Predicting impacts of climate change on biodiversity: a role for semi‐mechanistic community‐level modelling

Aim Robust and reliable predictions of the effects of climate change on biodiversity are required in formulating conservation and management strategies that best retain biodiversity into the future. Significant challenges in modelling climate change impacts arise from limitations in our current knowledge of biodiversity. Community‐level modelling can complement species‐level approaches in overcoming these limitations and predicting climate change impacts on biodiversity as a whole. However, the community‐level approaches applied to date have been largely correlative, ignoring the key processes that influence change in biodiversity over space and time. Here, we suggest that the development of new ‘semi‐mechanistic’ community‐level models would substantially increase our capacity to predict climate change impacts on biodiversity. Location Global. Methods Drawing on an expansive review of biodiversity modelling approaches and recent advances in semi‐mechanistic modelling at the species level, we outline the main elements of a new semi‐mechanistic community‐level modelling approach. Results Our quantitative review revealed a sharp divide between mechanistic and non‐mechanistic biodiversity modelling approaches, with very few semi‐mechanistic models developed to date. Main conclusions We suggest that the conceptual framework presented here for combining mechanistic and non‐mechanistic community‐level approaches offers a promising means of incorporating key processes into predictions of climate change impacts on biodiversity whilst working within the limits of our current knowledge.     

Testing metabolic scaling theory using intraspecific allometries in Antarctic microarthropods

Quantitative scaling relationships among body mass, temperature and metabolic rate of organisms are still controversial, while resolution may be further complicated through the use of different and possibly inappropriate approaches to statistical analysis. We propose the application of a modelling strategy based on the theoretical approach of Akaike's information criteria and non‐linear model fitting (nlm). Accordingly, we collated and modelled available data at intraspecific level on the individual standard metabolic rate of Antarctic microarthropods as a function of body mass (M), temperature (T), species identity (S) and high rank taxa to which species belong (G) and tested predictions from metabolic scaling theory (mass‐metabolism allometric exponent b = 0.75, activation energy range 0.2–1.2 eV). We also performed allometric analysis based on logarithmic transformations (lm). Conclusions from lm and nlm approaches were different. Best‐supported models from lm incorporated T, M and S. The estimates of the allometric scaling exponent linking body mass and metabolic rate resulted in a value of 0.696 ± 0.105 (mean ± 95% CI). In contrast, the four best‐supported nlm models suggested that both the scaling exponent and activation energy significantly vary across the high rank taxa (Collembola, Cryptostigmata, Mesostigmata and Prostigmata) to which species belong, with mean values of b ranging from about 0.6 to 0.8. We therefore reached two conclusions: 1, published analyses of arthropod metabolism based on logarithmic data may be biased by data transformation; 2, non‐linear models applied to Antarctic microarthropod metabolic rate suggest that intraspecific scaling of standard metabolic rate in Antarctic microarthropods is highly variable and can be characterised by scaling exponents that greatly vary within taxa, which may have biased previous interspecific comparisons that neglected intraspecific variability.     

Description of by-product inhibiton effects on biodesulfurization of dibenzothiophene in biphasic media

As several authors have reported previously, the Biodesulfurization of hydrodesulfurization recalcitrants, such as dibenzothiophene, is not yet commercially viable because mass transfer limitations and feedback inhibition effects are produced during the conversion. This work has been focused to investigate the inhibition process in aqueous and oil-water systems with two different aerobic biocatalysts types, Rhodococcus erythropolis IGTS8 and Pseudomonas putida CECT 5279. The results obtained have proven that global DBT desulfurization process using CECT 5279 was not clearly deactivated due to final product accumulation, under the experimental conditions assayed. Consistently, the desulfurization pattern has been described with the Michaelis-Menten equation, determining the kinetic parameters. On other hand, the assays have shown that important mass transfer limitations produced the decrease of the yields obtained with this Gram(-) strain in biphasic media. With strain IGTS8 it was observed lower mass transfer problems, but contrary the reaction was severely affected by the final product accumulation, in both aqueous and biphasic systems. Therefore it has been proposed an enzymatic kinetic model with competitive inhibition to describe the BDS evolution pattern when this Gram(+) strain was used.     

