1.
Micrograph
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A micrograph or photomicrograph is a photograph or digital image taken through a microscope or similar device to show a magnified image of an item. This is opposed to an image, which is at a scale that is visible to the naked eye. Micrography is the practice or art of using microscopes to make photographs, a micrograph contains extensive details that form the features of a microstructure. The neuropathologist Solomon C. Fuller designed and created the first photomicrograph in 1900, micrographs are widely used in all fields of microscopy. A light micrograph or photomicrograph is a micrograph prepared using an optical microscope, at a basic level, photomicroscopy may be performed simply by hooking up a regular camera to a microscope, thereby enabling the user to take photographs at reasonably high magnification. Roman Vishniac was a pioneer in the field of photomicroscopy, specializing in the photography of living creatures in full motion and he also made major developments in light-interruption photography and color photomicroscopy. An electron micrograph is a micrograph prepared using an electron microscope, however, the term electron micrograph is not used in electron microscopy. Digital micrography is a digital picture obtained either directly with a microscope or by scanning of a photomicrograph, digital micrographs are now commonly obtained using a USB microscope attached directly to a home computer or laptop. Today, an add-on three-in-one macro lens which has capability to take wide-angle, fish-eye and macro with 7x, 14x, micrographs usually have micron bars, or magnification ratios, or both. Magnification is a ratio between size of object on a picture and its real size, unfortunately, magnification is somewhat a misleading parameter. It depends on a size of a printed picture. Editors of journals and magazines routinely resize a figure to fit the page, a scale bar, or micron bar, is a bar of known length displayed on a picture. The bar can be used for measurements on a picture, when a picture is resized a bar is also resized. If a picture has a bar, the magnification can be easily calculated, ideally, all pictures destined for publication/presentation should be supplied with a scale bar, the magnification ratio is optional. All but one of the micrographs presented on this page do not have a bar, supplied magnification ratios are likely incorrect. The microscope has been used for scientific discovery. It has also linked to the arts since its invention in the 17th century. At first scientists used the microscope to view and draw objects not visible with the unaided eye, early adopters of the microscope, such as Robert Hooke and Antonie van Leeuwenhoek, were excellent illustrators
2.
Greek language
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Greek is an independent branch of the Indo-European family of languages, native to Greece and other parts of the Eastern Mediterranean. It has the longest documented history of any living language, spanning 34 centuries of written records and its writing system has been the Greek alphabet for the major part of its history, other systems, such as Linear B and the Cypriot syllabary, were used previously. The alphabet arose from the Phoenician script and was in turn the basis of the Latin, Cyrillic, Armenian, Coptic, Gothic and many other writing systems. Together with the Latin texts and traditions of the Roman world, during antiquity, Greek was a widely spoken lingua franca in the Mediterranean world and many places beyond. It would eventually become the official parlance of the Byzantine Empire, the language is spoken by at least 13.2 million people today in Greece, Cyprus, Italy, Albania, Turkey, and the Greek diaspora. Greek roots are used to coin new words for other languages, Greek. Greek has been spoken in the Balkan peninsula since around the 3rd millennium BC, the earliest written evidence is a Linear B clay tablet found in Messenia that dates to between 1450 and 1350 BC, making Greek the worlds oldest recorded living language. Among the Indo-European languages, its date of earliest written attestation is matched only by the now extinct Anatolian languages, the Greek language is conventionally divided into the following periods, Proto-Greek, the unrecorded but assumed last ancestor of all known varieties of Greek. The unity of Proto-Greek would have ended as Hellenic migrants entered the Greek peninsula sometime in the Neolithic era or the Bronze Age, Mycenaean Greek, the language of the Mycenaean civilisation. It is recorded in the Linear B script on tablets