title
stringlengths 1
251
| section
stringlengths 0
6.12k
| text
stringlengths 0
716k
|
|---|---|---|
American Airlines Flight 77
|
Rescue and recovery
|
Rescue and recovery
Rescue efforts began immediately after the crash. Almost all the successful rescues of survivors occurred within half an hour of the impact.Goldberg et al., p. 51. Initially, rescue efforts were led by the military and civilian employees within the building. Within minutes, the first fire companies arrived and found these volunteers searching near the impact site. The firefighters ordered them to leave as they were not properly equipped or trained to deal with the hazards.
The Arlington County Fire Department (ACFD) assumed command of the immediate rescue operation within ten minutes of the crash. ACFD Assistant Chief James Schwartz implemented an incident command system (ICS) to coordinate response efforts among multiple agencies.Goldberg et al., p. 72. It took about an hour for the ICS structure to become fully operational.Goldberg et al., p. 77. Firefighters from Fort Myer and Reagan National Airport arrived within minutes.Goldberg et al., p. 78. Rescue and firefighting efforts were impeded by rumors of additional incoming planes. Chief Schwartz ordered two evacuations during the day in response to these rumors.Goldberg et al., pp. 80–82.
thumb|left|alt=An injured victim being loaded into an ambulance at the Pentagon|An injured victim being loaded into an ambulance at the Pentagon
As firefighters attempted to extinguish the fires, they watched the building in fear of a structural collapse. One firefighter remarked that they "pretty much knew the building was going to collapse because it started making weird sounds and creaking." Officials saw a cornice of the building move and ordered an evacuation. Minutes later, at 10:10, the upper floors of the damaged area of the Pentagon collapsed. The collapsed area was about at its widest point and at its deepest. The amount of time between impact and collapse allowed everyone on the fourth and fifth levels to evacuate safely before the structure collapsed.Goldberg et al., p. 20.Goldberg et al., pp. 86–90. After 11:00, firefighters mounted a two-pronged attack against the fires. Officials estimated temperatures of up to . While progress was made against the interior fires by late afternoon, firefighters realized a flammable layer of wood under the Pentagon's slate roof had caught fire and begun to spread.Goldberg et al., pp. 91–95. Typical firefighting tactics were rendered useless by the reinforced structure as firefighters were unable to reach the fire to extinguish it. Firefighters instead made firebreaks in the roof on September 12 to prevent further spreading. At 18:00 on the 12th, Arlington County issued a press release stating the fire was "controlled" but not fully "extinguished". Firefighters continued to put out smaller fires that ignited in the succeeding days.
Various pieces of aircraft debris were found within the wreckage at the Pentagon. While on fire and escaping from the Navy Command Center, Lt. Kevin Shaeffer observed a chunk of the aircraft's nose cone and the nose landing gear in the service road between rings B and C. Early in the morning on Friday, September 14, Fairfax County Urban Search and Rescue Team members Carlton Burkhammer and Brian Moravitz came across an "intact seat from the plane's cockpit", while paramedics and firefighters located the two black boxes near the punch out hole in the A–E drive, nearly into the building. The cockpit voice recorder was too badly damaged and charred to retrieve any information, though the flight data recorder yielded useful information. Investigators also found a part of Nawaf al-Hazmi's driver's license in the North Parking Lot rubble pile. Personal effects belonging to victims were found and taken to Fort Myer.
|
American Airlines Flight 77
|
Remains
|
Remains
right|thumb|alt=Refer to caption|Diagram of body fragments found in the Pentagon. Most body fragments were found near the impact zone.
Army engineers determined by 17:30 on the first day that no survivors remained in the damaged section of the building.Goldberg et al., p. 97. In the days after the crash, news reports emerged that up to 800 people had died. Army soldiers from Fort Belvoir were the first teams to survey the interior of the crash site and noted the presence of human remains.Goldberg et al., p. 119. Federal Emergency Management Agency (FEMA) Urban Search and Rescue teams, including Fairfax County Urban Search and Rescue assisted the search for remains, working through the National Interagency Incident Management System (NIIMS). Kevin Rimrodt, a Navy photographer surveying the Navy Command Center after the attacks, remarked that "there were so many bodies, I'd almost step on them. So I'd have to really take care to look backwards as I'm backing up in the dark, looking with a flashlight, making sure I'm not stepping on somebody."Goldberg et al., pp. 121–122. Debris from the Pentagon was taken to the Pentagon's north parking lot for more detailed search for remains and evidence.
Remains recovered from the Pentagon were photographed, and turned over to the Armed Forces Medical Examiner office, located at Dover Air Force Base in Delaware. The medical examiner's office was able to identify remains belonging to 179 of the victims. Investigators eventually identified 184 of the 189 people who died in the attack. The remains of the five hijackers were identified through a process of elimination, and were turned over as evidence to the Federal Bureau of Investigation (FBI). On September 21, the ACFD relinquished control of the crime scene to the FBI. The Washington Field Office, National Capital Response Squad (NCRS), and the Joint Terrorism Task Force (JTTF) led the crime scene investigation at the Pentagon.
By October 2, 2001, the search for evidence and remains was complete and the site was turned over to Pentagon officials. In 2002, the remains of 25 victims were buried collectively at Arlington National Cemetery, with a five-sided granite marker inscribed with the names of all the victims in the Pentagon. The ceremony also honored the five victims whose remains were never found.
|
American Airlines Flight 77
|
Flight recorders
|
Flight recorders
right|thumb|alt=The cockpit voice recorder from American Airlines Flight 77, as used in an exhibit at the Moussaoui trial|The cockpit voice recorder from American Airlines Flight77, as used in an exhibit at the Moussaoui trial
About 03:40 on September 14, a paramedic and a firefighter who were searching through the debris of the impact site found two dark boxes, about long. They called for an FBI agent, who in turn called for someone from the National Transportation Safety Board (NTSB). The NTSB employee confirmed that these were the flight recorders ("black boxes") from American Airlines Flight77. Dick Bridges, deputy manager for Arlington County, Virginia, said the cockpit voice recorder was damaged on the outside and the flight data recorder was charred. Bridges said the recorders were found "right where the plane came into the building".
The cockpit voice recorder was transported to the NTSB lab in Washington, D.C., to see what data was salvageable. In its report, the NTSB identified the unit as an L-3 Communications, Fairchild Aviation Recorders model A-100A cockpit voice recordera device which records on magnetic tape. There were several loose pieces of magnetic tape that were found lying inside of the tape enclosure. No usable segments of tape were found inside the recorder; according to the NTSB's report, "[t]he majority of the recording tape was fused into a solid block of charred plastic". On the other hand, all the data from the flight data recorder, which used a solid-state drive, was recovered.
|
American Airlines Flight 77
|
Continuity of operations
|
Continuity of operations
At the moment of impact, Secretary of Defense Donald Rumsfeld was in his office on the other side of the Pentagon, away from the crash site. He ran to the site and assisted the injured. Rumsfeld returned to his office, and went to a conference room in the Executive Support Center where he joined a secure videoteleconference with Vice President Dick Cheney and other officials. On the day of the attacks, DoD officials considered moving their command operations to Site R, a backup facility in Pennsylvania. Secretary of Defense Rumsfeld insisted he remain at the Pentagon, and sent Deputy Secretary Paul Wolfowitz to Site R. The National Military Command Center (NMCC) continued to operate at the Pentagon, even as smoke entered the facility. Engineers and building managers manipulated the ventilation and other building systems that still functioned to draw smoke out of the NMCC and bring in fresh air.Creed and Newman, p. 278
During a press conference held inside the Pentagon at 18:42, Rumsfeld announced, "The Pentagon's functioning. It will be in business tomorrow." Pentagon employees returned the next day to offices in mostly unaffected areas of the building. By the end of September, more workers returned to the lightly damaged areas of the Pentagon.
|
American Airlines Flight 77
|
Aftermath
|
Aftermath
thumb|left|alt=Refer to caption|Damaged section of the Pentagon
Early estimates on rebuilding the damaged section of the Pentagon were that it would take three years to complete. However, the project moved forward at an accelerated pace and was completed by the first anniversary of the attack. The rebuilt section of the Pentagon includes a small indoor memorial and chapel at the point of impact. An outdoor memorial, commissioned by the Pentagon and designed by Julie Beckman and Keith Kaseman, was completed on schedule for its dedication on September 11, 2008.
|
American Airlines Flight 77
|
Security camera videos
|
Security camera videos
thumb|thumbtime=29|alt=A second security video, which shows the plane crashing 25 seconds into the video|Second security camera video; impact is at 0:25
The Department of Defense released filmed footage on May 16, 2006, that was recorded by a security camera of American Airlines Flight77 crashing into the Pentagon, with a plane visible in one frame, as a "thin white blur" and an explosion following. The images were made public in response to a December 2004 Freedom of Information Act request by Judicial Watch. Some still images from the video had previously been released and publicly circulated, but this was the first official release of the edited video of the crash.
A nearby Citgo service station also had security cameras, but a video released on September 15, 2006, did not show the crash because the camera was pointed away from the crash site.
The Doubletree Hotel in the nearby neighborhood of Crystal City also had a security camera video. The FBI released the video on December 4, 2006, in response to a FOIA lawsuit filed by Scott Bingham. The footage is "grainy and the focus is soft, but a rapidly growing tower of smoke is visible in the distance on the upper edge of the frame as the plane crashes into the building."
|
American Airlines Flight 77
|
Memorials
|
Memorials
left|thumb|A flag is used to memorialize the spot of the crash.
alt=Refer to caption|thumb|Panel S-69 of the National September 11 Memorial's South Pool, one of six on which the names of Pentagon victims are inscribed
thumb|right|The Pentagon Memorial, shortly before it opened on September 11, 2008
On September 12, 2002, Defense Secretary Donald Rumsfeld and General Richard Myers, Chairman of the Joint Chiefs of Staff, dedicated the Victims of Terrorist Attack on the Pentagon Memorial at Arlington National Cemetery.Garamone, Jim. "Remains of Pentagon Attack Victims Buried at Arlington". American Forces Press Service. September 12, 2002. Accessed September 7, 2011. The memorial specifically honors the five individuals for whom no identifiable remains were found.Cass, Connie. "Cremated Remains of Pentagon Victims Are Laid to Rest at National Cemetery". Associated Press. September 13, 2002. This included Dana Falkenberg, age three, who was aboard American Airlines Flight77 with her parents and older sister. A portion of the remains of 25 other victims are also buried at the site."Arlington Funeral Honors Unidentified Victims". CNN.com. September 12, 2002. Accessed September 7, 2011. The memorial is a pentagonalPusey, Allen. "Final Service Honors Victims of Pentagon Attack". Dallas Morning News. September 13, 2002. granite marker high. On five sides of the memorial along the top are inscribed the words "Victims of Terrorist Attack on the Pentagon September 11, 2001". Aluminum plaques, painted black, are inscribed with the names of the 184 victims of the terrorist attack. The site is located in Section 64,Vogel, Steve. "Lost and, Sometimes, Never Found". Washington Post. September 13, 2002. on a slight rise, which gives it a view of the Pentagon.
