Order Desmothoracida, the desmothoracids, are a group of heliozoan protists sessile and found in freshwater environments. The adult is a spherical cell around 10-20 μm in diameter surrounded by a perforated organic lorica, or shell, with many radial pseudopods projecting through the holes to capture food; these are supported by small bundles of microtubules that arise near a point on the nuclear membrane. Unlike other heliozoans, the microtubules are not in any regular geometric array, there does not appear to be a microtubule organizing center, there is no distinction between the outer and inner cytoplasm. Reproduction takes place by the budding-off of small motile cells with two flagella; these are lost, the pseudopods and lorica are formed. A single lengthened pseudopod will secrete a hollow stalk that attaches the cell to the substrate; the form of the flagella, the tubular cristae within the mitochondria, other characters have led to the suggestion that the desmothoracids belong among what is now the Cercozoa.
This was confirmed by genetic studies. As of the year 2000, the order Desmothoracida contained five genera with a total of 10 species. Order Desmothoracida Hartwig & Lesser 1874 emend. Honigberg et al. 1964 Family Clathrulinidae Claus 1874Genus Clathrulina Cienkowski 1867 Species Clathrulina elegans Cienkowski 1867 Species Clathrulina smaragdea Mikrjukov 2000 Genus Hedriocystis Hertwig & Lesser 1874 Species Hedriocystis pellucida Hertwig & Lesser 1874 Species Hedriocystis minor Siemensma 1991 Species Hedriocystis zhadani Mikrjukov 2000 Genus Penardiophrys Mikrjukov 2000 Species Penardiophrys reticulata Mikrjukov 2000 Species Penardiophrys spinifera Mikrjukov 2000 Genus Cienkowskya Schaudinn 1896 non Regel & Rach 1859 non Solms 1867 Species Cienkowskya mereschkovckii Schaudinn 1896 Species Cienkowskya brachypous Mikrjukov 2000 Genus Actinosphaeridium Zacharias 1893 Species Actinosphaeridium pedatus Zacharias 1893 Nikolaev, S. I.. "Genetic relationships between desmothoracid Heliozoa and gymnophryid amoebas as evidenced by comparison of 18S rRNA genes".
Doklady Biological Sciences. 393: 553–6. Doi:10.1023/B:DOBS.0000010322.33294.9f. PMID 14994549
A pseudopod or pseudopodium is a temporary arm-like projection of a eukaryotic cell membrane. Filled with cytoplasm, pseudopodia consist of actin filaments and may contain microtubules and intermediate filaments. Pseudopods are used for ingestion. Different types of pseudopodia can be classified by their distinct appearances. Lamellipodia are thin. Filopodia are slender, thread-like, are supported by microfilaments. Lobopodia are amoebic. Reticulopodia are complex structures bearing individual pseudopodia. Axopodia are the phagocytosis type with long, thin pseudopods supported by complex microtubule arrays enveloped with cytoplasm; however some pseudopodial cells are able to use multiple types of pseudopodia depending on the situation: Most of them use a combination of lamellipodia and filopodia to migrate. The human foreskin fibroblasts can either use lamellipodia- or lobopodia-based migration in a 3D matrix depending on the matrix elasticity. Several pseudopodia arise from the surface of the body, or, a single pseudopod may form on the surface of the body.
Cells which make pseudopods are referred to as amoeboids. To move towards a target, the cell uses chemotaxis, it senses extracellular signalling molecules, chemoattractants, to extend pseudopodia at the membrane area facing the source of these molecules. The chemoattractants bind to G protein-coupled receptors, which activate GTPases of the Rho family via G-proteins. Rho GTPases are able to activate WASp which in turn activate Arp2/3 complex which serve as nucleation sites for actin polymerization; the actin polymers push the membrane as they grow, forming the pseudopod. The pseudopodium can adhere to a surface via its adhesion proteins, pull the cell's body forward via contraction of an actin-myosin complex in the pseudopod; this type of locomotion is called Amoeboid movement. Rho GTPases can activate phosphatidylinositol 3-kinase which recruit PIP3 to the membrane at the leading edge and detach the PIP3-degrading enzyme PTEN from the same area of the membrane. PIP3 activate GTPases back via GEF stimulation.
