Automatic reconstruction of molecular and genetic networks from discrete time series data

We apply a mathematical algorithm which processes discrete time series data to generate a complete list of Petri net structures containing the minimal number of nodes required to reproduce the data set. The completeness of the list as guaranteed by a mathematical proof allows to define a minimal set of experiments required to discriminate between alternative network structures. This in principle allows to prove all possible minimal network structures by disproving all alternative candidate structures. The dynamic behaviour of the networks in terms of a switching rule for the transitions of the Petri net is part of the result. In addition to network reconstruction, the algorithm can be used to determine how many yet undetected components at least must be involved in a certain process. The algorithm also reveals all alternative structural modifications of a network that are required to generate a predefined behaviour.     

Automatic image segmentation of nuclear stained breast tissue sections using color active contour model and an improved watershed method

Automatic image segmentation of immunohistologically stained breast tissue sections helps pathologists to discover the cancer disease earlier. The detection of the real number of cancer nuclei in the image is a very tedious and time consuming task. Segmentation of cancer nuclei, especially touching nuclei, presents many difficulties to separate them by traditional segmentation algorithms. This paper presents a new automatic scheme to perform both classification of breast stained nuclei and segmentation of touching nuclei in order to get the total number of cancer nuclei in each class. Firstly, a modified geometric active contour model is used for multiple contour detection of positive and negative nuclear staining in the microscopic image. Secondly, a touching nuclei method based on watershed algorithm and concave vertex graph is proposed to perform accurate quantification of the different stains. Finally, benign nuclei are identified by their morphological features and they are removed automatically from the segmented image for positive cancer nuclei assessment. The proposed classification and segmentation schemes are tested on two datasets of breast cancer cell images containing different level of malignancy. The experimental results show the superiority of the proposed methods when compared with other existing classification and segmentation methods. On the complete image database, the segmentation accuracy in term of cancer nuclei number is over than 97%, reaching an improvement of 3–4% over earlier methods.     

Hopf bifurcation in the presomitic mesoderm during the mouse segmentation

Vertebrae and ribs arise from embryonic tissues called somites. Somites arise sequentially from the unsegmented embryo tail, called presomitic mesoderm (PSM). The pace of somite formation is controlled by gene products such as hairy and enhancer of split 7 (Hes7) whose expression oscillates in the PSM. In addition to the cyclic genes, there is a gradient of fibroblast growth factor 8 (Fgf8) mRNA from posterior to anterior PSM. Recent experiments have shown that in the absence of Fgf signaling, Hes7 oscillations in the anterior and posterior PSM are lost. On the other hand, Notch mutants reduce the amplitude of posterior Hes7 oscillations and abolish anterior Hes7 oscillations. To understand these phenotypes, we delineated and simulated a logical and a delay differential equation (DDE) model with similar network topology in wild-type and mutant situations. Both models reproduced most wild-type and mutant phenotypes suggesting that the chosen topology is robust to explain these phenotypes. Numerical continuation of the model showed that even in the wild-type situation, the system changed from sustained to damped, i.e. a Hopf bifurcation occurred, when the Fgf concentration decreased in the PSM. This numerical continuation analysis further indicated that the most sensitive parameters for the oscillations are the parameters of Hes7 followed by those of Lunatic fringe (Lfng) and Notch1. In the wild-type, the damping of Hes7 oscillations was not so strong so that cells reached the new somites before they lose Hes7 oscillations. By contrast, in the fibroblast growth factor receptor 1 (Fgfr1) conditional knock-out (cKO) mutant simulation, Notch signaling was not able to maintain sustained Hes7 oscillations. Our analysis suggests that Fgf signaling makes cells enter an oscillatory state of Hes7 expression. After moving to the anterior PSM, where Fgf signaling is missing, Notch signaling compensates the damping of Hes7 oscillations in the anterior PSM.     

Chemical mutagenesis of the mouse genome: an overview

The careful comparison of the phenotypic variations generated by different alleles at a given locus, including of course, those alleles with a deleterious effect, is often an important source of information for the understanding of gene functions. In fact, every time it is possible to match a specific alteration observed at the genomic level with a particular pathology, it is possible to establish a relationship between a gene and its function. When considered from this point of view, the production of new mutations by experimental mutagenesis appears as an alternative to the strategy of in vitro gene invalidation by homologous recombination in embryonic stem (ES) cells, with the advantage that experimental mutagenesis does not require any previous knowledge of the gene structure at the molecular level. Homologous recombination in ES cells is a gene driven approach, in which mutant alleles are produced for those genes that we already know. Experimental mutagenesis, on the contrary, is a phenotype driven approach, in which unknown genes are identified based on phenotypic changes. Also, while homologous recombination in ES cells requires a rather sophisticated technology, mutagenesis is simple to achieve but relies greatly on the efficiency of the mutagenic treatment as well as on the use of an accurate protocol for phenotyping. In this review, we will address a few comments about the different techniques that can be used for the induction of point mutations in the mouse germ line with special emphasis on chemical mutagenesis. We will also discuss the limitations of experimental mutagenesis and the necessity to look for alternative ways for the discovery of new genes and gene functions in the mouse.     

