Two-phase airlift fermentor operation with elicitation for the enhanced production of enzophenanthridine alkaloids in cell suspensions of Escherichia californica

Approaches to increasing the productivity of benzophenanthridine alkaloids in suspension cultures in Escherichia californica were made in an airlift fermentor under different culture conditions. Elicitation with yeast extract elicitor reduced the time required to obtain a certain amount of alkaloid production. In a two-phase airlift fermentor with compounded silicone fluid, total alkaloid concentration in silicone fluid was 153.1 mg/L and that in the aqueous cellular phase was 8.2 mg/L at day 21 from inoculation. The large accumulation capacity of silicone fluid made it possible to store correspondingly large amounts of total alkaloid and increased the alkaloid production. Act day 21 from inoculation, the volumetric alkaloid productivity and the netproduction in a two-phase airlift fermentor were 1.4 and 1.5 times higher than those of normal airlift fermentor operation. This performance was furthermore enhanced by elicitation. Elicitation in two-phase airlift fermentor operation increased the volumetric productivity and the new production 3.3- and 3.5-fold compared to those of normal airlift fermentor operation. (c) 1994 John Wiley & Sons, Inc.     

Experimental validation of the ANTS2 code for modelling optical photon transport in monolithic LYSO crystals

In this work the scintillation energy spectra originating from the background radioactivity from polished monolithic lutetium yttrium oxyorthosilicate coupled to position-sensitive silicon photomultipliers (SiPM) was studied using the open source Monte Carlo simulation package ANTS2. Two crystal sizes, fully and partially covering the photosensor area, three surface crystal wrappings (black, specular or diffuse) and the full signal formation process in the photosensor were considered. The simulation results were validated with experimental data acquired under the same geometric and detector operating conditions. In all cases ANTS2 simulated spectra have very good agreement with experimental results, reproducing the expected shape, with correct onset and end at 88 and 1190 keV, respectively, as well as sharp edges at the reference energies of 88, 88 + 202, 88 + 307 and 88 + 202 + 307 keV. The normalized root-mean square error between simulated and measured spectra varied between 4.3% and 10.4%.     

A New Version of the Insertion Particle Method for Determining the Chemical Potential by Monte Carlo Simulation

A new version of the test particle method for determining the chemical potential by Monte Carlo simulations is proposed. The method, applicable to any fluid at any density, combines the Widom's test particle insertion method with the ideas of the scaled particle theory, gradual insertion method and multistage sampling. Its applicability is exemplified by evaluating the chemical potential of the hard sphere fluid at a very high density in semi-grand-canonical and grand-canonical ensembles. A theory estimating the efficiency (i.e. statistical errors) of the method is proposed and the results are compared with the Widom's and gradual insertion methods, and the analytic results.     

Importance of anisotropy in detachment rates for force production and cargo transport by a team of motor proteins

Many cellular processes are driven by collective forces generated by a team consisting of multiple molecular motor proteins. One aspect that has received less attention is the detachment rate of molecular motors under mechanical force/load. While detachment rate of kinesin motors measured under backward force increases rapidly for forces beyond stall‐force; this scenario is just reversed for non‐yeast dynein motors where detachment rate from microtubule decreases, exhibiting a catch‐bond type behavior. It has been shown recently that yeast dynein responds anisotropically to applied load, i.e. detachment rates are different under forward and backward pulling. Here, we use computational modeling to show that these anisotropic detachment rates might help yeast dynein motors to improve their collective force generation in the absence of catch‐bond behavior. We further show that the travel distance of cargos would be longer if detachment rates are anisotropic. Our results suggest that anisotropic detachment rates could be an alternative strategy for motors to improve the transport properties and force production by the team.     

