Pyrenoids are sub-cellular micro-compartments found in chloroplasts of many algae, in a single group of land plants, the hornworts. Pyrenoids are associated with the operation of a carbon-concentrating mechanism, their main function is to act as centres of carbon dioxide fixation, by generating and maintaining a CO2 rich environment around the photosynthetic enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase. Pyrenoids therefore seem to have a role analogous to that of carboxysomes in cyanobacteria. Algae are restricted to aqueous environments in aquatic habitats, this has implications for their ability to access CO2 for photosynthesis. CO2 diffuses 10,000 times slower in water than in air, is slow to equilibrate; the result of this is that water, as a medium, is easily depleted of CO2 and is slow to gain CO2 from the air. CO2 equilibrates with bicarbonate when dissolved in water, does so on a pH-dependent basis. In sea water for example, the pH is such that dissolved inorganic carbon is found in the form of HCO3−.
The net result of this is a low concentration of free CO2, sufficient for an algal RuBisCO to run at a quarter of its maximum velocity, thus, CO2 availability may sometimes represent a major limitation of algal photosynthesis. Pyrenoids were first described in 1803 by Vaucher; the term was first coined by Schmitz who observed how algal chloroplasts formed de novo during cell division, leading Schimper to propose that chloroplasts were autonomous, to surmise that all green plants had originated through the “unification of a colourless organism with one uniformly tinged with chlorophyll". From these pioneering observations, Mereschkowski proposed, in the early 20th century, the symbiogenetic theory and the genetic independence of chloroplasts. In the following half-century, phycologists used the pyrenoid as a taxonomic marker, but physiologists long failed to appreciate the importance of pyrenoids in aquatic photosynthesis; the classical paradigm, which prevailed until the early 1980s, was that the pyrenoid was the site of starch synthesis.
Microscopic observations were misleading as a starch sheath encloses pyrenoids. The discovery of pyrenoid deficient mutants with normal starch grains in the green alga Chlamydomonas reinhardtii, as well as starchless mutants with formed pyrenoids discredited this hypothesis, it was not before the early 1970s that the proteinaceous nature of the pyrenoid was elucidated, when pyrenoids were isolated from a green alga, showed that up to 90% of it was composed of biochemically active RuBisCO. In the following decade and more evidence emerged that algae were capable of accumulating intracellular pools of DIC, converting these to CO2, in concentrations far exceeding that of the surrounding medium. Badger and Price first suggested the function of the pyrenoid to be analogous to that of the carboxysome in cyanobacteria, in being associated with CCM activity. CCM activity in algal and cyanobacterial photobionts of lichen associations was identified using gas exchange and carbon isotope isotopes and associated with the pyrenoid by Palmqvist and Badger et al.
The Hornwort CCM was characterized by Smith and Griffiths. From there on, the pyrenoid was studied in the wider context of carbon acquisition in algae, but has yet to be given a precise molecular definition. There is substantial diversity in pyrenoid morphology and ultrastructure between algal species. In the unicellular red alga Porphyridium purpureum and in the green alga Chlamydomonas reinhardtii, there is a single conspicuous pyrenoid in a single chloroplast, visible using light microscopy. By contrast, in diatoms and dinoflagellates, there can be multiple pyrenoids; when examined with transmission electron microscopy, pyrenoids appear as electron dense structures. The pyrenoid matrix, composed of RuBisCO, is traversed by thylakoids, which are in continuity with stromal thylakoids. In Porphyridium, these transpyrenoidal thylakoids are naked. Unlike carboxysomes, pyrenoids are not delineated by a protein shell. A starch sheath is formed or deposited at the periphery of pyrenoids when that starch is synthesised in the cytosol rather than in the chloroplast.
