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

Dicke-Type Energy Level Crossings in Cavity-Induced Atom Cooling: Another Superradiant Cooling

This paper is devoted to energy-spectral analysis for the system of a two-level atom coupled with photons in a cavity. It is shown that the Dicke-type energy level crossings take place when the atom-cavity interaction of the system undergoes changes between the weak coupling regime and the strong one. Using the phenomenon of the crossings we develop the idea of cavity-induced atom cooling proposed by the group of Ritsch, and we lay mathematical foundations of a possible mechanism for another superradiant cooling in addition to that proposed by Domokos and Ritsch. The process of our superradiant cooling can function well by cavity decay and by control of the position of the atom, at least in (mathematical) theory, even if there is neither atomic absorption nor atomic emission of photons.Comment: 15 pages; 8 figure

Complexity Bounds for Ordinal-Based Termination

`What more than its truth do we know if we have a proof of a theorem in a given formal system?' We examine Kreisel's question in the particular context of program termination proofs, with an eye to deriving complexity bounds on program running times. Our main tool for this are length function theorems, which provide complexity bounds on the use of well quasi orders. We illustrate how to prove such theorems in the simple yet until now untreated case of ordinals. We show how to apply this new theorem to derive complexity bounds on programs when they are proven to terminate thanks to a ranking function into some ordinal.Comment: Invited talk at the 8th International Workshop on Reachability Problems (RP 2014, 22-24 September 2014, Oxford

Absence of Ground States for a Class of Translation Invariant Models of Non-relativistic QED

We consider a class of translation invariant models of non-relativistic QED with net charge. Under certain natural assumptions we prove that ground states do not exist in the Fock space

First-order formative rules

This paper discusses the method of formative rules for first-order term rewriting, which was previously defined for a higher-order setting. Dual to the well-known usable rules, formative rules allow dropping some of the term constraints that need to be solved during a termination proof. Compared to the higher-order definition, the first-order setting allows for significant improvements of the technique

Formation and Interaction of Membrane Tubes

We show that the formation of membrane tubes (or membrane tethers), which is a crucial step in many biological processes, is highly non-trivial and involves first order shape transitions. The force exerted by an emerging tube is a non-monotonic function of its length. We point out that tubes attract each other, which eventually leads to their coalescence. We also show that detached tubes behave like semiflexible filaments with a rather short persistence length. We suggest that these properties play an important role in the formation and structure of tubular organelles.Comment: 4 pages, 3 figure

Infrared problem for the Nelson model on static space-times

We consider the Nelson model with variable coefficients and investigate the problem of existence of a ground state and the removal of the ultraviolet cutoff. Nelson models with variable coefficients arise when one replaces in the usual Nelson model the flat Minkowski metric by a static metric, allowing also the boson mass to depend on position. A physical example is obtained by quantizing the Klein-Gordon equation on a static space-time coupled with a non-relativistic particle. We investigate the existence of a ground state of the Hamiltonian in the presence of the infrared problem, i.e. assuming that the boson mass tends to 0 at infinity

Inner ear tissue preservation by rapid freezing: improving fixation by high-pressure freezing and hybrid methods

In the preservation of tissues in as ‘close to life’ state as possible, rapid freeze fixation has many benefits over conventional chemical fixation. One technique by which rapid freeze-fixation can be achieved, high pressure freezing (HPF), has been shown to enable ice crystal artefact-free freezing and tissue preservation to greater depths (more than 40μm) than other quick-freezing methods. Despite increasingly becoming routine in electron microscopy, the use of HPF for the fixation of inner ear tissue has been limited. Assessment of the quality of preservation showed routine HPF techniques were suitable for preparation of inner ear tissues in a variety of species. Good preservation throughout the depth of sensory epithelia was achievable. Comparison to chemically fixed tissue indicated that fresh frozen preparations exhibited overall superior structural preservation of cells. However, HPF fixation caused characteristic artefacts in stereocilia that suggested poor quality freezing of the actin bundles. The hybrid technique of pre-fixation and high pressure freezing was shown to produce cellular preservation throughout the tissue, similar to that seen in HPF alone. Pre-fixation HPF produced consistent high quality preservation of stereociliary actin bundles. Optimising the preparation of samples with minimal artefact formation allows analysis of the links between ultrastructure and function in inner ear tissues