At the National September 11 Memorial, the names of the Pentagon victims are inscribed on six panels at the South Pool.About: The Memorial Names Layout. Memorial Guide: National 9/11 Memorial. Retrieved December 11, 2011.
The Pentagon Memorial, located just southwest of The Pentagon in Arlington County, Virginia, is a permanent outdoor memorial to the 184 people who died as victims in the building and on American Airlines Flight77 during the September11 attacks. Designed by Julie Beckman and Keith Kaseman of the architectural firm of Kaseman Beckman Advanced Strategies with engineers Buro Happold, the memorial opened on September 11, 2008, seven years after the attack.
|
American Airlines Flight 77
|
Nationalities of victims on the aircraft
|
Nationalities of victims on the aircraft
The 53 passengers (excluding the hijackers) and six crew were from:
NationalityPassengersCrewTotalUnited States47653China202Australia101Ethiopia101South Korea101United Kingdom101Total53659
|
American Airlines Flight 77
|
See also
|
See also
Indian Airlines Flight 814
TWA Flight 847
Air France Flight 139
List of aircraft hijackings
|
American Airlines Flight 77
|
References
|
References
|
American Airlines Flight 77
|
Works cited
|
Works cited
|
American Airlines Flight 77
|
External links
|
External links
Picture of Aircraft Pre 9-11
Arlington County After-Action Report, July 23, 2002
(September 11, 2001)
(September 12, 2001)
Category:2001 fires in the United States
Category:2001 in Virginia
Category:2001 murders in the United States
Category:Accidents and incidents involving the Boeing 757
Category:Aircraft hijackings in the United States
Category:Airliner accidents and incidents caused by hijacking
Category:Airliner accidents and incidents in Virginia
Category:Airliner accidents and incidents involving deliberate crashes
Category:Airliners involved in the September 11 attacks
77
Category:Articles containing video clips
Category:Attacks on military installations in 2001
Category:Attacks in the United States in 2001
Category:Attacks on government buildings and structures in the United States
Category:Aviation accidents and incidents in the United States in 2001
Category:Dulles International Airport
Category:Filmed murder–suicides
Category:Islamic terrorism in the United States
Category:Mass murder in 2001
Category:Mass murder in Virginia
Category:Mass murder in the United States in the 2000s
Category:Murder–suicides in Virginia
Category:Murder–suicides in the United States
Category:September 2001 crimes in the United States
Category:Suicides in Virginia
Category:Terrorist incidents in the United States in 2001
Category:The Pentagon
Category:Filmed deaths during aviation accidents and incidents
|
American Airlines Flight 77
|
Table of Content
|
Short description, Background, Hijackers, Suspected accomplices, Flight, Boarding and departure, Hijacking, Calls, Crash, Rescue and recovery, Remains, Flight recorders, Continuity of operations, Aftermath, Security camera videos, Memorials, Nationalities of victims on the aircraft, See also, References, Works cited, External links
|
Ambush
|
short description
|
thumb|right|upright=1.3|French royalist rebels preparing an ambush during the War in the Vendée (The Ambush by Évariste Carpentier, 1889)
thumb|General Braddock's troops ambushed and decimated by the French and Indians in 1755
thumb|Depiction of a Zulu attack on a Boer camp in February 1838
thumb|Massacre of Elphinstone's army during the First Anglo-Afghan War in 1842
thumb|Ambush of Polish partisans against Russian forces during the January Uprising, 1863
An ambush is a surprise attack carried out by people lying in wait in a concealed position."Ambush" definition in the New Oxford American Dictionary The concealed position itself or the concealed person(s) may also be called an "". Ambushes as a basic fighting tactic of soldiers or of criminals have been used consistently throughout history, from ancient to modern warfare. The term "ambush" is also used in animal behavior studies, journalism, and marketing to describe methods of approach and strategy.
In the 20th century, a military ambush might involve thousands of soldiers on a large scale, such as at a choke point like a mountain pass. Conversely, it could involve a small irregular band or insurgent group attacking a regular armed-force patrol. Theoretically, a single well-armed, and concealed soldier could ambush other troops in a surprise attack.
In recent centuries, a military ambush can involve the exclusive or combined use of improvised explosive devices (IED). This allows attackers to hit enemy convoys or patrols while minimizing the risk of being exposed to return fire.
|
Ambush
|
History
|
History
The use of ambush tactics by early people dates as far back as two million years when anthropologists have recently suggested that ambush techniques were used to hunt large game.
One example from ancient times is the Battle of the Trebia River. Hannibal encamped within striking distance of the Romans with the Trebia River between them, and placed a strong force of cavalry and infantry in concealment, near the battle zone. He had noticed, says Polybius, a "place between the two camps, flat indeed and treeless, but well adapted for an ambuscade, as it was traversed by a water-course with steep banks, densely overgrown with brambles and other thorny plants, and here he proposed to lay a stratagem to surprise the enemy". When the Roman infantry became entangled in combat with his army, the hidden ambush force attacked the Roman infantry in the rear. The result was slaughter and defeat for the Romans. Nevertheless, the battle also displays the effects of good tactical discipline on the part of the ambushed force. Although most of the legions were lost, about 10,000 Romans cut their way through to safety, maintaining unit cohesion. This ability to maintain discipline and break out or maneuver away from a kill zone is a hallmark of good troops and training in any ambush situation.
Ambushes were widely used by the Lusitanians, in particular by their chieftain Viriathus. Their usual tactic, called concursare, involved repeatedly charging and retreating, forcing the enemy to eventually give them chase, to set up ambushes in difficult terrain where allied forces would be awaiting. In his first victory, he eluded the siege of Roman praetor Gaius Vetilius and attracted him to a narrow pass next to the Barbesuda river, where he destroyed his army and killed the praetor. Viriathus's ability to turn chases into ambushes would grant him victories over a number of Roman generals.
Another Lusitanian ambush was performed by Curius and Apuleius on Roman general Quintus Fabius Maximus Servilianus, who led a numerically superior army complete with war elephants and Numidian cavalry. The ambush allowed Curius and Apuleius to steal Servilianus's loot train. However, a tactic error in their retreat led to the Romans retaking the train and putting the Lusitanians to flight. Viriathus later defeated Servilianus with a surprise attack.
Germanic war chief Arminius sprung an ambush against the Romans at Battle of the Teutoburg Forest. This particular ambush was to affect the course of Western history. The Germanic forces demonstrated several principles needed for a successful ambush. They took cover in difficult forested terrain, allowing the warriors time and space to mass without detection. They had the element of surprise, and this was also aided by the defection of Arminius from Roman ranks prior to the battle. They sprang the attack when the Romans were most vulnerable; when they had left their fortified camp, and were on the march in a pounding rainstorm.
The Germans did not dawdle at the hour of decision but attacked quickly, using a massive series of short, rapid, vicious charges against the length of the whole Roman line, with charging units sometimes withdrawing to the forest to regroup while others took their place. The Germans also used blocking obstacles, erecting a trench and earthen wall to hinder Roman movement along the route of the killing zone. The result was a mass slaughter of the Romans and the destruction of three legions. The Germanic victory caused a limit on Roman expansion in the West. Ultimately, it established the Rhine as the boundary of the Roman Empire for the next four hundred years, until the decline of the Roman influence in the West. The Roman Empire made no further concerted attempts to conquer Germania beyond the Rhine.
There are many notable examples of ambushes during the Roman-Persian Wars. A year after their victory at Carrhae, the Parthians invaded Syria but were driven back after a Roman ambush near Antigonia. Roman Emperor Julian was mortally wounded in an ambush near Samarra in 363 during the retreat from his Persian campaign. A Byzantine invasion of Persian Armenia was repelled by a small force at Anglon who performed a meticulous ambush by using the rough terrain as a force multiplier and concealing in houses. Heraclius' discovery of a planned ambush by Shahrbaraz in 622 was a decisive factor in his campaign.
|
Ambush
|
Arabia during Muhammad's era
|
Arabia during Muhammad's era
According to Muslim tradition, Islamic Prophet Muhammad used ambush tactics in his military campaigns. His first such use was during the Caravan raids. In the Kharrar caravan raid, Sa'd ibn Abi Waqqas was ordered to lead a raid against the Quraysh. His group consisted of about twenty Muhajirs. This raid was about a month after the previous one. Sa'd, with his soldiers, set up an ambush in the valley of Kharrar on the road to Mecca and waited to raid a Meccan caravan returning from Syria. However, the caravan had already passed and the Muslims returned to Medina without any loot.Mubarakpuri, The Sealed Nectar (Free Version), p. 127.
Arab tribes during Muhammad's era also used ambush tactics. One example retold in Muslim tradition is said to have taken place during the First Raid on Banu Thalabah. The Banu Thalabah tribe were already aware of the impending attack; so they lay in wait for the Muslims. When Muhammad ibn Maslama arrived at the site, the Banu Thalabah with 100 men ambushed the Muslims while they were making preparation to sleep and, after a brief resistance, killed them all except for Muhammad ibn Maslama, who feigned death. A Muslim who happened to pass that way found him and assisted him to return to Medina. The raid was unsuccessful.
|
Ambush
|
Procedure
|
Procedure
In modern warfare, an ambush can be employed by ground troops up to platoon size against enemy targets, which may be other ground troops, or possibly vehicles. However, in some situations, especially when deep behind enemy lines, the actual attack will be carried out by a platoon. A company-sized unit will be deployed to support the attack group, setting up and maintaining a forward patrol harbour from which the attacking force will deploy, and to which they will retire after the attack.
|
Ambush
|
Planning
|
Planning
thumb|US Army idealised linear ambush plan
thumb|US Army idealised L-shaped ambush plan
Ambushes are complex multiphase operations and are therefore usually planned in some detail. First, a suitable killing zone is identified. This is where the ambush will be laid, where enemy units are expected to pass, and gives reasonable cover for the deployment, execution, and extraction phases of the ambush patrol. A path along a wooded valley floor would be a typical example.
Ambush can be described geometrically as:
Linear, when a number of firing units are equally distant from the linear kill zone. It can easily be controlled under all visibility conditions.
L-shaped, when a short leg of firing units are placed to enfilade (fire the length of) the sides of the linear kill zone.