Modeling of local dynamic behavior of phenol degradation in an internal loop airlift bioreactor by yeast Candida tropicalis

A coupled computational fluid dynamic (CFD) model, combining hydrodynamics with biochemical reactions, was developed to simulate the local transient flow patterns and the dynamic behaviors of cell growth and phenol biodegradation by yeast Candida tropicalis in an internal loop airlift reactor (ILALR). To validate this proposed model effectively, the simulated local hydrodynamic characteristics of the gas-mineral salt medium solution (gas-liquid) two-phase system, at a phenol concentration of 1,200 mg L(-1) and no presence of cells, was experimentally investigated in the ILALR using laser Doppler anemometer (LDA) measurements and conductivity probe. Furthermore, the validation of the simulated phenol biodegradation behavior by C. tropicalis at different initial concentrations of phenol and cell was also carried out in the ILALR. The time-averaged and transient results of the model simulations illustrated a satisfactory agreement with the experimental data. Finally, the local instantaneous flow and phenol biodegradation features, including gas holdup, gas velocity, liquid velocity, cell concentration, and phenol concentration inside the ILALR were successfully predicted by the proposed model.     

Effect of fuel concentration and force on collective transport by a team of dynein motors

Motor proteins are essential components of intracellular transport inside eukaryotic cells. These protein molecules use chemical energy obtained from hydrolysis of ATP to produce mechanical forces required for transporting cargos inside cells, from one location to another, in a directed manner. Of these motors, cytoplasmic dynein is structurally more complex than other motor proteins involved in intracellular transport, as it shows force and fuel (ATP) concentration dependent step‐size. Cytoplasmic dynein motors are known to work in a team during cargo transport and force generation. Here, we use a complete Monte‐Carlo model of single dynein constrained by in vitro experiments, which includes the effect of both force and ATP on stepping as well as detachment of motors under force. We then use our complete Monte‐Carlo model of single dynein motor to understand collective cargo transport by a team of dynein motors, such as dependence of cargo travel distance and velocity on applied force and fuel concentration. In our model, cargos pulled by a team of dynein motors do not detach rapidly under higher forces, confirming the experimental observation of longer persistence time of dynein team on microtubule under higher forces.     

Test of the Inverse Monte Carlo Method for the Calculation of Interatomic Potential Energies in Atomic Liquids

Abstract

The principle purpose of this paper is to demonstrate the use of the Inverse Monte Carlo technique for calculating pair interaction energies in monoatomic liquids from a given equilibrium property. This method is based on the mathematical relation between transition probability and pair potential given by the fundamental equation of the “importance sampling” Monte Carlo method. In order to have well defined conditions for the test of the Inverse Monte Carlo method a Metropolis Monte Carlo simulation of a Lennard Jones liquid is carried out to give the equilibrium pair correlation function determined by the assumed potential. Because an equilibrium configuration is prerequisite for an Inverse Monte Carlo simulation a model system is generated reproducing the pair correlation function, which has been calculated by the Metropolis Monte Carlo simulation and therefore representing the system in thermal equilibrium. This configuration is used to simulate virtual atom displacements. The resulting changes in atom distribution for each single simulation step are inserted in a set of non-linear equations defining the transition probability for the virtual change of configuration. The solution of the set of equations for pair interaction energies yields the Lennard Jones potential by which the equilibrium configuration has been determined.     

Two-phase culture for enhanced alkaloid synthesis and release in a new airlift reactor by Catharanthus roseus

A new airlift reactor was used to culture Catharanthus roseus cells, in which the draft tube was made up of polyurethane foam and acted as the immobilizing matrix. The reactor was connected in series to an adsorbent column with a neutral polymeric resin which absorbs these alkaloids. The synthesis of alkaloid was stimulated by adding the resin column and the total content of alkaloid secreted by cells reached 380 mg/L, which was 4.5 times of that in the control experiment. Meanwhile, most of the intracellular alkaloid produced by Catharanthus roseus was secreted into the medium.     