In Chlamydomonas, a high-molecular weight complex of two proteins forms an additional concentric layer around the pyrenoid, outside the starch sheath, this is hypothesised to act as a barrier to CO2-leakage or to recapture CO2 that escapes from the pyrenoid. The entire protein diversity and composition of the pyrenoid has yet to be elucidated, but thus far, a number of proteins other than RuBisCO have been shown to localise to the pyrenoid; however it is not yet known how the pyrenoid forms during cell division. Mutagenic work on Chlamydomonas has shown that the RuBisCO small subunit is important for pyrenoid assembly, that two solvent exposed alpha-helices of the RuBisCO small subunit are key to the process. Whether RuBisCO self-assembles into pyrenoids or requires additional chaperones is at present not known; the confinement of the CO2-fixing enzyme into a subcellular micro-compartment, in association with a mechanism to deliver CO2 to that site, is believed to enhance the efficacy of photosynthesis in an aqueous environment.
Having a CCM favours carboxylation over wasteful oxygenation by RuBisCO. The molecular basis of the pyrenoid and the CCM have been characterised to some detail in the model green alga Chlamydomonas reinhardtii; the current model of the biophysical CCM reliant upon a pyrenoid considers act
In scientific nomenclature, a synonym is a scientific name that applies to a taxon that goes by a different scientific name, although the term is used somewhat differently in the zoological code of nomenclature. For example, Linnaeus was the first to give a scientific name to the Norway spruce, which he called Pinus abies; this name is no longer in use: it is now a synonym of the current scientific name, Picea abies. Unlike synonyms in other contexts, in taxonomy a synonym is not interchangeable with the name of which it is a synonym. In taxonomy, synonyms have a different status. For any taxon with a particular circumscription and rank, only one scientific name is considered to be the correct one at any given time. A synonym cannot exist in isolation: it is always an alternative to a different scientific name. Given that the correct name of a taxon depends on the taxonomic viewpoint used a name, one taxonomist's synonym may be another taxonomist's correct name. Synonyms may arise whenever the same taxon is named more than once, independently.
They may arise when existing taxa are changed, as when two taxa are joined to become one, a species is moved to a different genus, a variety is moved to a different species, etc. Synonyms come about when the codes of nomenclature change, so that older names are no longer acceptable. To the general user of scientific names, in fields such as agriculture, ecology, general science, etc. A synonym is a name, used as the correct scientific name but, displaced by another scientific name, now regarded as correct, thus Oxford Dictionaries Online defines the term as "a taxonomic name which has the same application as another one, superseded and is no longer valid." In handbooks and general texts, it is useful to have synonyms mentioned as such after the current scientific name, so as to avoid confusion. For example, if the much advertised name change should go through and the scientific name of the fruit fly were changed to Sophophora melanogaster, it would be helpful if any mention of this name was accompanied by "".
Synonyms used in this way may not always meet the strict definitions of the term "synonym" in the formal rules of nomenclature which govern scientific names. Changes of scientific name have two causes: they may be taxonomic or nomenclatural. A name change may be caused by changes in the circumscription, position or rank of a taxon, representing a change in taxonomic, scientific insight. A name change may be due to purely nomenclatural reasons, that is, based on the rules of nomenclature. Speaking in general, name changes for nomenclatural reasons have become less frequent over time as the rules of nomenclature allow for names to be conserved, so as to promote stability of scientific names. In zoological nomenclature, codified in the International Code of Zoological Nomenclature, synonyms are different scientific names of the same taxonomic rank that pertain to that same taxon. For example, a particular species could, over time, have had two or more species-rank names published for it, while the same is applicable at higher ranks such as genera, orders, etc.
