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Etymology. Battle is a loanword from the Old French , first attested in 1297, from Late Latin , meaning "exercise of soldiers and gladiators in fighting and fencing", from Late Latin (taken from Germanic) "beat", from which the English word battery is also derived via Middle English . Characteristics. The defining characteristic of the fight as a concept in military science has changed with the variations in the organisation, employment and technology of military forces. The English military historian John Keegan suggested an ideal definition of battle as "something which happens between two armies leading to the moral then physical disintegration of one or the other of them" but the origins and outcomes of battles can rarely be summarized so neatly. Battle in the 20th and 21st centuries is defined as the combat between large components of the forces in a military campaign, used to achieve military objectives. Where the duration of the battle is longer than a week, it is often for reasons of planning called an operation. Battles can be planned, encountered or forced by one side when the other is unable to withdraw from combat.
A battle always has as its purpose the reaching of a mission goal by use of military force. A victory in the battle is achieved when one of the opposing sides forces the other to abandon its mission and surrender its forces, routs the other (i.e., forces it to retreat or renders it militarily ineffective for further combat operations) or annihilates the latter, resulting in their deaths or capture. A battle may end in a Pyrrhic victory, which ultimately favors the defeated party. If no resolution is reached in a battle, it can result in a stalemate. A conflict in which one side is unwilling to reach a decision by a direct battle using conventional warfare often becomes an insurgency. Until the 19th century the majority of battles were of short duration, many lasting a part of a day. (The Battle of Preston (1648), the Battle of Nations (1813) and the Battle of Gettysburg (1863) were exceptional in lasting three days.) This was mainly due to the difficulty of supplying armies in the field or conducting night operations. The means of prolonging a battle was typically with siege warfare. Improvements in transport and the sudden evolving of trench warfare, with its siege-like nature during the First World War in the 20th century, lengthened the duration of battles to days and weeks. This created the requirement for unit rotation to prevent combat fatigue, with troops preferably not remaining in a combat area of operations for more than a month.
The use of the term "battle" in military history has led to its misuse when referring to almost any scale of combat, notably by strategic forces involving hundreds of thousands of troops that may be engaged in either one battle at a time (Battle of Leipzig) or operations (Battle of Wuhan). The space a battle occupies depends on the range of the weapons of the combatants. A "battle" in this broader sense may be of long duration and take place over a large area, as in the case of the Battle of Britain or the Battle of the Atlantic. Until the advent of artillery and aircraft, battles were fought with the two sides within sight, if not reach, of each other. The depth of the battlefield has also increased in modern warfare with inclusion of the supporting units in the rear areas; supply, artillery, medical personnel etc. often outnumber the front-line combat troops. Battles are made up of a multitude of individual combats, skirmishes and small engagements and the combatants will usually only experience a small part of the battle. To the infantryman, there may be little to distinguish between combat as part of a minor raid or a big offensive, nor is it likely that he anticipates the future course of the battle; few of the British infantry who went over the top on the first day on the Somme, 1 July 1916, would have anticipated that the battle would last five months. Some of the Allied infantry who had just dealt a crushing defeat to the French at the Battle of Waterloo fully expected to have to fight again the next day (at the Battle of Wavre).
Battlespace. Battlespace is a unified strategic concept to integrate and combine armed forces for the military theatre of operations, including air, information, land, sea and space. It includes the environment, factors and conditions that must be understood to apply combat power, protect the force or complete the mission, comprising enemy and friendly armed forces; facilities; weather; terrain; and the electromagnetic spectrum. Factors. Battles are decided by various factors, the number and quality of combatants and equipment, the skill of commanders and terrain are among the most prominent. Weapons and armour can be decisive; on many occasions armies have achieved victory through more advanced weapons than those of their opponents. An extreme example was in the Battle of Omdurman, in which a large army of Sudanese Mahdists armed in a traditional manner were destroyed by an Anglo-Egyptian force equipped with Maxim machine guns and artillery. On some occasions, simple weapons employed in an unorthodox fashion have proven advantageous; Swiss pikemen gained many victories through their ability to transform a traditionally defensive weapon into an offensive one. Zulus in the early 19th century were victorious in battles against their rivals in part because they adopted a new kind of spear, the iklwa. Forces with inferior weapons have still emerged victorious at times, for example in the Wars of Scottish Independence. Disciplined troops are often of greater importance; at the Battle of Alesia, the Romans were greatly outnumbered but won because of superior training.
Battles can also be determined by terrain. Capturing high ground has been the main tactic in innumerable battles. An army that holds the high ground forces the enemy to climb and thus wear themselves down. Areas of jungle and forest, with dense vegetation act as force-multipliers, of benefit to inferior armies. Terrain may have lost importance in modern warfare, due to the advent of aircraft, though the terrain is still vital for camouflage, especially for guerrilla warfare. Generals and commanders also play an important role, Hannibal, Julius Caesar, Khalid ibn Walid, Subutai and Napoleon Bonaparte were all skilled generals and their armies were extremely successful at times. An army that can trust the commands of their leaders with conviction in its success invariably has a higher morale than an army that doubts its every move. The British in the naval Battle of Trafalgar owed its success to the reputation of Admiral Lord Nelson. Types. Battles can be fought on land, at sea, and in the air. Naval battles have occurred since before the 5th century BC. Air battles have been far less common, due to their late conception, the most prominent being the Battle of Britain in 1940. Since the Second World War, land or sea battles have come to rely on air support. During the Battle of Midway, five aircraft carriers were sunk without either fleet coming into direct contact.
Battles are usually hybrids of different types listed above. A "decisive battle" is one with political effects, determining the course of the war such as the Battle of Smolensk or bringing hostilities to an end, such as the Battle of Hastings or the Battle of Hattin. A decisive battle can change the balance of power or boundaries between countries. The concept of the "decisive battle" became popular with the publication in 1851 of Edward Creasy's "The Fifteen Decisive Battles of the World". British military historians J.F.C. Fuller ("The Decisive Battles of the Western World") and B.H. Liddell Hart ("Decisive Wars of History"), among many others, have written books in the style of Creasy's work. Land. There is an obvious difference in the way battles have been fought. Early battles were probably fought between rival hunting bands as unorganized crowds. During the Battle of Megiddo, the first reliably documented battle in the fifteenth century BC, both armies were organised and disciplined; during the many wars of the Roman Empire, barbarians continued to use mob tactics.
As the Age of Enlightenment dawned, armies began to fight in highly disciplined lines. Each would follow the orders from their officers and fight as a unit instead of individuals. Armies were divided into regiments, battalions, companies and platoons. These armies would march, line up and fire in divisions. Native Americans, on the other hand, did not fight in lines, using guerrilla tactics. American colonists and European forces continued using disciplined lines into the American Civil War. A new style arose from the 1850s to the First World War, known as trench warfare, which also led to tactical radio. Chemical warfare also began in 1915. By the Second World War, the use of the smaller divisions, platoons and companies became much more important as precise operations became vital. Instead of the trench stalemate of 1915–1917, in the Second World War, battles developed where small groups encountered other platoons. As a result, elite squads became much more recognized and distinguishable. Maneuver warfare also returned with an astonishing pace with the advent of the tank, replacing the cannon of the Enlightenment Age. Artillery has since gradually replaced the use of frontal troops. Modern battles resemble those of the Second World War, along with indirect combat through the use of aircraft and missiles which has come to constitute a large portion of wars in place of battles, where battles are now mostly reserved for capturing cities.
Naval. One significant difference of modern naval battles, as opposed to earlier forms of combat is the use of marines, which introduced amphibious warfare. Today, a marine is actually an infantry regiment that sometimes fights solely on land and is no longer tied to the navy. A good example of an ancient naval battle is the Battle of Salamis. Most ancient naval battles were fought by fast ships using the battering ram to sink opposing fleets or steer close enough for boarding in hand-to-hand combat. Troops were often used to storm enemy ships as used by Romans and pirates. This tactic was usually used by civilizations that could not beat the enemy with ranged weaponry. Another invention in the late Middle Ages was the use of Greek fire by the Byzantines, which was used to set enemy fleets on fire. Empty demolition ships utilized the tactic to crash into opposing ships and set it afire with an explosion. After the invention of cannons, naval warfare became useful as support units for land warfare. During the 19th century, the development of mines led to a new type of naval warfare. The ironclad, first used in the American Civil War, resistant to cannons, soon made the wooden ship obsolete. The invention of military submarines, during World War I, brought naval warfare to both above and below the surface. With the development of military aircraft during World War II, battles were fought in the sky as well as below the ocean. Aircraft carriers have since become the central unit in naval warfare, acting as a mobile base for lethal aircraft.
Aerial. Although the use of aircraft has for the most part always been used as a supplement to land or naval engagements, since their first major military use in World War I aircraft have increasingly taken on larger roles in warfare. During World War I, the primary use was for reconnaissance, and small-scale bombardment. Aircraft began becoming much more prominent in the Spanish Civil War and especially World War II. Aircraft design began specializing, primarily into two types: bombers, which carried explosive payloads to bomb land targets or ships; and fighter-interceptors, which were used to either intercept incoming aircraft or to escort and protect bombers (engagements between fighter aircraft were known as dog fights). Some of the more notable aerial battles in this period include the Battle of Britain and the Battle of Midway. Another important use of aircraft came with the development of the helicopter, which first became heavily used during the Vietnam War, and still continues to be widely used today to transport and augment ground forces. Today, direct engagements between aircraft are rare – the most modern fighter-interceptors carry much more extensive bombing payloads, and are used to bomb precision land targets, rather than to fight other aircraft. Anti-aircraft batteries are used much more extensively to defend against incoming aircraft than interceptors. Despite this, aircraft today are much more extensively used as the primary tools for both army and navy, as evidenced by the prominent use of helicopters to transport and support troops, the use of aerial bombardment as the "first strike" in many engagements, and the replacement of the battleship with the aircraft carrier as the center of most modern navies.
Naming. Battles are usually named after some feature of the battlefield geography, such as a town, forest or river, commonly prefixed "Battle of...". Occasionally battles are named after the date on which they took place, such as The Glorious First of June. In the Middle Ages it was considered important to settle on a suitable name for a battle which could be used by the chroniclers. After Henry V of England defeated a French army on October 25, 1415, he met with the senior French herald and they agreed to name the battle after the nearby castle and so it was called the Battle of Agincourt. In other cases, the sides adopted different names for the same battle, such as the Battle of Gallipoli which is known in Turkey as the Battle of Çanakkale. During the American Civil War, the Union tended to name the battles after the nearest watercourse, such as the Battle of Wilsons Creek and the Battle of Stones River, whereas the Confederates favoured the nearby towns, as in the Battles of Chancellorsville and Murfreesboro. Occasionally both names for the same battle entered the popular culture, such as the First Battle of Bull Run and the Second Battle of Bull Run, which are also referred to as the First and Second Battles of Manassas.
Sometimes in desert warfare, there is no nearby town name to use; map coordinates gave the name to the Battle of 73 Easting in the First Gulf War. Some place names have become synonymous with battles, such as the Passchendaele, Pearl Harbor, the Alamo, Thermopylae and Waterloo. Military operations, many of which result in battle, are given codenames, which are not necessarily meaningful or indicative of the type or the location of the battle. Operation Market Garden and Operation Rolling Thunder are examples of battles known by their military codenames. When a battleground is the site of more than one battle in the same conflict, the instances are distinguished by ordinal number, such as the First and Second Battles of Bull Run. An extreme case are the twelve Battles of the Isonzo—First to Twelfth—between Italy and Austria-Hungary during the First World War. Some battles are named for the convenience of military historians so that periods of combat can be neatly distinguished from one another. Following the First World War, the British Battles Nomenclature Committee was formed to decide on standard names for all battles and subsidiary actions. To the soldiers who did the fighting, the distinction was usually academic; a soldier fighting at Beaumont Hamel on November 13, 1916, was probably unaware he was taking part in what the committee named the Battle of the Ancre. Many combats are too small to be battles; terms such as "action", "affair", "skirmish", "firefight", "raid", or "offensive patrol" are used to describe small military encounters. These combats often take place within the time and space of a battle and while they may have an objective, they are not necessarily "decisive". Sometimes the soldiers are unable to immediately gauge the significance of the combat; in the aftermath of the Battle of Waterloo, some British officers were in doubt as to whether the day's events merited the title of "battle" or would be called an "action".
Effects. Battles affect the individuals who take part, as well as the political actors. Personal effects of battle range from mild psychological issues to permanent and crippling injuries. Some battle-survivors have nightmares about the conditions they encountered or abnormal reactions to certain sights or sounds and some experience flashbacks. Physical effects of battle can include scars, amputations, lesions, loss of bodily functions, blindness, paralysis and death. Battles affect politics; a decisive battle can cause the losing side to surrender, while a Pyrrhic victory such as the Battle of Asculum can cause the winning side to reconsider its goals. Battles in civil wars have often decided the fate of monarchs or political factions. Famous examples include the Wars of the Roses, as well as the Jacobite risings. Battles affect the commitment of one side or the other to the continuance of a war, for example the Battle of Inchon and the Battle of Huế during the Tet Offensive.
