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1.
《Journal of molecular biology》2022,434(17):167690
Accurate development of allosteric modulators of GPCRs require a thorough assessment of their sequence, structure, and dynamics, toward gaining insights into their mechanisms of actions shared by family members, as well as dynamic features that distinguish subfamilies. Building on recent progress in the characterization of the signature dynamics of proteins, we analyzed here a dataset of 160 Class A GPCRs to determine their sequence similarities, structural landscape, and dynamic features across different species (human, bovine, mouse, squid, and rat), different activation states (active/inactive), and different subfamilies. The two dominant directions of variability across experimentally resolved structures, identified by principal component analysis of the dataset, shed light to cooperative mechanisms of activation, subfamily differentiation, and speciation of Class A GPCRs. The analysis reveals the functional significance of the conformational flexibilities of specific structural elements, including: the dominant role of the intracellular loop 3 (ICL3) together with the cytoplasmic ends of the adjoining helices TM5 and TM6 in enabling allosteric activation; the role of particular structural motifs at the extracellular loop 2 (ECL2) connecting TM4 and TM5 in binding ligands specific to different subfamilies; or even the differentiation of the N-terminal conformation across different species. Detailed analyses of the modes of motions accessible to the members of the dataset and their variations across members demonstrate how the active and inactive states of GPCRs obey distinct conformational dynamics. The collective fluctuations of the GPCRs are robustly defined in the active state, while the inactive conformers exhibit broad variance among members. 相似文献
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Questions: Do differences in previous land use cause long-lasting changes in soil chemistry? Is vegetation composition affected by the previous land use after 50 years of secondary succession? Is the effect of previous land use caused by pre-existing differences in environmental conditions or mediated through changes in soil chemistry? How important is the effect of previous land use in relation to other factors? Location: Doupovské Mountains, Czech Republic. Methods: A stratified random sampling design was used to collect 91 vegetation relevés with accompanying soil samples. The effects of previous land use (arable field, meadow, pasture) on soil pH, organic carbon (C), total nitrogen (N), C:N ratio and available phosphorus were tested by an analysis of covariance. A canonical correspondence analysis and variation partitioning procedure were used to reveal relationships among previous land use, environmental factors and species composition. Results: Organic C, total N and C:N ratio were significantly influenced by previous land use, while available phosphorus and soil pH were not. Previous land use explained a significant part of the variation in species composition and its effects only partly overlapped with the effects of soil chemistry and terrain attributes. However, the species composition of post-agricultural forests was mostly determined by environmental factors not modified by previous land use. Conclusions: Forest communities that originate on abandoned agricultural land are primarily determined by natural environmental conditions. Nevertheless, the type of previous land use also modifies the species assemblages of these forests and needs to be considered as an important determinant of their composition. 相似文献
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Kalyani Nair Milind Gandhi Saif Khalil Karen Chang Yan Michele Marcolongo Kenneth Barbee Wei Sun Dr. 《Biotechnology journal》2009,4(8):1168-1177
Bioprinting is an emerging technology in the field of tissue engineering and regenerative medicine. The process consists of simultaneous deposition of cells, biomaterial and/or growth factors under pressure through a micro-scale nozzle. Cell viability can be controlled by varying the parameters like pressure and nozzle diameter. The process itself can be a very useful tool for evaluating an in vitro cell injury model. It is essential to understand the cell responses to process-induced mechanical disturbances because they alter cell morphology and function. We carried out analysis and quantification of the degree of cell injury induced by bioprinting process. A parametric study with different process parameters was conducted to analyze and quantify cell injury as well as to optimize the parameters for printing viable cells. A phenomenological model was developed correlating the percentage of live, apoptotic and necrotic cells to the process parameters. This study incorporates an analytical formulation to predict the cell viability through the system as a function of the maximum shear stress in the system. The study shows that dispensing pressure has a more significant effect on cell viability than the nozzle diameter. The percentage of live cells is reduced significantly (by 38.75%) when constructs are printed at 40 psi compared to those printed at 5 psi. 相似文献
