Early environment influences later performance in fishes

Conditions fish encounter during embryogenesis and early life history can leave lasting effects not only on morphology, but also on growth rate, life‐history and behavioural traits. The ecology of offspring can be affected by conditions experienced by their parents and mother in particular. This review summarizes such early impacts and their ecological influences for a variety of teleost species, but with special reference to salmonids. Growth and adult body size, sex ratio, egg size, lifespan and tendency to migrate can all be affected by early influences. Mechanisms behind such phenotypically plastic impacts are not well known, but epigenetic change appears to be one central mechanism. The thermal regime during development and incubation is particularly important, but also early food consumption and intraspecific density can all be responsible for later life‐history variation. For behavioural traits, early experiences with effects on brain, sensory development and cognition appear essential. This may also influence boldness and other social behaviours such as mate choice. At the end of the review, several issues and questions for future studies are given.     

Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

Type-3 functional response in limnetic suspension-feeders,as demonstrated by in situ grazing rates

Field-measured grazing rates (ml/animal/d) of cladocerans (mostly daphniids) and diaptomids were assembled from various published studies and plotted as a function of corresponding phytoplankton concentration (μg l⁻¹ f.w.). Filtering rates of both zooplankton groups initially increased with seston concentration until maximal grazing rates were observed at approximately 4 × 10² and 1 × 10² μg l⁻¹ for cladocerans and copepods, respectively; at higher algal concentrations, filtering rates of both declined as a function of food concentration. The shape of these curves are most consistent with Holling's (1966) Type 3 functional response. We found little support for the Type 3 functional response in published laboratory studies of Daphnia; most investigators report either a Type 1 or Type 2 response. The one study in which the Type 3 response was observed involved experiments where animals were acclimated at low food concentrations for 24 h, whereas those studies associated with response Types 1 or 2 had acclimation periods of only 1 to 3 h. We therefore assembled relevant data from the literature to examine the effect of acclimation period on the feeding rates of Daphnia at low food concentrations. In the absence of any acclimation, animals filtered at extremely low rates. After 2 h of acclimation, however, filtering rates increased 4 to 5-fold but declined again with longer durations; after > 70 h of pre-conditioning, filtering rates were almost as low as they had been with no acclimation. We also found little support for the Type 3 functional response in published studies of copepods. The only study associated with a Type 3 response involved a marine copepod that had been subjected to a starvation period of 48 h; however, an analysis of the effects of acclimation period did not yield conclusive evidence that filtering rates of freshwater copepods (Diaptomus and Eudiaptomus) decrease significantly with acclimation duration. The low filtering rates associated with long acclimation periods in laboratory experiments appears to be a direct result of animals becoming emaciated from prolonged exposure to low food concentrations, a situation which renders them incapable of high filtering rates. This may explain the Type 3 functional response for field cladocerans, since zooplankton in food-limiting situations are constantly exposed to low food concentrations, and would therefore have low body carbon and consequently less energy to filter-feed. We cannot, however, use this to explain the Type 3 response for field diaptomids, since copepods in the laboratory did not appear to lose body carbon even after 72 h of feeding at very low food levels, and there was inconclusive evidence that either Diaptomus or Eudiaptomus decrease their filtering rates with acclimation period. Although Incipient Limiting Concentrations (ILC) for Daphnia ranged from 1 to 8.5 × 10³ μg 1⁻¹, more than half of these fell between 1 and 3 × 10³ μg l⁻¹, bracketing the value of 2.7 × 10² μg l⁻¹ for field cladocerans. There was, however, a great deal of variation in reported maximum ingestion rates (MIR), maximum filtering rates (MFR) and ILC values for Daphnia magna. ILC values from the few laboratory studies of freshwater copepods ranged between 0.5 to 2.8 × 10³ μg 1⁻¹, and was higher than the ILC value of approximately 0.2 × 10³ μg l⁻¹ calculated for field populations of D. minutus. Generally, there was considerable agreement among laboratory studies regarding the shape of grazing-rate and ingestion-rate curves when data were converted to similar units and presented on standardized scales.     

An overview of indexes to evaluate terrestrial plants for phytoremediation purposes (Review)

This paper reviews the various factors, coefficients and indexes developed to evaluate terrestrial plant performance in respect to phytoremediation.A brief list of indexes includes the Accumulation factor, Bioabsorption coefficient, Bioaccumulation coefficient, Bioaccumulation factor, Bioconcentration, Bioconcentration coefficient, Bioconcentration factor, Biological absorption coefficient, Biological accumulation coefficient, Biological concentration factor, Biological transfer coefficient, Concentration factor, Enrichment coefficient, Enrichment factor, Extraction coefficient, Index of bioaccumulation, Mobility index, Shoot accumulation factor, Soil host transfer factor, Soil-plant transfer coefficient, Soil-plant transfer factor, Transfer factor and Translocation factor.These indexes represent the result of a ratio calculation between element concentrations in plant parts to that of substrata. In other cases indexes arise from the ratio calculation of element concentrations in two distinct plant parts.In the literature different terms have been attributed to the same ratio and this often represents an overlap in terminology. On the other hand the same term corresponds to several different ratios and this could create confusion and misinterpretation in data comparison.Furthermore, the evaluation of hyperaccumulation, phytostabilization or phytoextraction of plant species is not always performed in the same way. Different plant parts are considered as well as different extraction procedures for both plant and substrata element assessment. As a consequence, a direct comparison between obtained data is not always reliable and possible.In this paper the various available indexes are reviewed, highlighting both the similarity and differences between them with the aim of helping the community in choosing the appropriate term for both data evaluation and comparison. In this author’s opinion there is no need of new terms to define indexes. I would stress the need for conformity to the original definitions and criteria.     

Short-term variability of plant populations within a regularly disturbed habitat

The changing populations of weeds during 13 years of the Broadbalk continuous wheat experiment were analysed to investigate the extent of differences in shortterm variability of cover between species. The data were from two sections of the experiment where winter wheat was grown continuously under herbicide treatment for 13 and 6 years respectively. Logistic regressions were fitted to the data. Equisetum arvense showed significant long-term increases on both sections; long-term trends were also detected in the longer data run for Agrostis stolonifera, Cirsium arvensa, Poa trivialis, Ranunculus arvensis and Vicia sativa, and for Medicago lupulina on the shorter data run. Variation around long-term trends was low in the case of Equisetum, and, in the longer data run, for Cirsium and Tussilago farfara, and high for Poa spp. and Vicia. Cover values on the two sections were positively correlated for Alopecurus myosuroides, Equisetum, Poa annua and Tripleurospermum inodorum. There was a weak correlation between C-S-R strategy and short-term variability; the more competitive species displayed less variability than the ruderal species. Furthermore, species regenerating from persistent seed banks were more variable in the short term than those regenerating from short-lived seed or bud banks. This can be explained by differences in response to year-to-year variation in environmental conditions, those species with persistent seed banks being typically more sensitive to annual fluctuations in the environment than those without.