In each case, the earliest published name is called the senior synonym, while the name is the junior synonym. In the case where two names for the same taxon have been published the valid name is selected accorded to the principle of the first reviser such that, for example, of the names Strix scandiaca and Strix noctua, both published by Linnaeus in the same work at the same date for the taxon now determined to be the snowy owl, the epithet scandiaca has been selected as the valid name, with noctua becoming the junior synonym. One basic principle of zoological nomenclature is that the earliest published name, the senior synonym, by default takes precedence in naming rights and therefore, unless other restrictions interfere, must be used for the taxon. However, junior synonyms are still important to document, because if the earliest name cannot be used the next available junior synonym must be used for the taxon. For other purposes, if a researcher is interested in consulting or compiling all known information regarding a taxon, some of this may well have been published under names now regarded as outdated and so it is again useful to know a list of historic synonyms which may have been used for a given current taxon name.
Objective synonyms refer to taxa with same rank. This may be species-group taxa of the same rank with the same type specimen, genus-group taxa of the same rank with the same type species or if their type species are themselves objective synonyms, of family-group taxa with the same type genus, etc. In the case of subjective synonyms, there is no such shared type, so the synonymy is open to taxonomic judgement, meaning that th
Desmidiales called Desmids, are an order in the Charophyta, a division of green algae in which the land plants emerged. The desmids belong to the class Zygnematophyceae. Although they are sometimes grouped together as a single family Desmidiaceae, most classifications recognize three to five families, either within the order Zygnematales or as their own order Desmidiales; the Desmidiales comprise around 40 genera and 5,000 to 6,000 species, found but not in fresh water. Many species may be found in the fissures between patches of sphagnum moss in marshes. With a pH level of 4.0, sphagnum peat provides the ideal environment for this flora. The structure of these algae is unicellular, lacks flagella. Although most desmids are unicellular, the species Desmidium swartzii forms chains of cells resembling the algae genus Spirogyra. However, these filaments are arranged in a helix pattern; the cell of a desmid is divided into two symmetrical compartments separated by a narrow bridge or isthmus, wherein the spherical nucleus is located.
Each semi-cell houses a large folded chloroplast for photosynthesizing. One or more pyrenoids can be found; these form carbohydrates for energy storage. The cell-wall, of two halves, which, in a few species of Closterium and Penium, are of more than one piece, has two distinct layers, the inner composed of cellulose, the outer is stronger and thicker furnished with spines, warts et cetera, it is made up of a base of cellulose impregnated with other substances including iron compounds, which are prominent in some species of Closterium and Penium and is not soluble in an ammoniacal solution of copper oxide. Desmids assume a variety of symmetrical and attractive shapes, among those elongated, star-shaped and rotund configurations, which provide the basis for their classification; the largest among them may be visible to the unaided eye. Desmids possess characteristic crystals of barium sulphate at either end of the cell which exhibit a continuous Brownian type motion. Many desmids secrete translucent, gelatinous mucilage from pores in the cell wall that acts a protecting agent.
These pores are either, as in Micrasterias, uniformly distributed across the cell-wall but always appear to be absent in the region of the isthmus, or, in ornamented forms, as many genera of Cosmarium, grouped symmetrically around the bases of the spines, warts and so on with which the cell is provided. In the inner layer of the wall the pore is a simple canal, but in the outer, except in Closterium, the canal is surrounded by a specially differentiated cylindrical zone, not composed of cellulose, through which the canal passes; this is termed the pore-organ. The canals are no doubt. At the inner surface of the wall they terminate in lens- or button-shaped swellings, while from the outer end of the pore-organ there sometimes arise delicate radiating or club-shaped masses of mucilage through which the canal passes and which appear to be more or less permanent in character. In most cases, these are absent or only represented by small perforated buttons. Desmids reproduce by asexual fission, however, in adverse conditions, Desmidiales may reproduce sexually, through a process of conjugation, which are found among the related Zygnematales.
