Cell organisation in the colonic crypt: A theoretical comparison of the pedigree and niche concepts

The intestinal mucosa is a monolayer of rapidly self-renewing epithelial cells which is not only responsible for absorption of water and nutrients into the bloodstream but also acts as a protective barrier against harmful microbes entering the body. New functional epithelial cells are produced from stem cells, and their proliferating progeny. These stem cells are found within millions of crypts (tubular pits) spaced along the intestinal tract. The entire intestinal epithelium is replaced every 2–3 days in mice (3–5 days in humans) and hence cell production, differentiation, migration and turnover need to be tightly regulated. Malfunctions in this regulation are strongly linked to inflammatory bowel diseases and to the formation of adenomas and ultimately cancerous tumours. Despite a great deal of biological experimentation and observation, precisely how colonic crypts are regulated to produce mature colonocytes remains unclear. To assist in understanding how cell organisation in crypts is achieved, two very different conceptual models of cell behaviour are developed here, referred to as the ‘pedigree’ and the ‘niche’ models. The pedigree model proposes that crypt cells are largely preprogrammed and receive minimal prompting from the environment as they move through a routine of cell differentiation and proliferation to become mature colonocytes. The niche model proposes that crypt cells are primarily influenced by the local microenvironments along the crypt, and that predetermined cell behaviour plays a negligible role in their development. In this paper we present a computational model of colonic crypts in the mouse, which enables a comparison of the quality and controllability of mature coloncyte production by crypts operating under these two contrasting conceptual models of crypt regulation

Analysis of Wnt signaling β-catenin spatial dynamics in HEK293T cells

Background Wnt/β-catenin signaling is involved in different stages of mammalian development and implicated in various cancers (e.g. colorectal cancer). Recent experimental and computational studies have revealed characteristics of the pathway, however a cell-specific spatial perspective is lacking. In this study, a novel 3D confocal quantitation protocol is developed to acquire spatial (two cellular compartments: nucleus and cytosol-membrane) and temporal quantitative data on target protein (e.g. β-catenin) concentrations in Human Epithelial Kidney cells (HEK293T) during perturbation (with either cycloheximide or Wnt3A). Computational models of the Wnt pathway are constructed and interrogated based on this data. Results A single compartment Wnt pathway model is compared with a simple β-catenin two compartment model to investigate Wnt3A signaling in HEK293T cells. When protein synthesis is inhibited, β-catenin decreases at the same rate in both cellular compartments, suggesting diffusional transport is fast compared to β-catenin degradation in the cytosol. With Wnt3A stimulation, the total amount of β-catenin rises throughout the cell, however the increase is initially (~first hour) faster in the nuclear compartment. While both models were able to reproduce the whole cell changes in β-catenin, only the compartment model reproduced the Wnt3A induced changes in β-catenin distribution and it was also the best fit for the data obtained when active transport was included alongside passive diffusion transport. Conclusions This integrated 3D quantitation imaging protocol and computational modeling approach allowed cell-specific compartment models of the signaling pathways to be constructed and analyzed. The Wnt models constructed in this study are the first for HEK293T and have suggested potential roles of inter-compartment transport to the dynamics of signaling

Colon cryptogenesis: Asymmetric budding

The process of crypt formation and the roles of Wnt and cell-cell adhesion signaling in cryptogenesis are not well described; but are important to the understanding of both normal and cancer colon crypt biology. A quantitative 3D-microscopy and image analysis technique is used to study the frequency, morphology and molecular topography associated with crypt formation. Measurements along the colon reveal the details of crypt formation and some key underlying biochemical signals regulating normal colon biology. Our measurements revealed an asymmetrical crypt budding process, contrary to the previously reported symmetrical fission of crypts. 3D immunofluorescence analyses reveals heterogeneity in the subcellular distribution of E-cadherin and β-catenin in distinct crypt populations. This heterogeneity was also found in asymmetrical budding crypts. Singular crypt formation (i.e. no multiple new crypts forming from one parent crypt) were observed in crypts isolated from the normal colon mucosa, suggestive of a singular constraint mechanism to prevent aberrant crypt production. The technique presented improves our understanding of cryptogenesis and suggests that excess colon crypt formation occurs when Wnt signaling is perturbed (e.g. by truncation of adenomatous polyposis coli, APC protein) in most colon cancers

D-brane dynamics near compactified NS5-branes

We examine the dynamics of a $Dp$-brane in the background of $k$ coincident, parallel $NS$5-branes which have had one of their common transverse directions compactified. We find that for small energy, bound orbits can exist at sufficiently large distances where there will be no stringy effects. The orbits are dependent upon the energy density, angular momentum and electric field. The analysis breaks down at radial distances comparable with the compactification radius and we must resort to using a modified form of the harmonic function in this region.Comment: Latex, 20 pages, 6 figs, references adde

Discrete element framework for modelling extracellular matrix, deformable cells and subcellular components