Berry Berenson Berinthia "Berry" Berenson-Perkins ( Berenson; April 14, 1948 – September 11, 2001) was an American actress, model and photographer. She was the widow of actor Anthony Perkins. She died in the September 11 attacks, being a passenger on American Airlines Flight 11. Early life. Berry Berenson was born in Murray Hill, Manhattan, New York City. Her mother was born Maria-Luisa Yvonne Radha de Wendt de Kerlor, better known as Gogo Schiaparelli, a socialite of Italian, Swiss, & French ancestry. Her father, Robert Lawrence Berenson, was an American career diplomat turned shipping executive. He was of Russian-Jewish and Polish-Jewish descent, and his family's original surname was Valvrojenski. Berenson's maternal grandmother was the Italian-born fashion designer Elsa Schiaparelli, and her maternal grandfather was Wilhelm de Wendt de Kerlor, a Theosophist and psychic medium. Her elder sister, Marisa Berenson, became a well-known model and actress. She also was a great-grandniece of Giovanni Schiaparelli, an Italian astronomer who believed he had discovered canals on Mars, and a second cousin, once removed, of art expert Bernard Berenson (1865–1959), and his sister Senda Berenson (1868–1954), an athlete and educator who was one of the first two women elected to the Basketball Hall of Fame.
Career. Following a brief modeling career in the late 1960s, Berenson became a freelance photographer. In 1972, Berenson's fiancé Richard Bernstein was hired as the cover artist for Andy Warhol's "Interview" magazine. Berenson would recruit models for the cover and photograph them, and Bernstein illustrated the images. By 1973, her photographs had been published in "Life", "Glamour", "Vogue" and "Newsweek". Berenson studied acting at New York's The American Place Theatre with Wynn Handman along with Richard Gere, Philip Anglim, Penelope Milford, Robert Ozn, Ingrid Boulting and her sister Marisa. As an actress, Berenson starred opposite her husband Anthony Perkins in the 1978 Alan Rudolph film "Remember My Name". She also appeared with Jeff Bridges in the 1979 film "Winter Kills", and with Malcolm McDowell in "Cat People" (1982). Personal life. Berenson was engaged to artist Richard Bernstein. In 1972, Berenson had an affair with actor Anthony Perkins and they married on August 9, 1973, in Wellfleet, Massachusetts while she was three months pregnant. The couple raised two sons: actor-director Oz Perkins and folk/rock singer-songwriter Elvis Perkins. Although Perkins was gay, they remained married until Perkins died from AIDS-related complications on September 12, 1992.
Death. Berenson died on September 11, 2001, a day before the ninth anniversary of Perkins’ death, as she was returning home to Los Angeles from a vacation on Cape Cod. She and the other passengers and crew aboard American Airlines Flight 11 died when the plane was hijacked and deliberately crashed into the North Tower of the World Trade Center during the September 11 attacks on the US. At the National September 11 Memorial & Museum, Berenson's name is inscribed on Panel N-76 at the North Pool.
Botany Botany, also called plant science, is the branch of natural science and biology studying plants, especially their anatomy, taxonomy, and ecology. A botanist or plant scientist is a scientist who specialises in this field. "Plant" and "botany" may be defined more narrowly to include only land plants and their study, which is also known as phytology. Nowadays, phytologists or botanists (in the strict sense) study approximately 410,000 species of land plants, including some 391,000 species of vascular plants (of which approximately 369,000 are flowering plants) and approximately 20,000 bryophytes. Botany originated in prehistory as herbalism with the efforts of early humans to identify – and later cultivate – plants that were edible, poisonous, and possibly medicinal, making it one of the first endeavours of human investigation. Medieval physic gardens, often attached to monasteries, contained plants possibly having medicinal benefit. They were forerunners of the first botanical gardens attached to universities, founded from the 1540s onwards. One of the earliest was the Padua botanical garden. These gardens facilitated the academic study of plants. Efforts to catalogue and describe their collections were the beginnings of plant taxonomy and led in 1753 to the binomial system of nomenclature of Carl Linnaeus that remains in use to this day for the naming of all biological species.
In the 19th and 20th centuries, new techniques were developed for the study of plants, including methods of optical microscopy and live cell imaging, electron microscopy, analysis of chromosome number, plant chemistry and the structure and function of enzymes and other proteins. In the last two decades of the 20th century, botanists exploited the techniques of molecular genetic analysis, including genomics and proteomics and DNA sequences to classify plants more accurately. Modern botany is a broad subject with contributions and insights from most other areas of science and technology. Research topics include the study of plant structure, growth and differentiation, reproduction, biochemistry and primary metabolism, chemical products, development, diseases, evolutionary relationships, systematics, and plant taxonomy. Dominant themes in 21st-century plant science are molecular genetics and epigenetics, which study the mechanisms and control of gene expression during differentiation of plant cells and tissues. Botanical research has diverse applications in providing staple foods, materials such as timber, oil, rubber, fibre and drugs, in modern horticulture, agriculture and forestry, plant propagation, breeding and genetic modification, in the synthesis of chemicals and raw materials for construction and energy production, in environmental management, and the maintenance of biodiversity.
Etymology. The term "botany" comes from the Ancient Greek word ' () meaning "pasture", "herbs" "grass", or "fodder"; ' is in turn derived from "" (Greek: ), "to feed" or "to graze". Traditionally, botany has also included the study of fungi and algae by mycologists and phycologists respectively, with the study of these three groups of organisms remaining within the sphere of interest of the International Botanical Congress. History. Early botany. Botany originated as herbalism, the study and use of plants for their possible medicinal properties. The early recorded history of botany includes many ancient writings and plant classifications. Examples of early botanical works have been found in ancient texts from India dating back to before 1100 BCE, Ancient Egypt, in archaic Avestan writings, and in works from China purportedly from before 221 BCE. Modern botany traces its roots back to Ancient Greece specifically to Theophrastus (–287 BCE), a student of Aristotle who invented and described many of its principles and is widely regarded in the scientific community as the "Father of Botany". His major works, "Enquiry into Plants" and "On the Causes of Plants", constitute the most important contributions to botanical science until the Middle Ages, almost seventeen centuries later.
Another work from Ancient Greece that made an early impact on botany is , a five-volume encyclopedia about preliminary herbal medicine written in the middle of the first century by Greek physician and pharmacologist Pedanius Dioscorides. was widely read for more than 1,500 years. Important contributions from the medieval Muslim world include Ibn Wahshiyya's "Nabatean Agriculture", Abū Ḥanīfa Dīnawarī's (828–896) the "Book of Plants", and Ibn Bassal's "The Classification of Soils". In the early 13th century, Abu al-Abbas al-Nabati, and Ibn al-Baitar (d. 1248) wrote on botany in a systematic and scientific manner. In the mid-16th century, botanical gardens were founded in a number of Italian universities. The Padua botanical garden in 1545 is usually considered to be the first which is still in its original location. These gardens continued the practical value of earlier "physic gardens", often associated with monasteries, in which plants were cultivated for suspected medicinal uses. They supported the growth of botany as an academic subject. Lectures were given about the plants grown in the gardens. Botanical gardens came much later to northern Europe; the first in England was the University of Oxford Botanic Garden in 1621.
German physician Leonhart Fuchs (1501–1566) was one of "the three German fathers of botany", along with theologian Otto Brunfels (1489–1534) and physician Hieronymus Bock (1498–1554) (also called Hieronymus Tragus). Fuchs and Brunfels broke away from the tradition of copying earlier works to make original observations of their own. Bock created his own system of plant classification. Physician Valerius Cordus (1515–1544) authored a botanically and pharmacologically important herbal "Historia Plantarum" in 1544 and a pharmacopoeia of lasting importance, the "Dispensatorium" in 1546. Naturalist Conrad von Gesner (1516–1565) and herbalist John Gerard (1545 – ) published herbals covering the supposed medicinal uses of plants. Naturalist Ulisse Aldrovandi (1522–1605) was considered the "father of natural history", which included the study of plants. In 1665, using an early microscope, Polymath Robert Hooke discovered cells (a term he coined) in cork, and a short time later in living plant tissue. Early modern botany.
During the 18th century, systems of plant identification were developed comparable to dichotomous keys, where unidentified plants are placed into taxonomic groups (e.g. family, genus and species) by making a series of choices between pairs of characters. The choice and sequence of the characters may be artificial in keys designed purely for identification (diagnostic keys) or more closely related to the natural or phyletic order of the taxa in synoptic keys. By the 18th century, new plants for study were arriving in Europe in increasing numbers from newly discovered countries and the European colonies worldwide. In 1753, Carl Linnaeus published his Species Plantarum, a hierarchical classification of plant species that remains the reference point for modern botanical nomenclature. This established a standardised binomial or two-part naming scheme where the first name represented the genus and the second identified the species within the genus. For the purposes of identification, Linnaeus's "Systema Sexuale" classified plants into 24 groups according to the number of their male sexual organs. The 24th group, "Cryptogamia", included all plants with concealed reproductive parts, mosses, liverworts, ferns, algae and fungi.
Increasing knowledge of plant anatomy, morphology and life cycles led to the realisation that there were more natural affinities between plants than the artificial sexual system of Linnaeus. Adanson (1763), de Jussieu (1789), and Candolle (1819) all proposed various alternative natural systems of classification that grouped plants using a wider range of shared characters and were widely followed. The Candollean system reflected his ideas of the progression of morphological complexity and the later Bentham & Hooker system, which was influential until the mid-19th century, was influenced by Candolle's approach. Darwin's publication of the "Origin of Species" in 1859 and his concept of common descent required modifications to the Candollean system to reflect evolutionary relationships as distinct from mere morphological similarity. In the 19th century botany was a socially acceptable hobby for upper-class women. These women would collect and paint flowers and plants from around the world with scientific accuracy. The paintings were used to record many species that could not be transported or maintained in other environments. Marianne North illustrated over 900 species in extreme detail with watercolor and oil paintings. Her work and many other women's botany work was the beginning of popularizing botany to a wider audience.
Botany was greatly stimulated by the appearance of the first "modern" textbook, Matthias Schleiden's "", published in English in 1849 as "Principles of Scientific Botany". Schleiden was a microscopist and an early plant anatomist who co-founded the cell theory with Theodor Schwann and Rudolf Virchow and was among the first to grasp the significance of the cell nucleus that had been described by Robert Brown in 1831. In 1855, Adolf Fick formulated Fick's laws that enabled the calculation of the rates of molecular diffusion in biological systems. Late modern botany. Building upon the gene-chromosome theory of heredity that originated with Gregor Mendel (1822–1884), August Weismann (1834–1914) proved that inheritance only takes place through gametes. No other cells can pass on inherited characters. The work of Katherine Esau (1898–1997) on plant anatomy is still a major foundation of modern botany. Her books "Plant Anatomy" and "Anatomy of Seed Plants" have been key plant structural biology texts for more than half a century.
The discipline of plant ecology was pioneered in the late 19th century by botanists such as Eugenius Warming, who produced the hypothesis that plants form communities, and his mentor and successor Christen C. Raunkiær whose system for describing plant life forms is still in use today. The concept that the composition of plant communities such as temperate broadleaf forest changes by a process of ecological succession was developed by Henry Chandler Cowles, Arthur Tansley and Frederic Clements. Clements is credited with the idea of climax vegetation as the most complex vegetation that an environment can support and Tansley introduced the concept of ecosystems to biology. Building on the extensive earlier work of Alphonse de Candolle, Nikolai Vavilov (1887–1943) produced accounts of the biogeography, centres of origin, and evolutionary history of economic plants.
Modern morphology recognises a continuum between the major morphological categories of root, stem (caulome), leaf (phyllome) and trichome. Furthermore, it emphasises structural dynamics. Modern systematics aims to reflect and discover phylogenetic relationships between plants. Modern molecular phylogenetics largely ignores morphological characters, relying on DNA sequences as data. Molecular analysis of DNA sequences from most families of flowering plants enabled the Angiosperm Phylogeny Group to publish in 1998 a phylogeny of flowering plants, answering many of the questions about relationships among angiosperm families and species. The theoretical possibility of a practical method for identification of plant species and commercial varieties by DNA barcoding is the subject of active current research. Branches of botany. Botany is divided along several axes. Some subfields of botany relate to particular groups of organisms. Divisions related to the broader historical sense of botany include "bacteriology", "mycology" (or "fungology"), and "phycology" – respectively, the study of bacteria, fungi, and algae – with "lichenology" as a subfield of mycology. The narrower sense of botany as the study of embryophytes (land plants) is called "phytology". "Bryology" is the study of mosses (and in the broader sense also liverworts and hornworts). "Pteridology" (or "filicology") is the study of ferns and allied plants. A number of other taxa of ranks varying from family to subgenus have terms for their study, including "agrostology" (or "graminology") for the study of grasses, "synantherology" for the study of composites, and "batology" for the study of brambles.
Study can also be divided by guild rather than clade or grade. For example, "dendrology" is the study of woody plants. Many divisions of biology have botanical subfields. These are commonly denoted by prefixing the word plant (e.g. plant taxonomy, plant ecology, plant anatomy, plant morphology, plant systematics), or prefixing or substituting the prefix phyto- (e.g. phytochemistry, phytogeography). The study of fossil plants is called "palaeobotany". Other fields are denoted by adding or substituting the word botany (e.g. systematic botany). "Phytosociology" is a subfield of plant ecology that classifies and studies communities of plants. The intersection of fields from the above pair of categories gives rise to fields such as "bryogeography", the study of the distribution of mosses. Different parts of plants also give rise to their own subfields, including "xylology", "carpology" (or "fructology"), and "palynology", these being the study of wood, fruit and pollen/spores respectively. Botany also overlaps on the one hand with agriculture, horticulture and silviculture, and on the other hand with medicine and pharmacology, giving rise to fields such as "agronomy", "horticultural botany", "phytopathology", and "phytopharmacology".
