Protein Conformational Change Based on a Two-dimensional Generalized Langevin Equation

A two-dimensional generalized Langevin equation is proposed to describe the protein conformational change, compatible to the electron transfer process governed by atomic packing density model. We assume a fractional Gaussian noise and a white noise through bond and through space coordinates respectively, and introduce the coupling effect coming from both fluctuations and equilibrium variances. The general expressions for autocorrelation functions of distance fluctuation and fluorescence lifetime variation are derived, based on which the exact conformational change dynamics can be evaluated with the aid of numerical Laplace inversion technique. We explicitly elaborate the short time and long time approximations. The relationship between the two-diraensional description and the one-dimensional theory is also discussed.

Optimization of Two-Dimensional Gel Electrophoresis for Kenaf Leaf Proteins

To establish a suitable and effective protocol of protein extraction for two-dimensional gel electrophoresis （2-DE） analysis in kenaf leaf tissues, three extraction methods （trichloroacetic acid/acetone, urea/thiourea, and phenol extraction methods） were applied to the extraction of kenaf leaf protein. The results were compared in regard to protein extraction efficiency, sodiumdodecyl sulfate-polyacrylamide gel electrophoresis （SDS-PAGE）, and 2-DE gels. Furthermore, the 2-DE system was optimized for four aspects： the pH range of IPG （immobilized pH gradient） stripes, sampling methods, sample volumes, and concentration of polyacrylamide gels. The data presented showed that the phenol extraction method is the best method to perform 2-DE analysis of kenaf leaf protein. The protein extracted from phenol extraction method reached the purity of （26.40±0.859）%, showed （25.67±1.53） protein bands in one dimension SDS-PAGE gels, and （1 374±54.44） protein spots on 2-DE gels. The research also indicates that kenaf leaf protein spots were distributed mainly within the pH range of 4-8. More clear background with a better distribution effect and many protein spots could be obtained on 2-DE gels under the conditions of active rehydration loading, 24 cm IPG strips （linear pH gradient of 4-7）, 1.4 mg samples, and 12% SDS-PAGE gels.

Development and application of a two-dimensional water quality model for the Daqinghe River Mouth of the Dianchi Lake

Water quality models are important tools to support the optimization of aquatic ecosystem rehabilitation programs and assess their efficiency. Basing on the flow conditions of the Daqinghe River Mouth of the Dianchi Lake, China, a two-dimensional water quality model was developed in the research. The hydrodynamics module was numerically solved by the alternating direction iteration （ADI） method. The parameters of the water quality module were obtained through the in situ experiments and the laboratory analyses that were conducted from 2006 to 2007. The model was calibrated and verified by the observation data in 2007. Among the four modelled key variables, i.e., water level, COD （in CODcr）, NH4＋-N and PO43-P the minimum value of the coefficient of determination （COD） was 0.69, indicating the model performed reasonably well. The developed model was then applied to simulate the water quality changes at a downstream cross-section assuming that the designed restoration programs were implemented. According to the simulated results, the restoration programs could cut down the loads of COD and PO43-P about 15%. Such a load reduction, unfortunately, would have very little effect on the NH4^＋-N removal. Moreover, the water quality at the outlet cross-section would be still in class V （3838-02）, indicating more measures should be taken to further reduce the loads. The study demonstrated the capability of water quality models to support aquatic ecosystem restorations.

Simulation of two-dimensional interior ballistics model of solid propellant electrothermal-chem ical launch with discharge rod plasma generator