V-shaped, when the firing units are distant from the kill zone where the enemy enters and the firing units lay down bands of intersecting and interlocking fire. This ambush is normally triggered only when the enemy is well into the kill zone. The intersecting bands of fire prevent any attempt of moving out of the kill zone.
|
Ambush
|
Viet Cong ambush techniques
|
Viet Cong ambush techniques
thumb|right|The VC/NVA prepared the battlefield carefully. Siting automatic weapons at treetop level for example helped shoot down several US helicopters during the Battle of Dak To, 1967Terrence Maitland, A CONTAGION OF WAR: THE VIETNAM EXPERIENCE SERIES, (Boston Publishing Company), 1983, p. 180
|
Ambush
|
Ambush criteria
|
Ambush criteria
The terrain for the ambush had to meet strict criteria:
provide concealment to prevent detection from the ground or air
enable ambush force to deploy, encircle and divide the enemy
allow for heavy weapons emplacements to provide sustained fire
enable the ambush force to set up observation posts for early detection of the enemy
permit the secret movement of troops to the ambush position and the dispersal of troops during withdrawal
One important feature of the ambush was that the target units should 'pile up' after being attacked, thus preventing them any easy means of withdrawal from the kill zone and hindering their use of heavy weapons and supporting fire. Terrain was usually selected which would facilitate this and slow down the enemy. Any terrain around the ambush site which was not favourable to the ambushing force, or which offered some protection to the target, was heavily mined and booby trapped or pre-registered for mortars.
|
Ambush
|
Ambush units
|
Ambush units
The NVA/VC ambush formations consisted of:
lead-blocking element
main-assault element
rear-blocking element
observation posts
command post
Other elements might also be included if the situation demanded, such as a sniper screen along a nearby avenue of approach to delay enemy reinforcements.
|
Ambush
|
Command posts
|
Command posts
When deploying into an ambush site, the NVA first occupied several observation posts, placed to detect the enemy as early as possible and to report on the formation it was using, its strength and firepower, as well as to provide early warning to the unit commander. Usually, one main OP and numerous secondary OPs were established. Runners and radios were used to communicate between the OPs and the main command post. The OPs were located so that enemy movement into the ambush could be observed. They would remain in position throughout the ambush to report routes of reinforcement and withdrawal by the enemy, as well as his manoeuvre options. Frequently the OPs were reinforced to squad size and served as flank security. The command post was situated in a central location, frequently on terrain which afforded it a vantage point overlooking the ambush site.
|
Ambush
|
Recon methods
|
Recon methods
Reconnaissance elements observing a potential ambush target on the move generally stayed 300–500 meters away. A "leapfrogging" recon technique can be used. Surveillance units were echeloned one behind the other. As the enemy drew close to the first, it fell back behind the last recon team, leaving an advance group in its place. This one in turn fell back as the enemy again closed the gap, and the cycle rotated. This method helped keep the enemy under continuous observation from a variety of vantage points, and allowed the recon groups to cover one another.RAND Corp, "Insurgent Organization and Operations: A Case Study of the Viet Cong in the Delta, 1964–1966", (Santa Monica: August 1967)
|
Ambush
|
See also
|
See also
Ambush predator
Viet Cong and PAVN battle tactics
Flanking maneuver
Flypaper theory (strategy)
List of military tactics
Sniper
|
Ambush
|
References
|
References
Extract from Lt Col Anthony B. Herbert's Soldier's Handbook
Category:Assault tactics
Category:Military tactics
Category:Guerrilla warfare tactics
Category:Military operations by type
|
Ambush
|
Table of Content
|
short description, History, Arabia during Muhammad's era, Procedure, Planning, Viet Cong ambush techniques, Ambush criteria, Ambush units, Command posts, Recon methods, See also, References
|
Abzyme
|
Short description
|
An abzyme (from antibody and enzyme), also called catmab (from catalytic monoclonal antibody), and most often called catalytic antibody or sometimes catab, is a monoclonal antibody with catalytic activity. Abzymes are usually raised in lab animals immunized against synthetic haptens, but some natural abzymes can be found in normal humans (anti-vasoactive intestinal peptide autoantibodies) and in patients with autoimmune diseases such as systemic lupus erythematosus, where they can bind to and hydrolyze DNA. To date abzymes display only weak, modest catalytic activity and have not proved to be of any practical use.Barrera, G. J., Portillo, R., Mijares, A., Rocafull, M. A., del Castillo, J. R., & Thomas, L. E. (2009). Immunoglobulin A with protease activity secreted in human milk activates PAR-2 receptors, of intestinal epithelial cells HT-29, and promotes beta-defensin-2 expression. Immunology letters, 123(1), 52-59. They are, however, subjects of considerable academic interest. Studying them has yielded important insights into reaction mechanisms, enzyme structure and function, catalysis, and the immune system itself.
Enzymes function by lowering the activation energy of the transition state of a chemical reaction, thereby enabling the formation of an otherwise less-favorable molecular intermediate between the reactant(s) and the product(s). If an antibody is developed to bind to a molecule that is structurally and electronically similar to the transition state of a given chemical reaction, the developed antibody will bind to, and stabilize, the transition state, just like a natural enzyme, lowering the activation energy of the reaction, and thus catalyzing the reaction. By raising an antibody to bind to a stable transition-state analog, a new and unique type of enzyme is produced.
So far, all catalytic antibodies produced have displayed only modest, weak catalytic activity. The reasons for low catalytic activity for these molecules have been widely discussed. Possibilities indicate that factors beyond the binding site may play an important role, in particular through protein dynamics. Some abzymes have been engineered to use metal ions and other cofactors to improve their catalytic activity.
|
Abzyme
|
History
|
History
The possibility of catalyzing a reaction by means of an antibody which binds the transition state was first suggested by William P. Jencks in 1969. In 1994 Peter G. Schultz and Richard A. Lerner received the prestigious Wolf Prize in Chemistry for developing catalytic antibodies for many reactions and popularizing their study into a significant sub-field of enzymology.
|
Abzyme
|
Abzymes in healthy human breast milk
|
Abzymes in healthy human breast milk
There are a broad range of abzymes in healthy human breast milk with DNAse, RNAse, and protease activity.
|
Abzyme
|
Potential HIV treatment
|
Potential HIV treatment
In a June 2008 issue of the journal Autoimmunity Review, researchers S. Planque, Sudhir Paul, Ph.D., and Yasuhiro Nishiyama, Ph.D. of the University Of Texas Medical School at Houston announced that they have engineered an abzyme that degrades the superantigenic region of the gp120 CD4 binding site. This is the one part of the HIV virus outer coating that does not change, because it is the attachment point to T lymphocytes, the key cell in cell-mediated immunity. Once infected by HIV, patients produce antibodies to the more changeable parts of the viral coat. The antibodies are ineffective because of the virus' ability to change their coats rapidly. Because this protein gp120 is necessary for HIV to attach, it does not change across different strains and is a point of vulnerability across the entire range of the HIV variant population.
The abzyme does more than bind to the site: it catalytically destroys the site, rendering the virus inert, and then can attack other HIV viruses. A single abzyme molecule can destroy thousands of HIV viruses.
|
Abzyme
|
References
|
References
Category:Monoclonal antibodies
Category:Immune system
Category:Enzymes
|
Abzyme
|
Table of Content
|
Short description, History, Abzymes in healthy human breast milk, Potential HIV treatment, References
|
Adaptive radiation
|
Short description
|
thumb|Four of the 14 finch species found in the Galápagos Archipelago, which are thought to have evolved via an adaptive radiation that diversified their beak shapes, enabling them to exploit different food sources.|250x250px
In evolutionary biology, adaptive radiation is a process in which organisms diversify rapidly from an ancestral species into a multitude of new forms, particularly when a change in the environment makes new resources available, alters biotic interactions or opens new environmental niches. Starting with a single ancestor, this process results in the speciation and phenotypic adaptation of an array of species exhibiting different morphological and physiological traits. The prototypical example of adaptive radiation is finch speciation on the Galapagos ("Darwin's finches"), but examples are known from around the world.
|
Adaptive radiation
|
Characteristics
|
Characteristics
Four features can be used to identify an adaptive radiation:
A common ancestry of component species: specifically a recent ancestry. Note that this is not the same as a monophyly in which all descendants of a common ancestor are included.
A phenotype-environment correlation: a significant association between environments and the morphological and physiological traits used to exploit those environments.
Trait utility: the performance or fitness advantages of trait values in their corresponding environments.
Rapid speciation: presence of one or more bursts in the emergence of new species around the time that ecological and phenotypic divergence is underway.
|
Adaptive radiation
|
Conditions
|
Conditions
Adaptive radiations are thought to be triggered by an ecological opportunity or a new adaptive zone. Sources of ecological opportunity can be the loss of antagonists (competitors or predators), the evolution of a key innovation, or dispersal to a new environment. Any one of these ecological opportunities has the potential to result in an increase in population size and relaxed stabilizing (constraining) selection. As genetic diversity is positively correlated with population size the expanded population will have more genetic diversity compared to the ancestral population. With reduced stabilizing selection phenotypic diversity can also increase. In addition, intraspecific competition will increase, promoting divergent selection to use a wider range of resources. This ecological release provides the potential for ecological speciation and thus adaptive radiation.
Occupying a new environment might take place under the following conditions:
A new habitat has opened up: a volcano, for example, can create new ground in the middle of the ocean. This is the case in places like Hawaii and the Galapagos. For aquatic species, the formation of a large new lake habitat could serve the same purpose; the tectonic movement that formed the East African Rift, ultimately leading to the creation of the Rift Valley Lakes, is an example of this. An extinction event could effectively achieve this same result, opening up niches that were previously occupied by species that no longer exist.
This new habitat is relatively isolated. When a volcano erupts on the mainland and destroys an adjacent forest, it is likely that the terrestrial plant and animal species that used to live in the destroyed region will recolonize without evolving greatly. However, if a newly formed habitat is isolated, the species that colonize it will likely be somewhat random and uncommon arrivals.
