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The "QuantitatEVs: multiscale analyses, from bulk to single vesicle" workshop aimed to discuss quantitative strategies and harmonized wet and computational approaches toward the comprehensive analysis of extracellular vesicles (EVs) from bulk to single vesicle analyses with a special focus on emerging technologies. The workshop covered the key issues in the quantitative analysis of different EV‐associated molecular components and EV biophysical features, which are considered the core of EV‐associated biomarker discovery and validation for their clinical translation. The in‐person‐only workshop was held in Trento, Italy, from January 31st to February 2nd, 2023, and continued in Milan on February 3rd with "Next Generation EVs," a satellite event dedicated to early career researchers (ECR). This report summarizes the main topics and outcomes of the workshop. [ABSTRACT FROM AUTHOR]

Treatment of sensitive bacteria with beta‐lactam antibiotics often leads to two salient population‐level features: a transient increase in total population biomass before a subsequent decline, and a linear correlation between growth and killing rates. However, it remains unclear how these population‐level responses emerge from collective single‐cell responses. During beta‐lactam treatment, it is well‐recognized that individual cells often exhibit varying degrees of filamentation before lysis. We show that the cumulative probability of cell lysis increases sigmoidally with the extent of filamentation and that this dependence is characterized by unique parameters that are specific to bacterial strain, antibiotic dose, and growth condition. Modeling demonstrates how the single‐cell lysis probabilities can give rise to population‐level biomass dynamics, which were experimentally validated. This mapping provides insights into how the population biomass time‐kill curve emerges from single cells and allows the representation of both single‐ and population‐level responses with universal parameters. Synopsis: How do population‐level responses emerge from collective single‐cell responses upon antibiotic treatment? Measuring the kinetics of bacterial elongation and lysis in single cells treated with beta‐lactams allows quantitative mapping to temporal population biomass dynamics. When beta‐lactam antibiotics trigger bacterial filamentation and lysis, the cumulative lysis probability is sigmoidal over cell length.Parameters that describe such probability are unique to antibiotic conditions.Damage accumulation can describe how the probability arises from single‐cell responses.Mathematical mapping provides a quantitative understanding of population time‐kill curves from the single‐cell response parameters. [ABSTRACT FROM AUTHOR]

Interactomics aims to characterize all interactions formed between molecules that comprise our body. Although it emerged from quantitative biophysics, it has devolved into a predominantly qualitative field of science over the past decades. Due to technical limitations at its onset, almost all tools in interactomics are qualitative, which persists in defining the discipline. Here, we argue that interactomics needs to return to a quantitative direction because the technical achievements of the last decade have overcome the original limitations that forced its current path. In contrast to qualitative interactomics which is constrained to charting lists of observed interactions, quantitative interactomics can also uncover answers to key questions such as the strength of interactions or how many of certain complexes can form in cells, thus providing researchers with more immediate proxies for understanding and predicting biological processes. [ABSTRACT FROM AUTHOR]

The give and take between biology and physics is an important part of the history of modern science, with this partnership perhaps now more intimate than ever. In this essay, I explore the ways in which these different fields can strengthen each other through their distinct outlooks on some of the most important questions being asked about the living world. In particular, I highlight three areas where the perspective from physics might lead to deeper insights into the workings of cells. First, I consider what it means for two ostensibly unrelated problems to be the same, and how such sameness can provide unexpected insights into apparently unrelated phenomena. Second, I consider different conceptions of what constitutes a mechanistic understanding of a given phenomenon with an emphasis on nonmolecular notions of mechanism. The third idea is the importance of "toy problems" as a way of providing foundational insights into the real problems. Though my focus here is primarily on ways in which physics approaches might prove interesting in biology, I close with an example of how biology might substantially alter physics by providing a forum and the tools to uncover a fundamental understanding of nonequilibrium phenomena. [ABSTRACT FROM AUTHOR]