Instead of the capillary plasma generator(CPG),a discharge rod plasma generator(DRPG)is used in the30 mm electrothermal-chemical(ETC)gun to improve the ignition uniformity of the solid propellant.An axisymmetric two-dimensional interior ballistics model of the solid propellant ETC gun(2D-IB-SPETCG)is presented to describe the process of the ETC launch.Both calculated pressure and projectile muzzle velocity accord well with the experimental results.The feasibility of the 2D-IB-SPETCG model is proved.Depending on the experimental data and initial parameters,detailed distribution of the ballistics parameters can be simulated.With the distribution of pressure and temperature of the gas phase and the propellant,the influence of plasma during the ignition process can be analyzed.Because of the radial flowing plasma,the propellant in the area of the DRPG is ignited within 0.01 ms,while all propellant in the chamber is ignited within 0.09 ms.The radial ignition delay time is much less than the axial delay time.During the ignition process,the radial pressure difference is less than 5 MPa at the place 0.025 m away from the breech.The radial ignition uniformity is proved.The temperature of the gas increases from several thousand K(conventional ignition)to several ten thousand K(plasma ignition).Compare the distribution of the density and temperature of the gas,we know that low density and high temperature gas appears near the exits of the DRPG,while high density and low temperature gas appears at the wall near the breech.The simulation of the 2D-IB-SPETCG model is an effective way to investigate the interior ballistics process of the ETC launch.The 2D-IB-SPETC model can be used for prediction and improvement of experiments.

Performance assessment of two-dimensional hydraulic models for generation of flood inundation maps in mountain river basins

Hydraulic models for the generation of flood inundation maps are not commonly applied in mountain river basins because of the difficulty in modeling the hydraulic behavior and the complex topography. This paper presents a comparative analysis of the performance of four twodimensional hydraulic models (HEC-RAS 2D, Iber 2D, Flood Modeller 2D, and PCSWMM 2D) with respect to the generation of flood inundation maps. The study area covers a 5-km reach of the Santa B-arbara River located in the Ecuadorian Andes, at 2330 masl, in Gualaceo. The model's performance was evaluated based on the water surface elevation and flood extent, in terms of the mean absolute difference and measure of fit. The analysis revealed that, for a given case, Iber 2D has the best performance in simulating the water level and inundation for flood events with 20- and 50-year return periods, respectively, followed by Flood Modeller 2D, HEC-RAS 2D, and PCSWMM 2D in terms of their performance. Grid resolution, the way in which hydraulic structures are mimicked, the model code, and the default value of the parameters are considered the main sources of prediction uncertainty.

Protein Extraction Methods for Two-Dimensional Electrophoresis from Baphicacanthus cusia(Nees)Bremek Leaves-A Medicinal Plant with High Contents of Interfering Compounds

Protein extraction is a critical step for two-dimensional electrophoresis （2-DE）. Different plant samples require different and adaptive protein extraction protocols. The leaves of medicinal plant, Baphicacanthus cusia （Nees） Bremek are notoriously recalcitrant to common protein extraction methods due to high levels of interfering compounds （especially the secondary metabolites and pigments）. This study was aimed to establish a routine procedure for the proteomic analysis ofB. cusia leaves, and a new protocol for the protein extraction was developed by optimizing trichloroacetic acid （TCA）/ acetone extraction method. The efficiency of this protocol was demonstrated by comparison with 3 published protein extraction methods （chloroform/acetone, Mg/NP-40, Tris-base/acetone）. The results showed that the optimized TCA/ acetone precipitation extraction method gave a relatively high protein yield （9.263 mg g^-1 fresh weight）, high-resolution separation, clear protein profiles, the highest proteins spots （1 31 t protein spots）, and displayed less contamination in 2- DE gels. Therefore, the results suggested that the optimized TCA/acetone method was the most effective among the 4 methods for B. cusia leaves.

Establishing a protein expression profile database for the normal human pituitary gland using two-dimensional high-performance liquid chromatography combined with LTQ-Orbitrap mass spectrometry

