1.
Carrot
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The carrot is a root vegetable, usually orange in colour, though purple, black, red, white, and yellow cultivars exist. Carrots are a form of the wild carrot, Daucus carota, native to Europe. The plant probably originated in Persia and originally cultivated for its leaves, the most commonly eaten part of the plant is the taproot, although the greens are sometimes eaten as well. The domestic carrot has been bred for its greatly enlarged, more palatable. The carrot is a plant in the umbellifer family Apiaceae. At first, it grows a rosette of leaves while building up the enlarged taproot, fast-growing cultivars mature within three months of sowing the seed, while slower-maturing cultivars are harvested four months later. The United Nations Food and Agriculture Organization reports that production of carrots and turnips for the calendar year 2013 was 37.2 million tonnes. Carrots are widely used in many cuisines, especially in the preparation of salads, in Old English, carrots were not clearly distinguished from parsnips, the two were collectively called moru or more. Various languages still use the word for carrot as they do for root. Molecular and genetic studies, along with history, support the idea that the cultivated/domesticated carrot has a single origin in Central Asia. The wild ancestors of the carrot are likely to have originated in Persia, which remains the centre of diversity for Daucus carota, when they were first cultivated, carrots were grown for their aromatic leaves and seeds rather than their roots. Carrot seeds have been found in Switzerland and Southern Germany dating back to 2000–3000 BC, some close relatives of the carrot are still grown for their leaves and seeds, for example, parsley, cilantro/coriander, fennel, dill and cumin. Three different types of carrots are depicted, and the states of them that the root can be cooked. The plant appears to have been introduced into Spain by the Moors in the 8th century, in the 10th century, in worldwide locations like West Asia, India and Europe, the roots were purple. The modern carrot originated in Afghanistan at about this time, the Jewish scholar Simeon Seth describes both red and yellow carrots in the 11th century. The 12th-century Arab-Andalusian agriculturist, Ibn al-Awwam, also mentions roots of these colours, cultivated carrots appeared in China in the 14th century, and in Japan in the 18th century. Orange-coloured carrots appeared in the Netherlands in the 17th century, which has been related to the fact that the Dutch flag at the time, the Princes Flag, included orange. These, the carrots, were intended by the English antiquary John Aubrey when he noted in his memoranda
2.
Pollen
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Pollen is a fine to coarse powdery substance comprising pollen grains which are male microgametophytes of seed plants, which produce male gametes. If pollen lands on a compatible pistil or female cone, it germinates, individual pollen grains are small enough to require magnification to see detail. The study of pollen is called palynology and is useful in paleoecology, paleontology, archaeology. Pollen in plants is used for transferring haploid male genetic material from the anther of a flower to the stigma of another in cross-pollination. In a case of self-pollination, this takes place from the anther of a flower to the stigma of the same flower. Pollen itself is not the male gamete, each pollen grain contains vegetative cells and a generative cell. In flowering plants the vegetative tube cell produces the pollen tube, pollen is produced in the microsporangia in the male cone of a conifer or other gymnosperm or in the anthers of an angiosperm flower. Pollen grains come in a variety of shapes, sizes. Pollen grains of pines, firs, and spruces are winged, the smallest pollen grain, that of the forget-me-not, is around 6 µm in diameter. Wind-borne pollen grains can be as large as about 90–100 µm, in angiosperms, during flower development the anther is composed of a mass of cells that appear undifferentiated, except for a partially differentiated dermis. As the flower develops, four groups of cells form within the anther. The fertile sporogenous cells are surrounded by layers of cells that grow into the wall of the pollen sac. Some of the cells grow into nutritive cells that supply nutrition for the microspores that form by meiotic division from the sporogenous cells, in a process called microsporogenesis, four haploid microspores are produced from each diploid sporogenous cell, after meiotic division. After the formation of the four microspores, which are contained by callose walls, the exine is what is preserved in the fossil record. Two basic types of microsporogenesis are recognised, simultaneous and successive, in simultaneous microsporogenesis meiotic steps I and II are completed prior to cytokinesis, whereas in successive microsporogenesis cytokinesis follows. While there may be a continuum with intermediate forms, the type of microsporogenesis has systematic significance, the predominant form amongst the monocots is successive, but there are important exceptions. During microgametogenesis, the unicellular microspores undergo mitosis and develop into mature microgametophytes containing the gametes, in some flowering plants, germination of the pollen grain may begin even before it leaves the microsporangium, with the generative cell forming the two sperm cells. Except in the case of submerged aquatic plants, the mature pollen grain has a double wall
3.
