Algal blooms caused by Prorocentrum donghaiense occurred frequently in the East China Sea （ECS） during spring in recent years. In this study, a coupled biophysical model was used to hindcast a massive P. donghaiense...Algal blooms caused by Prorocentrum donghaiense occurred frequently in the East China Sea （ECS） during spring in recent years. In this study, a coupled biophysical model was used to hindcast a massive P. donghaiense bloom that occurred in 2005 and to determine the factors influencing bloom initiation and development. The model comprised the Regional Ocean Modeling System tailored for the ECS that utilized a multi-nested configuration and a population dynamics model for 19. donghaiense. Comparisons between simulations and observations revealed that the biological model is capable of reproducing the characteristics of 19. donghaiense growth under different irradiances and phosphorus limitation scenarios. The variation of intracellular phosphorus and the effects of 19. donghaiense on ambient nutrients conditions were also reproduced. The biophysical model hindcasted the hydrodynamics and spatiotemporal distributions of the P. donghaiense bloom reasonably well. Bloom development was consistent with observations reported in earlier studies. The results demonstrate the capability of the model in capturing subsurface incubation during bloom initiation. Then model＇s hindcast solutions were further used to diagnose the factors controlling the vertical distribution. Phosphate appeared to be one of the factors controlling the subsurface incubation, whereas surface wind fields played an important role in determining P. donghaiense distribution. The results highlight the importance of nutrient-limitation as a mechanism in the formation of P. donghaiense subsurface layers and the dispersing of P. donghaiense blooms. This coupled biophysical model should be improved and used to investigate 19. donghaiense blooms occurring in different scenarios.展开更多
In the East China Sea(ECS), the succession of causative species responsible for blooms is a recurrent phenomenon during the spring, which changes from diatoms to dinoflagellates. Observations from space and in situ cr...In the East China Sea(ECS), the succession of causative species responsible for blooms is a recurrent phenomenon during the spring, which changes from diatoms to dinoflagellates. Observations from space and in situ cruises captured this pattern of succession during spring of 2005. In this study, we coupled two biological models, which were developed previously for Skeletonema costatum and Prorocentrum donghaiense,into a circulation model tailored for the ECS. The coupled biophysical model was used to hindcast the blooms and to test the hypothesis proposed in earlier studies that phosphate(PO4 3–) is the first-order decider of the succession. The coupled model successfully reproduced the hydrodynamics(as described in a companion paper by Sun et al.(1), the spatiotemporal distribution of the chlorophyll a(Chl a) concentration, and the species succession reasonably well. By analyzing the effects of different factors on the surface Chl a distribution, we confirmed that the offshore boundaries of the blooms were confined by PO4 3–. In addition, we suggest that surface wind fields may modulate the horizontal distribution of blooms. Thus, during the dispersal of blooms, surface winds coupled with PO4 3– may control the succession of blooms in the ECS. The proposed coupled model provides a benchmark to facilitate future improvements by including more size classes for organisms, multiple nutrient schemes, and additional processes.展开更多
DNA double-strand breaks(DSBs)may result in cellular mutations,apoptosis,and cell death,making them critical determinants of cellular survival and functionality,as well as major mechanisms underlying cell death.The su...DNA double-strand breaks(DSBs)may result in cellular mutations,apoptosis,and cell death,making them critical determinants of cellular survival and functionality,as well as major mechanisms underlying cell death.The success of nanodosimetry lies in the reduction in the number of modeling parameters to be adjusted for the model to predict experimental data on radiation biology.Based on this background,this study modified and simplified the logistic nanodosimetry model(LNDM)based on radiation-induced DSB probability.The probability distribution of ionization cluster size P(v|Q)under irradiation with carbon-ion beams was obtained through a track-structure Monte Carlo(MC)simulation,and then,the nanodosimetric quantities and DSB probability were calculated.Combining the assumptions of the linear quadratic(LQ)model and LNDM,DSB probability-based modification and simplification of the LNDM were conducted.Additionally,based on the radiobiological experimental data of human salivary gland(HSG),Chinese hamster lung(V79),and Chinese hamster ovary(CHO-K1)cells,the least-squares method was used to optimize the parameters of the modified LNDM(mLNDM).The mLNDM accurately reproduced the experimental data of HSG,V79,and CHO-K1 cells,and the results showed that the