Scope and importance. The study of plants is vital because they underpin almost all animal life on Earth by generating a large proportion of the oxygen and food that provide humans and other organisms with aerobic respiration with the chemical energy they need to exist. Plants, algae and cyanobacteria are the major groups of organisms that carry out photosynthesis, a process that uses the energy of sunlight to convert water and carbon dioxide into sugars that can be used both as a source of chemical energy and of organic molecules that are used in the structural components of cells. As a by-product of photosynthesis, plants release oxygen into the atmosphere, a gas that is required by nearly all living things to carry out cellular respiration. In addition, they are influential in the global carbon and water cycles and plant roots bind and stabilise soils, preventing soil erosion. Plants are crucial to the future of human society as they provide food, oxygen, biochemicals, and products for people, as well as creating and preserving soil.
Historically, all living things were classified as either animals or plants and botany covered the study of all organisms not considered animals. Botanists examine both the internal functions and processes within plant organelles, cells, tissues, whole plants, plant populations and plant communities. At each of these levels, a botanist may be concerned with the classification (taxonomy), phylogeny and evolution, structure (anatomy and morphology), or function (physiology) of plant life. The strictest definition of "plant" includes only the "land plants" or embryophytes, which include seed plants (gymnosperms, including the pines, and flowering plants) and the free-sporing cryptogams including ferns, clubmosses, liverworts, hornworts and mosses. Embryophytes are multicellular eukaryotes descended from an ancestor that obtained its energy from sunlight by photosynthesis. They have life cycles with alternating haploid and diploid phases. The sexual haploid phase of embryophytes, known as the gametophyte, nurtures the developing diploid embryo sporophyte within its tissues for at least part of its life, even in the seed plants, where the gametophyte itself is nurtured by its parent sporophyte. Other groups of organisms that were previously studied by botanists include bacteria (now studied in bacteriology), fungi (mycology) – including lichen-forming fungi (lichenology), non-chlorophyte algae (phycology), and viruses (virology). However, attention is still given to these groups by botanists, and fungi (including lichens) and photosynthetic protists are usually covered in introductory botany courses.
Palaeobotanists study ancient plants in the fossil record to provide information about the evolutionary history of plants. Cyanobacteria, the first oxygen-releasing photosynthetic organisms on Earth, are thought to have given rise to the ancestor of plants by entering into an endosymbiotic relationship with an early eukaryote, ultimately becoming the chloroplasts in plant cells. The new photosynthetic plants (along with their algal relatives) accelerated the rise in atmospheric oxygen started by the cyanobacteria, changing the ancient oxygen-free, reducing, atmosphere to one in which free oxygen has been abundant for more than 2 billion years. Among the important botanical questions of the 21st century are the role of plants as primary producers in the global cycling of life's basic ingredients: energy, carbon, oxygen, nitrogen and water, and ways that our plant stewardship can help address the global environmental issues of resource management, conservation, human food security, biologically invasive organisms, carbon sequestration, climate change, and sustainability.
Human nutrition. Virtually all staple foods come either directly from primary production by plants, or indirectly from animals that eat them. Plants and other photosynthetic organisms are at the base of most food chains because they use the energy from the sun and nutrients from the soil and atmosphere, converting them into a form that can be used by animals. This is what ecologists call the first trophic level. The modern forms of the major staple foods, such as hemp, teff, maize, rice, wheat and other cereal grasses, pulses, bananas and plantains, as well as hemp, flax and cotton grown for their fibres, are the outcome of prehistoric selection over thousands of years from among wild ancestral plants with the most desirable characteristics. Botanists study how plants produce food and how to increase yields, for example through plant breeding, making their work important to humanity's ability to feed the world and provide food security for future generations. Botanists also study weeds, which are a considerable problem in agriculture, and the biology and control of plant pathogens in agriculture and natural ecosystems. Ethnobotany is the study of the relationships between plants and people. When applied to the investigation of historical plant–people relationships ethnobotany may be referred to as archaeobotany or palaeoethnobotany. Some of the earliest plant-people relationships arose between the indigenous people of Canada in identifying edible plants from inedible plants. This relationship the indigenous people had with plants was recorded by ethnobotanists.
Plant biochemistry. Plant biochemistry is the study of the chemical processes used by plants. Some of these processes are used in their primary metabolism like the photosynthetic Calvin cycle and crassulacean acid metabolism. Others make specialised materials like the cellulose and lignin used to build their bodies, and secondary products like resins and aroma compounds. Plants and various other groups of photosynthetic eukaryotes collectively known as "algae" have unique organelles known as chloroplasts. Chloroplasts are thought to be descended from cyanobacteria that formed endosymbiotic relationships with ancient plant and algal ancestors. Chloroplasts and cyanobacteria contain the blue-green pigment chlorophyll "a". Chlorophyll "a" (as well as its plant and green algal-specific cousin chlorophyll "b") absorbs light in the blue-violet and orange/red parts of the spectrum while reflecting and transmitting the green light that we see as the characteristic colour of these organisms. The energy in the red and blue light that these pigments absorb is used by chloroplasts to make energy-rich carbon compounds from carbon dioxide and water by oxygenic photosynthesis, a process that generates molecular oxygen (O2) as a by-product.
The light energy captured by chlorophyll "a" is initially in the form of electrons (and later a proton gradient) that is used to make molecules of ATP and NADPH which temporarily store and transport energy. Their energy is used in the light-independent reactions of the Calvin cycle by the enzyme rubisco to produce molecules of the 3-carbon sugar glyceraldehyde 3-phosphate (G3P). Glyceraldehyde 3-phosphate is the first product of photosynthesis and the raw material from which glucose and almost all other organic molecules of biological origin are synthesised. Some of the glucose is converted to starch which is stored in the chloroplast. Starch is the characteristic energy store of most land plants and algae, while inulin, a polymer of fructose is used for the same purpose in the sunflower family Asteraceae. Some of the glucose is converted to sucrose (common table sugar) for export to the rest of the plant. Unlike in animals (which lack chloroplasts), plants and their eukaryote relatives have delegated many biochemical roles to their chloroplasts, including synthesising all their fatty acids, and most amino acids. The fatty acids that chloroplasts make are used for many things, such as providing material to build cell membranes out of and making the polymer cutin which is found in the plant cuticle that protects land plants from drying out.
Plants synthesise a number of unique polymers like the polysaccharide molecules cellulose, pectin and xyloglucan from which the land plant cell wall is constructed. Vascular land plants make lignin, a polymer used to strengthen the secondary cell walls of xylem tracheids and vessels to keep them from collapsing when a plant sucks water through them under water stress. Lignin is also used in other cell types like sclerenchyma fibres that provide structural support for a plant and is a major constituent of wood. Sporopollenin is a chemically resistant polymer found in the outer cell walls of spores and pollen of land plants responsible for the survival of early land plant spores and the pollen of seed plants in the fossil record. It is widely regarded as a marker for the start of land plant evolution during the Ordovician period. The concentration of carbon dioxide in the atmosphere today is much lower than it was when plants emerged onto land during the Ordovician and Silurian periods. Many monocots like maize and the pineapple and some dicots like the Asteraceae have since independently evolved pathways like Crassulacean acid metabolism and the carbon fixation pathway for photosynthesis which avoid the losses resulting from photorespiration in the more common carbon fixation pathway. These biochemical strategies are unique to land plants.
Medicine and materials. Phytochemistry is a branch of plant biochemistry primarily concerned with the chemical substances produced by plants during secondary metabolism. Some of these compounds are toxins such as the alkaloid coniine from hemlock. Others, such as the essential oils peppermint oil and lemon oil are useful for their aroma, as flavourings and spices (e.g., capsaicin), and in medicine as pharmaceuticals as in opium from opium poppies. Many medicinal and recreational drugs, such as tetrahydrocannabinol (active ingredient in cannabis), caffeine, morphine and nicotine come directly from plants. Others are simple derivatives of botanical natural products. For example, the pain killer aspirin is the acetyl ester of salicylic acid, originally isolated from the bark of willow trees, and a wide range of opiate painkillers like heroin are obtained by chemical modification of morphine obtained from the opium poppy. Popular stimulants come from plants, such as caffeine from coffee, tea and chocolate, and nicotine from tobacco. Most alcoholic beverages come from fermentation of carbohydrate-rich plant products such as barley (beer), rice (sake) and grapes (wine). Native Americans have used various plants as ways of treating illness or disease for thousands of years. This knowledge Native Americans have on plants has been recorded by enthnobotanists and then in turn has been used by pharmaceutical companies as a way of drug discovery.
Plants can synthesise coloured dyes and pigments such as the anthocyanins responsible for the red colour of red wine, yellow weld and blue woad used together to produce Lincoln green, indoxyl, source of the blue dye indigo traditionally used to dye denim and the artist's pigments gamboge and rose madder. Sugar, starch, cotton, linen, hemp, some types of rope, wood and particle boards, papyrus and paper, vegetable oils, wax, and natural rubber are examples of commercially important materials made from plant tissues or their secondary products. Charcoal, a pure form of carbon made by pyrolysis of wood, has a long history as a metal-smelting fuel, as a filter material and adsorbent and as an artist's material and is one of the three ingredients of gunpowder. Cellulose, the world's most abundant organic polymer, can be converted into energy, fuels, materials and chemical feedstock. Products made from cellulose include rayon and cellophane, wallpaper paste, biobutanol and gun cotton. Sugarcane, rapeseed and soy are some of the plants with a highly fermentable sugar or oil content that are used as sources of biofuels, important alternatives to fossil fuels, such as biodiesel. Sweetgrass was used by Native Americans to ward off bugs like mosquitoes. These bug repelling properties of sweetgrass were later found by the American Chemical Society in the molecules phytol and coumarin.
Plant ecology. Plant ecology is the science of the functional relationships between plants and their habitats – the environments where they complete their life cycles. Plant ecologists study the composition of local and regional floras, their biodiversity, genetic diversity and fitness, the adaptation of plants to their environment, and their competitive or mutualistic interactions with other species. Some ecologists even rely on empirical data from indigenous people that is gathered by ethnobotanists. This information can relay a great deal of information on how the land once was thousands of years ago and how it has changed over that time. The goals of plant ecology are to understand the causes of their distribution patterns, productivity, environmental impact, evolution, and responses to environmental change. Plants depend on certain edaphic (soil) and climatic factors in their environment but can modify these factors too. For example, they can change their environment's albedo, increase runoff interception, stabilise mineral soils and develop their organic content, and affect local temperature. Plants compete with other organisms in their ecosystem for resources. They interact with their neighbours at a variety of spatial scales in groups, populations and communities that collectively constitute vegetation. Regions with characteristic vegetation types and dominant plants as well as similar abiotic and biotic factors, climate, and geography make up biomes like tundra or tropical rainforest.
Herbivores eat plants, but plants can defend themselves and some species are parasitic or even carnivorous. Other organisms form mutually beneficial relationships with plants. For example, mycorrhizal fungi and rhizobia provide plants with nutrients in exchange for food, ants are recruited by ant plants to provide protection, honey bees, bats and other animals pollinate flowers and humans and other animals act as dispersal vectors to spread spores and seeds. Plants, climate and environmental change. Plant responses to climate and other environmental changes can inform our understanding of how these changes affect ecosystem function and productivity. For example, plant phenology can be a useful proxy for temperature in historical climatology, and the biological impact of climate change and global warming. Palynology, the analysis of fossil pollen deposits in sediments from thousands or millions of years ago allows the reconstruction of past climates. Estimates of atmospheric concentrations since the Palaeozoic have been obtained from stomatal densities and the leaf shapes and sizes of ancient land plants. Ozone depletion can expose plants to higher levels of ultraviolet radiation-B (UV-B), resulting in lower growth rates. Moreover, information from studies of community ecology, plant systematics, and taxonomy is essential to understanding vegetation change, habitat destruction and species extinction.
Genetics. Inheritance in plants follows the same fundamental principles of genetics as in other multicellular organisms. Gregor Mendel discovered the genetic laws of inheritance by studying inherited traits such as shape in "Pisum sativum" (peas). What Mendel learned from studying plants has had far-reaching benefits outside of botany. Similarly, "jumping genes" were discovered by Barbara McClintock while she was studying maize. Nevertheless, there are some distinctive genetic differences between plants and other organisms. Species boundaries in plants may be weaker than in animals, and cross species hybrids are often possible. A familiar example is peppermint, "Mentha" × "piperita", a sterile hybrid between "Mentha aquatica" and spearmint, "Mentha spicata". The many cultivated varieties of wheat are the result of multiple inter- and intra-specific crosses between wild species and their hybrids. Angiosperms with monoecious flowers often have self-incompatibility mechanisms that operate between the pollen and stigma so that the pollen either fails to reach the stigma or fails to germinate and produce male gametes. This is one of several methods used by plants to promote outcrossing. In many land plants the male and female gametes are produced by separate individuals. These species are said to be dioecious when referring to vascular plant sporophytes and dioicous when referring to bryophyte gametophytes.
