Near-wall rheotaxis of the ciliate Tetrahymena induced by the kinesthetic sensing of cilia

泳ぐ微生物が海まで流されない理由 --SDGsに欠かせない小さな生物たちの振る舞いを解明--. 京都大学プレスリリース. 2021-10-21.To survive in harsh environments, single-celled microorganisms autonomously respond to external stimuli, such as light, heat, and flow. Here, we elucidate the flow response of Tetrahymena, a well-known single-celled freshwater microorganism. Tetrahymena moves upstream against an external flow via a behavior called rheotaxis. While micrometer-sized particles are swept away downstream in a viscous flow, what dynamics underlie the rheotaxis of the ciliate? Our experiments reveal that Tetrahymena slides along walls during upstream movement, which indicates that the cells receive rotational torque from shear flow to control cell orientation. To evaluate the effects of the shear torque and propelling speed, we perform a numerical simulation with a hydrodynamic model swimmer adopting cilia dynamics in a shear flow. The swimmer orientations converge to an upstream alignment, and the swimmer slides upstream along a boundary wall. The results suggest that Tetrahymena automatically responds to shear flow by performing rheotaxis using cilia-stalling mechanics

TRANSCRIPTIONAL REGULATION OF BONE FORMATION, MECHANOSENSING, AND EVOLUTION

Given that bone remodeling is a dynamic process, the output of which is dependent upon time, levels of mechanical input, and the ability of bones to respond to that mechanical stimulus, I assessed regulation of gene expression in the craniofacial region to determine how a response happens during mechanosensing and bone remodeling. To do this, I used African cichlids as a model, as they known for their rapid speciation rates, high phenotypic variation within and between species, and ability to remodel their bones in response to mechanical loading. In chapter 2, I combined RNA-seq and ATAC-seq datasets to determine with high confidence genes are responsible for plasticity and shape differences in cichlid species with different feeding morphologies. In particular, I found genes that were both differentially expressed and differentially accessible to transcriptional machinery that were implicated in cell cycle progression. In chapter 3, using qPCR, I was able to determine that time is a critical factor in assessing plasticity and the response of certain species to mechanical input. This was paired with 2D morphometrics for shape analysis over time to show that species that do not fall on the extreme end of phenotypic variation are more genetically plastic, and gives insights into the underpinnings of evolution in cichlid jaw morphology. Results from both chapters 2 and 3 suggested that certain environments facilitate larger changes in gene expression than others. In chapter 4, using molecular techniques such as qPCR coupled with enzymatic staining, I found that when mechanosensitive structures in the cell are ablated, gene expression regulation collapses over time, and specific sites of bone remodeling activity are less predictive. Taken together, this body of work supports previous research in the field and gives insight into the regulation of gene expression during bone remodeling, plasticity, and evolution

Stability of dancing Volvox

Biflagellate algal cells of the genus Volvox form spherical colonies that propel themselves, vertically upwards in still fluid, by the coordinated beating of thousands of flagella, that also cause the colonies to rotate about their vertical axes. When they are swimming in a chamber of finite depth, pairs (or more) of Volvox carteri colonies were observed by Drescher et al. [Phys. Rev. Lett. 102, 168101 (2009)] to exhibit hydrodynamic bound states when they are close to a rigid horizontal boundary. When the boundary is above, the colonies are attracted to each other and orbit around each other in a `waltz'; when the boundary is below they perform more complex `minuet' motions. These dances are simulated in the present paper, using a novel `spherical squirmer' model of a colony in which, instead of a time-independent but $\theta$-dependent tangential velocity being imposed on the spherical surface (radius $a$; $\theta$ is the polar angle), a time-independent and uniform tangential shear stress is applied to the fluid on a sphere of radius $(1+\epsilon)a, \epsilon \ll 1$, where $\epsilon a$ represents the length of the flagella. The fluid must satisfy the no-slip condition on the sphere at radius $a$. In addition to the shear stress, the motions depend on two dimensionless parameters that describe the effect of gravity on a colony: $F_g$, proportional to the ratio of the sedimentation speed of a non-swimming colony to its swimming speed, and $G_{bh}$, that represents the fact that colonies are bottom-heavy..

Squirmer hydrodynamics near a periodic surface topography

The behaviour of microscopic swimmers has previously been explored near large-scale confining geometries and in the presence of very small-scale surface roughness. Here, we consider an intermediate case of how a simple microswimmer, the tangential spherical squirmer, behaves adjacent to singly and doubly periodic sinusoidal surface topographies that spatially oscillate with an amplitude that is an order of magnitude less than the swimmer size and wavelengths that are also within an order of magnitude of this scale. The nearest neighbour regularised Stokeslet method is used for numerical explorations after validating its accuracy for a spherical tangential squirmer that swims stably near a flat surface. The same squirmer is then introduced to different surface topographies. The key governing factor in the resulting swimming behaviour is the size of the squirmer relative to the surface topography wavelength. For instance, directional guidance is not observed when the squirmer is much larger, or much smaller, than the surface topography wavelength. In contrast, once the squirmer size is on the scale of the topography wavelength, limited guidance is possible, often with local capture in the topography troughs. However, complex dynamics can also emerge, especially when the initial configuration is not close to alignment along topography troughs or above topography crests. In contrast to sensitivity in alignment and topography wavelength, reductions in the amplitude of the surface topography or variations in the shape of the periodic surface topography do not have extensive impacts on the squirmer behaviour. Our findings more generally highlight that the numerical framework provides an essential basis to elucidate how swimmers may be guided by surface topography