dating from the 15th century BC onwards, Ancient Greek, in its various dialects, the language of the Archaic and Classical periods of the ancient Greek civilisation. It was widely known throughout the Roman Empire, after the Roman conquest of Greece, an unofficial bilingualism of Greek and Latin was established in the city of Rome and Koine Greek became a first or second language in the Roman Empire. The origin of Christianity can also be traced through Koine Greek, Medieval Greek, also known as Byzantine Greek, the continuation of Koine Greek in Byzantine Greece, up to the demise of the Byzantine Empire in the 15th century. Much of the written Greek that was used as the language of the Byzantine Empire was an eclectic middle-ground variety based on the tradition of written Koine. Modern Greek, Stemming from Medieval Greek, Modern Greek usages can be traced in the Byzantine period and it is the language used by the modern Greeks, and, apart from Standard Modern Greek, there are several dialects of it. In the modern era, the Greek language entered a state of diglossia, the historical unity and continuing identity between the various stages of the Greek language is often emphasised. Greek speakers today still tend to regard literary works of ancient Greek as part of their own rather than a foreign language and it is also often stated that the historical changes have been relatively slight compared with some other languages. According to one estimation, Homeric Greek is probably closer to demotic than 12-century Middle English is to modern spoken English, Greek is spoken by about 13 million people, mainly in Greece, Albania and Cyprus, but also worldwide by the large Greek diaspora. Greek is the language of Greece, where it is spoken by almost the entire population
3.
Optical microscope
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The optical microscope, often referred to as light microscope, is a type of microscope which uses visible light and a system of lenses to magnify images of small samples. Optical microscopes are the oldest design of microscope and were invented in their present compound form in the 17th century. Basic optical microscopes can be simple, although there are many complex designs which aim to improve resolution. The image from a microscope can be captured by normal light-sensitive cameras to generate a micrograph. Originally images were captured by photographic film but modern developments in CMOS, purely digital microscopes are now available which use a CCD camera to examine a sample, showing the resulting image directly on a computer screen without the need for eyepieces. Alternatives to optical microscopy which do not use visible light include scanning electron microscopy, there are two basic types of optical microscopes, simple microscopes and compound microscopes. A simple microscope is one which uses a lens for magnification. A compound microscope uses several lenses to enhance the magnification of an object, the vast majority of modern research microscopes are compound microscopes while some cheaper commercial digital microscopes are simple single lens microscopes. Compound microscopes can be divided into a variety of other types of microscopes which differ in their optical configurations, cost. A simple microscope uses a lens or set of lenses to enlarge an object through angular magnification alone, the use of a single convex lens or groups of lenses are still found in simple magnification devices such as the magnifying glass, loupes, and eyepieces for telescopes and microscopes. A compound microscope uses a close to the object being viewed to collect light which focuses a real image of the object inside the microscope. That image is magnified by a second lens or group of lenses that gives the viewer an enlarged inverted virtual image of the object. The use of a compound objective/eyepiece combination allows for higher magnification. Common compound microscopes often feature exchangeable objective lenses, allowing the user to quickly adjust the magnification, a compound microscope also enables more advanced illumination setups, such as phase contrast. There are many variants of the optical microscope design for specialized purposes. Comparison microscope, which has two light paths allowing direct comparison of two samples via one image in each eye. Inverted microscope, for studying samples from below, useful for cell cultures in liquid, student microscope, designed for low cost, durability, and ease of use. Polarizing microscope, similar to the petrographic microscope, phase contrast microscope, which applies the phase contrast illumination method
4.