The new habitat has a wide availability of niche space. The rare colonist can only adaptively radiate into as many forms as there are niches.
|
Adaptive radiation
|
Relationship between mass-extinctions and mass adaptive radiations
|
Relationship between mass-extinctions and mass adaptive radiations
A 2020 study found there to be no direct causal relationship between the proportionally most comparable mass radiations and extinctions in terms of "co-occurrence of species", substantially challenging the hypothesis of "creative mass extinctions".
|
Adaptive radiation
|
Examples
|
Examples
|
Adaptive radiation
|
Darwin's finches
|
Darwin's finches
Darwin's finches on the Galapagos Islands are a model system for the study of adaptive radiation. Today represented by approximately 15 species, Darwin's finches are Galapagos endemics famously adapted for a specialized feeding behavior (although one species, the Cocos finch (Pinaroloxias inornata), is not found in the Galapagos but on the island of Cocos south of Costa Rica). Darwin's finches are not actually finches in the true sense, but are members of the tanager family Thraupidae, and are derived from a single ancestor that arrived in the Galapagos from mainland South America perhaps just 3 million years ago. Excluding the Cocos finch, each species of Darwin's finch is generally widely distributed in the Galapagos and fills the same niche on each island. For the ground finches, this niche is a diet of seeds, and they have thick bills to facilitate the consumption of these hard materials. The ground finches are further specialized to eat seeds of a particular size: the large ground finch (Geospiza magnirostris) is the largest species of Darwin's finch and has the thickest beak for breaking open the toughest seeds, the small ground finch (Geospiza fuliginosa) has a smaller beak for eating smaller seeds, and the medium ground finch (Geospiza fortis) has a beak of intermediate size for optimal consumption of intermediately sized seeds (relative to G. magnirostris and G. fuliginosa). There is some overlap: for example, the most robust medium ground finches could have beaks larger than those of the smallest large ground finches. Because of this overlap, it can be difficult to tell the species apart by eye, though their songs differ. These three species often occur sympatrically, and during the rainy season in the Galapagos when food is plentiful, they specialize little and eat the same, easily accessible foods. It was not well-understood why their beaks were so adapted until Peter and Rosemary Grant studied their feeding behavior in the long dry season, and discovered that when food is scarce, the ground finches use their specialized beaks to eat the seeds that they are best suited to eat and thus avoid starvation.
The other finches in the Galapagos are similarly uniquely adapted for their particular niche. The cactus finches (Geospiza sp.) have somewhat longer beaks than the ground finches that serve the dual purpose of allowing them to feed on Opuntia cactus nectar and pollen while these plants are flowering, but on seeds during the rest of the year. The warbler-finches (Certhidea sp.) have short, pointed beaks for eating insects. The woodpecker finch (Camarhynchus pallidus) has a slender beak which it uses to pick at wood in search of insects; it also uses small sticks to reach insect prey inside the wood, making it one of the few animals that use tools.
The mechanism by which the finches initially diversified is still an area of active research. One proposition is that the finches were able to have a non-adaptive, allopatric speciation event on separate islands in the archipelago, such that when they reconverged on some islands, they were able to maintain reproductive isolation. Once they occurred in sympatry, niche specialization was favored so that the different species competed less directly for resources. This second, sympatric event was adaptive radiation.
|
Adaptive radiation
|
Cichlids of the African Great Lakes
|
Cichlids of the African Great Lakes
The haplochromine cichlid fishes in the Great Lakes of the East African Rift (particularly in Lake Tanganyika, Lake Malawi, and Lake Victoria) form the most speciose modern example of adaptive radiation. These lakes are believed to be home to about 2,000 different species of cichlid, spanning a wide range of ecological roles and morphological characteristics. Cichlids in these lakes fill nearly all of the roles typically filled by many fish families, including those of predators, scavengers, and herbivores, with varying dentitions and head shapes to match their dietary habits. In each case, the radiation events are only a few million years old, making the high level of speciation particularly remarkable. Several factors could be responsible for this diversity: the availability of a multitude of niches probably favored specialization, as few other fish taxa are present in the lakes (meaning that sympatric speciation was the most probable mechanism for initial specialization). Also, continual changes in the water level of the lakes during the Pleistocene (which often turned the largest lakes into several smaller ones) could have created the conditions for secondary allopatric speciation.
|
Adaptive radiation
|
Tanganyika cichlids
|
Tanganyika cichlids
Lake Tanganyika is the site from which nearly all the cichlid lineages of East Africa (including both riverine and lake species) originated. Thus, the species in the lake constitute a single adaptive radiation event but do not form a single monophyletic clade. Lake Tanganyika is also the least speciose of the three largest African Great Lakes, with only around 200 species of cichlid; however, these cichlids are more morphologically divergent and ecologically distinct than their counterparts in lakes Malawi and Victoria, an artifact of Lake Tanganyika's older cichlid fauna. Lake Tanganyika itself is believed to have formed 9–12 million years ago, putting a recent cap on the age of the lake's cichlid fauna. Many of Tanganyika's cichlids live very specialized lifestyles. The giant or emperor cichlid (Boulengerochromis microlepis) is a piscivore often ranked the largest of all cichlids (though it competes for this title with South America's Cichla temensis, the speckled peacock bass). It is thought that giant cichlids spawn only a single time, breeding in their third year and defending their young until they reach a large size, before dying of starvation some time thereafter. The three species of Altolamprologus are also piscivores, but with laterally compressed bodies and thick scales enabling them to chase prey into thin cracks in rocks without damaging their skin. Plecodus straeleni has evolved large, strangely curved teeth that are designed to scrape scales off of the sides of other fish, scales being its main source of food. Gnathochromis permaxillaris possesses a large mouth with a protruding upper lip, and feeds by opening this mouth downward onto the sandy lake bottom, sucking in small invertebrates. A number of Tanganyika's cichlids are shell-brooders, meaning that mating pairs lay and fertilize their eggs inside of empty shells on the lake bottom. Lamprologus callipterus is a unique egg-brooding species, with 15 cm-long males amassing collections of shells and guarding them in the hopes of attracting females (about 6 cm in length) to lay eggs in these shells. These dominant males must defend their territories from three types of rival: (1) other dominant males looking to steal shells; (2) younger, "sneaker" males looking to fertilize eggs in a dominant male's territory; and (3) tiny, 2–4 cm "parasitic dwarf" males that also attempt to rush in and fertilize eggs in the dominant male's territory. These parasitic dwarf males never grow to the size of dominant males, and the male offspring of dominant and parasitic dwarf males grow with 100% fidelity into the form of their fathers. A number of other highly specialized Tanganyika cichlids exist aside from these examples, including those adapted for life in open lake water up to 200m deep.
|
Adaptive radiation
|
Malawi cichlids
|
Malawi cichlids
The cichlids of Lake Malawi constitute a "species flock" of up to 1000 endemic species. Only seven cichlid species in Lake Malawi are not a part of the species flock: the Eastern happy (Astatotilapia calliptera), the sungwa (Serranochromis robustus), and five tilapia species (genera Oreochromis and Coptodon). All of the other cichlid species in the lake are descendants of a single original colonist species, which itself was descended from Tanganyikan ancestors. The common ancestor of Malawi's species flock is believed to have reached the lake 3.4 million years ago at the earliest, making Malawi cichlids' diversification into their present numbers particularly rapid. Malawi's cichlids span a similarly range of feeding behaviors to those of Tanganyika, but also show signs of a much more recent origin. For example, all members of the Malawi species flock are mouth-brooders, meaning the female keeps her eggs in her mouth until they hatch; in almost all species, the eggs are also fertilized in the female's mouth, and in a few species, the females continue to guard their fry in their mouth after they hatch. Males of most species display predominantly blue coloration when mating. However, a number of particularly divergent species are known from Malawi, including the piscivorous Nimbochromis livingtonii, which lies on its side in the substrate until small cichlids, perhaps drawn to its broken white patterning, come to inspect the predator - at which point they are swiftly eaten.
|
Adaptive radiation
|
Victoria's cichlids
|
Victoria's cichlids
Lake Victoria's cichlids are also a species flock, once composed of some 500 or more species. The deliberate introduction of the Nile Perch (Lates niloticus) in the 1950s proved disastrous for Victoria cichlids, and the collective biomass of the Victoria cichlid species flock has decreased substantially and an unknown number of species have become extinct. However, the original range of morphological and behavioral diversity seen in the lake's cichlid fauna is still mostly present today, if endangered. These again include cichlids specialized for niches across the trophic spectrum, as in Tanganyika and Malawi, but again, there are standouts. Victoria is famously home to many piscivorous cichlid species, some of which feed by sucking the contents out of mouthbrooding females' mouths. Victoria's cichlids constitute a far younger radiation than even that of Lake Malawi, with estimates of the age of the flock ranging from 200,000 years to as little as 14,000.
|
Adaptive radiation
|
Adaptive radiation in Hawaii
|
Adaptive radiation in Hawaii
thumb|An ʻiʻiwi (Drepanis coccinea). Note the long, curved beak for sipping nectar from tubular flowers.Hawaii has served as the site of a number of adaptive radiation events, owing to its isolation, recent origin, and large land area. The three most famous examples of these radiations are presented below, though insects like the Hawaiian drosophilid flies and Hyposmocoma moths have also undergone adaptive radiation.
|
Adaptive radiation
|
Hawaiian honeycreepers
|
Hawaiian honeycreepers
The Hawaiian honeycreepers form a large, highly morphologically diverse species group of birds that began radiating in the early days of the Hawaiian archipelago. While today only 17 species are known to persist in Hawaii (3 more may or may not be extinct), there were more than 50 species prior to Polynesian colonization of the archipelago (between 18 and 21 species have gone extinct since the discovery of the islands by westerners). The Hawaiian honeycreepers are known for their beaks, which are specialized to satisfy a wide range of dietary needs: for example, the beak of the ʻakiapōlāʻau (Hemignathus wilsoni) is characterized by a short, sharp lower mandible for scraping bark off of trees, and the much longer, curved upper mandible is used to probe the wood underneath for insects. Meanwhile, the ʻiʻiwi (Drepanis coccinea) has a very long curved beak for reaching nectar deep in Lobelia flowers. An entire clade of Hawaiian honeycreepers, the tribe Psittirostrini, is composed of thick-billed, mostly seed-eating birds, like the Laysan finch (Telespiza cantans). In at least some cases, similar morphologies and behaviors appear to have evolved convergently among the Hawaiian honeycreepers; for example, the short, pointed beaks of Loxops and Oreomystis evolved separately despite once forming the justification for lumping the two genera together. The Hawaiian honeycreepers are believed to have descended from a single common ancestor some 15 to 20 million years ago, though estimates range as low as 3.5 million years.
|
Adaptive radiation
|
Hawaiian silverswords
|
Hawaiian silverswords
thumb|A mixture of blooming and non-blooming Haleakalā silverswords (Argyroxiphium sandwicense macrocephalum).
