1.
ChemSpider
–
ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses
ChemSpider
–
ChemSpider
2.
PubChem
–
PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information, a component of the National Library of Medicine, PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds, more than 80 database vendors contribute to the growing PubChem database. PubChem consists of three dynamically growing primary databases, as of 28 January 2016, Compounds,82.6 million entries, contains pure and characterized chemical compounds. Substances,198 million entries, contains also mixtures, extracts, complexes, bioAssay, bioactivity results from 1.1 million high-throughput screening programs with several million values. PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments. In the text search form the database fields can be searched by adding the name in square brackets to the search term. A numeric range is represented by two separated by a colon. The search terms and field names are case-insensitive, parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used, example,0,5000,50,10 -5,5 PubChem was released in 2004. The American Chemical Society has raised concerns about the publicly supported PubChem database and they have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the societys revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress, soon after PubChems creation, the American Chemical Society lobbied U. S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service
PubChem
–
PubChem
3.
International Chemical Identifier
–
Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure
International Chemical Identifier
–
L -
ascorbic acid
4.
Simplified molecular-input line-entry system
–
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
Simplified molecular-input line-entry system
–
Generation of SMILES: Break cycles, then write as branches off a main backbone. (Ciprofloxacin)
5.
Chemical formula
–
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
Chemical formula
–
Al 2 (SO 4) 3
6.
Nile blue
–
Nile blue is a stain used in biology and histology. It may be used live or fixed cells, and imparts a blue colour to cell nuclei. It may also be used in conjunction with fluorescence microscopy to stain for the presence of granules in prokaryotic or eukaryotic cells. Boiling a solution of Nile blue with sulfuric acid produces Nile red, Nile blue is a fluorescent dye. The fluorescence shows especially in nonpolar solvents with a quantum yield. The absorption and emission maxima of Nile blue are strongly dependent on pH and this is shorter than the corresponding value of Nile red with 3.65 ns. The fluorescence duration is independent on dilution in the range 10−3–10−8 mol/L, Nile blue is used for histological staining of biological preparations. It highlights the distinction between neutral lipids which are stained pink and acids which are stained blue, for better differentiation, it is dipped in 1% acetic acid for 10–20 minutes until the colors are pure. This might take only 1–2 minutes, then the sample is thoroughly rinsed in water. Afterwards, the specimen is taken on a microscope slide. The sample can be embedded in glycerol or glycerol gelatin, unsaturated glycerides are pink, nuclei and elastins dark, fatty acids and various fatty substances and fat mixtures are purple blue. The PHB granules in the cells of Pseudomonas solanacearum can be visualized by Nile blue A staining, Nile blue is also apparently used in a variety of commercial DNA staining formulations used for DNA electrophoresis. Derivatives of Nile blue are potential photosensitizers in photodynamic therapy of malignant tumors and these dyes aggregate in the tumor cells, especially in the lipid membranes, and/or are sequestered and concentrated in subcellular organelles. With the Nile blue derivative N-Ethyl-Nile Blue, normal and premalignant tissues in animal experiments can be distinguished by spectroscopy in fluorescence imaging. The following scheme illustrates the first of four approaches, leading to Nile Blue perchlorate
Nile blue
–
Nile blue hydrochloride in water. Concentrations, left to right: 1000
ppm, 100 ppm, 10 ppm, 1 ppm, 100 ppb.
Nile blue
–
Nile blue
7.
Sulfuric acid
–
Sulfuric acid is a highly corrosive strong mineral acid with the molecular formula H2SO4 and molecular weight 98.079 g/mol. It is a pungent-ethereal, colorless to slightly yellow liquid that is soluble in water at all concentrations. Sometimes, it is dyed dark brown during production to alert people to its hazards, the historical name of this acid is oil of vitriol. Sulfuric acid is an acid and shows different properties depending upon its concentration. Its corrosiveness on other materials, like metals, living tissues or even stones, can be ascribed to its strong acidic nature and, if concentrated. It is also hygroscopic, readily absorbing water vapour from the air, Sulfuric acid at a high concentration can cause very serious damage upon contact, since not only does it cause chemical burns via hydrolysis, but also secondary thermal burns through dehydration. It can lead to permanent blindness if splashed onto eyes and irreversible damage if swallowed, Sulfuric acid has a wide range of applications including in domestic acidic drain cleaners, as an electrolyte in lead-acid batteries and in various cleaning agents. It is also a central substance in the chemical industry, principal uses include mineral processing, fertilizer manufacturing, oil refining, wastewater processing, and chemical synthesis. It is widely produced with different methods, such as process, wet sulfuric acid process, lead chamber process. The study of vitriol, a category of glassy minerals from which the acid can be derived, sumerians had a list of types of vitriol that they classified according to the substances color. Some of the earliest discussions on the origin and properties of vitriol is in the works of the Greek physician Dioscorides, galen also discussed its medical use. Ibn Sina focused on its uses and different varieties of vitriol. Sulfuric acid was called oil of vitriol by medieval European alchemists because it was prepared by roasting green vitriol in an iron retort, there are references to it in the works of Vincent of Beauvais and in the Compositum de Compositis ascribed to Saint Albertus Magnus. A passage from Pseudo-Geber´s Summa Perfectionis was long considered to be the first recipe for sulfuric acid, in the seventeenth century, the German-Dutch chemist Johann Glauber prepared sulfuric acid by burning sulfur together with saltpeter, in the presence of steam. As saltpeter decomposes, it oxidizes the sulfur to SO3, in 1736, Joshua Ward, a London pharmacist, used this method to begin the first large-scale production of sulfuric acid. This process allowed the effective industrialization of sulfuric acid production, after several refinements, this method, called the lead chamber process or chamber process, remained the standard for sulfuric acid production for almost two centuries. Sulfuric acid created by John Roebucks process approached a 65% concentration, later refinements to the lead chamber process by French chemist Joseph Louis Gay-Lussac and British chemist John Glover improved concentration to 78%. However, the manufacture of dyes and other chemical processes require a more concentrated product
Sulfuric acid
–
Sulfuric acid
Sulfuric acid
Sulfuric acid
–
John Dalton 's 1808 sulfuric acid molecule shows a central
sulfur atom bonded to three oxygen atoms, or
sulfur trioxide, the
anhydride of sulfuric acid.