Classification of the families and genera in the Desmidiales: The family Gonatozygaceae is sometimes included within the Peniaceae, reducing the number of families from four to three. A fifth family Mesotaeniaceae was included in the Desmidiales, but analysis of cell wall structure and DNA sequences show that the group is more related to the Zygnemataceae, so is now placed together with that family in the order Zygnematales. However, the Zygnemataceae may have emerged in the Mesotaeniaceae. Survey of Clare Island 1990 - 2005, noting the Desmidiales recorded. Ed. Guiry, M. D. John, D. M. Rindi, F. and McCarthy, T. K. 2007. New Survey of Clare Island. Volume 6: The Freshwater and Terrestrial Algae. Royal Irish Academy. ISBN 978-1-904890-31-7 Microphotographs of desmids
Plants are multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. Plants were treated as one of two kingdoms including all living things that were not animals, all algae and fungi were treated as plants. However, all current definitions of Plantae exclude the fungi and some algae, as well as the prokaryotes. By one definition, plants form the clade Viridiplantae, a group that includes the flowering plants and other gymnosperms and their allies, liverworts and the green algae, but excludes the red and brown algae. Green plants obtain most of their energy from sunlight via photosynthesis by primary chloroplasts that are derived from endosymbiosis with cyanobacteria, their chloroplasts contain b, which gives them their green color. Some plants are parasitic or mycotrophic and have lost the ability to produce normal amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although asexual reproduction is common.
There are about 320 thousand species of plants, of which the great majority, some 260–290 thousand, are seed plants. Green plants provide a substantial proportion of the world's molecular oxygen and are the basis of most of Earth's ecosystems on land. Plants that produce grain and vegetables form humankind's basic foods, have been domesticated for millennia. Plants have many cultural and other uses, as ornaments, building materials, writing material and, in great variety, they have been the source of medicines and psychoactive drugs; the scientific study of plants is known as a branch of biology. All living things were traditionally placed into one of two groups and animals; this classification may date from Aristotle, who made the distincton between plants, which do not move, animals, which are mobile to catch their food. Much when Linnaeus created the basis of the modern system of scientific classification, these two groups became the kingdoms Vegetabilia and Animalia. Since it has become clear that the plant kingdom as defined included several unrelated groups, the fungi and several groups of algae were removed to new kingdoms.
However, these organisms are still considered plants in popular contexts. The term "plant" implies the possession of the following traits multicellularity, possession of cell walls containing cellulose and the ability to carry out photosynthesis with primary chloroplasts; when the name Plantae or plant is applied to a specific group of organisms or taxon, it refers to one of four concepts. From least to most inclusive, these four groupings are: Another way of looking at the relationships between the different groups that have been called "plants" is through a cladogram, which shows their evolutionary relationships; these are not yet settled, but one accepted relationship between the three groups described above is shown below. Those which have been called "plants" are in bold; the way in which the groups of green algae are combined and named varies between authors. Algae comprise several different groups of organisms which produce food by photosynthesis and thus have traditionally been included in the plant kingdom.
The seaweeds range from large multicellular algae to single-celled organisms and are classified into three groups, the green algae, red algae and brown algae. There is good evidence that the brown algae evolved independently from the others, from non-photosynthetic ancestors that formed endosymbiotic relationships with red algae rather than from cyanobacteria, they are no longer classified as plants as defined here; the Viridiplantae, the green plants – green algae and land plants – form a clade, a group consisting of all the descendants of a common ancestor. With a few exceptions, the green plants have the following features in common, they undergo closed mitosis without centrioles, have mitochondria with flat cristae. The chloroplasts of green plants are surrounded by two membranes, suggesting they originated directly from endosymbiotic cyanobacteria. Two additional groups, the Rhodophyta and Glaucophyta have primary chloroplasts that appear to be derived directly from endosymbiotic cyanobacteria, although they differ from Viridiplantae in the pigments which are used in photosynthesis and so are different in colour.
