Amoebozoa is a major taxonomic group containing about 2,400 described species of amoeboid protists possessing blunt, lobose pseudopods and tubular mitochondrial cristae. In most classification schemes, Amoebozoa is ranked as a phylum within either the kingdom Protista or the kingdom Protozoa. In the classification favored by the International Society of Protistologists, it is retained as an unranked "supergroup" within Eukaryota. Molecular genetic analysis supports Amoebozoa as a monophyletic clade. Most phylogenetic trees identify it as the sister group to Opisthokonta, another major clade which contains both fungi and animals as well as some 300 species of unicellular protists. Amoebozoa and Opisthokonta are sometimes grouped together in a high-level taxon, variously named Unikonta, Amorphea or Opimoda. Amoebozoa includes many of the best-known amoeboid organisms, such as Chaos, Entamoeba and the genus Amoeba itself. Species of Amoebozoa may be either shelled, or naked, cells may possess flagella.
Free-living species are common in both salt and freshwater as well as soil and leaf litter. Some live as parasites or symbiotes of other organisms, some are known to cause disease in humans and other organisms. While the majority of amoebozoan species are unicellular, the group includes several varieties of slime molds, which have a macroscopic, multicellular stage of life during which individual amoeboid cells aggregate to produce spores. Amoebozoa vary in size; some are only 10 -- 20 μm in diameter. The well-known species Amoeba proteus, which may reach 800 μm in length, is studied in schools and laboratories as a representative cell or model organism because of its convenient size. Multinucleate amoebae like Chaos and Pelomyxa may be several millimetres in length, some multicellular amoebozoa, such as the "dog vomit" slime mold Fuligo septica, can cover an area of several square meters. Amoebozoa is a large and diverse group; the amoebozoan cell is divided into a granular central mass, called endoplasm, a clear outer layer, called ectoplasm.
During locomotion, the endoplasm flows forwards and the ectoplasm runs backwards along the outside of the cell. In motion, many amoebozoans have a defined anterior and posterior and may assume a "monopodial" form, with the entire cell functioning as a single pseudopod. Large pseudopods may produce numerous clear projections called subpseudopodia, which are extended to a certain length and retracted, either for the purpose of locomotion or food intake. A cell may form multiple indeterminate pseudopodia, through which the entire contents of the cell flow in the direction of locomotion; these are more or less tubular and are filled with granular endoplasm. The cell mass flows into a leading pseudopod, the others retract, unless the organism changes direction. While most amoebozoans are "naked," like the familiar Amoeba and Chaos, or covered with a loose coat of minute scales, like Cochliopodium and Korotnevella, members of the order Arcellinida form rigid shells, or tests, equipped with a single aperture through which the pseudopods emerge.
Arcellinid tests may be secreted from organic materials, as in Arcella, or built up from collected particles cemented together, as in Difflugia. In all amoebozoa, the primary mode of nutrition is phagocytosis, in which the cell surrounds potential food particles with its pseudopods, sealing them into vacuoles within which they may be digested and absorbed; some amoebozoans have a posterior bulb called a uroid, which may serve to accumulate waste, periodically detaching from the rest of the cell. When food is scarce, most species can form cysts, which may be carried aerially and introduce them to new environments. In slime moulds, these structures are called spores, form on stalked structures called fruiting bodies or sporangia; the majority of Amoebozoa lack flagella and more do not form microtubule-supported structures except during mitosis. However, flagella do occur among the Archamoebae, many slime moulds produce biflagellate gametes; the flagellum is anchored by a cone of microtubules, suggesting a close relationship to the opisthokonts.
The mitochondria in amoebozoan cells characteristically have branching tubular cristae. However, among the Archamoebae, which are adapted to anoxic or microaerophilic habitats, mitochondria have been lost, it appears that the members of Amoebozoa form a sister group to animals and fungi, diverging from this lineage after it had split from the other groups, as illustrated below in a simplified diagram: Strong similarities between Amoebozoa and Opisthokonts lead to the hypothesis that they form a distinct clade. Thomas Cavalier-Smith proposed the name "unikonts" for this branch, whose members were believed to have been descended from a common ancestor possessing a single emergent flagellum rooted in one basal body. However, while the close relationship between Amoebozoa and Opisthokonta is robustly supported, recent work has shown that the hypothesis of a uniciliate ancestor is false. In their Revised Classification of Eukaryotes, Adl et al. proposed Amorphea as a more suitable name for a clade of the same composition, a sister group to the Diaphoretickes.