Arguably, one of the foremost distinctions between life and non-living matter is the ability to sense environmental changes and respond appropriately-an ability that is invested in every living cell. Within a single cell, this function is largely carried out by networks of signaling molecules. However, the details of how signaling networks help cells make complicated decisions are still not clear. For instance, how do cells read graded, analog stress signals but convert them into digital live-or-die responses? The answer to such questions may originate from the fact that signaling molecules are not static but dynamic entities, changing in numbers and activity over time and space. In the past two decades, researchers have been able to experimentally monitor signaling dynamics and use mathematical techniques to quantify and abstract general principles of how cells process information. In this review, the authors first introduce and discuss various experimental and computational methodologies that have been used to study signaling dynamics. The authors then discuss the different types of temporal dynamics such as oscillations and bistability that can be exhibited by signaling systems and highlight studies that have investigated such dynamics in physiological settings. Finally, the authors illustrate the role of spatial compartmentalization in regulating cellular responses with examples of second-messenger signaling in cardiac myocytes. [ABSTRACT FROM AUTHOR]

Descriptive terms are often used to characterize cells in culture, but the use of nonquantitative and poorly defined terms can lead to ambiguities when comparing data from different laboratories. Although recently there has been a good deal of interest in unambiguous identification of cell lines via their genetic markers, it is also critical to have definitive, quantitative metrics to describe cell phenotypic characteristics. Quantitative metrics of cell phenotype will aid the comparison of data from experiments performed at different times and in different laboratories where influences such as the age of the population and differences in culture conditions or protocols can potentially affect cellular metabolic state and gene expression in the absence of changes in the genetic profile. Here, we present examples of robust methodologies for quantitatively assessing characteristics of cell morphology and cell-cell interactions, and of growth rates of cells within the population. We performed these analyses with endothelial cell lines derived from dolphin, bovine and human, and with a mouse fibroblast cell line. These metrics quantify some characteristics of these cells lines that clearly distinguish them from one another, and provide quantitative information on phenotypic changes in one of the cell lines over large number of passages. Published 2012 American Institute of Chemical Engineers Biotechnol. Prog., 28: 1069-1078, 2012 [ABSTRACT FROM AUTHOR]

The idle assembly checkpoint acts to delay chromosome segregation until all duplicated sister chromatids are captured by the mitotic spindle. This pathway ensures that each daughter cell receives a complete copy of the genome. The high fidelity and robustness of this process have made it a subject of intense study in both the experimental and computational realms. A significant number of checkpoint proteins have been identified but how they orchestrate the communication between local spindle attachment and global cytoplasmic signalling to delay segregation is not yet understood. Here, we propose a systems view of the spindle assembly checkpoint to focus attention on the key regulators of the dynamics of this pathway. These regulators in turn have been the subject of detailed cellular measurements and computational modelling to connect molecular function to the dynamics of spindle assembly checkpoint signalling. A review of these efforts reveals the insights provided by such approaches and underscores the need for further interdisciplinary studies to reveal in full the quantitative underpinnings of this cellular control pathway. [ABSTRACT FROM AUTHOR]

The relationship between the binding affinity and specificity of modular interaction domains is potentially important in determining biological signaling responses. In signaling from the T-cell receptor (TCR), the Gads C-terminal SH3 domain binds a core RxxK sequence motif in the SLP-76 scaffold. We show that residues surrounding this motif are largely optimized for binding the Gads C-SH3 domain resulting in a high-affinity interaction (KD=8–20 nM) that is essential for efficient TCR signaling in Jurkat T cells, since Gads-mediated signaling declines with decreasing affinity. Furthermore, the SLP-76 RxxK motif has evolved a very high specificity for the Gads C-SH3 domain. However, TCR signaling in Jurkat cells is tolerant of potential SLP-76 crossreactivity, provided that very high-affinity binding to the Gads C-SH3 domain is maintained. These data provide a quantitative argument that the affinity of the Gads C-SH3 domain for SLP-76 is physiologically important and suggest that the integrity of TCR signaling in vivo is sustained both by strong selection of SLP-76 for the Gads C-SH3 domain and by a capacity to buffer intrinsic crossreactivity. [ABSTRACT FROM AUTHOR]

Abstract: During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this paper, we propose a scenario for chromatin structural reorganization during mitosis, which bridges all the different scales involved in chromatin architecture, from nucleosomes to chromatin loops. We build a model for chromatin, based on available data, taking into account both physical and topological constraints DNA has to deal with. Our results suggest that the mitotic chromosome condensation/decondensation process is induced by a structural change at the level of the nucleosome itself. [Copyright &y& Elsevier]