These groups differ from green plants in that the storage polysaccharide is floridean starch and is stored in the cytoplasm rather than in the plastids. They appear to have had a common origin with Viridiplantae and the three groups form the clade Archaeplastida, whose name implies that their chloroplasts were derived from a single ancient endosymbiotic event; this is the broadest modern definition of the term'plant'. In contrast, most other algae not only have different pigments but have chloroplasts with three or four surrounding membranes, they are not close relatives of the Archaeplastida having acquired chloroplasts separately from ingested or symbiotic green and red algae. They are thus not included in the broadest modern definition of the plant kingdom, although they were in the past; the green plants or Viridiplantae were traditionally divided into the green algae (including
The Desmidiaceae are one of four families of Charophyte green algae in the order Desmidiales. PubMed references for Desmidiaceae PubMed Central references for Desmidiaceae Google Scholar references for Desmidiaceae NCBI taxonomy page for Desmidiaceae Search Tree of Life taxonomy pages for Desmidiaceae Search Species2000 page for Desmidiaceae
In cell biology, the nucleus is a membrane-bound organelle found in eukaryotic cells. Eukaryotes have a single nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei, a few others including osteoclasts have many; the cell nucleus contains all of the cell's genome, except for a small fraction of mitochondrial DNA, organized as multiple long linear DNA molecules in a complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these chromosomes are structured in such a way to promote cell function; the nucleus maintains the integrity of genes and controls the activities of the cell by regulating gene expression—the nucleus is, the control center of the cell. The main structures making up the nucleus are the nuclear envelope, a double membrane that encloses the entire organelle and isolates its contents from the cellular cytoplasm, the nuclear matrix, a network within the nucleus that adds mechanical support, much like the cytoskeleton, which supports the cell as a whole.
Because the nuclear envelope is impermeable to large molecules, nuclear pores are required to regulate nuclear transport of molecules across the envelope. The pores cross both nuclear membranes, providing a channel through which larger molecules must be transported by carrier proteins while allowing free movement of small molecules and ions. Movement of large molecules such as proteins and RNA through the pores is required for both gene expression and the maintenance of chromosomes. Although the interior of the nucleus does not contain any membrane-bound subcompartments, its contents are not uniform, a number of nuclear bodies exist, made up of unique proteins, RNA molecules, particular parts of the chromosomes; the best-known of these is the nucleolus, involved in the assembly of ribosomes. After being produced in the nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA; the nucleus was the first organelle to be discovered. What is most the oldest preserved drawing dates back to the early microscopist Antonie van Leeuwenhoek.
He observed the nucleus, in the red blood cells of salmon. Unlike mammalian red blood cells, those of other vertebrates still contain nuclei; the nucleus was described by Franz Bauer in 1804 and in more detail in 1831 by Scottish botanist Robert Brown in a talk at the Linnean Society of London. Brown was studying orchids under the microscope when he observed an opaque area, which he called the "areola" or "nucleus", in the cells of the flower's outer layer, he did not suggest a potential function. In 1838, Matthias Schleiden proposed that the nucleus plays a role in generating cells, thus he introduced the name "cytoblast", he believed that he had observed new cells assembling around "cytoblasts". Franz Meyen was a strong opponent of this view, having described cells multiplying by division and believing that many cells would have no nuclei; the idea that cells can be generated de novo, by the "cytoblast" or otherwise, contradicted work by Robert Remak and Rudolf Virchow who decisively propagated the new paradigm that cells are generated by cells.
The function of the nucleus remained unclear. Between 1877 and 1878, Oscar Hertwig published several studies on the fertilization of sea urchin eggs, showing that the nucleus of the sperm enters the oocyte and fuses with its nucleus; this was the first time. This was in contradiction to Ernst Haeckel's theory that the complete phylogeny of a species would be repeated during embryonic development, including generation of the first nucleated cell from a "monerula", a structureless mass of primordial mucus. Therefore, the necessity of the sperm nucleus for fertilization was discussed for quite some time. However, Hertwig confirmed his observation in other animal groups, including amphibians and molluscs. Eduard Strasburger produced the same results for plants in 1884; this paved the way to assign the nucleus an important role in heredity. In 1873, August Weismann postulated the equivalence of the maternal and paternal germ cells for heredity; the function of the nucleus as carrier of genetic information became clear only after mitosis was discovered and the Mendelian rules were rediscovered at the beginning of the 20th century.
