Graviresponses of Paramecium biaurelia during parabolic flights

The thresholds of graviorientation and gravikinesis in Paramecium biaurelia were investigated during the 5th DLR (German Aerospace Center) parabolic-flight campaign at Bordeaux in June 2003. Parabolic flights are a useful tool for the investigation of swimming behaviour in protists at different accelerations. At normal gravity (1 g) and hypergravity (1 g to 1.8 g), precision of orientation and locomotion rates depend linearly on the applied acceleration as seen in earlier centrifuge experiments. After transition from hypergravity to decreased gravity (minimal residual acceleration of <10(-2) g), graviorientation as well as gravikinesis show a full relaxation with different kinetics. The use of twelve independent cell samples per flight guarantees high data numbers and secures the statistical significance of the obtained data. The relatively slow change of acceleration between periods of microgravity and hypergravity (0.4 g/s) enabled us to determine the thresholds of graviorientation at 0.6 g and of gravikinesis at 0.4 g. The gravity-unrelated propulsion rate of the sample was found to be 874 microm/s, exceeding the locomotion rate of horizontally swimming cells (855 microm/s). The measured thresholds of graviresponses were compared with data obtained from earlier centrifuge experiments on the sounding rocket Maxus-2. Measured thresholds of gravireactions indicate that small energies, close to the thermal noise level, are sufficient for the gravitransduction process. Data from earlier hypergravity experiments demonstrate that mechanosensitive ion channels are functioning over a relative wide range of acceleration. From this, we may speculate that gravireceptor channels derive from mechanoreceptor channels.     

Optospectroscopic detection of primary reactions associated with the graviperception of Phycomyces. Effects of micro- and hypergravity

The graviperception of sporangiophores of the fungus Phycomyces blakesleeanus involves gravity-induced absorbance changes (GIACs) that represent primary responses of gravitropism (Schmidt and Galland, 2000). GIACs (DeltaA(460-665)) of sporangiophores were measured in vivo with a micro-dual wavelength spectrometer at 460 and 665 nm. Sporangiophores that were placed horizontally displayed an instant increase of the GIACs while the return to the vertical position elicited an instant decrease. The GIACs are specific for graviperception, because they were absent in a gravitropism mutant with a defective madJ gene. During parabola flights hypergravity (1.8 g) elicited a decrease of the GIACs, while microgravity (0 +/- 3 x 10 (-2) g) elicited an instant increase. Hypergravity that was generated in a centrifuge (1.5-6.5 g) elicited also a decrease of the GIACs that saturated at about 5 g. The GIACs have a latency of about 20 ms or shorter and are thus the fastest graviresponses ever measured for fungi, protists, and plants. The threshold for eliciting the GIACs is near 3 x 10 (-2) g, which coincides numerically with the threshold for gravitropic bending. In contrast to gravitropic bending, which requires long-term stimulation, GIACs can be elicited by stimuli as short as 20 to 100 ms, leading to an extremely low threshold dose (acceleration x time) of about 3 x 10 (-3) g s, a value, which is four orders of magnitude below the ones described for other organisms and which makes the GIACs of Phycomyces blakesleeanus the most sensitive gravi-response in literature.     

Chemical information transfer between plants:: back to the future

Chemical information conveyance between organisms has been well established for a wide range of organisms including protozoa, invertebrates, vertebrates and plant-parasitic plants. During the past 20 years, various studies have addressed whether chemical information conveyance also occurs between damaged and undamaged plants and many interesting pieces of evidence have been presented. To date, this research field has been restricted to the question whether and how plants (in general) are involved in plant-to-plant communication. However, apart from mechanistic questions, evolutionary questions should be addressed asking why plants do (or do not) exploit their neighbour's information and whether their strategy is affected by e.g. environmental conditions or previous experience. Recent progress in the field of chemical information conveyance between damaged and undamaged plants warrants an intensified study of this exciting topic in chemical ecology.     

