Intracellular organelle networks: Understanding their organization and communication through systems-level modeling and analysis

Background

Membrane-bound intracellular organelles are biochemically distinct compartments used by eukaryotic cells for serving specialized physiological functions and organizing their internal environment. Recent studies revealed surprisingly extensive communication between these organelles and highlighted the network nature of their organization and communication. Since organization and communication of the organelles are carried out at the systems level through their networks, systems-level studies are essential for understanding the underlying mechanisms.

Methods

We reviewed recent studies that used systems-level quantitative modeling and analysis to understand organization and communication of intracellular organelle networks.

Results

We first review modeling and analysis studies on how fusion/fission and degradation/biogenesis, two essential and closely related classes of activities of individual organelles, collectively mediate the dynamic organization of their networks. We then turn to another important aspect of the dynamic organization of the organelle networks, namely how organelles are physically connected within their networks, a property referred to as the topology of the networks in mathematics, and summarize some of their distinct properties. Lastly, we briefly review modeling and analysis studies that aim to understand communication between different organelle networks, focusing on cellular calcium homeostasis as an example. We conclude with a brief discussion of future directions for research in this area.

Conclusion

Together, the reviewed studies provide critical insights into how diverse activities of individual organelles collectively mediate the organization and communication of their networks. They demonstrate the essential role of systemslevel modeling and analysis in understanding complex behavior of such networks.

     

Pest control through viral disease: mathematical modeling and analysis

This paper deals with the mathematical modeling of pest management under viral infection (i.e. using viral pesticide) and analysis of its essential mathematical features. As the viral infection induces host lysis which releases more virus into the environment, on the average 'kappa' viruses per host, kappain(1,infinity), the 'virus replication parameter' is chosen as the main parameter on which the dynamics of the infection depends. We prove that there exists a threshold value kappa(0) beyond which the endemic equilibrium bifurcates from the free disease one. Still for increasing kappa values, the endemic equilibrium bifurcates towards a periodic solution. We further analyse the orbital stability of the periodic orbits arising from bifurcation by applying Poor's condition. A concluding discussion with numerical simulation of the model is then presented.     

结构方程混合模型在SNP分析中的应用

采用结构方程混合模型(SEMM)对实际SNP数据进行分析,为遗传统计学提供一种新的有效的分析方法。本研究的数据是由GAW17提供的,包含697个个体的22条常染色体的上万个SNP和根据这些SNP所模拟的697个个体的性状特点。随机挑选了1号染色体上的4个SNP和3个定量性状作为研究变量,分别进行潜在类别分析和结构方程混合模型分析。根据4个SNP数据,人群被分为3个潜在类别,概率分别为0.53,0.34,0.13。潜在类别1、2和3中的因子均值Q分别为-4.029、-2.052和0,潜在类别1、2的因子均值均低于3(<0.001)。研究表明:结构方程混合模型(SEMM)综合了结构方程模型和潜在类别模型的思想,形成了自己的优势,可用于处理同时包含分类潜变量和连续潜变量的数据。     

Dissecting the molecular mechanism of drosophila odorant receptors through activity modeling and comparative analysis

To gain insight into the molecular mechanism of odorant receptors (ORs) in Drosophila species, we developed a Quantitative Structure Activity Relationship (QSAR) model that predicts experimentally measured electrophysiological activities between 24 D. melanogaster ORs and 108 odorants. Although the model is limited by the tested odorants,analyzing the model allowed dissection of specific topological and chemical properties necessary for an odorant to elicit excitatory or inhibitory receptor response. Linear odorants with five to eight nonhydrogen atoms at the main chain and hydrogen‐bond acceptor and/or hydrogen‐bond donor at its ends were found to stimulate strong excitatory response. A comparative sequence analysis of 90 ORs in 15 orthologous groups identified 15 putative specificity‐determining residues (SDRs) and 15 globally conserved residues that we postulate as functionally key residues. Mapping to a model of secondary structure resulted in 14 out of 30 key residues locating to the transmembrane (TM) domains. Twelve residues, including six SDRs and six conserved residues, are located at the extracellular halves of the TM domains. Combining the evidence from the QSAR modeling and the comparative sequence analysis, we hypothesize that the Drosophila ORs accept odorants into a binding pocket located on the extracellular halves of its TM domains. The QSAR modeling suggests that the binding pocket is around 15 Å in depth and about 6 Å in width. Twelve mainly polar or charged key residues, both SDRs and conserved, are located inthis pocket and postulated to distinguish docked odorants via primarily geometry fitting and hydrogen‐bond interaction. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

