Quantitative Analysis of Cell Nucleus Organisation

There are almost 1,300 entries for higher eukaryotes in the Nuclear Protein Database. The proteins' subcellular distribution patterns within interphase nuclei can be complex, ranging from diffuse to punctate or microspeckled, yet they all work together in a coordinated and controlled manner within the three-dimensional confines of the nuclear volume. In this review we describe recent advances in the use of quantitative methods to understand nuclear spatial organisation and discuss some of the practical applications resulting from this work

Quantification of the morphological characteristics of hESC colonies

The maintenance of the undifferentiated state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the displayed morphological features, such as prominent/abundant nucleoli and a colony with a tightly packed appearance and a well-defined edge. Using image analysis and computational tools, we precisely quantify these properties using phase-contrast images of hESC colonies of different sizes (0.1–1.1 mm2) during days 2, 3 and 4 after plating. Our analyses reveal noticeable differences in their structure influenced directly by the colony area A. Large colonies (A > 0.6 mm2) have cells with smaller nuclei and a short intercellular distance when compared with small colonies (A  0.6 mm2) due to the proliferation of the cells in the bulk. This increases the colony density and the number of nearest neighbours. We also detect the self-organisation of cells in the colonies where newly divided (smallest) cells cluster together in patches, separated from larger cells at the final stages of the cell cycle. This might influence directly cell-to-cell interactions and the community effects within the colonies since the segregation induced by size differences allows the interchange of neighbours as the cells proliferate and the colony grows. Our findings are relevant to efforts to determine the quality of hESC colonies and establish colony characteristics database

Quantification of the morphological characteristics of hESC colonies

The maintenance of the pluripotent state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the displayed morphological features, such as prominent/abundant nucleoli and a colony with a tightly packed appearance and a well-defined edge. Using image analysis and computational tools, we precisely quantify these properties using phase-contrast images of hESC colonies of different sizes (0.1 -- 1.1$\, \text{mm}^2$) during days 2, 3 and 4 after plating. Our analyses reveal noticeable differences in their structure influenced directly by the colony area $A$. Large colonies ($A > 0.6 \, \text{mm}^2$) have cells with smaller nuclei and a short intercellular distance when compared with small colonies ($A < 0.2 \, \text{mm}^2$). The gaps between the cells, which are present in small and medium sized colonies with $A \le 0.6 \, \text{mm}^2$, disappear in large colonies ($A > 0.6 \, \text{mm}^2$) due to the proliferation of the cells in the bulk. This increases the colony density and the number of nearest neighbours. We also detect the self-organisation of cells in the colonies where newly divided (smallest) cells cluster together in patches, separated from larger cells at the final stages of the cell cycle. This might influence directly cell-to-cell interactions and the community effects within the colonies since the segregation induced by size differences allows the interchange of neighbours as the cells proliferate and the colony grows. Our findings are relevant to efforts to determine the quality of hESC colonies and establish colony characteristics database

Modelling Cell Cycle using Different Levels of Representation

Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform computerised simulations of biological systems, which are called in silico experiments, to attain important insights and predictions about the system behaviour with a considerably lower cost. Computer visualisation is an important part of this approach, since it provides a realistic representation of the system behaviour. We define a formal methodology to model biological systems using different levels of representation: a purely formal representation, which we call molecular level, models the biochemical dynamics of the system; visualisation-oriented representations, which we call visual levels, provide views of the biological system at a higher level of organisation and are equipped with the necessary spatial information to generate the appropriate visualisation. We choose Spatial CLS, a formal language belonging to the class of Calculi of Looping Sequences, as the formalism for modelling all representation levels. We illustrate our approach using the budding yeast cell cycle as a case study

