Timing by rhythms: Daily clocks and developmental rulers

Information Theory as an Experimental Tool for Integrating Disparate Biophysical Signaling Modules

There is a growing appreciation in the fields of cell biology and developmental biology that cells collectively process information in time and space. While many powerful molecular tools exist to observe biophysical dynamics, biologists must find ways to quantitatively understand these phenomena at the systems level. Here, we present a guide for the application of well-established information theory metrics to biological datasets and explain these metrics using examples from cell, developmental and regenerative biology. We introduce a novel computational tool named after its intended purpose, calcium imaging, (CAIM) for simple, rigorous application of these metrics to time series datasets. Finally, we use CAIM to study calcium and cytoskeletal actin information flow patterns between Xenopus laevis embryonic animal cap stem cells. The tools that we present here should enable biologists to apply information theory to develop a systems-level understanding of information processing across a diverse array of experimental systems.

Scaling of internal organs during Drosophila embryonic development

Many species show a diverse range of sizes; for example, domestic dogs have large variation in body mass. Yet, the internal structure of the organism remains similar, i.e., the system scales to organism size. Drosophila melanogaster has been a powerful model system for exploring scaling mechanisms. In the early embryo, gene expression boundaries scale very precisely to embryo length. Later in development, the adult wings grow with remarkable symmetry and scale well with animal size. Yet, our knowledge of whether internal organs initially scale to embryo size remains largely unknown. Here, we utilize artificially small Drosophila embryos to explore how three critical internal organs-the heart, hindgut, and ventral nerve cord (VNC)-adapt to changes in embryo morphology. We find that the heart scales precisely with embryo length. Intriguingly, reduction in cardiac cell length, rather than number, appears to be important in controlling heart length. The hindgut, which is the first chiral organ to form, displays scaling with embryo size under large-scale changes in the artificially smaller embryos but shows few hallmarks of scaling within wild-type size variation. Finally, the VNC only displays weak scaling behavior; even large changes in embryo geometry result in only small shifts in VNC length. This suggests that the VNC may have an intrinsic minimal length that is largely independent of embryo length. Overall, our work shows that internal organs can adapt to embryo size changes in Drosophila, but the extent to which they scale varies significantly between organs.

Na+/Ca2+ exchanger mediates cold Ca2+ signaling conserved for temperature-compensated circadian rhythms

Circadian rhythms are based on biochemical oscillations generated by clock genes/proteins, which independently evolved in animals, fungi, plants, and cyanobacteria. Temperature compensation of the oscillation speed is a common feature of the circadian clocks, but the evolutionary-conserved mechanism has been unclear. Here, we show that Na⁺/Ca²⁺ exchanger (NCX) mediates cold-responsive Ca²⁺ signaling important for the temperature-compensated oscillation in mammalian cells. In response to temperature decrease, NCX elevates intracellular Ca²⁺, which activates Ca²⁺/calmodulin-dependent protein kinase II and accelerates transcriptional oscillations of clock genes. The cold-responsive Ca²⁺ signaling is conserved among mice, Drosophila, and Arabidopsis The mammalian cellular rhythms and Drosophila behavioral rhythms were severely attenuated by NCX inhibition, indicating essential roles of NCX in both temperature compensation and autonomous oscillation. NCX also contributes to the temperature-compensated transcriptional rhythms in cyanobacterial clock. Our results suggest that NCX-mediated Ca²⁺ signaling is a common mechanism underlying temperature-compensated circadian rhythms both in eukaryotes and prokaryotes.

From local resynchronization to global pattern recovery in the zebrafish segmentation clock

Integrity of rhythmic spatial gene expression patterns in the vertebrate segmentation clock requires local synchronization between neighboring cells by Delta-Notch signaling and its inhibition causes defective segment boundaries. Whether deformation of the oscillating tissue complements local synchronization during patterning and segment formation is not understood. We combine theory and experiment to investigate this question in the zebrafish segmentation clock. We remove a Notch inhibitor, allowing resynchronization, and analyze embryonic segment recovery. We observe unexpected intermingling of normal and defective segments, and capture this with a new model combining coupled oscillators and tissue mechanics. Intermingled segments are explained in the theory by advection of persistent phase vortices of oscillators. Experimentally observed changes in recovery patterns are predicted in the theory by temporal changes in tissue length and cell advection pattern. Thus, segmental pattern recovery occurs at two length and time scales: rapid local synchronization between neighboring cells, and the slower transport of the resulting patterns across the tissue through morphogenesis.

