Clearing the slate: RNA turnover to enable cell state switching?

The distribution of mRNA in tissue is determined by the balance between transcription and decay. Understanding the control of RNA decay during development has been somewhat neglected compared with transcriptional control. Here, we explore the potential for mRNA decay to trigger rapid cell state transitions during development, comparing a bistable switch model of cell state conversion with experimental evidence from different developmental systems. We also consider another potential role for large-scale RNA decay that has emerged from studies of stress-induced cell state transitions, in which removal of mRNA unblocks the translation machinery to prioritise the synthesis of proteins that establish the new cell state.

Controlling periodic long-range signalling to drive a morphogenetic transition.

Cells use signal relay to transmit information across tissue scales. However, the production of information carried by signal relay remains poorly characterised. To determine how the coding features of signal relay are generated, we used the classic system for long-range signalling: the periodic cAMP waves that drive Dictyostelium collective migration. Combining imaging and optogenetic perturbation of cell signalling states, we find that migration is triggered by an increase in wave frequency generated at the signalling centre. Wave frequency is regulated by cAMP wave circulation, which organises the long-range signal. To determine the mechanisms modulating wave circulation, we combined mathematical modelling, the general theory of excitable media, and mechanical perturbations to test competing models. Models in which cell density and spatial patterning modulate the wave frequency cannot explain the temporal evolution of signalling waves. Instead, our evidence leads to a model where wave circulation increases the ability for cells to relay the signal, causing further increase in the circulation rate. This positive feedback between cell state and signalling pattern regulates the long-range signal coding that drives morphogenesis.

Distributed and centralized control during differentiation.

A persistent view of cell fate choices during development entails centralized control by so-called master regulators. A recent single-cell study of the large-scale fate specification during mammalian gastrulation (Mittnenzweig et al., 2021) implies the prevalence of more distributed forms of control.

A lipid-structured model for macrophage populations in atherosclerotic plaques.

Atherosclerosis is a chronic inflammatory disease driven by the accumulation of pro-inflammatory, lipid-loaded macrophages at sites inside artery walls. These accumulations lead to the development of atherosclerotic plaques. The rupture of plaques that contain lipid-rich necrotic cores can trigger heart attacks and strokes via occlusion of blood vessels. We construct and analyse a system of partial integro-differential equations that model lipid accumulation by macrophages, the generation of apoptotic cells and the formation of the necrotic core. The model accounts for the following cell behaviours: monocyte recruitment into the plaque and differentiation into macrophages; macrophage ingestion of low density lipoproteins (LDL) and of apoptotic cells and necrotic material; lipid offloading to high density lipoproteins (HDL); macrophage emigration; and apoptosis of macrophages and necrosis of apoptotic cells. With this model, we study how changes in parameters predict the characteristic features of plaque pathology. In particular, we find the qualitative form of lipid distribution across the macrophage population and show that high lipid loads can occur in the absence of LDL ingestion. We also demonstrate the importance of macrophage emigration in mitigating and resolving inflammation and plaque lipid accumulation.

Efferocytosis perpetuates substance accumulation inside macrophage populations.

In both cells and animals, cannibalism can transfer harmful substances from the consumed to the consumer. Macrophages are immune cells that consume their own dead via a process called cannibalistic efferocytosis. Macrophages that contain harmful substances are found at sites of chronic inflammation, yet the role of cannibalism in this context remains unexplored. Here we take mathematical and experimental approaches to study the relationship between cannibalistic efferocytosis and substance accumulation in macrophages. Through mathematical modelling, we deduce that substances which transfer between individuals through cannibalism will concentrate inside the population via a coalescence process. This prediction was confirmed for macrophage populations inside a closed system. We used image analysis of whole slide photomicrographs to measure both latex microbead and neutral lipid accumulation inside murine bone marrow-derived macrophages (104-[Formula: see text]) following their stimulation into an inflammatory state ex vivo. While the total number of phagocytosed beads remained constant, cell death reduced cell numbers and efferocytosis concentrated the beads among the surviving macrophages. As lipids are also conserved during efferocytosis, these cells accumulated lipid derived from the membranes of dead and consumed macrophages (becoming macrophage foam cells). Consequently, enhanced macrophage cell death increased the rate and extent of foam cell formation. Our results demonstrate that cannibalistic efferocytosis perpetuates exogenous (e.g. beads) and endogenous (e.g. lipids) substance accumulation inside macrophage populations. As such, cannibalism has similar detrimental consequences in both cells and animals.