米心水青冈生长过程中的抑制和释放

米心水青冈生长过程中的抑制和释放江明喜,金义兴,张全发（中国科学院武汉植物研究所,武汉４３００７４）ＳｕｐｐｒｅｓｓｉｏｎａｎｄｒｅｌｅａｓｅｐｅｒｉｏｄｓｉｎｔｈｅｃｏｕｒｓｅｏｆＦａｇｕｓｅｎｇｌｅｒｉａｎａｇｒｏｗｔｈ￥．ＪｉａｎｇＭｉｎｇｘｉ...     

Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modeling

A novel hierarchical quantitative trait locus (QTL) mapping method using a polynomial growth function and a multiple-QTL model (with no dependence in time) in a multitrait framework is presented. The method considers a population-based sample where individuals have been phenotyped (over time) with respect to some dynamic trait and genotyped at a given set of loci. A specific feature of the proposed approach is that, instead of an average functional curve, each individual has its own functional curve. Moreover, each QTL can modify the dynamic characteristics of the trait value of an individual through its influence on one or more growth curve parameters. Apparent advantages of the approach include: (1) assumption of time-independent QTL and environmental effects, (2) alleviating the necessity for an autoregressive covariance structure for residuals and (3) the flexibility to use variable selection methods. As a by-product of the method, heritabilities and genetic correlations can also be estimated for individual growth curve parameters, which are considered as latent traits. For selecting trait-associated loci in the model, we use a modified version of the well-known Bayesian adaptive shrinkage technique. We illustrate our approach by analysing a sub sample of 500 individuals from the simulated QTLMAS 2009 data set, as well as simulation replicates and a real Scots pine (Pinus sylvestris) data set, using temporal measurements of height as dynamic trait of interest.     

On the flow of medical information through a hospital registration post

The health status of any inpatient of the Geneva hospital is appraised 3 times as follows: once before hospitalisation, then while registering, and last at discharge from hospital. Data about these 3 examinations were gathered in the registration post and then coded. The number of recorded ailments and their contents were statistically analysed. There is a notable increase in the number of diagnosed ailments and a large agreement about their nature. Simple models to describe the relations between those 2 variables were investigated, but turned up to be somewhat unsatisfying. Throughout the paper due allowance is made for a distinction between medicosurgical ailments and more specialised ones.     

Urinary steroids in the periparturient and postpartum periods through early pregnancy in llamas

Urinary steroids were determined daily in the periparturient and postpartum periods, including early pregnancy, in the female llama. Estrone sulfate (E(1)S) and pregnanediol glucuronide (PdG) concentrations were determined by enzyme immunoassay with values corrected for variations in urine concentration by creatinine. Estrone sulfate concentrations, elevated during the last 20 days of gestation through 12 hours before parturition, were declining at the time of delivery. Pregnanediol glucuronide concentrations followed a pattern similar to that of estrone sulfate except that values began to decrease 5 days before parturition. Values for both E(1)S and PdG were basal by 24 hours after delivery. The first significant elevation of estrone sulfate, indicative of initial follicle development, was observed 5 days after parturition. Pregnanediol glucuronide concentrations were low during the postpartum period until 4 to 5 days after breeding. The PdG values rose steadily following copulatory-induced ovulation, which was initiated at about 2 weeks postpartum; values continued to increase through the first 15 days of pregnancy.     

不同时期肠杆菌科细菌产ESBLS及耐药性的监测

目的对不同时期肠杆菌科细菌产超广谱β-内酰胺酶（ESBLS）及耐药性进行监测。方法采用生物梅里埃ATB药敏试验板测定肠杆菌科细菌中大肠埃希菌和肺炎克雷伯菌对抗生素的敏感性,同时用表型确证法检测ESBLS。结果肠杆菌科细菌2006-2008年与2009-2011年两个时期相比,ESBLS的检出率增长近50%。对亚胺配南、头孢吡肟、头孢西丁耐药率较低,对哌拉西林/他唑巴坦、阿米卡星的耐药率次之,对其他β-内酰胺类、氨基糖苷类、喹诺酮类及磺胺类抗生素的耐药率较高,且两个时期相比耐药率增加明显,差异具有统计学意义（P〈0.05）。结论临床产ESBLS菌株不断增多,多重耐药现象越来越严重,临床实验室应当把ESBLS的检测作为常规监测工作,有效指导临床选用抗菌药物。     

