An electrophysiological and kinematic model of Paramecium, the "swimming neuron".

Paramecium is a large unicellular organism that swims in fresh water using cilia. When stimulated by various means (mechanically, chemically, optically, thermally), it often swims backward then turns and swims forward again in a new direction: this is called the avoiding reaction. This reaction is triggered by a calcium-based action potential. For this reason, several authors have called Paramecium the "swimming neuron". Here we present an empirically constrained model of its action potential based on electrophysiology experiments on live immobilized paramecia, together with simultaneous measurement of ciliary beating using particle image velocimetry. Using these measurements and additional behavioral measurements of free swimming, we extend the electrophysiological model by coupling calcium concentration to kinematic parameters, turning it into a swimming model. In this way, we obtain a model of autonomously behaving Paramecium. Finally, we demonstrate how the modeled organism interacts with an environment, can follow gradients and display collective behavior. This work provides a modeling basis for investigating the physiological basis of autonomous behavior of Paramecium in ecological environments.

Evidence for a transition in the cortical membranes of Paramecium.

Ever since the pioneering studies in the 1960s and 70s, the importance of order transitions for cell membrane functions has remained a matter of debate. Recently, it has been proposed that the nonlinear stimulus-response curve of excitable cells, which manifests in all-or-none pulses (action potentials (AP)), is due to a transition in the cell membrane. Indeed, evidence for transitions has accumulated in plant cells and neurons, but studies with other excitable cells are expedient in order to show if this finding is of a general nature. Herein, we investigated intact, motile specimens of the "swimming neuron" Paramecium. The cellular membranes were labelled with the solvatochromic fluorophores LAURDAN or Di-4-ANEPPDHQ. Subsequently, a cell was trapped in a microfluidic channel and investigated by fluorescence spectroscopy. The generalized polarization (GP) of the fluorescence emission from cell cortical membranes (probably plasma and alveolar membranes) was extracted by an edge-finding algorithm. The thermo-optical state diagram, i.e. the dependence of GP on temperature, exhibited clear indications for a reversible transition. This transition had a width of ~10-15 °C and a midpoint that was located ~4 °C below the growth temperature. The state diagrams with LAURDAN and Di-4-ANEPPDHQ had widely identical characteristics. These results suggested that the cortical membranes of Paramecium reside in an order transition regime under physiological growth conditions. Based on these findings, membrane potential fluctuations, spontaneous depolarizing spikes, and thermal excitation of Paramecium was interpreted.

Micromanipulation in Paramecium: From non-mendelian inheritance to the outlook for versatile micromachines.

This review addresses nine areas of knowledge revealed by micromanipulations performed with Paramecium. Microinjection has shown that sexual maturation and senescence of Paramecium caudatum is a programmed process conducted by a specific gene and its product protein. In Paramecium tetraurelia, autogamy was revealed to depend on the number of DNA syntheses rather than the number of cell divisions in clonal aging. The cytoplasmic complementarity test established that microinjection of wild-type cytoplasm can correct genetic defects of mutants. The concept of complementarity together with protein chemistry revealed compounds that control membrane excitability. In non-Mendelian inheritance, noncoding small RNAs made from the parental micronucleus regulate the rearrangement of the progeny's macronuclear DNA. The macronucleus has the potential to be used as a factory for genetic engineering. The development and differentiation of progeny's nuclei in mating pairs are controlled by the parental macronucleus. The chemical reaction processes associated with exocytosis have been revealed by microinjection of various enzymes and antibodies. Using the fusion gene of histone H2B and yellow-fluorescence protein, it was revealed that the fusion gene-mRNA is transferred between cells during mating. Experiments with endosymbiotic bacteria and the host shed light on the conditions needed to establish sustainable symbiotic relationships.

Membrane traffic and Ca2+ signals in ciliates.