model parameters r and m_(0) were independent of the cell type,that is,the biological effects of cells with different radiosensitivities can be characterized by adjusting only the model parameters k and P_(s→l).Compared with HSG and CHO-K1 cells,V79 cells had smaller k and P_(s→l)values,indicating that that DSBs have a lower probability of eventually causing lethal damage,and sublethal events are less likely to interact to form lethal events,thereby having radioresistant characteristics.Compared with the LNDM,the mLNDM eliminates the tedious derivation process and connects the quantities characterizing radiation quality at the nanoscale level using radiation biological effects in a more direct and easy-to-understand manner,thus providing a simpler and more accurate method for calculating relative biological effectiveness for ion-beam treatment planning.展开更多
The impact of well watered mesoscale wheat over mid-latitude arid areas on mesoscale boundary layer structures (MBLS) and climate has been investigated in the study .using a mesoscale biophysical, meteorological model...The impact of well watered mesoscale wheat over mid-latitude arid areas on mesoscale boundary layer structures (MBLS) and climate has been investigated in the study .using a mesoscale biophysical, meteorological model (BM) developed in the current study. The BM is composed of six modules:mesoscale atmospheric module, soil module, vegetation module, snow-atmosphere interaction module, underlying surface meteorology module and subgrid scale flux parameterization module. The six modules constitute an interacting system by supplying boundary conditions to each other.The investigation indicates that a horizontal pressure gradient associated with mesoscale perturbations in temperature and humidity is created during the day, which results from more water transpired from the vegetation canopy (VC) and evaporated from underlying wet soil. Non-classical mesoscale circulations (called as vegetation-breeze) are forced by the pressure perturbations with wind speeds about 5 m / s, flowing from the VC to the adjacent bare soil in the low boundary layer.Specific attention in the study is given to study the MBLS at night caused by the interactions between these mesoscale vegetation-breezes.The impacts of the VC's scale and atmospheric background thermal stability (ABTS) on these thermally forced mesoscale vegetation-breezes are also investigated.展开更多
Biophysics as an immense spectrum comprehended by one of the most commonly applied borderland mental process embracing from the nature,through living systems up to spiritual processes brings it along inevitable that t...Biophysics as an immense spectrum comprehended by one of the most commonly applied borderland mental process embracing from the nature,through living systems up to spiritual processes brings it along inevitable that the reader will join issue here and there with the deductions of this book but in actual fact it was just one of the goals of this work.To get hold of the biophysical view is not an easy task,because it applies mathematical apparatus to biological systems;on the other hand as a reward it guides to fascinating results,recognizing theoretically which conformity of rules are valid on principle in the Universe in the inanimate-living-spiritual triple system from the lowest to the highest organizational level.In this way one can make up the reader’s claim to consider systematically those problems arising from the various fields of science and life in the countless variety of interrelations and in their very different consequences.展开更多
Modeling synthetic gene circuits to implement dynamic flux balancing is crucial in teaching and exploring metabolic engineering strategies to repartition metabolic precursors and construct efficient microbial cell fac...Modeling synthetic gene circuits to implement dynamic flux balancing is crucial in teaching and exploring metabolic engineering strategies to repartition metabolic precursors and construct efficient microbial cell factories.Microbial fitness and production rates are often complex phenotypes that are governed by highly nonlinear,multivariable functions which are intrinsically linked through carbon metabolism.The solution of such dynamic system can be difficult for synthetic biologists to visualize or conceptualize.Recently,researchers(Santala et al.,Metab.Eng.Comm.,2018)have implemented an arabinose based genetic switch to dynamically partition the central carbon flux between cell growth and product formation.The autonomous switch allowed dynamic shift from arabinose-associated cell growth to acetate-associated product(wax ester)formation.This system clearly demonstrates the effectiveness of using a genetic switch to decouple cell growth from product formation in a one-pot bioreactor to minimize operational cost.Coupled with Michaelis-Menten kinetics,and Luedeking-Piret equations,we were able to reconstruct and analyze this metabolic switch in silica and achieved graphical solutions that qualitatively match with the experimental data.By assessing physiologically-accessible parameter space,we observed a wide range of dynamic behavior and examined the different limiting cases.Graphical solutions for this dynamic system can be viewed simultaneously and resolved in real time via buttons on the graphical user interface(GUI).Metabolic bottlenecks in the system can be accurately predicted by varying the respective rate constants.The GUI serves as a diagnosis toolkit to troubleshoot genetic circuits design constraints and as an interactive workflow of using this arabinose based genetic switch to dynamically control carbon flux,which may provide a valuable computational toolbox for metabolic engineers and synthetic biologists to simulate and understand complex genetic-metabolic system.展开更多
