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     

不同分娩方式对产妇产后心理和生理的影响

目的:探讨不同分娩方式对产妇产后心理和生理的影响.方法:随机选择2011年1月～2011年12月在苏大附一院分娩的初产妇400例,其中剖宫产、阴道自然分娩各200例,对两组产妇产后42天心理状况、恶露持续时间、泌乳情况进行调查.结果:两种分娩方式对产妇产后42天发生焦虑和抑郁心理的影响无明显差别(P＞0.05);阴道自然分娩组产后恶露持续时间短于剖宫产组,差异有显著意义(P＜0.01).有抑郁、焦虑情绪的产妇泌乳始动时间显著长于正常产妇,24h泌乳量显著少于正常产妇(P＜0.01).结论:剖宫产对产妇身体生理创伤大过阴道自然分娩,应严格控制剖宫产的适应症,鼓励阴道自然分娩.     

Species Determination and Quantitation in Mixtures Using MRM Mass Spectrometry of Peptides Applied to Meat Authentication

We describe a simple protocol for identifying and quantifying the two components in binary mixtures of species possessing one or more similar proteins. Central to the method is the identification of ''corresponding proteins'' in the species of interest, in other words proteins that are nominally the same but possess species-specific sequence differences. When subject to proteolysis, corresponding proteins will give rise to some peptides which are likewise similar but with species-specific variants. These are ''corresponding peptides''. Species-specific peptides can be used as markers for species determination, while pairs of corresponding peptides permit relative quantitation of two species in a mixture. The peptides are detected using multiple reaction monitoring (MRM) mass spectrometry, a highly specific technique that enables peptide-based species determination even in complex systems. In addition, the ratio of MRM peak areas deriving from corresponding peptides supports relative quantitation. Since corresponding proteins and peptides will, in the main, behave similarly in both processing and in experimental extraction and sample preparation, the relative quantitation should remain comparatively robust. In addition, this approach does not need the standards and calibrations required by absolute quantitation methods. The protocol is described in the context of red meats, which have convenient corresponding proteins in the form of their respective myoglobins. This application is relevant to food fraud detection: the method can detect 1% weight for weight of horse meat in beef. The corresponding protein, corresponding peptide (CPCP) relative quantitation using MRM peak area ratios gives good estimates of the weight for weight composition of a horse plus beef mixture.     

Trait biogeography of marine copepods – an analysis across scales

Functional traits, rather than taxonomic identity, determine the fitness of individuals in their environment: traits of marine organisms are therefore expected to vary across the global ocean as a function of the environment. Here, we quantify such spatial and seasonal variations based on extensive empirical data and present the first global biogeography of key traits (body size, feeding mode, relative offspring size and myelination) for pelagic copepods, the major group of marine zooplankton. We identify strong patterns with latitude, season and between ocean basins that are partially (c. 50%) explained by key environmental drivers. Body size, for example decreases with temperature, confirming the temperature‐size rule, but surprisingly also with productivity, possibly driven by food‐chain length and size‐selective predation. Patterns unrelated to environmental predictors may originate from phylogenetic clustering. Our maps can be used as a test‐bed for trait‐based mechanistic models and to inspire next‐generation biogeochemical models.     

Detecting the native ligand orientation by interfacial rigidity: SiteInterlock

Understanding the physical attributes of protein‐ligand interfaces, the source of most biological activity, is a fundamental problem in biophysics. Knowing the characteristic features of interfaces also enables the design of molecules with potent and selective interactions. Prediction of native protein‐ligand interactions has traditionally focused on the development of physics‐based potential energy functions, empirical scoring functions that are fit to binding data, and knowledge‐based potentials that assess the likelihood of pairwise interactions. Here we explore a new approach, testing the hypothesis that protein‐ligand binding results in computationally detectable rigidification of the protein‐ligand interface. Our SiteInterlock approach uses rigidity theory to efficiently measure the relative interfacial rigidity of a series of small‐molecule ligand orientations and conformations for a number of protein complexes. In the majority of cases, SiteInterlock detects a near‐native binding mode as being the most rigid, with particularly robust performance relative to other methods when the ligand‐free conformation of the protein is provided. The interfacial rigidification of both the protein and ligand prove to be important characteristics of the native binding mode. This measure of rigidity is also sensitive to the spatial coupling of interactions and bond‐rotational degrees of freedom in the interface. While the predictive performance of SiteInterlock is competitive with the best of the five other scoring functions tested, its measure of rigidity encompasses cooperative rather than just additive binding interactions, providing novel information for detecting native‐like complexes. SiteInterlock shows special strength in enhancing the prediction of native complexes by ruling out inaccurate poses. Proteins 2016; 84:1888–1901. © 2016 Wiley Periodicals, Inc.     