An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis

In Arabidopsis, the root clock regulates the spacing of lateral organs along the primary root through oscillating gene expression. The core molecular mechanism that drives the root clock periodicity and how it is modified by exogenous cues such as auxin and gravity remain unknown. We identified the key elements of the oscillator (AUXIN RESPONSE FACTOR 7, its auxin-sensitive inhibitor IAA18/POTENT, and auxin) that form a negative regulatory loop circuit in the oscillation zone. Through multilevel computer modeling fitted to experimental data, we explain how gene expression oscillations coordinate with cell division and growth to create the periodic pattern of organ spacing. Furthermore, gravistimulation experiments based on the model predictions show that external auxin stimuli can lead to entrainment of the root clock. Our work demonstrates the mechanism underlying a robust biological clock and how it can respond to external stimuli.

Shaping Waves of Bone Morphogenetic Protein Inhibition During Vascular Growth

RATIONALE

The BMPs (bone morphogenetic proteins) are essential morphogens in angiogenesis and vascular development. Disruption of BMP signaling can trigger cardiovascular diseases, such as arteriovenous malformations.

OBJECTIVE

A computational model predicted that BMP4 and BMP9 and their inhibitors MGP (matrix gamma-carboxyglutamic acid [Gla] protein) and CV2 (crossveinless-2) would form a regulatory system consisting of negative feedback loops with time delays and that BMP9 would trigger oscillatory expression of the 2 inhibitors. The goal was to investigate this regulatory system in endothelial differentiation and vascular growth.

METHODS AND RESULTS

Oscillations in the expression of MGP and CV2 were detected in endothelial cells in vitro, using quantitative real-time polymerase chain reaction and immunoblotting. These organized temporally downstream BMP-related activities, including expression of stalk-cell markers and cell proliferation, consistent with an integral role of BMP9 in vessel maturation. In vivo, the inhibitors were located in distinct zones in relation to the front of the expanding retinal network, as determined by immunofluorescence. Time-dependent changes of the CV2 location in the retina and the existence of an endothelial population with signs of oscillatory MGP expression in developing vasculature supported the in vitro findings. Loss of MGP or its BMP4-binding capacity disrupted the retinal vasculature, resulting in poorly formed networks, especially in the venous drainage areas, and arteriovenous malformations as determined by increased cell coverage and functional testing.

CONCLUSIONS

Our results suggest a previously unknown mechanism of temporal orchestration of BMP4 and BMP9 activities that utilize the tandem actions of the extracellular antagonists MGP and CV2. Disruption of this mechanism may contribute to vascular malformations and disease.

Temporal Coordination of Collective Migration and Lumen Formation by Antagonism between Two Nuclear Receptors

During development, cells undergo multiple, distinct morphogenetic processes to form a tissue or organ, but how their temporal order and time interval are determined remain poorly understood. Here we show that the nuclear receptors E75 and DHR3 regulate the temporal order and time interval between the collective migration and lumen formation of a coherent group of cells named border cells during Drosophila oogenesis. We show that E75, in response to ecdysone signaling, antagonizes the activity of DHR3 during border cell migration, and DHR3 is necessary and sufficient for the subsequent lumen formation that is critical for micropyle morphogenesis. DHR3's lumen-inducing function is mainly mediated through βFtz-f1, another nuclear receptor and transcription factor. Furthermore, both DHR3 and βFtz-f1 are required for chitin secretion into the lumen, whereas DHR3 is sufficient for chitin secretion. Lastly, DHR3 and βFtz-f1 suppress JNK signaling in the border cells to downregulate cell adhesion during lumen formation.

