1.
Melting point
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The melting point of a solid is the temperature at which it changes state from solid to liquid at atmospheric pressure. At the melting point the solid and liquid phase exist in equilibrium, the melting point of a substance depends on pressure and is usually specified at standard pressure. When considered as the temperature of the change from liquid to solid. Because of the ability of some substances to supercool, the point is not considered as a characteristic property of a substance. For most substances, melting and freezing points are approximately equal, for example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures, for example, agar melts at 85 °C and solidifies from 31 °C to 40 °C, such direction dependence is known as hysteresis. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances the freezing point of water is the same as the melting point, the chemical element with the highest melting point is tungsten, at 3687 K, this property makes tungsten excellent for use as filaments in light bulbs. Many laboratory techniques exist for the determination of melting points, a Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip revealing its thermal behaviour at the temperature at that point, differential scanning calorimetry gives information on melting point together with its enthalpy of fusion. A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window, the several grains of a solid are placed in a thin glass tube and partially immersed in the oil bath. The oil bath is heated and with the aid of the melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, the measurement can also be made continuously with an operating process. For instance, oil refineries measure the point of diesel fuel online, meaning that the sample is taken from the process. This allows for more frequent measurements as the sample does not have to be manually collected, for refractory materials the extremely high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees, the spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source that has been previously calibrated as a function of temperature, in this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer, for temperatures above the calibration range of the source, an extrapolation technique must be employed
2.
Dye
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A dye is a colored substance that has an affinity to the substrate to which it is being applied. The dye is applied in an aqueous solution, and may require a mordant to improve the fastness of the dye on the fiber. Both dyes and pigments are colored because they absorb some wavelengths of light more than others, in contrast to dyes, pigments are insoluble and have no affinity for the substrate. Some dyes can be precipitated with a salt to produce a lake pigment. The majority of natural dyes are from plant sources, roots, berries, bark, leaves, and wood, fungi, textile dyeing dates back to the Neolithic period. Throughout history, people have dyed their textiles using common, locally available materials, scarce dyestuffs that produced brilliant and permanent colors such as the natural invertebrate dyes Tyrian purple and crimson kermes were highly prized luxury items in the ancient and medieval world. Plant-based dyes such as woad, indigo, saffron, and madder were raised commercially and were important trade goods in the economies of Asia, across Asia and Africa, patterned fabrics were produced using resist dyeing techniques to control the absorption of color in piece-dyed cloth. Dyes from the New World such as cochineal and logwood were brought to Europe by the Spanish treasure fleets, dyed flax fibers have been found in the Republic of Georgia in a prehistoric cave dated to 36,000 BP. Archaeological evidence shows that, particularly in India and Phoenicia, dyeing has been carried out for over 5,000 years. The dyes were obtained from animal, vegetable or mineral origin, by far the greatest source of dyes has been from the plant kingdom, notably roots, berries, bark, leaves and wood, but only a few have ever been used on a commercial scale. The discovery of synthetic dyes late in the 19th century ended the large-scale market for natural dyes. These dyes are made from synthetic resources such as petroleum by-products, the first human-made organic aniline dye, mauveine, was discovered serendipitously by William Henry Perkin in 1856, the result of a failed attempt at the total synthesis of quinine. Other aniline dyes followed, such as fuchsine, safranine, many thousands of synthetic dyes have since been prepared. These may be natural or synthetic, other than pigmentation, they have a range of applications including organic dye lasers, optical media and camera sensors. This is the basic classification Dyes are classified according to their solubility, acid dyes are water-soluble anionic dyes that are applied to fibers such as silk, wool, nylon and modified acrylic fibers using neutral to acid dye baths. Attachment to the fiber is attributed, at least partly, to salt formation between anionic groups in the dyes and cationic groups in the fiber, acid dyes are not substantive to cellulosic fibers. Most synthetic food colors fall in this category, basic dyes are water-soluble cationic dyes that are mainly applied to acrylic fibers, but find some use for wool and silk. Usually acetic acid is added to the dye bath to help the uptake of the dye onto the fiber, basic dyes are also used in the coloration of paper
3.
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
4.