Sulfuric acid
–
Drops of concentrated sulfuric acid rapidly decompose a piece of cotton towel by dehydration.
8.
Cell (biology)
–
The cell is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life that can replicate independently, the study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many such as proteins. Organisms can be classified as unicellular or multicellular, while the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion cells. Most plant and animal cells are only under a microscope. The cell was discovered by Robert Hooke in 1665, who named the unit for its resemblance to cells inhabited by Christian monks in a monastery. Cells emerged on Earth at least 3.5 billion years ago, Cells are of two types, eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular, prokaryotic cells were the first form of life on Earth, characterised by having vital biological processes including cell signaling and being self-sustaining. They are simpler and smaller than eukaryotic cells, and lack membrane-bound organelles such as the nucleus, prokaryotes include two of the domains of life, bacteria and archaea. The DNA of a prokaryotic cell consists of a chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid, most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 µm in diameter. Though most prokaryotes have both a cell membrane and a wall, there are exceptions such as Mycoplasma and Thermoplasma which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, the cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting from osmotic pressure due to a hypotonic environment, some eukaryotic cells also have a cell wall. Inside the cell is the region that contains the genome, ribosomes. The genetic material is found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular, linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a nucleoid, plasmids encode additional genes, such as antibiotic resistance genes
Cell (biology)
–
Onion (
Allium) cells in different phases of the cell cycle
Cell (biology)
–
Structure of an animal cell
Cell (biology)
–
A fluorescent image of an endothelial cell. Nuclei are stained blue,
mitochondria are stained red, and microfilaments are stained green.
Cell (biology)
–
Human cancer cells with nuclei (specifically the DNA) stained blue. The central and rightmost cell are in
interphase, so the entire nuclei are labeled. The cell on the left is going through
mitosis and its DNA has condensed.
9.
Lipid
–
In biology, lipids comprise a group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins, monoglycerides, diglycerides, triglycerides, phospholipids, and others. The main biological functions of lipids include storing energy, signaling, lipids have applications in the cosmetic and food industries as well as in nanotechnology. Biological lipids originate entirely or in part from two types of biochemical subunits or building-blocks, ketoacyl and isoprene groups. Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids called triglycerides, lipids also encompass molecules such as fatty acids and their derivatives, as well as other sterol-containing metabolites such as cholesterol. Although humans and other mammals use various biosynthetic pathways both to break down and to synthesize lipids, some essential lipids cannot be made this way, the word lipid stems etymologically from the Greek lipos. The fatty acid structure is one of the most fundamental categories of biological lipids, the carbon chain, typically between four and 24 carbons long, may be saturated or unsaturated, and may be attached to functional groups containing oxygen, halogens, nitrogen, and sulfur. If a fatty acid contains a double bond, there is the possibility of either a cis or trans geometric isomerism, cis-double bonds cause the fatty acid chain to bend, an effect that is compounded with more double bonds in the chain. This in turn plays an important role in the structure and function of cell membranes, most naturally occurring fatty acids are of the cis configuration, although the trans form does exist in some natural and partially hydrogenated fats and oils. Examples of biologically important fatty acids include the eicosanoids, derived primarily from arachidonic acid and eicosapentaenoic acid, that include prostaglandins, leukotrienes, docosahexaenoic acid is also important in biological systems, particularly with respect to sight. Other major lipid classes in the fatty acid category are the fatty esters, fatty esters include important biochemical intermediates such as wax esters, fatty acid thioester coenzyme A derivatives, fatty acid thioester ACP derivatives and fatty acid carnitines. The fatty amides include N-acyl ethanolamines, such as the cannabinoid neurotransmitter anandamide, glycerolipids are composed of mono-, di-, and tri-substituted glycerols, the best-known being the fatty acid triesters of glycerol, called triglycerides. The word triacylglycerol is sometimes used synonymously with triglyceride, in these compounds, the three hydroxyl groups of glycerol are each esterified, typically by different fatty acids. Because they function as a store, these lipids comprise the bulk of storage fat in animal tissues. The hydrolysis of the bonds of triglycerides and the release of glycerol. Additional subclasses of glycerolipids are represented by glycosylglycerols, which are characterized by the presence of one or more sugar residues attached to glycerol via a glycosidic linkage, examples of structures in this category are the digalactosyldiacylglycerols found in plant membranes and seminolipid from mammalian sperm cells. Glycerophospholipids, usually referred to as phospholipids, are ubiquitous in nature and are key components of the bilayer of cells, as well as being involved in metabolism. Neural tissue contains high amounts of glycerophospholipids, and alterations in their composition has been implicated in various neurological disorders. Examples of glycerophospholipids found in biological membranes are phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine, the major sphingoid base of mammals is commonly referred to as sphingosine
Lipid
–
Diving medicine:
Lipid
10.