The effect of constant darkness and short light periods on the survival and physiological fitness of two phytoplankton species and their growth potential after re-illumination

We tested the survival potential and fitness of two different algae strains (the diatom Thalassiosira weissflogii and the cryptophyceae Rhodomonas sp.) under different growth conditions (complete darkness and short light intervals, simulating conditions in a deep mixed water column) at different temperatures, plus the effect of these conditions on the physiological fitness and growth after re-illumination was examined. Both species survived the experimental conditions without significant cell loss or physiological damage. Two different survival strategies were observed: (1) the diatom T. weissflogii immediately reduced its metabolic rate and stopped cell division. The effect on chlorophyll a (chl-a) content and photosynthetic capacity was negligible. At 10 °C, T. weissflogii used the short light windows to metabolize carbohydrates and growth. (2) The cryptophyte Rhodomonas sp. initially continued to grow after transfer into all trials. However, the cell number decreased after day 6. Carbohydrate and chl-a content went on to decrease dramatically (70 and 50%, respectively). After 3 days of re-illumination, T. weissflogii grew faster than of Rhodomonas sp.. The diatom seemed to benefit from better start conditions and would out-compete the cryptophyte during a spring bloom. Our results highlight that these algae groups have different strategies in dealing with darkness, which potentially endow diatoms with a competitive advantage in deep mixed waters and in the season of early spring.     

Direct quantification of in vitro cell growth through image analysis

Summary Objective, accurate, non-intrusive measurement of in vitro cell growth was realized through microcomputerized video image analysis. Recently-released video and digitizing hardware and software were incorporated into an analytical system which accurately quantified visual differences between cultures on a cell number or fresh mass basis. Sequential measurements during culture incubation further detected and quantified subtle changes in colony area and density resulting from growth. Each measurement was acquired rapidly, without encroaching on the in vitro environment, so cell growth was undisturbed. Custom software routines coordinated the quantification of this detailed record into precise cumulative growth curves.     

Quantitation of in vitro ciliated cell growth through image analysis

Summary Ciliated cell cultures can be produced in outgrowths from explants of human respiratory epithelium. An image analysis technique was develope to quantify the percentage of active ciliated cells present in these cultures. The subtraction 2 by 2 of five successive video images of the cultures, followed by the addition of the resulting images, allowed the determinaton of the culture surface covered by ciliated cells. The percentage of this surface varied according to the regions of the explant (27.7% in the outgrowth near the explant and 4.1% at the periphery of the outgrowth). High variations were observed within the same region of an outgrowth, as well as from one outgrowth to another. However, maximal differentiation was observed after 4 d of culture. The quantitation techniques described in the present work might be useful for studying in vitro the respiratory epithelial injury and the subsequent repair processes. This work was supported by CEB-INSERM and SYNTHELABO-INSERM grants.     

Transformed cells have lost control of ribosome number through their growth cycle.

Previous studies on the synthesis and function of the protein synthetic machinery through the growth cycle of normal cultured hamster embryo fibroblasts (HA) were extended here to a series of four different clonal lines of polyoma virus-transformed HA cells. Under our culture conditions, these transformed cells could enter a stationary phase characterized by no mitotic cells, very low rates of DNA synthesis, and arrest in a post-mitotic pre-DNA synthetic state. Cellular viability was initially high in stationary phase but, unlike normal cells, transformed cells slowly lost viability. The rate of protein synthesis in the stationary phase of the transformed cells fell to 25-30% of the exponential rate. Though this reduction was similar to that seen in normal cells, it was accomplished by different means. The specific reduction in the ribosome complement per cell to values below that of any cycling cell seen in normal cells, was not seen in any of the transformed lines. This observation, which implies a loss of normal control of ribisome synthesis through the growth cycle after transformation, was confirmed in normal Chinese hamster embryo fibroblasts and transformed CHO cell lines. Normal control of ribosome synthesis was restored in L-73 and LR-73, growth control revertants of one of the transformed CHO lines. The transformed lines reduced their protein synthetic rates in stationary phase either by a greater reduction in the proportion of functioning ribosomes than that seen in normal cells or by a decrease in the elongation rate of functioning ribosomes; the latter effect was not seen in the normal cells. A model for growth control of normal cells and its derangement in transformed cells is presented.