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Fluorophore

A fluorophore (or fluorochrome, similarly to a chromophore) is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with several π bonds.

Fluorophores are sometimes used alone, as a tracer in fluids, as a dye for staining of certain structures, as a substrate of enzymes, or as a probe or indicator (when its fluorescence is affected by environmental aspects such as polarity or ions). More generally they are covalently bonded to macromolecules, serving as a markers (or dyes, or tags, or reporters) for affine or bioactive reagents (antibodies, peptides, nucleic acids). Fluorophores are notably used to stain tissues, cells, or materials in a variety of analytical methods, such as fluorescent imaging and spectroscopy.

Fluorescein, via its amine-reactive isothiocyanate derivative fluorescein isothiocyanate (FITC), has been one of the most popular fluorophores. From antibody labeling, the applications have spread to nucleic acids thanks to carboxyfluorescein. Other historically common fluorophores are derivatives of rhodamine (TRITC), coumarin, and cyanine. Newer generations of fluorophores, many of which are proprietary, often perform better, being more photostable, brighter, or less pH-sensitive than traditional dyes with comparable excitation and emission.

Fluorescence
The fluorophore absorbs light energy of a specific wavelength and re-emits light at a longer wavelength. The absorbed wavelengths, energy transfer efficiency, and time before emission depend on both the fluorophore structure and its chemical environment, since the molecule in its excited state interacts with surrounding molecules. Wavelengths of maximum absorption (≈ excitation) and emission (for example, Absorption/Emission = 485 nm/517 nm) are the typical terms used to refer to a given fluorophore, but the whole spectrum may be important to consider. The excitation wavelength spectrum may be a very narrow or broader band, or it may be all beyond a cutoff level. The emission spectrum is usually sharper than the excitation spectrum, and it is of a longer wavelength and correspondingly lower energy. Excitation energies range from ultraviolet through the visible spectrum, and emission energies may continue from visible light into the near infrared region.

The main characteristics of fluorophores are:
 * Maximum excitation and emission wavelength (expressed in nanometers (nm)): corresponds to the peak in the excitation and emission spectra (usually one peak each).
 * Molar absorption coefficient (in mol−1cm−1): links the quantity of absorbed light, at a given wavelength, to the concentration of fluorophore in solution.
 * Quantum yield: efficiency of the energy transferred from incident light to emitted fluorescence (the number of emitted photons per absorbed photons).
 * Lifetime (in picoseconds): duration of the excited state of a fluorophore before returning to its ground state. It refers to the time taken for a population of excited fluorophores to decay to 1/e (≈0.368) of the original amount.
 * Stokes shift: the difference between the maximum excitation and maximum emission wavelengths.
 * Dark fraction: the proportion of the molecules not active in fluorescence emission. For quantum dots, prolonged single-molecule microscopy showed that 20-90% of all particles never emit fluorescence. On the other hand, conjugated polymer nanoparticles (Pdots) show almost no dark fraction in their fluorescence. Fluorescent proteins can have a dark fraction from protein misfolding or defective chromophore formation.

These characteristics drive other properties, including photobleaching or photoresistance (loss of fluorescence upon continuous light excitation). Other parameters should be considered, as the polarity of the fluorophore molecule, the fluorophore size and shape (i.e. for polarization fluorescence pattern), and other factors can change the behavior of fluorophores.

Fluorophores can also be used to quench the fluorescence of other fluorescent dyes or to relay their fluorescence at even longer wavelengths.

Size (molecular weight)
Most fluorophores are organic small molecules of 20–100 atoms (200–1000 Dalton; the molecular weight may be higher depending on grafted modifications and conjugated molecules), but there are also much larger natural fluorophores that are proteins: green fluorescent protein (GFP) is 27 kDa, and several phycobiliproteins (PE, APC...) are ≈240kDa. As of 2020, the smallest known fluorophore was claimed to be 3-hydroxyisonicotinaldehyde, a compound of 14 atoms and only 123 Da.

Fluorescence particles like quantum dots (2–10 nm diameter, 100–100,000 atoms) are also considered fluorophores.

