An agent-based modelling approach to estimate error in gyrodactylid population growth

Comparative studies of gyrodactylid monogeneans on different host species or strains rely upon the observation of growth on individual fish maintained within a common environment, summarised using maximum likelihood statistical approaches. Here we describe an agent-based model of gyrodactylid population growth, which we use to evaluate errors due to stochastic reproductive variation in such experimental studies. Parameters for the model use available fecundity and mortality data derived from previously published life tables of Gyrodactylus salaris, and use a new data set of fecundity and mortality statistics for this species on the Neva stock of Atlantic salmon, Salmo salar. Mortality data were analysed using a mark-recapture analysis software package, allowing maximum-likelihood estimation of daily survivorship and mortality. We consistently found that a constant age-specific mortality schedule was most appropriate for G. salaris in experimental datasets, with a daily survivorship of 0.84 at 13°C. This, however, gave unrealistically low population growth rates when used as parameters in the model, and a schedule of constantly increasing mortality was chosen as the best compromise for the model. The model also predicted a realistic age structure for the simulated populations, with 0.32 of the population not yet having given birth for the first time (pre-first birth). The model demonstrated that the population growth rate can be a useful parameter for comparing gyrodactylid populations when these are larger than 20-30 individuals, but that stochastic error rendered the parameter unusable in smaller populations. It also showed that the declining parasite population growth rate typically observed during the course of G. salaris infections cannot be explained through stochastic error and must therefore have a biological basis. Finally, the study showed that most gyrodactylid-host studies of this type are too small to detect subtle differences in local adaptation of gyrodactylid monogeneans between fish stocks.     

根据野外调查资料评估鱼类的日摄食量

基于海洋渔业资源常规调查和河口定置网取样资料 ,将调查期间同一鱼种各取样时刻的消化道 (或胃 )内含物量视为发生在 2 4小时内的同一样本空间的不同事件 ,根据消化道内含物的变动确定鱼类的不摄食时段以计算排空率。为定量早期幼鱼及消化系统复杂的鱼类消化道内含物重量 ,建立了空消化道重 (EDW ) -体长(BL) -体重 (BW )经验关系式 ,即EDW =α BWBLβ δ。应用Eggers模型或Elliott Persson模型对日摄食量进行评估。研究获得以下鱼类的日摄食量 (约占体重百分比 ) :渤海大面调查所获幼鱼 ,蓝点马鲛 (Scomberomorusniphonius,16 0 1± 1 96cm ,3 0 95± 12 3 2 g ,n =159) 13 5%、黄鲫 (Setipinnataty ,7 2 6± 1 99cm ,2 89±4 0 8g ,n =2 3 9) 15%、小黄鱼 (Pseudosciaenapolyactis ,6 84± 1 41cm ,6 94± 4 0 7g ,n =2 72 ) 13 5% ,斑(Konosiruspunctatus ,9 49± 0 91cm ,10 0 8± 3 2 8g ,n =10 7) 110 % ;河口定置网所获早期幼鱼 ,斑 (1 77± 0 2 1cm ,0 0 4± 0 0 2g ,n =50 5) 40 % ,黄鳍刺虎鱼 (Acanthogobiusflavimanus ,1 82± 0 16cm ,0 0 6±0 0 1g ,n =93 0 ) 15%     

Dietary self-selection in fish: a new approach to studying fish nutrition and feeding behavior

The principles of modern aquaculture encourage the development of fish feeds containing low fish meal content and several types of plant ingredients plus nutrients to avoid depleting global fish stocks and to reduce costs. However, food constituents can affect animal nutrition and feeding behavior, so the effect of different diets on fish behavior and growth needs to be understood to optimize the use of nutrients and to improve fish welfare. The development of multiple-choice self-feeding systems led to a new perspective for investigating these issues in aquaculture species. Our purpose with this review is to summarize the information that has been published to date on this topic and to identify gaps in knowledge where research is needed. Key subjects are assessed under the following major headings: How do we study dietary selection in fish? What food signals do fish use to choose the right diet? and How do fish respond to food challenges? The present review will provide a picture of the main results obtained to date in these studies in aquaculture fish species, as well as perspectives for future research in the field.     