Morphological evidence for a direct innervation of the mouse vomeronasal glands

Summary The morphological evidence for a direct autonomic innervation of the mouse vomeronasal glands is presented. Axonal varicosities containing a few densecore vesicles and numerous clear vesicles (36–60 nm in diameter) make synaptic contacts with the secretory cells at the base of the glandular acini. The axonal presynaptic membrane is associated with a distinct dense material and it is separated from the secretory cell by a synaptic cleft of about 12–14 nm. At the postsynaptical level, coated vesicles can be found. Additional postsynaptical specializations have not been observed.     

Ultrastructural evidence for the presence of actin filaments in mouse eggs at fertilization

Summary Mouse eggs at fertilization were permeated with glycerol solutions and then reacted with heavy meromyosin to show actin filaments by electron microscopy. The meiotic area of the egg surface is devoid of microvilli and is supported by a thick layer (0.6–0.8 m in width) of submembranous filaments. A much thinner layer (less than 0.3 m) is present in the remaining non-meiotic microvillous area and underlying its membrane is a very thick layer of cross-filaments and filament bundles.     

合成未来：从大肠杆菌的重构看合成生物学的发展

合成生物学（synthetic biology）是伴随着基因工程、系统生物学以及生物信息学的发展而出现的一个新的交叉学科。大肠杆菌（Escherichia coli）作为一种宿主在合成生物学的发展中功不可没。从某种意义上讲,合成生物学的每一次进展都离不开大肠杆菌。从大肠杆菌的角度出发,对合成生物学的发展进行深入分析,并提出了合成生物学在中圉发展的重点。     

Elementary network reconstruction: A framework for the analysis of regulatory networks in biological systems

Complexity of regulatory networks arises from the high degree of interaction between network components such as DNA, RNA, proteins, and metabolites. We have developed a modeling tool, elementary network reconstruction (ENR), to characterize these networks. ENR is a knowledge-driven, steady state, deterministic, quantitative modeling approach based on linear perturbation theory. In ENR we demonstrate a novel means of expressing control mechanisms by way of dimensionless steady state gains relating input and output variables, which are purely in terms of species abundances (extensive variables). As a result of systematic enumeration of network species in n×n matrix, the two properties of linear perturbation are manifested in graphical representations: transitive property is evident in a special L-shape structure, and additive property is evident in multiple L-shape structures arriving at the same matrix cell. Upon imposing mechanistic (lowest-level) gains, network self-assembly through transitive and additive properties results in elucidation of inherent topology and explicit cataloging of higher level gains, which in turn can be used to predict perturbation results. Application of ENR to the regulatory network behind carbon catabolite repression in Escherichia coli is presented. Through incorporation of known molecular mechanisms governing transient and permanent repressions, the ENR model correctly predicts several key features of this regulatory network, including a 50% downshift in intracellular cAMP level upon exposure to glucose. Since functional genomics studies are mainly concerned with redistribution of species abundances in perturbed systems, ENR could be exploited in the system-level analysis of biological systems.     

Subcellular vesicular aggregations of GABA<Subscript>B</Subscript> R1a and R1b receptors increase with age in neurons of the developing mouse brain

GABA_B receptors play a critical neuromodulatory role in the central nervous system. It has been suggested that both the functional role and the cellular distribution of GABA_B receptors in the neuronal network change during post-natal maturation. In the present study, the cellular and subcellular distribution patterns of the GABA_B R1a/b receptors have been analysed in different brain regions of the mouse using immunocytochemistry with isoform-specific antisera. GABA_B R1-immunoreactivity (IR) was present from the first post-natal day (P0) on in most regions of the brain. Neurones exhibited diffuse GABA_B R1-IR labelling throughout somata and larger proximal dendrites as well as some fine neuronal processes. After P5, distinct punctuated staining was apparent. The number of such GABA_B IR granules per cell increased with age in a sigmoidal manner from P5 to P60. Electron microscopy revealed GABA_B IR as clusters of small clear vesicles of 30–50 nm diameter within the cytoplasm and close to the cell membrane at extrasynaptic locations, as well as at pre-synaptic and post-synaptic specialisations. The increase in GABA_B R1-IR punctuate staining during brain maturation points to increasing functional participation and heterogeneity of GABA_B receptors as the complexity of the central nervous system expands with growth and development.The first three authors contributed equally to the study. S.W.S. and W.Z. are co-senior authors.This project was supported by the Deutsche Forschungsgemeinschaft (CMPB to WZ).     