This serves as a feedback loop to amplify and maintain the presence of local GTPase at the leading edge. Otherwise, pseudopodia can't grow on other sides of the membrane than the leading edge because myosin filaments prevent them to extend; these myosin filaments are induced by cyclic GMP in D. discoideum or Rho kinase in neutrophils for example. In the case there is no extracellular cue, all moving cells navigate in random directions, but they can keep the same direction for some time before turning; this feature allows cells to explore large areas for colonization or searching for a new extracellular cue. In Dictyostelium cells, a pseudopodium can form either de novo as normal, or from an existing pseudopod, forming a Y-shaped pseudopodium; the Y-shaped pseudopods are used by Dictyostelium to advance straight forward by alternating between retraction of the left or right branch of the pseudopod. The de novo pseudopodia form at different sides than pre-existing ones, they are used by the cells to turn.
Y-shaped pseudopods are more frequent than de novo ones, which explain the preference of the cell to keep moving to the same direction. This persistence is modulated by PLA2 and cGMP signalling pathways; the functions of pseudopodia include locomotion and ingestion: Pseudopodia are critical in sensing targets which can be engulfed. A common example of this type of amoeboid cell is the macrophage, they are essential to amoeboid-like locomotion. Human mesenchymal stem cells are a good example of this function: these migratory cells are responsible for in-utero remodeling. Pseudopods can be classified into several varieties according to the number of projections, according to their appearance: Lamellipodia are broad and flat pseudopodia used in locomotion, they are supported by microfilaments which form at the leading edge, creating a mesh-like internal network. Filopodia are slender and filiform with pointed ends, consisting of ectoplasm; these formations are supported by microfilaments which, unlike the filaments of lamellipodia with their net-like actin, form loose bundles by cross-linking.
This formation is due to bundling proteins such as fimbrins and fascins. Filopodia are observed in some animal cells: in part of Filosa, in "Testaceafilosia", in Vampyrellidae and Pseudosporida and in Nucleariida. Lobopodia are bulbous and blunt in form; these finger-like, tubular pseudopodia contain both endoplasm. They can be found in different kind of cells, notably in Lobosa and other Amoebozoa and in some Heterolobosea. High-pressure lobopodia can be found in human fibroblasts travelling through a complex network of 3D matrix. Contrarily to other pseudopodia using the pressure exerted by actin polymerization on the membrane to extend, fibroblast lobopods use the nuclear piston mechanism consisting in pulling the nucleus via actomyosin contractility to push the cytoplasm that in turn push the membrane, leading to pseudopod formation. To occur, this lobopodia-based fibroblast migration needs nesprin 3, RhoA
The tectofilosids are a group of filose amoebae with shells. These are composed of organic materials and sometimes collected debris, in contrast to the euglyphids, which produce shells from siliceous scales; the shell has a single opening, but in Amphitrema and a few other genera it has two on opposite ends. The cell itself occupies most of the shell, they are most found on marsh plants such as Sphagnum. This group was classified as the Gromiida or Gromiina. However, molecular studies separate Gromia from the others, they are placed among the Cercozoa, developed from flagellates like Cryothecomonas, which has a similar test. However, only a few have been studied in detail, so their relationships and monophyly are not yet certain. In a recent classification, the group Tectofilosida was not used: Chlamydophryidae, Pseudodifflugiidae and Volutellidae were dispersally placed in Thecofilosea, while Amphitremidae was included in Labyrinthulomycetes. Order Tectofilosida Cavalier-Smith & Chao 2003 Suborder Lithocollina Cavalier-Smith 2012Family Lithocollidae Schulze 1874 Suborder Unitremina Cavalier-Smith 2012 Family Rhizaspididae Howe et al. 2011 Family Fiscullidae Dumack et al. 2017 Family Pseudodifflugiidae De Saedeleer 1934 Family Psammonobiotidae Golemansky 1974 emend Meisterfeld 2002 Family Chlamydophryidae de Saedeleer 1934 emend.