Protist taxonomy: an ecological perspective

This is an exploration of contemporary protist taxonomy within an ecological perspective. As it currently stands, the 'morphospecies' does not accommodate the information that might support a truly ecological species concept for the protists. But the 'morphospecies' is merely a first step in erecting a taxonomy of the protists, and it is expected to become more meaningful in the light of genetic, physiological and ecological research in the near future. One possible way forward lies in the recognition that sexual and asexual protists may all be subject to forces of cohesion that result in (DNA) sequence-similarity clusters. A starting point would then be the detection of 'ecotypes'--where genotypic and phenotypic clusters correspond; but for that we need better information regarding the extent of clonality in protists, and better characterization of ecological niches and their boundaries. There is some progress with respect to the latter. Using the example of a community of ciliated protozoa living in the stratified water column of a freshwater pond, it is shown to be possible to gauge the potential of protists to partition their local environment into ecological niches. Around 40 morphospecies can coexist in the superimposed water layers, which presumably represent different ecological niches, but we have yet to discover if these are discrete or continuously variable. It is a myth that taxonomic problems are more severe for protists than for animals and plants. Most of the fundamental problems associated with species concepts (e.g. asexuals, sibling species, phenotypic variation) are distributed across biota in general. The recent history of the status of Pfiesteria provides a model example of an integrated approach to solving what are essentially taxonomic problems.     

Molecular Identification of Nanoplanktonic Protists Based on Small Subunit Ribosomal RNA Gene Sequences for Ecological Studies1

Nanoplanktonic protists are comprised of a diverse assemblage of species which are responsible for a variety of trophic processes in marine and freshwater ecosystems. Current methods for identifying small protists by electron microscopy do not readily permit both identification and enumeration of nanoplanktonic protists in field samples. Thus, one major goal in the application of molecular approaches in protistan ecology has been the detection and quantification of individual species in natural water samples. Sequences of small subunit ribosomal RNA (SSU rRNA) genes have proven to be useful towards achieving this goal. Comparison of sequences from clone libraries of protistan SSU rRNA genes amplified from natural assemblages of protists by the polymerase chain reaction (PCR) can be used to examine protistan diversity. Furthermore, oligonucleotide probes complementary to short sequence regions unique to species of small protists can be designed by comparative analysis of rRNA gene sequences. These probes may be used to either detect the RNA of particular species of protists in total nucleic acid extracts immobilized on membranes, or the presence of target species in water samples via in situ hybridization of whole cells. Oligonucleotide probes may also serve as primers for the selective amplification of target sequences from total population DNA by PCR. Thus, molecular sequence information is becoming increasingly useful for identifying and enumerating protists, and for studying their spatial and temporal distribution in nature. Knowledge of protistan species composition, abundance and variability in an environment can ultimately be used to relate community structure to various aspects of community function and biogeochemical activity.     

Kin Discrimination in Protists: From Many Cells to Single Cells and Backwards

During four decades (1960–1990s), the conceptualization and experimental design of studies in kin recognition relied on work with multicellular eukaryotes, particularly Unikonta (including invertebrates and vertebrates) and some Bikonta (including plants). This pioneering research had an animal behavior approach. During the 2000s, work on taxa‐, clone‐ and kin‐discrimination and recognition in protists produced genetic and molecular evidence that unicellular organisms (e.g. Saccharomyces, Dictyostelium, Polysphondylium, Tetrahymena, Entamoeba and Plasmodium) could distinguish between same (self or clone) and different (diverse clones), as well as among conspecifics of close or distant genetic relatedness. Here, we discuss some of the research on the genetics of kin discrimination/recognition and highlight the scientific progress made by switching emphasis from investigating multicellular to unicellular systems (and backwards). We document how studies with protists are helping us to understand the microscopic, cellular origins and evolution of the mechanisms of kin discrimination/recognition and their significance for the advent of multicellularity. We emphasize that because protists are among the most ancient organisms on Earth, belong to multiple taxonomic groups and occupy all environments, they can be central to reexamining traditional hypotheses in the field of kin recognition, reformulating concepts, and generating new knowledge.     

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.     

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.     