Charles Darwin in his 1878 book The Effects of Cross and Self-Fertilization in the Vegetable Kingdom at the start of chapter XII noted "The first and most important of the conclusions which may be drawn from the observations given in this volume, is that generally cross-fertilisation is beneficial and self-fertilisation often injurious, at least with the plants on which I experimented." An important adaptive benefit of outcrossing is that it allows the masking of deleterious mutations in the genome of progeny. This beneficial effect is also known as hybrid vigor or heterosis. Once outcrossing is established, subsequent switching to inbreeding becomes disadvantageous since it allows expression of the previously masked deleterious recessive mutations, commonly referred to as inbreeding depression. Unlike in higher animals, where parthenogenesis is rare, asexual reproduction may occur in plants by several different mechanisms. The formation of stem tubers in potato is one example. Particularly in arctic or alpine habitats, where opportunities for fertilisation of flowers by animals are rare, plantlets or bulbs, may develop instead of flowers, replacing sexual reproduction with asexual reproduction and giving rise to clonal populations genetically identical to the parent. This is one of several types of apomixis that occur in plants. Apomixis can also happen in a seed, producing a seed that contains an embryo genetically identical to the parent.
Most sexually reproducing organisms are diploid, with paired chromosomes, but doubling of their chromosome number may occur due to errors in cytokinesis. This can occur early in development to produce an autopolyploid or partly autopolyploid organism, or during normal processes of cellular differentiation to produce some cell types that are polyploid (endopolyploidy), or during gamete formation. An allopolyploid plant may result from a hybridisation event between two different species. Both autopolyploid and allopolyploid plants can often reproduce normally, but may be unable to cross-breed successfully with the parent population because there is a mismatch in chromosome numbers. These plants that are reproductively isolated from the parent species but live within the same geographical area, may be sufficiently successful to form a new species. Some otherwise sterile plant polyploids can still reproduce vegetatively or by seed apomixis, forming clonal populations of identical individuals. Durum wheat is a fertile tetraploid allopolyploid, while bread wheat is a fertile hexaploid. The commercial banana is an example of a sterile, seedless triploid hybrid. Common dandelion is a triploid that produces viable seeds by apomictic seed.
As in other eukaryotes, the inheritance of endosymbiotic organelles like mitochondria and chloroplasts in plants is non-Mendelian. Chloroplasts are inherited through the male parent in gymnosperms but often through the female parent in flowering plants. Molecular genetics. A considerable amount of new knowledge about plant function comes from studies of the molecular genetics of model plants such as the Thale cress, "Arabidopsis thaliana", a weedy species in the mustard family (Brassicaceae). The genome or hereditary information contained in the genes of this species is encoded by about 135 million base pairs of DNA, forming one of the smallest genomes among flowering plants. "Arabidopsis" was the first plant to have its genome sequenced, in 2000. The sequencing of some other relatively small genomes, of rice ("Oryza sativa") and "Brachypodium distachyon", has made them important model species for understanding the genetics, cellular and molecular biology of cereals, grasses and monocots generally. Model plants such as "Arabidopsis thaliana" are used for studying the molecular biology of plant cells and the chloroplast. Ideally, these organisms have small genomes that are well known or completely sequenced, small stature and short generation times. Corn has been used to study mechanisms of photosynthesis and phloem loading of sugar in plants. The single celled green alga "Chlamydomonas reinhardtii", while not an embryophyte itself, contains a green-pigmented chloroplast related to that of land plants, making it useful for study. A red alga "Cyanidioschyzon merolae" has also been used to study some basic chloroplast functions. Spinach, peas, soybeans and a moss "Physcomitrella patens" are commonly used to study plant cell biology.
"Agrobacterium tumefaciens", a soil rhizosphere bacterium, can attach to plant cells and infect them with a callus-inducing Ti plasmid by horizontal gene transfer, causing a callus infection called crown gall disease. Schell and Van Montagu (1977) hypothesised that the Ti plasmid could be a natural vector for introducing the Nif gene responsible for nitrogen fixation in the root nodules of legumes and other plant species. Today, genetic modification of the Ti plasmid is one of the main techniques for introduction of transgenes to plants and the creation of genetically modified crops. Epigenetics. Epigenetics is the study of heritable changes in gene function that cannot be explained by changes in the underlying DNA sequence but cause the organism's genes to behave (or "express themselves") differently. One example of epigenetic change is the marking of the genes by DNA methylation which determines whether they will be expressed or not. Gene expression can also be controlled by repressor proteins that attach to silencer regions of the DNA and prevent that region of the DNA code from being expressed. Epigenetic marks may be added or removed from the DNA during programmed stages of development of the plant, and are responsible, for example, for the differences between anthers, petals and normal leaves, despite the fact that they all have the same underlying genetic code. Epigenetic changes may be temporary or may remain through successive cell divisions for the remainder of the cell's life. Some epigenetic changes have been shown to be heritable, while others are reset in the germ cells.
Epigenetic changes in eukaryotic biology serve to regulate the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells. A single fertilised egg cell, the zygote, gives rise to the many different plant cell types including parenchyma, xylem vessel elements, phloem sieve tubes, guard cells of the epidermis, etc. as it continues to divide. The process results from the epigenetic activation of some genes and inhibition of others. Unlike animals, many plant cells, particularly those of the parenchyma, do not terminally differentiate, remaining totipotent with the ability to give rise to a new individual plant. Exceptions include highly lignified cells, the sclerenchyma and xylem which are dead at maturity, and the phloem sieve tubes which lack nuclei. While plants use many of the same epigenetic mechanisms as animals, such as chromatin remodelling, an alternative hypothesis is that plants set their gene expression patterns using positional information from the environment and surrounding cells to determine their developmental fate.
Epigenetic changes can lead to paramutations, which do not follow the Mendelian heritage rules. These epigenetic marks are carried from one generation to the next, with one allele inducing a change on the other. Plant evolution. The chloroplasts of plants have a number of biochemical, structural and genetic similarities to cyanobacteria, (commonly but incorrectly known as "blue-green algae") and are thought to be derived from an ancient endosymbiotic relationship between an ancestral eukaryotic cell and a . The algae are a polyphyletic group and are placed in various divisions, some more closely related to plants than others. There are many differences between them in features such as cell wall composition, biochemistry, pigmentation, chloroplast structure and nutrient reserves. The algal division Charophyta, sister to the green algal division Chlorophyta, is considered to contain the ancestor of true plants. The Charophyte class Charophyceae and the land plant sub-kingdom Embryophyta together form the monophyletic group or clade Streptophytina.
Nonvascular land plants are embryophytes that lack the vascular tissues xylem and phloem. They include mosses, liverworts and hornworts. Pteridophytic vascular plants with true xylem and phloem that reproduced by spores germinating into free-living gametophytes evolved during the Silurian period and diversified into several lineages during the late Silurian and early Devonian. Representatives of the lycopods have survived to the present day. By the end of the Devonian period, several groups, including the lycopods, sphenophylls and progymnosperms, had independently evolved "megaspory" – their spores were of two distinct sizes, larger megaspores and smaller microspores. Their reduced gametophytes developed from megaspores retained within the spore-producing organs (megasporangia) of the sporophyte, a condition known as endospory. Seeds consist of an endosporic megasporangium surrounded by one or two sheathing layers (integuments). The young sporophyte develops within the seed, which on germination splits to release it. The earliest known seed plants date from the latest Devonian Famennian stage. Following the evolution of the seed habit, seed plants diversified, giving rise to a number of now-extinct groups, including seed ferns, as well as the modern gymnosperms and angiosperms. Gymnosperms produce "naked seeds" not fully enclosed in an ovary; modern representatives include conifers, cycads, "Ginkgo", and Gnetales. Angiosperms produce seeds enclosed in a structure such as a carpel or an ovary. Ongoing research on the molecular phylogenetics of living plants appears to show that the angiosperms are a sister clade to the gymnosperms.
Plant physiology. Plant physiology encompasses all the internal chemical and physical activities of plants associated with life. Chemicals obtained from the air, soil and water form the basis of all plant metabolism. The energy of sunlight, captured by oxygenic photosynthesis and released by cellular respiration, is the basis of almost all life. Photoautotrophs, including all green plants, algae and cyanobacteria gather energy directly from sunlight by photosynthesis. Heterotrophs including all animals, all fungi, all completely parasitic plants, and non-photosynthetic bacteria take in organic molecules produced by photoautotrophs and respire them or use them in the construction of cells and tissues. Respiration is the oxidation of carbon compounds by breaking them down into simpler structures to release the energy they contain, essentially the opposite of photosynthesis. Molecules are moved within plants by transport processes that operate at a variety of spatial scales. Subcellular transport of ions, electrons and molecules such as water and enzymes occurs across cell membranes. Minerals and water are transported from roots to other parts of the plant in the transpiration stream. Diffusion, osmosis, and active transport and mass flow are all different ways transport can occur. Examples of elements that plants need to transport are nitrogen, phosphorus, potassium, calcium, magnesium, and sulfur. In vascular plants, these elements are extracted from the soil as soluble ions by the roots and transported throughout the plant in the xylem. Most of the elements required for plant nutrition come from the chemical breakdown of soil minerals. Sucrose produced by photosynthesis is transported from the leaves to other parts of the plant in the phloem and plant hormones are transported by a variety of processes.
Plant hormones. Plants are not passive, but respond to external signals such as light, touch, and injury by moving or growing towards or away from the stimulus, as appropriate. Tangible evidence of touch sensitivity is the almost instantaneous collapse of leaflets of "Mimosa pudica", the insect traps of Venus flytrap and bladderworts, and the pollinia of orchids. The hypothesis that plant growth and development is coordinated by plant hormones or plant growth regulators first emerged in the late 19th century. Darwin experimented on the movements of plant shoots and roots towards light and gravity, and concluded "It is hardly an exaggeration to say that the tip of the radicle . . acts like the brain of one of the lower animals . . directing the several movements". About the same time, the role of auxins (from the Greek , to grow) in control of plant growth was first outlined by the Dutch scientist Frits Went. The first known auxin, indole-3-acetic acid (IAA), which promotes cell growth, was only isolated from plants about 50 years later. This compound mediates the tropic responses of shoots and roots towards light and gravity. The finding in 1939 that plant callus could be maintained in culture containing IAA, followed by the observation in 1947 that it could be induced to form roots and shoots by controlling the concentration of growth hormones were key steps in the development of plant biotechnology and genetic modification.
Cytokinins are a class of plant hormones named for their control of cell division (especially cytokinesis). The natural cytokinin zeatin was discovered in corn, "Zea mays", and is a derivative of the purine adenine. Zeatin is produced in roots and transported to shoots in the xylem where it promotes cell division, bud development, and the greening of chloroplasts. The gibberelins, such as gibberelic acid are diterpenes synthesised from acetyl CoA via the mevalonate pathway. They are involved in the promotion of germination and dormancy-breaking in seeds, in regulation of plant height by controlling stem elongation and the control of flowering. Abscisic acid (ABA) occurs in all land plants except liverworts, and is synthesised from carotenoids in the chloroplasts and other plastids. It inhibits cell division, promotes seed maturation, and dormancy, and promotes stomatal closure. It was so named because it was originally thought to control abscission. Ethylene is a gaseous hormone that is produced in all higher plant tissues from methionine. It is now known to be the hormone that stimulates or regulates fruit ripening and abscission, and it, or the synthetic growth regulator ethephon which is rapidly metabolised to produce ethylene, are used on industrial scale to promote ripening of cotton, pineapples and other climacteric crops.
Another class of phytohormones is the jasmonates, first isolated from the oil of "Jasminum grandiflorum" which regulates wound responses in plants by unblocking the expression of genes required in the systemic acquired resistance response to pathogen attack. In addition to being the primary energy source for plants, light functions as a signalling device, providing information to the plant, such as how much sunlight the plant receives each day. This can result in adaptive changes in a process known as photomorphogenesis. Phytochromes are the photoreceptors in a plant that are sensitive to light. Plant anatomy and morphology. Plant anatomy is the study of the structure of plant cells and tissues, whereas plant morphology is the study of their external form. All plants are multicellular eukaryotes, their DNA stored in nuclei. The characteristic features of plant cells that distinguish them from those of animals and fungi include a primary cell wall composed of the polysaccharides cellulose, hemicellulose and pectin, larger vacuoles than in animal cells and the presence of plastids with unique photosynthetic and biosynthetic functions as in the chloroplasts. Other plastids contain storage products such as starch (amyloplasts) or lipids (elaioplasts). Uniquely, streptophyte cells and those of the green algal order Trentepohliales divide by construction of a phragmoplast as a template for building a cell plate late in cell division.
The bodies of vascular plants including clubmosses, ferns and seed plants (gymnosperms and angiosperms) generally have aerial and subterranean subsystems. The shoots consist of stems bearing green photosynthesising leaves and reproductive structures. The underground vascularised roots bear root hairs at their tips and generally lack chlorophyll. Non-vascular plants, the liverworts, hornworts and mosses do not produce ground-penetrating vascular roots and most of the plant participates in photosynthesis. The sporophyte generation is nonphotosynthetic in liverworts but may be able to contribute part of its energy needs by photosynthesis in mosses and hornworts. The root system and the shoot system are interdependent – the usually nonphotosynthetic root system depends on the shoot system for food, and the usually photosynthetic shoot system depends on water and minerals from the root system. Cells in each system are capable of creating cells of the other and producing adventitious shoots or roots. Stolons and tubers are examples of shoots that can grow roots. Roots that spread out close to the surface, such as those of willows, can produce shoots and ultimately new plants. In the event that one of the systems is lost, the other can often regrow it. In fact it is possible to grow an entire plant from a single leaf, as is the case with plants in "Streptocarpus" sect. "Saintpaulia", or even a single cell – which can dedifferentiate into a callus (a mass of unspecialised cells) that can grow into a new plant.
