Symmetry and Asymmetry Models for Rectangular Tables

The models of complete, quasi and conditional symmetry as well as marginal homogeneity and diagonal asymmetry, applicable to square contingency tables are extended to non-square ones. Several properties of the models are investigated and estimation and test theory is presented. The utility of the new proposed models is discussed and illustrated by reanalyzing classical data sets.     

TrkB/BDNF signaling regulates photoreceptor progenitor cell fate decisions

Neurotrophins, via activation of Trk receptor tyrosine kinases, serve as mitogens, survival factors and regulators of arborization during retinal development. Brain-derived neurotrophic factor (BDNF) and TrkB regulate neuronal arborization and survival in late retinal development. However, TrkB is expressed during early retinal development where its functions are unclear. To assess TrkB/BDNF actions in the early chick retina, replication-incompetent retroviruses were utilized to over-express a dominant negative truncated form of TrkB (trunc TrkB), or BDNF and effects were assessed at E15. Clones expressing trunc TrkB were smaller than controls, and proliferation and apoptosis assays suggest that decreased clone size correlated with increased cell death when BDNF/TrkB signaling was impaired. Analysis of clonal composition revealed that trunc TrkB over-expression decreased photoreceptor numbers (41%) and increased cell numbers in the middle third of the inner nuclear layer (INL) (23%). Conversely, BDNF over-expression increased photoreceptor numbers (25%) and decreased INL numbers (17%). Photoreceptors over-expressing trunc TrkB demonstrated no increase in apoptosis nor abnormalities in lamination suggesting that TrkB activation is not required for photoreceptor cell survival or migration. These studies suggest that TrkB signaling regulates commitment to and/or differentiation of photoreceptor cells from retinal progenitor cells, identifying a novel role for TrkB/BDNF in regulating cell fate decisions.     

Effects of dispersal in a tri-trophic metapopulation model

The aim of this paper is to understand how dispersal in a patchy environment influences the stability properties of tri-trophic metapopulations. Differential equation models for tri-trophic metapopulations are formulated and analysed. The patchy nature of the metapopulations is incorporated through dispersal phases. Two variants are studied: one with a dispersal phase for the top and one with a dispersal phase for the middle level. A complete characterisation of stable and unstable equilibria is given and the possibility of invasion in these food chains is studied. A dispersal phase for the middle level can destabilize the bottom level-middle level interaction, because of the delay that dispersal causes in the reaction to the resource. When the middle level is not efficiently controlled by the top level, the unstable bottom level-middle level pair can destabilize the entire food chain. Dispersal for the top level can destabilize in the same way. A characterisation of the long term behaviour of the models is given. Bistability with a stable three species equilibrium and a stable limit cycle is one of the possibilities.     

Year-class coexistence in biennial plants

I extend the well known and biologically well motivated Skellam model of plant population dynamics to biennial plants. The model has two attractors: either one year class competitively excludes the other, resulting in 2-cycles with only vegetative vs only flowering plants in alternating years, or the two year classes coexist at an interior equilibrium. Contrary to earlier models, these two attractors can exist also simultaneously. I investigate the robustness of the model by including delayed flowering, a common phenomenon in plants, and provide a full numerical bifurcation analysis of the generalized model. High fecundity implies strong competition within year classes and promotes coexistence, whereas high survival results in strong competition between year classes and promotes competitive exclusion. Delayed flowering tends to stabilize the interior equilibrium, but (unlike in density-independent matrix models) the population cycles are robust with respect to some delay in flowering.     

Balance between noise and adaptation in competition models of perceptual bistability

Perceptual bistability occurs when a physical stimulus gives rise to two distinct interpretations that alternate irregularly. Noise and adaptation processes are two possible mechanisms for switching in neuronal competition models that describe the alternating behaviors. Either of these processes, if strong enough, could alone cause the alternations in dominance. We examined their relative role in producing alternations by studying models where by smoothly varying the parameters, one can change the rhythmogenesis mechanism from being adaptation-driven to noise-driven. In consideration of the experimental constraints on the statistics of the alternations (mean and shape of the dominance duration distribution and correlations between successive durations) we ask whether we can rule out one of the mechanisms. We conclude that in order to comply with the observed mean of the dominance durations and their coefficient of variation, the models must operate within a balance between the noise and adaptation strength—both mechanisms are involved in producing alternations, in such a way that the system operates near the boundary between being adaptation-driven and noise-driven.     