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E75 antagonizes DHR3's function in inducing lumen formation of border cells (BCs)

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E75 and DHR3 temporally coordinate collective migration and lumen formation of BCs

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DHR3 is required and sufficient for chitin secretion into the lumen

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DHR3 and βFtz-f1 downregulate JNK signaling and cell adhesion in the BCs

Circadian Rhythm of Deaths in a Cardiology Department: A Five-Year Analysis

BACKGROUND

Previous studies have described a circadian pattern of death from cardiovascular causes with a morning peak. Our aim is to describe the daytime oscillations in mortality in hospitalized patients with cardiovascular diseases.

METHODS

Our retrospective registry including all patients who died in the Cardiology Department, including the cardiac intensive care unit, Madrid, Spain.

RESULTS

From a total of 500 patients, time of death was registered in 373 (74.6%), which are the focus of our study; 354 (70.8%) died in the cardiac intensive care unit and 146 (29.2%) in the conventional ward. Mean age was 74.2 ± 13.1 years, and 239 (64.1%) were male. Cardiovascular causes were the leading cause of death (308 patients; 82.6%). Mortality followed a circadian biphasic pattern with a peak at dawn (00.00-05.59 a.m.: 104 patients [27.9%]) and in the afternoon (12.00-17.59 p.m.: 135 patients [36.2%]), irrespective of the cause of death. The peak of mortality occurred in the afternoon (12.00-17.59 p.m.) in the case of cardiovascular mortality (119 deaths [38.6%]) and in the evening (18.00-23.59 p.m.) for non-cardiovascular deaths (21 deaths [32.3%], p = 0.03). This pattern was present regardless from the place of death (conventional ward or cardiac intensive care unit) and also throughout the four seasons.

CONCLUSIONS

Mortality in hospitalized patients with cardiovascular diseases follows a circadian biphasic pattern.

Association Between Three Polymorphisms in BMAL1 Genes and Risk of Lung Cancer in a Northeast Chinese Population

The connection between cancer and circadian rhythms has garnered recent attention. BMAL1 is a core factor in the regulation of circadian rhythms, and its variants have frequently been associated with human diseases, including cancer. Our study first clarifies the relationship of three single-nucleotide polymorphisms (rs3816360, rs2290035, and rs3816358) in BMAL1 with the risk of lung cancer, as well as the gene-environment interaction between the polymorphisms and tobacco exposure in a Northeast Chinese population. A case-control study of 409 new diagnosis patients and 417 controls was performed in Shenyang, Liaoning province. The gene-environment interactions were explored on both additive and multiplicative scale. After Bonferroni correction, rs3816360 and rs2290035 were evidently associated with lung cancer risk. For rs3816360, subjects carrying CC (adjusted odds ratio [OR] = 2.163, 95% confidence interval [CI] = 1.413-3.310, p = 0.004) genotype showed an increased risk of lung cancer compared to the subjects carrying homozygous TT genotype. As for rs2290035, homozygous carriers of AA genotype (OR = 1.908, 95% CI = 1.207-3.017, p = 0.006) showed a significantly increased risk of lung cancer. The dominant models and recessive models of rs3816360 and rs2290035 showed significant associations (p < 0.01). In the stratified analysis, our results revealed that rs3816360 and rs2290035 were associated with the risk of lung adenocarcinoma. However, rs3816358 polymorphism was not significantly associated with lung cancer risk. The measures of additive interaction and logistic models suggested that the gene-environment interactions were not statistically significant on both additive and multiplicative scales.

Rhythmicity and waves in the cortex of single cells

Emergence of dynamic patterns in the form of oscillations and waves on the cortex of single cells is a fascinating and enigmatic phenomenon. Here we outline various theoretical frameworks used to model pattern formation with the goal of reducing complex, heterogeneous patterns into key parameters that are biologically tractable. We also review progress made in recent years on the quantitative and molecular definitions of these terms, which we believe have begun to transform single-cell dynamic patterns from a purely observational and descriptive subject to more mechanistic studies. Specifically, we focus on the nature of local excitable and oscillation events, their spatial couplings leading to propagating waves and the role of active membrane. Instead of arguing for their functional importance, we prefer to consider such patterns as basic properties of dynamic systems. We discuss how knowledge of these patterns could be used to dissect the structure of cellular organization and how the network-centric view could help define cellular functions as transitions between different dynamical states. Last, we speculate on how these patterns could encode temporal and spatial information.