More recent work places the members of Amorphea together with the malawimonids and collodictyonids in a proposed clade called Opimoda, which comprises one of two major lineages diverging at the root of the eukaryote tree of life. Traditionally all amoebozoa with lobose pseudopods were grouped together in the class L
Cyclic cellular automaton
A cyclic cellular automaton is a kind of cellular automaton rule developed by David Griffeath and studied by several other cellular automaton researchers. In this system, each cell remains unchanged until some neighboring cell has a modular value one unit larger than that of the cell itself, at which point it copies its neighbor's value. One-dimensional cyclic cellular automata can be interpreted as systems of interacting particles, while cyclic cellular automata in higher dimensions exhibit complex spiraling behavior; as with any cellular automaton, the cyclic cellular automaton consists of a regular grid of cells in one or more dimensions. The cells can take on any of n states, ranging from 0 to n − 1; the first generation starts out with random states in each of the cells. In each subsequent generation, if a cell has a neighboring cell whose value is the successor of the cell's value, the cell is "consumed" and takes on the succeeding value. More general forms of this type of rule include a threshold parameter, only allow a cell to be consumed when the number of neighbors with the successor value exceeds this threshold.
The one-dimensional cyclic cellular automaton has been extensively studied by Robert Fisch, a student of Griffeath. Starting from a random configuration with n = 3 or n = 4, this type of rule can produce a pattern which, when presented as a time-space diagram, shows growing triangles of values competing for larger regions of the grid; the boundaries between these regions can be viewed as moving particles which collide and interact with each other. In the three-state cyclic cellular automaton, the boundary between regions with values i and i + 1 can be viewed as a particle that moves either leftwards or rightwards depending on the ordering of the regions; this type of ballistic annihilation process occurs in several other cellular automata and related systems, including Rule 184, a cellular automaton used to model traffic flow. In the n = 4 automaton, the same two types of particles and the same annihilation reaction occur. Additionally, a boundary between regions with values i and i + 2 can be viewed as a third type of particle, that remains stationary.
A collision between a moving and a stationary particle results in a single moving particle moving in the opposite direction. However, for n ≥ 5, random initial configurations tend to stabilize rather than forming any non-trivial long-range dynamics. Griffeath has nicknamed this dichotomy between the long-range particle dynamics of the n = 3 and n = 4 automata on the one hand, the static behavior of the n ≥ 5 automata on the other hand, "Bob's dilemma", after Bob Fisch. In two dimensions, with no threshold and the von Neumann neighborhood or Moore neighborhood, this cellular automaton generates three general types of patterns sequentially, from random initial conditions on sufficiently large grids, regardless of n. At first, the field is purely random; as cells consume their neighbors and get within range to be consumed by higher-ranking cells, the automaton goes to the consuming phase, where there are blocks of color advancing against remaining blocks of randomness. Important in further development are objects called demons, which are cycles of adjacent cells containing one cell of each state, in the cyclic order.
The third stage, the demon stage, is dominated by these cycles. The demons with shorter cycles consume demons with longer cycles until surely, every cell of the automaton enters a repeating cycle of states, where the period of the repetition is either n or n + 1; the same eventually-periodic behavior occurs in higher dimensions. Small structures can be constructed with any period between n and 3n/2. Merging these structures, configurations can be built with a global super-polynomial period. For larger neighborhoods, similar spiraling behavior occurs for low thresholds, but for sufficiently high thresholds the automaton stabilizes in the block of color stage without forming spirals. At intermediate values of the threshold, a complex mix of color blocks and partial spirals, called turbulence, can form. For appropriate choices of the number of states and the size of the neighborhood, the spiral patterns formed by this automaton can be made to resemble those of the Belousov-Zhabotinsky reaction in chemistry, or other systems of autowaves, although other cellular automata more model the excitable medium that leads to this reaction.