New tools for quantitative analysis of nuclear architecture

The cell nucleus houses a wide variety of macromolecular substructures including the cell’s genetic material. The spatial configuration of these substructures is thought to be fundamentally associated with nuclear function, yet the architectural organisation of the cell nucleus is only poorly understood. Advances in microscopy and associated fluorescence techniques have provided a wealth of nuclear image data. Such images offer the opportunity for both visualising nuclear substructures and quantitative investigation of the spatial configuration of these objects. In this thesis, we present new tools to study and explore the subtle principles behind nuclear architecture. We describe a novel method to segment fluorescent microscopy images of nuclear objects. The effectiveness of this segmentation algorithm is demonstrated using extensive simulation. Additionally, we show that the method performs as well as manual-thresholding, which is considered the gold standard. Next, randomisationbased tests from spatial point pattern analysis are employed to inspect spatial interactions of nuclear substructures. The results suggest new and interesting spatial relationships in the nucleus. However, this approach probes only relative nuclear organisation and cannot readily yield a description of absolute spatial preference, which may be a key component of nuclear architecture. To address this problem we have developed methodology based on techniques employed in statistical shape analysis and image registration. The approach proposes that the nuclear boundary can be used to align nuclei from replicate images into a common coordinate system. Each nucleus and its contents can therefore be registered to the sample mean shape using rigid and non-rigid deformations. This aggregated data allows inference regarding global nuclear spatial organisation. For example, the kernel smoothed intensity function is computed to return an estimate of the intensity function of the registered nuclear object. Simulation provides evidence that the registration procedure is sensible and the results accurate. Finally, we have investigated a large database of nuclear substructures using conventional methodology as well as our new tools. We have identified novel spatial relationships between nuclear objects that offer significant clues to their function. We have also examined the absolute spatial configuration of these substructures in registered data. The results reveal dramatic underlying spatial preferences and present new and clear insights into nuclear architecture

The organisation of spinoparabrachial neurons in the mouse

The anterolateral tract (ALT), which originates from neurons in lamina I and the deep dorsal horn, represents a major ascending output through which nociceptive information is transmitted to brain areas involved in pain perception. Although there is detailed quantitative information concerning the ALT in the rat, much less is known about this system in the mouse, which is increasingly being used for studies of spinal pain mechanisms because of the availability of genetically modified lines. The aim of this study was therefore to determine the extent to which information about the ALT in the rat can be extrapolated to the mouse. Our results suggest that as in the rat, most lamina I ALT projection neurons in the lumbar enlargement can be retrogradely labelled from the lateral parabrachial area, that the great majority of these cells (~90%) express the neurokinin 1 receptor (NK1r), and that these are larger than other NK1r-expressing neurons in this lamina. This means that many lamina I spinoparabrachial cells can be identified in NK1r-immunostained sections from animals that have not received retrograde tracer injections. However, we also observed certain species differences, in particular we found that many spinoparabrachial cells in lamina III-IV lack the NK1r, meaning that they cannot be identified based solely on expression of this receptor. We also provide evidence that the vast majority of spinoparabrachial cells are glutamatergic, and that some express substance P. These findings will be important for studies designed to unravel the complex neuronal circuitry that underlies spinal pain processing

Catecholaminergic neurons in medullary nuclei are among the post-synaptic targets of descending projections from infralimbic area 25 of the rat medial prefrontal cortex

The infralimbic (IL) 'visceromotor' area of the rat medial prefrontal cortex projects to strategic subcortical nuclei involved in autonomic functions. Central among these targets are the nucleus tractus solitarius (NTS) and the rostral ventrolateral medulla (rVLM). By combining tract-tracing using the anterograde tracer biotinylated dextran amine (BDA) with immunolabeling for tyrosine hydroxylase (TH; an enzyme marker of catecholaminergic neurons), a limited proportion of BDA-labeled IL axonal boutons in the NTS and rVLM was found to be closely associated with TH immunopositive (+) target structures. Such structural appositions were mainly located proximally over the labeled dendritic arbors of identified TH+ neurons. Quantitative ultrastructural examination revealed that in NTS, TH+ dendritic shafts comprised 7.0% of the overall post-synaptic target population innervated by BDA-labeled IL boutons, whereas TH+ dendritic spines represented 1.25% of targets. In rVLM, TH+ shafts represented 9.0% and TH+ spines 2.5% of IL targets. Labeled IL boutons established exclusively asymmetric Gray Type 1 (presumed excitatory) synaptic junctions. The results indicate that subpopulations of catecholaminergic neurons in the NTS and rVLM are among the spectrum of post-synaptic neurons monosynaptically innervated by descending 'excitatory' input from IL cortex. Such connectivity, albeit restricted, identifies the potential direct influence of IL cortex on the processing and distribution of cardiovascular, respiratory and related autonomic information by catecholaminergic neurons in the NTS and VLM of the rat

Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organisation

BACKGROUND: X chromosome inactivation, the mechanism used by mammals to equalise dosage of X-linked genes in XX females relative to XY males, is triggered by chromosome-wide localisation of a cis-acting non-coding RNA, Xist. The mechanism of Xist RNA spreading and Xist-dependent silencing is poorly understood. A large body of evidence indicates that silencing is more efficient on the X chromosome than on autosomes, leading to the idea that the X chromosome has acquired sequences that facilitate propagation of silencing. LINE-1 (L1) repeats are relatively enriched on the X chromosome and have been proposed as candidates for these sequences. To determine the requirements for efficient silencing we have analysed the relationship of chromosome features, including L1 repeats, and the extent of silencing in cell lines carrying inducible Xist transgenes located on one of three different autosomes. RESULTS: Our results show that the organisation of the chromosome into large gene-rich and L1-rich domains is a key determinant of silencing efficiency. Specifically genes located in large gene-rich domains with low L1 density are relatively resistant to Xist-mediated silencing whereas genes located in gene-poor domains with high L1 density are silenced more efficiently. These effects are observed shortly after induction of Xist RNA expression, suggesting that chromosomal domain organisation influences establishment rather than long-term maintenance of silencing. The X chromosome and some autosomes have only small gene-rich L1-depleted domains and we suggest that this could confer the capacity for relatively efficient chromosome-wide silencing. CONCLUSIONS: This study provides insight into the requirements for efficient Xist mediated silencing and specifically identifies organisation of the chromosome into gene-rich L1-depleted and gene-poor L1-dense domains as a major influence on the ability of Xist-mediated silencing to be propagated in a continuous manner in cis

Interphase chromosome positioning in in vitro porcine cells and ex vivo porcine tissues

Copyright @ 2012 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and 85 reproduction in any medium, provided the original author and source are credited. The article was made available through the Brunel University Open Access Publishing Fund.BACKGROUND: In interphase nuclei of a wide range of species chromosomes are organised into their own specific locations termed territories. These chromosome territories are non-randomly positioned in nuclei which is believed to be related to a spatial aspect of regulatory control over gene expression. In this study we have adopted the pig as a model in which to study interphase chromosome positioning and follows on from other studies from our group of using pig cells and tissues to study interphase genome re-positioning during differentiation. The pig is an important model organism both economically and as a closely related species to study human disease models. This is why great efforts have been made to accomplish the full genome sequence in the last decade. RESULTS: This study has positioned most of the porcine chromosomes in in vitro cultured adult and embryonic fibroblasts, early passage stromal derived mesenchymal stem cells and lymphocytes. The study is further expanded to position four chromosomes in ex vivo tissue derived from pig kidney, lung and brain. CONCLUSIONS: It was concluded that porcine chromosomes are also non-randomly positioned within interphase nuclei with few major differences in chromosome position in interphase nuclei between different cell and tissue types. There were also no differences between preferred nuclear location of chromosomes in in vitro cultured cells as compared to cells in tissue sections. Using a number of analyses to ascertain by what criteria porcine chromosomes were positioned in interphase nuclei; we found a correlation with DNA content.This study is partly supported by Sygen International PLC

Neuronal circuitry for pain processing in the dorsal horn

Neurons in the spinal dorsal horn process sensory information, which is then transmitted to several brain regions, including those responsible for pain perception. The dorsal horn provides numerous potential targets for the development of novel analgesics and is thought to undergo changes that contribute to the exaggerated pain felt after nerve injury and inflammation. Despite its obvious importance, we still know little about the neuronal circuits that process sensory information, mainly because of the heterogeneity of the various neuronal components that make up these circuits. Recent studies have begun to shed light on the neuronal organization and circuitry of this complex region