A Paramecium cell has as many types of membrane interactions as mammalian cells, as established with monoclonal antibodies by R. Allen and A. Fok. Since then, we have identified key players, such as SNARE proteins, Ca2+ -regulating proteins, including Ca2+ -channels, Ca2+ -pumps, Ca2+ -binding proteins of different affinity, etc., at the molecular level, probed their function and localized them at the light and electron microscopy level. SNARE proteins, in conjunction with a synaptotagmin-like Ca2+ -sensor protein, mediate membrane fusion. This interaction is additionally regulated by monomeric GTPases whose spectrum in Tetrahymena and Paramecium has been established by A. Turkewitz. As known from mammalian cells, GTPases are activated on membranes in conjunction with lumenal acidification by an H+ -ATPase. For these complex molecules, we found in Paramecium an unsurpassed number of 17 a-subunit paralogs which connect the polymeric head and basis part, V1 and V0. (This multitude may reflect different local functional requirements.) Together with plasmalemmal Ca2+ -influx channels, locally enriched intracellular InsP3 -type (InsP3 R, mainly in osmoregulatory system) and ryanodine receptor-like Ca2+ -release channels (ryanodine receptor-like proteins, RyR-LP), this complexity mediates Ca2+ signals for most flexible local membrane-to-membrane interactions. As we found, the latter channel types miss a substantial portion of the N-terminal part. Caffeine and 4-chloro-meta-cresol (the agent used to probe mutations of RyRs in man during surgery in malignant insomnia patients) initiate trichocyst exocytosis by activating Ca2+ -release channels type CRC-IV in the peripheral part of alveolar sacs. This is superimposed by Ca2+ -influx, that is, a mechanism called "store-operated Ca2+ -entry" (SOCE). For the majority of key players, we have mapped paralogs throughout the Paramecium cell, with features in common or at variance in the different organelles participating in vesicle trafficking. Local values of free Ca2+ -concentration, [Ca2+ ]i , and their change, for example, upon exocytosis stimulation, have been registered by flurochromes and chelator effects. In parallel, we have registered release of Ca2+ from alveolar sacs by quenched-flow analysis combined with cryofixation and X-ray microanalysis.

Ion channels of cilia: Paramecium as a model.

Holotrichous ciliates, like Paramecium, swim through their aqueous environment by beating their many cilia. They can alter swimming speed and direction, which seems to have mesmerized early microscopists of the 1600s. We know from extensive and elegant physiological studies and generation of mutants that these cells can be considered little swimming neurons because their ciliary beating is under bioelectric control of ion channels in the cilia. This chapter will focus on the ionic control of swimming behavior by ciliary ion channels, primarily in the holotrichous ciliate Paramecium. Voltage-gated and calcium-activated channels for calcium, magnesium, sodium, and potassium are regulated in a closely orchestrated manner that allows cilia to bend and propel the cell forward or backward. Sensory input that generates receptor potentials feeds into the control of this channel activity and allows the cell to turn or speed up. This in turn helps the cell to avoid predators or toxic conditions. While the focus is on P. tetraurelia and P. caudatum, the principles of ciliary ion channel activity and control are easily extendable to other ciliates and protists. The high conservation of channel and ion pump structures also extends the lessons from Paramecium to higher organisms.

Using Paramecium as a Model for Ciliopathies.

Paramecium has served as a model organism for the studies of many aspects of genetics and cell biology: non-Mendelian inheritance, genome duplication, genome rearrangements, and exocytosis, to name a few. However, the large number and patterning of cilia that cover its surface have inspired extraordinary ultrastructural work. Its swimming patterns inspired exquisite electrophysiological studies that led to a description of the bioelectric control of ciliary motion. A genetic dissection of swimming behavior moved the field toward the genes and gene products underlying ciliary function. With the advent of molecular technologies, it became clear that there was not only great conservation of ciliary structure but also of the genes coding for ciliary structure and function. It is this conservation and the legacy of past research that allow us to use Paramecium as a model for cilia and ciliary diseases called ciliopathies. However, there would be no compelling reason to study Paramecium as this model if there were no new insights into cilia and ciliopathies to be gained. In this review, we present studies that we believe will do this. For example, while the literature continues to state that immotile cilia are sensory and motile cilia are not, we will provide evidence that Paramecium cilia are clearly sensory. Other examples show that while a Paramecium protein is highly conserved it takes a different interacting partner or conducts a different ion than expected. Perhaps these exceptions will provoke new ideas about mammalian systems.

Efficient isolation and cultivation of endosymbiotic Chlorella from Paramecium bursaria on agar plates by co-culture with yeast cells.