This paper presents a framework for modelling biological tissues based on discrete particles. Cell components (e.g. cell membranes, cell cytoskeleton, cell nucleus) and extracellular matrix (e.g. collagen) are represented using collections of particles. Simple particle to particle interaction laws are used to simulate and control complex physical interaction types (e.g. cell-cell adhesion via cadherins, integrin basement membrane attachment, cytoskeletal mechanical properties). Particles may be given the capacity to change their properties and behaviours in response to changes in the cellular microenvironment (e.g., in response to cell-cell signalling or mechanical loadings). Each particle is in effect an 'agent', meaning that the agent can sense local environmental information and respond according to pre-determined or stochastic events. The behaviour of the proposed framework is exemplified through several biological problems of ongoing interest. These examples illustrate how the modelling framework allows enormous flexibility for representing the mechanical behaviour of different tissues, and we argue this is a more intuitive approach than perhaps offered by traditional continuum methods. Because of this flexibility, we believe the discrete modelling framework provides an avenue for biologists and bioengineers to explore the behaviour of tissue systems in a computational laboratory

SD-brane gravity fields and rolling tachyons

S(pacelike)D-branes are objects arising naturally in string theory when Dirichlet boundary conditions are imposed on the time direction. SD-brane physics is inherently time-dependent. Previous investigations of gravity fields of SD-branes have yielded undesirable naked spacelike singularities. We set up the problem of coupling the most relevant open-string tachyonic mode to massless closed-string modes in the bulk, with backreaction and Ramond-Ramond fields included. We find solutions numerically in a self-consistent approximation; our solutions are naturally asymptotically flat and time-reversal asymmetric. We find completely nonsingular evolution; in particular, the dilaton and curvature are well-behaved for all time. The essential mechanism for spacetime singularity resolution is the inclusion of full backreaction between the bulk fields and the rolling tachyon. Our analysis is not the final word on the story, because we have to make some significant approximations, most notably homogeneity of the tachyon on the unstable branes. Nonetheless, we provide significant progress in plugging a gaping hole in prior understanding of the gravity fields of SD-branes.Comment: References added. Analysis for much broader range of solutions presented. Conclusions unchanged. Time-reversal symmetric examples ruled out, new examples are provide

Semi-Analytic Stellar Structure in Scalar-Tensor Gravity

Precision tests of gravity can be used to constrain the properties of hypothetical very light scalar fields, but these tests depend crucially on how macroscopic astrophysical objects couple to the new scalar field. We develop quasi-analytic methods for solving the equations of stellar structure using scalar-tensor gravity, with the goal of seeing how stellar properties depend on assumptions made about the scalar coupling at a microscopic level. We illustrate these methods by applying them to Brans-Dicke scalars, and their generalization in which the scalar-matter coupling is a weak function of the scalar field. The four observable parameters that characterize the fields external to a spherically symmetric star (the stellar radius, R, mass, M, scalar `charge', Q, and the scalar's asymptotic value, phi_infty) are subject to two relations because of the matching to the interior solution, generalizing the usual mass-radius, M(R), relation of General Relativity. We identify how these relations depend on the microscopic scalar couplings, agreeing with earlier workers when comparisons are possible. Explicit analytical solutions are obtained for the instructive toy model of constant-density stars, whose properties we compare to more realistic equations of state for neutron star models.Comment: 39 pages, 9 figure

The health-related quality of life in a Swedish sample of HIV-infected persons

The purposes of the present study are (1) to assess the health-related quality of life (HRQOL) and the subjective health status in a sample of human immunodeficiency virus (HIV)-infected persons (2) to relate the results to different population groups and (3) to investigate the relationship of medical and demographic variables with HRQOL. A total of 72 HIV-infected men were included. They answered the Swedish health-related quality of life questionnaire and the health index. Demographic and medical data were obtained from the medical records. The data collection took place before entering a therapeutic HIV vaccine trial. The results showed a more negative impact on the HRQOL and subjective health status in the HIV-positive subjects, compared with male population groups. The dimensions of emotional well-being were most affected. When comparisons were made according to the medical and demographic variables for different subgroups within the HIV sample, differences in the physical-dimension scales were most prominent. Symptomatic HIV infection or acquired immunodeficiency syndrome (AIDS), anti-retroviral treatment, sick leave or disability pension, low income and basic education were associated with worse HRQOL and health status. In conclusion, it is of utmost importance to take into account, aspects of the patients' emotional well-being in nursing, as well as in medical care and interventions. Moreover, individualized caring programs are needed because the disruptions in HRQOL fluctuated within the HIV sample

D-terms and D-strings in open string models

We study the Fayet-Iliopoulos (FI) D-terms on D-branes in type II Calabi-Yau backgrounds. We provide a simple worldsheet proof of the fact that, at tree level, these terms only couple to scalars in closed string hypermultiplets. At the one-loop level, the D-terms get corrections only if the gauge group has an anomalous spectrum, with the anomaly cancelled by a Green-Schwarz mechanism. We study the local type IIA model of D6-branes at SU(3) angles and show that, as in field theory, the one-loop correction suffers from a quadratic divergence in the open string channel. By studying the closed string channel, we show that this divergence is related to a closed string tadpole, and is cancelled when the tadpole is cancelled. Next, we study the cosmic strings that arise in the supersymmetric phases of these systems in light of recent work of Dvali et. al. In the type IIA intersecting D6-brane examples, we identify the D-term strings as D4-branes ending on the D6-branes. Finally, we use N=1 dualities to relate these results to previous work on the FI D-term of heterotic strings.Comment: 29 pages, 5 figures; v2: improved referencin