The nucleus is the largest organelle in animal cells. In mammalian cells, the average diameter of the nucleus is 6 micrometres, which occupies about 10% of the total cell volume; the contents of the nucleus are held in the nucleoplasm similar to the cytoplasm in the rest of the cell. The fluid component of this is termed the nucleosol, similar to the cytosol in the cytoplasm. In most types of granulocyte, a white blood cell, the nucleus is lobated and can be bi-lobed, tri-lobed or multi-lobed; the nuclear envelope, otherwise known as nuclear membrane, consists of two cellular membranes, an inner and an outer membrane, arranged parallel to one another and separated by 10 to 50 nanometres. The nuclear envelope encloses the nucleus and separates the cell's genetic material from the surrounding cytoplasm, serving as a barrier to prevent macromolecules from diffusing between the nucleoplasm and the cytoplasm; the outer nuclear membrane is continuous with the membrane of the rough endoplasmic reticulum, is studded with ribosomes.
The space between the membranes is called the perinuclear space and is continuous with the RER lumen. Nuclear pores, which provide aqueous cha
In zoological nomenclature, a type species is the species name with which the name of a genus or subgenus is considered to be permanently taxonomically associated, i.e. the species that contains the biological type specimen. A similar concept is used for suprageneric groups called a type genus. In botanical nomenclature, these terms have no formal standing under the code of nomenclature, but are sometimes borrowed from zoological nomenclature. In botany, the type of a genus name is a specimen, the type of a species name; the species name that has that type can be referred to as the type of the genus name. Names of genus and family ranks, the various subdivisions of those ranks, some higher-rank names based on genus names, have such types. In bacteriology, a type species is assigned for each genus; every named genus or subgenus in zoology, whether or not recognized as valid, is theoretically associated with a type species. In practice, there is a backlog of untypified names defined in older publications when it was not required to specify a type.
A type species is both a concept and a practical system, used in the classification and nomenclature of animals. The "type species" represents the reference species and thus "definition" for a particular genus name. Whenever a taxon containing multiple species must be divided into more than one genus, the type species automatically assigns the name of the original taxon to one of the resulting new taxa, the one that includes the type species; the term "type species" is regulated in zoological nomenclature by article 42.3 of the International Code of Zoological Nomenclature, which defines a type species as the name-bearing type of the name of a genus or subgenus. In the Glossary, type species is defined as The nominal species, the name-bearing type of a nominal genus or subgenus; the type species permanently attaches a formal name to a genus by providing just one species within that genus to which the genus name is permanently linked. The species name in turn is fixed, to a type specimen. For example, the type species for the land snail genus Monacha is Helix cartusiana, the name under which the species was first described, known as Monacha cartusiana when placed in the genus Monacha.
That genus is placed within the family Hygromiidae. The type genus for that family is the genus Hygromia; the concept of the type species in zoology was introduced by Pierre André Latreille. The International Code of Zoological Nomenclature states that the original name of the type species should always be cited, it gives an example in Article 67.1. Astacus marinus Fabricius, 1775 was designated as the type species of the genus Homarus, thus giving it the name Homarus marinus. However, the type species of Homarus should always be cited using its original name, i.e. Astacus marinus Fabricius, 1775. Although the International Code of Nomenclature for algae and plants does not contain the same explicit statement, examples make it clear that the original name is used, so that the "type species" of a genus name need not have a name within that genus, thus in Article 10, Ex. 3, the type of the genus name Elodes is quoted as the type of the species name Hypericum aegypticum, not as the type of the species name Elodes aegyptica.
Glossary of scientific naming Genetypes – genetic sequence data from type specimens. Holotype Paratype Principle of Typification Type Type genus