A novel approach to estimate trabecular bone anisotropy using a database approach

Continuum finite element (FE) models of bones have become a standard pre-clinical tool to estimate bone strength. These models are usually based on clinical CT scans and material properties assigned are chosen as isotropic based only on the density distribution. It has been shown, however, that trabecular bone elastic behavior is best described as orthotropic. Unfortunately, the use of orthotropic models in FE analysis derived from CT scans is hampered by the fact that the measurement of a trabecular orientation (fabric) is not possible from clinical CT images due to the low resolution of such images. In this study, we explore the concept of using a database (DB) of high-resolution bone models to derive the fabric information that is missing in clinical images. The goal of this study was to investigate if models with fabric derived from a relatively small database can already produce more accurate results than isotropic models.     

Production and food consumption of predatory fish in the Vistula River

Vital statistics for six predatory fish species occurring in the Vistula River were estimated. The mixed, six species population, in its predatory phase, had an average biomass of 0-96 g/m2 and produced 043 g/ma. Less than 45% of annual production was exploited by man and eggs shed amounted to about 10% of the production. Annual consumption by the population amounted to about 3 -44 kcal or g/ma. Accuracy of all estimates is low.     

A new single work bout test to estimate critical power and anaerobic work capacity

The purpose of this study was to develop a 3-minute, all-out test protocol using the Monark cycle ergometer for estimating the critical power (CP) and anaerobic work capacity (AWC) with the resistance based on body weight. Twelve moderately trained adults (mean age ± SD = 23.2 ± 3.5 years) performed an incremental cycle ergometer test to exhaustion. The CP and AWC were estimated from the original work limit (W(lim)) vs. time limit (T(lim)) relationship (CP(PT)) and a 3-minute all-out test (CP(3min)) against a fixed resistance and compared with the CP and AWC estimated from the new 3-minute tests on the Monark cycle ergometer (CP(3.5%) and CP(4.5%)). The resistance values for the CP(3.5%) and CP(4.5%) tests were set at 3.5 and 4.5% of the subject's body weight (kilograms). The results indicated that there were no significant differences (p > 0.05) among mean CP values for CP(PT) (178 ± 47 W), CP(3.5%) (173 ± 40 W), and CP(4.5%) (186 ± 44 W). The mean CP(3min) (193 ± 54 W), however, was significantly greater than CP(PT) and CP(3.5%). There were no significant differences in AWC for the CP(PT) (13,412 ± 6,247 J), CP(3min) (10,895 ± 2,923 J), and CP(4.5%) (9,842 ± 4,394 J). The AWC values for the CP(PT) and CP(3min), however, were significantly greater than CP(3.5%) (8,357 ± 2,946 J). The results of this study indicated that CP and AWC could be estimated from a single 3-minute work bout test on the Monark cycle ergometer with the resistance set at 4.5% of the body weight. A single work bout test with the resistance based on the individual's body weight provides a practical and accessible method to estimate CP and AWC.     

An in situ estimate of food consumption of five cyprinid species in Lake Balaton

Daily rations of five cyprinid species, bream Abramis brama , silver bream Blicca bjoerkna , roach Rutilus rutilus , gibel Carassius auratus gibelio and carp Cyprinus carpio , in Lake Balaton, a large shallow lake, estimated by the Eggers model differed from that of the Elliott – Persson model by only − 4.3 to +7.3% (the differences were insignificant). Daily rations varied within the range of 0.23–0.69 in bream, 0.55–3.61 in silver bream, 0.69–4.65 in roach, 0.38–3.16 in gibel and 0.50–9.74 g dry 100 g wet fish mass⁻¹ day ⁻¹ in carp at temperatures ranging from 8.7–25.8% C. Daily ration was related exponentially with temperature in silver bream, roach, gibel and carp. For bream, a significant relationship was obtained only when a daily ration value was excluded from the analysis. Annual rations were assessed using the relationships between the daily ration estimates from the Elliott—Persson model and water temperature, and the long-term averages of the monthly water temperature data. From these estimates the bream population consumed 104%, silver bream 424%, roach 487%, gibel 363% and carp 913% dry mass of food of its wet biomass annually.     

