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The extent to which water availability can be used to predict the enlargement and final dimensions of xylem conduits remains an open issue. We reconstructed the time course of tracheid enlargement in Pinus sylvestris trees in central Spain by repeated measurements of tracheid diameter on microcores sampled weekly during a 2 yr period. We analyzed the role of water availability in these dynamics empirically through time-series correlation analysis and mechanistically by building a model that simulates daily tracheid enlargement rate and duration based on Lockhart's equation and water potential as the sole input. Tracheid enlargement followed a sigmoid-like time course, which varied intra- and interannually. Our empirical analysis showed that final tracheid diameter was strongly related to water availability during tracheid enlargement. The mechanistic model was calibrated and successfully validated (R-2 = 0.92) against the observed tracheid enlargement time course. The model was also able to reproduce the seasonal variations of tracheid enlargement rate, duration and final diameter (R-2 = 0.84-0.99). Our results support the hypothesis that tracheid enlargement and final dimensions can be modeled based on the direct effect of water potential on turgor-driven cell expansion. We argue that such a mechanism is consistent with other reported patterns of tracheid dimension variation.

Soil nitrous oxide (N2O) is an important greenhouse gas contributing to climate change. Many processes produce N2O in soil and the production rate of each process is affected by climatic-edaphic factors, making the soil-to-atmosphere N2O flux extremely dynamic. Experimental approaches, including natural and enriched isotopic methods, have been developed to separate and quantify the N2O production from different processes. However, these methods are often costly and tedious, hampering their wide application. This study aimed to develop a mechanistic model quantifying the soil N2O production from nitrifier nitrification (NN), nitrifier denitrification (ND), and heterotrophic denitrification (HD), which are considered as the most important biological processes, and to investigate how climatic-edaphic factors affect N2O production from individual process as well as total N2O production. The developed model demonstrated its robustness and capability by reliably reproducing the N2O production from NN, ND, and HD in different types of soils under various moisture contents or oxygen concentrations. The model simulations unraveled how environmental conditions and soil properties control the total N2O production rate by variably regulating individual processes. Therefore, the mechanistic model can potentially elucidate the large spatiotemporal variances of in-situ soil N2O flux and improve the assessment of soil N2O emission at regional and global scales.

Plants continually adjust the photosynthetic functions in their leaves to fluctuating light, thereby optimizing the use of photosynthetic nitrogen (Nph ) at the canopy level. To investigate the complex interplay between external signals during the acclimation processes, a mechanistic model based on the concept of protein turnover (synthesis and degradation) was proposed and parameterized using cucumber grown under nine combinations of nitrogen and light in growth chambers. Integrating this dynamic model into a multi-layer canopy model provided accurate predictions of photosynthetic acclimation of greenhouse cucumber canopies grown under high and low nitrogen supply in combination with day-to-day fluctuations in light at two different levels. This allowed us to quantify the degree of optimality in canopy nitrogen use for maximizing canopy carbon assimilation, which was influenced by Nph distribution along canopy depth or Nph partitioning between functional pools. Our analyses suggest that Nph distribution is close to optimum and Nph reallocation is more important under low nitrogen. Nph partitioning is only optimal under a light level similar to the average light intensity during acclimation, meaning that day-to-day light fluctuations inevitably result in suboptimal Nph partitioning. Our results provide insights into photoacclimation and can be applied to crop model improvement.

There has been considerable recent interest in modelling the potential distributions of invasive species. However, research has developed in two opposite directions: the first, focusing on screening, utilizes phenomenological models; the second, focusing on predictions of invasion dynamics, utilizes mechanistic models. Here, we present hybrid modelling as an approach to bridge the gap and to integrate the advantages of both research directions. Global. First, we briefly summarize the characteristics and limitations of both approaches (screening vs. understanding). Then, we review the recent developments of hybrid models, discuss their current problems and offer suggestions to improve them. Generally, hybrid models are able to combine the advantages of currently used phenomenological and mechanistic approaches. Main challenges in building hybrid models are the choices of the appropriate degree of detail and efficiency and the decision on how to connect the different sub-models. Given these challenges, we discuss the links between the phenomenological and the mechanistic model parameters, the underlying concepts of fundamental and realized niches and the problem of feedback loops between population dynamics and environmental factors. Once the above challenges have been addressed and the necessary framework has been developed, hybrid models will provide outstanding tools for overcoming past limitations and will provide the means to make reliable and robust predictions of the potential distribution of invasive species, their population dynamics and the potential outcomes of the overall invasion process.