The size of the fluorophore might sterically hinder the tagged molecule and affect the fluorescence polarity.

Families
Fluorophore molecules could be either utilized alone, or serve as a fluorescent motif of a functional system. Based on molecular complexity and synthetic methods, fluorophore molecules could be generally classified into four categories: proteins and peptides, small organic compounds, synthetic oligomers and polymers, and multi-component systems.

Fluorescent proteins GFP, YFP, and RFP (green, yellow, and red, respectively) can be attached to other specific proteins to form a fusion protein, synthesized in cells after transfection of a suitable plasmid carrier.

Non-protein organic fluorophores belong to following major chemical families:
 * Xanthene derivatives: fluorescein, rhodamine, Oregon green, eosin, and Texas red
 * Cyanine derivatives: cyanine, indocarbocyanine, oxacarbocyanine, thiacarbocyanine, and merocyanine
 * Squaraine derivatives and ring-substituted squaraines, including Seta and Square dyes
 * Squaraine rotaxane derivatives: See Tau dyes
 * Naphthalene derivatives (dansyl and prodan derivatives)
 * Coumarin derivatives
 * Oxadiazole derivatives: pyridyloxazole, nitrobenzoxadiazole, and benzoxadiazole
 * Anthracene derivatives: anthraquinones, including DRAQ5, DRAQ7, and CyTRAK Orange
 * Pyrene derivatives: cascade blue, etc.
 * Oxazine derivatives: Nile red, Nile blue, cresyl violet, oxazine 170, etc.
 * Acridine derivatives: proflavin, acridine orange, acridine yellow, etc.
 * Arylmethine derivatives: auramine, crystal violet, malachite green
 * Tetrapyrrole derivatives: porphin, phthalocyanine, bilirubin
 * Dipyrromethene derivatives: BODIPY, aza-BODIPY

These fluorophores fluoresce due to delocalized electrons which can jump a band and stabilize the energy absorbed. For example, benzene, one of the simplest aromatic hydrocarbons, is excited at 254 nm and emits at 300 nm. This discriminates fluorophores from quantum dots, which are fluorescent semiconductor nanoparticles.

They can be attached to proteins to specific functional groups, such as amino groups (active ester, carboxylate, isothiocyanate, hydrazine), carboxyl groups (carbodiimide), thiol (maleimide, acetyl bromide), and organic azide (via click chemistry or non-specifically (glutaraldehyde)).

Additionally, various functional groups can be present to alter their properties, such as solubility, or confer special properties, such as boronic acid which binds to sugars or multiple carboxyl groups to bind to certain cations. When the dye contains an electron-donating and an electron-accepting group at opposite ends of the aromatic system, this dye will probably be sensitive to the environment's polarity (solvatochromic), hence called environment-sensitive. Often dyes are used inside cells, which are impermeable to charged molecules; as a result of this, the carboxyl groups are converted into an ester, which is removed by esterases inside the cells, e.g., fura-2AM and fluorescein-diacetate.

The following dye families are trademark groups, and do not necessarily share structural similarities.
 * CF dye (Biotium)
 * DRAQ and CyTRAK probes (BioStatus)
 * BODIPY (Invitrogen)
 * EverFluor (Setareh Biotech)
 * Alexa Fluor (Invitrogen)
 * Bella Fluor (Setareh Biotech)
 * DyLight Fluor (Thermo Scientific, Pierce)
 * Atto and Tracy (Sigma Aldrich)
 * FluoProbes (Interchim)
 * Abberior Dyes (Abberior)
 * DY and MegaStokes Dyes (Dyomics)
 * Sulfo Cy dyes (Cyandye)
 * HiLyte Fluor (AnaSpec)
 * Seta, SeTau and Square Dyes (SETA BioMedicals)
 * Quasar and Cal Fluor dyes (Biosearch Technologies)
 * SureLight Dyes (APC, RPEPerCP, Phycobilisomes) (Columbia Biosciences)
 * APC, APCXL, RPE, BPE (Phyco-Biotech, Greensea, Prozyme, Flogen)
 * Vio Dyes (Miltenyi Biotec)