Epifluorescence microscope
–
The specimen is illuminated with light of a specific wavelength which is absorbed by the fluorophores, causing them to emit light of longer wavelengths. The illumination light is separated from the much weaker emitted fluorescence through the use of an emission filter. Typical components of a microscope are a light source, the excitation filter, the dichroic mirror. The filters and the dichroic beamsplitter are chosen to match the spectral excitation and emission characteristics of the used to label the specimen. In this manner, the distribution of a fluorophore is imaged at a time. Multi-color images of types of fluorophores must be composed by combining several single-color images. Most fluorescence microscopes in use are epifluorescence microscopes, where excitation of the fluorophore and these microscopes are widely used in biology and are the basis for more advanced microscope designs, such as the confocal microscope and the total internal reflection fluorescence microscope. The majority of fluorescence microscopes, especially used in the life sciences, are of the epifluorescence design shown in the diagram. Light of the wavelength is focused on the specimen through the objective lens. Fluorescence microscopy requires intense, near-monochromatic, illumination which some widespread light sources, four main types of light source are used, including xenon arc lamps or mercury-vapor lamps with an excitation filter, lasers, supercontinuum sources, and high-power LEDs. In order for a sample to be suitable for fluorescence microscopy it must be fluorescent, there are several methods of creating a fluorescent sample, the main techniques are labelling with fluorescent stains or, in the case of biological samples, expression of a fluorescent protein. Alternatively the intrinsic fluorescence of a sample can be used, as a result, there is a diverse range of techniques for fluorescent staining of biological samples. Many fluorescent stains have been designed for a range of biological molecules, some of these are small molecules which are intrinsically fluorescent and bind a biological molecule of interest. Major examples of these are nucleic acid stains like DAPI and Hoechst and DRAQ5 and DRAQ7 which all bind the minor groove of DNA, others are drugs or toxins which bind specific cellular structures and have been derivatised with a fluorescent reporter. A major example of class of fluorescent stain is phalloidin which is used to stain actin fibres in mammalian cells. Immunofluorescence is a technique which uses the specific binding of an antibody to its antigen in order to label specific proteins or other molecules within the cell. A sample is treated with an antibody specific for the molecule of interest. A fluorophore can be conjugated to the primary antibody
Epifluorescence microscope
–
An upright fluorescence microscope (Olympus BX61) with the fluorescent filter cube turret above the objective lenses, coupled with a digital camera.
Epifluorescence microscope
–
A sample of
herring sperm stained with
SYBR green in a
cuvette illuminated by blue light in an epifluorescence microscope. The SYBR green in the sample binds to the herring sperm
DNA and, once bound, fluoresces giving off green light when illuminated by blue light.
Epifluorescence microscope
–
Epifluorescent imaging of the three components in a dividing human cancer cell.
DNA is stained blue, a
protein called
INCENP is green, and the
microtubules are red. Each
fluorophore is imaged separately using a different combination of excitation and emission filters, and the images are captured sequentially using a digital
CCD camera, then overlaid to give a complete image.
Epifluorescence microscope
–
Endothelial cells under the microscope. Nuclei are stained blue with DAPI, microtubules are marked green by an antibody bound to FITC and actin filaments are labeled red with phalloidin bound to TRITC. Bovine pulmonary artery endothelial (BPAE) cells
11.