Inclusion bodies (IBs) are protein aggregates formed as a result of overexpression of recombinant protein in E. coli. The formation of IBs is a valuable strategy of recombinant protein production despite the need for additional processing steps, i.e., isolation, solubilization and refolding. Industrial process development of protein refolding is a labor-intensive task based largely on empirical approaches rather than knowledge-driven strategies. A prerequisite for knowledge-driven process development is a reliable monitoring strategy. This work explores the potential of intrinsic tryptophan and tyrosine fluorescence for real-time and in situ monitoring of protein refolding. In contrast to commonly established process analytical technology (PAT), this technique showed high sensitivity with reproducible measurements for protein concentrations down to 0.01 g L-1. The change of protein conformation during refolding is reflected as a shift in the position of the maxima of the tryptophan and tyrosine fluorescence spectra as well as change in the signal intensity. The shift in the peak position, expressed as average emission wavelength of a spectrum, was correlated to the amount of folding intermediates whereas the intensity integral correlates to the extent of aggregation. These correlations were implemented as an observation function into a mechanistic model. The versatility and transferability of the technique were demonstrated on the refolding of three different proteins with varying structural complexity. The technique was also successfully applied to detect the effect of additives and process mode on the refolding process efficiency. Thus, the methodology presented poses a generic and reliable PAT tool enabling real-time process monitoring of protein refolding.Real-time intrinsic fluorescence monitoring in protein refolding

Therapeutic monoclonal antibodies are mainly produced in mammalian cells to date. However, unglycosylated antibody fragments can also be produced in the bacterium Escherichia coli which brings several advantages, like growth on cheap media and high productivity. One of the most popular E. coli strains for recombinant protein production is E. coli BL21(DE3) which is usually used in combination with the pET expression system. However, it is well known that induction by isopropyl β- d -1-thiogalactopyranoside (IPTG) stresses the cells and can lead to the formation of insoluble inclusion bodies. In this study, we revisited the pET expression system for the production of a novel antibody single-chain variable fragment (scFv) with the goal of maximizing the amount of soluble product. Thus, we (1) investigated whether lactose favors the recombinant production of soluble scFv compared to IPTG, (2) investigated whether the formation of soluble product can be influenced by the specific glucose uptake rate ( q s,glu ) during lactose induction, and (3) determined the mechanistic correlation between the specific lactose uptake rate ( q s,lac ) and q s,glu . We found that lactose induction gave a much greater amount of soluble scFv compared to IPTG, even when the growth rate was increased. Furthermore, we showed that the production of soluble protein could be tuned by varying q s,glu during lactose induction. Finally, we established a simple model describing the mechanistic correlation between q s,lac and q s,glu allowing tailored feeding and prevention of sugar accumulation. We believe that this mechanistic model might serve as platform knowledge for E. coli .

Background The mosquito Aedes albopitus is a competent vector for the transmission of many blood-borne pathogens. An important factor that affects the mosquitoes’ development and spreading is climate, such as temperature, precipitation and photoperiod. Existing climate-driven mechanistic models overlook the seasonal pattern of diapause, referred to as the survival strategy of mosquito eggs being dormant and unable to hatch under extreme weather. With respect to diapause, several issues remain unaddressed, including identifying the time when diapause eggs are laid and hatched under different climatic conditions, demarcating the thresholds of diapause and non-diapause periods, and considering the mortality rate of diapause eggs. Methods Here we propose a generic climate-driven mechanistic population model of Ae. albopitus applicable to most Ae. albopictus -colonized areas. The new model is an improvement over the previous work by incorporating the diapause behaviors with many modifications to the stage-specific mechanism of the mosquitoes’ life-cycle. monthly Container Index (CI) of Ae. albopitus collected in two Chinese cities, Guangzhou and Shanghai is used for model validation. Results The simulation results by the proposed model is validated with entomological field data by the Pearson correlation coefficient r 2 in Guangzhou ( r 2  = 0.84) and in Shanghai ( r 2  = 0.90). In addition, by consolidating the effect of diapause-related adjustments and temperature-related parameters in the model, the improvement is significant over the basic model. Conclusions The model highlights the importance of considering diapause in simulating Ae. albopitus population. It also corroborates that temperature and photoperiod are significant in affecting the population dynamics of the mosquito. By refining the relationship between Ae. albopitus population and climatic factors, the model serves to establish a mechanistic relation to the growth and decline of the species . Understanding this relationship in a better way will benefit studying the transmission and the spatiotemporal distribution of mosquito-borne epidemics and eventually facilitating the early warning and control of the diseases.