A comparison of statistical approaches for modelling fish species distributions

SUMMARY 1. The prediction of species distributions is of primary importance in ecology and conservation biology. Statistical models play an important role in this regard; however, researchers have little guidance when choosing between competing methodologies because few comparative studies have been conducted. 2. We provide a comprehensive comparison of traditional and alternative techniques for predicting species distributions using logistic regression analysis, linear discriminant analysis, classification trees and artificial neural networks to model: (1) the presence/absence of 27 fish species as a function of habitat conditions in 286 temperate lakes located in south‐central Ontario, Canada and (2) simulated data sets exhibiting deterministic, linear and non‐linear species response curves. 3. Detailed evaluation of model predictive power showed that approaches produced species models that differed in overall correct classification, specificity (i.e. ability to correctly predict species absence) and sensitivity (i.e. ability to correctly predict speciespresence) and in terms of which of the study lakes they correctly classified. Onaverage, neural networks outperformed the other modelling approaches, although all approaches predicted species presence/absence with moderate to excellent success. 4. Based on simulated non‐linear data, classification trees and neural networks greatly outperformed traditional approaches, whereas all approaches exhibited similar correct classification rates when modelling simulated linear data. 5. Detailed evaluation of model explanatory insight showed that the relative importance of the habitat variables in the species models varied among the approaches, where habitat variable importance was similar among approaches for some species and very different for others. 6. In general, differences in predictive power (both correct classification rate and identity of the lakes correctly classified) among the approaches corresponded with differences in habitat variable importance, suggesting that non‐linear modelling approaches (i.e. classification trees and neural networks) are better able to capture and model complex, non‐linear patterns found in ecological data. The results from the comparisons using simulated data further support this notion. 7. By employing parallel modelling approaches with the same set of data and focusing on comparing multiple metrics of predictive performance, researchers can begin to choose predictive models that not only provide the greatest predictive power, but also best fit the proposed application.     

Cell growth patterns in immobilization matrices

Within an immobilized cell matrix, mass transfer limitations on substrate delivery or product removal can often lead to a wide range of local chemical environments. As immobilized living cell populations actively grow and adapt to their surroundings, these mass transfer effects often lead to strong, time-dependent spatial variations in substrate concentration and biomass densities and growth rates. This review focuses on the methods that have been devised, both experimentally and theoretically, to study the non-uniform growth patterns that arise in the mass transfer limited environment of an immobilization matrix, with particular attention being paid to cell growth in polysaccharide gels.     

Kinetic study of the concentration dependence of the mass transfer rate coefficient in anion-exchange chromatography of bovine serum albumin.

The experimental results of a previous study of the mass transfer kinetics of bovine serum albumin (BSA) in ion-exchange chromatography under nonlinear conditions are reevaluated. The analysis of the concentration dependence of the lumped mass-transfer rate coefficient (k(m,L)) provides information on the kinetics of axial dispersion, fluid-to-particle mass transfer, intraparticle mass transfer, and adsorption/desorption. The new analysis shows that the contribution of intraparticle mass transfer is the dominant one. Similar to k(m,L), the surface diffusivity (D(s)) of BSA increases with increasing concentration. The linear concentration dependence of k(m,L) seems to originate in a similar dependence of D(s). The use of an heterogeneous-surface model for the anion-exchange resin provides an explanation of the positive concentration dependence of D(s). This work illustrates how frontal analysis data can be used for a detailed investigation of the kinetics of mass transfer between the phases of a chromatographic column, in addition to its conventional use in the determination of the thermodynamic characteristics of the phase equilibrium.     