Fate mapping
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When carried out at single-cell resolution, this process is termed cell lineage tracing. The first attempts at fate mapping were made by inferences based on the examination of embryos that had fixed, sectioned. The disadvantage of this technique was that observation of single points in time provide only snapshots of what cell movements are actually occurring. Early embryologists thus had to infer which cells became what tissues at later stages, early embryologists used vital dyes to follow movements of individual cells or groups of cells over time in Xenopus frog embryos. The tissue to which the cells contribute would thus be labeled, the first person to develop and use this technique to study cell fate was embryologist Walter Vogt in 1929. Once the cells were effectively labeled, the chip could be removed. With this method, Vogt was able to discern movements of cell populations. Additionally, the cell or cell population of interest must be superficial, the information Vogt gathered from his tracing experiments of distinct cells and populations of cells in Xenopus was then pooled to construct a fate map. The map was a representation of an embryo that has particular regions highlighted which are known to give rise to specific tissues in the adult organism. For instance, in Figure 1, Nile Blue staining of a 32-cell blastula at the side of the animal pole yields a blue-stained brain. All progeny of the cells could later be discerned by staining for HRP using benzidine substrate or visualized by fluorescence microscopy. This technique allowed the experimenter greater control and selectivity over what cell was labeled and traced, however, the opaque character of the HRP stain prevented use of vital dye nuclear counter-stains such as Hoechst 33258 to observe the mitotic state of the injected cells progeny. Also, embryos had to be fixed in order to stain for the HRP, leech embryos injected with the fluorescent tracers could be visualized, and images collected of the same specimen at multiple timepoints, without fixation. The fluorescent tracers could also be combined with nuclear Hoechst staining to visualize the status of the progeny of injected cells. For this purpose, specific cells were ablated by microinjection with Pronase to ablate the cell, the single-cell injection technique is now also in use by researchers studying other model organisms such as Xenopus, Danio rerio, and Caenorhabditis elegans. Subsequent studies have used the Cre-lox system in mice and zebrafish to create tissue specific conditional knockouts. A second transgenic line must be created, in which loxP recognition sites flank a portion of a particular critical housekeeping gene such as DNA polymerase-β. However, in some cases a particular gene of interest is turned on multiple times during development, in this scenario, it is possible to use an inducible version of the transgene, the Cre-ERt loxP approach
5.
Sodium dodecyl sulfate
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Sodium dodecyl sulfate, synonymously sodium lauryl sulfate, is a synthetic organic compound with the formula CH311SO4Na. It is a surfactant used in many cleaning and hygiene products. The sodium salt is of a class of organics. It consists of a 12-carbon tail attached to a group, i. e. it is the sodium salt of dodecyl hydrogen sulfate. Its hydrocarbon tail combined with a polar headgroup give the compound amphiphilic properties, SDS is in the family of organosulfate compounds, and has the formula, CH311SO4Na, that is, it is the sodium salt of a 12-carbon alcohol that has been esterified to sulfuric acid. An alternative description is that it is a group with a pendant. As a result of its tail, and its anionic head group, it has amphiphilic properties that allow it to form micelles. The critical micelle concentration in water at 25 °C is 8.2 mM. The micelle ionization fraction is around 0.3, SDS is synthesized by treating lauryl alcohol with sulfur trioxide gas, oleum, or chlorosulfuric acid to produce hydrogen lauryl sulfate. The resulting product is then neutralized through the addition of sodium hydroxide or sodium carbonate, lauryl alcohol can be used in pure form or may be derived from either coconut or palm kernel oil by hydrolysis, followed by hydrogenation. When produced from these sources, commercial samples of these SDS products are not pure SDS. For instance, SDS is a component, along with other chain-length amphiphiles, when produced from coconut oil, SDS is available commercially in powder, pellet, and other forms, as well as in aqueous solutions of varying concentrations. SDS is mainly used in detergents for laundry with many cleaning applications and it is used as an emulsifying agent and whipping aid. SLS is reported to temporarily diminish perception of sweetness, the electrostatic repulsion that is created by SDS binding forces proteins into a rod-like shape, thereby eliminating differences in shape as a factor for electrophoretic separation in gels. SDS is used in a technique for preparing brain tissues for study by optical microscopy. Along with sodium dodecylbenzene sulfonate and Triton X-100, aqueous solutions of SDS are popular for dispersing or suspending nanotubes, in products intended for prolonged contact with skin, concentrations should not exceed 1%. Like all detergent surfactants, sodium lauryl sulfate removes oils from the skin and it has been shown to irritate the skin of the face, with prolonged and constant exposure in young adults. SDS may worsen skin problems in individuals with chronic skin hypersensitivity, in animal studies SDS appears to cause skin and eye irritation
6.