Adaptive radiation is not a strictly vertebrate phenomenon, and examples are also known from among plants. The most famous example of adaptive radiation in plants is quite possibly the Hawaiian silverswords, named for alpine desert-dwelling Argyroxiphium species with long, silvery leaves that live for up to 20 years before growing a single flowering stalk and then dying. The Hawaiian silversword alliance consists of twenty-eight species of Hawaiian plants which, aside from the namesake silverswords, includes trees, shrubs, vines, cushion plants, and more. The silversword alliance is believed to have originated in Hawaii no more than 6 million years ago, making this one of Hawaii's youngest adaptive radiation events. This means that the silverswords evolved on Hawaii's modern high islands, and descended from a single common ancestor that arrived on Kauai from western North America. The closest modern relatives of the silverswords today are California tarweeds of the family Asteraceae.
|
Adaptive radiation
|
Hawaiian lobelioids
|
Hawaiian lobelioids
Hawaii is also the site of a separate major floral adaptive radiation event: the Hawaiian lobelioids. The Hawaiian lobelioids are significantly more speciose than the silverswords, perhaps because they have been present in Hawaii for so much longer: they descended from a single common ancestor who arrived in the archipelago up to 15 million years ago. Today the Hawaiian lobelioids form a clade of over 125 species, including succulents, trees, shrubs, epiphytes, etc. Many species have been lost to extinction and many of the surviving species endangered.
|
Adaptive radiation
|
Caribbean anoles
|
Caribbean anoles
Anole lizards are distributed broadly in the New World, from the Southeastern US to South America. With over 400 species currently recognized, often placed in a single genus (Anolis), they constitute one of the largest radiation events among all lizards. Anole radiation on the mainland has largely been a process of speciation, and is not adaptive to any great degree, but anoles on each of the Greater Antilles (Cuba, Hispaniola, Puerto Rico, and Jamaica) have adaptively radiated in separate, convergent ways. On each of these islands, anoles have evolved with such a consistent set of morphological adaptations that each species can be assigned to one of six "ecomorphs": trunk–ground, trunk–crown, grass–bush, crown–giant, twig, and trunk. Take for example crown–giants from each of these islands: the Cuban Anolis luteogularis, Hispaniola's Anolis ricordii, Puerto Rico's Anolis cuvieri, and Jamaica's Anolis garmani (Cuba and Hispaniola are both home to more than one species of crown–giant). These anoles are all large, canopy-dwelling species with large heads and large lamellae (scales on the undersides of the fingers and toes that are important for traction in climbing), and yet none of these species are particularly closely related and appear to have evolved these similar traits independently. The same can be said of the other five ecomorphs across the Caribbean's four largest islands. Much like in the case of the cichlids of the three largest African Great Lakes, each of these islands is home to its own convergent Anolis adaptive radiation event.
|
Adaptive radiation
|
Other examples
|
Other examples
Presented above are the most well-documented examples of modern adaptive radiation, but other examples are known. Populations of three-spined sticklebacks have repeatedly diverged and evolved into distinct ecotypes.Bell, M. A., and W. E. Aguirre. 2013. Contemporary evolution, allelic recycling, and adaptive radiation of the threespine stickleback. Evolutionary Ecology Research 15:377–411. On Madagascar, birds of the family Vangidae are marked by very distinct beak shapes to suit their ecological roles. Madagascan mantellid frogs have radiated into forms that mirror other tropical frog faunas, with the brightly colored mantellas (Mantella) having evolved convergently with the Neotropical poison dart frogs of Dendrobatidae, while the arboreal Boophis species are the Madagascan equivalent of tree frogs and glass frogs. The pseudoxyrhophiine snakes of Madagascar have evolved into fossorial, arboreal, terrestrial, and semi-aquatic forms that converge with the colubroid faunas in the rest of the world. These Madagascan examples are significantly older than most of the other examples presented here: Madagascar's fauna has been evolving in isolation since the island split from India some 88 million years ago, and the Mantellidae originated around 50 mya. Older examples are known: the K-Pg extinction event, which caused the disappearance of the dinosaurs and most other reptilian megafauna 65 million years ago, is seen as having triggered a global adaptive radiation event that created the mammal diversity that exists today. Also the Cambrian Explosion, where vacant niches left by the extinction of Ediacaran biota during End-Ediacaran mass extinction were filled up by the emergence of new phyla.
|
Adaptive radiation
|
See also
|
See also
Cambrian explosion—the most notable evolutionary radiation event
Evolutionary radiation—a more general term to describe any radiation
List of adaptive radiated Hawaiian honeycreepers by form
List of adaptive radiated marsupials by form
Nonadaptive radiation
|
Adaptive radiation
|
References
|
References
|
Adaptive radiation
|
Further reading
|
Further reading
Wilson, E. et al. Life on Earth, by Wilson, E.; Eisner, T.; Briggs, W.; Dickerson, R.; Metzenberg, R.; O'Brien, R.; Susman, M.; Boggs, W. (Sinauer Associates, Inc., Publishers, Stamford, Connecticut), c 1974. Chapters: The Multiplication of Species; Biogeography, pp 824–877. 40 Graphs, w species pictures, also Tables, Photos, etc. Includes Galápagos Islands, Hawaii, and Australia subcontinent, (plus St. Helena Island, etc.).
Leakey, Richard. The Origin of Humankind—on adaptive radiation in biology and human evolution, pp. 28–32, 1994, Orion Publishing.
Grant, P.R. 1999. The ecology and evolution of Darwin's Finches. Princeton University Press, Princeton, NJ.
Mayr, Ernst. 2001. What evolution is. Basic Books, New York, NY.
Gavrilets, S. and A. Vose. 2009. Dynamic patterns of adaptive radiation: evolution of mating preferences. In Butlin, R.K., J. Bridle, and D. Schluter (eds) Speciation and Patterns of Diversity, Cambridge University Press, page. 102–126.
Pinto, Gabriel, Luke Mahler, Luke J. Harmon, and Jonathan B. Losos. "Testing the Island Effect in Adaptive Radiation: Rates and Patterns of Morphological Diversification in Caribbean and Mainland Anolis Lizards." NCBI (2008): n. pag. Web. 28 Oct. 2014.
Schluter, Dolph. The ecology of adaptive radiation. Oxford University Press, 2000.
Category:Speciation
Category:Evolutionary biology terminology
|
Adaptive radiation
|
Table of Content
|
Short description, Characteristics, Conditions, Relationship between mass-extinctions and mass adaptive radiations, Examples, Darwin's finches, Cichlids of the African Great Lakes, Tanganyika cichlids, Malawi cichlids, Victoria's cichlids, Adaptive radiation in Hawaii, Hawaiian honeycreepers, Hawaiian silverswords, Hawaiian lobelioids, Caribbean anoles, Other examples, See also, References, Further reading
|
Agarose gel electrophoresis
|
Short description
|
200px|thumb|right|Digital image of 3 plasmid restriction digests run on a 1% w/v agarose gel, 3 volt/cm, stained with ethidium bromide. The DNA size marker is a commercial 1 kbp ladder. The position of the wells and direction of DNA migration is noted.
Agarose gel electrophoresis is a method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main components of agar. The proteins may be separated by charge and/or size (isoelectric focusing agarose electrophoresis is essentially size independent), and the DNA and RNA fragments by length. Biomolecules are separated by applying an electric field to move the charged molecules through an agarose matrix, and the biomolecules are separated by size in the agarose gel matrix.Sambrook J, Russel DW (2001). Molecular Cloning: A Laboratory Manual 3rd Ed. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, NY.
Agarose gel is easy to cast, has relatively fewer charged groups, and is particularly suitable for separating DNA of size range most often encountered in laboratories, which accounts for the popularity of its use. The separated DNA may be viewed with stain, most commonly under UV light, and the DNA fragments can be extracted from the gel with relative ease. Most agarose gels used are between 0.7–2% dissolved in a suitable electrophoresis buffer.
|
Agarose gel electrophoresis
|
Properties of agarose gel
|
Properties of agarose gel
right|thumb|An agarose gel cast in tray, to be used for gel electrophoresis
Agarose gel is a three-dimensional matrix formed of helical agarose molecules in supercoiled bundles that are aggregated into three-dimensional structures with channels and pores through which biomolecules can pass. The 3-D structure is held together with hydrogen bonds and can therefore be disrupted by heating back to a liquid state. The melting temperature is different from the gelling temperature, depending on the sources, agarose gel has a gelling temperature of and a melting temperature of . Low-melting and low-gelling agaroses made through chemical modifications are also available.
Agarose gel has large pore size and good gel strength, making it suitable as an anticonvection medium for the electrophoresis of DNA and large protein molecules. The pore size of a 1% gel has been estimated from 100 nm to 200–500 nm, and its gel strength allows gels as dilute as 0.15% to form a slab for gel electrophoresis. Low-concentration gels (0.1–0.2%) however are fragile and therefore hard to handle. Agarose gel has lower resolving power than polyacrylamide gel for DNA but has a greater range of separation, and is therefore used for DNA fragments of usually 50–20,000 bp in size. The limit of resolution for standard agarose gel electrophoresis is around 750 kb, but resolution of over 6 Mb is possible with pulsed field gel electrophoresis (PFGE). It can also be used to separate large proteins, and it is the preferred matrix for the gel electrophoresis of particles with effective radii larger than 5–10 nm. A 0.9% agarose gel has pores large enough for the entry of bacteriophage T4.
The agarose polymer contains charged groups, in particular pyruvate and sulfate. These negatively charged groups create a flow of water in the opposite direction to the movement of DNA in a process called electroendosmosis (EEO), and can therefore retard the movement of DNA and cause blurring of bands. Higher concentration gels would have higher electroendosmotic flow. Low EEO agarose is therefore generally preferred for use in agarose gel electrophoresis of nucleic acids, but high EEO agarose may be used for other purposes. The lower sulfate content of low EEO agarose, particularly low-melting point (LMP) agarose, is also beneficial in cases where the DNA extracted from gel is to be used for further manipulation as the presence of contaminating sulfates may affect some subsequent procedures, such as ligation and PCR. Zero EEO agaroses however are undesirable for some applications as they may be made by adding positively charged groups and such groups can affect subsequent enzyme reactions. Electroendosmosis is a reason agarose is used in preference to agar as the agaropectin component in agar contains a significant amount of negatively charged sulfate and carboxyl groups. The removal of agaropectin in agarose substantially reduces the EEO, as well as reducing the non-specific adsorption of biomolecules to the gel matrix. However, for some applications such as the electrophoresis of serum proteins, a high EEO may be desirable, and agaropectin may be added in the gel used.
|
Agarose gel electrophoresis
|
Migration of nucleic acids in agarose gel
|
Migration of nucleic acids in agarose gel
|
Agarose gel electrophoresis
|
Factors affecting migration of nucleic acid in gel
|
Factors affecting migration of nucleic acid in gel
thumb|280px|Gels of plasmid preparations usually show a major band of supercoiled DNA with other fainter bands in the same lane. Note that by convention DNA gel is displayed with smaller DNA fragments nearer to the bottom of the gel. This is because historically DNA gels were run vertically and the smaller DNA fragments move downwards faster.
A number of factors can affect the migration of nucleic acids: the dimension of the gel pores (gel concentration), size of DNA being electrophoresed, the voltage used, the ionic strength of the buffer, and the concentration of intercalating dye such as ethidium bromide if used during electrophoresis.