Belitzky, Vladimir. "Ballistic annihilation and deterministic surface growth". Journal of Statistical Physics. 80: 517–543. Bibcode:1995JSP....80..517B. Doi:10.1007/BF02178546. Bunimovich L. A.. E.. "Rotators and absence of diffusion in cyclic cellular automata". Journal of Statistical Physics. 74: 1–10. Bibcode:1994JSP....74....1B. Doi:10.1007/BF02186804. Dewdney, A. K.. "Computer Recreations: A cellular universe of debris, droplets and demons". Scientific American: 102–105. Fisch, R.. "The one-dimensional cyclic cellular automaton: A system with deterministic dynamics that emulates an interacting particle system with stochastic dynamics". Journal of Theoretical Probability. 3: 311–338. Doi:10
A cytoskeleton is present in the cytoplasm of all cells, including bacteria, archaea. It is a complex, dynamic network of interlinking protein filaments that extends from the cell nucleus to the cell membrane; the cytoskeletal systems of different organisms are composed of similar proteins. In eukaryotes, the cytoskeletal matrix is a dynamic structure composed of three main proteins, which are capable of rapid growth or disassembly dependent on the cell's requirements; the structure and dynamic behavior of the cytoskeleton can be different, depending on organism and cell type. Within one cell the cytoskeleton can change through association with other proteins and the previous history of the network. A multitude of functions can be performed by the cytoskeleton, its primary function is to give the cell its shape and mechanical resistance to deformation, through association with extracellular connective tissue and other cells it stabilizes entire tissues. The cytoskeleton can contract, thereby deforming the cell and the cell's environment and allowing cells to migrate.
Moreover, it is involved in many cell signaling pathways: in the uptake of extracellular material, segregates chromosomes during cellular division, is involved in cytokinesis, provides a scaffold to organize the contents of the cell in space and for intracellular transport. Furthermore, it forms specialized structures, such as flagella, cilia and podosomes. A large-scale example of an action performed by the cytoskeleton is muscle contraction; this is carried out by groups of specialized cells working together. A main component in the cytoskeleton that helps show the true function of this muscle contraction is the microfilament. Microfilaments are composed of the most abundant cellular protein known as actin. During contraction of a muscle, within each muscle cell, myosin molecular motors collectively exert forces on parallel actin filaments. Muscle contraction starts from nerve impulses which causes increased amounts of calcium to be released from the sarcoplasmic reticulum. Increases in calcium in the cytosol allows muscle contraction to begin with the help of two proteins and troponin.
Tropomyosin inhibits the interaction between actin and myosin, while troponin senses the increase in calcium and releases the inhibition. This action contracts the muscle cell, through the synchronous process in many muscle cells, the entire muscle. In 1903, Nikolai K. Koltsov proposed that the shape of cells was determined by a network of tubules that he termed the cytoskeleton; the concept of a protein mosaic that dynamically coordinated cytoplasmic biochemistry was proposed by Rudolph Peters in 1929 while the term was first introduced by French embryologist Paul Wintrebert in 1931. When the cytoskeleton was first introduced, it was thought to be an uninteresting gel-like substance that helps organelles stay in place. Much research took place to try to understand the purpose of its components. With the help of Stuart Hameroff and Roger Penrose, they discovered that microtubules vibrate within neurons in the brain which suggest that brain waves come from deeper microtubule vibrations; this discovery showed that the cytoskeleton is not just a gel like substance but it has a purpose.
It was thought that the cytoskeleton was exclusive to eukaryotes but in 1992, it was discovered to be present in prokaryotes as well. This discovery came after the realization that bacteria possess proteins that are homologous to tubulin and actin. Eukaryotic cells contain three main kinds of cytoskeletal filaments: microfilaments and intermediate filaments; each type is formed by the polymerization of a distinct type of protein subunit and has its own characteristic shape and intracellular distribution. Microfilaments are 7 nm in diameter. Microtubules are 25 nm in diameter. Intermediate filaments are composed of various proteins, depending on the type of cell in which they are found; the cytoskeleton provides the cell with structure and shape, by excluding macromolecules from some of the cytosol, it adds to the level of macromolecular crowding in this compartment. Cytoskeletal elements interact intimately with cellular membranes. Research into neurodegenerative disorders such as Parkinson's disease, Alzheimer's disease, Huntington's disease, amyotrophic lateral sclerosis indicate that the cytoskeleton is affected in these diseases.
