Experimental evidence of size-selective harvest and environmental stochasticity effects on population demography,fluctuations and non-linearity

Theory and analyses of fisheries data sets indicate that harvesting can alter population structure and destabilise non-linear processes, which increases population fluctuations. We conducted a factorial experiment on the population dynamics of Daphnia magna in relation to size-selective harvesting and stochasticity of food supply. Harvesting and stochasticity treatments both increased population fluctuations. Timeseries analysis indicated that fluctuations in control populations were non-linear, and non-linearity increased substantially in response to harvesting. Both harvesting and stochasticity induced population juvenescence, but harvesting did so via the depletion of adults, whereas stochasticity increased the abundance of juveniles. A fitted fisheries model indicated that harvesting shifted populations towards higher reproductive rates and larger-magnitude damped oscillations that amplify demographic noise. These findings provide experimental evidence that harvesting increases the non-linearity of population fluctuations and that both harvesting and stochasticity increase population variability and juvenescence.     

Water conditions influence the detectability of Crossodactylus gaudichaudii (Anura,Hylodidae) in streams of the Atlantic Forest

Stream-dwelling amphibians' occurrence, behaviour and reproductive success are strongly influenced by dynamic abiotic factors, for example, water flow and spray. These factors can disproportionately affect these frogs due to their dependency on specific favourable conditions for development and incapacity to disperse from unfavourable environments. We analysed the influence of environmental covariates on the detectability of Crossodactylus gaudichaudii, an amphibian species endemic to streams in the Brazilian Atlantic Forest. We conducted sampling in the streams of the Duas Bocas Biological Reserve, Brazil, and we measured air and water temperature, air humidity and pH of water on each sampling occasion. We estimated the effects of variables on the detectability of the species using single-season occupancy models. Our results indicated that the detectability of the species increases on occasions with higher water temperatures (24–26°C) and lower pH (5.0–5.5). We investigated the influence of these covariates only on the detectability of adult frogs, but it is likely that the physiochemical properties of stream water are more important to aquatic larvae, and hence, the probability of their detection. Given this, further studies should examine the relevance of covariates on the detectability of adult frogs as well as larvae.     

Protein structure dynamics by crosslinking mass spectrometry

Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can be reduced by photo-crosslinking, and adding information from protein structure models, or quantitative crosslinking reveals conformation-specific crosslinks. As a consequence, crosslinking MS has proven useful already in the context of multiple dynamic protein systems. We foresee a breakthrough in the resolution and scale of studying protein dynamics when crosslinks are used to guide deep-learning-based protein modelling. Advances in crosslinking MS, such as photoactivatable crosslinking and in-situ crosslinking, will then reveal protein conformation dynamics in the cellular context, at a pseudo-atomic resolution, and plausibly in a time-resolved manner.     

Particle size influences decay rates of environmental DNA in aquatic systems

Environmental DNA (eDNA) analysis is a powerful tool for remote detection of target organisms. However, obtaining quantitative and longitudinal information from eDNA data is challenging, requiring a deep understanding of eDNA ecology. Notably, if the various size components of eDNA decay at different rates, and we can separate them within a sample, their changing proportions could be used to obtain longitudinal dynamics information on targets. To test this possibility, we conducted an aquatic mesocosm experiment in which we separated fish-derived eDNA components using sequential filtration to evaluate the decay rate and changing proportion of various eDNA particle sizes over time. We then fit four alternative mathematical decay models to the data, building towards a predictive framework to interpret eDNA data from various particle sizes. We found that medium-sized particles (1–10 μm) decayed more slowly than other size classes (i.e., <1 and > 10 μm), and thus made up an increasing proportion of eDNA particles over time. We also observed distinct eDNA particle size distribution (PSD) between our Common carp and Rainbow trout samples, suggesting that target-specific assays are required to determine starting eDNA PSDs. Additionally, we found evidence that different sizes of eDNA particles do not decay independently, with particle size conversion replenishing smaller particles over time. Nonetheless, a parsimonious mathematical model where particle sizes decay independently best explained the data. Given these results, we suggest a framework to discern target distance and abundance with eDNA data by applying sequential filtration, which theoretically has both metabarcoding and single-target applications.     

Comparison of mechanistic and hybrid modeling approaches for characterization of a CHO cultivation process: Requirements,pitfalls and solution paths

Despite the advantages of mathematical bioprocess modeling, successful model implementation already starts with experimental planning and accordingly can fail at this early stage. For this study, two different modeling approaches (mechanistic and hybrid) based on a four-dimensional antibody-producing CHO fed-batch process are compared. Overall, 33 experiments are performed in the fractional factorial four-dimensional design space and separated into four different complex data partitions subsequently used for model comparison and evaluation. The mechanistic model demonstrates the advantage of prior knowledge (i.e., known equations) to get informative value relatively independently of the utilized data partition. The hybrid approach displayes a higher data dependency but simultaneously yielded a higher accuracy on all data partitions. Furthermore, our results demonstrate that independent of the chosen modeling framework, a smart selection of only four initial experiments can already yield a very good representation of a full design space independent of the chosen modeling structure. Academic and industry researchers are recommended to pay more attention to experimental planning to maximize the process understanding obtained from mathematical modeling.     

