Process model comparison and transferability across bioreactor scales and modes of operation for a mammalian cell bioprocess

A Monod kinetic model, logistic equation model, and statistical regression model were developed for a Chinese hamster ovary cell bioprocess operated under three different modes of operation (batch, bolus fed‐batch, and continuous fed‐batch) and grown on two different bioreactor scales (3 L bench‐top and 15 L pilot‐scale). The Monod kinetic model was developed for all modes of operation under study and predicted cell density, glucose glutamine, lactate, and ammonia concentrations well for the bioprocess. However, it was computationally demanding due to the large number of parameters necessary to produce a good model fit. The transferability of the Monod kinetic model structure and parameter set across bioreactor scales and modes of operation was investigated and a parameter sensitivity analysis performed. The experimentally determined parameters had the greatest influence on model performance. They changed with scale and mode of operation, but were easily calculated. The remaining parameters, which were fitted using a differential evolutionary algorithm, were not as crucial. Logistic equation and statistical regression models were investigated as alternatives to the Monod kinetic model. They were less computationally intensive to develop due to the absence of a large parameter set. However, modeling of the nutrient and metabolite concentrations proved to be troublesome due to the logistic equation model structure and the inability of both models to incorporate a feed. The complexity, computational load, and effort required for model development has to be balanced with the necessary level of model sophistication when choosing which model type to develop for a particular application. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

An evolutionary computing approach for parameter estimation investigation of a model for cholera

We consider the problem of using time-series data to inform a corresponding deterministic model and introduce the concept of genetic algorithms (GA) as a tool for parameter estimation, providing instructions for an implementation of the method that does not require access to special toolboxes or software. We give as an example a model for cholera, a disease for which there is much mechanistic uncertainty in the literature. We use GA to find parameter sets using available time-series data from the introduction of cholera in Haiti and we discuss the value of comparing multiple parameter sets with similar performances in describing the data.     

An SEI model for sarcoptic mange among chamois

We consider a simple model to study the dynamics of sarcoptic mange in a population of chamois. The epidemiological patterns observed during an epidemic in Italy are reconstructed and key parameters of the model are estimated from field data. In particular, we calculate the basic reproductive ratio R ₀, a threshold value for chamois density for the occurrence of an epidemic and the speed of propagation of the epidemic wave. The model is then used to obtain indications on the effect of culling as a possible control measure in a closed population and extended to analyse the spatial diffusion of the epidemic. Our results are in agreement with mange epidemiology and observations, and suggest that intervention could be efficacious in reducing the impact of an epidemic.     

GAP promoter‐based fed‐batch production of highly bioactive core streptavidin by Pichia pastoris

Streptavidin is a homotetrameric protein binding the vitamin biotin and peptide analogues with an extremely high affinity, which leads to a large variety of applications. The biotin‐auxotrophic yeast Pichia pastoris has recently been identified as a suitable host for the expression of the streptavidin gene, allowing both high product concentrations and productivities. However, so far only methanol‐based expression systems have been applied, bringing about increased oxygen demand, strong heat evolution and high requirements for process safety, causing increased cost. Moreover, common methanol‐based processes lead to large proportions of biotin‐blocked binding sites of streptavidin due to biotin‐supplemented media. Targeting these problems, this paper provides strategies for the methanol‐free production of highly bioactive core streptavidin by P. pastoris under control of the constitutive GAP promoter. Complex were superior to synthetic production media regarding the proportion of biotin‐blocked streptavidin. The optimized, easily scalable fed‐batch process led to a tetrameric product concentration of up to 4.16 ± 0.11 µM of biotin‐free streptavidin and a productivity of 57.8 nM h^?1 based on constant glucose feeding and a successive shift of temperature and pH throughout the cultivation, surpassing the concentration in un‐optimized conditions by a factor of 3.4. Parameter estimation indicates that the optimized conditions caused a strongly increased accumulation of product at diminishing specific growth rates (μ ≈ D < 0.01 h^?1), supporting the strategy of feeding. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:855–864, 2016     

A comparison of four different conformations adopted by human telomeric G‐quadruplex using computer simulations