Tissue (biology)
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In biology, tissue is a cellular organizational level intermediate between cells and a complete organ. A tissue is an ensemble of similar cells from the origin that together carry out a specific function. Organs are then formed by the grouping together of multiple tissues. The study of tissue is known as histology or, in connection with disease, the classical tools for studying tissues are the paraffin block in which tissue is embedded and then sectioned, the histological stain, and the optical microscope. In the last couple of decades, developments in microscopy, immunofluorescence. With these tools, the appearances of tissues can be examined in health and disease. Animal tissues are grouped into four types, connective, muscle, nervous. Collections of tissues joined in structural units to serve a common function compose organs, while all animals can generally be considered to contain the four tissue types, the manifestation of these tissues can differ depending on the type of organism. For example, the origin of the cells comprising a particular type may differ developmentally for different classifications of animals. By contrast, a true epithelial tissue is present only in a layer of cells held together via occluding junctions called tight junctions. This tissue covers all surfaces that come in contact with the external environment such as the skin, the airways. It serves functions of protection, secretion, and absorption, and is separated from other tissues below by a basal lamina and they are made up of cells separated by non-living material, which is called an extracellular matrix. This matrix can be liquid or rigid, for example, blood contains plasma as its matrix and bones matrix is rigid. Connective tissue gives shape to organs and holds them in place, blood, bone, tendon, ligament, adipose and areolar tissues are examples of connective tissues. One method of classifying tissues is to divide them into three types, fibrous connective tissue, skeletal connective tissue, and fluid connective tissue. Muscle cells form the active contractile tissue of the known as muscle tissue or muscular tissue. Muscle tissue functions to force and cause motion, either locomotion or movement within internal organs. Cells comprising the nervous system and peripheral nervous system are classified as nervous tissue
5.
Disease
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A disease is a particular abnormal condition, a disorder of a structure or function, that affects part or all of an organism. The study of disease is called pathology which includes the study of cause, Disease is often construed as a medical condition associated with specific symptoms and signs. When caused by pathogens, even in the literature, the term disease is often misleadingly used in the place of its causal agent. This language habitat can cause confusion in the communication of the principle in epidemiology. Diseases can affect not only physically, but also emotionally. Death due to disease is called death by natural causes, there are four main types of disease, infectious diseases, deficiency diseases, genetic diseases, and physiological diseases. Diseases can also be classified as communicable and non-communicable, the deadliest diseases in humans are coronary artery disease, followed by cerebrovascular disease and lower respiratory infections. In many cases, terms such as disease, disorder, morbidity, there are situations, however, when specific terms are considered preferable. Disease The term disease broadly refers to any condition that impairs the normal functioning of the body, for this reason, diseases are associated with dysfunctioning of the bodys normal homeostatic processes. The term disease has both a count sense and a noncount sense, by contrast, an infection that is asymptomatic during its incubation period, but expected to produce symptoms later, is usually considered a disease. Non-infectious diseases are all other diseases, including most forms of cancer, heart disease, acquired disease disease that began at some point during ones lifetime, as opposed to disease that was already present at birth, which is congenital disease. Acquired sounds like it could mean caught via contagion, but it simply means acquired sometime after birth and it also sounds like it could imply secondary disease, but acquired disease can be primary disease. It is often, genetic and can be inherited and it can also be the result of a vertically transmitted infection from the mother such as HIV/AIDS. Genetic disease disease that is caused by genetic mutation and it is often inherited, but some mutations are random and de novo. Hereditary or inherited disease a type of disease caused by mutation that is hereditary Iatrogenic disease A disease condition caused by medical intervention. Idiopathic disease disease whose cause is unknown, as medical science has advanced, many diseases whose causes were formerly complete mysteries have been somewhat explained or even extensively explained. Bacterial infections can be primary or secondary to a viral infection or burn. Terminal disease disease with death as an inevitable result Illness Illness is generally used as a synonym for disease, however, this term is occasionally used to refer specifically to the patients personal experience of his or her disease
6.