Diversification of the Microtubule System in the Early Stage of Eukaryote Evolution: Elongation Factor 1α and α-Tubulin Protein Phylogeny of Termite Symbiotic Oxymonad and Hypermastigote Protists

The symbiotic protists of the lower termite have been regarded as a model of early-branched eukaryotes because of their simple cellular systems and morphological features. However, cultivation of these symbiotic protists is very difficult. For this reason, these interesting protists have not been well characterized in terms of their molecular biology. In research on these organisms which have not yet been cultivated, we developed a method for retrieving specific genes from a small number of cells, through micromanipulation without axenic cultivation, and we obtained EF-1 alpha and alpha-tubulin genes from members of the Hypermastigida--the parabasalid protist Trichonympha agilis and the oxymonad protists Pyrsonympha grandis and Dinenympha exilis--from the termite Reticulitermes speratus gut community. Results of phylogenetic analysis of the amino acid sequences of both proteins, EF-1 alpha and alpha-tubulin, indicate that the hypermastigid, parabasalid, and oxymonad protists do not share a close common ancestor. In addition, although the EF-1 alpha phylogeny indicates that these two groups of protists branched at an early stage of eukaryotic evolution, the alpha-tubulin phylogeny indicates that these protists can be assigned to two diversified clades. As shown in a recent investigation of alpha-tubulin phylogeny, eukaryotic organisms can be divided into three classes: an animal--parabasalids clade, a plant--protists clade, and the diplomonads. In this study, we show that parabasalids, including hypermastigids, can be classified as belonging to the animal--parabasalids clade and the early-branching eukaryote oxymonads can be classified as belonging to the plant--protists clade. Our findings suggest that these protists have a cellular microtubule system that has diverged considerably, and it seems that such divergence of the microtubule system occurred in the earliest stage of eukaryotic evolution.     

Rewiring and regulation of cross-compartmentalized metabolism in protists

Plastid acquisition, endosymbiotic associations, lateral gene transfer, organelle degeneracy or even organelle loss influence metabolic capabilities in many different protists. Thus, metabolic diversity is sculpted through the gain of new metabolic functions and moderation or loss of pathways that are often essential in the majority of eukaryotes. What is perhaps less apparent to the casual observer is that the sub-compartmentalization of ubiquitous pathways has been repeatedly remodelled during eukaryotic evolution, and the textbook pictures of intermediary metabolism established for animals, yeast and plants are not conserved in many protists. Moreover, metabolic remodelling can strongly influence the regulatory mechanisms that control carbon flux through the major metabolic pathways. Here, we provide an overview of how core metabolism has been reorganized in various unicellular eukaryotes, focusing in particular on one near universal catabolic pathway (glycolysis) and one ancient anabolic pathway (isoprenoid biosynthesis). For the example of isoprenoid biosynthesis, the compartmentalization of this process in protists often appears to have been influenced by plastid acquisition and loss, whereas for glycolysis several unexpected modes of compartmentalization have emerged. Significantly, the example of trypanosomatid glycolysis illustrates nicely how mathematical modelling and systems biology can be used to uncover or understand novel modes of pathway regulation.     

A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis

Sexual reproduction in eukaryotes is accomplished by meiosis, a complex and specialized process of cell division that results in haploid cells (e.g., gametes). The stereotypical reductive division in meiosis is a major evolutionary innovation in eukaryotic cells, and delineating its history is key to understanding the evolution of sex. Meiosis arose early in eukaryotic evolution, but when and how meiosis arose and whether all eukaryotes have meiosis remain open questions. The known phylogenetic distribution of meiosis comprises plants, animals, fungi, and numerous protists. Diplomonads including Giardia intestinalis (syn. G. lamblia) are not known to have a sexual cycle; these protists may be an early-diverging lineage and could represent a premeiotic stage in eukaryotic evolution. We surveyed the ongoing G. intestinalis genome project data and have identified, verified, and analyzed a core set of putative meiotic genes-including five meiosis-specific genes-that are widely present among sexual eukaryotes. The presence of these genes indicates that: (1) Giardia is capable of meiosis and, thus, sexual reproduction, (2) the evolution of meiosis occurred early in eukaryotic evolution, and (3) the conserved meiotic machinery comprises a large set of genes that encode a variety of component proteins, including those involved in meiotic recombination.     

Conservation of protists: is it needed at all?