In this study, we selected adult normal pituitary gland tissues from six patients during operations for pituitary microadenomas via the transsphenoidal approach for extended normal pituitary tissue resection around the tumor, and analyzed the protein expression of human normal pituitary using two-dimensional high-performance liquid chromatography combined with LTQ-Orbitrap mass spectrometry proteomics technology. The ten most highly expressed proteins in normal human pituitary were： alpha 3 type VI collagen isoform 5 precursor （abundance among tall pituitary proteins 1.30%）, fibrinogen beta chain preproprotein （0.99%）, vimentin （0.73%）, prolactin （0.69%）, ATP synthase, H~ transporting and mitochondrial F1 complex beta subunit precursor （0.52%）, keratin I （0.49%）, growth hormone （0.45%）, carbonic anhydrase I （0.40%）, heat shock protein 90 kDa I （0.31%）, and annexin V （0.30%）. Based on the biological function classifications of these proteins, the top three categories by content were neuroendocrine proteins （abundance among all pituitary proteins, 40.1%）, catalytic and metabolic proteins （28.3%）, and cell signal transduction proteins （9.8%）. Based on cell positioning classification, the top three categories were cell organelle （24.5%） membrane （20.8%）, and cytoplasm （13.0%）. Based on biological process classification, the top three categories of proteins are involved in physiological processes （42.9%）, cellular processes （40.4%）, and regulation of biological processes （9.1%）. Our experimental findings indicate that a protein expression profile database of normal human pituitary can be precisely and efficiently established by proteomics technology.

HIGH RESOLUTION PARAMETRIC MODELLING FOR TWO-DIMENSIONAL RADAR TARGET USING PRONY ALGORITHM

On the conditions of low-resolution radar, a parametric model for two-dimensional radar target is described here according to the theory of electromagnetic scattering and the geometrical theory of diffraction. A high resolution estimation algorithm to extract the model parameters is also developed by building the relation of the scattering model and Prony model. The analysis of Cramer-Rao bound and simulation show that the method here has better statistical performance. The simulated analysis also indicates that the accurate extraction of the diffraction coefficient of scattering center is restricted by signal to noise ratio, radar center frequency and radar bandwidth.

Analysis of Male Sterility-Related Proteins of Young Panicle in Rice (Oryza sativa L.) by Two-Dimensional Electrophoresis

For searching out male sterility-related proteins (polypeptides) in rice(Oryza sativa L. ), we examined the difference of panicle protein (polypeptides) between hybrid rice( Wujin2A/R168, Wujin5A/R988) and their parents (male-sterile line Wujin2A, Wujin5A, and restorerline R168, R988) at the formation stage of pollen mother cell by two-dimensional electrophoresis(2-DE). The results revealed that the 2-DE polypeptide maps were similar among these experimentalmaterials. A small group of polypeptides were disappeared in 2-DE polypeptide maps of male-sterileline (Wu-jin2A, WujinSA) by comparing to restorer line (R168, R988) and the first filial (F, )generation (Wujin2A/R168, Wujin5A/R988). The isoelectric points of these polypeptides were pl5.8-6.5, molecular weight 42. 7 X 10~3-66. 2 X 10~3.

A Numerical Algorithm Based on Quadratic Finite Element for Two-Dimensional Nonlinear Time Fractional Thermal Diffusion Model

In this article,a high-order scheme,which is formulated by combining the quadratic finite element method in space with a second-order time discrete scheme,is developed for looking for the numerical solution of a two-dimensional nonlinear time fractional thermal diffusion model.The time Caputo fractional derivative is approximated by using the L2-1formula,the first-order derivative and nonlinear term are discretized by some second-order approximation formulas,and the quadratic finite element is used to approximate the spatial direction.The error accuracy O(h3+
t2)is obtained,which is verified by the numerical results.

Global Two-Dimensional Chemistry Model and Simulation of Atmospheric Chemical Composition

A global two-dimensional zonally averaged chemistry model is developed to study the chemi-cal composition of atmosphere. The region of the model is from 90°S to 90°N and from the ground to the altitude of 20 km with a resolution of 5° x 1 km. The wind field is residual circulation calcu-lated from diabatic rate. 34 species and 104 chemical and photochemical reactions are considered in the model. The sources of CH4, CO and NOx, which are divided into seasonal sources and non-seasonal sources, are parameterized as a function of latitude and time. The chemical composi-tion of atmosphere was simulated with emission level of CH4, CO and NOx in 1990. The results are compared with observations and other model results, showing that the model is successful to simu-late the atmospheric chemical composition and distribution of CH4. Key words Global two-dimensional chemistry model - Atmospheric composition - Emission This work was supported by the State Key Program for basic research “ Climate Dynamics and Cli-mate Prediction Theory” (Pandeng-yu-21).The authors would like to express their thanks to the National Oceanic and Atmospheric Administration (NOAA), Climate Monitoring and Diagnostics Laboratory (CMDL), Carbon Cycle Group for providing the observational data of CO and CH4.