Pathology
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Pathology is a significant component of the causal study of disease and a major field in modern medicine and diagnosis. Similarly, a condition is one caused by disease, rather than occurring physiologically. A physician practicing pathology is called a pathologist, as a field of general inquiry and research, pathology addresses four components of disease, cause, mechanisms of development, structural alterations of cells, and the consequences of changes. Further divisions in specialty exist on the basis of the involved sample types, organs, the sense of the word pathology as a synonym of disease or pathosis is very common in health care. The persistence of this usage despite attempted proscription is discussed elsewhere, the study of pathology, including the detailed examination of the body, including dissection and inquiry into specific maladies, dates back to antiquity. Notably, many advances were made in the era of Islam, during which numerous texts of complex pathologies were developed. By the 17th century, the study of microscopy was underway and examination of tissues had led British Royal Society member Robert Hooke to coin the word cell, setting the stage for later germ theory. However, pathology as an area of specialty was not fully developed until the late 19th and early 20th centuries. This realization led to the understanding that diseases are able to replicate themselves. To determine causes of diseases, medical experts used the most common and widely accepted assumptions or symptoms of their times, by the late 1920s to early 1930s pathology was deemed a medical specialty. The modern practice of pathology is divided into a number of subdisciplines within the discrete but deeply interconnected aims of biological research, anatomical pathology is itself divided into subfields, the main divisions being surgical pathology, cytopathology, and forensic pathology. Sometimes, pathologists practice both anatomical and clinical pathology, a known as general pathology. Cytopathology is a branch of pathology that studies and diagnoses diseases on the cellular level, however, cytology samples may be prepared in other ways, including cytocentrifugation. Dermatopathology is a subspecialty of pathology that focuses on the skin. It is unique, in there are two paths a physician can take to obtain the specialization. The completion of this allows one to take a subspecialty board examination. Dermatologists are able to recognize most skin diseases based on their appearances, anatomic distributions, sometimes, however, those criteria do not lead to a conclusive diagnosis, and a skin biopsy is taken to be examined under the microscope using usual histological tests. One of the greatest challenges of dermatopathology is its scope, more than 1500 different disorders of the skin exist, including cutaneous eruptions and neoplasms
7.
Histological section
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Histology is the study of the microscopic anatomy of cells and tissues of plants and animals. It is commonly performed by examining cells and tissues under a microscope or electron microscope, the specimen having been sectioned, stained. Histological studies may be conducted using tissue culture, where human or animal cells are isolated and maintained in an artificial environment for various research projects. The ability to visualize or differentially identify microscopic structures is frequently enhanced through the use of histological stains, histology is an essential tool of biology and medicine. Trained physicians, frequently licensed pathologists, are the personnel who perform histopathological examination and their field of study is called histotechnology. In the 17th century, Italian Marcello Malpighi invented one of the first microscopes for studying tiny biological entities, Malpighi analysed several parts of the organs of bats, frogs and other animals under the microscope. Malpighi, while studying the structure of the lung, noticed its membranous alveoli and his discovery established how the oxygen we breathe enters the blood stream and serves the body. In the 19th century, histology was a discipline in its own right. The French anatomist Bichat introduced the concept of tissue in anatomy in 1801, the 1906 Nobel Prize in Physiology or Medicine was awarded to histologists Camillo Golgi and Santiago Ramon y Cajal. They had dueling interpretations of the structure of the brain based in differing interpretations of the same images. Cajal won the prize for his theory and Golgi for the staining technique he invented to make it possible. There are four types of animal tissues, muscle tissue, nervous tissue, connective tissue. All tissue types are subtypes of these four basic tissue types and their structure is very different from animal tissues. The most common fixative for light microscopy is 10% neutral buffered formalin, for electron microscopy, the most commonly used fixative is glutaraldehyde, usually as a 2. 5% solution in phosphate buffered saline. These fixatives preserve tissues or cells mainly by irreversibly cross-linking proteins and this can be detrimental to certain histological techniques. Further fixatives are often used for electron microscopy such as osmium tetroxide or uranyl acetate Formalin fixation leads to degradation of mRNA, miRNA and DNA in tissues, however, extraction, amplification and analysis of these nucleic acids from formalin-fixed, paraffin-embedded tissues is possible using appropriate protocols. Frozen section procedure is a way to fix and mount histology sections using a refrigeration device called a cryostat. It is often used after surgical removal of tumors to allow determination of margin
8.