Parkinson's disease is marked by the degradation of neurons, resulting in tremors and other non-motor symptoms. Research has shown that microtubule assembly and stability in the cytoskeleton is compromised causing the neurons to degrade over time. In Alzheimer's disease, tau proteins which stabilize microtubules, malfunction in the progression of the disease, causing pathology with the cytoskeleton. Excess glutamine in the Huntington protein, involved with linking vesicles to the cytoskeleton is proposed to be a factor in the development of Huntington's disease. Amyotrophic lateral sclerosis which results in a loss of movement caused by the degradation of motor neurons is seen to involve defects in the cytoskeleton. A number of small-molecule cytoskeletal drugs have been discovered that interact with actin and microtubules; these compounds have proven useful in studying the cytoskeleton and several have clinical applications. All filaments interact with accessory prote
Cellular differentiation is the process where a cell changes from one cell type to another. The cell changes to a more specialized type. Differentiation occurs numerous times during the development of a multicellular organism as it changes from a simple zygote to a complex system of tissues and cell types. Differentiation continues in adulthood as adult stem cells divide and create differentiated daughter cells during tissue repair and during normal cell turnover; some differentiation occurs in response to antigen exposure. Differentiation changes a cell's size, membrane potential, metabolic activity, responsiveness to signals; these changes are due to controlled modifications in gene expression and are the study of epigenetics. With a few exceptions, cellular differentiation never involves a change in the DNA sequence itself. Thus, different cells can have different physical characteristics despite having the same genome. A specialized type of differentiation, known as'terminal differentiation', is of importance in some tissues, for example vertebrate nervous system, striated muscle and gut.
During terminal differentiation, a precursor cell capable of cell division, permanently leaves the cell cycle, dismantles the cell cycle machinery and expresses a range of genes characteristic of the cell's final function. Differentiation may continue to occur after terminal differentiation if the capacity and functions of the cell undergo further changes. Among dividing cells, there are multiple levels of cell potency, the cell's ability to differentiate into other cell types. A greater potency indicates a larger number of cell types. A cell that can differentiate into all cell types, including the placental tissue, is known as totipotent. In mammals, only the zygote and subsequent blastomeres are totipotent, while in plants, many differentiated cells can become totipotent with simple laboratory techniques. A cell that can differentiate into all cell types of the adult organism is known as pluripotent; such cells are called meristematic cells in higher plants and embryonic stem cells in animals, though some groups report the presence of adult pluripotent cells.
Virally induced expression of four transcription factors Oct4, Sox2, c-Myc, KIF4 is sufficient to create pluripotent cells from adult fibroblasts. A multipotent cell is one that can differentiate into multiple different, but related cell types. Oligopotent cells are more restricted than multipotent, but can still differentiate into a few related cell types. Unipotent cells can differentiate into only one cell type, but are capable of self-renewal. In cytopathology, the level of cellular differentiation is used as a measure of cancer progression. "Grade" is a marker of. Three basic categories of cells make up the mammalian body: germ cells, somatic cells, stem cells; each of the 37.2 trillion cells in an adult human has its own copy or copies of the genome except certain cell types, such as red blood cells, that lack nuclei in their differentiated state. Most cells are diploid; such cells, called somatic cells, make up most such as skin and muscle cells. Cells differentiate to specialize for different functions.
Germ line cells are any line of cells that give rise to gametes—eggs and sperm—and thus are continuous through the generations. Stem cells, on the other hand, have the ability to divide for indefinite periods and to give rise to specialized cells, they are best described in the context of normal human development. Development begins when a sperm fertilizes an egg and creates a single cell that has the potential to form an entire organism. In the first hours after fertilization, this cell divides into identical cells. In humans four days after fertilization and after several cycles of cell division, these cells begin to specialize, forming a hollow sphere of cells, called a blastocyst; the blastocyst has an outer layer of cells, inside this hollow sphere, there is a cluster of cells called the inner cell mass. The cells of the inner cell mass go on to form all of the tissues of the human body. Although the cells of the inner cell mass can form every type of cell found in the human body, they cannot form an organism.
These cells are referred to as pluripotent. Pluripotent stem cells undergo further specialization into multipotent progenitor cells that give rise to functional cells. Examples of stem and progenitor cells include: Radial glial cells that give rise to excitatory neurons in the fetal brain through the process of neurogenesis. Hematopoietic stem cells from the bone marrow that give rise to red blood cells, white blood cells, platelets Mesenchymal stem cells from the bone marrow that give rise to stromal cells, fat cells, types of bone cells Epithelial stem cells that give rise to the various types of skin cells Muscle satellite cells that contribute to differentiated muscle tissue. A pathway, guided by the cell adhesion molecules consisting of four amino acids, glycine and serine, is created as the cellular blastomere differentiates from the single-layered blastula to the three primary layers of germ cells in mammals, namely the ectoderm and endoderm; the ectoderm ends up forming the skin and the nervous system, the mesoderm forms the bones and muscular tissue, the endoderm forms the internal organ tissues.
