Model-based predictions of anaerobic digestion of agricultural substrates for biogas production

A modified Anaerobic Digestion Model No. 1 (ADM1), calibrated on a laboratory digester with a feeding mix of 30% weight of cow manure and 70% weight of corn silage, was implemented, showing its performances of simulation as a decision-making and planning-supporting tool for the anaerobic digestion of agricultural substrates. The virtual fermenter obtained was used to conduct simulations with different feeding compositions and loading rates of cow manure, corn silage, grass silage and rape oil. All simulations were started at the same initial state which was represented by a steady state with an organic loading rate of 2.5 kg ODM/(). The effects of the different feeding combinations on biogas composition and biogas yield were predicted reasonably, and partly verified with the available literature data. Results demonstrated that the simulations could be helpful for taking decisions on agricultural biogas plant operation or experimental set-ups, if used advisedly.     

Microbial community structure and dynamics in a mixotrophic nitrogen removal process using recycled spent caustic under different loading conditions

A laboratory-scale Bardenpho process was established to investigate the proper nitrogen loading rate (NLR) when modified spent caustic (MSC) is applied as electron donor and alkalinity source for denitrification. MSC injection induced autotrophic nitrogen removal with sulfur as electron donor and heterotrophic denitrification. The nitrogen removal rate (NRR) did not increase proportionally to NLR. Based on the total nitrogen concentration in the effluent observed in the trials with MSC, the NLR in the influent should not exceed 0.15 kg N/m³ d in order to satisfy water quality regulations. Microbial communities in the anoxic reactors were characterized by pyrosequencing of 16S rRNA gene sequences amplified by the polymerase chain reaction of DNA extracted from sludge samples. Microbial diversity was lower as MSC dosage was increased, and the injection of MSC caused an increase in SOB belonging to the genus Thiobacillus which is responsible for denitrification using sulfur.     

Hydraulic residence time computation for constructed wetland design

Hydraulic residence time (HRT) is one of the key design parameters controlling the removal efficiency of contaminants and nutrients in stormwater and wastewater wetlands. The paper presents a new approach to the estimation of HRT using the variable residence time (VART) model. The VART model is employed to simulate the major processes (including advection, dispersion, and transient storage of contaminants/nutrients in vegetated zones) affecting HRT and thereby to produce a hydraulic residence time distribution (HRTD) for a design wetland. The HRTD in combination with a moment-based method is then utilized to find a mean design HRT for the design wetland. Methods for estimation of parameters governing the HRTD are proposed. The new approach to HRT computation is demonstrated through a case study for the Tres Rios Demonstration (TRD) Wetlands in Arizona, USA. Modeling results show that the design HRTs for the Hayfield wetland (H1) and the Cobble wetlands (C1 and C2) are 4.04, 4.66, and 2.65 days, respectively. The computed HRTs agree well with those reported by previous studies, confirming the efficacy of the new approach to hydraulic design of constructed wetlands.     

Thermal performance curves of Paramecium caudatum: a model selection approach

The ongoing climate change has motivated numerous studies investigating the temperature response of various organisms, especially that of ectotherms. To correctly describe the thermal performance of these organisms, functions are needed which sufficiently fit to the complete optimum curve. Surprisingly, model-comparisons for the temperature-dependence of population growth rates of an important ectothermic group, the protozoa, are still missing. In this study, temperature reaction norms of natural isolates of the freshwater protist Paramecium caudatum were investigated, considering nearly the entire temperature range. These reaction norms were used to estimate thermal performance curves by applying a set of commonly used model functions. An information theory approach was used to compare models and to identify the best ones for describing these data. Our results indicate that the models which can describe negative growth at the high- and low-temperature branch of an optimum curve are preferable. This is a prerequisite for accurately calculating the critical upper and lower thermal limits. While we detected a temperature optimum of around 29 °C for all investigated clonal strains, the critical thermal limits were considerably different between individual clones. Here, the tropical clone showed the narrowest thermal tolerance, with a shift of its critical thermal limits to higher temperatures.     

Predicting kinetic constants of protein-protein interactions based on structural properties

Elucidating kinetic processes of protein–protein interactions (PPI) helps to understand how basic building blocks affect overall behavior of living systems. In this study, we used structure‐based properties to build predictive models for kinetic constants of PPI. A highly diverse PPI dataset, protein–protein kinetic interaction data and structures (PPKIDS), was built. PPKIDS contains 62 PPI with complex structures and kinetic constants measured experimentally. The influence of structural properties on kinetics of PPI was studied using 35 structure‐based features, describing different aspects of complex structures. Linear models for the prediction of kinetic constants were built by fitting with selected subsets of structure‐based features. The models gave correlation coefficients of 0.801, 0.732, and 0.770 for k_off, k_on, and K_d, respectively, in leave‐one‐out cross validations. The predictive models reported here use only protein complex structures as input and can be generally applied in PPI studies as well as systems biology modeling. Our study confirmed that different properties play different roles in the kinetic process of PPI. For example, k_on was affected by overall structural features of complexes, such as the composition of secondary structures, the change of translational and rotational entropy, and the electrostatic interaction; while k_off was determined by interfacial properties, such as number of contacted atom pairs per 100 Ų. This information provides useful hints for PPI design. Proteins 2010;79:720–734. © 2010 Wiley‐Liss, Inc.     