In vascular plants, the xylem and phloem are the conductive tissues that transport resources between shoots and roots. Roots are often adapted to store food such as sugars or starch, as in sugar beets and carrots. Stems mainly provide support to the leaves and reproductive structures, but can store water in succulent plants such as cacti, food as in potato tubers, or reproduce vegetatively as in the stolons of strawberry plants or in the process of layering. Leaves gather sunlight and carry out photosynthesis. Large, flat, flexible, green leaves are called foliage leaves. Gymnosperms, such as conifers, cycads, "Ginkgo", and gnetophytes are seed-producing plants with open seeds. Angiosperms are seed-producing plants that produce flowers and have enclosed seeds. Woody plants, such as azaleas and oaks, undergo a secondary growth phase resulting in two additional types of tissues: wood (secondary xylem) and bark (secondary phloem and cork). All gymnosperms and many angiosperms are woody plants. Some plants reproduce sexually, some asexually, and some via both means.
Although reference to major morphological categories such as root, stem, leaf, and trichome are useful, one has to keep in mind that these categories are linked through intermediate forms so that a continuum between the categories results. Furthermore, structures can be seen as processes, that is, process combinations. Systematic botany. Systematic botany is part of systematic biology, which is concerned with the range and diversity of organisms and their relationships, particularly as determined by their evolutionary history. It involves, or is related to, biological classification, scientific taxonomy and phylogenetics. Biological classification is the method by which botanists group organisms into categories such as genera or species. Biological classification is a form of scientific taxonomy. Modern taxonomy is rooted in the work of Carl Linnaeus, who grouped species according to shared physical characteristics. These groupings have since been revised to align better with the Darwinian principle of common descent – grouping organisms by ancestry rather than superficial characteristics. While scientists do not always agree on how to classify organisms, molecular phylogenetics, which uses DNA sequences as data, has driven many recent revisions along evolutionary lines and is likely to continue to do so. The dominant classification system is called Linnaean taxonomy. It includes ranks and binomial nomenclature. The nomenclature of botanical organisms is codified in the International Code of Nomenclature for algae, fungi, and plants (ICN) and administered by the International Botanical Congress.
Kingdom Plantae belongs to Domain Eukaryota and is broken down recursively until each species is separately classified. The order is: Kingdom; Phylum (or Division); Class; Order; Family; Genus (plural "genera"); Species. The scientific name of a plant represents its genus and its species within the genus, resulting in a single worldwide name for each organism. For example, the tiger lily is "Lilium columbianum". "Lilium" is the genus, and "columbianum" the specific epithet. The combination is the name of the species. When writing the scientific name of an organism, it is proper to capitalise the first letter in the genus and put all of the specific epithet in lowercase. Additionally, the entire term is ordinarily italicised (or underlined when italics are not available). The evolutionary relationships and heredity of a group of organisms is called its phylogeny. Phylogenetic studies attempt to discover phylogenies. The basic approach is to use similarities based on shared inheritance to determine relationships. As an example, species of "Pereskia" are trees or bushes with prominent leaves. They do not obviously resemble a typical leafless cactus such as an "Echinocactus". However, both "Pereskia" and "Echinocactus" have spines produced from areoles (highly specialised pad-like structures) suggesting that the two genera are indeed related.
Judging relationships based on shared characters requires care, since plants may resemble one another through convergent evolution in which characters have arisen independently. Some euphorbias have leafless, rounded bodies adapted to water conservation similar to those of globular cacti, but characters such as the structure of their flowers make it clear that the two groups are not closely related. The cladistic method takes a systematic approach to characters, distinguishing between those that carry no information about shared evolutionary history – such as those evolved separately in different groups (homoplasies) or those left over from ancestors (plesiomorphies) – and derived characters, which have been passed down from innovations in a shared ancestor (apomorphies). Only derived characters, such as the spine-producing areoles of cacti, provide evidence for descent from a common ancestor. The results of cladistic analyses are expressed as cladograms: tree-like diagrams showing the pattern of evolutionary branching and descent.
From the 1990s onwards, the predominant approach to constructing phylogenies for living plants has been molecular phylogenetics, which uses molecular characters, particularly DNA sequences, rather than morphological characters like the presence or absence of spines and areoles. The difference is that the genetic code itself is used to decide evolutionary relationships, instead of being used indirectly via the characters it gives rise to. Clive Stace describes this as having "direct access to the genetic basis of evolution." As a simple example, prior to the use of genetic evidence, fungi were thought either to be plants or to be more closely related to plants than animals. Genetic evidence suggests that the true evolutionary relationship of multicelled organisms is as shown in the cladogram below – fungi are more closely related to animals than to plants. In 1998, the Angiosperm Phylogeny Group published a phylogeny for flowering plants based on an analysis of DNA sequences from most families of flowering plants. As a result of this work, many questions, such as which families represent the earliest branches of angiosperms, have now been answered. Investigating how plant species are related to each other allows botanists to better understand the process of evolution in plants. Despite the study of model plants and increasing use of DNA evidence, there is ongoing work and discussion among taxonomists about how best to classify plants into various taxa. Technological developments such as computers and electron microscopes have greatly increased the level of detail studied and speed at which data can be analysed. Symbols. A few symbols are in current use in botany. A number of others are obsolete; for example, Linnaeus used planetary symbols (Mars) for biennial plants, (Jupiter) for herbaceous perennials and (Saturn) for woody perennials, based on the planets' orbital periods of 2, 12 and 30 years; and Willd used (Saturn) for neuter in addition to (Mercury) for hermaphroditic. The following symbols are still used:
Bacillus thuringiensis Bacillus thuringiensis (or Bt) is a gram-positive, soil-dwelling bacterium, the most commonly used biological pesticide worldwide. "B. thuringiensis" also occurs naturally in the gut of caterpillars of various types of moths and butterflies, as well on leaf surfaces, aquatic environments, animal feces, insect-rich environments, flour mills and grain-storage facilities. It has also been observed to parasitize moths such as "Cadra calidella"—in laboratory experiments working with "C. calidella", many of the moths were diseased due to this parasite. During sporulation, many Bt strains produce crystal proteins (proteinaceous inclusions), called delta endotoxins, that have insecticidal action. This has led to their use as insecticides, and more recently to genetically modified crops using Bt genes, such as Bt corn. Many crystal-producing Bt strains, though, do not have insecticidal properties. The subspecies "israelensis" is commonly used for control of mosquitoes and of fungus gnats. As a toxic mechanism, "cry" proteins bind to specific receptors on the membranes of mid-gut (epithelial) cells of the targeted pests, resulting in their rupture. Other organisms (including humans, other animals and non-targeted insects) that lack the appropriate receptors in their gut cannot be affected by the "cry" protein, and therefore are not affected by Bt.
Taxonomy and discovery. In 1902, "B. thuringiensis" was first discovered in silkworms by Japanese sericultural engineer . He named it "B. sotto", using the Japanese word , here referring to bacillary paralysis. In 1911, German microbiologist Ernst Berliner rediscovered it when he isolated it as the cause of a disease called "" in flour moth caterpillars in Thuringia (hence the specific name "thuringiensis", "Thuringian"). "B. sotto" would later be reassigned as "B. thuringiensis" var. "sotto". In 1976, Robert A. Zakharyan reported the presence of a plasmid in a strain of "B. thuringiensis" and suggested the plasmid's involvement in endospore and crystal formation. "B. thuringiensis" is closely related to "B. cereus", a soil bacterium, and "B. anthracis", the cause of anthrax; the three organisms differ mainly in their plasmids. Like other members of the genus, all three are capable of producing endospores. Species group placement. "B. thuringiensis" is placed in the "Bacillus cereus" group which is variously defined as: seven closely related species: "B. cereus" "sensu stricto" ("B. cereus"), "B. anthracis", "B. thuringiensis", "B. mycoides", "B. pseudomycoides", and "B. cytotoxicus"; or as six species in a "Bacillus cereus" sensu lato: "B. weihenstephanensis", "B. mycoides", "B. pseudomycoides", "B. cereus", "B. thuringiensis", and "B. anthracis". Within this grouping "B.t." is more closely related to "B.ce." It is more distantly related to "B.w.", "B.m.", "B.p.", and "B.cy."
Subspecies. There are several dozen recognized subspecies of "B. thuringiensis". Subspecies commonly used as insecticides include "B. thuringiensis" subspecies "kurstaki" (Btk), subspecies "israelensis" (Bti) and (Bta). Some Bti lineages are clonal. Genetics. Some strains are known to carry the same genes that produce enterotoxins in "B. cereus", and so it is possible that the entire "B. cereus" sensu lato group may have the potential to be enteropathogens. The proteins that "B. thuringiensis" is most known for are encoded by "cry" genes. In most strains of "B. thuringiensis", these genes are located on a plasmid (in other words "cry" is not a chromosomal gene in most strains). If these plasmids are lost it becomes indistinguishable from "B. cereus" as "B. thuringiensis" has no other species characteristics. Plasmid exchange has been observed both naturally and experimentally both within "B.t." and between "B.t." and two congeners, "B. cereus" and "B. mycoides". plcR is an indispensable transcription regulator of most virulence factors, its absence greatly reducing virulence and toxicity. Some strains do naturally complete their life cycle with an inactivated plcR. It is half of a two-gene operon along with the heptapeptide . papR is part of quorum sensing in "B. thuringiensis".
Various strains including "Btk" ATCC 33679 carry plasmids belonging to the wider pXO1-like family. (The pXO1 family being a "B. cereus"-common family with members of ≈330kb length. They differ from pXO1 by replacement of the pXO1 pathogenicity island.) The insect parasite "Btk" HD73 carries a pXO2-like plasmid (pBT9727) lacking the 35kb pathogenicity island of pXO2 itself, and in fact having no identifiable virulence factors. (The pXO2 family does not have replacement of the pathogenicity island, instead simply lacking that part of pXO2.) The genomes of the "B. cereus" group may contain two types of introns, dubbed group I and group II. "B.t" strains have variously 0–5 group Is and 0–13 group IIs. There is still insufficient information to determine whether chromosome-plasmid coevolution to enable adaptation to particular environmental niches has occurred or is even possible. Common with "B. cereus" but so far not found elsewhere – including in other members of the species group – are the efflux pump BC3663, the "N"-acyl--amino-acid amidohydrolase BC3664, and the methyl-accepting chemotaxis protein BC5034.
Proteome. It has a similar proteome diversity to its close relative "B. cereus". Into the BT Cotton protein is 'Crystal protein'. Mechanism of insecticidal action. Upon sporulation, "B. thuringiensis" forms crystals of two types of proteinaceous insecticidal delta endotoxins (δ-endotoxins) called crystal proteins or Cry proteins, which are encoded by "cry" genes, and Cyt proteins. Cry toxins have specific activities against insect species of the orders Lepidoptera (moths and butterflies), Diptera (flies and mosquitoes), Coleoptera (beetles) and Hymenoptera (wasps, bees, ants and sawflies), as well as against nematodes. A specific example of "B. thuringiensis" use against beetles is the fight against Colorado Potato Beetles in potato crops. Thus, "B. thuringiensis" serves as an important reservoir of Cry toxins for production of biological insecticides and insect-resistant genetically modified crops. When insects ingest toxin crystals, their alkaline digestive tracts denature the insoluble crystals, making them soluble and thus amenable to being cut with proteases found in the insect gut, which liberate the toxin from the crystal. The Cry toxin is then inserted into the insect gut cell membrane, paralyzing the digestive tract and forming a pore. The insect stops eating and starves to death; live Bt bacteria may also colonize the insect, which can contribute to death. Death occurs within a few hours or weeks. The midgut bacteria of susceptible larvae may be required for "B. thuringiensis" insecticidal activity.
A "B. thuringiensis" small RNA called BtsR1 can silence the Cry5Ba toxin expression when outside the host by binding to the RBS site of the Cry5Ba toxin transcript to avoid nematode behavioral defenses. The silencing results in an increase of the bacteria ingestion by "C. elegans". The expression of BtsR1 is then reduced after ingestion, resulting in Cry5Ba toxin production and host death. In 1996 another class of insecticidal proteins in Bt was discovered: the vegetative insecticidal proteins (Vip; ). Vip proteins do not share sequence homology with Cry proteins, in general do not compete for the same receptors, and some kill different insects than do Cry proteins. In 2000, a novel subgroup of Cry protein, designated parasporin, was discovered from non-insecticidal "B. thuringiensis" isolates. The proteins of parasporin group are defined as "B. thuringiensis" and related bacterial parasporal proteins that are not hemolytic, but capable of preferentially killing cancer cells. As of January 2013, parasporins comprise six subfamilies: PS1 to PS6.