Paramecium bursaria is a ciliate that harbors Chlorella-like unicellular green algae as endosymbionts. The relationship between the host P. bursaria and the endosymbiotic Chlorella is facultative; therefore, both partners can be cultured independently and re-combined to re-establish symbiosis, making this system suitable for studying algal endosymbiosis. However, despite many previous studies, cultivation of endosymbiotic Chlorella remains difficult, particularly on agar plates. Here we describe a simple agar plate method for efficiently isolating and culturing cells of the endosymbiotic alga Chlorella variabilis from an individual P. bursaria cell, by co-culturing them with yeast Saccharomyces cerevisiae. The co-culture with the yeast significantly improved the colony-forming efficiency of the alga on agar. Growth assays suggest that the main role of the co-cultured yeast cells is not to provide nutrients for the algal cells, but to protect the algal cells from some environmental stresses on the agar surface. Using the algal cells grown on the plates and a set of specially designed primers, direct colony PCR can be performed for screening of multiple endosymbiont clones isolated from a single host ciliate. These methods may provide a useful tool for studying endosymbiotic Chlorella species within P. bursaria and various other protists.

Changes in geometrical aspects of a simple model of cilia synchronization control the dynamical state, a possible mechanism for switching of swimming gaits in microswimmers.

Active oscillators, with purely hydrodynamic coupling, are useful simple models to understand various aspects of motile cilia synchronization. Motile cilia are used by microorganisms to swim and to control the flow fields in their surroundings; the patterns observed in cilia carpets can be remarkably complex, and can be changed over time by the organism. It is often not known to what extent the coupling between cilia is due to just hydrodynamic forces, and neither is it known if it is biological or physical triggers that can change the dynamical collective state. Here we treat this question from a very simplified point of view. We describe three possible mechanisms that enable a switch in the dynamical state, in a simple scenario of a chain of oscillators. We find that shape-change provides the most consistent strategy to control collective dynamics, but also imposing small changes in frequency produces some unique stable states. Demonstrating these effects in the abstract minimal model proves that these could be possible explanations for gait switching seen in ciliated micro organisms like Paramecium and others. Microorganisms with many cilia could in principle be taking advantage of hydrodynamic coupling, to switch their swimming gait through either a shape change that manifests in decreased coupling between groups of cilia, or alterations to the beat style of a small subset of the cilia.

Polarization grating based on diffraction phase microscopy for quantitative phase imaging of paramecia.

This study presents a polarization grating based diffraction phase microscopy (PG-DPM) and its application in bio-imaging. Compared with traditional diffraction phase microscopy (DPM) of which the fringe contrast is sample-dependent, the fringe contrast of PG-DPM is adjustable by changing the polarization of the illumination beam. Moreover, PG-DPM has been applied to real-time phase imaging of live paramecia for the first time. The study reveals that paramecium has self-helical forward motion characteristics, or more specifically, 77% clockwise and 23% anti-clockwise rotation when moving forward. We can envisage that PG-DPM will be applied to many different fields.

Roles of Adenylate Cyclases in Ciliary Responses of Paramecium to Mechanical Stimulation.

Paramecium shows rapid forward swimming due to increased beat frequency of cilia in normal (forward swimming) direction in response to various kinds of stimuli applied to the cell surface that cause K+ -outflow accompanied by a membrane hyperpolarization. Some adenylate cyclases are known to be functional K+ channels in the membrane. Using gene-specific knockdown methods, we examined nine paralogues of adenylate cyclases in P. tetraurelia to ascertain whether and how they are involved in the mechanical stimulus-induced hyperpolarization-coupled acceleration of forward swimming. Results demonstrated that knockdown of the adenylate cyclase 1 (ac1)-gene and 2 (ac2)-gene inhibited the acceleration of forward swimming in response to mechanical stimulation of the cell, whereas that spared the acceleration response to external application of 8-Br-cAMP and dilution of extracellular [K+ ] induced hyperpolarization. Electrophysiological examination of the knockdown cells revealed that the hyperpolarization-activated inward K+ current is smaller than that of a normal cell. Our results suggest that AC1 and AC2 are involved in the mechanical stimulus-induced acceleration of ciliary beat in Paramecium.

Paramecium Biology.