A Method for Assessing Environmental Risks of Oil-Mineral-Aggregate to Benthic Organisms

Previous studies have shown that Oil-Mineral-Aggregate (OMA) formation enhances the dispersion of marine oil spills, but the potential impacts of settled OMAs on benthic organisms are not well known. A comprehensive numerical approach is proposed here to model the transport of OMAs and assesses their potential risks. The predicted environmental concentrations (PEC) of settled oil in OMAs was calculated using a random walk particle tracking model and the benchmark concentrations (BCs) of individual hydrocarbon groups were computed based on a equilibrium partitioning (EqP) approach. The likely of risks in terms of Hazard Quotient (HQ) were then determined using a Monte Carlo simulation method. HQ for both aliphatic and aromatic hydrocarbon groups were calculated for OMAs formed with two sediments, Mississippi River Delta (MRD) and Standard Reference Material (SRM). Mean total HQs were also determined by a simple sum of individual HQ. The predicted results from a case study based on a spill of 1000 tons of South Louisiana crude oil in the Gulf of St. Lawrence with a water depth of 80 m show that the SRM is unlikely to cause adverse impacts but this may not be the case for MRD. Furthermore, it has been found that the application of chemical dispersant (CD) increased the risks of MRD but it had little effects on SRM.     

Connectivity effects for slit pores linked by a channel

This paper describes a Monte Carlo computer simulation study of connectivity effects in a system of two parallel slit pores and a quasi-one-dimensional joint. A numerical method for evaluation of accessible volume in computer simulation studies of adsorption in pores is presented and applied to simple slit pores and systems of interconnected pores. A local version of the grand canonical ensemble Monte Carlo method is used to study adsorption under conditions mimicking mass transfer limitations.     

Hybrid maize breeding with doubled haploids: I. One-stage versus two-stage selection for testcross performance

Optimum allocation of resources is of fundamental importance for the efficiency of breeding programs. The objectives of our study were to (1) determine the optimum allocation for the number of lines and test locations in hybrid maize breeding with doubled haploids (DHs) regarding two optimization criteria, the selection gain ΔG _k and the probability P _k of identifying superior genotypes, (2) compare both optimization criteria including their standard deviations (SDs), and (3) investigate the influence of production costs of DHs on the optimum allocation. For different budgets, number of finally selected lines, ratios of variance components, and production costs of DHs, the optimum allocation of test resources under one- and two-stage selection for testcross performance with a given tester was determined by using Monte Carlo simulations. In one-stage selection, lines are tested in field trials in a single year. In two-stage selection, optimum allocation of resources involves evaluation of (1) a large number of lines in a small number of test locations in the first year and (2) a small number of the selected superior lines in a large number of test locations in the second year, thereby maximizing both optimization criteria. Furthermore, to have a realistic chance of identifying a superior genotype, the probability P _k of identifying superior genotypes should be greater than 75%. For budgets between 200 and 5,000 field plot equivalents, P _k > 75% was reached only for genotypes belonging to the best 5% of the population. As the optimum allocation for P _k (5%) was similar to that for ΔG _k , the choice of the optimization criterion was not crucial. The production costs of DHs had only a minor effect on the optimum number of locations and on values of the optimization criteria. C. Friedrich H. Longin and H. Friedrich Utz contributed equally to this work.     

Prediction of protein conformation in water and on surfaces by Monte Carlo simulations using united-atom method

The united-atom method has been used to model an avian pancreatic polypeptide (APP) in water and the adsorption process of an albumin subdomain (AS) onto graphite surface to observe the capability of this lumped modelling approach to generate structures observed in protein data bank (PDB) and from atomistic modelling. The subdomain structure of a protein is simplified by the united-atom approximation where the side chains and peptide groups are represented by lumped spheres. The total potential energy of the adsorption process involves the interaction between these lumped spheres by means of virtual bond chain interaction and the interaction of the spheres with the graphite surface by means of Lennard-Jones potential. The protein/polypeptide structure has been perturbed by Monte Carlo with energy minimisation to obtain the global minimum. Results on the APP in water showed a near-to-experimental PDB conformation revealing the two α-helix structures of this small protein molecule with the root mean square deviation among carbon backbone atoms of 5.9 Å. Protein adsorption on biosurfaces has been made by modelling AS, which has 60 amino acids. The surface is graphite, which is characterised by its hydrophobicity. Graphite was chosen because of its widely used applications in certain implants that interact with blood. Our simulation results showed final conformation close to that obtained by atomistic modelling. It also proved that the whole pattern of intramolecular hydrogen bonds was distorted. The model also demonstrated the random conformation of the original α-helix secondary structures of AS consistent with experimental and atomistic results. While atomistic simulation works well for simulating individual small proteins, the united-atom model is more efficient when simulating macromolecular and multiple protein adsorption where time and limiting computer capacity are key factors.     