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Many macrophyte-dominated clear lakes switch to a phytoplankton-dominated turbid state when the lake becomes eutrophic. An existing Yuqiao Reservoir Water Quality Model (YRWQM) and the macrophyte submodel were coupled to simulate the effect of submerged macrophytes on nutrients and dissolve oxygen cycles in a shallow reservoir in China. The level of phosphorus loading in a transition from a clear to turbid state was addressed using the integrated model. The model runs from seedling establishment until dying out, from March 1 to July 18 in 2009. The simulations were performed for a contingent range of P loadings, starting from three different initial conditions. The results indicated that the integrated model improves accuracy of predictions compared to YRWQM. The concentrations of nutrients declined slightly during the macrophyte growth period in the reservoir and dissolved oxygen increased slightly. Although nutrient concentrations increased by submerged macrophyte release during the extinction period, the effect on the nutrients was less than that of transfer with nutrient-rich water. More released nutrients may enhance increases in substantial abundance. The critical phosphorus loading level during a switch from the clear to turbid state was estimated by these scenarios. The threshold for the switch is ∼6.1 mgP m−2 d−1 with an initial total phosphorus concentration of 160 μg l−1. Moreover, the results demonstrated that the switch was also dependent on the initial total phosphorus concentration. These results suggest that the reservoir in a clear water state is at risk of a switch as nutrient levels are close to the critical levels. 相似文献
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REDD+ reference levels directly impact the benefits which a country may receive. However, the existing “Compensation Reduction” (CR) and “Compensated Successful Efforts” (CSE) are only considered from a unilateral perspective of outputs or inputs. The combination of these two approaches is considered to estimate the REDD+ reference levels through the Zero-Sum-Gains Data Envelopment Analysis in this paper. The agricultural labor force and agricultural land area are used as input variables, and the gross agricultural production and carbon emissions from deforestation are considered as output variables. The REDD+ reference levels of 89 countries are calculated and classified through the Zero-Sum-Gains DEA model. The results demonstrate that the REDD+ reference levels are estimated efficiently through the Zero-Sum-Gains DEA model, and all countries with deforestation are in the Zero-Sum-Gains DEA frontier, indicating the overall Pareto optimality has been achieved. The empirical results also indicate that the use of Zero-Sum-Gains DEA model is more beneficial for Latin American and the Caribbean, while the countries that may see a revenue drop in REDD+ are in Africa, Asia and Oceania. Consequently, the final REDD+ reference levels should take into account both efficiency and fairness by selecting the appropriate fairness-efficiency weighting factor. 相似文献
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This study presents a complex approach for modeling the natural evolution of a population in terms of population number and dynamics of the genetic structure. A set of dynamic models that consider various types of natural selection was applied to describe possible mechanisms underlying the formation of existing genetic variations in litter sizes in coastal, inland, and farmed arctic fox populations (Alopex lagopus, family Canidae, order Carnivora). The r–K selection model for uniform population and the models with natural selection were assessed on various life cycle stages in a two-age population. The life cycle of arctic fox was fitted to the population model with two age stages. The different reproductive potentials and survivability of progeny on the early stage of life cycle were genetically determined using the model with a single diallelic gene. A monomorphism was obtained for a considered characteristic in a population of coastal arctic fox with constant food supply. Meanwhile, a polymorphism with cyclic fluctuations in population number and gene frequency was obtained in inland arctic fox populations, which could be due to cyclic fluctuations of prey. In farmed fox populations, the considered gene becomes pleiotropic (defines the survival rate of individuals on early and late stages of the life cycle) because of artificial selection performed by farmers to increase the reproductive success of breeders. The application of an appropriate model (with selection by pleiotropic gene) can be used to determine the elimination rate of low litter size alleles from the farmed populations. The possible applications of the proposed models for formulating and solving optimal control tasks in arctic fox populations are discussed too. 相似文献
8.
The contrasting effects of short‐ and long‐term habitat drainage on the population dynamics of freshwater turtles in a human‐dominated landscape 下载免费PDF全文
Zoey Owen‐Jones Pauline Priol Stephanie Thienpont Marc Cheylan Gabrielle Sauret Christophe Coïc Aurélien Besnard 《Freshwater Biology》2016,61(1):121-132
- Most studies on the effect of drought on the biodiversity of freshwater systems have focussed on natural droughts. We sought to assess the effects of artificial drainage on the population dynamics of the European pond turtle (Emys orbicularis). We investigated whether the probability of survival and emigration/immigration was affected by short‐term drawdown (for a few months over winter) or long‐term habitat drainage (a full year of drying out) in this long‐lived species of low dispersal ability.
- The study was replicated in two different areas using a Capture–Recapture monitoring programme over 5 years. In the two areas, we marked 1412 and 282 individuals, respectively. Short‐term drawdown had no impact on the vital rates of this species, while long‐term drainage promoted greater mobility among the ponds in both areas. This increase in movement might reduce survival, due to road mortality, or result in turtles leaving the study area.
- Moreover, as the transition probability between ponds was higher when ponds were close together and directly connected, for instance by a ditch, the construction and maintenance of ditches might reduce the effects of drainage. To implement effective conservation plans, studies that aim to assess the effect of human disturbance should monitor population dynamics and vital rates to allow a more complete picture of the real impacts.
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