Search for: All records

Synopsis The cumulative outcome of bacteria-phytoplankton cell-cell interactions has global-scale consequences that necessitate a more comprehensive understanding of the species that form these relationships, the chemical exchanges that govern them, and the chemical cues that trigger them. However, the diffuse liquid environment supporting these exchanges is inherently difficult to interrogate, which has moved researchers to combine multi-omics analyses, genome mining tools, genetic probes, and mathematical models to gain insight into the species and chemical networks existing around individual phytoplankton cells. Yet, fundamental questions still remain about these micro-scale interactions, creating an opportunity for innovating new methods where biology and chemistry interface with engineering and mathematics. 

Synopsis Cells are the fundamental unit of biological organization. Although it may be easy to think of them as little more than the simple building blocks of complex organisms such as animals, single cells are capable of behaviors of remarkable apparent sophistication. This is abundantly clear when considering the diversity of form and function among the microbial eukaryotes, the protists. How might we navigate this diversity in the search for general principles of cellular behavior? Here, we review cases in which the intensive study of protists from the perspective of cellular biophysics has driven insight into broad biological questions of morphogenesis, navigation and motility, and decision making. We argue that applying such approaches to questions of evolutionary cell biology presents rich, emerging opportunities. Integrating and expanding biophysical studies across protist diversity, exploiting the unique characteristics of each organism, will enrich our understanding of general underlying principles. 

Synopsis In animals, epithelial tissues are barriers against the external environment, providing protection against biological, chemical, and physical damage. Depending on the organism’s physiology and behavior, these tissues encounter different types of mechanical forces and need to provide a suitable adaptive response to ensure success. Therefore, understanding tissue mechanics in different contexts is an important research area. Here, we review recent tissue mechanics discoveries in three early divergent non-bilaterian systems—Trichoplax adhaerens, Hydra vulgaris, and Aurelia aurita. We highlight each animal’s simple body plan and biology and unique, rapid tissue remodeling phenomena that play a crucial role in its physiology. We also discuss the emergent large-scale mechanics in these systems that arise from small-scale phenomena. Finally, we emphasize the potential of these non-bilaterian animals to be model systems in a bottom-up approach for further investigation in tissue mechanics. 

Synopsis Motility is an essential factor for an organism’s survival and diversification. With the advent of novel single-cell technologies, analytical frameworks, and theoretical methods, we can begin to probe the complex lives of microscopic motile organisms and answer the intertwining biological and physical questions of how these diverse lifeforms navigate their surroundings. Herein, we summarize the main mechanisms of microscale motility and give an overview of different experimental, analytical, and mathematical methods used to study them across different scales encompassing the molecular-, individual-, to population-level. We identify transferable techniques, pressing challenges, and future directions in the field. This review can serve as a starting point for researchers who are interested in exploring and quantifying the movements of organisms in the microscale world. 

Synopsis The shift of funding organizations to prioritize interdisciplinary work points to the need for workflow models that better accommodate interdisciplinary studies. Most scientists are trained in a specific field and are often unaware of the kind of insights that other disciplines could contribute to solving various problems. In this paper, we present a perspective on how we developed an experimental pipeline between a microscopy and image analysis/bioengineering lab. Specifically, we connected microscopy observations about a putative mechanosensing protein, obscurin, to image analysis techniques that quantify cell changes. While the individual methods used are well established (fluorescence microscopy; ImageJ WEKA and mTrack2 programs; MATLAB), there are no existing best practices for how to integrate these techniques into a cohesive, interdisciplinary narrative. Here, we describe a broadly applicable workflow of how microscopists can more easily quantify cell properties (e.g., perimeter, velocity) from microscopy videos of eukaryotic (MDCK) adherent cells. Additionally, we give examples of how these foundational measurements can create more complex, customizable cell mechanics tools and models. 