A Quantitative Model of Early Atherosclerotic Plaques Parameterized Using In Vitro Experiments.

There are a growing number of studies that model immunological processes in the artery wall that lead to the development of atherosclerotic plaques. However, few of these models use parameters that are obtained from experimental data even though data-driven models are vital if mathematical models are to become clinically relevant. We present the development and analysis of a quantitative mathematical model for the coupled inflammatory, lipid and macrophage dynamics in early atherosclerotic plaques. Our modeling approach is similar to the biologists' experimental approach where the bigger picture of atherosclerosis is put together from many smaller observations and findings from in vitro experiments. We first develop a series of three simpler submodels which are least-squares fitted to various in vitro experimental results from the literature. Subsequently, we use these three submodels to construct a quantitative model of the development of early atherosclerotic plaques. We perform a local sensitivity analysis of the model with respect to its parameters that identifies critical parameters and processes. Further, we present a systematic analysis of the long-term outcome of the model which produces a characterization of the stability of model plaques based on the rates of recruitment of low-density lipoproteins, high-density lipoproteins and macrophages. The analysis of the model suggests that further experimental work quantifying the different fates of macrophages as a function of cholesterol load and the balance between free cholesterol and cholesterol ester inside macrophages may give valuable insight into long-term atherosclerotic plaque outcomes. This model is an important step toward models applicable in a clinical setting.

Orientation of migratory birds under ultraviolet light.

In view of the finding that cryptochrome 1a, the putative receptor molecule for the avian magnetic compass, is restricted to the ultraviolet single cones in European Robins, we studied the orientation behaviour of robins and Australian Silvereyes under monochromatic ultraviolet (UV) light. At low intensity UV light of 0.3 mW/m(2), birds showed normal migratory orientation by their inclination compass, with the directional information originating in radical pair processes in the eye. At 2.8 mW/m(2), robins showed an axial preference in the east-west axis, whereas silvereyes preferred an easterly direction. At 5.7 mW/m(2), robins changed direction to a north-south axis. When UV light was combined with yellow light, robins showed easterly 'fixed direction' responses, which changed to disorientation when their upper beak was locally anaesthetised with xylocaine, indicating that they were controlled by the magnetite-based receptors in the beak. Orientation under UV light thus appears to be similar to that observed under blue, turquoise and green light, albeit the UV responses occur at lower light levels, probably because of the greater light sensitivity of the UV cones. The orientation under UV light and green light suggests that at least at the level of the retina, magnetoreception and vision are largely independent of each other.

Avian orientation: the pulse effect is mediated by the magnetite receptors in the upper beak.

Migratory silvereyes treated with a strong magnetic pulse shift their headings by approximately 90 degrees , indicating an involvement of magnetite-based receptors in the orientation process. Structures containing superparamagnetic magnetite have been described in the inner skin at the edges of the upper beak of birds, while single-domain magnetite particles are indicated in the nasal cavity. To test which of these structures mediate the pulse effect, we subjected migratory silvereyes, Zosterops l. lateralis, to a strong pulse, and then tested their orientation, while the skin of their upper beak was anaesthetized with a local anaesthetic to temporarily deactivate the magnetite-containing structures there. After the pulse, birds without anaesthesia showed the typical shift, whereas when their beak was anaesthetized, they maintained their original headings. This indicates that the superparamagnetic magnetite-containing structures in the skin of the upper beak are most likely the magnetoreceptors that cause the change in headings observed after pulse treatment.

Light-dependent magnetoreception: orientation behaviour of migratory birds under dim red light.

Magnetic compass orientation in migratory birds has been shown to be based on radical pair processes and to require light from the short wavelength part of the spectrum up to 565 nm Green. Under dim red light of 645 nm wavelength and 1 mW m(-2) intensity, Australian silvereyes and European robins showed a westerly tendency that did not change between spring and autumn, identifying it as a 'fixed direction' response. A thorough analysis revealed that this orientation did not involve the inclination compass, but was a response based on the polarity of the magnetic field. Furthermore, in contrast to the orientation under short-wavelength light, it could be disrupted by local anaesthesia of the upper beak where iron-containing receptors are located, indicating that it is controlled by these receptors. The similarity of the response under dim red light to the response in total darkness suggests that the two responses may be identical. These findings indicate that the observed 'fixed direction' response under dim red light is fundamentally different from the normal compass orientation, which is based on radical pair processes.