In vivo evidence of role of bone morphogenetic protein-4 in the mouse ovary

The transition of a primordial follicle to a primary follicle is an early step in folliculogenesis. All female mammals are born with a fixed stock of primordial follicles, and exhaustion of that stock leads to menopause or infertility. Recently, several in vitro studies have indicated that BMP-4, BMP-7, and several other growth factors affect the transition of primordial to primary follicles. The aim of our present study was to investigate role of BMP-4 in this process using passive immunization to investigate the role of BMP-4 in a prepubertal mouse model. After seven days of treatment, the weight of antiBMP-4 treated ovaries was significantly lower than the ovaries from mice treated with nonimmune Ig. The number of primary follicles was lower, and the numbers of primordial follicles were higher in antiBMP-4 treated ovaries compared to control ovaries. Treatment with equine chorionic gonadotrophin (eCG) showed no influence on the effects of antiBMP-4 in the mouse ovary. Thus, the results of our study indicate that in vivo BMP-4 acts as transition factor in transition of primordial to primary follicle.     

The integrated development of network complexity modulates the diverse evolutionary mutation rates of individual proteins

The rate of evolution-related mutation varies widely among proteins while the unity of the organism implies an integrated evolution of its protein network. Focusing on the yeast interactome, we monitored the structural impact of amino acid substitution on yeast proteins with reported structure. The impact of mutation in creating or deleting structural markers for interactivity varies across proteins and modulates the evolutionary rates, yielding a unified kinetic law of accumulation of connectivities consistent with an integrated evolution of the interactome.     

网络教学在研究生细胞培养实验中的应用

细胞培养技术是研究生开展科研工作的基础技术。充分利用网络教学的优势,以丰富的知识体系,多样的授课形式、生动形象的表现手段,有助于学生创造性理解和掌握,同时教师自身素质也得到相应的提高,达到教学相长的目的。     

Immunocytochemical evidence of a met-enkephalin-like substance in the dense-core granules of mouse Merkel cells

Summary The electron-microscopic immunogold method was applied to Merkel cells of adult mice to demonstrate the subcellular localization of met-enkephalin-like immunoreactivity. Post-embedding incubation with metenkephalin antisera showed that the gold particles were associated with the dense-core granules of the Merkel cells. The majority, but not all, of the dense-core granules were strongly labelled. Osmication caused a significant reduction in the number of gold particles on these granules. The nerve terminal associated with the Merkel cell did not show met-enkephalin-like immunoreactivity. To the best of our knowledge, this is the first report of the ultrastructural localization of a positive met-enkephalin immunoreactivity in the dense-core granules of Merkel cells in mice.     

不同浓度卵蛋白变应原对小鼠哮喘模型建立的影响

目的研究不同浓度卵蛋白(ovalbumin,OVA)变应原对小鼠的哮喘造模影响。方法 96只6～8周龄SPF级雌性BALB/c小鼠随机分为8组,分别为PBS组(对照组)、10μg组(A组)、20μg组(B组)、50μg组(C组)、100μg组(D组)、200μg组(E组)、500μg组(F组)、1000μg组(G组)。A～G组分别用含1%明矾的PBS配制相应浓度的OVA于第0、7和第14天对小鼠进行腹腔注射。于第21～27天连续7 d用含1%的OVA的PBS溶液雾化吸入激发各组小鼠。正常对照组使用PBS溶液致敏和激发。最后一次雾化吸入激发后24 h内,计数各组小鼠支气管肺泡灌洗液(BLAF)中嗜酸性粒细胞的含量,ELISA法检测IL-4、IL-5的分泌量及其血清IgG2a、IgE抗体的水平;肺组织病理切片观察各组小鼠哮喘模型的效果,评价最优哮喘造模的OVA浓度。结果 A～G组小鼠肺泡灌洗液中IL-4、IL-5含量均高于正常对照组(P<0.01),细胞因子水平随着OVA浓度的增高而逐渐下降;A～G组小鼠肺泡灌洗液中嗜酸性粒细胞数均高于正常对照组(P<0.01),从低浓度组至高浓度组嗜酸性粒细胞数从高向低变化;A～G组小鼠血清中总抗体IgE的水平均显著高于正常对照组(P<0.01),且随着OVA浓度的增高IgE水平逐渐下降。血清中IgG2a的水平则随OVA给药浓度的增高而逐渐增高;低浓度OVA致敏组小鼠肺组织标本可观察到明显的炎症浸润性病理表现,而高浓度组肺部组织病理变化不明显。结论低浓度的OVA连续致敏小鼠造成过敏性哮喘病理改变较为明显,随着OVA浓度的增高,造模效果逐渐降低,而高浓度的OVA则会导致模型小鼠发生免疫耐受。     