Reactive and conjugated dyes
Abbreviations:
 * Ex (nm): Excitation wavelength in nanometers
 * Em (nm): Emission wavelength in nanometers
 * MW: Molecular weight
 * QY: Quantum yield

Fluorescent proteins
Abbreviations:
 * Ex (nm): Excitation wavelength in nanometers
 * Em (nm): Emission wavelength in nanometers
 * MW: Molecular weight
 * QY: Quantum yield
 * BR: Brightness: Molar absorption coefficient * quantum yield / 1000
 * PS: Photostability: time [sec] to reduce brightness by 50%

Applications
Fluorophores have particular importance in the field of biochemistry and protein studies, for example, in immunofluorescence, cell analysis, immunohistochemistry, and small molecule sensors.

Uses outside the life sciences
Fluorescent dyes find a wide use in industry, going under the name of "neon colors", such as:
 * Multi-ton scale usages in textile dyeing and optical brighteners in laundry detergents
 * Advanced cosmetic formulations
 * Safety equipment and clothing
 * Organic light-emitting diodes (OLEDs)
 * Fine arts and design (posters and paintings)
 * Synergists for insecticides and experimental drugs
 * Dyes in highlighters to give off a glow-like effect
 * Solar panels to collect more light / wavelengths
 * Fluorescent sea dye is used to help airborne search and rescue teams locate objects in the water

title: Fluorophore


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HMAS Strahan

HMAS Strahan (J363/M363), named for the town of Strahan, Tasmania, was one of 60 Bathurst-class corvettes constructed during World War II, and one of 36 initially manned and commissioned solely by the Royal Australian Navy (RAN).

Design and construction
In 1938, the Australian Commonwealth Naval Board (ACNB) identified the need for a general purpose 'local defence vessel' capable of both anti-submarine and mine-warfare duties, while easy to construct and operate. The vessel was initially envisaged as having a displacement of approximately 500 tons, a speed of at least 10 kn, and a range of 2000 nmi The opportunity to build a prototype in the place of a cancelled Bar-class boom defence vessel saw the proposed design increased to a 680-ton vessel, with a 15.5 kn top speed, and a range of 2850 nmi, armed with a 4-inch gun, equipped with asdic, and able to fitted with either depth charges or minesweeping equipment depending on the planned operations: although closer in size to a sloop than a local defence vessel, the resulting increased capabilities were accepted due to advantages over British-designed mine warfare and anti-submarine vessels. Construction of the prototype HMAS Kangaroo did not go ahead, but the plans were retained. The need for locally built 'all-rounder' vessels at the start of World War II saw the "Australian Minesweepers" (designated as such to hide their anti-submarine capability, but popularly referred to as "corvettes") approved in September 1939, with 60 constructed during the course of the war: 36 (including Strahan) ordered by the RAN, 20 ordered by the British Admiralty but manned and commissioned as RAN vessels, and 4 for the Royal Indian Navy.

Strahan was laid down by the State Dockyard at Newcastle, New South Wales on 9 October 1942. She was launched on 12 July 1943 by Mrs. J. J. Cahill, wife of the Minister for Public Works and Local Government, and commissioned into the RAN on 14 March 1944.

Operational history
Strahan began her career in May 1944, arriving in New Guinea after completing trials to serve as an escort and anti-submarine vessel. In October 1944, Strahan was present in Morotai Harbour when the recently captured island was attacked by Japanese aircraft. The corvette was attacked by a dive-bomber, but was able to drive off the Japanese plane before she was damaged. The aircraft was then destroyed by an American Bofors shore installation, but there claims that Strahan's 4-inch gun had seriously damaged the aircraft, and that it was in an uncontrollable dive when the Bofors blew it up.

In May 1945, Strahan travelled to Adelaide via Sydney, where she underwent a refit. Following this, she was immediate deployed back in New Guinea, and in June 1945 fired upon Japanese gun emplacements on Kairiru Island. In August, the corvette sank a Japanese supply craft off Tarakan, and captured three survivors.