Apples(Malus domestica)are one of the major fruits cultivated in South Korea and worldwide.To both sustain the productivity of apple trees and preserve the land,a land suitability assessment has been conducted.Two met...Apples(Malus domestica)are one of the major fruits cultivated in South Korea and worldwide.To both sustain the productivity of apple trees and preserve the land,a land suitability assessment has been conducted.Two methods were used to analyze land suitability,a Most-Limiting Characteristic Method(MLCM)and an Analytic Hierarchy Process(AHP)with integrated soil and climate information based on the FAO classification framework.The most-limiting characteristic analysis showed that almost all areas were classified as marginally suitable(S3)or not suitable(N),which together accounted for 94.54%of the land in the Republic of Korea.On the contrary,AHP showed that S1(34.1%)and S2(44.17%)account for the majority of the land.展开更多
Background:Previous studies have surveyed golf courses to determine nitrogen(N)fertilizer application rates on golf courses,but no previous studies have attempted to quantify how efficiently golf courses use nitrogen....Background:Previous studies have surveyed golf courses to determine nitrogen(N)fertilizer application rates on golf courses,but no previous studies have attempted to quantify how efficiently golf courses use nitrogen.Methods:This study tests the ability of the growth potential(GP)N Requirement model as a benchmarking tool to predict a target level of N use on 76 golf courses in 5 regions of the US(Midwest,Northeast,East Texas,Florida,Northwest)and 3 countries in Europe(Denmark,Norway,UK).Results:The ratio of the golf course-wide N application rate to the GP N requirement prediction(termed the nitrogen efficiency score or NES)was 0.27,indicating that golf courses used 73%less N than predicted by the model.As such,the GP N Requirement model needs to be recalibrated to predict N use on golf courses.This was achieved by adjusting the Nmax coefficient in the model.N rates on golf courses were widely variable both within and across regions.All regions had a coefficient of variation in N rates of 0.46 or greater.Conclusions:The high variation in N rates,which is largely unexplained by climate,economic factors,grass type,and soil type,may be indicative of inefficient N use in golf course management.展开更多
基金The National Natural Science Foundation of China(NSFC)under contract Nos 41276186,41506015 and 41606038the NSFC-Shandong Joint Fund for Marine Science Research Centers under contract No.U1606405the Postdoctoral Innovation Foundation of Shandong Province under contract No.201502031
文摘Algal blooms caused by Prorocentrum donghaiense occurred frequently in the East China Sea （ECS） during spring in recent years. In this study, a coupled biophysical model was used to hindcast a massive P. donghaiense bloom that occurred in 2005 and to determine the factors influencing bloom initiation and development. The model comprised the Regional Ocean Modeling System tailored for the ECS that utilized a multi-nested configuration and a population dynamics model for 19. donghaiense. Comparisons between simulations and observations revealed that the biological model is capable of reproducing the characteristics of 19. donghaiense growth under different irradiances and phosphorus limitation scenarios. The variation of intracellular phosphorus and the effects of 19. donghaiense on ambient nutrients conditions were also reproduced. The biophysical model hindcasted the hydrodynamics and spatiotemporal distributions of the P. donghaiense bloom reasonably well. Bloom development was consistent with observations reported in earlier studies. The results demonstrate the capability of the model in capturing subsurface incubation during bloom initiation. Then model＇s hindcast solutions were further used to diagnose the factors controlling the vertical distribution. Phosphate appeared to be one of the factors controlling the subsurface incubation, whereas surface wind fields played an important role in determining P. donghaiense distribution. The results highlight the importance of nutrient-limitation as a mechanism in the formation of P. donghaiense subsurface layers and the dispersing of P. donghaiense blooms. This coupled biophysical model should be improved and used to investigate 19. donghaiense blooms occurring in different scenarios.