This article is part of the theme issue ‘Self-organization in cell biology’.

Bone development in laboratory mammals used in developmental toxicity studies

Evaluation of the skeleton in laboratory animals is a standard component of developmental toxicology testing. Standard methods of performing the evaluation have been established, and modification of the evaluation using imaging technologies is under development. The embryology of the rodent, rabbit, and primate skeleton has been characterized in detail and summarized herein. The rich literature on variations and malformations in skeletal development that can occur in the offspring of normal animals and animals exposed to test articles in toxicology studies is reviewed. These perturbations of skeletal development include ossification delays, alterations in number, shape, and size of ossification centers, and alterations in numbers of ribs and vertebrae. Because the skeleton is undergoing developmental changes at the time fetuses are evaluated in most study designs, transient delays in development can produce apparent findings of abnormal skeletal structure. The determination of whether a finding represents a permanent change in embryo development with adverse consequences for the organism is important in study interpretation. Knowledge of embryological processes and schedules can assist in interpretation of skeletal findings.

Epigenetic Basis of Circadian Rhythm Disruption in Cancer

Self-sustained and synchronized to environmental stimuli, circadian clocks are under genetic and epigenetic regulation. Recent findings have greatly increased our understanding of epigenetic plasticity governed by circadian clock. Thus, the link between circadian clock and epigenetic machinery is reciprocal. Circadian clock can affect epigenetic features including genomic DNA methylation, noncoding RNA, mainly miRNA expression, and histone modifications resulted in their 24-h rhythms. Concomitantly, these epigenetic events can directly modulate cyclic system of transcription and translation of core circadian genes and indirectly clock output genes. Significant findings interlocking circadian clock, epigenetics, and cancer have been revealed, particularly in breast, colorectal, and blood cancers. Aberrant methylation of circadian gene promoter regions and miRNA expression affected circadian gene expression, together with 24-h expression oscillation pace have been frequently observed.

Evaluating the Autonomy of the Drosophila Circadian Clock in Dissociated Neuronal Culture

Circadian behavioral rhythms offer an excellent model to study intricate interactions between the molecular and neuronal mechanisms of behavior. In mammals, pacemaker neurons in the suprachiasmatic nucleus (SCN) generate rhythms cell-autonomously, which are synchronized by the network interactions within the circadian circuit to drive behavioral rhythms. However, whether this principle is universal to circadian systems in animals remains unanswered. Here, we examined the autonomy of the Drosophila circadian clock by monitoring transcriptional and post-transcriptional rhythms of individual clock neurons in dispersed culture with time-lapse microscopy. Expression patterns of the transcriptional reporter show that CLOCK/CYCLE (CLK/CYC)-mediated transcription is constantly active in dissociated clock neurons. In contrast, the expression profile of the post-transcriptional reporter indicates that PERIOD (PER) protein levels fluctuate and ~10% of cells display rhythms in PER levels with periods in the circadian range. Nevertheless, PER and TIM are enriched in the cytoplasm and no periodic PER nuclear accumulation was observed. These results suggest that repression of CLK/CYC-mediated transcription by nuclear PER is impaired, and thus the negative feedback loop of the molecular clock is incomplete in isolated clock neurons. We further demonstrate that, by pharmacological assays using the non-amidated form of neuropeptide pigment-dispersing factor (PDF), which could be specifically secreted from larval LNvs and adult s-LNvs, downstream events of the PDF signaling are partly impaired in dissociated larval clock neurons. Although non-amidated PDF is likely to be less active than the amidated one, these results point out the possibility that alteration in PDF downstream signaling may play a role in dampening of molecular rhythms in isolated clock neurons. Taken together, our results suggest that Drosophila clocks are weak oscillators that need to be in the intact circadian circuit to generate robust 24-h rhythms.