Smaller molecules travel faster than larger molecules in gel, and double-stranded DNA moves at a rate that is inversely proportional to the logarithm of the number of base pairs. This relationship however breaks down with very large DNA fragments, and separation of very large DNA fragments requires the use of pulsed field gel electrophoresis (PFGE), which applies alternating current from different directions and the large DNA fragments are separated as they reorient themselves with the changing field.
For standard agarose gel electrophoresis, larger molecules are resolved better using a low concentration gel while smaller molecules separate better at high concentration gel. Higher concentration gels, however, require longer run times (sometimes days).
The movement of the DNA may be affected by the conformation of the DNA molecule, for example, supercoiled DNA usually moves faster than relaxed DNA because it is tightly coiled and hence more compact. In a normal plasmid DNA preparation, multiple forms of DNA may be present. Gel electrophoresis of the plasmids would normally show the negatively supercoiled form as the main band, while nicked DNA (open circular form) and the relaxed closed circular form appears as minor bands. The rate at which the various forms move however can change using different electrophoresis conditions, and the mobility of larger circular DNA may be more strongly affected than linear DNA by the pore size of the gel.
Ethidium bromide which intercalates into circular DNA can change the charge, length, as well as the superhelicity of the DNA molecule, therefore its presence in gel during electrophoresis can affect its movement. For example, the positive charge of ethidium bromide can reduce the DNA movement by 15%. Agarose gel electrophoresis can be used to resolve circular DNA with different supercoiling topology.
DNA damage due to increased cross-linking will also reduce electrophoretic DNA migration in a dose-dependent way.
The rate of migration of the DNA is proportional to the voltage applied, i.e. the higher the voltage, the faster the DNA moves. The resolution of large DNA fragments however is lower at high voltage. The mobility of DNA may also change in an unsteady field – in a field that is periodically reversed, the mobility of DNA of a particular size may drop significantly at a particular cycling frequency. This phenomenon can result in band inversion in field inversion gel electrophoresis (FIGE), whereby larger DNA fragments move faster than smaller ones.
|
Agarose gel electrophoresis
|
Migration anomalies
|
Migration anomalies
"Smiley" gels - this edge effect is caused when the voltage applied is too high for the gel concentration used.
Overloading of DNA - overloading of DNA slows down the migration of DNA fragments.
Contamination - presence of impurities, such as salts or proteins can affect the movement of the DNA.
|
Agarose gel electrophoresis
|
Mechanism of migration and separation
|
Mechanism of migration and separation
The negative charge of its phosphate backbone moves the DNA towards the positively charged anode during electrophoresis. However, the migration of DNA molecules in solution, in the absence of a gel matrix, is independent of molecular weight during electrophoresis. The gel matrix is therefore responsible for the separation of DNA by size during electrophoresis, and a number of models exist to explain the mechanism of separation of biomolecules in gel matrix. A widely accepted one is the Ogston model which treats the polymer matrix as a sieve. A globular protein or a random coil DNA moves through the interconnected pores, and the movement of larger molecules is more likely to be impeded and slowed down by collisions with the gel matrix, and the molecules of different sizes can therefore be separated in this sieving process.
The Ogston model however breaks down for large molecules whereby the pores are significantly smaller than size of the molecule. For DNA molecules of size greater than 1 kb, a reptation model (or its variants) is most commonly used. This model assumes that the DNA can crawl in a "snake-like" fashion (hence "reptation") through the pores as an elongated molecule. A biased reptation model applies at higher electric field strength, whereby the leading end of the molecule become strongly biased in the forward direction and pulls the rest of the molecule along. Real-time fluorescence microscopy of stained molecules, however, showed more subtle dynamics during electrophoresis, with the DNA showing considerable elasticity as it alternately stretching in the direction of the applied field and then contracting into a ball, or becoming hooked into a U-shape when it gets caught on the polymer fibres.
|
Agarose gel electrophoresis
|
General procedure
|
General procedure
The details of an agarose gel electrophoresis experiment may vary depending on methods, but most follow a general procedure.
thumb|none|Video showing assembly of the rig and loading/running of the gel.
|
Agarose gel electrophoresis
|
Casting of gel
|
Casting of gel
thumb|180px|Loading DNA samples into the wells of an agarose gel using a multi-channel pipette.
The gel is prepared by dissolving the agarose powder in an appropriate buffer, such as TAE or TBE, to be used in electrophoresis. The agarose is dispersed in the buffer before heating it to near-boiling point, but avoid boiling. The melted agarose is allowed to cool sufficiently before pouring the solution into a cast as the cast may warp or crack if the agarose solution is too hot. A comb is placed in the cast to create wells for loading sample, and the gel should be completely set before use.
The concentration of gel affects the resolution of DNA separation. The agarose gel is composed of microscopic pores through which the molecules travel, and there is an inverse relationship between the pore size of the agarose gel and the concentration – pore size decreases as the density of agarose fibers increases. High gel concentration improves separation of smaller DNA molecules, while lowering gel concentration permits large DNA molecules to be separated. The process allows fragments ranging from 50 base pairs to several mega bases to be separated depending on the gel concentration used. The concentration is measured in weight of agarose over volume of buffer used (g/ml). For a standard agarose gel electrophoresis, a 0.8% gel gives good separation or resolution of large 5–10kb DNA fragments, while 2% gel gives good resolution for small 0.2–1kb fragments. 1% gels is often used for a standard electrophoresis. High percentage gels are often brittle and may not set evenly, while low percentage gels (0.1-0.2%) are fragile and not easy to handle. Low-melting-point (LMP) agarose gels are also more fragile than normal agarose gel. Low-melting point agarose may be used on its own or simultaneously with standard agarose for the separation and isolation of DNA. PFGE and FIGE are often done with high percentage agarose gels.
|
Agarose gel electrophoresis
|
Loading of samples
|
Loading of samples
Once the gel has set, the comb is removed, leaving wells where DNA samples can be loaded. Loading buffer is mixed with the DNA sample before the mixture is loaded into the wells. The loading buffer contains a dense compound, which may be glycerol, sucrose, or Ficoll, that raises the density of the sample so that the DNA sample may sink to the bottom of the well. If the DNA sample contains residual ethanol after its preparation, it may float out of the well. The loading buffer also includes colored dyes such as xylene cyanol and bromophenol blue used to monitor the progress of the electrophoresis. The DNA samples are loaded using a pipette.
|
Agarose gel electrophoresis
|
Electrophoresis
|
Electrophoresis
thumb|Agarose gel slab in electrophoresis tank with bands of dyes indicating progress of the electrophoresis. The DNA moves towards anode.
Agarose gel electrophoresis is most commonly done horizontally in a subaquaeous mode whereby the slab gel is completely submerged in buffer during electrophoresis. It is also possible, but less common, to perform the electrophoresis vertically, as well as horizontally with the gel raised on agarose legs using an appropriate apparatus. The buffer used in the gel is the same as the running buffer in the electrophoresis tank, which is why electrophoresis in the subaquaeous mode is possible with agarose gel.
For optimal resolution of DNA greater than 2kb in size in standard gel electrophoresis, 5 to 8 V/cm is recommended (the distance in cm refers to the distance between electrodes, therefore this recommended voltage would be 5 to 8 multiplied by the distance between the electrodes in cm). Voltage may also be limited by the fact that it heats the gel and may cause the gel to melt if it is run at high voltage for a prolonged period, especially if the gel used is LMP agarose gel. Too high a voltage may also reduce resolution, as well as causing band streaking for large DNA molecules. Too low a voltage may lead to broadening of band for small DNA fragments due to dispersion and diffusion.
Since DNA is not visible in natural light, the progress of the electrophoresis is monitored using colored dyes. Xylene cyanol (light blue color) comigrates large DNA fragments, while Bromophenol blue (dark blue) comigrates with the smaller fragments. Less commonly used dyes include Cresol Red and Orange G which migrate ahead of bromophenol blue. A DNA marker is also run together for the estimation of the molecular weight of the DNA fragments. Note however that the size of a circular DNA like plasmids cannot be accurately gauged using standard markers unless it has been linearized by restriction digest, alternatively a supercoiled DNA marker may be used.
|
Agarose gel electrophoresis
|
Staining and visualization
|
Staining and visualization
thumb|Agarose gel with UV illumination: DNA stained with ethidium bromide appears as glowing orange bands.
DNA as well as RNA are normally visualized by staining with ethidium bromide, which intercalates into the major grooves of the DNA and fluoresces under UV light. The intercalation depends on the concentration of DNA and thus, a band with high intensity will indicate a higher amount of DNA compared to a band of less intensity. The ethidium bromide may be added to the agarose solution before it gels, or the DNA gel may be stained later after electrophoresis. Destaining of the gel is not necessary but may produce better images. Other methods of staining are available; examples are MIDORI Green, SYBR Green, GelRed, methylene blue, brilliant cresyl blue, Nile blue sulfate, and crystal violet. SYBR Green, GelRed and other similar commercial products are sold as safer alternatives to ethidium bromide as it has been shown to be mutagenic in Ames test, although the carcinogenicity of ethidium bromide has not actually been established. SYBR Green requires the use of a blue-light transilluminator. DNA stained with crystal violet can be viewed under natural light without the use of a UV transilluminator which is an advantage, however it may not produce a strong band.
When stained with ethidium bromide, the gel is viewed with an ultraviolet (UV) transilluminator. The UV light excites the electrons within the aromatic ring of ethidium bromide, and once they return to the ground state, light is released, making the DNA and ethidium bromide complex fluoresce. Standard transilluminators use wavelengths of 302/312-nm (UV-B), however exposure of DNA to UV radiation for as little as 45 seconds can produce damage to DNA and affect subsequent procedures, for example reducing the efficiency of transformation, in vitro transcription, and PCR. Exposure of DNA to UV radiation therefore should be limited. Using a higher wavelength of 365 nm (UV-A range) causes less damage to the DNA but also produces much weaker fluorescence with ethidium bromide. Where multiple wavelengths can be selected in the transilluminator, shorter wavelength can be used to capture images, while longer wavelength should be used if it is necessary to work on the gel for any extended period of time.
The transilluminator apparatus may also contain image capture devices, such as a digital or polaroid camera, that allow an image of the gel to be taken or printed.
For gel electrophoresis of protein, the bands may be visualised with Coomassie or silver stains.
thumb|Cutting out agarose gel slices. Protective equipment must be worn when using UV transilluminator.
|
Agarose gel electrophoresis
|
Downstream procedures
|
Downstream procedures
The separated DNA bands are often used for further procedures, and a DNA band may be cut out of the gel as a slice, dissolved and purified. Contaminants however may affect some downstream procedures such as PCR, and low melting point agarose may be preferred in some cases as it contains fewer of the sulfates that can affect some enzymatic reactions. The gels may also be used for blotting techniques.
|
Agarose gel electrophoresis
|
Buffers
|
Buffers
In general, the ideal buffer should have good conductivity, produce less heat and have a long life. There are a number of buffers used for agarose electrophoresis; common ones for nucleic acids include tris/acetate/EDTA (TAE) and tris/borate/EDTA (TBE). The buffers used contain EDTA to inactivate many nucleases which require divalent cation for their function. The borate in TBE buffer can be problematic as borate can polymerize, and/or interact with cis diols such as those found in RNA. TAE has the lowest buffering capacity, but it provides the best resolution for larger DNA. This means a lower voltage and more time, but a better product.