Meisterfeld 2002 Family Volutellidae Sudzuki 1979
Wagneria is a genus of flies in the family Tachinidae. More junior homonyms exist of Wagneria than any other animal genus name; these 20 species belong to the genus Wagneria: Data sources: i = ITIS, c = Catalogue of Life, g = GBIF, b = Bugguide.net
Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes, which have no membrane-bound organelles. Eukaryotes belong to Eukarya, their name comes from the Greek εὖ and κάρυον. Eukaryotic cells contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may be multicellular and include organisms consisting of many cell types forming different kinds of tissue. Animals and plants are the most familiar eukaryotes. Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, DNA replication is followed by two rounds of cell division to produce four haploid daughter cells; these act as sex cells. Each gamete has just one set of chromosomes, each a unique mix of the corresponding pair of parental chromosomes resulting from genetic recombination during meiosis.
The domain Eukaryota appears to be monophyletic, makes up one of the domains of life in the three-domain system. The two other domains and Archaea, are prokaryotes and have none of the above features. Eukaryotes represent a tiny minority of all living things. However, due to their much larger size, their collective worldwide biomass is estimated to be about equal to that of prokaryotes. Eukaryotes evolved 1.6–2.1 billion years ago, during the Proterozoic eon. The concept of the eukaryote has been attributed to the French biologist Edouard Chatton; the terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1937 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes; however he mentioned this in only one paragraph, the idea was ignored until Chatton's statement was rediscovered by Stanier and van Niel.
In 1905 and 1910, the Russian biologist Konstantin Mereschkowski argued that plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, itself formed by symbiosis between an amoeba-like host and a bacterium-like cell that formed the nucleus. Plants had thus inherited photosynthesis from cyanobacteria. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in eukaryotic cells in her paper, On the origin of mitosing cells. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA; this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles and chloroplasts. In 1977, Woese and George Fox introduced a "third form of life", which they called the Archaebacteria. In 1979, G. W. Gould and G. J. Dring suggested that the eukaryotic cell's nucleus came from the ability of Gram-positive bacteria to form endospores. In 1987 and papers, Thomas Cavalier-Smith proposed instead that the membranes of the nucleus and endoplasmic reticulum first formed by infolding a prokaryote's plasma membrane.
In the 1990s, several other biologists proposed endosymbiotic origins for the nucleus reviving Mereschkowski's theory. Eukaryotic cells are much larger than those of prokaryotes having a volume of around 10,000 times greater than the prokaryotic cell, they have a variety of internal membrane-bound structures, called organelles, a cytoskeleton composed of microtubules and intermediate filaments, which play an important role in defining the cell's organization and shape. Eukaryotic DNA is divided into several linear bundles called chromosomes, which are separated by a microtubular spindle during nuclear division. Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system. Simple compartments, called vesicles and vacuoles, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and pinches off to form a vesicle, it is probable that most other membrane-bound organelles are derived from such vesicles.
Alternatively some products produced by the cell can leave in a vesicle through exocytosis. The nucleus is surrounded with pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form the endoplasmic reticulum, involved in protein transport and maturation, it includes the rough endoplasmic reticulum where ribosomes are attached to synthesize proteins, which enter the interior space or lumen. Subsequently, they enter vesicles, which bud off from the smooth endoplasmic reticulum. In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles, the Golgi apparatus. Vesicles may be specialized for various purposes. For instance, lysosomes contain digestive enzymes that break down most biomolecules in the cytoplasm. Peroxisomes are used to break down peroxide, otherwise toxic. Many protozoans have contractile vacuoles, which collect and expel excess water, extrusomes, which expel material used to deflect predators or capture prey.
In higher plants, most of a cell's volume is taken up by a central vacuole, whi
A flagellum is a lash-like appendage that protrudes from the cell body of certain bacteria and eukaryotic cells termed as flagellates. A flagellate can have several flagella; the primary function of a flagellum is that of locomotion, but it often functions as a sensory organelle, being sensitive to chemicals and temperatures outside the cell. The similar structure in the archaea functions in the same way but is structurally different and has been termed the archaellum. Flagella are organelles defined by function rather than structure. Flagella vary greatly. Both prokaryotic and eukaryotic flagella can be used for swimming but they differ in protein composition and mechanism of propulsion; the word flagellum in Latin means whip. An example of a flagellated bacterium is the ulcer-causing Helicobacter pylori, which uses multiple flagella to propel itself through the mucus lining to reach the stomach epithelium. An example of a eukaryotic flagellate cell is the mammalian sperm cell, which uses its flagellum to propel itself through the female reproductive tract.