Phylogenetic conservatism of environmental niches in mammals

Phylogenetic niche conservatism is the pattern where close relatives occupy similar niches, whereas distant relatives are more dissimilar. We suggest that niche conservatism will vary across clades in relation to their characteristics. Specifically, we investigate how conservatism of environmental niches varies among mammals according to their latitude, range size, body size and specialization. We use the Brownian rate parameter, σ(2), to measure the rate of evolution in key variables related to the ecological niche and define the more conserved group as the one with the slower rate of evolution. We find that tropical, small-ranged and specialized mammals have more conserved thermal niches than temperate, large-ranged or generalized mammals. Partitioning niche conservatism into its spatial and phylogenetic components, we find that spatial effects on niche variables are generally greater than phylogenetic effects. This suggests that recent evolution and dispersal have more influence on species' niches than more distant evolutionary events. These results have implications for our understanding of the role of niche conservatism in species richness patterns and for gauging the potential for species to adapt to global change.     

Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence

The relationship between genotypic and phenotypic divergence over evolutionary time varies widely, and cases of rapid phenotypic differentiation despite genetic similarity have attracted much attention. Here, we report an extreme case of the reverse pattern--morphological stasis in a tropical fish despite massive genetic divergence. We studied the enigmatic African freshwater butterfly fish (Pantodon buchholzi), whose distinctive morphology earns it recognition as a monotypic family. We sequenced the mitochondrial genome of Pantodon from the Congo basin and nine other osteoglossomorph taxa for comparison with previous mitogenomic profiles of Pantodon from the Niger basin and other related taxa. Pantodon populations form a monophyletic group, yet their mitochondrial coding sequences differ by 15.2 per cent between the Niger and Congo basins. The mitogenomic divergence time between these populations is estimated to be greater than 50 Myr, and deep genetic divergence was confirmed by nuclear sequence data. Among six sister-group comparisons of osteoglossomorphs, Pantodon exhibits the slowest rate of morphological divergence despite a level of genetic differentiation comparable to both species-rich (e.g. Mormyridae) and species-poor (e.g. Osteoglossidae) families. Morphological stasis in these two allopatric lineages of Pantodon offers a living vertebrate model for investigating phenotypic stability over millions of generations in the face of profound fluctuations in environmental conditions.     

The genome as a life-history character: why rate of molecular evolution varies between mammal species

DNA sequences evolve at different rates in different species. This rate variation has been most closely examined in mammals, revealing a large number of characteristics that can shape the rate of molecular evolution. Many of these traits are part of the mammalian life-history continuum: species with small body size, rapid generation turnover, high fecundity and short lifespans tend to have faster rates of molecular evolution. In addition, rate of molecular evolution in mammals might be influenced by behaviour (such as mating system), ecological factors (such as range restriction) and evolutionary history (such as diversification rate). I discuss the evidence for these patterns of rate variation, and the possible explanations of these correlations. I also consider the impact of these systematic patterns of rate variation on the reliability of the molecular date estimates that have been used to suggest a Cretaceous radiation of modern mammals, before the final extinction of the dinosaurs.     

UV-C irradiation as a tool to eradicate algae in caves

Algal proliferation has commonly been reported to occur on monuments, such as crypts, churches, and caves, as soon as artificial lighting is used. In this work we study the effects of UV-C irradiation on algae collected in different caves in Dordogne (southwest of France). First, the effect of UV-C irradiation was tested on algal cell suspensions during increasing exposure times. After treatment, the photosynthetic capacity was assayed using a polarometric method, and algal cell viability was then estimated using a Trypan blue test after a rest period of 15 h. UV-C irradiation was then studied on algal cells cultivated on a solid support consisting of pieces of calcareous stone. Drops of concentrated algal cells were inoculated on stone and exposed to UV-C radiation for 3, 6, or 9 h. After this irradiation, half of the samples were submitted to a high white light intensity (1400 ??mol m⁻² s⁻¹ of photosynthetically active radiation, PAR) for 6 h while the other half were incubated in the culture room. Subsequently, algal macroscopic parameters such as covering rate and colonized area were measured by macro photography. Both experiments led to the conclusion that UV-C irradiation has deleterious effects on photosynthetic parameters and growth of algal cells.     

光呼吸和谷氨酰胺合成酶抑制剂对水稻冠层NH3挥发的影响

在营养液培养条件下,对两个不同氮效率基因型水稻品种扬稻6号和武育粳3号采用光呼吸抑制剂异烟肼（INH）和谷氨酰胺合成酶（GS）抑制剂蛋氨酸亚砜亚胺（MSO）处理,研究其对水稻光合速率、光呼吸速率、GS酶活性及冠层的NH。挥发速率的影响。结果发现：（1）MSO导致剑叶光合速率下降,光呼吸速率升高;INH导致光呼吸速率显著下降,同时一定程度上引起光合速率降低。（2）MSO处理显著降低了GS酶活性,相应地引起NH。挥发速率增加;INH在一定程度上导致NH。挥发速率降低。（3）扬稻6号NH。挥发速率比武育粳3号低的生理原因是光呼吸速率较低和GS酶活性较高。