Many other buffers have been proposed, e.g. lithium borate (LB), iso electric histidine, pK matched goods buffers, etc.; in most cases the purported rationale is lower current (less heat) and or matched ion mobilities, which leads to longer buffer life. Tris-phosphate buffer has high buffering capacity but cannot be used if DNA extracted is to be used in phosphate sensitive reaction. LB is relatively new and is ineffective in resolving fragments larger than 5 kbp; However, with its low conductivity, a much higher voltage could be used (up to 35 V/cm), which means a shorter analysis time for routine electrophoresis. As low as one base pair size difference could be resolved in 3% agarose gel with an extremely low conductivity medium (1 mM lithium borate).
Other buffering system may be used in specific applications, for example, barbituric acid-sodium barbiturate or tris-barbiturate buffers may be used for in agarose gel electrophoresis of proteins, for example in the detection of abnormal distribution of proteins.
|
Agarose gel electrophoresis
|
Applications
|
Applications
Estimation of the size of DNA molecules following digestion with restriction enzymes, e.g., in restriction mapping of cloned DNA.
Estimation of the DNA concentration by comparing the intensity of the nucleic acid band with the corresponding band of the size marker.
Analysis of products of a polymerase chain reaction (PCR), e.g., in molecular genetic diagnosis or genetic fingerprinting
Separation of DNA fragments for extraction and purification.
Separation of restricted genomic DNA prior to Southern transfer, or of RNA prior to Northern transfer.
Separation of proteins, for example, screening of protein abnormalities in clinical chemistry.
Agarose gels are easily cast and handled compared to other matrices and nucleic acids are not chemically altered during electrophoresis. Samples are also easily recovered. After the experiment is finished, the resulting gel can be stored in a plastic bag in a refrigerator.
Electrophoresis is performed in buffer solutions to reduce pH changes due to the electric field, which is important because the charge of DNA and RNA depends on pH, but running for too long can exhaust the buffering capacity of the solution. Further, different preparations of genetic material may not migrate consistently with each other, for morphological or other reasons.
|
Agarose gel electrophoresis
|
See also
|
See also
Gel electrophoresis
Immunodiffusion, Immunoelectrophoresis
SDD-AGE
Northern blot
SDS-polyacrylamide gel electrophoresis
Southern blot
|
Agarose gel electrophoresis
|
References
|
References
|
Agarose gel electrophoresis
|
External links
|
External links
How to run a DNA or RNA gel
Animation of gel analysis of DNA restriction fragments
Video and article of agarose gel electrophoresis
Step by step photos of running a gel and extracting DNA
Drinking straw electrophoresis!
A typical method from wikiversity
Building a gel electrophoresis chamber
Category:Biological techniques and tools
Category:Molecular biology
Category:Electrophoresis
Category:Polymerase chain reaction
Category:Articles containing video clips
|
Agarose gel electrophoresis
|
Table of Content
|
Short description, Properties of agarose gel, Migration of nucleic acids in agarose gel, Factors affecting migration of nucleic acid in gel, Migration anomalies, Mechanism of migration and separation, General procedure, Casting of gel, Loading of samples, Electrophoresis, Staining and visualization, Downstream procedures, Buffers, Applications, See also, References, External links
|
Allele
|
Short description
|
An allele is a variant of the sequence of nucleotides at a particular location, or locus, on a DNA molecule.
Alleles can differ at a single position through single nucleotide polymorphisms (SNP), but they can also have insertions and deletions of up to several thousand base pairs.
Most alleles observed result in little or no change in the function or amount of the gene product(s) they code or regulate for. However, sometimes different alleles can result in different observable phenotypic traits, such as different pigmentation. A notable example of this is Gregor Mendel's discovery that the white and purple flower colors in pea plants were the result of a single gene with two alleles.
Nearly all multicellular organisms have two sets of chromosomes at some point in their biological life cycle; that is, they are diploid. For a given locus, if the two chromosomes contain the same allele, they, and the organism, are homozygous with respect to that allele. If the alleles are different, they, and the organism, are heterozygous with respect to those alleles.
Popular definitions of 'allele' typically refer only to different alleles within genes. For example, the ABO blood grouping is controlled by the ABO gene, which has six common alleles (variants). In population genetics, nearly every living human's phenotype for the ABO gene is some combination of just these six alleles.
|
Allele
|
Etymology
|
Etymology
The word "allele" is a short form of "allelomorph" ("other form", a word coined by British geneticists William Bateson and Edith Rebecca Saunders) in the 1900s,Bateson, W. and Saunders, E. R. (1902) "The facts of heredity in the light of Mendel’s discovery." Reports to the Evolution Committee of the Royal Society, I. pp. 125–160 which was used in the early days of genetics to describe variant forms of a gene detected in different phenotypes and identified to cause the differences between them. It derives from the Greek prefix ἀλληλο-, allelo-, meaning "mutual", "reciprocal", or "each other", which itself is related to the Greek adjective ἄλλος, allos (cognate with Latin alius), meaning "other".
|
Allele
|
Alleles that lead to dominant or recessive phenotypes
|
Alleles that lead to dominant or recessive phenotypes
In many cases, genotypic interactions between the two alleles at a locus can be described as dominant or recessive, according to which of the two homozygous phenotypes the heterozygote most resembles. Where the heterozygote is indistinguishable from one of the homozygotes, the allele expressed is the one that leads to the "dominant" phenotype, and the other allele is said to be "recessive". The degree and pattern of dominance varies among loci. This type of interaction was first formally-described by Gregor Mendel. However, many traits defy this simple categorization and the phenotypes are modelled by co-dominance and polygenic inheritance.
The term "wild type" allele is sometimes used to describe an allele that is thought to contribute to the typical phenotypic character as seen in "wild" populations of organisms, such as fruit flies (Drosophila melanogaster). Such a "wild type" allele was historically regarded as leading to a dominant (overpowering – always expressed), common, and normal phenotype, in contrast to "mutant" alleles that lead to recessive, rare, and frequently deleterious phenotypes. It was formerly thought that most individuals were homozygous for the "wild type" allele at most gene loci, and that any alternative "mutant" allele was found in homozygous form in a small minority of "affected" individuals, often as genetic diseases, and more frequently in heterozygous form in "carriers" for the mutant allele. It is now appreciated that most or all gene loci are highly polymorphic, with multiple alleles, whose frequencies vary from population to population, and that a great deal of genetic variation is hidden in the form of alleles that do not produce obvious phenotypic differences. Wild type alleles are often denoted by a superscript plus sign (i.e., p for an allele p).
|
Allele
|
Multiple alleles
|
Multiple alleles
thumb|upright=1.45|In the ABO blood group system, a person with Type A blood displays A-antigens and may have a genotype IAIA or IAi. A person with Type B blood displays B-antigens and may have the genotype IBIB or IBi. A person with Type AB blood displays both A- and B-antigens and has the genotype IAIB and a person with Type O blood, displaying neither antigen, has the genotype ii.
A population or species of organisms typically includes multiple alleles at each locus among various individuals. Allelic variation at a locus is measurable as the number of alleles (polymorphism) present, or the proportion of heterozygotes in the population. A null allele is a gene variant that lacks the gene's normal function because it either is not expressed, or the expressed protein is inactive.
For example, at the gene locus for the ABO blood type carbohydrate antigens in humans, classical genetics recognizes three alleles, IA, IB, and i, which determine compatibility of blood transfusions. Any individual has one of six possible genotypes (IAIA, IAi, IBIB, IBi, IAIB, and ii) which produce one of four possible phenotypes: "Type A" (produced by IAIA homozygous and IAi heterozygous genotypes), "Type B" (produced by IBIB homozygous and IBi heterozygous genotypes), "Type AB" produced by IAIB heterozygous genotype, and "Type O" produced by ii homozygous genotype. (It is now known that each of the A, B, and O alleles is actually a class of multiple alleles with different DNA sequences that produce proteins with identical properties: more than 70 alleles are known at the ABO locus. Hence an individual with "Type A" blood may be an AO heterozygote, an AA homozygote, or an AA heterozygote with two different "A" alleles.)
|
Allele
|
Genotype frequencies
|
Genotype frequencies
The frequency of alleles in a diploid population can be used to predict the frequencies of the corresponding genotypes (see Hardy–Weinberg principle). For a simple model, with two alleles;
where p is the frequency of one allele and q is the frequency of the alternative allele, which necessarily sum to unity. Then, p2 is the fraction of the population homozygous for the first allele, 2pq is the fraction of heterozygotes, and q2 is the fraction homozygous for the alternative allele. If the first allele is dominant to the second then the fraction of the population that will show the dominant phenotype is p2 + 2pq, and the fraction with the recessive phenotype is q2.
With three alleles:
and
In the case of multiple alleles at a diploid locus, the number of possible genotypes (G) with a number of alleles (a) is given by the expression:
|
Allele
|
Allelic dominance in genetic disorders
|
Allelic dominance in genetic disorders
A number of genetic disorders are caused when an individual inherits two recessive alleles for a single-gene trait. Recessive genetic disorders include albinism, cystic fibrosis, galactosemia, phenylketonuria (PKU), and Tay–Sachs disease. Other disorders are also due to recessive alleles, but because the gene locus is located on the X chromosome, so that males have only one copy (that is, they are hemizygous), they are more frequent in males than in females. Examples include red–green color blindness and fragile X syndrome.