高校互动式教学模式探讨

互动式教学模式是指以学生为主体,立足于培养学生创新能力的一种教学模式。高等医学院校是高素质医学人才培养的主要单位,研究高校互动式教学模式的内涵及医学意义、病理生理学中互动式教学模式的应用、互动式教学模式的制约瓶颈、探究高校互动式教学模式的实施策略有利于促进高校互动式教学模式的创新及医学人才培养质量的提高。     

Interspecies Comparison of the Bacterial Response to Allicin Reveals Species‐Specific Defense Strategies

Allicin, a broad‐spectrum antimicrobial agent from garlic, disrupts thiol and redox homeostasis, proteostasis, and cell membrane integrity. Since medicine demands antimicrobials with so far unexploited mechanisms, allicin is a promising lead structure. While progress is being made in unraveling its mode of action, little is known on bacterial adaptation strategies. Some isolates of Pseudomonas aeruginosa and Escherichia coli withstand exposure to high allicin concentrations due to as yet unknown mechanisms. To elucidate resistance and sensitivity‐conferring cellular processes, the acute proteomic responses of a resistant P. aeruginosa strain and the sensitive species Bacillus subtilis are compared to the published proteomic response of E. coli to allicin treatment. The cellular defense strategies share functional features: proteins involved in translation and maintenance of protein quality, redox homeostasis, and cell envelope modification are upregulated. In both Gram‐negative species, protein synthesis of the majority of proteins is downregulated while the Gram‐positive B. subtilis responded by upregulation of multiple regulons. A comparison of the B. subtilis proteomic response to a library of responses to antibiotic treatment reveals 30 proteins specifically upregulated by allicin. Upregulated oxidative stress proteins are shared with nitrofurantoin and diamide. Microscopy‐based assays further indicate that in B. subtilis cell wall integrity is impaired.     

ENSO and NAO affect long‐term leaf litter dynamics and stoichiometry of Scots pine and European beech mixedwoods

Litterfall dynamics (production, seasonality and nutrient composition) are key factors influencing nutrient cycling. Leaf litter characteristics are modified by species composition, site conditions and water availability. However, significant evidence on how large‐scale, global circulation patterns affect ecophysiological processes at tree and ecosystem level remains scarce due to the difficulty in separating the combined influence of different factors on local climate and tree phenology. To fill this gap, we studied links between leaf litter dynamics with climate and other forest processes, such as tree‐ring width (TRW) and intrinsic water‐use efficiency (iWUE) in two mixtures of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) in the south‐western Pyrenees. Temporal series (18 years) of litterfall production and elemental chemical composition were decomposed following the ensemble empirical mode decomposition method and relationships with local climate, large‐scale climatic indices, TRW and Scots pine's iWUE were assessed. Temporal trends in N:P ratios indicated increasing P limitation of soil microbes, thus affecting nutrient availability, as the ecological succession from a pine‐dominated to a beech‐dominated forest took place. A significant influence of large‐scale patterns on tree‐level ecophysiology was explained through the impact of the North Atlantic Oscillation (NAO) and El Niño–Southern Oscillation (ENSO) on water availability. Positive NAO and negative ENSO were related to dry conditions and, consequently, to early needle shedding and increased N:P ratio of both species. Autumn storm activity appears to be related to premature leaf abscission of European beech. Significant cascading effects from large‐scale patterns on local weather influenced pine TRW and iWUE. These variables also responded to leaf stoichiometry fallen 3 years prior to tree‐ring formation. Our results provide evidence of the cascading effect that variability in global climate circulation patterns can have on ecophysiological processes and stand dynamics in mixed forests.     

Balancing competing life‐stage requirements in salmon habitat rehabilitation: between a rock and a hard place

Gravel augmentation is often applied to rivers and streams to rehabilitate salmonid spawning and incubation habitat. However, the effect of gravel size on salmon spawning utilization and embryo survival during incubation is not well understood. We conducted an experiment on a regulated and previously mined Northern California salmonid‐bearing stream in which different sized gravel (small, medium, and large) patches were placed into the stream's degraded spawning reach. We documented Oncorhynchus tshawytscha (Chinook salmon) spawning activity within the three gravel sizes for two seasons. In addition, we deployed Chinook salmon embryos into each gravel size patch and allowed them to incubate until estimated emergence time. Although all experimental gravel sizes were predicted to be within the spawning population's mobilization capabilities, model results indicated the probability of salmon building redds decreased as substrate size increased. Conversely, embryo survival increased as gravel size increased. A possible mechanism of disparate Chinook salmon embryo survival is provided by an observed decrease in embryo survival correlating with greater presence of embryo predators (leeches), which are associated with smaller gravel. Our results indicate a parent‐offspring conflict in optimal spawning gravel size for Chinook salmon, and suggest that an intermediate gravel size would maximize overall reproductive success across both spawning and incubation life stages.