Establishment of two-dimensional gel electrophoresis for soybean protein isolate and its application

To optimize the conditions for the establishment of two-dimensional gel electrophoresis(2-DE)of soybean protein isolate(SPI),we investigated Ampholine mixture,anodic and cathodic electrolytes,loading amount of sample,acrylamide concentration,p H gradient and gel staining method in twodimensional gel electrophoresis to optimize the protein imaging conditions in two-dimensional gel.The results of mixed-level design experiments showed that Ampholine,loading amount and gel staining method had significant effect(P<0.05)on 2-DE of SPI.The optimal conditions were Ampholine mixture(pH 3–10+pH 5–7 or pH 4–6+pH 5–7),loading amount of 2 mg sample and silver staining.Although the acrylamide concentration of the gel,the p H gradient,the anodic and cathodic electrolyte solutions had significant statistical effects on the protein separation degree,the complexity of the protein composition and the visibility of the gel images were more inclined to the 12%gel,the 3–10 pH gradient and the H3PO4/NaOH electrolyte.According to the established conditions,the hydrolyzed products of SPI emulsion were determined by 2-DE,and the dynamic changes of protein in the process of enzymatic hydrolysis were described.

Effects of invigorating-spleen and anticancer prescription on extracellular signal-regulated kinase/mitogen-activated protein kinase signaling pathway in colon cancer mice model

BACKGROUND Colon cancer(CC)is one of the most common malignant tumors in the gastrointestinal system.Overall,CC had the third highest incidence but the second highest mortality rate globally in 2020.Nowadays,CC is mainly treated with capecitabine chemotherapy regimen,supplemented by radiotherapy,immunotherapy and targeted therapy,but there are still limitations,so Chinese medicine plays an important role.AIM To investigate the effects of invigorating-spleen and anticancer prescription(ISAP)on body weight,tumor inhibition rate and expression levels of proteins in extracellular-signal-regulated kinase(ERK)/mitogen-activated protein kinase(MAPK)signaling pathway in CC mice model.METHODS The CC mice model were established and the mice were randomly divided into 5 groups,including the control group,capecitabine group,the low-dose,mediumdose and high-dose groups of ISAP,with 8 mice in each group,respectively.After 2 weeks of intervention,the body weight and tumor inhibition rate of mice were observed,and the expression of RAS,ERK,phosphorylated ERK(p-ERK),C-MYC and matrix metalloproteinase 2(MMP2)proteins in the tissues of tumors were detected.RESULTS Compared with the control group,the differences of body weight before and after treatment was much smaller in the groups of ISAP,with the smallest difference in the high-dose group of ISAP,while the capecitabine group had the greatest difference,indicating ISAP had a significant inhibiting effect on the growth of transplanted tumor in mice.The expression of RAS protein was decreased in the low-and medium-dose groups of ISAP,and the change of p-ERK was significant in the medium-and high-dose groups of ISAP.MMP2 protein expression was significantly decreased in both the low-dose and medium-dose groups of ISAP.There were no significant changes in ERK in the ISAP group compared to the capecitabine group,while RAS,MMP2,and C-MYC protein expression were reduced in the ISAP group.The expression level of C-MYC protein decreased after treated with ISAP,and the decrease was the most significant in the medium-dose group of ISAP.CONCLUSION ISAP has a potential inhibiting effect on transplanted tumor in mice,and could maintain the general conditions,physical strength and body weight of mice.The expression levels of RAS,p-ERK,MMP2 and c-myc were also decreased to a certain extent.By inhibiting the expression of upstream proteins,the expression levels of downstream proteins in ERK/MAPK signaling pathway were significantly decreased.Therefore,it can be concluded that ISAP may exert an anti-tumor effect by blocking the ERK/MAPK signaling pathway and inhibiting the expression of MMP2 and c-myc proteins.