Nile Blue
–
Nile blue is a stain used in biology and histology. It may be used live or fixed cells, and imparts a blue colour to cell nuclei. It may also be used in conjunction with fluorescence microscopy to stain for the presence of granules in prokaryotic or eukaryotic cells. Boiling a solution of Nile blue with sulfuric acid produces Nile red, Nile blue is a fluorescent dye. The fluorescence shows especially in nonpolar solvents with a quantum yield. The absorption and emission maxima of Nile blue are strongly dependent on pH and this is shorter than the corresponding value of Nile red with 3.65 ns. The fluorescence duration is independent on dilution in the range 10−3–10−8 mol/L, Nile blue is used for histological staining of biological preparations. It highlights the distinction between neutral lipids which are stained pink and acids which are stained blue, for better differentiation, it is dipped in 1% acetic acid for 10–20 minutes until the colors are pure. This might take only 1–2 minutes, then the sample is thoroughly rinsed in water. Afterwards, the specimen is taken on a microscope slide. The sample can be embedded in glycerol or glycerol gelatin, unsaturated glycerides are pink, nuclei and elastins dark, fatty acids and various fatty substances and fat mixtures are purple blue. The PHB granules in the cells of Pseudomonas solanacearum can be visualized by Nile blue A staining, Nile blue is also apparently used in a variety of commercial DNA staining formulations used for DNA electrophoresis. Derivatives of Nile blue are potential photosensitizers in photodynamic therapy of malignant tumors and these dyes aggregate in the tumor cells, especially in the lipid membranes, and/or are sequestered and concentrated in subcellular organelles. With the Nile blue derivative N-Ethyl-Nile Blue, normal and premalignant tissues in animal experiments can be distinguished by spectroscopy in fluorescence imaging. The following scheme illustrates the first of four approaches, leading to Nile Blue perchlorate
Nile Blue
–
Nile blue hydrochloride in water. Concentrations, left to right: 1000
ppm, 100 ppm, 10 ppm, 1 ppm, 100 ppb.
Nile Blue
–
Nile blue
12.
2-naphthol
–
2-Naphthol, or β-naphthol, is a fluorescent colorless crystalline solid with the formula C10H7OH. It is an isomer of 1-naphthol, differing by the location of the group on the naphthalene ring. The naphthols are naphthalene homologues of phenol, but more reactive, both isomers are soluble in simple alcohols, ethers, and chloroform. 2-Naphthol is a widely used intermediate for the production of dyes, 2-Naphthol can also be produced by a method analogous to the cumene process. The Sudan dyes are popular dyes noted for being soluble in organic solvents, several of the Sudan dyes are derived from 2-naphthol by coupling with diazonium salts. Sudan dyes I -IV and Sudan Red G consist of arylazo-substituted naphthols, selected 2-Naphthol-derived dyes They can be also used in the production of dyes and in organic synthesis. For example, 2-naphthol reacts to form BINOL, naphthols are used as biomarkers for livestock and humans exposed to polycyclic aromatic hydrocarbons
2-naphthol
–
2-Naphthol
13.
Water
–
Water is a transparent and nearly colorless chemical substance that is the main constituent of Earths streams, lakes, and oceans, and the fluids of most living organisms. Its chemical formula is H2O, meaning that its molecule contains one oxygen, Water strictly refers to the liquid state of that substance, that prevails at standard ambient temperature and pressure, but it often refers also to its solid state or its gaseous state. It also occurs in nature as snow, glaciers, ice packs and icebergs, clouds, fog, dew, aquifers, Water covers 71% of the Earths surface. It is vital for all forms of life. Only 2. 5% of this water is freshwater, and 98. 8% of that water is in ice and groundwater. Less than 0. 3% of all freshwater is in rivers, lakes, and the atmosphere, a greater quantity of water is found in the earths interior. Water on Earth moves continually through the cycle of evaporation and transpiration, condensation, precipitation. Evaporation and transpiration contribute to the precipitation over land, large amounts of water are also chemically combined or adsorbed in hydrated minerals. Safe drinking water is essential to humans and other even though it provides no calories or organic nutrients. There is a correlation between access to safe water and gross domestic product per capita. However, some observers have estimated that by 2025 more than half of the population will be facing water-based vulnerability. A report, issued in November 2009, suggests that by 2030, in developing regions of the world. Water plays an important role in the world economy, approximately 70% of the freshwater used by humans goes to agriculture. Fishing in salt and fresh water bodies is a source of food for many parts of the world. Much of long-distance trade of commodities and manufactured products is transported by boats through seas, rivers, lakes, large quantities of water, ice, and steam are used for cooling and heating, in industry and homes. Water is an excellent solvent for a variety of chemical substances, as such it is widely used in industrial processes. Water is also central to many sports and other forms of entertainment, such as swimming, pleasure boating, boat racing, surfing, sport fishing, Water is a liquid at the temperatures and pressures that are most adequate for life. Specifically, at atmospheric pressure of 1 bar, water is a liquid between the temperatures of 273.15 K and 373.15 K
Water
–
Water in three states: liquid, solid (
ice), and gas (invisible
water vapor in the air).
Clouds are accumulations of water droplets,
condensed from vapor-saturated air.
Water
–
Impact from a water drop causes an upward "rebound" jet surrounded by circular
capillary waves.
Water
–
Snowflakes by
Wilson Bentley, 1902.
Water
–
Dew drops adhering to a
spider web.