Neural fate decisions mediated by combinatorial regulation of Hes1 and miR-9

In the nervous system, Hes1 shows an oscillatory manner in neural progenitors but a persistent one in neurons. Many models involving Hes1 have been provided for the study of neural differentiation but few of them take the role of microRNA into account. It is known that a microRNA, miR-9, plays crucial roles in modulating Hes1 oscillations. However, the roles of miR-9 in controlling Hes1 oscillations and inducing transition between different cell fates still need to be further explored. Here we provide a mathematical model to show the interaction between miR-9 and Hes1, with the aim of understanding how the Hes1 oscillations are produced, how they are controlled, and further, how they are terminated. Based on the experimental findings, the model demonstrates the essential roles of Hes1 and miR-9 in regulating the dynamics of the system. In particular, the model suggests that the balance between miR-9 and Hes1 plays important roles in the choice between progenitor maintenance and neural differentiation. In addition, the synergistic (or antagonistic) effects of several important regulations are investigated so as to elucidate the effects of combinatorial regulation in neural decision-making. Our model provides a qualitative mechanism for understanding the process in neural fate decisions regulated by Hes1 and miR-9.     

The use of gene function to identify the rate-limiting steps controlling cell fate

The size and complexity of the genomes of mammals in general, and humans in particular, is such that it will take many years to utilise this information to produce a genuine understanding of the control of cell behaviour. Since there are tens of thousands of genes to consider, the task of identifying those which play the most significant roles, biologically and medically, is both crucial and very demanding. Here we emphasise the importance of functional approaches to answering this question, i.e. the application of techniques which use the function of the gene itself in identifying the critical rate-limiting steps in biological processes. In this review, we use the functional analysis of one of the most important of these processes, the control of survival and apoptosis, to illustrate the power of a number of functional genomic strategies.This work was presented at the first Cancer Immunology and Immunotherapy Summer School, 8–13 September 2003, Ionian Village, Bartholomeio, Peloponnese, Greece.     

Neural crest and placode interaction during the development of the cranial sensory system

In the vertebrate head, the peripheral components of the sensory nervous system are derived from two embryonic cell populations, the neural crest and cranial sensory placodes. Both arise in close proximity to each other at the border of the neural plate: neural crest precursors abut the future central nervous system, while placodes originate in a common preplacodal region slightly more lateral. During head morphogenesis, complex events organise these precursors into functional sensory structures, raising the question of how their development is coordinated. Here we review the evidence that neural crest and placode cells remain in close proximity throughout their development and interact repeatedly in a reciprocal manner. We also review recent controversies about the relative contribution of the neural crest and placodes to the otic and olfactory systems. We propose that a sequence of mutual interactions between the neural crest and placodes drives the coordinated morphogenesis that generates functional sensory systems within the head.     

Bilateral asymmetry in bone measurements of the hand and lateral hand dominance

Two hundred thirty–five (235) normal male participants of the Baltimore Longitudinal Study were classified as right handed, left handed, and ambidextrous on the basis of their grip–strength performance. Their left and right hands were also radiographed and the measurements of the second metacarpal bones were evaluated on the basis of hand dominance. The results indicated that, as a rule, the right hand measurements are higher than those of the left hand, regardless of hand dominance. The bilateral differences in total width, length, total area and cortical area are significant among the right hand dominant and nonsignificant among the left hand dominant. Regardless off hand dominance the bilateral differences in medullary width are nonsignificant. These results suggest an inherent tendency of the right second metacarpal to have more bone than the left regardless of hand dominance. Differential stress due to hand dominance will increase the bilateral difference in the right handed and reduce it in the left handed.     

Delayed transition to new cell fates during cellular reprogramming

In many embryos specification toward one cell fate can be diverted to a different cell fate through a reprogramming process. Understanding how that process works will reveal insights into the developmental regulatory logic that emerged from evolution. In the sea urchin embryo, cells at gastrulation were found to reprogram and replace missing cell types after surgical dissections of the embryo. Non-skeletogenic mesoderm (NSM) cells reprogrammed to replace missing skeletogenic mesoderm cells and animal caps reprogrammed to replace all endomesoderm. In both cases evidence of reprogramming onset was first observed at the early gastrula stage, even if the cells to be replaced were removed earlier in development. Once started however, the reprogramming occurred with compressed gene expression dynamics. The NSM did not require early contact with the skeletogenic cells to reprogram, but the animal cap cells gained the ability to reprogram early in gastrulation only after extended contact with the vegetal halves prior to that time. If the entire vegetal half was removed at early gastrula, the animal caps reprogrammed and replaced the vegetal half endomesoderm. If the animal caps carried morpholinos to either hox11/13b or foxA (endomesoderm specification genes), the isolated animal caps failed to reprogram. Together these data reveal that the emergence of a reprogramming capability occurs at early gastrulation in the sea urchin embryo and requires activation of early specification components of the target tissues.     