Following the end of World War II, Strahan was assigned to the 21st Minesweeping Flotilla in Hong Kong, and performed in minesweeping and anti-piracy patrols. On 26 September, an acoustic mine detonated under Strahan's stern while the corvette was pursuing Chinese pirates. Her rudder was damaged, and she had to be towed into Hong Kong Harbour by sister ship HMAS Wagga. She was repaired, and returned to Australia. In November, Strahan visited her namesake town. During the visit, a leading seaman drowned; the only casualty in the ship's life. Strahan was decommissioned into reserve in Sydney on 25 January 1946, having sailed almost 60,000 nmi in her two-year career.

The corvette received two battle honours for her wartime service: "Pacific 1944–45" and "New Guinea 1944".

Fate
Strahan was sold to the Kinoshita Australia company for scrap on 6 January 1961. She was broken up at Green Point in Sydney during March 1963.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: HMAS Strahan


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Pinus arizonica

Pinus arizonica, commonly known as the Arizona pine, is a medium-sized pine in northern Mexico, southeast Arizona, southwest New Mexico, and western Texas in the United States. It is a tree growing to 25–35 m tall, with a trunk diameter of up to 1.2 m. The needles are in bundles of 3, 4, or 5, with 5-needle fascicles being the most prevalent. This variability may be a sign of hybridization with the closely related ponderosa pine (Pinus ponderosa). The cones are single, paired, or in whorls of three, and 5–11 cm long.

Taxonomy
The Arizona pine was commonly thought to be a variant of Ponderosa pine, but since at least 1997 it is now recognized as a distinct species by most authorities.

Three varieties are described;
 * Pinus arizonica var. arizonica, primarily in the Sierra Madre Occidental from Arizona and New Mexico south through Chihuahua to Durango and Zacatecas, west to Sonora and Sinaloa, and east through Coahuila to Nuevo León.
 * Pinus arizonica var. stormiae, in the Sierra Madre Oriental from Coahuila and Nuevo León south to southwest Tamaulipas (in Miquihuana) and parts of San Luis Potosí. Possibly in the Big Bend National Park in Texas.
 * Pinus arizonica var. cooperi, in the Sierra Madre Occidental in Chihuahua and Durango. This variety was originally described as a distinct species, but was subsumed under Pinus arizonica by Farjon in 1997. Among some primarily Mexican botanists this change has not proved popular. It has also been reclassified as a subspecies by Silba in 2009 on the basis of it being more distinct than var. stormiae, although this taxonomy is followed by even fewer authors. Some authors regard this as more closely related to Hartweg's pine (Pinus hartwegii).

Uses
This pine is a source of construction timber, and is heavily harvested for firewood. Extensive cutting has reduced the formerly widespread Arizona pine forests, particularly in Mexico.

title: Pinus arizonica


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Westminster University (Utah)

Westminster University is a private university in Salt Lake City, Utah, United States. It was founded in 1875 and comprises four schools.

History
Westminster University was founded in 1875 as the Salt Lake Collegiate Institute, a preparatory school. Westminster first offered college classes in 1897 as Sheldon Jackson College. Named in honor of its primary benefactor and a Presbyterian minister, Sheldon Jackson, the college operated for many years on the Collegiate Institute campus in downtown Salt Lake City under the supervision of the First Presbyterian Church of Salt Lake City.

The college changed its name to Westminster College in 1902 to better reflect a more general Protestant education. The name is derived from the Westminster Confession of Faith, a Presbyterian confession of faith, which was named for the district of London where it was devised. The University of Westminster, London is a separate higher education institution in the United Kingdom and is not affiliated with Westminster College.

High school level classes ceased to be offered in 1945, and Westminster became the first accredited two-year junior college in the intermountain area. In 1935, Westminster modified its curriculum to qualify as a four-year junior college and in 1949 became a four-year liberal arts university offering baccalaureate degrees in the arts and sciences.

On September 19, 2022, President Bethami Dobkin announced that starting Fall semester 2023, Westminster College would be known as Westminster University to reflect the comprehensive institutional offerings of the school.

