The Polynomial Model in the Multivariate Analysis of Variance

Assuming that the independent variables (factors) are quantitative, there exist besides the coding schemes generally used for the multivariate analysis of variance (dummy-coded or effect-coded design matrices) the so-called polynomial models. The advantage of these polynomial models are the full rank design matrices, which allow a more comprehensible analysis, i.e. the unambiguous interpretation of tested hypotheses and simultaneous confidence intervals.     

磁性细胞分选技术的应用与生物学评价

磁性细胞分选技术是一种利用超顺磁性纳米复合材料进行细胞分选的细胞高度特异性快速分选技术,在免疫学、干细胞学、肿瘤学和临床医学等领域应用广泛。本文综合阐述了磁性细胞分选技术的分类和应用,讨论了近几年出现的几项基于磁性细胞分选的新技术和面临的挑战。重点分析了磁性细胞分选产品生物学评价的必要性,并提出了10项与磁性细胞分选产品相关的生物学评价技术参数：得率、纯度、无菌、细胞毒性、细胞形态、活率、细胞的光散射特性、细胞的荧光抗体标记能力、细胞活化、细胞增殖,该评价技术参数的提出对磁性细胞分选规范化应用具有重要的推动作用。     

Dissecting the Biological Role of Mucin-type O-Glycosylation Using RNA Interference in Drosophila Cell Culture

Mucin type O-glycosylation is a highly conserved form of post-translational modification initiated by the family of enzymes known as the polypeptide α-N-acetylgalactosaminyltransferases (ppGalNAcTs in mammals and PGANTs in Drosophila). To address the cellular functions of the many PGANT family members, RNA interference (RNAi) to each pgant gene was performed in two independent Drosophila cell culture lines. We demonstrate that RNAi to individual pgant genes results in specific reduction in gene expression without affecting the expression of other family members. Cells with reduced expression of individual pgant genes were then examined for changes in viability, morphology, adhesion, and secretion to assess the contribution of each family member to these cellular functions. Here we find that RNAi to pgant3, pgant6, or pgant7 resulted in reduced secretion, further supporting a role for O-glycosylation in proper secretion. Additionally, RNAi to pgant3 or pgant6 resulted in altered Golgi organization, suggesting a role for each in establishing or maintaining proper secretory apparatus structure. Other subcellular effects observed included multinucleated cells seen after RNAi to either pgant2 or pgant35A, suggesting a role for these genes in the completion of cytokinesis. These studies demonstrate the efficient and specific knockdown of pgant gene expression in two Drosophila cell culture systems, resulting in specific morphological and functional effects. Our work provides new information regarding the biological roles of O-glycosylation and illustrates a new platform for interrogating the cellular and subcellular effects of this form of post-translational modification.     

Synthesis and Biological Evaluation of Some Succinimide Hybrid Molecules

Russian Journal of Bioorganic Chemistry - In this study, a new series of succinimide hybrid molecules containing isothiocyanate, coumarin, isatin, and furan moieties was synthesized and screened...     

Synthesis and Biological Evaluation of Some D-Arabino- and D-Lyxofuranosyl-Pyridine C-Nucleosides

Abstract

The addition reaction of either 3-bromo-5-lithiopyridine (2a) or 3-cyano-5-lithiopyridine (2b) to 2,3:4,5-di-O-isopropylidene-aldehydo-D-arabinose (1) or 2,4:3,5-di-O-benzylidene-aldehydo-D-lyxose (8) gave respectively a D-gluco/D-manno mixture of 3-bromo- and 3-cyano-5-(2,3:4,5-di-O-isopropylidene-pentitol-1-yl)pyridine (3a,b) or a D-galacto/D-talo mixture of respectively 3-bromo- and 3-cyano-5-(2,4:3,5-di-O-benzylidene-pentitol-1-yl)pyridine (9a,b). Mesylation of C-1′ followed by reaction with CF₃COOH/H₂O resulted in the formation of the corresponding D-arabino- or D-lyxofuranosyl pyridine C-nucleosides. The cyano group of (5b) and (11b) was converted into a carbamoyl group using Amberlite IRA 400 (OH^?). 3-Cyano-5-D-arabinofuianosylpyridine (5b) was converted into 3-thiocarbamoyl-5-D-arabinofuranosyl-pyridine (7) using H₂S and triethylamine.