Mass transfer effects in solvent-free fat interesterification reactions: influences on catalyst design

The use of solvent-free systems in the oil and fats industry is commonplace. Initial studies on interesterification were carried out in solvent systems because the lipase was immobilized solely by adsorption onto particles of diatomaceous earth. In this study, the mass transfer characteristics associated with the continuous interesterification of olive oil in a solvent-free system have been examined, for lipase immobilized on the three ion-exchange materials: Duolite ES562, Duolite ES568, and Spheroil DEA. The process of immobilization is influenced by the internal structure of the material and this in turn influences the interesterification activity of the catalyst. Individually prepared catalysts for the three support materials have shown that external mass transfer limitations are unlikely even at low flowrates.In the case of Spherosil DEA, with a mean pore diameter of 1480 A, the wide pores would be expected to reduce internal mass transfer limitations; however, it is more likely that the reduction in activity with increased catalyst loading is due to the lipase molecules being immobilized in a tightly packed monolayer. In such a situation, some active sites of the lipase molecules would become inaccessible to substrate molecules leading to an observed reduction in activity. For Duolite ES568, the observed results are very similar to those seen for Spherosil DEA, however, the pore structure of this support material indicate that some internal mass transfer limitations may also be occurring. Yet the contribution of the individual effects cannot be determined. The results observed for the support Duolite ES562 are different than those observed for the other materials and reflect the heterogeneity of Duolite ES562. The large proportion of narrow pores in the support mean that, for the catalysts examined, immobilization is most likely to have occurred in the external pores of the particles, and as such no internal mass transfer limitation is observed.It is clear that for interesterification the material chosen for enzyme immobilization will have an important role in determining the catalyst efficiency. External mass transfer limitations are very minor and observed internal mass transfer limitations may be caused by both internal mass transfer and the manner in which the immobilization process occurs. (c) 1994 John Wiley & Sons, Inc.     

Liquid chromatography modelling: a review

Liquid chromatography modelling represents a real challenge to understand the phenomena encountered in the separation process of biomolecules, especially in non-linear adsorption cases, and to enhance production rates and recovery yields in preparative chromatography.

The three major ways to describe liquid chromatography are presented, i.e. the continuity equations, the theory of interferences and the plate theory. The former is described in detail, since it permits the inclusion of various physical and thermodynamical phenomena, and to handle non-linear adsorption problems. The numerical ways of solving the differential equations stated by the different models are also considered. The interference theory, despite its limitations to ideal situations, is still considered as a useful tool in non-linear multicomponents liquid chromatography modelling. The plate theory is not developed, for it is restricted to linear adsorption cases.     

Allometric scaling of seed retention time in seed dispersers and its application to estimation of seed dispersal potentials of theropod dinosaurs

Seed retention time (SRT), the time interval between seed ingestion and defaecation, is a critical parameter that determines the spatial pattern of seed dispersal created by an animal, and is therefore, an essential component of trait‐based modelling of seed dispersal functions. However, no simple predictive model of SRT for any given animal exists. We explored the linkage between animal traits and SRT. We collected previously published data on mean SRT for 112 species of birds, mammals, reptiles and fishes and investigated the general allometric scaling of mean SRT with body mass for each taxon. Moreover, we analysed the effects of food habit and digestive strategy on mean SRT for birds and mammals. In general, mean SRT increased with body mass in all four taxa, whereas the pattern of allometric scaling varied greatly among the taxa. Birds had a smaller intercept and larger slope than those of mammals, whereas reptiles had a much larger intercept and smaller slope than those of either birds or mammals. For birds, food habit was also detected as an important factor affecting SRT. We applied the allometric scaling that was obtained for birds to estimate mean SRT of extinct Mesozoic dinosaurs (Theropoda) – few of which are assumed to have acted as seed dispersers. SRT for large carnivorous theropods was estimated to be 4–5 days, when considering only body mass. The present study provides allometric scaling parameters of mean SRT for a variety of seed‐dispersing animals, and highlights large variations in scaling among taxa. The allometric scaling obtained could be a critical component of further trait‐based modelling of seed dispersal functions. Further, the potential and limitations of the scaling of animal SRT with body mass and a future pathway to the development of trait‐based modelling are discussed.     