Cyanine
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Cyanine is the non-systematic name of a synthetic dye family belonging to polymethine group. Cyanines were and are used in industry, and more recently in biotechnology. Cyanines have many uses as fluorescent dyes, particularly in biomedical imaging, depending on the structure, they cover the spectrum from IR to UV. There are a number reported in the literature. Both nitrogens are each part of a heteroaromatic moiety, such as pyrrole, imidazole, thiazole, pyridine, quinoline, indole, benzothiazole. Cyanines were first synthesized over a century ago, cyanines are also used in CD-R and DVD-R media. The ones used are green or light blue in color. These discs are often rated with a life of 75 years or more. The other dyes used in CD-Rs are phthalocyanine and azo, labeling is done for visualization and quantification purposes. Cyanines dyes are available with different modifications such as methyl, ethyl or butyl substituent, carboxyl, acetylmethoxy, Cy 3 and Cy5 are the most popular, used typically combined for 2 colors detection. Cy3 fluoresces greenish yellow, while Cy5 is fluorescent in the red region, Cy3 can be detected by various fluorometers, imagers, and microscopes with standard filters for Tetramethylrhodamine. Due to inherently high extinction coefficient, this dye is also detected by naked eye on gels. The scanners actually use different laser emission wavelengths and filter wavelengths to avoid background contamination and they are thus able to easily distinguish colors from Cy3 and from Cy5, and also able to quantify the amount of Cy3 and Cy5 labeling in one sample. Other cyanine dyes are useful, Cy3.5 can replace SulfoRhodamine 101, Cy5.5 is a near-infrared fluorescence-emitting dye. Cy7 is a near-IR fluor that is invisible to the naked eye and it is used in in vivo imaging applications, as well as the Cy7.5 dye. Sulfo–Cyanine dyes bear classically one or two Sulfo groups, rendering the Cy dye water-soluble, but tri- and quadri-sulfonated forms are available for even higher hydrosolubility, pEGylation is another modification that confers hydrophilicity, not only to the dye but also to the labeled conjugate. Standard chemical names specify exactly the structure of the molecule. The Cy3 and Cy5 nomenclature was first proposed by Ernst, et al. in 1989, in the original paper the number designated the count of the methines, and the side chains were unspecified
7.
Single-molecule experiment
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A single-molecule experiment is an experiment that investigates the properties of individual molecules. Indeed, since the 90s, many techniques for probing individual molecules have been developed, the first single-molecule experiments were patch clamp experiments performed in the 70s, but these were limited to studying ion channels. Biological polymers conformations have been measured using atomic force microscopy, using force spectroscopy, single molecules, usually polymers, can be mechanically stretched and their elastic response recorded in real time. In the gas phase at pressures, single-molecule experiments have been around for decades. One year later Michel Orrit and Jacky Bernard were able to also the detection of the absorption of single molecules by their fluorescence. Many techniques have the ability to observe one molecule at a time, most notably mass spectrometry, where single ions are detected. In addition one of the earliest means of detecting single molecules, came about in the field of ion channels with the development of the patch clamp technique by Erwin Neher and Bert Sakmann. However, the idea of measuring conductance to look at single molecules placed a limitation on the kind of systems which could be observed. Fluorescence is a convenient means of observing one molecule at a time, mostly due to the sensitivity of commercial optical detectors, the most studied protein has been the class of myosin/actin enzymes found in muscle tissues. Through single-molecule techniques the step mechanism has been observed and characterized in many of these proteins, nanomanipulators such as the atomic force microscope are also suited to single-molecule experiments of biological significance, since they work on the same length scale of most biological polymers. Besides, atomic force microscopy is appropriate for the studies of synthetic polymer molecules, AFM provides a unique possibility of 3D visualization of polymer chains. For instance, AFM tapping mode is gentle enough for the recording of adsorbed polyelectrolyte molecules under liquid medium, the location of two-chain-superposition correspond in these experiments to twice the thickness of single chain. At the application of proper scanning parameters, conformation of such molecules remain unchanged for hours that allows the performance of experiments under liquid media having various properties. Furthermore, by controlling the force between the tip and the high resolution images can be obtained. Optical tweezers have also been used to study. Single-molecule fluorescence spectroscopy uses the fluorescence of a molecule for obtaining information on its environment, structure, the technique affords the ability of obtaining information otherwise not available due to ensemble averaging. The results in experiments of individual molecules are two-state trajectories. Specifically, ion channels alternate between conducting and non-conducting classes, which differ in conformation, therefore, the functional state of ion channels can be directly measured with sufficiently sensitive electronics, provided that proper precautions are taken to minimize noise. In turn, each of these classes may be divided into one or more states with direct bearing on the underlying function of the ion channel
8.
