Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle.

Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ∼20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control and changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level.

RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size.

A fundamental feature of cellular growth is that total protein and RNA amounts increase with cell size to keep concentrations approximately constant. A key component of this is that global transcription rates increase in larger cells. Here, we identify RNA polymerase II (RNAPII) as the limiting factor scaling mRNA transcription with cell size in budding yeast, as transcription is highly sensitive to the dosage of RNAPII but not to other components of the transcriptional machinery. Our experiments support a dynamic equilibrium model where global RNAPII transcription at a given size is set by the mass action recruitment kinetics of unengaged nucleoplasmic RNAPII to the genome. However, this only drives a sub-linear increase in transcription with size, which is then partially compensated for by a decrease in mRNA decay rates as cells enlarge. Thus, limiting RNAPII and feedback on mRNA stability work in concert to scale mRNA amounts with cell size.

Eukaryotic Cell Size Control and Its Relation to Biosynthesis and Senescence.

The most fundamental feature of cellular form is size, which sets the scale of all cell biological processes. Growth, form, and function are all necessarily linked in cell biology, but we often do not understand the underlying molecular mechanisms nor their specific functions. Here, we review progress toward determining the molecular mechanisms that regulate cell size in yeast, animals, and plants, as well as progress toward understanding the function of cell size regulation. It has become increasingly clear that the mechanism of cell size regulation is deeply intertwined with basic mechanisms of biosynthesis, and how biosynthesis can be scaled (or not) in proportion to cell size. Finally, we highlight recent findings causally linking aberrant cell size regulation to cellular senescence and their implications for cancer therapies.

Importin α Partitioning to the Plasma Membrane Regulates Intracellular Scaling.

Early embryogenesis is accompanied by reductive cell divisions requiring that subcellular structures adapt to a range of cell sizes. The interphase nucleus and mitotic spindle scale with cell size through both physical and biochemical mechanisms, but control systems that coordinately scale intracellular structures are unknown. We show that the nuclear transport receptor importin α is modified by palmitoylation, which targets it to the plasma membrane and modulates its binding to nuclear localization signal (NLS)-containing proteins that regulate nuclear and spindle size in Xenopus egg extracts. Reconstitution of importin α targeting to the outer boundary of extract droplets mimicking cell-like compartments recapitulated scaling relationships observed during embryogenesis, which were altered by inhibitors that shift levels of importin α palmitoylation. Modulation of importin α palmitoylation in human cells similarly affected nuclear and spindle size. These experiments identify importin α as a conserved surface area-to-volume sensor that scales intracellular structures to cell size.

Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria.

The scaling of organelles with cell size is thought to be exclusive to eukaryotes. Here, we demonstrate that similar scaling relationships hold for the bacterial nucleoid. Despite the absence of a nuclear membrane, nucleoid size strongly correlates with cell size, independent of changes in DNA amount and across various nutrient conditions. This correlation is observed in diverse bacteria, revealing a near-constant ratio between nucleoid and cell size for a given species. As in eukaryotes, the nucleocytoplasmic ratio in bacteria varies greatly among species. This spectrum of nucleocytoplasmic ratios is independent of genome size, and instead it appears linked to the average population cell size. Bacteria with different nucleocytoplasmic ratios have a cytoplasm with different biophysical properties, impacting ribosome mobility and localization. Together, our findings identify new organizational principles and biophysical features of bacterial cells, implicating the nucleocytoplasmic ratio and cell size as determinants of the intracellular organization of translation.

Keeping Your Brain in Balance: Homeostatic Regulation of Network Function.

To perform computations with the efficiency necessary for animal survival, neocortical microcircuits must be capable of reconfiguring in response to experience, while carefully regulating excitatory and inhibitory connectivity to maintain stable function. This dynamic fine-tuning is accomplished through a rich array of cellular homeostatic plasticity mechanisms that stabilize important cellular and network features such as firing rates, information flow, and sensory tuning properties. Further, these functional network properties can be stabilized by different forms of homeostatic plasticity, including mechanisms that target excitatory or inhibitory synapses, or that regulate intrinsic neuronal excitability. Here we discuss which aspects of neocortical circuit function are under homeostatic control, how this homeostasis is realized on the cellular and molecular levels, and the pathological consequences when circuit homeostasis is impaired. A remaining challenge is to elucidate how these diverse homeostatic mechanisms cooperate within complex circuits to enable them to be both flexible and stable.

Increasing cell size remodels the proteome and promotes senescence.