Imagine that in 1678 you are Christiaan Huygens or Antonie van Leeuwenhoek seeing paramecia swim gracefully across the field of view of your new microscope. These unicellular, free-living, and swimming cells might have remained a curiosity if not for the ability of H.S. Jennings (Behavior of the lower organisms. Indiana University Press, Bloomington, 1906) and T.M. Sonneborn (Proc Natl Acad Sci USA 23:378-385, 1937) to recognize them for their behavior and genetics, both Mendelian and non-Mendelian. Following many years of painstaking work by Sonneborn and other researchers, Paramecium now serves as a modern model organism that has made specific contributions to cell and molecular biology and development. We will review the continuing usefulness and contributions of Paramecium species in this chapter.Even without a microscope, Paramecium species is visible to the naked eye because of their size (50-300 µ long). Paramecia are holotrichous ciliates, that is, unicellular organisms in the phylum Ciliophora that are covered with cilia. It was the beating of these cilia that propelled them across the slides of the first microscopes and continue to fascinate us today. Over time, Paramecium became a favorite model organism for a large variety of studies. Denis Lyn has called Paramecium the "white rat" of the Ciliophora for their manipulability and amenity to research. We will touch upon the use of Paramecium species to examine swimming behavior, ciliary structure and function, ion channel function, basal body duplication and patterning, non-Mendelian cortical inheritance, programmed DNA rearrangements, regulated secretion and exocytosis, and cell trafficking. In particular, we will focus on the use of P. tetraurelia and P. caudatum.

Deianiraea, an extracellular bacterium associated with the ciliate Paramecium, suggests an alternative scenario for the evolution of Rickettsiales.

Rickettsiales are a lineage of obligate intracellular Alphaproteobacteria, encompassing important human pathogens, manipulators of host reproduction, and mutualists. Here we report the discovery of a novel Rickettsiales bacterium associated with Paramecium, displaying a unique extracellular lifestyle, including the ability to replicate outside host cells. Genomic analyses show that the bacterium possesses a higher capability to synthesise amino acids, compared to all investigated Rickettsiales. Considering these observations, phylogenetic and phylogenomic reconstructions, and re-evaluating the different means of interaction of Rickettsiales bacteria with eukaryotic cells, we propose an alternative scenario for the evolution of intracellularity in Rickettsiales. According to our reconstruction, the Rickettsiales ancestor would have been an extracellular and metabolically versatile bacterium, while obligate intracellularity would have evolved later, in parallel and independently, in different sub-lineages. The proposed new scenario could impact on the open debate on the lifestyle of the last common ancestor of mitochondria within Alphaproteobacteria.

Towards an ecological understanding of the killer trait - A reproducible protocol for testing its impact on freshwater ciliates.

Paramecium strains with the ability to kill other paramecia often harbour intracellular bacteria belonging to the genera Caedibacter or Caedimonas. Central structures of this killer trait are refractile bodies (R-bodies) produced by the endosymbionts. Once ingested by a sensitive Paramecium, R-bodies presumably act as delivery system for an unidentified toxin which causes the death of endosymbiont-free paramecia while those infected gain resistance from their symbionts. The killer trait is therefore considered as competitive advantage for the hosts of R-body producers. While its effectiveness against paramecia is well documented, the effects on other aquatic ciliates are much less studied. In order to address the broadness of the killer trait, a reproducible killer test assay considering the effects on predatory ciliates (Climacostomum virens and Dileptus jonesi) as well as potential bacterivorous Paramecium competitors (Dexiostoma campyla, Euplotes aediculatus, Euplotes woodruffi, and Spirostomum teres) as possibly susceptible species was established. All used organisms were molecularly characterized to increase traceability and reproducibility. The absence of any lethal effects in both predators and competitors after exposure to killer paramecia strongly suggests a narrow action range for the killer trait. Thus, R-body producing bacteria provide their host with a complex, costly strategy to outcompete symbiont-free congeners only.

Genetic basis for the establishment of endosymbiosis in Paramecium.