14.
Ethanol
–
Ethanol, also called alcohol, ethyl alcohol, and drinking alcohol, is the principal type of alcohol found in alcoholic beverages. It is a volatile, flammable, colorless liquid with a characteristic odor. Its chemical formula is C 2H 6O, which can be written also as CH 3-CH 2-OH or C 2H 5-OH, ethanol is mostly produced by the fermentation of sugars by yeasts, or by petrochemical processes. It is a psychoactive drug, causing a characteristic intoxication. It is widely used as a solvent, as fuel, and as a feedstock for synthesis of other chemicals, the eth- prefix and the qualifier ethyl in ethyl alcohol originally come from the name ethyl assigned in 1834 to the group C 2H 5- by Justus Liebig. He coined the word from the German name Aether of the compound C 2H 5-O-C 2H5, according to the Oxford English Dictionary, Ethyl is a contraction of the Ancient Greek αἰθήρ and the Greek word ύλη. The name ethanol was coined as a result of a resolution that was adopted at the International Conference on Chemical Nomenclature that was held in April 1892 in Geneva, Switzerland. The term alcohol now refers to a class of substances in chemistry nomenclature. The Oxford English Dictionary claims that it is a loan from Arabic al-kuḥl, a powdered ore of antimony used since aniquity as a cosmetic. The use of alcohol for ethanol is modern, first recorded 1753, the systematic use in chemistry dates to 1850. Ethanol is used in medical wipes and most common antibacterial hand sanitizer gels as an antiseptic, ethanol kills organisms by denaturing their proteins and dissolving their lipids and is effective against most bacteria and fungi, and many viruses. However, ethanol is ineffective against bacterial spores, ethanol may be administered as an antidote to methanol and ethylene glycol poisoning. Ethanol, often in high concentrations, is used to dissolve many water-insoluble medications, as a central nervous system depressant, ethanol is one of the most commonly consumed psychoactive drugs. The amount of ethanol in the body is typically quantified by blood alcohol content, small doses of ethanol, in general, produce euphoria and relaxation, people experiencing these symptoms tend to become talkative and less inhibited, and may exhibit poor judgment. Ethanol is commonly consumed as a drug, especially while socializing. The largest single use of ethanol is as a fuel and fuel additive. Brazil in particular relies heavily upon the use of ethanol as an engine fuel, gasoline sold in Brazil contains at least 25% anhydrous ethanol. Hydrous ethanol can be used as fuel in more than 90% of new gasoline fueled cars sold in the country, Brazilian ethanol is produced from sugar cane and noted for high carbon sequestration
Ethanol
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USP grade ethanol for laboratory use.
Ethanol
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Ethanol pump station in
São Paulo, Brazil
Ethanol
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A
Ford Taurus fueled by ethanol in
New York City
Ethanol
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USPS truck running on
E85 in
Minnesota
15.
Ethyl acetate
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Ethyl acetate is the organic compound with the formula CH3–COO–CH2–CH3, simplified to C4H8O2. This colorless liquid has a sweet smell and is used in glues, nail polish removers, decaffeinating tea and coffee. Ethyl acetate is the ester of ethanol and acetic acid, it is manufactured on a scale for use as a solvent. The combined annual production in 1985 of Japan, North America, in 2004, an estimated 1.3 million tonnes were produced worldwide. Ethyl acetate is synthesized in industry mainly via the classic Fischer esterification reaction of ethanol and this method is more cost effective than the esterification but is applied with surplus ethanol in a chemical plant. Typically, dehydrogenation is conducted with copper at an elevated temperature, the copper may have its surface area increased by depositing it on zinc, promoting the growth of snowflake-like fractal structures. Surface area can be increased by deposition onto a zeolite. Traces of rare earth and alkali metals are beneficial to the process, byproducts of the dehydrogenation include diethyl ether, which is thought to arise primarily due to aluminum sites in the catalyst, acetaldehyde and its aldol products, higher esters, and ketones. These azeotropes are broken by pressure swing distillation or membrane distillation, ethyl acetate is used primarily as a solvent and diluent, being favored because of its low cost, low toxicity, and agreeable odor. For example, it is used to clean circuit boards. Coffee beans and tea leaves are decaffeinated with this solvent and it is also used in paints as an activator or hardener. Ethyl acetate is present in confectionery, perfumes, and fruits, in perfumes, it evaporates quickly, leaving only the scent of the perfume on the skin. In the laboratory, mixtures containing ethyl acetate are used in column chromatography. Ethyl acetate is rarely selected as a solvent because it is prone to hydrolysis. Ethyl acetate is volatile at room temperature and has a boiling point of 77 °C. Due to these properties, it can be removed from a sample by heating in a hot water bath and providing ventilation with compressed air. Ethyl acetate is the most common ester in wine, being the product of the most common organic acid – acetic acid. The aroma of ethyl acetate is most vivid in younger wines and contributes towards the general perception of fruitiness in the wine, sensitivity varies, with most people having a perception threshold around 120 mg/L
Ethyl acetate
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Ethyl acetate
16.