基金The National Natural Science Foundation of China under contract Nos 41276186,41506015 and 41606038the NSFC-Shandong Joint Fund for Marine Science Research Centers under contract No.U1406404the Postdoctoral Innovation Foundation of Shandong Province under contract No.201502031
文摘In the East China Sea(ECS), the succession of causative species responsible for blooms is a recurrent phenomenon during the spring, which changes from diatoms to dinoflagellates. Observations from space and in situ cruises captured this pattern of succession during spring of 2005. In this study, we coupled two biological models, which were developed previously for Skeletonema costatum and Prorocentrum donghaiense,into a circulation model tailored for the ECS. The coupled biophysical model was used to hindcast the blooms and to test the hypothesis proposed in earlier studies that phosphate(PO4 3–) is the first-order decider of the succession. The coupled model successfully reproduced the hydrodynamics(as described in a companion paper by Sun et al.(1), the spatiotemporal distribution of the chlorophyll a(Chl a) concentration, and the species succession reasonably well. By analyzing the effects of different factors on the surface Chl a distribution, we confirmed that the offshore boundaries of the blooms were confined by PO4 3–. In addition, we suggest that surface wind fields may modulate the horizontal distribution of blooms. Thus, during the dispersal of blooms, surface winds coupled with PO4 3– may control the succession of blooms in the ECS. The proposed coupled model provides a benchmark to facilitate future improvements by including more size classes for organisms, multiple nutrient schemes, and additional processes.
基金supported by the National Key Research and Development Program of China(No.2022YFC2401503)Key Research and Development Program of Gansu Province(No.23YFFA0010)+1 种基金Natural Science Foundation of Gansu Province(No.23JRRA625)Special Project of Science and Technology Cooperation between Hubei Province and Chinese Academy of Sciences(No.42000021817T300000050)。
文摘DNA double-strand breaks(DSBs)may result in cellular mutations,apoptosis,and cell death,making them critical determinants of cellular survival and functionality,as well as major mechanisms underlying cell death.The success of nanodosimetry lies in the reduction in the number of modeling parameters to be adjusted for the model to predict experimental data on radiation biology.Based on this background,this study modified and simplified the logistic nanodosimetry model(LNDM)based on radiation-induced DSB probability.The probability distribution of ionization cluster size P(v|Q)under irradiation with carbon-ion beams was obtained through a track-structure Monte Carlo(MC)simulation,and then,the nanodosimetric quantities and DSB probability were calculated.Combining the assumptions of the linear quadratic(LQ)model and LNDM,DSB probability-based modification and simplification of the LNDM were conducted.Additionally,based on the radiobiological experimental data of human salivary gland(HSG),Chinese hamster lung(V79),and Chinese hamster ovary(CHO-K1)cells,the least-squares method was used to optimize the parameters of the modified LNDM(mLNDM).The mLNDM accurately reproduced the experimental data of HSG,V79,and CHO-K1 cells,and the results showed that the model parameters r and m_(0) were independent of the cell type,that is,the biological effects of cells with different radiosensitivities can be characterized by adjusting only the model parameters k and P_(s→l).Compared with HSG and CHO-K1 cells,V79 cells had smaller k and P_(s→l)values,indicating that that DSBs have a lower probability of eventually causing lethal damage,and sublethal events are less likely to interact to form lethal events,thereby having radioresistant characteristics.Compared with the LNDM,the mLNDM eliminates the tedious derivation process and connects the quantities characterizing radiation quality at the nanoscale level using radiation biological effects in a more direct and easy-to-understand manner,thus providing a simpler and more accurate method for calculating relative biological effectiveness for ion-beam treatment planning.
基金This project is supported by National Natureal Science Foundation of China,LASC and LAPC.
文摘The impact of well watered mesoscale wheat over mid-latitude arid areas on mesoscale boundary layer structures (MBLS) and climate has been investigated in the study .using a mesoscale biophysical, meteorological model (BM) developed in the current study. The BM is composed of six modules:mesoscale atmospheric module, soil module, vegetation module, snow-atmosphere interaction module, underlying surface meteorology module and subgrid scale flux parameterization module. The six modules constitute an interacting system by supplying boundary conditions to each other.The investigation indicates that a horizontal pressure gradient associated with mesoscale perturbations in temperature and humidity is created during the day, which results from more water transpired from the vegetation canopy (VC) and evaporated from underlying wet soil. Non-classical mesoscale circulations (called as vegetation-breeze) are forced by the pressure perturbations with wind speeds about 5 m / s, flowing from the VC to the adjacent bare soil in the low boundary layer.Specific attention in the study is given to study the MBLS at night caused by the interactions between these mesoscale vegetation-breezes.The impacts of the VC's scale and atmospheric background thermal stability (ABTS) on these thermally forced mesoscale vegetation-breezes are also investigated.