基于改进SW模型的千烟洲人工林蒸散组分拆分及其特征

蒸散组分拆分是准确评估陆地生态系统生产力以及估算水分利用效率的重要基础。利用改进后的Shuttleworth-Wallace模型,将蒸散拆分为植被蒸腾、土壤蒸发和冠层截留蒸发,并采用Monte Carlo随机参数化方案对模型参数进行优化。将模型与千烟洲亚热带人工针叶林站点的2011年涡度相关及小气候观测资料结合,对千烟洲人工林蒸散及其组分进行模拟。研究结果表明:半小时尺度上蒸散量模拟值与实测值的一致性在晴天和雨天都较高。半小时尺度上全年蒸散模拟值与实测值的决定系数、均方根误差和平均偏差为0.73、1.55 mmol m~(-2)s~(-1)和0.21 mmol m~(-2)s~(-1)。蒸散是该生态系统水分输出的最主要贡献项,占全年降水的80%。在蒸散中,植被蒸腾约占总蒸散量的85%,可推测2011年千烟洲人工林生态系统有较高的水分利用效率。该生态系统的蒸腾量季节变化明显,主要受饱和水汽压差和气温两种环境因素以及植被的叶面积指数影响且与三者均呈正相关;土壤蒸发约占总蒸散量的5%,季节变化平缓;模拟的冠层截留蒸发量约占总蒸散量的10%,季节变化大,与降水量呈正相关,与暴雨频次呈负相关,说明冠层无法有效截留强降水。该模型参数较少、时间分辨率高且可以有效模拟蒸散及其组分特征,是陆地生态系统水分循环过程研究有力的模型工具。     

Optimization of GATE simulations for whole-body planar scintigraphic acquisitions using the XCAT male phantom with 177Lu-DOTATATE biokinetics in a Siemens Symbia T2

Simulations of planar whole body acquisitions in therapeutic procedures are often extensively time-consuming and therefore rarely used. However, optimising tools and variance reduction techniques can be employed to overcome this problem. In this paper, a variety of features available in GATE are explored and their capabilities to reduce simulation time are evaluated. For this purpose, the male XCAT phantom was used as a virtual patient with ¹⁷⁷Lu-DOTATATE pharmacokinetic for whole body planar acquisition simulations in a Siemens Symbia T2 model. Activity distribution was divided into 8 compartments that were simulated separately. GATE optimization techniques included reducing the amount of time spent in both voxel and detector tracking. Some acceleration techniques led to a decrease of CPU-time by a factor of 167, while image statistics were kept constant. In that context, the simulation of therapeutic procedure imaging would still require 46 days on a single CPU, but this could be reduced to hours on a dedicated cluster.     

Joint Modeling for Cognitive Trajectory and Risk of Dementia in the Presence of Death

Summary .  Dementia is characterized by accelerated cognitive decline before and after diagnosis as compared to normal aging. It has been known that cognitive impairment occurs long before the diagnosis of dementia. For individuals who develop dementia, it is important to determine the time when the rate of cognitive decline begins to accelerate and the subsequent gap time to dementia diagnosis. For normal aging individuals, it is also useful to understand the trajectory of cognitive function until their death. A Bayesian change-point model is proposed to fit the trajectory of cognitive function for individuals who develop dementia. In real life, people in older ages are subject to two competing risks, e.g., dementia and dementia-free death. Because the majority of people do not develop dementia, a mixture model is used for survival data with competing risks, which consists of dementia onset time after the change point of cognitive function decline for demented individuals and death time for nondemented individuals. The cognitive trajectories and the survival process are modeled jointly and the parameters are estimated using the Markov chain Monte Carlo method. Using data from the Honolulu Asia Aging Study, we show the trajectories of cognitive function and the effect of education, apolipoprotein E 4 genotype, and hypertension on cognitive decline and the risk of dementia.     

