BioNetSim:a Petri net-based modeling tool for simulations of biochemical processes

BioNetSim,a Petri net-based software for modeling and simulating biochemistry processes,is developed,whose design and implement are presented in this pa-per,including logic construction,real-time access to KEGG(Kyoto Encyclopedia of Genes and Genomes),and BioModel database.Furthermore,glycolysis is simulated as an example of its application.BioNetSim is a helpful tool for researchers to download data,model biological network,and simulate complicated biochemistry processes.Gene regulatory networks,metabolic pathways,signaling pathways,and kinetics of cell interaction are all available in BioNetSim,which makes modeling more efficient and effective.Similar to other Petri net-based softwares,BioNetSim does well in graphic application and mathematic construction.Moreover,it shows several powerful predominances.(1)It creates models in database.(2)It realizes the real-time access to KEGG and BioModel and transfers data to Petri net.(3)It provides qualitative analysis,such as computation of constants.(4)It generates graphs for tracing the concentration of every molecule during the simulation processes.

Recent Progress of Commercially Available Biosensors in China and Their Applications in Fermentation Processes

Biosensors, which are the products of the biotechnology industry, are among the key projects of the 7th, 8th, and 9th Fiveyear Plans of China Science ＆ Technology Developing Programs, respectively, and they play an important role in developing and reforming traditional biotechnology. SBA series biosensor analyzer, as the only one commercial biosensor in China, has attracted lots of attention in the process of information gathering and measurement for biological industry with the development of technology and society. In this paper, we presented an overview of the most important contributions dealing with the monitoring of the biochemical analytes in fermentation processes using SBA series biosensor analyzers in China. Future trends of the biosensor analyzer in China were also mentioned in the last section.

DYNAMIC MODEL AND SIMULATION OF THE PLATELETS'ROLE IN BLOOD COAGULATION

In order to confirm which process is the most important in the blood coagulation cascade,a dynamic model on the function of platelets in blood coagulation is presented based on biochemical experiments.Based on qualitative analysis and mathematical simulation,a series of conclusions about the influence of the activation rate of factor VIII and factor IX on the generation of thrombin(IIa)are drawn.It is evident that the pro-coagulation stimulus must exceed a threshold value to initiate the coagulation cascade.The value is related to the binding constant d_2 of the platelet. The stability of the equilibrium value is also related to the pro-coagulation stimulus. This article also evaluates the influence of the stimulus strength and the activated rate parameter of platelets on thrombin.The proportion of platelets activated at any given time is designated c.To each c,we obtain a maximum concentration of thrombin.It is evident that when the level of factor IX is below 1% of the normal level,the rate of thrombin generation reduces dramatically,resulting in severe bleeding tendency.

Experimental study on pressurized activated sludge process for high concentration pesticide wastewater

Pressurized biochemical process derived from traditional activated sludge processes is an innovative technology for wastewater treatment. The main advantage of the pressurized process is that the oxygen transfer barrier can be overcome by increasing the dissolved oxygen level. In this study, high concentration pesticide wastewater was treated by pressurized activated sludge process. It was found that the removal of chemical oxygen demand （COD） increased steadily with the increase of operating pressure, aeration time, and sludge concentration. When the operation pressure was 0.30 MPa and the aeration time was 6 hr, 85.0%-92.5% COD, corresponding to an effluent COD of 230-370 mg/L, was removed from an influent COD of 2500-5000 mg/L. The obtained outlet COD concentration was lower than 350-450 mg/L for the identical process operated under the atmospheric pressure. In addition, pressurized biochemical process could produce a higher COD volumetric loading rate at 5.8-7.6 kg COD/（m^3.day）, compared with 2.0-2.8 kg COD/（ma.day） using the same equipment at the atmospheric pressure. The COD concentration followed a modified Monod model with Vmax 2.31 day-1 and Ks 487 mg/L.

Fluorescence resonance energy transfer-based nanomaterials for the sensing in biological systems

The applications of fluorescence resonance energy transfer(FRET)are coming to be one of the simplest and most accessible strategy with super-resolved optical measurements.Meanwhile,nanomaterials have become ideal for constructing FRET-based system,due to their unique advantages of tunable emission,broad absorption,and long fluorescence(FL)lifetime.The limitations of traditional FRET-based detections,such as the intrinsic FL,auto-FL,as well as the short FL lifetime,could be overcome with nanomaterials.Consequently,numbers of FRET-based nanomaterials have been constructed for precise,sensitive and selective detections in biological systems.They could act as both energy donors and/or acceptors in the optical energy transfer process for biological detections.Some other nanomaterials would not participate in the energy transfer process,but act as the excellent matrix for modifications.The review will be roughly classified into nanomaterial-involved and uninvolved ones.Different detection targets,such as nucleic acids,pathogenic microorganisms,proteins,heavy metal ions,and other applications will be reviewed.Finally,the other biological applications,including environmental evaluation and mechanism studies would also be summarized.