Cell size is tightly controlled in healthy tissues, but it is unclear how deviations in cell size affect cell physiology. To address this, we measured how the cell's proteome changes with increasing cell size. Size-dependent protein concentration changes are widespread and predicted by subcellular localization, size-dependent mRNA concentrations, and protein turnover. As proliferating cells grow larger, concentration changes typically associated with cellular senescence are increasingly pronounced, suggesting that large size may be a cause rather than just a consequence of cell senescence. Consistent with this hypothesis, larger cells are prone to replicative, DNA-damage-induced, and CDK4/6i-induced senescence. Size-dependent changes to the proteome, including those associated with senescence, are not observed when an increase in cell size is accompanied by an increase in ploidy. Together, our findings show how cell size could impact many aspects of cell physiology by remodeling the proteome and provide a rationale for cell size control and polyploidization.

Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size.

Biosynthesis scales with cell size such that protein concentrations generally remain constant as cells grow. As an exception, synthesis of the cell-cycle inhibitor Whi5 "sub-scales" with cell size so that its concentration is lower in larger cells to promote cell-cycle entry. Here, we find that transcriptional control uncouples Whi5 synthesis from cell size, and we identify histones as the major class of sub-scaling transcripts besides WHI5 by screening for similar genes. Histone synthesis is thereby matched to genome content rather than cell size. Such sub-scaling proteins are challenged by asymmetric cell division because proteins are typically partitioned in proportion to newborn cell volume. To avoid this fate, Whi5 uses chromatin-binding to partition similar protein amounts to each newborn cell regardless of cell size. Disrupting both Whi5 synthesis and chromatin-based partitioning weakens G1 size control. Thus, specific transcriptional and partitioning mechanisms determine protein sub-scaling to control cell size.

Modular control of vertebrate axis segmentation in time and space.

How the timing of development is linked to organismal size is a longstanding question. Although numerous studies have reported a correlation of temporal and spatial traits, the developmental or selective constraints underlying this link remain largely unexplored. We address this question by studying the periodic process of embryonic axis segmentation in-vivo in Oryzias fish. Interspecies comparisons reveal that the timing of segmentation correlates to segment, tissue and organismal size. Segment size in turn scales according to tissue and organism size. To probe for underlying causes, we genetically hybridised two closely related species. Quantitative analysis in ~600 phenotypically diverse F2 embryos reveals a decoupling of timing from size control, while spatial scaling is preserved. Using developmental quantitative trait loci (devQTL) mapping we identify distinct genetic loci linked to either the control of segmentation timing or tissue size. This study demonstrates that a developmental constraint mechanism underlies spatial scaling of axis segmentation, while its spatial and temporal control are dissociable modules.

RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting.

RNA polymerase II (RNA Pol II) contains a disordered C-terminal domain (CTD) whose length enigmatically correlates with genome size. The CTD is crucial to eukaryotic transcription, yet the functional and evolutionary relevance of this variation remains unclear. Here, we investigate how CTD length and disorder influence transcription. We find that length modulates the size and frequency of transcriptional bursting. Disorder is highly conserved and facilitates CTD-CTD interactions, an ability we show is separable from protein sequence and necessary for efficient transcription. We build a data-driven quantitative model, simulations of which recapitulate experiments and support that CTD length promotes initial polymerase recruitment to the promoter and slows down its release from it and that CTD-CTD interactions enable recruitment of multiple polymerases. Our results reveal how these parameters provide access to a range of transcriptional activity, offering a new perspective for the mechanistic significance of CTD length and disorder in transcription across eukaryotes.

Hypertranscription: the invisible hand in stem cell biology.

Stem cells are the fundamental drivers of growth during development and adult organ homeostasis. The properties that define stem cells - self-renewal and differentiation - are highly biosynthetically demanding. In order to fuel this demand, stem and progenitor cells engage in hypertranscription, a global amplification of the transcriptome. While standard normalization methods in transcriptomics typically mask hypertranscription, new approaches are beginning to reveal a remarkable range in global transcriptional output in stem and progenitor cells. We discuss technological advancements to probe global transcriptional shifts, review recent findings that contribute to defining hallmarks of stem cell hypertranscription, and propose future directions in this field.

The cell cycle and cell size influence the rates of global cellular translation and transcription in fission yeast.

How the production of biomass is controlled as cells increase in size and proceed through the cell cycle events is important for understanding the regulation of global cellular growth. This has been studied for decades but has not yielded consistent results, probably due to perturbations induced by the synchronisation methods used in most previous studies. To avoid this problem, we have developed a system to analyse unperturbed exponentially growing populations of fission yeast cells. We generated thousands of fixed single-cell measurements of cell size, cell cycle stage and the levels of global cellular translation and transcription. We show that translation scales with size, and additionally, increases at late S-phase/early G2 and early in mitosis and decreases later in mitosis, suggesting that cell cycle controls are also operative over global cellular translation. Transcription increases with both size and the amount of DNA, suggesting that the level of transcription of a cell may be the result of a dynamic equilibrium between the number of RNA polymerases associating and disassociating from DNA.

