in the same directions) than with asymmetrical interactions (neighbors affect each other in different directions). We conclude by discussing potential extension of the present framework to a general dynamic model of spatially structured organism development.     

Stigmatic pollen delivery by flies and bees: Methods comparing multiple species within a pollinator community

A wide variety of insect species provide pollination services in natural and agricultural ecosystems, but in order to quantify their contribution it is necessary to evaluate their effectiveness. An important component of this is to determine their ability to transfer pollen to stigmas which typically requires observers to wait for insects to visit focal flowers (static approach); a time-consuming process not amenable to obtaining measures for pollinating species of low local abundance. An alternative method (active approach) is to detach test flowers and present them to the targeted flower visitor. This offers a number of advantages (e.g. increased speed and flexibility), but may alter insect behaviour. We compared pollen deposition within flowering onion crops using three bee (Apoidea) and three fly (Diptera) species. The two approaches resulted in similar numbers of pollen grains being deposited onto stigmas for each insect species, thereby supporting the validity of the active as an alternative to the static approach in our test crop. The ability to rapidly assess stigmatic pollen deposition of a broad range of insects using the active approach can greatly assist assessments of pollinator contribution within plant pollinator assemblages.     

Nitrogen storage and remobilization in Brassica napus L. during the growth cycle: nitrogen fluxes within the plant and changes in soluble protein patterns

Oilseed rape (Brassica napus L.) is commonly grown for oil or bio-fuel production, while the seed residues can be used for animal feed. It can also be grown as a catch crop because of its efficiency in extracting mineral N from the soil profile. However, the N harvest index is usually low, due in part to a low ability to remobilize N from leaves and to the fall of N-rich leaves which allows a significant amount of N to return to the environment. In order to understand how N filling of pods occurs, experiments were undertaken to quantify N flows within the plant by (15)N labelling and to follow the changes in soluble protein profiles of tissues presumed to store and subsequently to remobilize N. Whereas N uptake increased as a function of growth, N uptake capacity decreased at flowering to a non-significant level during pod filling. However, large amounts of endogenous N were transferred from the leaves to the stems and to taproots which acted as a buffering storage compartment later used to supply the reproductive tissue. About 15% of the total N cycling through the plant were lost through leaf fall and 48%, nearly all of which had been remobilized from vegetative tissues, were finally recovered in the mature pods. SDS-PAGE analysis revealed that large amounts of a 23 kDa polypeptide accumulated in the taproots during flowering and was later fully hydrolysed. Its putative function of storage protein is further supported by the fact that when plants were grown at lower temperature, both flowering, its accumulation and further mobilization were delayed. The overall results are discussed in relation to plant strategies which optimize N cycling to reproductive sinks by means of buffering vegetative tissues such as stems and taproots.     

The distribution of rotifers (Rotifera) within a single Myriophyllum bed

The research on the spatial distribution of rotifers between the central and border part of the Myriophyllum bed (M. verticillatum) was carried out between 1998 and 1999 in the shallow part (approx. 1 m depth) of Budzyńskie Lake (Wielkopolski National Park, Poland). The comparison of both species composition and the numbers of individuals between both of the examined zones have not revealed statistically significant differences. However, a higher number of rotifer species and their higher densities, as well as increased participation of littoral species were observed in the middle of the vegetation bed. The structure of the dominating species also differed between both areas. Seven rotifer species were found to have significantly greater numbers in the central part of the Myriophyllum bed, while only one species was significantly correlated with the border part of the macrophyte stand. These differences in the behaviour of particular groups of rotifers may be dependent on the structure of their microhabitat and their position in relation to the open water zone. They may also be related to young fish predation in both habitats and better refuge conditions inside the thick macrophyte stand, as well as typical adaptation to littoral or limnetic life.

     

A water network within a protein: temperature-dependent water ligation in H64V-metmyoglobin and relaxation to deoxymyoglobin

The sperm whale myoglobin mutant H64V, where the distal histidine is mutated to valine, is known to be five coordinated in the ferric state at room temperature and physiological pH. A change of the ligation in this H64V-Mbmet has been observed by optical absorption spectroscopy as a function of temperature from 20 K to 300 K. Above the dynamical transition at about 180 K one observes the temperature-dependent equilibrium between five- and six-ligated heme. Below the dynamical transition the equilibrium is frozen-in at about 50% of six-coordinate molecules. The water ligation of the iron occurs at temperatures where protein-specific motions are present, as monitored by M?ssbauer spectroscopy. The X-ray structures of H64V-Mbmet at 300 K and 110 K are reported with a resolution of 1.5 A and 1.3 A, respectively. The measurements at high resolutions are possible owing to crystallization in the space group P2(1), whereas all mutant myoglobins studies up to now have been carried out with crystals in the space group P6. The overall structure at both temperatures is very close to the native myoglobin. The binding of water at the sixth coordination site at lower temperatures is possible owing to a stabilizing water network extending from the protein surface to the active centre. The reduction of the H64V-Mbmet by electrons obtained by X-ray irradiation of the water-glycerol solvent at 85 K produces an intermediate low-spin state of the water-ligated molecules where Fe(II) retains the six-fold coordination. M?ssbauer spectroscopy shows that the relaxation of the metastable low-spin state to high-spin H64V-Mbdeoxy with dissociation of the Fe(II)-H(2)O bond starts at about 115 K and is completed at about 170 K. Differences in the dynamics properties of the native and mutant myoglobin and the connection to the dynamical transition around 180 K are discussed.