Eukaryotic flagella are structurally identical to eukaryotic cilia, although distinctions are sometimes made according to function or length. Fimbriae and pili are thin appendages, but have different functions and are smaller. Three types of flagella have so far been distinguished: bacterial and eukaryotic; the main differences among these three types are: Bacterial flagella are helical filaments, each with a rotary motor at its base which can turn clockwise or counterclockwise. They provide two of several kinds of bacterial motility. Archaeal flagella are superficially similar to bacterial flagella, but are different in many details and considered non-homologous. Eukaryotic flagella—those of animal and protist cells—are complex cellular projections that lash back and forth. Eukaryotic flagella are classed along with eukaryotic motile cilia as undulipodia to emphasize their distinctive wavy appendage role in cellular function or motility. Primary cilia are immotile, are not undulipodia; the bacterial flagellum is made up of the protein flagellin.
Its shape is a 20-nanometer-thick hollow tube. It has a sharp bend just outside the outer membrane. A shaft runs between the hook and the basal body, passing through protein rings in the cell's membrane that act as bearings. Gram-positive organisms have two of these basal body rings, one in the peptidoglycan layer and one in the plasma membrane. Gram-negative organisms have four such rings: the L ring associates with the lipopolysaccharides, the P ring associates with peptidoglycan layer, the M ring is embedded in the plasma membrane, the S ring is directly attached to the plasma membrane; the filament ends with a capping protein. The flagellar filament is the long, helical screw that propels the bacterium when rotated by the motor, through the hook. In most bacteria that have been studied, including the Gram-negative Escherichia coli, Salmonella typhimurium, Caulobacter crescentus, Vibrio alginolyticus, the filament is made up of 11 protofilaments parallel to the filament axis; each protofilament is a series of tandem protein chains.
However, Campylobacter jejuni has seven protofilaments. The basal body has several traits in common with some types of secretory pores, such as the hollow, rod-like "plug" in their centers extending out through the plasma membrane; the similarities between bacterial flagella and bacterial secretory system structures and proteins provide scientific evidence supporting the theory that bacterial flagella evolved from the type-three secretion system. The bacterial flagellum is driven by a rotary engine made up of protein, located at the flagellum's anchor point on the inner cell membrane; the engine is powered by proton motive force, i.e. by the flow of protons across the bacterial cell membrane due to a concentration gradient set up by the cell's metabolism. The rotor transports protons across the membrane, is turned in the process; the rotor alone can operate at 6,000 to 17,000 rpm, but with the flagellar filament attached only reaches 200 to 1000 rpm. The direction of rotation can be changed by the flagellar motor switch instantaneously, caused by a slight change in the position of a protein, FliG, in the rotor.
The flagellum is energy efficient and uses little energy. The exact mechanism for torque generation is still poorly understood; because the flagellar motor has no on-off switch, the protein epsE is used as a mechanical clutch to disengage the motor from the rotor, thus stopping the flagellum and allowing the bacterium to remain in one place. The cylindrical shape of flagella is suited to locomotion of microscopic organisms; the rotational speed of flagella varies in response to the intensity of the proton motive force, thereby permitting certain forms of speed control, permitting some types of bacteria to attain remarkable speeds in proportion to their size. At such a speed, a bacterium would take about 245 days to cover 1 km. In comparison to macroscopic life forms, it is fast indeed when expressed in terms of number of body lengths p
The Cercozoa are a group of single-celled eukaryotes. They lack shared morphological characteristics at the microscopic level, being defined by molecular phylogenies of rRNA and actin or polyubiquitin; the group flagellates that feed by means of filose pseudopods. These may be restricted to part of the cell surface, but there is never a true cytostome or mouth as found in many other protozoa, they show a variety of forms and have proven difficult to define in terms of structural characteristics, although their unity is supported by genetic studies. Cercozoa are related to Foraminifera and Radiolaria, amoeboids that have complex shells, together with them form a supergroup called the Rhizaria, they are sometimes grouped by whether they are "filose" or "reticulose". The best-known Cercozoa are the euglyphids, filose amoebae with shells of siliceous scales or plates, which are found in soils, nutrient-rich waters, on aquatic plants; some other filose amoebae produce organic shells, including Gromia.