细胞命运抉择的数学模型:活性氧与p53的关系及其意义(英文)

生物体内的细胞生活在复杂的环境中。在生物体内,活性氧是普遍存在的。生物体内的活性氧可以诱导DNA损伤,最终破坏基因组稳定性。其中,对基因组损伤最严重的是DNA双链断裂损伤。肿瘤抑制因子p53是细胞内介导DNA损伤反应的重要因子。p53可以修复损伤DNA,保护轻度受损细胞。而当细胞受到严重损伤时,p53能够诱发细胞凋亡,从而维持机体稳态。p53的动力学对于细胞的反应性具有重要影响,然而对这方面却缺少系统的认识。因此在本文中,我们主要关注运用数学模型方法研究p53脉冲的动力学性质,从而揭示细胞内潜在的生死选择机制。     

Transformation of peripheral inputs by the first-order lateral line brainstem nucleus

Extracellular recording techniques were used to record the responses of medial nucleus cells and posterior lateral line nerve fibers in mottled sculpin, Cottus bairdi, and goldfish, Carassius auratus, to a 50-Hz dipole source (vibrating sphere). Responses were characterized in terms of (1) receptive fields that relate responsiveness (spike rate and phase-locking) to the location of the source along the length of the fish, (2) input-output functions that relate responsiveness to vibration amplitude for a fixed source location, and (3) peri-stimulus time histograms that relate responsiveness to time during a sustained period of vibration. Relative to posterior lateral line nerve fibers, medial nucleus cells in both species were similar in showing (1) lower spontaneous and evoked rates of spike activity, (2) greater degrees of adaptation, (3) greater heterogeneity in all response characteristics, and (4) evidence for inhibitory/excitatory interactions. Whereas receptive fields of nerve fibers in both species faithfully reflect both pressure gradient amplitudes (with rate changes) and directions (with phase-angle changes) in the stimulus field, receptive fields of medial nucleus were more difficult to relate to the stimulus field. Some, but not all, receptive fields could be modeled with excitatory center/inhibitory surround and inhibitory center/excitatory surround organizations. Accepted: 26 November 1997     

CAMBIUM, a process-based model of daily xylem development in Eucalyptus

In hardwoods such as Eucalyptus spp., xylem (wood) is a heterogeneous tissue consisting of multiple cell types. As such, xylem development involves multiple complex interactions. To describe and understand xylem development, and ultimately predict the resultant wood properties, a process-based approach to modelling wood property variation is potentially very useful. In this paper, a new model (CAMBIUM), which incorporates concepts of these processes, is described. CAMBIUM predicts how wood density and fibre and vessel anatomical properties vary from pith-to-bark at a daily time step as a function of changing environmental conditions and a set of simulated physiological processes. Simulations from an existing process-based model of stand development (CABALA) are used as inputs. A key feature of CAMBIUM is a model of the interaction between different xylem cell types. Some weaknesses were identified in the ability of the model to simulate vessel spatial patterns and frequencies, emphasizing the complexities inherent in this aspect of angiosperm wood formation. The model was, however, able to provide realistic estimates of short-term variation and temporal ranges in eucalypt fibre diameter and secondary wall development and wood density.     

EGF–FGF2 stimulates the proliferation and improves the neuronal commitment of mouse epidermal neural crest stem cells (EPI-NCSCs)

Epidermal neural crest stem cells (EPI-NCSCs), which reside in the bulge of hair follicles, are attractive candidates for several applications in cell therapy, drug screening and tissue engineering. As suggested remnants of the embryonic neural crest (NC) in an adult location, EPI-NCSCs are able to generate a wide variety of cell types and are readily accessible by a minimally invasive procedure. Since the combination of epidermal growth factor (EGF) and fibroblast growth factor type 2 (FGF₂) is mitogenic and promotes the neuronal commitment of various stem cell populations, we examined its effects in the proliferation and neuronal potential of mouse EPI-NCSCs. By using a recognized culture protocol of bulge whiskers follicles, we were able to isolate a population of EPI-NCSCs, characterized by the migratory potential, cell morphology and expression of phenotypic markers of NC cells. EPI-NCSCs expressed neuronal, glial and smooth muscle markers and exhibited the NC-like fibroblastic morphology. The treatment with the combination EGF and FGF₂, however, increased their proliferation rate and promoted the acquisition of a neuronal-like morphology accompanied by reorganization of neural cytoskeletal proteins βIII-tubulin and nestin, as well as upregulation of the pan neuronal marker βIII-tubulin and down regulation of the undifferentiated NC, glial and smooth muscle cell markers. Moreover, the treatment enhanced the response of EPI-NCSCs to neurogenic stimulation, as evidenced by induction of GAP43, and increased expression of Mash-1 in neuron-like cell, both neuronal-specific proteins. Together, the results suggest that the combination of EGF–FGF2 stimulates the proliferation and improves the neuronal potential of EPI-NCSCs similarly to embryonic NC cells, ES cells and neural progenitor/stem cells of the central nervous system and highlights the advantage of using EGF–FGF₂ in neuronal differentiation protocols.