Use of spores and proteins in pest control. Spores and crystalline insecticidal proteins produced by "B. thuringiensis" have been used to control insect pests since the 1920s and are often applied as liquid sprays. They are now used as specific insecticides under trade names such as DiPel and Thuricide. Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators, and most other beneficial insects, and are used in organic farming; however, the manuals for these products do contain many environmental and human health warnings, and a 2012 European regulatory peer review of five approved strains found, while data exist to support some claims of low toxicity to humans and the environment, the data are insufficient to justify many of these claims. New strains of Bt are developed and introduced over time as insects develop resistance to Bt, or the desire occurs to force mutations to modify organism characteristics, or to use homologous recombinant genetic engineering to improve crystal size and increase pesticidal activity, or broaden the host range of Bt and obtain more effective formulations. Each new strain is given a unique number and registered with the U.S. EPA and allowances may be given for genetic modification depending on "its parental strains, the proposed pesticide use pattern, and the manner and extent to which the organism has been genetically modified". Formulations of Bt that are approved for organic farming in the US are listed at the website of the Organic Materials Review Institute (OMRI) and several university extension websites offer advice on how to use Bt spore or protein preparations in organic farming.
Use of Bt genes in genetic engineering of plants for pest control. The Belgian company Plant Genetic Systems (now part of Bayer CropScience) was the first company (in 1985) to develop genetically modified crops (tobacco) with insect tolerance by expressing "cry" genes from "B. thuringiensis"; the resulting crops contain delta endotoxin. The Bt tobacco was never commercialized; tobacco plants are used to test genetic modifications since they are easy to manipulate genetically and are not part of the food supply. Usage. In 1995, were approved safe by the Environmental Protection Agency, making it the first human-modified pesticide-producing crop to be approved in the US, though many plants produce pesticides naturally, including tobacco, coffee plants, cocoa, cotton and black walnut. This was the 'New Leaf' potato, and it was removed from the market in 2001 due to lack of interest. In 1996, was approved, which killed the European corn borer and related species; subsequent Bt genes were introduced that killed corn rootworm larvae.
The Bt genes engineered into crops and approved for release include, singly and stacked: Cry1A.105, CryIAb, CryIF, Cry2Ab, Cry3Bb1, Cry34Ab1, Cry35Ab1, mCry3A, and VIP, and the engineered crops include corn and cotton. Corn genetically modified to produce VIP was first approved in the US in 2010. In India, by 2014, more than seven million cotton farmers, occupying twenty-six million acres, had adopted . Monsanto developed a and the glyphosate-resistance gene for the Brazilian market, which completed the Brazilian regulatory process in 2010. - specifically "Populus" hybrids - have been developed. They do suffer lesser leaf damage from insect herbivory. The results have not been entirely positive however: The intended result - better timber yield - was not achieved, with no growth advantage despite that reduction in herbivore damage; one of their major pests still preys upon the transgenic trees; and besides that, their leaf litter decomposes differently due to the transgenic toxins, resulting in alterations to the aquatic insect populations nearby.
Safety studies. The use of Bt toxins as plant-incorporated protectants prompted the need for extensive evaluation of their safety for use in foods and potential unintended impacts on the environment. Dietary risk assessment. Concerns over the safety of consumption of genetically modified plant materials that contain Cry proteins have been addressed in extensive dietary risk assessment studies. As a toxic mechanism, "cry" proteins bind to specific receptors on the membranes of mid-gut (epithelial) cells of the targeted pests, resulting in their rupture. While the target pests are exposed to the toxins primarily through leaf and stalk material, Cry proteins are also expressed in other parts of the plant, including trace amounts in maize kernels which are ultimately consumed by both humans and animals. However, other organisms (including humans, other animals and non-targeted insects) that lack the appropriate receptors in their gut cannot be affected by the "cry" protein, and therefore are not affected by Bt. Toxicology studies.
Animal models have been used to assess human health risk from consumption of products containing Cry proteins. The United States Environmental Protection Agency recognizes mouse acute oral feeding studies where doses as high as 5,000 mg/kg body weight resulted in no observed adverse effects. Research on other known toxic proteins suggests that , further suggesting that Bt toxins are not toxic to mammals. The results of toxicology studies are further strengthened by the lack of observed toxicity from decades of use of "B. thuringiensis" and its crystalline proteins as an insecticidal spray. Allergenicity studies. Introduction of a new protein raised concerns regarding the potential for allergic responses in sensitive individuals. Bioinformatic analysis of known allergens has indicated there is no concern of allergic reactions as a result of consumption of Bt toxins. Additionally, skin prick testing using purified Bt protein resulted in no detectable production of toxin-specific IgE antibodies, even in atopic patients.
Digestibility studies. Studies have been conducted to evaluate the fate of Bt toxins that are ingested in foods. Bt toxin proteins have been shown to digest within minutes of exposure to simulated gastric fluids. The instability of the proteins in digestive fluids is an additional indication that Cry proteins are unlikely to be allergenic, since most known food allergens resist degradation and are ultimately absorbed in the small intestine. Persistence in environment. Concerns over possible environmental impact from accumulation of Bt toxins from plant tissues, pollen dispersal, and direct secretion from roots have been investigated. Bt toxins may persist in soil for over 200 days, with half-lives between 1.6 and 22 days. Much of the toxin is initially degraded rapidly by microorganisms in the environment, while some is adsorbed by organic matter and persists longer. Some studies, in contrast, claim that the toxins do not persist in the soil. Bt toxins are less likely to accumulate in bodies of water, but pollen shed or soil runoff may deposit them in an aquatic ecosystem. Fish species are not susceptible to Bt toxins if exposed.
Impact on non-target organisms. The toxic nature of Bt proteins has an adverse impact on many major crop pests, but some ecological risk assessments has been conducted to ensure safety of beneficial non-target organisms that may come into contact with the toxins. Toxicity for the monarch butterfly, has been shown to not reach dangerous levels. Most soil-dwelling organisms, potentially exposed to Bt toxins through root exudates, are probably not impacted by the growth of Bt crops. Insect resistance. Multiple insects have developed a resistance to "B. thuringiensis". In November 2009, Monsanto scientists found the pink bollworm had become resistant to the first-generation Bt cotton in parts of Gujarat, India - that generation expresses one Bt gene, "Cry1Ac". This was the first instance of Bt resistance confirmed by Monsanto anywhere in the world. Monsanto responded by introducing a second-generation cotton with multiple Bt proteins, which was rapidly adopted. Bollworm resistance to first-generation Bt cotton was also identified in Australia, China, Spain, and the United States. Additionally, resistance to Bt was documented in field population of diamondback moth in Hawaii, the continental US, and Asia. Studies in the cabbage looper have suggested that a mutation in the membrane transporter ABCC2 can confer resistance to Bt "Cry1Ac".
Secondary pests. Several studies have documented surges in "sucking pests" (which are not affected by Bt toxins) within a few years of adoption of Bt cotton. In China, the main problem has been with mirids, which have in some cases "completely eroded all benefits from Bt cotton cultivation". The increase in sucking pests depended on local temperature and rainfall conditions and increased in half the villages studied. The increase in insecticide use for the control of these secondary insects was far smaller than the reduction in total insecticide use due to Bt cotton adoption. Another study in five provinces in China found the reduction in pesticide use in Bt cotton cultivars is significantly lower than that reported in research elsewhere, consistent with the hypothesis suggested by recent studies that more pesticide sprayings are needed over time to control emerging secondary pests, such as aphids, spider mites, and lygus bugs. Similar problems have been reported in India, with both mealy bugs and aphids although a survey of small Indian farms between 2002 and 2008 concluded Bt cotton adoption has led to higher yields and lower pesticide use, decreasing over time.
Controversies. The controversies surrounding Bt use are among the many genetically modified food controversies more widely. Lepidopteran toxicity. The most publicised problem associated with Bt crops is the claim that pollen from Bt maize could kill the monarch butterfly. The paper produced a public uproar and demonstrations against Bt maize; however by 2001 several follow-up studies coordinated by the USDA had asserted that "the most common types of Bt maize pollen are not toxic to monarch larvae in concentrations the insects would encounter in the fields." Similarly, "B. thuringiensis" has been widely used for controlling "Spodoptera littoralis" larvae growth due to their detrimental pest activities in Africa and Southern Europe. However, "S. littoralis" showed resistance to many strains of "B. thuriginesis" and were only effectively controlled by a few strains. Wild maize genetic mixing. A study published in "Nature" in 2001 reported Bt-containing maize genes were found in maize in its center of origin, Oaxaca, Mexico. Another "Nature" paper published in 2002 claimed that the previous paper's conclusion was the result of an artifact caused by an inverse polymerase chain reaction and that "the evidence available is not sufficient to justify the publication of the original paper." A significant controversy happened over the paper and "Nature"s unprecedented notice.
A subsequent large-scale study in 2005 failed to find any evidence of genetic mixing in Oaxaca. A 2007 study found the "transgenic proteins expressed in maize were found in two (0.96%) of 208 samples from farmers' fields, located in two (8%) of 25 sampled communities." Mexico imports a substantial amount of maize from the U.S., and due to formal and informal seed networks among rural farmers, many potential routes are available for transgenic maize to enter into food and feed webs. One study found small-scale (about 1%) introduction of transgenic sequences in sampled fields in Mexico; it did not find evidence for or against this introduced genetic material being inherited by the next generation of plants. That study was immediately criticized, with the reviewer writing, "Genetically, any given plant should be either non-transgenic or transgenic, therefore for leaf tissue of a single transgenic plant, a GMO level close to 100% is expected. In their study, the authors chose to classify leaf samples as transgenic despite GMO levels of about 0.1%. We contend that results such as these are incorrectly interpreted as positive and are more likely to be indicative of contamination in the laboratory."
Colony collapse disorder. As of 2007, a new phenomenon called colony collapse disorder (CCD) began affecting bee hives all over North America. Initial speculation on possible causes included new parasites, pesticide use, and the use of Bt transgenic crops. The Mid-Atlantic Apiculture Research and Extension Consortium found no evidence that pollen from Bt crops is adversely affecting bees. According to the USDA, "Genetically modified (GM) crops, most commonly Bt corn, have been offered up as the cause of CCD. But there is no correlation between where GM crops are planted and the pattern of CCD incidents. Also, GM crops have been widely planted since the late 1990s, but CCD did not appear until 2006. In addition, CCD has been reported in countries that do not allow GM crops to be planted, such as Switzerland. German researchers have noted in one study a possible correlation between exposure to Bt pollen and compromised immunity to "Nosema"." The actual cause of CCD was unknown in 2007, and scientists believe it may have multiple exacerbating causes.
Beta-exotoxins. Some isolates of "B. thuringiensis" produce a class of insecticidal small molecules called beta-exotoxin, the common name for which is thuringiensin. A consensus document produced by the OECD says: "Beta-exotoxins are known to be toxic to humans and almost all other forms of life and its presence is prohibited in "B. thuringiensis" microbial products". Thuringiensins are nucleoside analogues. They inhibit RNA polymerase activity, a process common to all forms of life, in rats and bacteria alike. Other hosts. This bacterium is an opportunistic pathogen of animals other than insects, causing necrosis, pulmonary infection, and/or food poisoning. It is unknown how common this is, because these infections are always taken to be "B. cereus" infections and are rarely tested for the "Cry" and "Cyt" proteins that are the only factor distinguishing "B. thuringiensis" from "B. cereus". New nomenclature for pesticidal proteins (Bt toxins). "Bacillus thuringiensis" is no longer the sole source of pesticidal proteins. The Bacterial Pesticidal Protein Resource Center (BPPRC) provides information on the rapidly expanding field of pesticidal proteins for academics, regulators, and research and development personnel.
Bacteriophage A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria and archaea. The term is derived . Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes (e.g. MS2) and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere. Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 1031 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined. Viruses are the most abundant biological entity in the water column of the world's oceans, and the second largest component of biomass after prokaryotes, where up to 9x108 virions per millilitre have been found in microbial mats at the surface, and up to 70% of marine bacteria may be infected by bacteriophages.
Bacteriophages were used from the 1920s as an alternative to antibiotics in the former Soviet Union and Central Europe, as well as in France and Brazil. They are seen as a possible therapy against multi-drug-resistant strains of many bacteria (see phage therapy). Bacteriophages are known to interact with the immune system both indirectly via bacterial expression of phage-encoded proteins and directly by influencing innate immunity and bacterial clearance. Phage–host interactions are becoming increasingly important areas of research. Classification. Bacteriophages occur abundantly in the biosphere, with different genomes and lifestyles. Phages are classified by the International Committee on Taxonomy of Viruses (ICTV) according to morphology and nucleic acid. It has been suggested that members of "Picobirnaviridae" infect bacteria, but not mammals. There are also many unassigned genera of the class "Leviviricetes": "Chimpavirus", "Hohglivirus", "Mahrahvirus", "Meihzavirus", "Nicedsevirus", "Sculuvirus", "Skrubnovirus", "Tetipavirus" and "Winunavirus" containing linear ssRNA genomes and the unassigned genus "Lilyvirus" of the order "Caudovirales" containing a linear dsDNA genome.