Protists have scarcely been considered in traditional perspectives and strategies in environmental management and biodiversity conservation. This is a remarkable omission given that these tiny organisms are highly diverse, and have performed as key ecological players in evolutionary theatres for over a billion years of Earth history. Protists hold key roles in nearly all ecosystems, notably as participants in fluxes of energy and matter through foodwebs that centre on their predation on microbes. In spite of this, they have been largely ignored in conservation issues due to a widespread, naive belief that protists are ubiquitous and cosmopolitanously distributed. Nevertheless, recent research shows that many protists have markedly restricted distributions. These range from palaeoendemics (Gondwanan-Laurasian distribution) to local endemics. Our ignorance about the ultimate and proximate causes of such acute disparities in scale-dependent distributions of protists can be flagged as a singular reason to preserve these more cryptic participants in ecological and evolutionary dynamics. This argument is disturbing when one considers anthropogenic modifications of landscapes and the very poorly understood roles of protists in ecological processes in soils, not least in agroecolandscapes and hydrological systems. Major concerns include host specific symbiotic, symphoric and parasitic species which become extinct, unseen and largely unknown, alongside their metazoan hosts; change or loss of habitats; massive change or loss of type localities; and losses of unique genetic resources and evolutionary potential. These concerns are illustrated by examples to argue that conservation of protists should be integral to any strategy that traditionally targets vascular plants and animals. The ongoing decline in research capacity to inventory and classify protist diversity exemplifies a most acute symptom of the failures, at local, national and international levels, to support scientific responses to the biodiversity crisis. Responsible responses to these severe problems need to centre on the revival of natural history as the core discipline in biology. F. P. D. Cotterill: Formerly Principal Curator of Vertebrates, Natural History Museum of Zimbabwe, P.O. Box 240, Bulawayo, Zimbabwe Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner     

Molecular characterization of nucleocytosolic O-GlcNAc transferases of Giardia lamblia and Cryptosporidium parvum

O-Linked N-acetylglucosaminyltransferase (OGT) catalyzes the transfer of a single GlcNAc to the Ser or Thr of nucleocytoplasmic proteins. OGT activity, which may compete with that of kinases, is involved in signaling in animals and plants, and abnormalities in OGT activities have been associated with type 2 diabetes. Here, we show that ogt genes that predict enzymes with characteristic tetratricopeptide repeats and a spindly domain are present in some protists (Giardia, Cryptosporidium, Toxoplasma, and Dictyostelium) but are absent from the majority of protists examined (e.g., Plasmodium, Trypanosoma, Entamoeba, and Trichomonas). Similarly, ogt genes are present in some fungi but are absent from numerous other fungi, suggesting that secondary loss is an important contributor to the evolution of ogt genes. Nucleocytosolic extracts of Giardia and Cryptosporidium show OGT activity, and recombinant Giardia and Cryptosporidium OGTs are active in yeast and bacteria, respectively. These results suggest the possibility that O-GlcNAc modification of nucleocytosolic proteins also has function(s) in simple eukaryotes.     

Human mesenchymal stem cells are sensitive to abnormal gravity and exhibit classic apoptotic features

The aim of the present study was to investigate the effects of abnormal gravity on human mesenchymal stem cells (hMSCs). Strong magnetic field and magnetic field gradient generate a magnetic force that can add to or subtract from the gravitational force. In this study, this is defined as a high-magneto-gravitational environment (HMGE). The HMGE provides three apparent gravity levels, i.e. hypogravity (μg), hypergravity (2g) and normal gravity with strong magnetic field (1g) conditions. After hMSCs were subject to HMGE for 12 h, the proliferation, morphology, structure and apoptosis were investigated. Results showed that the proliferation of hMSCs was inhibited under μg condition. The abnormal gravity induced morphologic characteristics of apoptosis cells, such as cell shrinkage, membrane blebbing, nuclear chromatin condensation and margination, decreased cell viability, and increased caspase-3/7 activity. The rate of apoptosis under μg condition is up to 56.95%. The F-actin stress fibers and microtubules were disrupted under abnormal gravity condition. Under μg-condition, the expression of p53 at mRNA and protein levels was up-regulated more than 9- and 6 folds, respectively. The Pifithrin-α, an specific inhibitor of p53, inhibited the apoptosis and prevented the disruption of cytoskeleton induced by abnormal gravity. These results implied that hMSCs were sensitive to abnormal gravity and exhibited classic apoptotic features, which might be associated with p53 signaling.     