Determining the impact of cell mixing on signaling during development

Cell movement and intercellular signaling occur simultaneously to organize morphogenesis during embryonic development. Cell movement can cause relative positional changes between neighboring cells. When intercellular signals are local such cell mixing may affect signaling, changing the flow of information in developing tissues. Little is known about the effect of cell mixing on intercellular signaling in collective cellular behaviors and methods to quantify its impact are lacking. Here we discuss how to determine the impact of cell mixing on cell signaling drawing an example from vertebrate embryogenesis: the segmentation clock, a collective rhythm of interacting genetic oscillators. We argue that comparing cell mixing and signaling timescales is key to determining the influence of mixing. A signaling timescale can be estimated by combining theoretical models with cell signaling perturbation experiments. A mixing timescale can be obtained by analysis of cell trajectories from live imaging. After comparing cell movement analyses in different experimental settings, we highlight challenges in quantifying cell mixing from embryonic timelapse experiments, especially a reference frame problem due to embryonic motions and shape changes. We propose statistical observables characterizing cell mixing that do not depend on the choice of reference frames. Finally, we consider situations in which both cell mixing and signaling involve multiple timescales, precluding a direct comparison between single characteristic timescales. In such situations, physical models based on observables of cell mixing and signaling can simulate the flow of information in tissues and reveal the impact of observed cell mixing on signaling.

Delta-Notch signalling in segmentation

Modular body organization is found widely across multicellular organisms, and some of them form repetitive modular structures via the process of segmentation. It's vastly interesting to understand how these regularly repeated structures are robustly generated from the underlying noise in biomolecular interactions. Recent studies from arthropods reveal similarities in segmentation mechanisms with vertebrates, and raise the possibility that the three phylogenetic clades, annelids, arthropods and chordates, might share homology in this process from a bilaterian ancestor. Here, we discuss vertebrate segmentation with particular emphasis on the role of the Notch intercellular signalling pathway. We introduce vertebrate segmentation and Notch signalling, pointing out historical milestones, then describe existing models for the Notch pathway in the synchronization of noisy neighbouring oscillators, and a new role in the modulation of gene expression wave patterns. We ask what functions Notch signalling may have in arthropod segmentation and explore the relationship between Notch-mediated lateral inhibition and synchronization. Finally, we propose open questions and technical challenges to guide future investigations into Notch signalling in segmentation.

Gene expression boundary scaling and organ size regulation in the Drosophila embryo

How the shape and size of tissues and organs is regulated during development is a major question in developmental biology. Such regulation relies upon both intrinsic cues (such as signaling networks) and extrinsic inputs (such as from neighboring tissues). Here, we focus on pattern formation and organ development during Drosophila embryogenesis. In particular, we outline the importance of both biochemical and mechanical tissue-tissue interactions in size regulation. We describe how the Drosophila embryo can potentially provide novel insights into how shape and size are regulated during development. We focus on gene expression boundary scaling in the early embryo and how size is regulated in three organs (hindgut, trachea, and ventral nerve cord) later in development, with particular focus on the role of tissue-tissue interactions. Overall, we demonstrate that Drosophila embryogenesis provides a suitable model system for studying spatial and temporal scaling and size control in vivo.

Is the Epididymis a Series of Organs Placed Side By Side?

The mammalian epididymis is more than a highly convoluted tube divided into four regions: initial segment, caput, corpus and cauda. It is a highly segmented structure with each segment expressing its own and overlapping genes, proteins, and signal transduction pathways. Therefore, the epididymis may be viewed as a series of organs placed side by side. In this review we discuss the contributions of septa that divide the epididymis into segments and present hypotheses as to the mechanism by which septa form. The mechanisms of Wolffian duct segmentation are likened to the mechanisms of segmentation of the renal nephron and somites. The renal nephron may provide valuable clues as to how the Wolffian duct is patterned during development, whereas somitogenesis may provide clues as to the timing of the development of each segment. Emphasis is also placed upon how segments are differentially regulated, in support of the idea that the epididymis can be considered a series of multiple organs placed side by side. One region in particular, the initial segment, which consists of 2 or 4 segments in mice and rats, respectively, is unique with respect to its regulation and vascularity compared to other segments; loss of development of these segments leads to male infertility. Different ways of thinking about how the epididymis functions may provide new directions and ideas as to how sperm maturation takes place.