None of the test compounds showed a marked cytostatic or antiviral activity in vitro.     

Discovery of Some of the Biological Effects of Nitric Oxide and its Role in Cell Signaling

The role of nitric oxide in cellular signaling in the past 22 years has become one of the most rapidly growing areas in biology with more than 20,000 publications to date. Nitric oxide is a gas and free radical with an unshared electron that can regulate an ever-growing list of biological processes. In many instances nitric oxide mediates its biological effects by activating guanylyl cyclase and increasing cyclic GMP synthesis from GTP. However, the list of effects of nitric oxide that are independent of cyclic GMP is also growing at a rapid rate. For example, nitric oxide can interact with transition metals such as iron, thiol groups, other free radicals, oxygen, superoxide anion, unsaturated fatty acids and other molecules. Some of these reactions result in the oxidation of nitric oxide to nitrite and nitrate to terminate its effect, while other reactions can lead to altered protein structure, function, and/or catalytic capacity. These diverse effects of nitric oxide that are either cyclic GMP dependent or independent can alter and regulate important physiological and biochemical events in cell regulation and function. Nitric oxide can function as an intracellular messenger, an autacoid, a paracrine substance, a neurotransmitter, or as a hormone that can be carried to distant sites for effects. Thus, it is a unique simple molecule with an array of signaling functions. However, as with any messenger molecule, there can be too little or too much of the substance and pathological events result. Some of the methods to regulate either nitric oxide formation, metabolism, or function have been in clinical use for more than a century as with the use of organic nitrates and nitroglycerin in angina pectoris that was initiated in the 1870's. Current and future research with nitric oxide and cyclic GMP will undoubtedly expand the clinicians' therapeutic armamentarium to manage a number of important diseases by perturbing nitric oxide and cyclic GMP formation and metabolism. Such promise and expectations have obviously fueled the interests in these signaling molecules for a growing list of potential therapeutic applications.John S. Dunn Distinguished Chair in Medicine and Physiology, Regental Professor and Chair of Department of Integrative Biology, Pharmacology, and Physiology and Director of the Institute of Molecular Medicine     

Discovery of Some of the Biological Effects of Nitric Oxide and its Role in Cell Signaling

The role of nitric oxide in cellular signaling in the past 22 years has become one of the most rapidly growing areas in biology with more than 20,000 publications to date. Nitric oxide is a gas and free radical with an unshared electron that can regulate an ever-growing list of biological processes. In many instances nitric oxide mediates its biological effects by activating guanylyl cyclase and increasing cyclic GMP synthesis from GTP. However, the list of effects of nitric oxide that are independent of cyclic GMP is also growing at a rapid rate. For example, nitric oxide can interact with transition metals such as iron, thiol groups, other free radicals, oxygen, superoxide anion, unsaturated fatty acids and other molecules. Some of these reactions result in the oxidation of nitric oxide to nitrite and nitrate to terminate its effect, while other reactions can lead to altered protein structure, function, and/or catalytic capacity. These diverse effects of nitric oxide that are either cyclic GMP dependent or independent can alter and regulate important physiological and biochemical events in cell regulation and function. Nitric oxide can function as an intracellular messenger, an autacoid, a paracrine substance, a neurotransmitter, or as a hormone that can be carried to distant sites for effects. Thus, it is a unique simple molecule with an array of signaling functions. However, as with any messenger molecule, there can be too little or too much of the substance and pathological events result. Some of the methods to regulate either nitric oxide formation, metabolism, or function have been in clinical use for more than a century as with the use of organic nitrates and nitroglycerin in angina pectoris that was initiated in the 1870’s. Current and future research with nitric oxide and cyclic GMP will undoubtedly expand the clinicians’ therapeutic armamentarium to manage a number of important diseases by perturbing nitric oxide and cyclic GMP formation and metabolism. Such promise and expectations have obviously fueled the interests in these signaling molecules for a growing list of potential therapeutic applications.     

Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling

A fundamental property of cell populations is their growth rate as well as the time needed for cell division and its variance. The eukaryotic cell cycle progresses in an ordered sequence through the phases and and is regulated by environmental cues and by intracellular checkpoints. Reflecting this regulatory complexity, the length of each phase varies considerably in different kinds of cells but also among genetically and morphologically indistinguishable cells. This article addresses the question of how to describe and quantify the mean and variance of the cell cycle phase lengths. A phase-resolved cell cycle model is introduced assuming that phase completion times are distributed as delayed exponential functions, capturing the observations that each realization of a cycle phase is variable in length and requires a minimal time. In this model, the total cell cycle length is distributed as a delayed hypoexponential function that closely reproduces empirical distributions. Analytic solutions are derived for the proportions of cells in each cycle phase in a population growing under balanced growth and under specific non-stationary conditions. These solutions are then adapted to describe conventional cell cycle kinetic assays based on pulse labelling with nucleoside analogs. The model fits well to data obtained with two distinct proliferating cell lines labelled with a single bromodeoxiuridine pulse. However, whereas mean lengths are precisely estimated for all phases, the respective variances remain uncertain. To overcome this limitation, a redesigned experimental protocol is derived and validated in silico. The novelty is the timing of two consecutive pulses with distinct nucleosides that enables accurate and precise estimation of both the mean and the variance of the length of all phases. The proposed methodology to quantify the phase length distributions gives results potentially equivalent to those obtained with modern phase-specific biosensor-based fluorescent imaging.     

Synthesis and Biological Evaluation of Some Acyclic Pyridine C-Nucleosides. Part Two

Abstract

3-Bromo-5-(2-hydroxyethylthiomethyl)pyridine (7) was synthesized by reaction of 3-bromo-5-chloromethylpyridine hydrochloride (6) with the mono sodium salt of 2-mercaptoethanol. 3-Bromo-5-hydroxymethylpyridine (10) was, after protection as a silyl ether, converted to the 3-carboxy analogue using BuLi and CO₂. After deprotection with NH₄F, the alcohol function was chlorinated using SOCl₂. Finally, attachment of the acyclic chain and ammonolysis gave the acyclic nicotinamide nucleosides. Treatment of the latter compounds with Lawesson's reagent gave the thioamide analogues. All compounds were identified by NMR and DCI-MS. The acyclic pyridine C-nucleosides were evaluated against a series of tumor-cell lines and a variety of viruses. No marked biological activity was found.     

Synthesis and Biological Evaluation of Some N-Substituted Quinoxaline Derivatives as Antitumor Agents

Russian Journal of Bioorganic Chemistry - A new hybrid molecules containing 1-(N-substituted)-quinoxaline derivatives were synthesized from condensation of 3-hydroxy-2-oxo quinoxaline with...     

人红细胞生成素(EPO)工程细胞建立及特性分析

构建了EPO真核表达质粒,成功地实现了其在CHOdhfr-细胞中的表达,所得到的EPO工程细胞株的形态与CHOdhfr-细胞相似,细胞株小瓶静止培养时最高表达水平为2～3μg/106cells/24h,而且细胞表达稳定,连续传代三个月和反复冻存复苏三次,细胞表达水平无明显下降。经过对细胞的一系列特性分析表明,该细胞株无支原体、真菌及细菌污染,无致瘤性,形态正常,染色体畸变率与出发株相当。     

Causal Efficacy and the Analysis of Variance

The causal impacts of genes and environment on any one biological trait are inextricably entangled, and consequently it is widely accepted that it makes no sense in singleton cases to privilege either factor for particular credit. On the other hand, at a population level it may well be the case that one of the factors is responsible for more variation than the other. Standard methodological practice in biology uses the statistical technique of analysis of variance to measure this latter kind of causal efficacy. In this paper, I argue that: 1) analysis of variance is in fact badly suited to this role; and 2) a superior alternative definition is available that readily reconciles both the entangled-singleton and the population-variation senses of causal efficacy.     

Information-Theoretic Analysis of the Dynamics of an Executable Biological Model

To facilitate analysis and understanding of biological systems, large-scale data are often integrated into models using a variety of mathematical and computational approaches. Such models describe the dynamics of the biological system and can be used to study the changes in the state of the system over time. For many model classes, such as discrete or continuous dynamical systems, there exist appropriate frameworks and tools for analyzing system dynamics. However, the heterogeneous information that encodes and bridges molecular and cellular dynamics, inherent to fine-grained molecular simulation models, presents significant challenges to the study of system dynamics. In this paper, we present an algorithmic information theory based approach for the analysis and interpretation of the dynamics of such executable models of biological systems. We apply a normalized compression distance (NCD) analysis to the state representations of a model that simulates the immune decision making and immune cell behavior. We show that this analysis successfully captures the essential information in the dynamics of the system, which results from a variety of events including proliferation, differentiation, or perturbations such as gene knock-outs. We demonstrate that this approach can be used for the analysis of executable models, regardless of the modeling framework, and for making experimentally quantifiable predictions.     