Synopsis The symposium “Large-scale biological phenomena arising from small-scale biophysical processes” at the SICB 2023 Annual General Meeting focused on the cross-disciplinary exploration of emergent phenomena in biology. Interactions between cells or organisms at small scales within a system can govern patterns occurring at larger scales in space, time, or biological complexity. This theme recurs in many sub-disciplines of biology, including cell and developmental biology, evolution, and ecology. This symposium, and the associated special issue introduced here, showcases a wide range of cross-disciplinary collaborations among biologists, physicists, and engineers. Technological advancements in microscopy and microfluidics, as well as complementary advances in mathematical modeling and associated theory demonstrate the timeliness of this issue. This introduction seeks to provide useful background information to place the studies within this issue in a broader biophysical context and highlight similarities in ideas and approaches across systems and sub-disciplines. We hope to demonstrate that cross-disciplinary research linking small-scale biophysics to larger-scale emergent phenomena can help us understand problems ranging from single-cell behaviors to tissue formation and function, evolution of form, and the dynamics of communities. 

Synopsis While the modern framework of evolutionary development (evo-devo) has been decidedly genetic, historic analyses have also considered the importance of mechanics in the evolution of form. With the aid of recent technological advancements in both quantifying and perturbing changes in the molecular and mechanical effectors of organismal shape, how molecular and genetic cues regulate the biophysical aspects of morphogenesis is becoming increasingly well studied. As a result, this is an opportune time to consider how the tissue-scale mechanics that underlie morphogenesis are acted upon through evolution to establish morphological diversity. Such a focus will enable a field of evo-devo mechanobiology that will serve to better elucidate the opaque relations between genes and forms by articulating intermediary physical mechanisms. Here, we review how the evolution of shape is measured and related to genetics, how recent strides have been made in the dissection of developmental tissue mechanics, and how we expect these areas to coalesce in evo-devo studies in the future. 

Synopsis Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities, is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems. 

Synopsis Cross-disciplinary research enables us to tackle complex problems that require expertise from different fields. Such collaborations involve researchers who have different perspectives, communication styles, and knowledge bases, and can produce results far greater than the sum of their parts. However, in an era of increasing scientific specialization, there exist many barriers for students and early-career researchers (ECRs) interested in training and undertaking interdisciplinary research endeavors. This perspective examines the challenges that students and ECRs perceive and experience in cross-disciplinary work and proposes pathways to create more inclusive and welcoming research environments. This work emerges from a National Science Foundation (NSF)-funded workshop held during the Society for Integrative and Comparative Biology (SICB) Annual Meeting in January 2023 in Austin, TX. The workshop brought together seasoned interdisciplinary scientists with undergraduate and graduate students to identify and discuss perceived challenges through small group discussions and experience sharing. Through summarizing a range of student concerns about embarking on careers as interdisciplinary scientists and identifying ways to dismantle institutional and lab management-level barriers, we aim to promote an inclusive and collaborative problem-solving environment for scientists of all experience levels. 

Synopsis The freshwater cnidarian Hydra can regenerate from wounds, small tissue fragments and even from aggregated cells. This process requires the de novo development of a body axis and oral–aboral polarity, a fundamental developmental process that involves chemical patterning and mechanical shape changes. Gierer and Meinhardt recognized that Hydra’s simple body plan and amenability to in vivo experiments make it an experimentally and mathematically tractable model to study developmental patterning and symmetry breaking. They developed a reaction-diffusion model, involving a short-range activator and a long-range inhibitor, which successfully explained patterning in the adult animal. In 2011, HyWnt3 was identified as a candidate for the activator. However, despite the continued efforts of both physicists and biologists, the predicted inhibitor remains elusive. Furthermore, the Gierer-Meinhardt model cannot explain de novo axis formation in cellular aggregates that lack inherited tissue polarity. The aim of this review is to synthesize the current knowledge on Hydra symmetry breaking and patterning. We summarize the history of patterning studies and insights from recent biomechanical and molecular studies, and highlight the need for continued validation of theoretical assumptions and collaboration across disciplinary boundaries. We conclude by proposing new experiments to test current mechano-chemical coupling models and suggest ideas for expanding the Gierer-Meinhardt model to explain de novo patterning, as observed in Hydra aggregates. The availability of a fully sequenced genome, transgenic fluorescent reporter strains, and modern imaging techniques, that enable unprecedented observation of cellular events in vivo, promise to allow the community to crack Hydra’s secret to patterning.