Cytopathology
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Cytopathology is a branch of pathology that studies and diagnoses diseases on the cellular level. The discipline was founded by George Nicolas Papanicolaou in 1928, a common application of cytopathology is the Pap smear, used as a screening tool, to detect precancerous cervical lesions and prevent cervical cancer. Cytopathology is also used to investigate thyroid lesions, diseases involving sterile body cavities. It is usually used to aid in the diagnosis of cancer, cytopathology is generally used on samples of free cells or tissue fragments, in contrast to histopathology, which studies whole tissues. Cytopathologic tests are sometimes called smear tests because the samples may be smeared across a glass slide for subsequent staining. However, cytology samples may be prepared in ways, including cytocentrifugation. Different types of tests may also be used for cancer diagnosis. In this sense, it is termed a cytologic smear, cytopathology is frequently, less precisely, called cytology, which means the study of cells. An example of spontaneous exfoliation is when cells of the cavity or peritoneal cavity are shed into the pleural or peritoneal fluid. This fluid can be collected via various methods for examination, liquid-based cytology collects the samples in the same way but places them in liquid that is then treated to allow for improved results. In interventional cytology the pathologist intervenes into the body for sample collection, nowadays FNAC has become synonymous to interventional cytology. Fine-Needle Aspiration Cytology or Needle aspiration biopsy, a needle attached to a syringe is used to collect cells from lesions or masses in various body organs by microcoring, often with the application of negative pressure to increase yield. FNAC is widely used in countries, but success rate is dependent on the skill of the practitioner. If performed by a pathologist alone, or as team with pathologist-cytotechnologist and this may be due to the pathologists ability to immediately evaluate specimens under a microscope and immediately repeat the procedure if sampling was inadequate. Fine needles are 23 to 27 gauge, because needles as small as 27 gauge can almost always yield diagnostic material, FNAC is often the least injurious way to obtain diagnostic tissue from a lesion. Sometime a syringe holder may be used to using one hand to perform the biopsy while the other hand is immobilizing the mass. Imaging equipment such as a CT scanner or ultrasound may be used to assist in locating the region to be biopsied, sediment cytology – Here, the sample is collected from the fixative that was used for processing the biopsy or autopsy specimen. The fixative is mixed properly and taken into a tube and is centrifuged
9.
Surgery
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An act of performing surgery may be called a surgical procedure, operation, or simply surgery. In this context, the verb means to perform surgery. The adjective surgical means pertaining to surgery, e. g. surgical instruments or surgical nurse, the patient or subject on which the surgery is performed can be a person or an animal. A surgeon is a person who practices surgery and an assistant is a person who practices surgical assistance. A surgical team is made up of surgeon, surgeons assistant, anesthesia provider, circulating nurse, Surgery usually spans minutes to hours, but it is typically not an ongoing or periodic type of treatment. The term surgery can also refer to the place where surgery is performed, or simply the office of a physician, dentist, Surgery is a technology consisting of a physical intervention on tissues. As a general rule, a procedure is considered surgical when it involves cutting of a patients tissues or closure of a previously sustained wound, surgical procedures are commonly categorized by urgency, type of procedure, body system involved, degree of invasiveness, and special instrumentation. Based on timing, Elective surgery is done to correct a condition, and is carried out at the patients request, subject to the surgeons. A semi-elective surgery is one that must be done to avoid permanent disability or death, emergency surgery is surgery which must be done promptly to save life, limb, or functional capacity. Based on purpose, Exploratory surgery is performed to aid or confirm a diagnosis, therapeutic surgery treats a previously diagnosed condition. Cosmetic surgery is done to improve the appearance of an otherwise normal structure. By type of procedure, Amputation involves cutting off a part, usually a limb or digit. Resection is the removal of all or part of an organ or part of the body. Replantation involves reattaching a severed body part, reconstructive surgery involves reconstruction of an injured, mutilated, or deformed part of the body. Excision is the cutting out or removal of an organ, tissue, transplant surgery is the replacement of an organ or body part by insertion of another from different human into the patient. Removing an organ or body part from a human or animal for use in transplant is also a type of surgery. By body part, When surgery is performed on one system or structure. Examples include cardiac surgery, gastrointestinal surgery, and orthopedic surgery, by contrast, an open surgical procedure such as a laparotomy requires a large incision to access the area of interest
10.