Comprehensive two-dimensional river ice model based on boundary-fitted coordinate transformation method

River ice is a natural phenomenon in cold regions, influenced by meteorology, geomorphology, and hydraulic conditions. River ice processes involve complex interactions between hydrodynamic, mechanical, and thermal processes, and they are also influenced by weather and hydrologic conditions. Because natural rivers are serpentine, with bends, narrows, and straight reaches, the commonly-used one-dimensional river ice models and two-dimensional models based on the rectangular Cartesian coordinates are incapable of simulating the physical phenomena accurately. In order to accurately simulate the complicated river geometry and overcome the difficulties of numerical simulation resulting from both complex boundaries and differences between length and width scales, a two-dimensional river ice numerical model based on a boundary-fitted coordinate transformation method was developed. The presented model considers the influence of the frazil ice accumulation under ice cover and the shape of the leading edge of ice cover during the freezing process. The model is capable of determining the velocity field, the distribution of water temperature, the concentration distribution of frazil ice, the transport of floating ice, the progression, stability, and thawing of ice cover, and the transport, accumulation, and erosion of ice under ice cover. A MacCormack scheme was used to solve the equations numerically. The model was validated with field observations from the Hequ Reach of the Yellow River. Comparison of simulation results with field data indicates that the model is capable of simulating the river ice process with high accuracy.

DETERMINATION OF PARAMETERS IN A TWO-DIMENSIONAL MODEL FOR FIXED-BED ADSORBERS

A new method is proposed for the determination of the parameters in a two-dimensionalmodel which characterizes the properties of axial and radial mixing and mass transport in afixed-bed adsorber.Parameter estimation for the model is carried out with methane-air-5A molecularsieve in a bed under the condition of step injection of tracer from a point on the main axis of thebed by the curve fitting method in the time domain.

Two-dimensional hydrodynamic robust numerical model of soil erosion based on slopes and river basins

Erosion is an important issue in soil science and is related to many environmental problems,such as soil erosion and sediment transport.Establishing a simulation model suitable for soil erosion prediction is of great significance not only to accurately predict the process of soil separation by runoff,but also improve the physical model of soil erosion.In this study,we develop a graphic processing unit(GPU)-based numerical model that combines two-dimensional(2D)hydrodynamic and Green-Ampt(G-A)infiltration modelling to simulate soil erosion.A Godunov-type scheme on a uniform and structured square grid is then generated to solve the relevant shallow water equations(SWEs).The highlight of this study is the use of GPU-based acceleration technology to enable numerical models to simulate slope and watershed erosion in an efficient and high-resolution manner.The results show that the hydrodynamic model performs well in simulating soil erosion process.Soil erosion is studied by conducting calculation verification at the slope and basin scales.The first case involves simulating soil erosion process of a slope surface under indoor artificial rainfall conditions from 0 to 1000 s,and there is a good agreement between the simulated values and the measured values for the runoff velocity.The second case is a river basin experiment(Coquet River Basin)that involves watershed erosion.Simulations of the erosion depth change and erosion cumulative amount of the basin during a period of 1-40 h show an elevation difference of erosion at 0.5-3.0 m,especially during the period of 20-30 h.Nine cross sections in the basin are selected for simulation and the results reveal that the depth of erosion change value ranges from-0.86 to-2.79 m and the depth of deposition change value varies from 0.38 to 1.02 m.The findings indicate that the developed GPU-based hydrogeomorphological model can reproduce soil erosion processes.These results are valuable for rainfall runoff and soil erosion predictions on rilled hillslopes and river basins.

Differential analysis of two-dimensional gel electrophoresis profiles of spermatozoa protein in human normal motility sperm and idiopathic asthenospermia

Objective: To evaluate the application of two-dimensional electrophoresis in the research of differentially expressed proteins in the human asthenospermia. Methods: Two-dimensional gel electrophoresis was performed on 4 normal sperm samples from healthy men and 4 sperm samples from 4 asthenospermia patients. After silver staining, the differential expression proteins were analyzed by PDQuest 2D analysis software. Results: Six differential protein spots were identified. Four spots showed increased expression in the control gels compared with the patient gels. Conclusion: The protein profiles of differential expression between the normal spermatozoa and idiopathic asthenospermia were established and some differential proteins were found. The data of this study would establish the better fundament for further isolation and identification of differentially expressed proteins in human asthenospermia sperm.