They were classified with the euglyphids as the Testaceafilosia. This group is not monophyletic, but nearly all studied members fall in or near the Cercozoa, related to shelled flagellates. Other notable filose cercozoans include the cercomonads. Another important group placed here are the chlorarachniophytes, strange amoebae that form a reticulating net, they are set apart by the presence of chloroplasts, which developed from an ingested green alga. They still possess a vestigial nucleus, called a nucleomorph; as such, they have been of great interest to researchers studying the endosymbiotic origins of organelles. Chlorarachniophytes are sometimes considered Filosa, rather than Endomyxa, while groups such as Gromia are considered Endomyxa. Filosa is a monophyletic group, but Endomyxa is paraphyletic. In addition, three groups that are traditionally considered heliozoans belong here: the Heliomonadida and Gymnosphaerida, which were grouped into the new class of Granofilosea. Cercozoans include the Phaeodarea, marine protozoa that were considered radiolarians.
The exact composition and classification of the Cercozoa are still being worked out. A general scheme is: In addition two groups of parasites, the Phytomyxea and Ascetosporea, the shelled amoeba Gromia may be basal Cercozoa, although some trees place them closer to the Foraminifera; the spongomonads have been included here, but more have been considered Amoebozoa. Some other small groups of protozoans are considered Cercozoa but are of uncertain placement, it is many obscure genera will turn out to be cercozoans with further study. Phylogeny based on al.. 2009, Howe etal. 2011 and Silar 2016. In 2019, Cercozoa were recognized as sister to Retaria in Rhizaria. Phylum Cercozoa Family? Gymnophrydiidae Family? Gymnophryidae Mikrjukov & Mylnikov 1996 Family? Rhizoplasmidae Cavalier-Smith & Bass 2009 Order? Gymnosphaerida Poche 1913 emend. Mikrjukov 2000 Family Gymnosphaeridae Poche 1913 Clade Marimyxia Cavalier-Smith 2017 Order Reticulosida Cavalier-Smith 2003 emend. Bass et al. 2009 Family Filoretidae Cavalier-Smith & Bass 2009 Class Gromiidea Cavalier-Smith 2003 Order Gromiida Claparède & Lachmann 1856 s.s.
Class Ascetosporea Desportes & Ginsburger-Vogel, 1977 emend. Cavalier-Smith 2009 Order Claustrosporida Cavalier-Smith 2003 Order Paradiniida Cavalier-Smith 2009 Order Mikrocytida Hartikainen et al. 2014 Order Paramyxida Chatton 1911 Order Haplosporida Caullery & Mesnil 1899 Class Phytomyxea Engler & Prantl 1897 em. Cavalier-Smith 1993 Order Phagomyxida Cavalier-Smith 1993 Order Plasmodiophorida Cook 1928 em. Cavalier-Smith 1993 Class Vampyrellidea Cavalier-Smith 2017 Order Vampyrellida West 1901 emend. Hess et al. 2012 Subphylum Filosa Leidy 1879 emend. Cavalier-Smith 2003 Class Skiomonadea Cavalier-Smith 2012 Order Tremulida Cavalier-Smith & Howe 2011 Class Chlorarachnea Hibberd & Norris 1984 Order Minorisida Cavalier-Smith 2017 Order Chlorarachniida Hibberd & Norris 1984 Class Granofilosea Cavalier-Smith & Bass 2009 Family? Microgromiidae De Saedeleer 1934 Order? Axomonadida Order Desmothoracida Honigberg et al. 1964 Order Cryptofilida Cavalier-Smith & Bass 2009 Order Limnofilida Cavalier-Smith & Bass 2009 Order Leucodictyida Cavalier-Smith 1993 emend.
2003 Infraphylum Monadofilosa Cavalier-Smith 1997 Family? Katabiidae Cavalier-Smith 2012 Family? Krakenidae Dumack, Mylnikov & Bonkowski 2017 Order? Pseudodimorphida Class Helkesea Cavalier-Smith 2017 Order Ventricleftida Cavalier-Smith 2011 Order Helkesida Cavalier-Smith 2017 Order Cercomonadida Poche 1913 emend. Karpov et al. 2006 Class Metromonadea Cavalier-Smith 2007 s.s. Order Metromonadida Bass & Cavalier-Smith 2004 Order Metopiida Cavalier-Smith 2003 Clade Glissomonadida-Pansomonadida Order Glissomonadida Howe & Cavalie