Performance optimization of continuous countercurrent tangential chromatography for antibody capture

Recent studies have demonstrated that continuous countercurrent tangential chromatography (CCTC) can effectively purify monoclonal antibodies from clarified cell culture fluid. CCTC has the potential to overcome many of the limitations of conventional packed bed protein A chromatography. This paper explores the optimization of CCTC in terms of product yield, impurity removal, overall productivity, and buffer usage. Modeling was based on data from bench‐scale process development and CCTC experiments for protein A capture of two clarified Chinese Hamster Ovary cell culture feedstocks containing monoclonal antibodies provided by industrial partners. The impact of resin binding capacity and kinetics, as well as staging strategy and buffer recycling, was assessed. It was found that optimal staging in the binding step provides better yield and increases overall system productivity by 8–16%. Utilization of higher number of stages in the wash and elution steps can lead to significant decreases in buffer usage (～40% reduction) as well as increased removal of impurities (～2 log greater removal). Further reductions in buffer usage can be obtained by recycling of buffer in the wash and regeneration steps (～35%). Preliminary results with smaller particle size resins show that the productivity of the CCTC system can be increased by 2.5‐fold up to 190 g of mAb/L of resin/hr due to the reduction in mass transfer limitations in the binding step. These results provide a solid framework for designing and optimizing CCTC technology for capture applications. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:430–439, 2016     

Purification and characterization of a novel phospholipid transfer protein from filamentous fungi

1. We have isolated from mycelia of Mucor mucedo, a filamentous fungus, a phospholipid transfer protein. 2. The purification steps were gel filtration, hydroxyapatite chromatography, blue affinity column and fast protein liquid chromatography on anion exchanger. 3. A purified protein was obtained with a molecular mass of 24 kDa and a pI of 5.05 and its N-terminal sequence was established. 4. This protein transfers phosphatidylinositol, as well as phosphatidylcholine and phosphatidylethanolamine.     

Effects of climate change and horticultural use on the spread of naturalized alien garden plants in Europe

Climate warming is supposed to enlarge the area climatically suitable to the naturalization of alien garden plants in temperate regions. However, the effects of a changing climate on the spread of naturalized ornamentals have not been evaluated by spatially and temporarily explicit range modelling at larger scales so far. Here, we assess how climate change and the frequency of cultivation interactively determine the spread of 15 ornamental plants over the 21st century in Europe. We coupled species distribution modelling with simulations of demography and dispersal to predict range dynamics of these species in annual steps across a 250 × 250 m raster of the study area. Models were run under four scenarios of climate warming and six levels of cultivation intensity. Cultivation frequency was implemented as size of the area used for planting a species. Although the area climatically suitable to the 15 species increases, on average, the area predicted to be occupied by them in 2090 shrinks under two of the three climate change scenarios. This contradiction obviously arises from dispersal limitations that were pronounced although we assumed that cultivation is spatially adapting to the changing climate. Cultivation frequency had a much stronger effect on species spread than climate change, and this effect was non‐linear. The area occupied increased sharply from low to moderate levels of cultivation intensity, but levelled off afterwards. Our simulations suggest that climate warming will not necessarily foster the spread of alien garden plants in Europe over the next decades. However, climatically suitable areas do increase and hence an invasion debt is likely accumulating. Restricting cultivation of species can be effective in preventing species spread, irrespective of how the climate develops. However, for being successful, they depend on high levels of compliance to keep propagule pressure at a low level.     