A simple approach to estimate similarity in ecosystem analysis

A simple rank similarity index is proposed to use in estimation of ecological community similarities. The analysis of similarities is based on hypergeometric probabilities of the coincidence of dominant species in the samples. When 4 dominant species are ranked in samples, two sets of ranks can be compared in 133 different ways. In the case of total similarity rank similarity index M=10 and for dissimilarity M=0. Critical levels of M are given for total amount of species from 10 to 300. The proposed approach useful in rapid similarity analysis of planktonic communities.     

Bacterial clogging of porous media: A new modelling approach

A comparison is made between existing mathematical models and experimental data that relate the reduction of the saturated hydraulic conductivity (K) of a porous medium to the porosity reduction caused by microbial growth. The models yielded a realistic prediction of a data set obtained with a model porous medium consisting of millimeter‐size glass spheres, but failed to predict the clogging behaviour observed in smaller‐than‐1‐mm sand. A new modelling approach, semi‐mechanistic in nature, is proposed that gives good predictions of fine sand media as well. It relaxes the assumption about uniformly‐thick biofilms by allowing a second arrangement to occur, i.e. discrete plugs filling the pore lumen. The new model requires input data on two intrinsic properties of the system, which renders it sufficiently flexible as to fit very different data sets. The two model parameters are K_min, the minimum K value when all porosity is filled with microorganisms, and B_c, the biovolume fraction at which most cell detachment from biofilm occurs.     

Revised food consumption estimate of a bluegill sunfish population in Wyland Lake, Indiana, U.S.A.

The estimate of food consumption by the bluegill sunfish ( Lepomis macrochirus ) population of Wyland Lake, Indiana, was examined with reference to recent research on the length of the growing season and the effect of body weight, ration and activity on growth efficiency. Growth efficiency was measured in the laboratory in terms of protein, comparing nitrogen assimilated with nitrogen accumulated over a period of about 30 days.
The revised consumption of protein was 134.9kg (or 1407kg live weight of aquatic organisms, 444 kg/ha) during a growing season of 111 days compared with the original estimate of 127.3 kg calculated for an assumed growing season of 150 days, a difference of only 6%. The correspondence between the two estimates was coincidental. The original estimate was made at a time when the growing season had not been measured and the effect of ration and body size on growth efficiency was not precisely known. Corrections for these factors plus that for activity compensated for one another, closely approaching, by chance, the original value.     

A new baseline of organic carbon stock in European agricultural soils using a modelling approach

Proposed European policy in the agricultural sector will place higher emphasis on soil organic carbon (SOC), both as an indicator of soil quality and as a means to offset CO₂ emissions through soil carbon (C) sequestration. Despite detailed national SOC data sets in several European Union (EU) Member States, a consistent C stock estimation at EU scale remains problematic. Data are often not directly comparable, different methods have been used to obtain values (e.g. sampling, laboratory analysis) and access may be restricted. Therefore, any evolution of EU policies on C accounting and sequestration may be constrained by a lack of an accurate SOC estimation and the availability of tools to carry out scenario analysis, especially for agricultural soils. In this context, a comprehensive model platform was established at a pan‐European scale (EU + Serbia, Bosnia and Herzegovina, Croatia, Montenegro, Albania, Former Yugoslav Republic of Macedonia and Norway) using the agro‐ecosystem SOC model CENTURY. Almost 164 000 combinations of soil‐climate‐land use were computed, including the main arable crops, orchards and pasture. The model was implemented with the main management practices (e.g. irrigation, mineral and organic fertilization, tillage) derived from official statistics. The model results were tested against inventories from the European Environment and Observation Network (EIONET) and approximately 20 000 soil samples from the 2009 LUCAS survey, a monitoring project aiming at producing the first coherent, comprehensive and harmonized top‐soil data set of the EU based on harmonized sampling and analytical methods. The CENTURY model estimation of the current 0–30 cm SOC stock of agricultural soils was 17.63 Gt; the model uncertainty estimation was below 36% in half of the NUTS2 regions considered. The model predicted an overall increase of this pool according to different climate‐emission scenarios up to 2100, with C loss in the south and east of the area (involving 30% of the whole simulated agricultural land) compensated by a gain in central and northern regions. Generally, higher soil respiration was offset by higher C input as a consequence of increased CO₂ atmospheric concentration and favourable crop growing conditions, especially in northern Europe. Considering the importance of SOC in future EU policies, this platform of simulation appears to be a very promising tool to orient future policymaking decisions.     