Properties of polar and apolar cells from the 16-cell mouse morula

Summary The surface properties of newly formed, isolated 1/16 mouse blastomeres have been analyzed over the 10–12 h period prior to their division to 2/32 cells. Two populations of cells are formed at the 8- to 16-cell transition and their surface phenotypes vary with their relative position within the morula. Outer cells are polar, relatively non-adhesive and relatively large; inner cells are apolar, adhesive and smaller. The surface phenotypes of both inner and outer 1/16 cells are stable during culture for 11 h in isolation. However, the surface phenotypes can be induced to change by culture in combination with a second 1/16 cell, in a manner that is dependent upon the identity of the second cell. Two aggregated polar cells never flatten completely against each other, and both cells retain a clearly defined polar phenotype for 11–12 h. In aggregates of two apolar cells, cell outlines are lost as a result of intercellular flattening and microvilli are displaced away from areas of cell contact. However, if the two apolar cells are subsequently separated an even distribution of microvilli is restored. In most aggregates of an apolar and a polar cell, the polar cell envelops the apolar cell completely. These results are discussed in the context of the normal fate and potential of each cell type within the morula.     

Characterization of isolated villus and crypt cells from the small intestine of the adult mouse

Summary Suspensions of sequentially isolated villus and crypt cells were obtained in order to study certain biochemical changes associated with differentiation of epithelial cells in the small intestine of the mouse. Microscopic observation of the various cell fractions reveals that the epithelial cells detach as individual cells or small sheets of epithelium from the tip to the base of the villus, whereas cells in the crypt regions are separated as entire crypt units. The isolated cells retain their ultrastructural integrity as judged by electron microscopy. Chemical characterization of the various fractions shows that the total cellular protein content, expressed in activity per cell, remains relatively constant throughout the villus region followed by a noticeable drop in the crypt zone. On the other hand, sharp variations in values of cell DNA content are observed in the crypt zone depending on the reference of activity being used. Activity profiles of several brush border enzymes confirm the biochemical changes that occur during the migration of cells from the crypt to the villus tip, as observed in other species, with maximum activity of sucrase in the mid-villus region, of glucoamylase, trehalase, lactase and maltase in the upper third region, and of alkaline phosphatase at the villus tip. Forty-eight-hour suspension cultures of cell fractions corresponding to cells at the base of the villus and crypt zones show a moderate decrease in protein and enzyme activities to approximately 70% of their original value, with DNA content remaining stable throughout the incubation period. The use of biochemical activities as indicators of cellular integrity during cell culture is discussed.Supported by a research grant from the Medical Research Council of Canada (J.H.)     

Regulation of mouse hepatic ATP-citrate lyase activity by dietary fat evidence for the presence of inactive enzyme

The induction of ATP-citrate lyase activity in mouse liver by dietary carbohydrate (glucose) is markedly reduced by including in the diet a source of polyunsaturated fatty acids. Within 72 h after changing from a standard mouse chow diet to a high carbohydrate diet containing 15% (w/w) of hydrogenated cottonseed oil (as a source of saturated fatty acids), the activity of mouse liver ATP-citrate lyase per milligram cytosolic protein was approx. 3-fold higher than that from mice fed a similar diet containing 15% (w/w) of corn oil. The rate of synthesis of ATP-citrate lyase relative to that for total protein and the rate of degradation of the enzyme were similar for both dietary groups. Elevated levels of enzyme activity in the hydrogenated cottonseed oil-fed livers were not accompanied by a similar increase in the amount of enzyme protein. To explain such findings, we propose that the activity of hepatic ATP-citrate lyase is regulated by dietary polyunsaturated fatty acids through a mechanism involving the conversion of a catalytically active form of the enzyme to a catalytically inactive form. A reversal of this conversion (inactive-active)_is evident within 72 h of removing the mice from the corn oil diet and placing them on the hydrogenated cottonseed oil diet. Futhermore, the conversion appears to be independent of the in vivo rate of synthesis of the enzyme.