Other disorders, such as Huntington's disease, occur when an individual inherits only one dominant allele.
|
Allele
|
Epialleles
|
Epialleles
While heritable traits are typically studied in terms of genetic alleles, epigenetic marks such as DNA methylation can be inherited at specific genomic regions in certain species, a process termed transgenerational epigenetic inheritance. The term epiallele is used to distinguish these heritable marks from traditional alleles, which are defined by nucleotide sequence. A specific class of epiallele, the metastable epialleles, has been discovered in mice and in humans which is characterized by stochastic (probabilistic) establishment of epigenetic state that can be mitotically inherited.
|
Allele
|
Idiomorph
|
Idiomorph
The term "idiomorph", from Greek 'morphos' (form) and 'idio' (singular, unique), was introduced in 1990 in place of "allele" to denote sequences at the same locus in different strains that have no sequence similarity and probably do not share a common phylogenetic relationship. It is used mainly in the genetic research of mycology.
|
Allele
|
See also
|
See also
|
Allele
|
References and notes
|
References and notes
|
Allele
|
External links
|
External links
ALFRED: The ALlele FREquency Database
Category:Classical genetics
Category:Genetic genealogy
|
Allele
|
Table of Content
|
Short description, Etymology, Alleles that lead to dominant or recessive phenotypes, Multiple alleles, Genotype frequencies, Allelic dominance in genetic disorders, Epialleles, Idiomorph, See also, References and notes, External links
|
Ampicillin
|
Short description
|
Ampicillin is an antibiotic belonging to the aminopenicillin class of the penicillin family. The drug is used to prevent and treat several bacterial infections, such as respiratory tract infections, urinary tract infections, meningitis, salmonellosis, and endocarditis. It may also be used to prevent group B streptococcal infection in newborns. It is used by mouth, by injection into a muscle, or intravenously.
Common side effects include rash, nausea, and diarrhea. It should not be used in people who are allergic to penicillin. Serious side effects may include Clostridioides difficile colitis or anaphylaxis. While usable in those with kidney problems, the dose may need to be decreased. Its use during pregnancy and breastfeeding appears to be generally safe.
Ampicillin was discovered in 1958 and came into commercial use in 1961. It is on the World Health Organization's List of Essential Medicines. The World Health Organization classifies ampicillin as critically important for human medicine. It is available as a generic medication.
|
Ampicillin
|
Medical uses
|
Medical uses
|
Ampicillin
|
Diseases
|
Diseases
Bacterial meningitis; an aminoglycoside can be added to increase efficacy against gram-negative meningitis bacteria
Endocarditis by enterococcal strains (off-label use); often given with an aminoglycoside
Gastrointestinal infections caused by contaminated water or food (for example, by Salmonella)
Genito-urinary tract infections
Healthcare-associated infections that are related to infections from using urinary catheters and that are unresponsive to other medications
Otitis media (middle ear infection)
Prophylaxis (i.e. to prevent infection) in those who previously had rheumatic heart disease or are undergoing dental procedures, vaginal hysterectomies, or C-sections. It is also used in pregnant woman who are carriers of group B streptococci to prevent early-onset neonatal infections.
Respiratory infections, including bronchitis, pharyngitis
Sinusitis
Sepsis
Whooping cough, to prevent and treat secondary infections
Ampicillin used to also be used to treat gonorrhea, but there are now too many strains resistant to penicillins.
|
Ampicillin
|
Bacteria
|
Bacteria
Ampicillin is used to treat infections by many gram-positive and gram-negative bacteria. It was the first "broad spectrum" penicillin with activity against gram-positive bacteria, including Streptococcus pneumoniae, Streptococcus pyogenes, some isolates of Staphylococcus aureus (but not penicillin-resistant or methicillin-resistant strains), Trueperella, and some Enterococcus. It is one of the few antibiotics that works against multidrug resistant Enterococcus faecalis and E. faecium. Activity against gram-negative bacteria includes Neisseria meningitidis, some Haemophilus influenzae, and some of the Enterobacteriaceae (though most Enterobacteriaceae and Pseudomonas are resistant). Its spectrum of activity is enhanced by co-administration of sulbactam, a drug that inhibits beta lactamase, an enzyme produced by bacteria to inactivate ampicillin and related antibiotics. It is sometimes used in combination with other antibiotics that have different mechanisms of action, like vancomycin, linezolid, daptomycin, and tigecycline.
|
Ampicillin
|
Available forms
|
Available forms
Ampicillin can be administered by mouth, an intramuscular injection (shot) or by intravenous infusion. The oral form, available as capsules or oral suspensions, is not given as an initial treatment for severe infections, but rather as a follow-up to an IM or IV injection. For IV and IM injections, ampicillin is kept as a powder that must be reconstituted.
IV injections must be given slowly, as rapid IV injections can lead to convulsive seizures.
|
Ampicillin
|
Specific populations
|
Specific populations
Ampicillin is one of the most used drugs in pregnancy, and has been found to be generally harmless both by the Food and Drug Administration in the U.S. (which classified it as category B) and the Therapeutic Goods Administration in Australia (which classified it as category A). It is the drug of choice for treating Listeria monocytogenes in pregnant women, either alone or combined with an aminoglycoside. Pregnancy increases the clearance of ampicillin by up to 50%, and a higher dose is thus needed to reach therapeutic levels.
Ampicillin crosses the placenta and remains in the amniotic fluid at 50–100% of the concentration in maternal plasma; this can lead to high concentrations of ampicillin in the newborn.
While lactating mothers secrete some ampicillin into their breast milk, the amount is minimal.
In newborns, ampicillin has a longer half-life and lower plasma protein binding. The clearance by the kidneys is lower, as kidney function has not fully developed.
|
Ampicillin
|
Contraindications
|
Contraindications
Ampicillin is contraindicated in those with a hypersensitivity to penicillins, as they can cause fatal anaphylactic reactions. Hypersensitivity reactions can include frequent skin rashes and hives, exfoliative dermatitis, erythema multiforme, and a temporary decrease in both red and white blood cells.
Ampicillin is not recommended in people with concurrent mononucleosis, as over 40% of patients develop a skin rash.
|
Ampicillin
|
Side effects
|
Side effects
Ampicillin is comparatively less toxic than other antibiotics, and side effects are more likely in those who are sensitive to penicillins and those with a history of asthma or allergies. In very rare cases, it causes severe side effects such as angioedema, anaphylaxis, and C. difficile infection (that can range from mild diarrhea to serious pseudomembranous colitis). Some develop black "furry" tongue. Serious adverse effects also include seizures and serum sickness. The most common side effects, experienced by about 10% of users are diarrhea and rash. Less common side effects can be nausea, vomiting, itching, and blood dyscrasias. The gastrointestinal effects, such as hairy tongue, nausea, vomiting, diarrhea, and colitis, are more common with the oral form of penicillin. Other conditions may develop up several weeks after treatment.
|
Ampicillin
|
Overdose
|
Overdose
Ampicillin overdose can cause behavioral changes, confusion, blackouts, and convulsions, as well as neuromuscular hypersensitivity, electrolyte imbalance, and kidney failure.
|
Ampicillin
|
Interactions
|
Interactions
Ampicillin reacts with probenecid and methotrexate to decrease renal excretion. Large doses of ampicillin can increase the risk of bleeding with concurrent use of warfarin and other oral anticoagulants, possibly by inhibiting platelet aggregation. Ampicillin has been said to make oral contraceptives less effective, but this has been disputed. It can be made less effective by other antibiotic, such as chloramphenicol, erythromycin, cephalosporins, and tetracyclines. For example, tetracyclines inhibit protein synthesis in bacteria, reducing the target against which ampicillin acts. If given at the same time as aminoglycosides, it can bind to it and inactivate it. When administered separately, aminoglycosides and ampicillin can potentiate each other instead.
Ampicillin causes skin rashes more often when given with allopurinol.
Both the live cholera vaccine and live typhoid vaccine can be made ineffective if given with ampicillin. Ampicillin is normally used to treat cholera and typhoid fever, lowering the immunological response that the body has to mount.
|
Ampicillin
|
Pharmacology
|
Pharmacology
|
Ampicillin
|
Mechanism of action
|
Mechanism of action
class=skin-invert-image|thumb|The amino group (highlighted in magenta) is present on ampicillin but not penicillin G.
Ampicillin is in the penicillin group of beta-lactam antibiotics and is part of the aminopenicillin family. It is roughly equivalent to amoxicillin in terms of activity. Ampicillin is able to penetrate gram-positive and some gram-negative bacteria. It differs from penicillin G, or benzylpenicillin, only by the presence of an amino group. This amino group, present on both ampicillin and amoxicillin, helps these antibiotics pass through the pores of the outer membrane of gram-negative bacteria, such as Escherichia coli, Proteus mirabilis, Salmonella enterica, and Shigella.
Ampicillin acts as an irreversible inhibitor of the enzyme transpeptidase, which is needed by bacteria to make the cell wall. It inhibits the third and final stage of bacterial cell wall synthesis in binary fission, which ultimately leads to cell lysis; therefore, ampicillin is usually bacteriolytic.
|
Ampicillin
|
Pharmacokinetics
|
Pharmacokinetics
Ampicillin is well-absorbed from the GI tract (though food reduces its absorption), and reaches peak concentrations in one to two hours. The bioavailability is around 62% for parenteral routes. Unlike other penicillins, which usually bind 60–90% to plasma proteins, ampicillin binds to only 15–20%.
Ampicillin is distributed through most tissues, though it is concentrated in the liver and kidneys. It can also be found in the cerebrospinal fluid when the meninges become inflamed (such as, for example, meningitis). Some ampicillin is metabolized by hydrolyzing the beta-lactam ring to penicilloic acid, though most of it is excreted unchanged. In the kidneys, it is filtered out mostly by tubular secretion; some also undergoes glomerular filtration, and the rest is excreted in the feces and bile.
Hetacillin and pivampicillin are ampicillin esters that have been developed to increase bioavailability.
|
Ampicillin
|
History
|
History
Ampicillin has been used extensively to treat bacterial infections since 1961. Until the introduction of ampicillin by the British company Beecham, penicillin therapies had only been effective against gram-positive organisms such as staphylococci and streptococci. Ampicillin (originally branded as "Penbritin") also demonstrated activity against gram-negative organisms such as H. influenzae, coliforms, and Proteus spp.
|
Ampicillin
|
Society and culture
|
Society and culture
|
Ampicillin
|
Economics
|
Economics
Ampicillin is relatively inexpensive. In the United States, it is available as a generic medication.
|
Ampicillin
|
Veterinary use
|
Veterinary use
In veterinary medicine, ampicillin is used in cats, dogs, and farm animals to treat:
Anal gland infections
Cutaneous infections, such as abscesses, cellulitis, and pustular dermatitis
E. coli and Salmonella infections in cattle, sheep, and goats (oral form). Ampicillin use for this purpose had declined as bacterial resistance has increased.
Mastitis in sows
Mixed aerobic–anaerobic infections, such as from cat bites
Multidrug-resistant Enterococcus faecalis and E. faecium
Prophylactic use in poultry against Salmonella and sepsis from E. coli or Staphylococcus aureus
Respiratory tract infections, including tonsilitis, bovine respiratory disease, shipping fever, bronchopneumonia, and calf and bovine pneumonia
Urinary tract infections in dogs
Horses are generally not treated with oral ampicillin, as they have low bioavailability of beta-lactams.
The half-life in animals is around that same of that in humans (just over an hour). Oral absorption is less than 50% in cats and dogs, and less than 4% in horses.
|
Ampicillin
|
References
|
References
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.