Two-dimensional Electrophoresis Analysis of Proteins Extracted from Alexandrium sp. LC3

Two-dimensional electrophoresis（2-DE） of protein extracted and purified from Alexandrium sp. LC3 was conducted. In the SDS-PAGE study, the relative molecular weights of the proteins were mainly in the range of 14 kDa-31 kDa and 43 kDa-66 kDa, and more proteins were detected between 14kDa and 31 kDa. With the improved protein preparation, the two-dimensional electrophoresis patterns indicated that the relative molecular weights of the proteins were between 14kDa and 100kDa, and most of them ranged from 14 kDa to 31 kDa. This was consistent with the result of the SDS-PAGE analysis. The isoelectric points were found to lie between 3.0 and 8.0, and most of them were in the range of 3.0-6.0. Better separation effect was acquired with pre-prepared immobilized gradient （IPG） strip （pH 3-5.6）, and about 320 protein spots could be visualized on the 2-DE map by staining. Within pH 3-l0 and pH 3-5.6 strips, the protein samples of Alexandrium sp. LC3 could be separated well.

Reduced mesencephalic astrocyte-derived neurotrophic factor expression by mutant androgen receptor contributes to neurodegeneration in a model of spinal and bulbar muscular atrophy pathology

Spinal and bulbar muscular atrophy is a neurodegenerative disease caused by extended CAG trinucleotide repeats in the androgen receptor gene,which encodes a ligand-dependent transcription facto r.The mutant androgen receptor protein,characterized by polyglutamine expansion,is prone to misfolding and forms aggregates in both the nucleus and cytoplasm in the brain in spinal and bulbar muscular atrophy patients.These aggregates alter protein-protein interactions and compromise transcriptional activity.In this study,we reported that in both cultured N2a cells and mouse brain,mutant androgen receptor with polyglutamine expansion causes reduced expression of mesencephalic astrocyte-de rived neurotrophic factor.Overexpressio n of mesencephalic astrocyte-derived neurotrophic factor amelio rated the neurotoxicity of mutant androgen receptor through the inhibition of mutant androgen receptor aggregation.Conversely.knocking down endogenous mesencephalic astrocyte-derived neurotrophic factor in the mouse brain exacerbated neuronal damage and mutant androgen receptor aggregation.Our findings suggest that inhibition of mesencephalic astrocyte-derived neurotrophic factor expression by mutant androgen receptor is a potential mechanism underlying neurodegeneration in spinal and bulbar muscular atrophy.

Impact of Large Fresh Water Discharges into Hakata Bay Due to Torrential Rain Using Nested Two-Dimensional Convective-Dispersive Model

In this study, numerical simulation of a two-dimensional convective-dispersive model in Hakata Bay, Japan, is performed to analyze the impact of major river discharges due to torrential rain in Fukuoka City. Tank models are applied to calculate river discharges, which are taken into consideration as river inflow in the hydrodynamic model of Hakata Bay. A two-way nesting “edge” technique is developed and applied in the model in order to consider the influence of narrow and complex geographical features. The area around “Island City” and Imazu Bay are calculated in high resolution. The resulting model has high reproducibility since the calculated river discharges, tidal current, and salinity show good agreement with observed data. To analyze the impact of large river discharges, the calculation period is set from 11 September 2002 to 21 September 2002 since there was torrential rain on September 16 in the given year in Fukuoka City (163.5 mm/d). The results show that low-salinity water covered the whole of the inner part of Hakata Bay, and water of lower salinity than outer sea water (<34.0 psu) spread out to the bay’s mouth two days after the torrential rain event. Fresh water covered the entire area of Imazu Bay and flowed out from the mouth of the Bay after the torrential rain event. The behavior of fresh water after a few days of torrential rain was remarkably different from normal discharge river flow. These results indicate that the environment in Imazu Bay can be degraded severely by torrential rain. Therefore, countermeasures to protect ecosystems in Hakata Bay must be examined immediately.