Use of Monte Carlo simulations for improved facility fit planning in downstream biomanufacturing and technology transfer

Biologics manufacturing is capital and consumable intensive with need for advanced inventory planning to account for supply chain constraints. Early-stage process design and technology transfer are often challenging due to limited information on process variability regarding bioreactor titer, process yield, and product quality. Monte Carlo (MC) methods offer a stochastic modeling approach for process optimization where probabilities of occurrence for process inputs are incorporated into a deterministic model to simulate more likely scenarios for process outputs. In this study, we explore MC simulation-based design of a monoclonal antibody downstream manufacturing process. We demonstrate that this probabilistic approach offers more representative outcomes over the conventional worst-case approach where the theoretical minimum and maximum values of each process parameter are used without consideration for their probability of occurrence. Our work demonstrates case studies on more practically sizing unit operations to improve consumable utilization, thereby reducing manufacturing costs. We also used MC simulations to minimize process cadence by constraining the number of cycles per unit operation to fit facility preferences. By factoring in process uncertainty, we have implemented MC simulation-based facility fit analyses to efficiently plan for inventory when accounting for process constraints during technology transfer from lab-scale to clinical or commercial manufacturing.     

Size and Power of Test Statistics for Gene Correlation in 2 × 2 Contingency Tables

Monte Carlo simulation of size and power of two proposed tests for linkage disequilibrium between two genes each with two alleles were investigated. Results were compared with two commonly used statistics, the correlation coefficient r and the log-odds ratio tests. Depending on the sign of the linkage disequilibrium, the new tests were found to be more powerful than either of the correlation or log-odds ratio tests. However, on average (positive and negative linkage disequilibrium) the Chi-square test using the correlation coefficient was to a small extent more powerful than the other tests.     

Development of an x-ray-opaque-marker system for quantitative phantom positioning in patient-specific quality assurance

PurposeWe developed an x-ray-opaque-marker (XOM) system with inserted fiducial markers for patient-specific quality assurance (QA) in CyberKnife (Accuray) and a general-purpose linear accelerator (linac). The XOM system can be easily inserted or removed from the existing patient-specific QA phantom. Our study aimed to assess the utility of the XOM system by evaluating the recognition accuracy of the phantom position error and estimating the dose perturbation around a marker.MethodsThe recognition accuracy of the phantom position error was evaluated by comparing the known error values of the phantom position with the values measured by matching the images with target locating system (TLS; Accuray) and on-board imager (OBI; Varian). The dose perturbation was evaluated for 6 and 10 MV single-photon beams through experimental measurements and Monte Carlo simulations.ResultsThe root mean squares (RMSs) of the residual position errors for the recognition accuracy evaluation in translations were 0.07 mm with TLS and 0.30 mm with OBI, and those in rotations were 0.13° with TLS and 0.15° with OBI. The dose perturbation was observed within 1.5 mm for 6 MV and 2.0 mm for 10 MV from the marker.ConclusionsSufficient recognition accuracy of the phantom position error was achieved using our system. It is unnecessary to consider the dose perturbation in actual patient-specific QA. We concluded that the XOM system can be utilized to ensure quantitative and accurate phantom positioning in patient-specific QA with CyberKnife and a general-purpose linac.     

在DH或RIL群体中两对重叠基因控制性状的定位

在DH或RIL群体中,若只找到与两对重叠基因控制性状连锁的1个分子标记,可采用极大似然法估计控制性状的一对基因与分子标记间的重组率,并推导出重组率估计值的标准误公式。Monte Carlo模拟显示,重组率估计值的无偏性较好,其变异随时样本容量或重组率的增加而减少。