Students from all religions are welcome, as Westminster severed its official ties to the Presbyterian church in 1974. In 2019 the college replaced its traditional crest emblem, a shield emblazoned with the term Pro Christo et Libertate ("For Christ and Liberty"), for a new seal bearing the motto Discendo Vita Abundantior ("Life Made More Abundant by Learning").

Campus
Originally located in downtown Salt Lake City, the college moved to its present campus on 27 acre in the Sugar House neighborhood of the city in 1911 where it is still located today. Emigration Creek runs through the campus. This land was donated by Civil War Veteran Colonel William M. Ferry Jr.

On campus are two gyms each equipped with a basketball court, weight room, and studio.

The larger of the buildings, the Eccles Health Wellness and Athletics Center (HWAC), also has an indoor pool, three story rock climbing wall, and racket ball court.

As Westminster University is located on 27 acres in the heart of Salt Lake City, administration has had to be careful and smart about the growing student population. The sixteenth president of Westminster College, Michael S. Bassis, saw a need for growing into and connecting with the Sugar House community. During his presidency he acquired Garfield School to the east, with plans on converting it into a center for the arts. However, it was sold to the Elizabeth Academy, a private Montessori school in February 2017.

Bassis also struck a deal to have Westminster on the Draw built on 1300 East, directly across the street from Sugar House Park. This seven-floor space has many uses. The bottom level is used as academic and event space, the second floor (street level) is used as business space, and the remaining floors are used as housing for upper-classmen and graduate students.

Administration
Westminster University has had nineteen presidents since its founding; the current president, Bethami Dobkin, was appointed in July 2018. It has an endowment of $79 million as of June 30, 2020. The Board of Trustees added Amy C. Wadsworth, the founding CAO of Salt Lake Arts Academy, after her retirement in June 2019, known for her historical novel reviewed by American western historian Will Bagley.

Academics
Westminster University comprises four schools: the School of Arts and Sciences, the Bill and Vieve Gore School of Business, the School of Education, and the School of Nursing and Health Sciences. It operates on a fall and spring semester system with a mini term in May and eight- and twelve-week summer terms.

Westminster offers 38 undergraduate majors conferring BS, BBA, BA, and BFA degrees, which do not include its customized majors and pre-med, pre-law, and pre-dental programs. In addition to a number of post-baccalaureate certificate programs in various fields, Westminster also offers 13 graduate degrees: Master of Business Administration (MBA), Project-Based Master of Business Administration (MBA), Master of Business Administration in Technology Commercialization (MBATC), Master of Accountancy (MAcc), Master of Arts in Community Leadership (MACL), Master of Arts in Teaching (MAT), Master of Education (MEd), Doctor of Nursing Practice (DNP), Doctor of Nursing Practice - Nurse Anesthesia (DNAP), Master of Public Health (MPH), Master of Science in Mental Health Counseling (MSMHC), Master of Science in Nursing: Family Nurse Practitioner (MSN), and Master of Strategic Communication (MSC).

Westminster University recently launched a new program within the Gore School of Business focusing on training students to be entrepreneurs. The Center for New Enterprise will offer graduate and undergraduate degrees as well as community education programs in entrepreneurship.

The university is accredited by the Northwest Commission on Colleges and Universities. Programs throughout the university are accredited as well.

Recognition
U.S. News & World Report ranked Westminster in its 2022 "Best College" guide in the following lists: "Best Regional Universities" (No. 18); "Best Value Schools" (No. 19); "Best College for Veterans" (No. 9); and "Best Undergraduate Teaching" (No. 15).

Student life
The university has over 70 campus clubs and organizations. The Associated Students of Westminster is the student association on campus. The school newspaper is a bi-weekly called "The Forum". There is also a nationally recognized literary journal known as Ellipsis. The Estonian, Westminster's student yearbook, was last published in 1987. The university publishes an alumni magazine, The Westminster Review, on a bi-annual schedule.

Athletics
The Westminster athletic teams are called the Griffins. The university is a member of the NCAA Division II ranks, primarily competing in the Rocky Mountain Athletic Conference (RMAC) for most of its sports since the 2015–16 academic year (which they were a member on a previous stint from 1967–68 to 1978–79 before suspending its athletics program); while its men's and women's alpine skiing teams compete in the Rocky Mountain Intercollegiate Ski Association (RMISA) affiliated with the NCAA. The Griffins previously competed in the Frontier Conference of the National Association of Intercollegiate Athletics (NAIA) from 1998–99 to 2014–15.