Plant
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Plants are mainly multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. The term is generally limited to the green plants, which form an unranked clade Viridiplantae. This includes the plants, conifers and other gymnosperms, ferns, clubmosses, hornworts, liverworts, mosses and the green algae. Green plants have cell walls containing cellulose and obtain most of their energy from sunlight via photosynthesis by primary chloroplasts and their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic and have lost the ability to produce amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although reproduction is also common. There are about 300–315 thousand species of plants, of which the great majority, green plants provide most of the worlds molecular oxygen and are the basis of most of Earths ecologies, especially on land. Plants that produce grains, fruits and vegetables form humankinds basic foodstuffs, Plants play many roles in culture. They are used as ornaments and, until recently and in variety, they have served as the source of most medicines. The scientific study of plants is known as botany, a branch of biology, Plants are one of the two groups into which all living things were traditionally divided, the other is animals. The division goes back at least as far as Aristotle, who distinguished between plants, which generally do not move, and animals, which often are mobile to catch their food. Much later, when Linnaeus created the basis of the system of scientific classification. Since then, it has become clear that the plant kingdom as originally defined included several unrelated groups, however, these organisms are still often considered plants, particularly in popular contexts. When the name Plantae or plant is applied to a group of organisms or taxon. The evolutionary history of plants is not yet settled. Those which have been called plants are in bold, the way in which the groups of green algae are combined and named varies considerably between authors. Algae comprise several different groups of organisms which produce energy through photosynthesis, most conspicuous among the algae are the seaweeds, multicellular algae that may roughly resemble land plants, but are classified among the brown, red and green algae. Each of these groups also includes various microscopic and single-celled organisms
11.
Decomposition
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Decomposition is the process by which organic substances are broken down into simpler matter. The process is a part of nutrient cycle and is essential for recycling the matter that occupies physical space in the biosphere. Bodies of living organisms begin to decompose shortly after death, animals, such as worms, also help decompose the organic materials. Organisms that do this are known as decomposers, although no two organisms decompose in the same way, they all undergo the same sequential stages of decomposition. The science which studies decomposition is referred to as taphonomy from the Greek word τάφος taphos. One can differentiate abiotic from biotic decomposition, the former means degradation of a substance by chemical or physical processes, e. g. hydrolysis. The latter means the metabolic breakdown of materials into simpler components by living organisms and these processes release gases, such as cadaverine and putrescine, that are the chief source of the unmistakably putrid odor of decaying animal tissue. Prime decomposers are bacteria or fungi, though larger scavengers also play an important role in decomposition if the body is accessible to insects, mites and other animals. The most important arthropods that are involved in the process include carrion beetles, mites, the most important non-insect animals that are typically involved in the process include mammal and bird scavengers, such as coyotes, dogs, wolves, foxes, rats, crows and vultures. Some of these scavengers also remove and scatter bones, which they ingest at a later time, aquatic and marine environments have break-down agents that include bacteria, fish, crustaceans, Diptera larvae and other carrion scavengers. Five general stages are used to describe the process of decomposition in vertebrate animals, fresh, bloat, active and advanced decay, the general stages of decomposition are coupled with two stages of chemical decomposition, autolysis and putrefaction. These two stages contribute to the process of decomposition, which breaks down the main components of the body. The fresh stage begins immediately after the heart stops beating, from the moment of death, the body begins cooling or warming to match the temperature of the ambient environment, during a stage called algor mortis. Shortly after death, within three to six hours, the tissues become rigid and incapable of relaxing, during a stage called rigor mortis. Once the heart stops, the blood can no longer supply oxygen or remove carbon dioxide from the tissues and this process is known as autolysis. Visible changes caused by decomposition are limited during the fresh stage and these multiply, consuming the bodys carbohydrates, lipids, and proteins, to produce a variety of substances including propionic acid, lactic acid, methane, hydrogen sulfide, and ammonia. The process of microbial proliferation within a body is referred to as putrefaction and leads to the stage of decomposition. Blowflies and flesh flies are the first carrion insects to arrive, the bloat stage provides the first clear visual sign that microbial proliferation is underway
12.