History. In 1896, Ernest Hanbury Hankin reported that something in the waters of the Ganges and Yamuna rivers in India had a marked antibacterial action against cholera and it could pass through a very fine porcelain filter. In 1915, British bacteriologist Frederick Twort, superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria. He believed the agent must be one of the following: Twort's research was interrupted by the onset of World War I, as well as a shortage of funding and the discoveries of antibiotics. Independently, French-Canadian microbiologist Félix d'Hérelle, working at the Pasteur Institute in Paris, announced on 3 September 1917 that he had discovered "an invisible, antagonistic microbe of the dysentery bacillus". For d'Hérelle, there was no question as to the nature of his discovery: "In a flash I had understood: what caused my clear spots was in fact an invisible microbe... a virus parasitic on bacteria." D'Hérelle called the virus a bacteriophage, a bacterium-eater (from the Greek "", meaning "to devour"). He also recorded a dramatic account of a man suffering from dysentery who was restored to good health by the bacteriophages. It was d'Hérelle who conducted much research into bacteriophages and introduced the concept of phage therapy. In 1919, in Paris, France, d'Hérelle conducted the first clinical application of a bacteriophage, with the first reported use in the United States being in 1922.
Nobel prizes awarded for phage research. In 1969, Max Delbrück, Alfred Hershey, and Salvador Luria were awarded the Nobel Prize in Physiology or Medicine for their discoveries of the replication of viruses and their genetic structure. Specifically the work of Hershey, as contributor to the Hershey–Chase experiment in 1952, provided convincing evidence that DNA, not protein, was the genetic material of life. Delbrück and Luria carried out the Luria–Delbrück experiment which demonstrated statistically that mutations in bacteria occur randomly and thus follow Darwinian rather than Lamarckian principles. Uses. Phage therapy. Phages were discovered to be antibacterial agents and were used in the former Soviet Republic of Georgia (pioneered there by Giorgi Eliava with help from the co-discoverer of bacteriophages, Félix d'Hérelle) during the 1920s and 1930s for treating bacterial infections. D'Herelle "quickly learned that bacteriophages are found wherever bacteria thrive: in sewers, in rivers that catch waste runoff from pipes, and in the stools of convalescent patients."
They had widespread use, including treatment of soldiers in the Red Army. However, they were abandoned for general use in the West for several reasons: The use of phages has continued since the end of the Cold War in Russia, Georgia, and elsewhere in Central and Eastern Europe. The first regulated, randomized, double-blind clinical trial was reported in the "Journal of Wound Care" in June 2009, which evaluated the safety and efficacy of a bacteriophage cocktail to treat infected venous ulcers of the leg in human patients. The FDA approved the study as a Phase I clinical trial. The study's results demonstrated the safety of therapeutic application of bacteriophages, but did not show efficacy. The authors explained that the use of certain chemicals that are part of standard wound care (e.g. lactoferrin or silver) may have interfered with bacteriophage viability. Shortly after that, another controlled clinical trial in Western Europe (treatment of ear infections caused by "Pseudomonas aeruginosa") was reported in the journal "Clinical Otolaryngology" in August 2009. The study concludes that bacteriophage preparations were safe and effective for treatment of chronic ear infections in humans. Additionally, there have been numerous animal and other experimental clinical trials evaluating the efficacy of bacteriophages for various diseases, such as infected burns and wounds, and cystic fibrosis-associated lung infections, among others. On the other hand, phages of "Inoviridae" have been shown to complicate biofilms involved in pneumonia and cystic fibrosis and to shelter the bacteria from drugs meant to eradicate disease, thus promoting persistent infection.
Meanwhile, bacteriophage researchers have been developing engineered viruses to overcome antibiotic resistance, and engineering the phage genes responsible for coding enzymes that degrade the biofilm matrix, phage structural proteins, and the enzymes responsible for lysis of the bacterial cell wall. There have been results showing that T4 phages that are small in size and short-tailed can be helpful in detecting "E. coli" in the human body. Therapeutic efficacy of a phage cocktail was evaluated in a mouse model with nasal infection of multi-drug-resistant (MDR) "A. baumannii". Mice treated with the phage cocktail showed a 2.3-fold higher survival rate compared to those untreated at seven days post-infection. In 2017, a 68-year-old diabetic patient with necrotizing pancreatitis complicated by a pseudocyst infected with MDR "A. baumannii" strains was being treated with a cocktail of Azithromycin, Rifampicin, and Colistin for 4 months without results and overall rapidly declining health. Because discussion had begun of the clinical futility of further treatment, an Emergency Investigational New Drug (eIND) was filed as a last effort to at the very least gain valuable medical data from the situation, and approved, so he was subjected to phage therapy using a percutaneously (PC) injected cocktail containing nine different phages that had been identified as effective against the primary infection strain by rapid isolation and testing techniques (a process which took under a day). This proved effective for a very brief period, although the patient remained unresponsive and his health continued to worsen; soon isolates of a strain of "A. baumannii" were being collected from drainage of the cyst that showed resistance to this cocktail, and a second cocktail which was tested to be effective against this new strain was added, this time by intravenous (IV) injection as it had become clear that the infection was more pervasive than originally thought.
Once on the combination of the IV and PC therapy the patient's downward clinical trajectory reversed, and within two days he had awoken from his coma and become responsive. As his immune system began to function he had to be temporarily removed from the cocktail because his fever was spiking to over , but after two days the phage cocktails were re-introduced at levels he was able to tolerate. The original three-antibiotic cocktail was replaced by minocycline after the bacterial strain was found not to be resistant to this and he rapidly regained full lucidity, although he was not discharged from the hospital until roughly 145 days after phage therapy began. Towards the end of the therapy it was discovered that the bacteria had become resistant to both of the original phage cocktails, but they were continued because they seemed to be preventing minocycline resistance from developing in the bacterial samples collected so were having a useful synergistic effect. Other. Food industry. Phages have increasingly been used to safen food products and to forestall spoilage bacteria. Since 2006, the United States Food and Drug Administration (FDA) and United States Department of Agriculture (USDA) have approved several bacteriophage products. LMP-102 (Intralytix) was approved for treating ready-to-eat (RTE) poultry and meat products. In that same year, the FDA approved LISTEX (developed and produced by Micreos) using bacteriophages on cheese to kill "Listeria monocytogenes" bacteria, in order to give them generally recognized as safe (GRAS) status. In July 2007, the same bacteriophage were approved for use on all food products. In 2011 USDA confirmed that LISTEX is a clean label processing aid and is included in USDA. Research in the field of food safety is continuing to see if lytic phages are a viable option to control other food-borne pathogens in various food products.
Water indicators. Bacteriophages, including those specific to "Escherichia coli", have been employed as indicators of fecal contamination in water sources. Due to their shared structural and biological characteristics, coliphages can serve as proxies for viral fecal contamination and the presence of pathogenic viruses such as rotavirus, norovirus, and HAV. Research conducted on wastewater treatment systems has revealed significant disparities in the behavior of coliphages compared to fecal coliforms, demonstrating a distinct correlation with the recovery of pathogenic viruses at the treatment's conclusion. Establishing a secure discharge threshold, studies have determined that discharges below 3000 PFU/100 mL are considered safe in terms of limiting the release of pathogenic viruses. Diagnostics. In 2011, the FDA cleared the first bacteriophage-based product for in vitro diagnostic use. The KeyPath MRSA/MSSA Blood Culture Test uses a cocktail of bacteriophage to detect "Staphylococcus aureus" in positive blood cultures and determine methicillin resistance or susceptibility. The test returns results in about five hours, compared to two to three days for standard microbial identification and susceptibility test methods. It was the first accelerated antibiotic-susceptibility test approved by the FDA.
Counteracting bioweapons and toxins. Government agencies in the West have for several years been looking to Georgia and the former Soviet Union for help with exploiting phages for counteracting bioweapons and toxins, such as anthrax and botulism. Developments are continuing among research groups in the U.S. Other uses include spray application in horticulture for protecting plants and vegetable produce from decay and the spread of bacterial disease. Other applications for bacteriophages are as biocides for environmental surfaces, e.g., in hospitals, and as preventative treatments for catheters and medical devices before use in clinical settings. The technology for phages to be applied to dry surfaces, e.g., uniforms, curtains, or even sutures for surgery now exists. Clinical trials reported in "Clinical Otolaryngology" show success in veterinary treatment of pet dogs with otitis. Bacterium sensing and identification. The sensing of phage-triggered ion cascades (SEPTIC) bacterium sensing and identification method uses the ion emission and its dynamics during phage infection and offers high specificity and speed for detection.
Phage display. Phage display is a different use of phages involving a library of phages with a variable peptide linked to a surface protein. Each phage genome encodes the variant of the protein displayed on its surface (hence the name), providing a link between the peptide variant and its encoding gene. Variant phages from the library may be selected through their binding affinity to an immobilized molecule (e.g., botulism toxin) to neutralize it. The bound, selected phages can be multiplied by reinfecting a susceptible bacterial strain, thus allowing them to retrieve the peptides encoded in them for further study. Antimicrobial drug discovery. Phage proteins often have antimicrobial activity and may serve as leads for peptidomimetics, i.e. drugs that mimic peptides. Phage-ligand technology makes use of phage proteins for various applications, such as binding of bacteria and bacterial components (e.g. endotoxin) and lysis of bacteria. Basic research. Bacteriophages are important model organisms for studying principles of evolution and ecology.
Detriments. Dairy industry. Bacteriophages present in the environment can cause cheese to not ferment. In order to avoid this, mixed-strain starter cultures and culture rotation regimes can be used. Genetic engineering of culture microbes – especially "Lactococcus lactis" and "Streptococcus thermophilus" – have been studied for genetic analysis and modification to improve phage resistance. This has especially focused on plasmid and recombinant chromosomal modifications. Some research has focused on the potential of bacteriophages as antimicrobial against foodborne pathogens and biofilm formation within the dairy industry. As the spread of antibiotic resistance is a main concern within the dairy industry, phages can serve as a promising alternative. Replication. The life cycle of bacteriophages tends to be either a lytic cycle or a lysogenic cycle. In addition, some phages display pseudolysogenic behaviors. With "lytic phages" such as the T4 phage, bacterial cells are broken open (lysed) and destroyed after immediate replication of the virion. As soon as the cell is destroyed, the phage progeny can find new hosts to infect. Lytic phages are more suitable for phage therapy. Some lytic phages undergo a phenomenon known as lysis inhibition, where completed phage progeny will not immediately lyse out of the cell if extracellular phage concentrations are high. This mechanism is not identical to that of the temperate phage going dormant and usually is temporary.
In contrast, the "lysogenic cycle" does not result in immediate lysing of the host cell. Those phages able to undergo lysogeny are known as temperate phages. Their viral genome will integrate with host DNA and replicate along with it, relatively harmlessly, or may even become established as a plasmid. The virus remains dormant until host conditions deteriorate, perhaps due to depletion of nutrients, then, the endogenous phages (known as prophages) become active. At this point they initiate the reproductive cycle, resulting in lysis of the host cell. As the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is replicated in all offspring of the cell. An example of a bacteriophage known to follow the lysogenic cycle and the lytic cycle is the phage lambda of "E. coli." Sometimes prophages may provide benefits to the host bacterium while they are dormant by adding new functions to the bacterial genome, in a phenomenon called lysogenic conversion. Examples are the conversion of harmless strains of "Corynebacterium diphtheriae" or "Vibrio cholerae" by bacteriophages to highly virulent ones that cause diphtheria or cholera, respectively. Strategies to combat certain bacterial infections by targeting these toxin-encoding prophages have been proposed.
Attachment and penetration. Bacterial cells are protected by a cell wall of polysaccharides, which are important virulence factors protecting bacterial cells against both immune host defenses and antibiotics. Host growth conditions also influence the ability of the phage to attach and invade them. As phage virions do not move independently, they must rely on random encounters with the correct receptors when in solution, such as blood, lymphatic circulation, irrigation, soil water, etc. Myovirus bacteriophages use a hypodermic syringe-like motion to inject their genetic material into the cell. After contacting the appropriate receptor, the tail fibers flex to bring the base plate closer to the surface of the cell. This is known as reversible binding. Once attached completely, irreversible binding is initiated and the tail contracts, possibly with the help of ATP present in the tail, injecting genetic material through the bacterial membrane. The injection is accomplished through a sort of bending motion in the shaft by going to the side, contracting closer to the cell and pushing back up. Podoviruses lack an elongated tail sheath like that of a myovirus, so instead, they use their small, tooth-like tail fibers enzymatically to degrade a portion of the cell membrane before inserting their genetic material.
Synthesis of proteins and nucleic acid. Within minutes, bacterial ribosomes start translating viral mRNA into protein. For RNA-based phages, RNA replicase is synthesized early in the process. Proteins modify the bacterial RNA polymerase so it preferentially transcribes viral mRNA. The host's normal synthesis of proteins and nucleic acids is disrupted, and it is forced to manufacture viral products instead. These products go on to become part of new virions within the cell, helper proteins that contribute to the assemblage of new virions, or proteins involved in cell lysis. In 1972, Walter Fiers (University of Ghent, Belgium) was the first to establish the complete nucleotide sequence of a gene and in 1976, of the viral genome of bacteriophage MS2. Some dsDNA bacteriophages encode ribosomal proteins, which are thought to modulate protein translation during phage infection. Virion assembly. In the case of the T4 phage, the construction of new virus particles involves the assistance of helper proteins that act catalytically during phage morphogenesis. The base plates are assembled first, with the tails being built upon them afterward. The head capsids, constructed separately, will spontaneously assemble with the tails. During assembly of the phage T4 virion, the morphogenetic proteins encoded by the phage genes interact with each other in a characteristic sequence. Maintaining an appropriate balance in the amounts of each of these proteins produced during viral infection appears to be critical for normal phage T4 morphogenesis. The DNA is packed efficiently within the heads. The whole process takes about 15 minutes.