Arabidopsis thaliana
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Arabidopsis thaliana is a small flowering plant native to Eurasia. A. thaliana is considered a weed, it is found by roadsides, a winter annual with a relatively short life cycle, A. thaliana is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, A. thaliana has a small genome of approximately 135 megabase pairs. It was the first plant to have its genome sequenced, and is a tool for understanding the molecular biology of many plant traits, including flower development. Arabidopsis thaliana is a plant, usually growing to 20–25 cm tall. The leaves form a rosette at the base of the plant, leaves are covered with small, unicellular hairs. The flowers are 3 mm in diameter, arranged in a corymb, the fruit is a siliqua 5–20 mm long, containing 20–30 seeds. Roots are simple in structure, with a primary root that grows vertically downward. These roots form interactions with rhizosphere bacteria such as Bacillus megaterium, a. thaliana can complete its entire lifecycle in six weeks. The central stem produces flowers grows after about three weeks, and the flowers naturally self-pollinate. In the lab, A. thaliana may be grown in Petri plates, pots, or hydroponics, the plant was first described in 1577 in the Harz Mountains by Johannes Thal, a physician from Nordhausen, Thüringen, Germany, who called it Pilosella siliquosa. In 1753, Carl Linnaeus renamed the plant Arabis thaliana in honor of Thal, in 1842, the German botanist Gustav Heynhold erected the new genus Arabidopsis and placed the plant in that genus. The genus name, Arabidopsis, comes from Greek, meaning resembling Arabis, thousands of natural inbred accessions of A. thaliana have been collected from throughout its natural and introduced range. These accessions exhibit considerable genetic and phenotypic variation which can be used to study the adaptation of species to different environments. A. thaliana is native to Europe, Asia, and northwestern Africa and it also appears to be native in tropical afroalpine ecosystems. It has been introduced and naturalized worldwide, a. thaliana readily grows and often pioneers rocky, sandy and calcareous soils. It is generally considered a weed, due to its distribution in agricultural fields, roadside, railway lines, waste ground. Like most Brassicaceae species, A. thaliana is edible by humans as a salad or cooked, the first mutant in A. thaliana was documented in 1873 by Alexander Braun, describing a double flower phenotype
4.
Aspergillus terreus
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Aspergillus terreus, also known as Aspergillus terrestris, is a fungus found worldwide in soil. Although thought to be strictly asexual until recently, A. terreus is now known to be capable of sexual reproduction and this saprotrophic fungus is prevalent in warmer climates such as tropical and subtropical regions. Aside from being located in soil, A. terreus has also found in habitats such as decomposing vegetation. A. terreus is commonly used in industry to produce important organic acids, such as acid and cis-aconitic acid, as well as enzymes. It was also the source for the drug mevinolin, a drug for lowering serum cholesterol. A. terreus can cause infection in people with deficient immune systems. It is relatively resistant to amphotericin B, an antifungal drug. Aspergillus terreus also produces aspterric acid and 6-hydroxymellein, inhibitors of pollen development in Arabidopsis thaliana, a. terreus is brownish in colour and gets darker as it ages on culture media. On Czapek or malt extract agar medium at 25 °C, colonies have the conditions to grow rapidly and have smooth-like walls, in some cases, they are able to become floccose, achieving hair-like soft tufts. Colonies on malt extract agar grow faster and sporulate more densely than on other media. A. terreus has conidial heads that are compact, biseriate, conidiophores of A. terreus are smooth and hyaline up to 100–250 × 4–6 µm in diameter. The conidia of A. terreus are small, about 2 µm in diameter, globose-shaped, smooth-walled, unique to this species is the production of aleurioconidia, asexual spores produced directly on the hyphae that are larger than the phialoconidia. This structure might be influential in the way A. terreus presents itself clinically as it can induce elevated inflammatory responses and this fungus is readily distinguished from the other species of Aspergillus by its cinnamon-brown colony colouration and its production of aleurioconidia. The morphology of this provides an accessible way for spores to disperse globally in air current. Elevation of the sporulating head atop a stalk above the growing surface may facilitate spore dispersal through the air. Normally, spores in fungi are discharged into still air, but in A. terreus, it resolves this problem with a long stalk and it allows the spores to discharge into air currents like wind. In turn, A. terreus has a chance to disperse its spores amongst a vast geography which subsequently explains for the worldwide prevalence of the fungus. Despite A. terreus being found worldwide in warm, arable soil, eventually, the dispersed fungal spores come into contact with either liquid or solid material and settle onto it, but only when the conditions are right do the spores germinate
5.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
6.