The telomeric G‐quadruplexes for their unique structural features are considered as potential anticancer drug targets. These, however, exhibit structural polymorphism as different topology types for the intra‐molecular G‐quadruplexes from human telomeric G‐rich sequences have been reported based on NMR spectroscopy and X‐ray crystallography. These techniques provide detailed atomic‐level information about the molecule but relative conformational stability of the different topologies remains unsolved. Therefore, to understand the conformational preference, we have carried out quantum chemical calculations on G‐quartets; used all‐atom molecular dynamics (MD) simulations and steered molecular dynamics (SMD) simulations to characterize the four human telomeric G‐quadruplex topologies based on its G‐tetrad core‐types, viz., parallel, anti‐parallel, mixed‐(3 + 1)‐form1 and mixed‐(3 + 1)‐form2. We have also studied a non‐telomeric sequence along with these telomeric forms giving a comparison between the two G‐rich forms. The structural properties such as base pairing, stacking geometry and backbone conformations have been analyzed. The quantum calculations indicate that presence of a sodium ion inside the G‐tetrad plane or two potassium ions on both sides of the plane give it an overall planarity which is much needed for good stacking to form a helix. MD simulations indicate that capping of the G‐tetrad core by the TTA loops keep the terminal guanine bases away from water. The SMD simulations along with equilibrium MD studies indicate that the parallel and non‐telomeric forms are comparatively less stable. We could come to the conclusion that the anti‐parallel form and also the mixed‐(3 + 1)‐form1 topology are most likely to represent the major conformation., 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 83–99, 2016     

乳酸链球菌素对瘤胃体外发酵、甲烷生成及功能菌群数量的影响北大核心CSCD

【目的】旨在通过体外静态模拟瘤胃发酵法研究乳酸链球菌素(NI)对瘤胃发酵、甲烷生成及功能菌群数量的影响。【方法】以不添加任何添加剂处理做阴性对照(NC),以莫能菌素(MON,5μmol/L)做阳性对照,试验组NI添加水平分别为3(NI-3)、9(NI-9)和27 mg/100 m L(NI-27),每个处理4个重复,分别于培养后的0、3、6、9、12、24 h测定产气量和甲烷产量。培养24 h后,采集发酵液样品,用于发酵参数和菌群数量的测定。【结果】与NC组相比,添加NI和MON均能显著降低产气量和甲烷产量(P<0.05);添加NI对pH值、干物质消失率(DMD)和有机物消失率(OMD)无显著影响(P>0.05);NI-9处理组与NC组相比氨态氮浓度显著降低(P<0.05),而NI-3和NI-27组氨氮浓度没有显著变化(P>0.05);相比而言,MON处理组DMD、OMD和氨氮浓度与NC组相比均显著降低(P<0.05),而pH值与其他各处理组相比没有差异(P>0.05);与NC组相比,NI各处理组和MON组乙酸浓度及乙丙比均显著降低(P<0.05),丙酸浓度显著提高(P<0.05)。功能菌方面,qPCR结果显示添加NI和MON对总菌和拟杆菌门数量均无显著影响(P>0.05);与NC相比,添加NI对原虫、甲烷菌、真菌和厚壁菌门数量均无显著影响(P>0.05),而MON组原虫、甲烷菌、真菌和厚壁菌门数量显著降低(P<0.05);NI和MON处理均显著提高了硫还原菌和C.aminophilum数量(P<0.05),但C.sticklandii数量不受影响(P>0.05)。【结论】添加适宜浓度的NI可降低瘤胃甲烷与氨的生成,但并不影响饲料消化,这种发酵模式的改变可能与瘤胃功能菌群数量与多样性的变化密切相关。     

Effect of surface-screening parameter of the Yukawa potential model on vapour–liquid phase coexistence and critical-point properties of confined Yukawa fluid

We report the effect of surface-screening parameter of Yukawa potential model on vapour–liquid phase coexistence and critical-point properties of slit–pore-confined Yukawa fluid, using grand canonical transition-matrix Monte Carlo along with the histogram reweighting method. The effect of surface-screening parameter on the vapour–phase coexistence density is insignificant for the studied system. On the other hand, significant effect of surface-screening parameter is observed on liquid phase coexistence density. With increasing surface-screening parameter, liquid phase coexistence density decreases. Critical-point properties have shown monotonic decreasing trends with increase in surface-screening parameter. Moreover, the effect of change of surface-screening parameter is least on critical temperature changes as compared to critical density and critical pressure changes for the studied Yukawa system in this work.     