文摘Biophysics as an immense spectrum comprehended by one of the most commonly applied borderland mental process embracing from the nature,through living systems up to spiritual processes brings it along inevitable that the reader will join issue here and there with the deductions of this book but in actual fact it was just one of the goals of this work.To get hold of the biophysical view is not an easy task,because it applies mathematical apparatus to biological systems;on the other hand as a reward it guides to fascinating results,recognizing theoretically which conformity of rules are valid on principle in the Universe in the inanimate-living-spiritual triple system from the lowest to the highest organizational level.In this way one can make up the reader’s claim to consider systematically those problems arising from the various fields of science and life in the countless variety of interrelations and in their very different consequences.
基金The authors would like to acknowledge the Bill and Melinda Gates Foundation(OPP1188443)National Science Foundation under grant number 1805139 for financially supporting this project.
文摘Modeling synthetic gene circuits to implement dynamic flux balancing is crucial in teaching and exploring metabolic engineering strategies to repartition metabolic precursors and construct efficient microbial cell factories.Microbial fitness and production rates are often complex phenotypes that are governed by highly nonlinear,multivariable functions which are intrinsically linked through carbon metabolism.The solution of such dynamic system can be difficult for synthetic biologists to visualize or conceptualize.Recently,researchers(Santala et al.,Metab.Eng.Comm.,2018)have implemented an arabinose based genetic switch to dynamically partition the central carbon flux between cell growth and product formation.The autonomous switch allowed dynamic shift from arabinose-associated cell growth to acetate-associated product(wax ester)formation.This system clearly demonstrates the effectiveness of using a genetic switch to decouple cell growth from product formation in a one-pot bioreactor to minimize operational cost.Coupled with Michaelis-Menten kinetics,and Luedeking-Piret equations,we were able to reconstruct and analyze this metabolic switch in silica and achieved graphical solutions that qualitatively match with the experimental data.By assessing physiologically-accessible parameter space,we observed a wide range of dynamic behavior and examined the different limiting cases.Graphical solutions for this dynamic system can be viewed simultaneously and resolved in real time via buttons on the graphical user interface(GUI).Metabolic bottlenecks in the system can be accurately predicted by varying the respective rate constants.The GUI serves as a diagnosis toolkit to troubleshoot genetic circuits design constraints and as an interactive workflow of using this arabinose based genetic switch to dynamically control carbon flux,which may provide a valuable computational toolbox for metabolic engineers and synthetic biologists to simulate and understand complex genetic-metabolic system.
基金support of“Research Program for Agricultural Science&Technology Development(Project No.PJ01000701)”National Institute of Agricultural Science,Rural Development Administration,the Republic of Korea.
文摘Apples(Malus domestica)are one of the major fruits cultivated in South Korea and worldwide.To both sustain the productivity of apple trees and preserve the land,a land suitability assessment has been conducted.Two methods were used to analyze land suitability,a Most-Limiting Characteristic Method(MLCM)and an Analytic Hierarchy Process(AHP)with integrated soil and climate information based on the FAO classification framework.The most-limiting characteristic analysis showed that almost all areas were classified as marginally suitable(S3)or not suitable(N),which together accounted for 94.54%of the land in the Republic of Korea.On the contrary,AHP showed that S1(34.1%)and S2(44.17%)account for the majority of the land.
文摘Background:Previous studies have surveyed golf courses to determine nitrogen(N)fertilizer application rates on golf courses,but no previous studies have attempted to quantify how efficiently golf courses use nitrogen.Methods:This study tests the ability of the growth potential(GP)N Requirement model as a benchmarking tool to predict a target level of N use on 76 golf courses in 5 regions of the US(Midwest,Northeast,East Texas,Florida,Northwest)and 3 countries in Europe(Denmark,Norway,UK).Results:The ratio of the golf course-wide N application rate to the GP N requirement prediction(termed the nitrogen efficiency score or NES)was 0.27,indicating that golf courses used 73%less N than predicted by the model.As such,the GP N Requirement model needs to be recalibrated to predict N use on golf courses.This was achieved by adjusting the Nmax coefficient in the model.N rates on golf courses were widely variable both within and across regions.All regions had a coefficient of variation in N rates of 0.46 or greater.Conclusions:The high variation in N rates,which is largely unexplained by climate,economic factors,grass type,and soil type,may be indicative of inefficient N use in golf course management.