CONSTRAINTS OF THE IMAGINATION: HOW PHENOTYPES ARE SHAPED THROUGH GENETICS, THE ENVIRONMENT, AND DEVELOPMENT

Phenotypic constraints are ubiquitous throughout nature, being found throughout all stages of life and at multiple different biological levels including cellular, genetic, environmental, behavioral, evolutionary, and developmental. These constraints have shaped, not only the natural world, but the way that we perceive what is possible, or impossible, an observation made clear by François Jacob in his 1977 paper “Evolution and Tinkering”. This is reflected in the literature, repeatedly, by the regular occurrence of densely packed visualization of phenotypic space that seemingly always have large areas that go unoccupied. Despite constrained regions of space being observable across countless taxa, identifying the mechanisms of those constraints remains elusive. Given that constraints are widespread and have influenced how evolution may work, my aim was to identify mechanisms of constraint throughout multiple biological levels. Chapter one is divided into two parts, sections A and B, but largely focuses on how constraints are influenced by genetics. For this, we investigated crocc2, a protein that encodes for a structural component of the ciliary rootlet which in turn plays a major role as a mechanosensory for nearly all cells. We found dysfunctional crocc2 resulted in both dysmorphic bone development and a decrease in the plastic response potential of zebrafish (section A), as well as altered developmental trajectories in juvenile morphology, presumably due to alterations in cellular polarity and inadequate extracellular communication. Importantly, all results from this chapter point toward crocc2 play a canalizing role in the production of phenotypes at multiple life-history stages. Chapter 2 takes a different approach into understanding constrains by looking at broad ecological alterations and how those alterations may alter morphology of resident taxa. Here, we utilized the heavily altered habitat of the Tocantins River in the Amazon and the existing museum collections to evaluate how select representatives of the cichlid community had responded to such change. We found significant changes in contemporary morphology across all included cichlid species compared to their historical counterparts. These data show that alterations to the environment have resulted in changes to the local resident species, and possibly an alteration to their future evolutionary trajectories. Among the species included, one was found to have the most substantial morphological changes, which is what we followed up in the next chapter. Chapter 3 dug into the morphological changes of Satanoperca, a Geophagine cichlid with a unique feeding mechanism known as winnowing. Winnowing is a poorly understood mechanical process involving substrate manipulation. Given that anthropogenic alterations to local hydrology oft result in changes to the benthic sediment composition, we wanted to know if differing substrates was enough to induce a plastic response in winnowing fishes, and if so which traits were effected. We found significant differences across our experimental populations in both shape and disparity and present evidence in support of wide-spread integration across craniofacial traits. In addition, these data suggest that the novel anatomical structure, the epibranchial lobe, is more modular than other craniofacial traits involved in the winnowing process. Chapters 4 and 5 utilize a unique lineage of fishes, the Bramidae, to understand how developmental and evolutionary constraints are broken to produce morphological novelties. We used a combination of DNA sequences from GenBank and numerous museum specimens to illuminate constraints and determine how constraints are broken to produce complex phenotypic novelties. In Chapter 4, we found that the fanfishes had experienced greater rates of morphological evolution than other members of the Bramidae family, resulting in their occupation of an entirely novel region of phenotypic space. In Chapter 5, we elaborated on this by investigating the developmental processes involved in producing an extreme morphological novelty. The data presented in Chapter 5 provide evidence suggesting that the fanfishes have broken various constraints, resulting in prominent anatomical and morphological changes to accommodate their novel phenotype. In all, my dissertation provides examples of how constraints have shaped the variability that we see throughout life and shows examples of how constraints can be identified, what happens when they are broken, and how they work to control the pace and trajectory of evolutionary processes

Origins of eukaryotic excitability

This is the final version. Available on open access from the Royal Society via the DOI in this recordAll living cells interact dynamically with a constantly changing world. Eukaryotes in particular, evolved radically new ways to sense and react to their environment. These advances enabled new and more complex forms of cellular behavior in eukaryotes, including directional movement, active feeding, mating, or responses to predation. But what are the key events and innovations during eukaryogenesis that made all of this possible? Here we describe the ancestral repertoire of eukaryotic excitability and discuss five major cellular innovations that enabled its evolutionary origin. The innovations include a vastly expanded repertoire of ion channels, the emergence of cilia and pseudopodia, endomembranes as intracellular capacitors, a flexible plasma membrane, and the relocation of chemiosmotic ATP synthesis to mitochondria that liberated the plasma membrane for more complex electrical signaling involved in sensing and reacting. We conjecture that together with an increase in cell size, these new forms of excitability greatly amplified the degrees of freedom associated with cellular responses, allowing eukaryotes to vastly outperform prokaryotes in terms of both speed and accuracy. This comprehensive new perspective on the evolution of excitability enriches our view of eukaryogenesis and emphasizes behaviour and sensing as major contributors to the success of eukaryotes.European Commissio