Material properties of the cornea and sclera: a modelling approach to test experimental analysis

Material properties of cornea and sclera are important for maintaining the shape of the eye and the requisite surface curvatures for optics. They also need to withstand the forces of external and internal musculature and fluctuations in intraocular pressure (IOP). These properties are difficult to measure and variable results have been reported. A previously published experimental procedure, from which the material properties of the eyeball coats were obtained, has been modelled in this paper using Finite Element Analysis, in order to test the accuracy of the experiment. Material parameters were calculated from the model and the resulting relationships between stress and strain for the cornea and sclera compared to their experimentally obtained counterparts. The comparison between model and experiment was close for the sclera but more varied for the cornea. The pressure vessel model can be applied for measuring the material properties of the sclera but is less accurate for the cornea.     

Estimation of food consumption from field observations of fish feeding cycles

The available methods of estimating food consumption by fish require that experiments be performed on confined animals and that experimental results may be validly applied to free fish. A method is described by which food consumption in periodically feeding fish may be estimated without performing laboratory experiments. A relatively simple input–output model of stomach contents is fitted to the observed time trajectory of stomach fullness, and food consumption is calculated from the estimated model parameters. Feeding is considered to be restricted to a distinct feeding period, and the rate of feeding during that period can be either constant or linearly decreased with the quantity of food already present in the stomach.
The method is applied to three examples. The model appears robust, and generally provides very similar food consumption estimates to those obtained from methods requiring an independent estimate of gastric evacuation rate. However, the described method is sensitive to violation of the assumption that feeding occurs only during a discrete feeding period.     

A new method to estimate the relative bioavailability of individual amino acids in fish larvae using 13C-NMR spectroscopy

In comparison to mammals, fish, and in particular young stages, are thought to have higher amino acid (AA) requirements. Still, little is known about AA requirements of fish larvae, largely due to difficulties in applying traditional methodologies to these fast growing small animals. This study presents a new method to study the qualitative AA requirements of fish larvae. This method combines the use of 13C-labelled live food and 13C-NMR spectroscopy. It allows the simultaneous estimation of the relative bioavailability of several individual AAs. The present study shows that the relative bioavailabilies of various AAs do differ between AAs in larval seabream (Sparus aurata). Threonine has a low relative bioavailability, while aspartate, glutamate and lysine had high relative bioavailabilies compared to other AAs. These results are here attributed to differences in absorption rates by the gut, and/or selective catabolism. The results from the present study suggest that when rotifers are used as the diet for larval seabream, they should be enriched with products rich in threonine and leucine. Information on the relative bioavailability of individual AAs together with the AA profile of the larval protein should allow defining the ideal dietary AA profile for a given species.     

A novel in vitro approach to test the effectiveness of fish oil in ameliorating type 1 diabetes

Molecular and Cellular Biochemistry - Diabetes type 1 (T1D) characterized by destruction of pancreatic β-cells results in inadequate insulin production and hyperglycaemia. Generation...     

A continuum approach to modelling cell-cell adhesion

Cells adhere to each other through the binding of cell adhesion molecules at the cell surface. This process, known as cell-cell adhesion, is fundamental in many areas of biology, including early embryo development, tissue homeostasis and tumour growth. In this paper we develop a new continuous mathematical model of this phenomenon by considering the movement of cells in response to the adhesive forces generated through binding. We demonstrate that our model predicts the aggregation behaviour of a disassociated adhesive cell population. Further, when the model is extended to represent the interactions between multiple populations, we demonstrate that it is capable of replicating the different types of cell sorting behaviour observed experimentally. The resulting pattern formation is a direct consequence of the relative strengths of self-population and cross-population adhesive bonds in the model. While cell sorting behaviour has been captured previously with discrete approaches, it has not, until now, been observed with a fully continuous model.