Westminster competes in 15 intercollegiate varsity sports: Men's sports include alpine ski, basketball, cross country, golf, lacrosse, soccer and track & field; while women's sports include alpine ski, basketball, cross country, golf, lacrosse, soccer, track & field and volleyball. Current non-NCAA sports include cheerleading, cycling, dance, men's soccer (club) and snowboard.

Olympians
More than 50 Olympians have pursued their educational aspirations at Westminster, earning degrees along with 10 medals. The Griffins have competed in at least four Winter Olympic Games. Most of them as part of a 2005–2018 partnership between the college and U.S. Ski and Snowboard. Twenty-three Westminster students made up 10% of Team USA in Sochi and 18 students competed in the 2018 Pyeongchang games. In the 2022 Winter Olympics, 8 Olympians from Westminster will represent four different countries in Beijing: the U.S., Philippines, Ireland and Slovenia. One alum will compete in qualifying races for the 2022 USA Paralympic alpine skiing team.

History
The intercollegiate athletic teams were formerly called the Parsons, and Westminster was a member of the RMAC (in the NAIA), joining the conference in the summer of 1967 for football, basketball, and other team sports. A financial crisis at the school in 1979 caused it to discontinue intercollegiate athletics. Beginning in the 1990s, Westminster gradually began to restore its intercollegiate athletic program in the NAIA as the Griffins; it joined NCAA Division II in 2015 and returned to the RMAC, gaining full member status in 2018.

Notable alumni

 * Maude Adams – first American actress to play Peter Pan on Broadway; theatrical lighting and color photography researcher; LGBTQ luminary
 * Mildred J. Berryman – pioneering researcher of the lesbian and gay community in post-WWI Utah
 * Maddie Bowman – 2014 Olympic gold medalist in ski halfpipe; Team USA, Freestyle Skiing; Two-time Olympian for the US (2014, 2018)
 * Les Brown – Tight end for the Miami Dolphins
 * Janet H. Clark -Minnesota state legislator
 * Joss Christensen – 2014 Olympic gold medalist in slopestyle; Team USA, Freestyle Skiing; One-time Olympian for the US (2014)
 * Alex Deibold (2019) – 2014 Olympic bronze medalist in snowboardcross; Team USA, Snowboarding; One-time Olympian for the US (2014)
 * Jim Eliopulos – Linebacker for the New York Jets
 * Kaitlyn Farrington (2012) – 2014 Olympic gold medalist in halfpipe; Team USA, Snowboarding; One-time Olympian for the US (2014)
 * Otto Harbach – Broadway lyricist/librettist
 * David Litvack (1994) – Utah State House Representative for the 26th district and Alumni Board member
 * Devin Logan (2023) – 2014 Olympic silver medalist in slopestyle; Team USA, Freestyle Skiing; Three-time Olympian for the US (2014, 2018, 2022)
 * Jonathan Midol – 2014 Olympic bronze medalist in ski-cross; Team France, Freestyle Skiing; One-time Olympian for France (2014)
 * Colby Stevenson – 2022 Olympic silver medalist in big air; Team USA, Freestyle Skiing; One-time Olympian for the US (2022)
 * Michael Stockton (2011) – Professional basketball player for Budivelnyk of the Ukrainian Basketball Super League
 * Geoff Stradling – Hollywood composer and orchestrator for TV series and movies. Stradling frequently works on movie scores with Ladd McIntosh, a former Westminster professor who led the Westminster Jazz Band to numerous awards in the early 1970s
 * Spencer West – Motivational speaker and disability advocate
 * Vic Wild – 2014 Olympic gold medalist in parallel giant slalom; Team Russia, Snowboarding; One-time Olympian for Russia (2014)
 * Richard D. Wood (1977) – Molecular biologist and winner of the 1998 Meyenburg Prize

title: Westminster University (Utah)