Dichloromethane
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Dichloromethane is an organic compound with the formula CH2Cl2. This colorless, volatile liquid with a sweet aroma is widely used as a solvent. Although it is not miscible with water, it is miscible with organic solvents. One of the most well-known applications of dichloromethane is in the drinking bird heat engine, natural sources of dichloromethane include oceanic sources, macroalgae, wetlands, and volcanoes. However, the majority of dichloromethane in the environment is the result of industrial emissions, DCM is produced by treating either chloromethane or methane with chlorine gas at 400–500 °C. At these temperatures, both methane and chloromethane undergo a series of reactions producing progressively more chlorinated products, in this way, an estimated 400,000 tons were produced in the US, Europe, and Japan in 1993. These compounds are separated by distillation, DCM was first prepared in 1839 by the French chemist Henri Victor Regnault, who isolated it from a mixture of chloromethane and chlorine that had been exposed to sunlight. DCMs volatility and ability to dissolve a wide range of organic compounds makes it a useful solvent for chemical processes. It is widely used as a paint stripper and a degreaser, in the food industry, it has been used to decaffeinate coffee and tea as well as to prepare extracts of hops and other flavorings. Its volatility has led to its use as an aerosol spray propellant, the chemical compounds low boiling point allows the chemical to function in a heat engine that can extract mechanical energy from small temperature differences. An example of a DCM heat engine is the drinking bird, the toy works at room temperature. For example, it is used to seal the casing of electric meters, often sold as a main component of plastic welding adhesives, it is also used extensively by model building hobbyists for joining plastic components together. It is commonly referred to as Di-clo and it is used in the garment printing industry for removal of heat-sealed garment transfers, and its volatility is exploited in novelty items, bubble lights and jukebox displays. DCM is the least toxic of the simple chlorohydrocarbons, but it is not without health risks and it can also be absorbed through the skin. More severe consequences can include suffocation, loss of consciousness, coma, DCM is also metabolized by the body to carbon monoxide potentially leading to carbon monoxide poisoning. Acute exposure by inhalation has resulted in optic neuropathy and hepatitis, prolonged skin contact can result in DCM dissolving some of the fatty tissues in skin, resulting in skin irritation or chemical burns. It may be carcinogenic, as it has linked to cancer of the lungs, liver. Other animal studies showed breast cancer and salivary gland cancer, research is not yet clear as to what levels may be carcinogenic
Dichloromethane
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Dichloromethane
17.
MTBE
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Methyl tert-butyl ether is an organic compound with a structural formula 3COCH3. MTBE is a volatile, flammable, and colorless liquid that is soluble in water. It has a minty odor vaguely reminiscent of diethyl ether, leading to unpleasant taste, MTBE is a gasoline additive, used as an oxygenate to raise the octane number. Its use is controversial because of its contamination of groundwater and legislation favoring ethanol, however, worldwide production of MTBE has been constant owing to growth in Asian markets. MTBE is manufactured via the reaction of methanol and isobutylene. Methanol is derived from gas, and isobutylene is derived from butane obtained from crude oil or natural gas. In the United States, it is produced in large quantities during its use as a fuel additive. MTBE is used as a component in fuel for gasoline engines. It is one of a group of chemicals known as oxygenates because they raise the oxygen content of gasoline. In the US it has used in gasoline at low levels since 1979 to replace tetraethyl lead. Before the incoming of other oxygenates and octane enhancing components most refiners had chosen MTBE primarily for its blending characteristics, other oxygenates are available as additives for gasoline including ethanol and other ethers such as ETBE. Ethanol has been advertised as an alternative by agricultural and other interest groups in the US. In 2003, California was the first US state to start replacing MTBE with ethanol, an alternative to ethanol is ETBE, which is manufactured from ethanol and isobutene. Its performance as an additive is similar to MTBE, but due to the price of ethanol compared to methanol. Higher quality gasoline is also an alternative, so that such as MTBE are unnecessary. MTBE plants can be retrofitted to produce iso-octane from isobutylene, MTBE is extensively used in industry as a safer alternative to diethyl ether as the tert-butyl group prevents MTBE from forming potentially explosive peroxides. It is also used as a solvent in research, although it is less commonly used than diethyl ether. Although an ether, MTBE is a poor Lewis base and does not support formation of Grignard reagents and it is also unstable toward strong acids
MTBE
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Methyl tert -butyl ether
18.