Density dependence in blowfly populations: experimental evaluation of non‐parametric time‐series modelling

Two approaches for describing density dependence in demographic rates of stage‐structured populations are compared in this study. Time‐series data from laboratory blowfly populations (Lucilia sericata) have been analysed in a separate study, with a statistical modelling approach that incorporated density dependences as unspecified (non‐parametric) functions. In this study, we assessed density‐dependent structures by manipulating densities of larvae and adults in cohorts of blowflies and measuring the demographic rates. We here compare the density‐dependent structures revealed by the cohort experiments with those estimated by the non‐parametric model. This model estimates the demographic rates to have the following density‐dependent structures: (i) larval survival was non‐linearly density‐dependent (a ‘humped’ function), (ii) adult survival was density‐independent, and (iii) reproductive rate decreased with adult density. In the cohort experiments reported here, (i) juvenile survival exhibited a positive density dependence in low densities (facilitation), which became negative at higher densities (competition). Pupal and adult size decreased with initial larval density. (ii) Adult survival was reduced by high initial larval density, but it was independent of adult density. (iii) Reproductive rate was reduced by high initial larval density, and by high adult density in populations of large individuals (from low larval density). Hence, the results from these experiments support the non‐parametric model estimates regarding density‐dependent structures of demographic rates in the blowfly populations. The mean demographic rates, however, were apparently underestimated by the model. We conclude that non‐parametric modelling is a useful first approach for exploratory analysis of ecological time‐series data.     

Punching above their weight: low-biomass non-native plant species alter soil properties during primary succession

Non‐native invasive plants can greatly alter community and ecosystem properties, but efforts to predict which invasive species have the greatest impacts on these properties have been generally unsuccessful. An hypothesis that has considerable promise for predicting the effects of invasive non‐native plant species is the mass ratio hypothesis (i.e. that dominant species exert the strongest effects). We tested this hypothesis using data from a four year removal experiment in which the presence of two dominant shrub species (one native and the other not), and subordinate plant species, were manipulated in factorial combinations over four years in a primary successional floodplain system. We measured the effects of these manipulations on the plant community, soil nutrient status and soil biota in different trophic levels of the soil food web. Our experiment showed that after four years, low‐biomass non‐native plant species exerted disproportionate belowground effects relative to their contribution to total biomass in the plant community, most notably by increasing soil C, soil microbial biomass, altering soil microbial community structure and increasing the abundance of microbial‐feeding and predatory nematodes. Low‐biomass, non‐native plant species had distinct life history strategies and foliar traits (higher foliar N concentrations and higher leaf area per unit mass) compared with the two dominant shrub species (97% of total plant mass). Our results have several implications for understanding species’ effects in communities and on soil properties. First, high‐biomass species do not necessarily exert the largest impacts on community or soil properties. Second, low‐biomass, inconspicuous non‐native species can influence community composition and have important trophic consequences belowground through effects on soil nutrient status or resource availability to soil biota. Our finding that low‐biomass non‐native species influence belowground community structure and soil properties more profoundly than dominant species demonstrates that the mass ratio hypothesis does not accurately predict the relative effects of different coexisting species on community‐ and ecosystem‐level properties.     

Experimental and theoretical evidence for convective nutrient transport in an immobilized cell support.

Even though immobilized-cell reactors possess several engineering advantages over free-cell reactors, their full potential has not been realized because mass transfer often limits the rate of nutrient supply and product removal from immobilized cell supports. We studied the interaction between mass transfer and reaction kinetics in the anaerobic conversion of glucose to CO2 and ethanol by yeast immobilized in a porous rotating disk on the agitator shaft of a conventional CSTR. A Sherwood number correlation was used to show that external mass-transfer resistances were negligible under typical operating conditions. The modulus of Weisz based on observable reaction parameters was used to gauge the importance of pore diffusion limitations. Under conditions for which significant pore diffusion effects and hence low effectiveness factors (eta = ca. 0.1) would be predicted, the observed reaction rates were much higher than expected (eta = ca. 1), suggesting that pore diffusion limitations were at least partially relieved by convective transport of glucose into the support. Two possible mechanisms of convective transport are discussed. We hypothesize that gas evolution was responsible for the convective enhancement of glucose supply.     