1. Climate change will alter the distribution and abundance of many species, including those of concern to human health. Accurate predictions of these impacts must be based on an understanding of the mechanistic links between climate and organisms, and a consideration of evolutionary responses. 2. Here we use biophysical models of energy and mass transfer to predict climatic impacts on the potential range of the dengue fever vector, Aedes aegypti, in Australia. We develop a first-principles approach to calculate water depth and daily temperature cycles in containers differing in size, catchment and degree of shading to assess habitat suitability for the aquatic life cycle phase. We also develop a method to predict potential climatic impacts on the evolutionary response of traits limiting distribution. 3. Our predictions show strong correspondence with the current and historical distribution and abundance of Ae. aegypti in Australia, suggesting that inland and northern limits are set by water availability and egg desiccation resistance, and southern limits by adult and larval cold tolerance. 4. While we predict that climate change will directly increase habitat suitability throughout much of Australia, the potential indirect impact of changed water storage practices by humans in response to drought may have a greater effect. 5. In northern Australia, we show that evolutionary changes in egg desiccation resistance could potentially increase the chances of establishment in a major centre (Darwin) under climate change. 6. Our study demonstrates how biophysical models of climate-animal interactions can be applied to make decisions about managing biotic responses to climate change. Mechanistic models of the kind we apply here can provide more robust and general predictions than correlative analyses. They can also explicitly incorporate evolutionary responses, the outcomes of which may significantly alter management decisions.

Owing to the late Pleistocene extinctions, the megafauna of Europe, Australia and the Americas disappeared, and with them the dispersal service they offered megafaunal fruit. The African savanna elephant, the largest remaining megaherbivore, offers valuable insights into the seed dispersal services provided by extinct megafauna in prehistoric times. Elephant seed dispersal studies have for the most part concentrated on African and Asian forest elephants. African savanna elephants are morphologically distinct from their forest counterparts. Like the forest elephants they consume large quantities of fruit from a large number of tree species. Despite this little is known of the savanna trees that rely on elephants for their dispersal or the spatial scale at which these seeds are dispersed. We combined information from feeding trials conducted on four park elephants with field telemetry data from 38 collared elephants collected over an 8-year period in APNR/Kruger National Park to assess the seed dispersal service provided by savanna elephants. This study provides the first detailed account of the spatial scale at which African savanna elephants disperse seeds. Our mechanistic model predicts that 50 percent of seeds are carried over 2.5 km, and distances up to 65 km are achievable in maximum gut passage time. These findings suggest the savanna elephant as the longest distance terrestrial vertebrate disperser yet investigated. Maintaining their ecological role as a seed disperser may prove a significant factor in the conservation of large-fruited tree diversity within the savannas. These results suggest that extinct megafauna offered a functionally unique dispersal service to megafaunal fruit.

Aim Identify climate change impacts on spawning and settlement of a tropical herbivore (Tripneustes), optimal habitat of a temperate kelp (Ecklonia) and implications for these species regions of interaction under future climate. Location Along eastern Australia and into the Tasman Sea including Lord Howe Island (LHI). Time period A contemporary scenario (2006–2015) and future “business as usual” RCP 8.5 climate change scenario (2090–2100). Major taxa studied The tropical sea urchin, Tripneustes gratilla, and the temperate kelp, Ecklonia radiata. Methods We combined mechanistic models to create a predictive map of Ecklonia and Tripneustes distributions, and their future potential to co‐occur. We use 3D velocity and temperature fields produced with a state‐of‐the‐art configuration of the Ocean Forecasting Model version 3 that simulates the contemporary oceanic environment and projects it under an RCP 8.5 climate change scenario. We map the contemporary and future Ecklonia's realized and fundamental thermal niche; and simulate Tripneustes larval dispersal under both climate scenarios. Results Based on the thermal affinity of kelp and increases in projected temperatures, we predict a poleward range contraction of ~530 km by 2100 for kelp on Australia's east coast. Climate‐driven changes in dispersal of Tripneustes lead to its range expansion into Bass Strait and poleward, ~340–650 km further into Ecklonia's habitat range inducing new areas of co‐occurrence in the future. We find warming decreases spawning and settlement of Tripneustes in the tropics by 43%, and causes significant connectivity changes for LHI with future reliance on self‐recruitment. Major conclusions We predict novel regions of co‐occurrence between a temperate Ecklonia and tropical Tripneustes species which may lead to greater loss of kelp. Our results provide a new modelling approach for predicting species range shifts that is transferable to other marine ecosystems; it considers species response to abiotic change, predicts spatial spread and anticipates new regions for species interactions.