Phenols
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In organic chemistry, phenols, sometimes called phenolics, are a class of chemical compounds consisting of a hydroxyl group bonded directly to an aromatic hydrocarbon group. The simplest of the class is phenol, which is also called carbolic acid C 6H 5OH, phenolic compounds are classified as simple phenols or polyphenols based on the number of phenol units in the molecule. Synonyms are arenols or aryl alcohols, phenolic compounds are synthesized industrially, they also are produced by plants and microorganisms, with variation between and within species. Although similar to alcohols, phenols have unique properties and are not classified as alcohols and they have higher acidities due to the aromatic rings tight coupling with the oxygen and a relatively loose bond between the oxygen and hydrogen. The acidity of the group in phenols is commonly intermediate between that of aliphatic alcohols and carboxylic acids. Phenols can have two or more hydroxy groups bonded to the ring in the same molecule. The simplest examples are the three benzenediols, each having two groups on a benzene ring. Organisms that synthesize phenolic compounds do so in response to pressures such as pathogen and insect attack, UV radiation. As they are present in food consumed in human diets and in used in traditional medicine of several cultures, their role in human health. Some phenols are germicidal and are used in formulating disinfectants, others possess estrogenic or endocrine disrupting activity. They can also be classified on the basis of their number of phenol groups and they can therefore be called simple phenols or monophenols, with only one phenolic group, or di-, tri- and oligophenols, with two, three or several phenolic groups respectively. The phenolic unit can be found dimerized or further polymerized, creating a new class of polyphenol, two natural phenols from two different categories, for instance a flavonoid and a lignan, can combine to form a hybrid class like the flavonolignans. Nomenclature of polymers, Plants in the genus Humulus and Cannabis produce terpenophenolic metabolites, phenolic lipids are long aliphatic chains bonded to a phenolic moiety. The majority of compounds are solubles molecules but the smaller molecules can be volatiles. Many natural phenols present chirality within their molecule, an example of such molecules is catechin. Cavicularin is an unusual macrocycle because it was the first compound isolated from nature displaying optical activity due to the presence of planar chirality, natural phenols chemically interact with many other substances. Stacking, a property of molecules with aromaticity, is seen occurring between phenolic molecules. When studied in mass spectrometry, phenols easily form adduct ions with halogens and they can also interact with the food matrices or with different forms of silica
7.
Simplified molecular-input line-entry system
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The simplified molecular-input line-entry system is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules, the original SMILES specification was initiated in the 1980s. It has since modified and extended. In 2007, a standard called OpenSMILES was developed in the open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. The Environmental Protection Agency funded the project to develop SMILES. It has since modified and extended by others, most notably by Daylight Chemical Information Systems. In 2007, a standard called OpenSMILES was developed by the Blue Obelisk open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, in July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI, the term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also used to refer to both a single SMILES string and a number of SMILES strings, the exact meaning is usually apparent from the context. The terms canonical and isomeric can lead to confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive, typically, a number of equally valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol, algorithms have been developed to generate the same SMILES string for a given molecule, of the many possible strings, these algorithms choose only one of them. This SMILES is unique for each structure, although dependent on the algorithm used to generate it. These algorithms first convert the SMILES to a representation of the molecular structure. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database, there is currently no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, and these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES
8.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
9.
Monocerin
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Monocerin is a dihydroisocoumarin and a polyketide metabolite that originates from various fungal species. It has been shown to display antifungal, plant pathogenic, Monocerin has been isolated from Dreschlera monoceras, D. ravenelii, Exserohilum turcicum, and Fusarium larvarum. Polyketide synthases of fungi are Type I PKSs, Monocerin has been confirmed by biosynthesis studies to have heptaketide origins. Monocerin PKS produces an intermediate with initially a high degree of reductive modification, dihydroisocoumarin is the first PKS-free intermediate which would be formed from the reduced heptaketide whose assembly pathway is shown in figure 1. Ketosynthase, ketoreductase, dehydrates, enol reductases and cyclisases are shown as domains of the Monocerin PKS, formation of an enolate ion on the carbon three carbons away from sulfur allows aldol addition onto the carbonyl six carbons distant along the chain. Dehydration proceeds to give the alkene, enolization then occurs to reach the stability of the aromatic ring. The modified chain is transferred to the TE domain and this will allow lactonization and release from the enzyme. Hydroxylation occurs at ortho-position to two substituents, o-methylation Cyclic-ether formation Monocerin produced by Exserohilum turcicum causes Northern Corn Leaf blight disease in maize. The maize will develop brown lesions on its leaves and will have decreased viability in its root cap cells, Monocerin has also been shown to be an effective insecticide against wooly aphids. Monocerin is also a herbicide against Johnson grass by inhibiting seedling growth. It has an effect against cucumber. Polyketide synthase Fungicide use in the United States Setosphaeria turcica