Early studies of bactioriophage T4 (1962-1964) provided an opportunity to gain understanding of virtually all of the genes that are essential for growth of the bacteriophage under laboratory conditions. These studies were made possible by the availability of two classes of conditional lethal mutants. One class of such mutants was referred to as amber mutants. The other class of conditional lethal mutants was referred to as temperature-sensitive mutants Studies of these two classes of mutants led to considerable insight into the functions and interactions of the proteins employed in the machinery of DNA replication, repair and recombination, and on how viruses are assembled from protein and nucleic acid components (molecular morphogenesis). Release of virions. Phages may be released via cell lysis, by extrusion, or, in a few cases, by budding. Lysis, by tailed phages, is achieved by an enzyme called endolysin, which attacks and breaks down the cell wall peptidoglycan. An altogether different phage type, the filamentous phage, makes the host cell continually secrete new virus particles. Released virions are described as free, and, unless defective, are capable of infecting a new bacterium. Budding is associated with certain "Mycoplasma" phages. In contrast to virion release, phages displaying a lysogenic cycle do not kill the host and instead become long-term residents as prophages.
Communication. Research in 2017 revealed that the bacteriophage Φ3T makes a short viral protein that signals other bacteriophages to lie dormant instead of killing the host bacterium. Arbitrium is the name given to this protein by the researchers who discovered it. Genome structure. Given the millions of different phages in the environment, phage genomes come in a variety of forms and sizes. RNA phages such as MS2 have the smallest genomes, with only a few kilobases. However, some DNA phages such as T4 may have large genomes with hundreds of genes; the size and shape of the capsid varies along with the size of the genome. The largest bacteriophage genomes reach a size of 735 kb.Bacteriophage genomes can be highly mosaic, i.e. the genome of many phage species appear to be composed of numerous individual modules. These modules may be found in other phage species in different arrangements. Mycobacteriophages, bacteriophages with mycobacterial hosts, have provided excellent examples of this mosaicism. In these mycobacteriophages, genetic assortment may be the result of repeated instances of site-specific recombination and illegitimate recombination (the result of phage genome acquisition of bacterial host genetic sequences). Evolutionary mechanisms shaping the genomes of bacterial viruses vary between different families and depend upon the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the viral life cycle.
Some marine roseobacter phages, also known as roseophages, contain deoxyuridine (dU) instead of deoxythymidine (dT) in their genomic DNA. There is some evidence that this unusual component is a mechanism to evade bacterial defense mechanisms such as restriction endonucleases and CRISPR/Cas systems which evolved to recognize and cleave sequences within invading phages, thereby inactivating them. Other phages have long been known to use unusual nucleotides. In 1963, Takahashi and Marmur identified a "Bacillus" phage that has dU substituting dT in its genome, and in 1977, Kirnos et al. identified a cyanophage containing 2-aminoadenine (Z) instead of adenine (A). Systems biology. The field of systems biology investigates the complex networks of interactions within an organism, usually using computational tools and modeling. For example, a phage genome that enters into a bacterial host cell may express hundreds of phage proteins which will affect the expression of numerous host genes or the host's metabolism. All of these complex interactions can be described and simulated in computer models.
For instance, infection of "Pseudomonas aeruginosa" by the temperate phage PaP3 changed the expression of 38% (2160/5633) of its host's genes. Many of these effects are probably indirect, hence the challenge becomes to identify the direct interactions among bacteria and phage. Several attempts have been made to map protein–protein interactions among phage and their host. For instance, bacteriophage lambda was found to interact with its host, "E. coli", by dozens of interactions. Again, the significance of many of these interactions remains unclear, but these studies suggest that there most likely are several key interactions and many indirect interactions whose role remains uncharacterized. Host resistance. Bacteriophages are a major threat to bacteria and prokaryotes have evolved numerous mechanisms to block infection or to block the replication of bacteriophages within host cells. The CRISPR system is one such mechanism as are retrons and the anti-toxin system encoded by them. The Thoeris defense system is known to deploy a unique strategy for bacterial antiphage resistance via NAD+ degradation.
Bacteriophage–host symbiosis. Temperate phages are bacteriophages that integrate their genetic material into the host as extrachromosomal episomes or as a prophage during a lysogenic cycle. Some temperate phages can confer fitness advantages to their host in numerous ways, including giving antibiotic resistance through the transfer or introduction of antibiotic resistance genes (ARGs), protecting hosts from phagocytosis, protecting hosts from secondary infection through superinfection exclusion, enhancing host pathogenicity, or enhancing bacterial metabolism or growth. Bacteriophage–host symbiosis may benefit bacteria by providing selective advantages while passively replicating the phage genome. In the environment. Metagenomics has allowed the in-water detection of bacteriophages that was not possible previously. Also, bacteriophages have been used in hydrological tracing and modelling in river systems, especially where surface water and groundwater interactions occur. The use of phages is preferred to the more conventional dye marker because they are significantly less absorbed when passing through ground waters and they are readily detected at very low concentrations. Non-polluted water may contain approximately 2×108 bacteriophages per ml.
Bacteriophages are thought to contribute extensively to horizontal gene transfer in natural environments, principally via transduction, but also via transformation. Metagenomics-based studies also have revealed that viromes from a variety of environments harbor antibiotic-resistance genes, including those that could confer multidrug resistance. Recent findings have mapped the complex and intertwined arsenal of anti-phage defense tools in environmental bacteria. In humans. Although phages do not infect humans, there are countless phage particles in the human body, given the extensive human microbiome. One's phage population has been called the human phageome, including the "healthy gut phageome" (HGP) and the "diseased human phageome" (DHP). The active phageome of a healthy human (i.e., actively replicating as opposed to nonreplicating, integrated prophage) has been estimated to comprise dozens to thousands of different viruses. There is evidence that bacteriophages and bacteria interact in the human gut microbiome both antagonistically and beneficially.
Preliminary studies have indicated that common bacteriophages are found in 62% of healthy individuals on average, while their prevalence was reduced by 42% and 54% on average in patients with ulcerative colitis (UC) and Crohn's disease (CD). Abundance of phages may also decline in the elderly. The most common phages in the human intestine, found worldwide, are crAssphages. CrAssphages are transmitted from mother to child soon after birth, and there is some evidence suggesting that they may be transmitted locally. Each person develops their own unique crAssphage clusters. CrAss-like phages also may be present in primates besides humans. Commonly studied bacteriophages. Among the countless phages, only a few have been studied in detail, including some historically important phage that were discovered in the early days of microbial genetics. These, especially the T-phage, helped to discover important principles of gene structure and function.
Bactericide A bactericide or bacteriocide, sometimes abbreviated Bcidal, is a substance which kills bacteria. Bactericides are disinfectants, antiseptics, or antibiotics. However, material surfaces can also have bactericidal properties based solely on their physical surface structure, as for example biomaterials like insect wings. Disinfectants. The most used disinfectants are those applying Antiseptics. As antiseptics (i.e., germicide agents that can be used on human or animal body, skin, mucosae, wounds and the like), few of the above-mentioned disinfectants can be used, under proper conditions (mainly concentration, pH, temperature and toxicity toward humans and animals). Among them, some important are Others are generally not applicable as safe antiseptics, either because of their corrosive or toxic nature. Antibiotics. Bactericidal antibiotics kill bacteria; bacteriostatic antibiotics slow their growth or reproduction. Bactericidal antibiotics that inhibit cell wall synthesis: the beta-lactam antibiotics (penicillin derivatives (penams), cephalosporins (cephems), monobactams, and carbapenems) and vancomycin.
Also bactericidal are daptomycin, fluoroquinolones, metronidazole, nitrofurantoin, co-trimoxazole, telithromycin. Aminoglycosidic antibiotics are usually considered bactericidal, although they may be bacteriostatic with some organisms. As of 2004, the distinction between bactericidal and bacteriostatic agents appeared to be clear according to the basic/clinical definition, but this only applies under strict laboratory conditions and it is important to distinguish microbiological and clinical definitions. The distinction is more arbitrary when agents are categorized in clinical situations. The supposed superiority of bactericidal agents over bacteriostatic agents is of little relevance when treating the vast majority of infections with gram-positive bacteria, particularly in patients with uncomplicated infections and noncompromised immune systems. Bacteriostatic agents have been effectively used for treatment that are considered to require bactericidal activity. Furthermore, some broad classes of antibacterial agents considered bacteriostatic can exhibit bactericidal activity against some bacteria on the basis of in vitro determination of MBC/MIC values. At high concentrations, bacteriostatic agents are often bactericidal against some susceptible organisms. The ultimate guide to treatment of any infection must be clinical outcome.
Surfaces. Material surfaces can exhibit bactericidal properties because of their crystallographic surface structure. Somewhere in the mid-2000s it was shown that metallic nanoparticles can kill bacteria. The effect of a silver nanoparticle for example depends on its size with a preferential diameter of about 1–10 nm to interact with bacteria. In 2013, cicada wings were found to have a selective anti-gram-negative bactericidal effect based on their physical surface structure. Mechanical deformation of the more or less rigid nanopillars found on the wing releases energy, striking and killing bacteria within minutes, hence called a mechano-bactericidal effect. In 2020 researchers combined cationic polymer adsorption and femtosecond laser surface structuring to generate a bactericidal effect against both gram-positive "Staphylococcus aureus" and gram-negative "Escherichia coli" bacteria on borosilicate glass surfaces, providing a practical platform for the study of the bacteria-surface interaction.
Brion Gysin Brion Gysin (19 January 1916 – 13 July 1986) was a British-Canadian painter, writer, sound poet, performance artist and inventor of experimental devices. He is best known for his use of the cut-up technique, alongside his close friend, the novelist William S. Burroughs. With the engineer Ian Sommerville he also invented the Dreamachine, a flicker device designed as an art object to be viewed with the eyes closed. It was in painting and drawing, however, that Gysin devoted his greatest efforts, creating calligraphic works inspired by cursive Japanese "grass" script and Arabic script. Burroughs later stated that "Brion Gysin was the only man I ever respected." Biography. Early years. John Clifford Brian Gysin was born at the Canadian military hospital in Taplow, Buckinghamshire, England. His mother, Stella Margaret Martin, was a Canadian from Deseronto, Ontario. His father, Leonard Gysin, a captain with the Canadian Expeditionary Force, was killed in action eight months after his son's birth. Stella returned to Canada and settled in Edmonton, Alberta where her son became "the only Catholic day-boy at an Anglican boarding school". Leaving that school at the age of fifteen, Gysin was sent next to Downside School in Stratton-on-the-Fosse, near Bath in England, a prestigious school for boys run by Benedictine monks. Despite attending both Anglican and Roman Catholic schools, Gysin was already an atheist when he left St Joseph's.
Surrealism. In 1934, he moved to Paris to study "La Civilisation Française", an open course given at the Sorbonne where he made literary and artistic contacts through Marie Berthe Aurenche, Max Ernst's second wife. He joined the Surrealist Group and began associating with Valentine Hugo, Leonor Fini, Salvador Dalí, Picasso and Dora Maar. A year later, he had his first exhibition at the "Galérie Quatre Chemins" in Paris with Ernst, Picasso, Hans Arp, Hans Bellmer, Victor Brauner, Giorgio de Chirico, Dalí, Marcel Duchamp, René Magritte, Man Ray and Yves Tanguy. On the day of the preview, however, he was expelled from the Surrealist Group by André Breton, who ordered the poet Paul Éluard to take down his pictures. Gysin was 19 years old. His biographer, John Geiger, suggests the arbitrary expulsion "had the effect of a curse. Years later, he blamed other failures on the Breton incident. It gave rise to conspiracy theories about the powerful interests who seek control of the art world. He gave various explanations for the expulsion, the more elaborate involving 'insubordination' or "lèse majesté" towards Breton".
After World War II. After serving in the U.S. army during World War II, Gysin published a biography of Josiah "Uncle Tom" Henson titled, "To Master, a Long Goodnight: The History of Slavery in Canada" (1946). A gifted draughtsman, he took an 18-month course learning the Japanese language (including calligraphy) that would greatly influence his artwork. In 1949, he was among the first Fulbright Fellows. His goal was to research, at the University of Bordeaux and in the Archivo de Indias in Seville, Spain, the history of slavery, a project that he later abandoned. He moved to Tangier, Morocco, after visiting the city with novelist and composer Paul Bowles in 1950. In 1952/3 he met the travel writer and sexual adventurer Anne Cumming and they remained friends until his death. Morocco and the Beat Hotel. In 1954 in Tangier, Gysin opened a restaurant called The 1001 Nights, with his friend Mohamed Hamri, who was the cook. Gysin hired the Master Musicians of Jajouka from the village of Jajouka to perform alongside entertainment that included acrobats, a dancing boy and fire eaters. The musicians performed there for an international clientele that included William S. Burroughs. Gysin lost the business in 1958, and the restaurant closed permanently. That same year, Gysin returned to Paris, taking lodgings in a flophouse located at 9 rue Gît-le-Cœur that would become famous as the Beat Hotel. Working on a drawing, he discovered a Dada technique by accident:

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