Allometry in limb regeneration and scale-invariant patterning as the basis of normal morphogenesis from different sizes of blastemas.

Axolotl (Ambystoma mexicanum) limb regeneration begins with blastemas of various sizes, in contrast to the limb developmental process. Despite this size variation, normal limb morphology, consistent with a limb stump size, is regenerated. This outcome suggests the existence of underlying scale-invariant mechanisms. To identify such mechanisms, we examined the allometric relationships between blastema size, and Sonic Hedgehog (Shh) and Fibroblast Growth Factor 8 (Fgf8) expression patterns against limb stump size. We found that all factors showed allometric rather than isometric scaling; specifically, their relative sizes decrease with an increase in limb stump size. However, the ratio of Shh/Fgf8 signaling dominant region was nearly constant, independent of blastema/body size. Furthermore, the relative spatial patterns of cell density and proliferation activity and the relative position of first digit formation were scale-invariant in the summed Shh/Fgf8 crosstalk region. This scale-invariant nature may underlie the morphogenesis of normal limbs from different sizes of blastemas.

Quantum network utility: A framework for benchmarking quantum networks.

The central aim of quantum networks is to facilitate user connectivity via quantum channels, but there is an open need for benchmarking metrics to compare diverse quantum networks. Here, we propose a general framework for quantifying the performance of a quantum network by estimating the value created by connecting users through quantum channels. In this framework, we define the quantum network utility metric [Formula: see text] to capture the social and economic value of quantum networks. The proposed framework accommodates a variety of applications from secure communications to distributed sensing. As a case study, we investigate the example of distributed quantum computing in detail. We determine the scaling laws of quantum network utility, which suggest that distributed edge quantum computing has more potential for success than its classical equivalent. We believe the proposed utility-based framework will serve as a foundation for guiding and assessing the development of quantum network technologies and designs.

Length control emerges from cytoskeletal network geometry.

Many cytoskeletal networks consist of individual filaments that are organized into elaborate higher-order structures. While it is appreciated that the size and architecture of these networks are critical for their biological functions, much of the work investigating control over their assembly has focused on mechanisms that regulate the turnover of individual filaments through size-dependent feedback. Here, we propose a very different, feedback-independent mechanism to explain how yeast cells control the length of their actin cables. Our findings, supported by quantitative cell imaging and mathematical modeling, indicate that actin cable length control is an emergent property that arises from the cross-linked and bundled organization of the filaments within the cable. Using this model, we further dissect the mechanisms that allow cables to grow longer in larger cells and propose that cell length-dependent tuning of formin activity allows cells to scale cable length with cell length. This mechanism is a significant departure from prior models of cytoskeletal filament length control and presents a different paradigm to consider how cells control the size, shape, and dynamics of higher-order cytoskeletal structures.

Basal forebrain cholinergic activity is necessary for upward firing rate homeostasis in the rodent visual cortex.

Bidirectional homeostatic plasticity allows neurons and circuits to maintain stable firing in the face of developmental or learning-induced perturbations. In the primary visual cortex (V1), upward firing rate homeostasis (FRH) only occurs during active wake (AW) and downward during sleep, but how this behavioral state-dependent gating is accomplished is unknown. Here, we focus on how AW enables upward FRH in V1 of juvenile Long Evans rats. A major difference between quiet wake (QW), when upward FRH is absent, and AW, when it is present, is increased cholinergic (ACh) tone, and the main cholinergic projections to V1 arise from the horizontal diagonal band of the basal forebrain (HDB ACh). We therefore chemogenetically inhibited HDB ACh neurons while inducing upward homeostatic compensation using direct activity-suppression in V1. We found that synaptic scaling up and intrinsic homeostatic plasticity, two important cellular mediators of upward FRH, were both impaired when HDB ACh neurons were inhibited. Most strikingly, HDB ACh inhibition flipped the sign of intrinsic plasticity so that it became anti-homeostatic, and this effect was phenocopied by knockdown of the M1 ACh receptor in V1, indicating that this modulation of intrinsic plasticity is the result of direct actions of ACh within V1. Finally, we found that upward FRH induced by visual deprivation was completely prevented by HDB ACh inhibition. Together, our results show that HDB ACh modulation is a key enabler of upward homeostatic plasticity and FRH, and more broadly suggest that neuromodulatory inputs can segregate upward and downward homeostatic plasticity into distinct behavioral states.