Cyclohexane
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Cyclohexane is a cycloalkane with the molecular formula C6H12. Cyclohexane is mainly used for the production of adipic acid and caprolactam. Cyclohexane is a colourless, flammable liquid with a distinctive detergent-like odor, on an industrial scale, cyclohexane is produced by hydrogenation of benzene. Producers of cyclohexane accounts for approximately 11. 4% of global demand for benzene, the reaction is highly exothermic, with ΔH =216.37 kJ/mol). Dehydrogenation commenced noticeably above 300 °C, reflecting the favorable entropy for dehydrogenation, unlike benzene, cyclohexane is not easily obtained from natural resources such as coal. For this reason, early investigators synthesized their cyclohexane samples, in 1867 Marcellin Berthelot reduced benzene with hydroiodic acid at elevated temperatures. In 1894 Baeyer synthesized cyclohexane starting with a Dieckmann condensation of pimelic acid followed by multiple reductions, In the same year E. Haworth, perkin Jr. prepared it via a Wurtz reaction of 1, 6-dibromohexane. Cyclohexane is rather unreactive, being a non-polar, hydrophobic hydrocarbon and it reacts with superacids, such as HF + SbF5, which will lead to cracking. Substituted cyclohexanes, however, may be reactive under a variety of conditions, commercially most of cyclohexane produced is converted into cyclohexanone–cyclohexanol mixture by catalytic oxidation. KA oil is used as a raw material for adipic acid. It is used as a solvent in some brands of correction fluid, cyclohexane is sometimes used as an organic solvent. Cyclohexane is also used for calibration of differential scanning calorimetry instruments, cyclohexane vapour is used in vacuum carburizing furnaces, in heat treating equipment manufacture. The 6-vertex edge ring does not conform to the shape of a perfect hexagon, therefore, to reduce torsional strain, cyclohexane adopts a three-dimensional structure known as the chair conformation. There are also two other intermediate conformers, half chair, which is the most unstable conformer, and twist boat and this was first proposed as early as 1890 by Hermann Sachse, but only gained widespread acceptance much later. The new conformation puts the carbons at an angle of 109. 5°, half of the hydrogens are in the plane of the ring while the other half are perpendicular to the plane. This conformation allows for the most stable structure of cyclohexane, another conformation of cyclohexane exists, known as boat conformation, but it interconverts to the slightly more stable chair formation. If cyclohexane is mono-substituted with a substituent, then the substituent will most likely be found attached in an equatorial position. Cyclohexane has the lowest angle and torsional strain of all the cycloalkanes, the high-temperature phase I, stable between 186 K and the melting point 280 K, is a plastic crystal, which means the molecules retain some rotational degree of freedom
Cyclohexane
19.
Toluene
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Toluene /ˈtɒljuːiːn/, also known as toluol /ˈtɒljuːɒl/, is a colorless, water-insoluble liquid with the smell associated with paint thinners. It is a benzene derivative, consisting of a CH3 group attached to a phenyl group. As such, its IUPAC systematic name is methylbenzene, Toluene is widely used as an industrial feedstock and a solvent. In 2013, worldwide sales of toluene amounted to about 24.5 billion US-dollars, as the solvent in some types of paint thinner, contact cement and model airplane glue, toluene is sometimes used as a recreational inhalant and has the potential of causing severe neurological harm. The compound was first isolated in 1837 through a distillation of oil by a Polish chemist named Filip Walter. In 1843, Jöns Jacob Berzelius recommended the name toluin, in 1850, French chemist Auguste Cahours isolated from a distillate of wood a hydrocarbon which he recognized as similar to Devilles benzoène and which Cahours named toluène. Toluene reacts as an aromatic hydrocarbon in electrophilic aromatic substitution. Because the methyl group has greater electron-releasing properties than an atom in the same position. It undergoes sulfonation to give p-toluenesulfonic acid, and chlorination by Cl2 in the presence of FeCl3 to give ortho, importantly, the methyl side chain in toluene is susceptible to oxidation. Toluene reacts with Potassium permanganate to yield benzoic acid, and with chromyl chloride to yield benzaldehyde, the methyl group undergoes halogenation under free radical conditions. For example, N-bromosuccinimide heated with toluene in the presence of AIBN leads to benzyl bromide, the same conversion can be effected with elemental bromine in the presence of UV light or even sunlight. Toluene may also be brominated by treating it with HBr and H2O2 in the presence of light. C6H5CH3 + Br2 → C6H5CH2Br + HBr C6H5CH2Br + Br2 → C6H5CHBr2 + HBr The methyl group in toluene undergoes deprotonation only with strong bases. Catalytic hydrogenation of toluene gives methylcyclohexane, the reaction requires a high pressure of hydrogen and a catalyst. Final separation and purification is done by any of the distillation or solvent extraction processes used for BTX aromatics, Toluene is so inexpensively produced industrially that it is not prepared in the laboratory. In principle it could be prepared by a variety of methods, Toluene is mainly used as a precursor to benzene via hydrodealkylation, C6H5CH3 + H2 → C6H6 + CH4 The second ranked application involves its disproportionation to a mixture of benzene and xylene. When oxidized it yields benzaldehyde and benzoic acid, two important intermediates in chemistry, in addition to the synthesis of benzene and xylene, toluene is a feedstock for toluene diisocyanate, trinitrotoluene, and a number of synthetic drugs. Toluene is a solvent, e. g. for paints, paint thinners, silicone sealants, many chemical reactants, rubber, printing ink, adhesives, lacquers, leather tanners
Toluene
20.