North Sea cod and climate change – modelling the effects of temperature on population dynamics

In order to examine the likely impacts of climate change on fish stocks, it is necessary to couple the output from large‐scale climate models to fisheries population simulations. Using projections of future North Sea surface temperatures for the period 2000–2050 from the Hadley General Circulation Model, we estimate the likely effects of climate change on the North Sea cod population. Output from the model suggests that increasing temperatures will lead to an increased rate of decline in the North Sea cod population compared with simulations that ignore environmental change. Although the simulation developed here is relatively simplistic, we demonstrate that inclusion of environmental factors in population models can markedly alter one's perception of how the population will behave. The development of simulations incorporating environment effects will become increasingly important as the impacts of climate change on the marine ecosystem become more pronounced.     

Early needle senescence and thinning of the crown structure of Picea abies as induced by chronic SO2 pollution. II. Field data basis, model results and tolerance limits

Field data on the sulphur and cation budget of growing Norway spruce canopies (Picea abies [L.] Karst.) are summarized. They are used to test a spruce decline model capable of quantifying effects of chronic SO₂ pollution on spruce forests. At ambient SO₂ concentrations, acute SO₂ damage is rare, but exposure to polluted air produces reversible thinning of the canopy structure with a half-time of a few years. Canopy thinning in the spruce decline model is highest (i) at elevated SO₂ pollution, (ii) in the mountains, (iii) at unfertilized sites with poor K⁺, Mg²⁺ or Zn²⁺ supply, (iv) at low spruce litter decomposition rates, and (v) acidic, shallow soils at high annual precipitation rates in the field and vice versa. Model application using field data from Würzburg (moderate SO₂ pollution, alkaline soils, no spruce decline) and from the Erzgebirge (extreme SO₂ pollution, acidic soils in the mountains, massive spruce decline) predicts canopy thinning by 2–11% in Würzburg and by 45–70% in the Erzgebirge. The model also predicts different SO₂-tolerance limits for Norway spruce depending on the site elevation and on the nutritional status of the needles. If needle loss of more than 25% (damage class 2) is taken to indicate ‘real damage’ exceeding natural variances, then for optimum soil conditions SO₂ tolerance limits range from (27.3 ± 7.4) μg m^?3 to (62.6 ± 16.5) μg m^?3. For shallow and acidic soils, SO₂ tolerance limits range from (22.0 ± 5.5) μg m^?3 to (37.4 ± 7.5) μ m^?3. These tolerance limits, which are calculated on an ecophysiological data basis for Norway spruce are close to epidemiological SO₂-toIerance limits as recommended by the IUFRO, UN-ECE and WHO. The observed statistical regression slope of the plot (damaged spruce trees vs. SO₂-pollution) in west Germany is confirmed by modelling (6% error). Model application to other forest trees allows deduction of the observed sequence of SO₂-sensitivity: Abies > Picea > Pinus > Fagus > Quercus. Thus, acute phytotoxicity of SO₂ seems not to be involved in ‘forest decline’. Chronic SO₂-pollution induces massive canopy thinning of Abies alba and Picea abies only at unfavourable sites, where natural stress factors and secondary effects of SO₂pollution act together to produce tree decline.     

鼠抗人纤维蛋白抗体单链Fv片断的三维结构模建

用Biosym公司开发的计算机辅助分子设计系统模建了鼠抗人纤维蛋白抗体Fv片断的三维结构。Fv是由重链可变区(Vh)和轻链可变区(Vl)两个结构域组成的具有抗原结合能力的最小抗体片断。先分别模建了Vh和Vl两个结构域,然后搭建出Fv片断的整体三维结构,并对模建的结构进行了分子力学和动力学优化。对结构的合理性验证显示模建结构是合理的。本研究为鼠抗人纤维蛋白抗体Fv片断的人源化的分子设计打下了基础。     

Prediction of B-cell epitopes forSalmonella typhi OmpC

The possible B-cell epitopes of the outer membrane porin OmpC ofSalmonella typhi have been identified, using the primary structure of the protein, by means of multiple sequence alignment and the known molecular structure of two other porins. From the analysis, 8 regions were identified as immunodominant and these were ranked based on antigenic index and the ratio of the number of nonconserved residues to the fragment length. Model building of the top two ranked regions show the tendency to form loop structures supporting the possibility of these being candidate epitopes.     

Statistical analysis of algal and water quality data

Data on cyanobacteria (blue-green algae) are generallycollected on a reactive basis, frequently in responseto bloom events. Such data presents a biased andincomplete snapshot of water quality. This paper looksat two typical data sets for UK waters showing thatwhile statistics may be used to describe the data theyare of limited use in forecasting. Suggestions ofappropriate tests for small and sparse data sets aremade.