Rhodamine
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Rhodamine /ˈroʊdəmiːn/ is a family of related chemical compounds, fluorone dyes. Examples are Rhodamine 6G and Rhodamine B and they are used as dyes and as dye laser gain media. They are often used as a tracer dye within water to determine the rate and direction of flow, Rhodamine dyes fluoresce and can thus be detected easily and inexpensively with instruments called fluorometers. Rhodamine dyes are used extensively in biotechnology applications such as microscopy, flow cytometry, fluorescence correlation spectroscopy. Rhodamine dyes are generally toxic, and are soluble in water, the laser dye rhodamine 123 is also used in biochemistry to inhibit mitochondrion function. Rhodamine 123 seems to bind to the membranes and inhibit transport processes, especially the electron transport chain. It is a substrate of P-glycoprotein, which is overexpressed in cancer cells. Recent reports indicate that rhodamine 123 may be also a substrate of multidrug resistance-associated protein, or more specifically, TRITC is the base rhodamine molecule functionalized with an isothiocyanate group, replacing a hydrogen atom on the bottom ring of the structure. This derivative is reactive towards amine groups on proteins inside cells, a succinimidyl-ester functional group attached to the rhodamine core, creating NHS-rhodamine, forms another common amine-reactive derivative
9.
Solubility
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Solubility is the property of a solid, liquid, or gaseous chemical substance called solute to dissolve in a solid, liquid, or gaseous solvent. The solubility of a substance depends on the physical and chemical properties of the solute and solvent as well as on temperature, pressure. The solubility of a substance is a different property from the rate of solution. Most often, the solvent is a liquid, which can be a substance or a mixture. One may also speak of solid solution, but rarely of solution in a gas, the extent of solubility ranges widely, from infinitely soluble such as ethanol in water, to poorly soluble, such as silver chloride in water. The term insoluble is often applied to poorly or very poorly soluble compounds, a common threshold to describe something as insoluble is less than 0.1 g per 100 mL of solvent. Under certain conditions, the solubility can be exceeded to give a so-called supersaturated solution. Metastability of crystals can also lead to apparent differences in the amount of a chemical that dissolves depending on its form or particle size. A supersaturated solution generally crystallises when seed crystals are introduced and rapid equilibration occurs, phenylsalicylate is one such simple observable substance when fully melted and then cooled below its fusion point. Solubility is not to be confused with the ability to dissolve a substance, for example, zinc dissolves in hydrochloric acid as a result of a chemical reaction releasing hydrogen gas in a displacement reaction. The zinc ions are soluble in the acid, the smaller a particle is, the faster it dissolves although there are many factors to add to this generalization. Crucially solubility applies to all areas of chemistry, geochemistry, inorganic, physical, organic, in all cases it will depend on the physical conditions and the enthalpy and entropy directly relating to the solvents and solutes concerned. By far the most common solvent in chemistry is water which is a solvent for most ionic compounds as well as a range of organic substances. This is a factor in acidity/alkalinity and much environmental and geochemical work. According to the IUPAC definition, solubility is the composition of a saturated solution expressed as a proportion of a designated solute in a designated solvent. Solubility may be stated in units of concentration such as molarity, molality, mole fraction, mole ratio, mass per volume. Solubility occurs under dynamic equilibrium, which means that solubility results from the simultaneous and opposing processes of dissolution, the solubility equilibrium occurs when the two processes proceed at a constant rate. The term solubility is used in some fields where the solute is altered by solvolysis
. PMID 27597115.