Bacillus subtilis
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Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants and humans. A member of the genus Bacillus, B. subtilis is rod-shaped, B. subtilis has historically been classified as an obligate aerobe, though evidence exists that it is a facultative aerobe. B. subtilis is considered the best studied Gram-positive bacterium and an organism to study bacterial chromosome replication. It is one of the champions in secreted enzyme production. Bacillus subtilis is a Gram-positive bacterium, rod-shaped and catalase-positive and it was originally named Vibrio subtilis by Christian Gottfried Ehrenberg, and renamed Bacillus subtilis by Ferdinand Cohn in 1872. B. subtilis cells are typically rod-shaped, and are about 4-10 micrometers long and 0. 25–1.0 μm in diameter, as with other members of the genus Bacillus, it can form an endospore, to survive extreme environmental conditions of temperature and desiccation. B. subtilis is a facultative anaerobe and had considered as an obligate aerobe until 1998. B. subtilis is heavily flagellated, which gives it the ability to move quickly in liquids, in terms of popularity as a laboratory model organism, B. subtilis is often considered as the Gram-positive equivalent of Escherichia coli, an extensively studied Gram-negative bacterium. This species is found in the upper layers of the soil. A2009 study compared the density of spores found in soil to that found in human feces, the number of spores found in the human gut was too high to be attributed solely to consumption through food contamination. The endospore is formed at times of stress, allowing the organism to persist in the environment until conditions become favourable. Prior to the process of sporulation the cells might become motile by producing flagella, take up DNA from the environment, under stressful conditions, such as nutrient deprivation, B. subtilis undergoes the process of sporulation. This process has very well studied and has served as a model organism for studying sporulation. B. subtilis is a model used to study bacterial chromosome replication. Replication of the circular chromosome initiates at a single locus. Replication proceeds bidirectionally and two replication forks progress in clockwise and counterclockwise directions along the chromosome, chromosome replication is completed when the forks reach the terminus region, which is positioned opposite to the origin on the chromosome map. The terminus region contains several short DNA sequences that promote replication arrest, specific proteins mediate all the steps in DNA replication. Comparison between the involved in chromosomal DNA replication in B. subtilis and in Escherichia coli reveals similarities and differences
Bacillus subtilis
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Bacillus subtilis
Bacillus subtilis
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Sporulating B. subtilis.
Bacillus subtilis
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Gram-stained B. subtilis
Bacillus subtilis
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Colonies of B. subtilis grown on a
culture dish in a
molecular biology laboratory
21.
Journal of Cell Biology
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The Journal of Cell Biology is an international, peer-reviewed journal owned by The Rockefeller University and published by The Rockefeller University Press. In the early 1950s, a group of biologists began to explore intracellular anatomy using the emerging technology of electron microscopy. Many of these researchers were at The Rockefeller Institute of Medicine, in 1954, the Director of the Rockefeller Institute, Detlev Bronk, convened a luncheon to discuss the creation of a new journal as a venue for publication of this type of work. The first issue of The Journal of Biophysical and Biochemical Cytology was published less than a year later on January 25,1955, a subscription cost $15 per year. The list of editors comprised Richard S. Bear, H. Stanley Bennett, Albert L. Lehninger, George E. Palade, Keith R. Porter, Francis O. Schmitt, Franz Schrader, and Arnold M. Seligman. It will give attention to reports on cellular organization at the colloidal and molecular levels. Recognizing that they needed a title, the editors changed the name to The Journal of Cell Biology in 1962. January 25,1955, Publication of the first issue of The Journal of Biophysical and Biochemical Cytology, January 1961 – December 1983, Ray Griffiths is Executive Editor. January 1962, Journal name changed to The Journal of Cell Biology, January 1984 – December 1998, Bernie Gilula is Editor in Chief. January 13,1997, First issue of the JCB is published online, April 1997 – April 2007, Mike Rossner is Managing Editor. January 1999 – December 2008, Ira Mellman is Editor in Chief, July 2000, Authors allowed to post the final, published pdf file of their articles on their own websites. January 2001, JCB begins to make its online content free to the six months after publication. July 2002, JCB adopts completely electronic workflow, september 2002, JCB begins screening all digital images for evidence of manipulation. January 2003, JCB pioneers RGB workflow for digital images. June 2003, JCB releases all of its back content older than six months for free to the back to volume 1. May 2007 – July 2010, Emma Hill is Executive Editor, November 2007, JCB begins posting all of its content on PubMed Central, where it is available for free to the public six months after publication. May 1,2008, New copyright policy allows authors to retain copyright to their own works, December 2008, JCB launches Dataviewer January 2009 – October 2014, Tom Misteli is Editor in Chief. September 2010 – December 2014, Elizabeth H. Williams is Executive Editor, October 2013 – August 2015, Alan Hall is Editor in Chief
Journal of Cell Biology
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The Journal of Cell Biology
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