Magnetite-based magnetoreception: the effect of repeated pulsing on the orientation of migratory birds.

Previous studies have shown that a magnetic pulse affected the orientation of passerine migrants for a short period only: for about 3 days, the birds' headings were deflected eastward from their migratory direction, followed by a phase of disorientation, with the birds returning to their normal migratory direction after about 10 days. To analyze the processes involved in the fading of the pulse effect, migratory birds were subjected to a second, identical pulse 16 days after the first pulse, when the effect of that pulse had disappeared. This second pulse affected the birds' behavior in a different way: it caused an increase in the scatter of the birds' headings for 2 days, after which the birds showed normal migratory orientation again. These observations are at variance with the hypothesis that the magnetite-based receptor had been fully restored, but also with the hypothesis that the input of this receptor was ignored. They rather indicate dynamic processes, which include changes in the affected receptor, but at the same time cause the birds to weigh and rate the altered input differently. The bearing of these findings on the question of whether single domains or superparamagnetic particles are involved in the magnetite-based receptors is discussed.

Bird navigation: what type of information does the magnetite-based receptor provide?

Previous experiments have shown that a short, strong magnetic pulse caused migratory birds to change their headings from their normal migratory direction to an easterly direction in both spring and autumn. In order to analyse the nature of this pulse effect, we subjected migratory Australian silvereyes, Zosterops lateralis, to a magnetic pulse and tested their subsequent response under different magnetic conditions. In the local geomagnetic field, the birds preferred easterly headings as before, and when the horizontal component of the magnetic field was shifted 90 degrees anticlockwise, they altered their headings accordingly northwards. In a field with the vertical component inverted, the birds reversed their headings to westwards, indicating that their directional orientation was controlled by the normal inclination compass. These findings show that although the pulse strongly affects the magnetite particles, it leaves the functional mechanism of the magnetic compass intact. Thus, magnetite-based receptors seem to mediate magnetic 'map'-information used to determine position, and when affected by a pulse, they provide birds with false positional information that causes them to change their course.

Possible human impacts on adaptive radiation: beak size bimodality in Darwin's finches.

Adaptive radiation is facilitated by a rugged adaptive landscape, where fitness peaks correspond to trait values that enhance the use of distinct resources. Different species are thought to occupy the different peaks, with hybrids falling into low-fitness valleys between them. We hypothesize that human activities can smooth adaptive landscapes, increase hybrid fitness and hamper evolutionary diversification. We investigated this possibility by analysing beak size data for 1755 Geospiza fortis measured between 1964 and 2005 on the island of Santa Cruz, Galápagos. Some populations of this species can display a resource-based bimodality in beak size, which mirrors the greater beak size differences among species. We first show that an historically bimodal population at one site, Academy Bay, has lost this property in concert with a marked increase in local human population density. We next show that a nearby site with lower human impacts, El Garrapatero, currently manifests strong bimodality. This comparison suggests that bimodality can persist when human densities are low (Academy Bay in the past, El Garrapatero in the present), but not when they are high (Academy Bay in the present). Human activities may negatively impact diversification in 'young' adaptive radiations, perhaps by altering adaptive landscapes.

Magnetic orientation in birds: non-compass responses under monochromatic light of increased intensity.

Migratory Australian silvereyes (Zosterops lateralis) were tested under monochromatic light at wavelengths of 424 nm blue and 565 nm green. At a low light level of 7 x 10(15) quanta m(-2) s(-1) in the local geomagnetic field, the birds preferred their seasonally appropriate southern migratory direction under both wavelengths. Their reversal of headings when the vertical component of the magnetic field was inverted indicated normal use of the avian inclination compass. A higher light intensity of 43 x 10(15) quanta m(-2) s(-1), however, caused a fundamental change in behaviour: under bright blue, the silvereyes showed an axial tendency along the east-west axis; under bright green, they showed a unimodal preference of a west-northwesterly direction that followed a shift in magnetic north, but was not reversed by inverting the vertical component of the magnetic field. Hence it is not based on the inclination compass. The change in behaviour at higher light intensities suggests a complex interaction between at least two receptors. The polar nature of the response under bright green cannot be explained by the current models of light-dependent magnetoreception and will lead to new considerations on these receptive processes.