LJH-OS人骨肉瘤裸鼠原位移植模型的建立及其生物学特性

用人成骨肉瘤细胞系LJH- OS的传代移植瘤组织作为移植材料,进行胫骨原位移植及皮下移植。结果发现胫骨原位移植的潜伏期较短,生长快。皮下移植瘤呈局限性膨胀性生长,有不完整的纤维包膜,未见肺转移,观察7 周无明显消瘦;而胫骨原位移植瘤浸润基层,无纤维包膜,且发生肺转移,7 周时有明显消瘦。原位移植的裸鼠血清ALP水平高于皮下移植者。说明裸鼠胫骨微环境较皮下组织更适于人骨肉瘤的浸润及转移表达,裸鼠胫骨原位移植模型的恶性生物学行为更接近临床骨肉瘤患者的实际情况,该原位移植模型的建立为骨肉瘤的研究提供了良好的实验模型。     

Improving Embryonic Stem Cell Expansion through the Combination of Perfusion and Bioprocess Model Design

Background

High proliferative and differentiation capacity renders embryonic stem cells (ESCs) a promising cell source for tissue engineering and cell-based therapies. Harnessing their potential, however, requires well-designed, efficient and reproducible expansion and differentiation protocols as well as avoiding hazardous by-products, such as teratoma formation. Traditional, standard culture methodologies are fragmented and limited in their fed-batch feeding strategies that afford a sub-optimal environment for cellular metabolism. Herein, we investigate the impact of metabolic stress as a result of inefficient feeding utilizing a novel perfusion bioreactor and a mathematical model to achieve bioprocess improvement.

Methodology/Principal Findings

To characterize nutritional requirements, the expansion of undifferentiated murine ESCs (mESCs) encapsulated in hydrogels was performed in batch and perfusion cultures using bioreactors. Despite sufficient nutrient and growth factor provision, the accumulation of inhibitory metabolites resulted in the unscheduled differentiation of mESCs and a decline in their cell numbers in the batch cultures. In contrast, perfusion cultures maintained metabolite concentration below toxic levels, resulting in the robust expansion (>16-fold) of high quality ‘naïve’ mESCs within 4 days. A multi-scale mathematical model describing population segregated growth kinetics, metabolism and the expression of selected pluripotency (‘stemness’) genes was implemented to maximize information from available experimental data. A global sensitivity analysis (GSA) was employed that identified significant (6/29) model parameters and enabled model validation. Predicting the preferential propagation of undifferentiated ESCs in perfusion culture conditions demonstrates synchrony between theory and experiment.

Conclusions/Significance

The limitations of batch culture highlight the importance of cellular metabolism in maintaining pluripotency, which necessitates the design of suitable ESC bioprocesses. We propose a novel investigational framework that integrates a novel perfusion culture platform (controlled metabolic conditions) with mathematical modeling (information maximization) to enhance ESC bioprocess productivity and facilitate bioprocess optimization.     

Analysis of State-Dependent Transitions in Frequency and Long-Distance Coordination in a Model Oscillatory Cortical Circuit

Changes in behavioral state are typically accompanied by changes in the frequency and spatial coordination of rhythmic activity in the neocortex. In this article, we analyze the effects of neuromodulation on ionic conductances in an oscillating cortical circuit model. The model consists of synaptically-coupled excitatory and inhibitory neurons and supports rhythmic activity in the alpha, beta, and gamma ranges. We find that the effects of neuromodulation on ionic conductances are, by themselves, sufficient to induce transitions between synchronous gamma and beta rhythms and asynchronous alpha rhythms. Moreover, these changes are consistent with changes in behavioral state, with the rhythm transitioning from the slower alpha to the faster gamma and beta as arousal increases. We also observe that it is the same set of underlying intrinsic and network mechanisms that appear to be simultaneously responsible for both the observed transitions between the rhythm types and between their synchronization properties. Spike time response curves (STRCs) are used to study the relationship between the transitions in rhythm and the underlying biophysics.