Membrane adsorbers as purification tools for monoclonal antibody purification

Downstream purification processes for monoclonal antibody production typically involve multiple steps; some of them are conventionally performed by bead-based column chromatography. Affinity chromatography with Protein A is the most selective method for protein purification and is conventionally used for the initial capturing step to facilitate rapid volume reduction as well as separation of the antibody. However, conventional affinity chromatography has some limitations that are inherent with the method, it exhibits slow intraparticle diffusion and high pressure drop within the column. Membrane-based separation processes can be used in order to overcome these mass transfer limitations. The ligand is immobilized in the membrane pores and the convective flow brings the solute molecules very close to the ligand and hence minimizes the diffusional limitations associated with the beads. Nonetheless, the adoption of this technology has been slow because membrane chromatography has been limited by a lower binding capacity than that of conventional columns, even though the high flux advantages provided by membrane adsorbers would lead to higher productivity. This review considers the use of membrane adsorbers as an alternative technology for capture and polishing steps for the purification of monoclonal antibodies. Promising industrial applications as well as new trends in research will be addressed.     

基因治疗中关于非病毒载体的最新设计策略

基因转移的非病毒技术近来发展迅速。与病毒转染细胞的方法相比,非病毒转移方法比较简便,安全,毒性小。这种方法大体可分为两种：完全非病毒方法和病毒增强的转移方式。本文主要介绍一些最近两三年来新兴的技术方案的优点和不足。     

Influence of chain architecture on the mechanochemical degradation of macromolecules

We detail here studies into the nature of mechanochemical degradation of macromolecules, effected by means of ultrasonic (US) irradiation. Specifically, we have investigated the effect of long-chain branching (LCB), in the star configuration, on the degradation mechanism of polystyrene dissolved in DMAc/LiCl. The information obtained from size-exclusion chromatography with triple detection (refractometry, viscometry, multi-angle light scattering) shows that the degradation mechanism of stars is radically different from that of linear polymers. Whereas in the latter, from a macromolecular standpoint, it is merely necessary for the molar mass to be greater than some limiting value (M(lim)), in the former both molar mass and structural factors affect ultrasonic degradation. We have examined the effects of arm number and of arm molar mass on star degradation, and propose the concept of a spanning molar mass (M(span) approximately 2M(arm)) such that, even in the event that M(arm)M(lim). This mechanism has been extended to other types of architecture (e.g., H-branched, dendritic), where it is proposed that a continuous path must exist with M(path)>M(lim) for degradation to occur. Examination of the different radii afforded by viscometric and light-scattering detection gives insight into the solution thermodynamics and conformation of the stars with differing arm number and molar mass and of the effects of insonation on macromolecular structure.     

Determination of external and internal mass transfer limitation in nitrifying microbial aggregates

In this article we present a study of the effects of external and internal mass transfer limitation of oxygen in a nitrifying system. The oxygen uptake rates (OUR) were measured on both a macro-scale with a respirometric reactor using off-gas analysis (Titrimetric and Off-Gas Analysis (TOGA) sensor) and on a micro-scale with microsensors. These two methods provide independent, accurate measurements of the reaction rates and concentration profiles around and in the granules. The TOGA sensor and microsensor measurements showed a significant external mass transfer effect at low dissolved oxygen (DO) concentrations in the bulk liquid while it was insignificant at higher DO concentrations. The oxygen distribution with anaerobic or anoxic conditions in the center clearly shows major mass transfer limitation in the aggregate interior. The large drop in DO concentration of 22-80% between the bulk liquid and aggregate surface demonstrates that the external mass transfer resistance is also highly important. The maximum OUR even for floccular biomass was only attained at much higher DO concentrations (approximately 8 mg/L) than typically used in such systems. For granules, the DO required for maximal activity was estimated to be >20 mg/L, clearly indicating the effects of the major external and internal mass transfer limitations on the overall biomass activity. Smaller aggregates had a larger volumetric OUR indicating that the granules may have a lower activity in the interior part of the aggregate.