The single-celled ciliate Paramecium bursaria is an indispensable model for investigating endosymbiosis between protists and green-algal symbionts. To elucidate the mechanism of this type of endosymbiosis, we combined PacBio and Illumina sequencing to assemble a high-quality and near-complete macronuclear genome of P. bursaria. The genomic characteristics and phylogenetic analyses indicate that P. bursaria is the basal clade of the Paramecium genus. Through comparative genomic analyses with its close relatives, we found that P. bursaria encodes more genes related to nitrogen metabolism and mineral absorption, but encodes fewer genes involved in oxygen binding and N-glycan biosynthesis. A comparison of the transcriptomic profiles between P. bursaria with and without endosymbiotic Chlorella showed differential expression of a wide range of metabolic genes. We selected 32 most differentially expressed genes to perform RNA interference experiment in P. bursaria, and found that P. bursaria can regulate the abundance of their symbionts through glutamine supply. This study provides novel insights into Paramecium evolution and will extend our knowledge of the molecular mechanism for the induction of endosymbiosis between P. bursaria and green algae.

Is the Virus Important? And Some Other Questions.

The motivation for focusing on a specific virus is often its importance in terms of impact on human interests. The chlorella viruses are a notable exception and 40 years of research has made them the undisputed model system for large icosahedral dsDNA viruses infecting eukaryotes. Their status has changed from inconspicuous and rather odd with no ecological relevance to being the Phycodnaviridae type strain possibly affecting humans and human cognitive functioning in ways that remain to be understood. The Van Etten legacy is the backbone for research on Phycodnaviridae. After highlighting some of the peculiarities of chlorella viruses, we point to some issues and questions related to the viruses we choose for our research, our prejudices, what we are still missing, and what we should be looking for.

The remembrance of the things past: Conserved signalling pathways link protozoa to mammalian nervous system.

The aim of the present article is to analyse the evolutionary links between protozoa and neuronal and neurosecretory cells. To this effect we employ functional and topological data available for ciliates, in particular for Paramecium. Of note, much less data are available for choanoflagellates, the progenitors of metazoans, which currently are in the focus of metazoan genomic data mining. Key molecular players are found from the base to the highest levels of eukaryote evolution, including neurones and neurosecretory cells. Several common fundamental mechanisms, such as SNARE proteins and assembly of exocytosis sites, GTPases, Ca2+-sensors, voltage-gated Ca2+-influx channels and their inhibition by the forming Ca2+/calmodulin complex are conserved, albeit with different subcellular channel localisation, from protozoans to man. Similarly, Ca2+-release channels represented by InsP3 receptors and putative precursors of ryanodine receptors, which all emerged in protozoa, serve for focal intracellular Ca2+ signalling from ciliates to mammalian neuronal cells, eventually in conjunction with store-operated Ca2+-influx. Restriction of Ca2+ signals by high capacity/low affinity Ca2+-binding proteins is maintained throughout the evolutionary tree although the proteins involved differ between the taxa. Phosphatase 2B/calcineurin appears to be involved in signalling and in membrane recycling throughout evolution. Most impressive example of evolutionary conservation is the sub-second dynamics of exocytosis-endocytosis coupling in Paramecium cells, with similar kinetics in neuronal and neurosecretory systems. Numerous cell surface receptors and channels that emerge in protozoa operate in the human nervous system, whereas a variety of cell adhesion molecules are newly "invented" during evolution, enabled by an increase in gene numbers, alternative splice forms and transcription factors. Thereby, important regulatory and signalling molecules are retained as a protozoan heritage.

Phylogenetic relationships among endosymbiotic R-body producer: Bacteria providing their host the killer trait.

R-body producing bacterial endosymbionts of Paramecium spp. transform their hosts into "killer" paramecia and provide them a selective advantage. This killer trait is connected to the presence of R-bodies, which are peculiar, tightly coiled protein ribbons capable of rapid unrolling. Based mainly on those two characteristics the respective obligate intracellular bacteria have been comprised in the genus Caedibacter and additional traits such as host species, subcellular localization, and R-body dimensions and mode of unrolling were used for species discrimination. Previous studies applying the full-cycle rRNA approach demonstrated the polyphyly of this assemblage. Following this approach, we obtained new sequences and in situ hybridizations for five strains of Caedibacter taeniospiralis and four strains associated to Caedibacter varicaedens and Caedibacter caryophilus. Detailed phylogenetic reconstructions confirm the association of C. taeniospiralis to Fastidiosibacteraceae and to Holosporales in case of the others. Therefore, we critically revise the taxonomy of the latter group. The high 16S rRNA gene sequence similarity among the type strains of Caedibacter varicaedens and C. caryophilus indicate that they should be classified within a single species for which we propose Caedimonas varicaedens comb. nov. owing to the priority of Caedibacter varicaedens. Moreover, we propose to establish the new family Caedimonadaceae fam. nov. to encompass Caedimonas varicaedens, "Ca. Paracaedimonas acanthamoebae" comb. nov. and "Ca. Nucleicultrix amoebiphila" within the order Holosporales.