The Drosophila tracheal terminal cell as a model for branching morphogenesis.

The terminal cells of the Drosophila larval tracheal system are perhaps the simplest delivery networks, providing an analogue for mammalian vascular growth and function in a system with many fewer components. These cells are a prime example of single-cell morphogenesis, branching significantly over time to adapt to the needs of the growing tissue they supply. While the genetic mechanisms governing local branching decisions have been studied extensively, an understanding of the emergence of a global network architecture is still lacking. Mapping out the full network architecture of populations of terminal cells at different developmental times of Drosophila larvae, we find that cell growth follows scaling laws relating the total edge length, supply area, and branch density. Using time-lapse imaging of individual terminal cells, we identify that the cells grow in three ways: by extending branches, by the side budding of new branches, and by internally growing existing branches. A generative model based on these modes of growth recapitulates statistical properties of the terminal cell network data. These results suggest that the scaling laws arise from the coupled contributions of branching and internal growth. This study establishes the terminal cell as a uniquely tractable model system for further studies of transportation and distribution networks.

Correlation-informed ordered dictionary learning for imaging in complex media.

We propose a method for imaging in scattering media when large and diverse datasets are available. It has two steps. Using a dictionary learning algorithm the first step estimates the true Green's function vectors as columns in an unordered sensing matrix. The array data comes from many sparse sets of sources whose location and strength are not known to us. In the second step, the columns of the estimated sensing matrix are ordered for imaging using the multidimensional scaling algorithm with connectivity information derived from cross-correlations of its columns, as in time reversal. For these two steps to work together, we need data from large arrays of receivers so the columns of the sensing matrix are incoherent for the first step, as well as from sub-arrays so that they are coherent enough to obtain connectivity needed in the second step. Through simulation experiments, we show that the proposed method is able to provide images in complex media whose resolution is that of a homogeneous medium.

Formation of human kinship structures depending on population size and cultural mutation rate.

How does social complexity depend on population size and cultural transmission? Kinship structures in traditional societies provide a fundamental illustration, where cultural rules between clans determine people's marriage possibilities. Here, we propose a simple model of kinship interactions that considers kin and in-law cooperation and sexual rivalry. In this model, multiple societies compete. Societies consist of multiple families with different cultural traits and mating preferences. These values determine interactions and hence the growth rate of families and are transmitted to offspring with mutations. Through a multilevel evolutionary simulation, family traits and preferences are grouped into multiple clans with interclan mating preferences. It illustrates the emergence of kinship structures as the spontaneous formation of interdependent cultural associations. Emergent kinship structures are characterized by the cycle length of marriage exchange and the number of cycles in society. We numerically and analytically clarify their parameter dependence. The relative importance of cooperation versus rivalry determines whether attraction or repulsion exists between families. Different structures evolve as locally stable attractors. The probabilities of formation and collapse of complex structures depend on the number of families and the mutation rate, showing characteristic scaling relationships. It is now possible to explore macroscopic kinship structures based on microscopic interactions, together with their environmental dependence and the historical causality of their evolution. We propose the basic causal mechanism of the formation of typical human social structures by referring to ethnographic observations and concepts from statistical physics and multilevel evolution. Such interdisciplinary collaboration will unveil universal features in human societies.

A bifurcation integrates information from many noisy ion channels and allows for milli-Kelvin thermal sensitivity in the snake pit organ.

In various biological systems, information from many noisy molecular receptors must be integrated into a collective response. A striking example is the thermal imaging organ of pit vipers. Single nerve fibers in the organ reliably respond to milli-Kelvin (mK) temperature increases, a thousand times more sensitive than their molecular sensors, thermo-transient receptor potential (TRP) ion channels. Here, we propose a mechanism for the integration of this molecular information. In our model, amplification arises due to proximity to a dynamical bifurcation, separating a regime with frequent and regular action potentials (APs), from a regime where APs are irregular and infrequent. Near the transition, AP frequency can have an extremely sharp dependence on temperature, naturally accounting for the thousand-fold amplification. Furthermore, close to the bifurcation, most of the information about temperature available in the TRP channels' kinetics can be read out from the times between consecutive APs even in the presence of readout noise. A key model prediction is that the coefficient of variation in the distribution of interspike times decreases with AP frequency, and quantitative comparison with experiments indeed suggests that nerve fibers of snakes are located very close to the bifurcation. While proximity to such bifurcation points typically requires fine-tuning of parameters, we propose that having feedback act from the order parameter (AP frequency) onto the control parameter robustly maintains the system in the vicinity of the bifurcation. This robustness suggests that similar feedback mechanisms might be found in other sensory systems which also need to detect tiny signals in a varying environment.