A model organism is a non-human species, extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. Model organisms are used to research human disease when human experimentation would be unfeasible or unethical; this strategy is made possible by the common descent of all living organisms, the conservation of metabolic and developmental pathways and genetic material over the course of evolution. Studying model organisms can be informative, but care must be taken when generalizing from one organism to another. In researching human disease, model organisms allow for better understanding the disease process without the added risk of harming an actual human; the species chosen will meet a determined taxonomic equivalency to humans, so as to react to disease or its treatment in a way that resembles human physiology as needed. Although biological activity in a model organism does not ensure an effect in humans, many drugs and cures for human diseases are developed in part with the guidance of animal models.
There are three main types of disease models: homologous and predictive. Homologous animals have the same causes and treatment options as would humans who have the same disease. Isomorphic animals share the same treatments. Predictive models are similar to a particular human disease in only a couple of aspects, but are useful in isolating and making predictions about mechanisms of a set of disease features; the use of animals in research dates back to ancient Greece, with Aristotle and Erasistratus among the first to perform experiments on living animals. Discoveries in the 18th and 19th centuries included Antoine Lavoisier's use of a guinea pig in a calorimeter to prove that respiration was a form of combustion, Louis Pasteur's demonstration of the germ theory of disease in the 1880s using anthrax in sheep. Research using animal models has been central to many of the achievements of modern medicine, it has contributed most of the basic knowledge in fields such as human physiology and biochemistry, has played significant roles in fields such as neuroscience and infectious disease.
For example, the results have included the near-eradication of polio and the development of organ transplantation, have benefited both humans and animals. From 1910 to 1927, Thomas Hunt Morgan's work with the fruit fly Drosophila melanogaster identified chromosomes as the vector of inheritance for genes. Drosophila became one of the first, for some time the most used, model organisms, Eric Kandel wrote that Morgan's discoveries "helped transform biology into an experimental science." D. melanogaster remains one of the most used eukaryotic model organisms. During the same time period, studies on mouse genetics in the laboratory of William Ernest Castle in collaboration with Abbie Lathrop led to generation of the DBA inbred mouse strain and the systematic generation of other inbred strains; the mouse has since been used extensively as a model organism and is associated with many important biological discoveries of the 20th and 21st centuries. In the late 19th century, Emil von Behring isolated the diphtheria toxin and demonstrated its effects in guinea pigs.
He went on to develop an antitoxin against diphtheria in animals and in humans, which resulted in the modern methods of immunization and ended diphtheria as a threatening disease. The diphtheria antitoxin is famously commemorated in the Iditarod race, modeled after the delivery of antitoxin in the 1925 serum run to Nome; the success of animal studies in producing the diphtheria antitoxin has been attributed as a cause for the decline of the early 20th-century opposition to animal research in the United States. Subsequent research in model organisms led to further medical advances, such as Frederick Banting's research in dogs, which determined that the isolates of pancreatic secretion could be used to treat dogs with diabetes; this led to the 1922 discovery of insulin and its use in treating diabetes, which had meant death. John Cade's research in guinea pigs discovered the anticonvulsant properties of lithium salts, which revolutionized the treatment of bipolar disorder, replacing the previous treatments of lobotomy or electroconvulsive therapy.
Modern general anaesthetics, such as halothane and related compounds, were developed through studies on model organisms, are necessary for modern, complex surgical operations. In the 1940s, Jonas Salk used rhesus monkey studies to isolate the most virulent forms of the polio virus, which led to his creation of a polio vaccine; the vaccine, made publicly available in 1955, reduced the incidence of polio 15-fold in the United States over the following five years. Albert Sabin improved the vaccine by passing the polio virus through animal hosts, including monkeys, it has been estimated that developing and producing the vaccines required the use of 100,000 rhesus monkeys, with 65 doses of vaccine produced from each monkey. Sabin wrote in 1992, "Without the use of animals and human beings, it would have been impossible to acquire the important knowledge needed to prevent much suffering and premature death not only among humans, but among animals."Other 20th-century medical advances and treatments that relied on research performed in animals include organ transplant techniques, the heart-lung machine and the whooping cough vaccine.
Treatments for animal diseases have been developed, including for rabies, anthrax