Protist homologs of the meiotic Spo11 gene and topoisomerase VI reveal an evolutionary history of gene duplication and lineage-specific loss

Spo11 is a meiotic protein of fundamental importance as it is a conserved meiosis-specific transesterase required for meiotic recombination initiation in fungi, animals, and plants. Spo11 is homologous to the archaebacterial topoisomerase VIA (Top6A) gene, and its homologs are broadly distributed among eukaryotes, with some eukaryotes having more than one homolog. However, the evolutionary relationships among these genes are unclear, with some debate as to whether eukaryotic homologs originated by lateral gene transfer. We have identified and characterized protist Spo11 homologs by degenerate polymerase chain reaction (PCR) and sequencing and by analyses of sequences from public databases. Our phylogenetic analyses show that Spo11 homologs evolved by two ancient eukaryotic gene duplication events prior to the last common ancestor of extant eukaryotes, resulting in three eukaryotic paralogs: Spo11-1, Spo11-2, and Spo11-3. Spo11-1 orthologs encode meiosis-specific proteins and are distributed broadly among eukaryotic lineages, though Spo11-1 is absent from some protists. This absence coincides with the presence of Spo11-2 orthologs, which are meiosis-specific in Arabidopsis and are found in plants, red algae, and some protists but absent in animals and fungi. Spo11-3 encodes a Top6A subunit that interacts with topoisomerase VIB (Top6B) subunits, which together play a role in vegetative growth in Arabidopsis. We identified Spo11-3 (Top6A) and Top6B homologs in plants, red algae, and a few protists, establishing a broader distribution of these genes among eukaryotes, indicating their likely vertical descent followed by lineage-specific loss.     

Protist diversity and distribution: some basic considerations

This essay discusses protist species number and geographic distribution, both heavily influenced by undersampling and human introductions. The features of the ubiquity model and the moderate endemicity model are compared. I recognize five main flaws of the ubiquity model, viz., the ignorance of the extraordinary possibilities protists have to speciate due to their short generation time and the likelihood that many persisted over geological time scales; that all protist species have high abundances; that their small size is a main reason for global distribution; the ignorance of human introductions; and the rejection of literature evidence on the occurrence of flagship species with restricted distribution in a wide variety of protists. Thus, the data available support the moderate endemicity model which proposes about 300,000 extant, free-living protist species, of which one third might have a restricted distribution, i.e., is not cosmopolitan in spite of suitable habitats. To sum up, the distribution of protists, flowering plants, and larger animals has much in common, but protists usually have wider ranges and thus a higher proportion of cosmopolites. Future research should reconcile morphologic, genetic, and ecological species concepts because this is crucial for determining the number of protist species. Further, greatly intensified research is required on morphospecies in heterotrophic protists because their diversity has never been investigated in large areas of the earth. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Preface to special issue: "Molecular mechanism of the adaptation of terrestrial plants to gravity environment on Earth"]

Organisms borne in the primitive sea about 30 million years ago had evolved in water without a large influence of gravity on earth. About 4 million years ago, the first terrestrial organisms, plants appeared on the land from the sea. The terrestrial plants have adapted to and evolved on the land environment so that they can extend their roots downward in soil and their shoots upward against 1 g gravity. At least two functions that were acquired during the process of evolution helped the terrestrial plants to adapt to gravity environment on earth. One is gravitropism. The other is the reinforcement of the cell wall, particularly the secondary cell wall. In the present feature articles, the molecular mechanism of the adaptation of terrestrial plants to gravity environment on earth will be reviewed, paying special attention to the mechanism of the genetic control of the signaling of gravity stimulus in gravitropism, automorphogenesis, genes involved in auxin transport, gravity effect on cell wall properties and gravimorphogenesis in terrestrial plants.