Probing the effect of nitro groups in nitramine based energetic molecules: a DFT and charge density study

The structure, electron density distribution, energetic and electrostatic properties of simple nitramine based energetic TMA, DMNA, MDA and TNA molecules were determined using density functional theory (B3LYP) with the 6-311G^** and aug-cc-pVDZ basis sets coupled with Bader's theory of atoms in molecules. In the NO₂ group substituted molecules, the N–N bond distance increases with the increase of NO₂ groups, whereas in C–N bonds, this effect is relatively less, and the distances are almost equal. The topological analysis of electron density reveals that the electron density ρ_bcp(r) of C–N and N–N bonds are significantly decreasing with the increase of NO₂ groups in the nitramine molecules. The Laplacian of electron density ▽²ρ_bcp(r) of N–NO₂ bonds [DMNA: ? 16.7 eÅ^? 5, MDA: ? 12.8 eÅ^? 5 and TNA: ? 7.9 eÅ^? 5] of the molecules are relatively less negative, and the values also decrease with the increase of NO₂ groups; this implies that the charge concentration decreases with the increase of NO₂ groups, which leads to weakening the N–N bonds of the molecules. The isosurface of molecular electrostatic potential displays high electronegative regions around the NO₂ groups. The oxygen balance OB₁₀₀ of the molecules increases as the number of NO₂ group increases in the molecules, in which, the TNA molecule having maximum OB₁₀₀ value [+7.89]. The band gap, heat of detonation, bond dissociation energy and charge imbalance are predominantly depends on the number of NO₂ group present in the molecule. The charge imbalance parameter (ν) has been calculated for all molecules, which reveals that TNA is a highly sensitive molecule, the corresponding ν value is 0.047.     

皮下种植黑色素瘤对小鼠血液中脂肪和氨基酸代谢的影响*

目的:探讨皮下种植黑色素瘤对小鼠血液中相关脂肪和氨基酸代谢的影响。方法:野生型小鼠皮下种植B16黑色素瘤细胞,两周后观察小鼠并取不同的组织称重,检测血液中甘油三酯、葡萄糖、脂肪酸、炎症因子的水平。利用质谱方法检测血液中氨基酸的水平。结果:野生型小鼠皮下肿瘤种植2周后体重没有明显变化,脾脏和肝脏的重量明显增加,皮下脂肪组织和腹腔脂肪组织的重量没有明显变化。血液中甘油三酯的水平明显增高,葡萄糖和甘油的水平明显下降。血液中炎症因子Interleukin 6(IL6)和Interferon gamma(IFNγ)的水平明显增加。血液的质谱结果显示有四种氨基酸的水平有明显变化,其中胱氨酸(Cystine)增加了约30倍,丝氨酸(Serine)、谷氨酰胺(Glutamine)和色氨酸(Tryptophan)分别有不同程度的降低。结论:皮下黑色素瘤显著影响小鼠机体营养状态和炎症,并特异性影响血液中氨基酸的代谢。     

米槁幼苗光合作用及光响应曲线模拟对干旱胁迫的响应

为阐明米槁光合作用对干旱胁迫的响应规律与适应机制,以一年生米槁幼苗为研究对象,进行盆栽试验研究设置3种不同土壤含水量梯度,利用Li-6400便携式光合作用系统测定干旱胁迫下的光合生理指标及光响应过程,光响应曲线模拟采用直角双曲线模型、非直角双曲线模型、指数模型和直角双曲线修正模型进行拟合并对比,以期选出适用于干旱环境下的光响应模型。结果表明(1)光响应曲线模型对干旱胁迫下米槁幼苗的光合作用拟合中直角双曲线、非直角双曲线和指数模型适用于低光合有效辐射(PAR),但拟合光响应参数与实测值相差大,只有直角双曲线修正模型能够很好的拟合各个处理且拟合参数比较精确米槁幼苗。(2)光合作用的表观量子效率(Φ)小于一般植物的光合量子效率,则其对弱光的光能利用效率相对较低。(3)在较强的光合有效辐射条件下,严重干旱胁迫下的米槁净光合速率P_n显著下降,出现了明显的光抑制现象;中度胁迫下净光合速率(P_n)、最大净光合速率(P_(nmax))、光补偿点(LSP)最大,米槁具有较宽的抗旱适应范围,有一定的抗旱性;严重胁迫下P_n、P_(nmax)、LSP降低,蒸腾速率(T_r)与气孔导度(G_s)下降幅度更大,但仍具有较高的水分利用效率(WUE),米槁在严重的干旱胁迫下光合机构受到一定的损伤,但自身可以通过生理调节来积极适应不良环境,减少光合机构伤害。(4)综合来看,在人工管理或种植米槁时,为了适应米槁生长发育,建议土壤含水量保持在23.05%到14.92%之间。