More than the "Killer Trait": Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host.

Endosymbiosis is a widespread phenomenon and hosts of bacterial endosymbionts can be found all-over the eukaryotic tree of life. Likely, this evolutionary success is connected to the altered phenotype arising from a symbiotic association. The potential variety of symbiont's contributions to new characteristics or abilities of host organisms are largely unstudied. Addressing this aspect, we focused on an obligate bacterial endosymbiont that confers an intraspecific killer phenotype to its host. The symbiosis between Paramecium tetraurelia and Caedibacter taeniospiralis, living in the host's cytoplasm, enables the infected paramecia to release Caedibacter symbionts, which can simultaneously produce a peculiar protein structure and a toxin. The ingestion of bacteria that harbor both components leads to the death of symbiont-free congeners. Thus, the symbiosis provides Caedibacter-infected cells a competitive advantage, the "killer trait." We characterized the adaptive gene expression patterns in symbiont-harboring Paramecium as a second symbiosis-derived aspect next to the killer phenotype. Comparative transcriptomics of infected P. tetraurelia and genetically identical symbiont-free cells confirmed altered gene expression in the symbiont-bearing line. Our results show up-regulation of specific metabolic and heat shock genes whereas down-regulated genes were involved in signaling pathways and cell cycle regulation. Functional analyses to validate the transcriptomics results demonstrated that the symbiont increases host density hence providing a fitness advantage. Comparative transcriptomics shows gene expression modulation of a ciliate caused by its bacterial endosymbiont thus revealing new adaptive advantages of the symbiosis. Caedibacter taeniospiralis apparently increases its host fitness via manipulation of metabolic pathways and cell cycle control.

Phenomena of synchronized response in biosystems and the possible mechanism.

Phenomena of synchronized response is common among organs, tissues and cells in biosystems. We have analyzed and discussed three examples of synchronization in biosystems, including the direction-changing movement of paramecia, the prey behavior of flytraps, and the simultaneous discharge of electric eels. These phenomena and discussions support an electrical communication mechanism that in biosystems, the electrical signals are mainly soliton-like electromagnetic pulses, which are generated by the transient transmembrane ionic current through the ion channels and propagate along the dielectric membrane-based softmaterial waveguide network to complete synchronized responses. This transmission model implies that a uniform electrical communication mechanism might have been naturally developed in biosystem.

Scaling from Metabolism to Population Growth Rate to Understand How Acclimation Temperature Alters Thermal Performance.

SYNOPSIS: The mean and variance of environmental temperature are changing as a consequence of human activities. Ectotherms are sensitive to these temperature changes in the short term, typically displaying a unimodal response of most biological rates to temperature (thermal performance curves; TPCs). Many organisms, however, may acclimate or evolve in response to new temperature regimes. In particular, population growth rate TPCs (r TPCs) reflect the ability to maintain positive growth under a range of temperatures, and therefore shifts in r TPCs due to acclimation are fundamental to our understanding of how ectotherms will respond to changes in climate. Here, we derive a model for r TPCs rooted in temperature dependent metabolic rate (through enzyme kinetics and activity). We then use this model to interpret the effects of acclimation to different temperatures on r TPCs of the protist Paramecium bursaria. Intermediate acclimation temperatures generally resulted in higher upper critical thermal limits, thermal optima, maximum population growth rate, and the area under the TPC. Lower critical thermal limits increased linearly with acclimation temperature, causing a decrease in thermal breadth with increased acclimation temperature. Thus, rather than showing improved performance at the acclimation temperature, P. bursaria appeared to pay a price at all temperatures for acclimating to higher temperatures. The fits of our data to our model also suggest that changes in the structure and function of metabolic enzymes may underlie the changes in the TPCs. Specifically, our results suggest that both the delta heat capacity and delta enthalpy of formation of metabolic enzymes may have increased with acclimation. Since these two factors are correlated across acclimation temperatures, our data also suggest potential trade-offs that may constrain changes in TPCs.