Histology
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Histology is the study of the microscopic anatomy of cells and tissues of plants and animals. It is commonly performed by examining cells and tissues under a microscope or electron microscope, the specimen having been sectioned, stained. Histological studies may be conducted using tissue culture, where human or animal cells are isolated and maintained in an artificial environment for various research projects. The ability to visualize or differentially identify microscopic structures is frequently enhanced through the use of histological stains, histology is an essential tool of biology and medicine. Trained physicians, frequently licensed pathologists, are the personnel who perform histopathological examination and their field of study is called histotechnology. In the 17th century, Italian Marcello Malpighi invented one of the first microscopes for studying tiny biological entities, Malpighi analysed several parts of the organs of bats, frogs and other animals under the microscope. Malpighi, while studying the structure of the lung, noticed its membranous alveoli and his discovery established how the oxygen we breathe enters the blood stream and serves the body. In the 19th century, histology was a discipline in its own right. The French anatomist Bichat introduced the concept of tissue in anatomy in 1801, the 1906 Nobel Prize in Physiology or Medicine was awarded to histologists Camillo Golgi and Santiago Ramon y Cajal. They had dueling interpretations of the structure of the brain based in differing interpretations of the same images. Cajal won the prize for his theory and Golgi for the staining technique he invented to make it possible. There are four types of animal tissues, muscle tissue, nervous tissue, connective tissue. All tissue types are subtypes of these four basic tissue types and their structure is very different from animal tissues. The most common fixative for light microscopy is 10% neutral buffered formalin, for electron microscopy, the most commonly used fixative is glutaraldehyde, usually as a 2. 5% solution in phosphate buffered saline. These fixatives preserve tissues or cells mainly by irreversibly cross-linking proteins and this can be detrimental to certain histological techniques. Further fixatives are often used for electron microscopy such as osmium tetroxide or uranyl acetate Formalin fixation leads to degradation of mRNA, miRNA and DNA in tissues, however, extraction, amplification and analysis of these nucleic acids from formalin-fixed, paraffin-embedded tissues is possible using appropriate protocols. Frozen section procedure is a way to fix and mount histology sections using a refrigeration device called a cryostat. It is often used after surgical removal of tumors to allow determination of margin
13.
Microscope
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A microscope is an instrument used to see objects that are too small for the naked eye. The science of investigating small objects using such an instrument is called microscopy, microscopic means invisible to the eye unless aided by a microscope. There are many types of microscopes, the most common is the optical microscope, which uses light to image the sample. Other major types of microscopes are the microscope, the ultramicroscope. The earliest microscopes were single lens magnifying glasses with limited magnification which date at least as far back as the wide use of lenses in eyeglasses in the 13th century. Compound microscopes, which combine an objective lens with an eyepiece to view a real image, the actual inventor of the compound microscope is unknown although many claims have been made over the years. These include what may be a claim by the son of Zacharias Janssen that his father invented the microscope and telescope as early as 1590. Historians note the compound microscope did not appear in the Netherlands until the 1620s, giovanni Faber coined the name microscope for the compound microscope Galileo submitted to the Accademia dei Lincei in 1625. The first detailed account of the construction of living tissue based on the use of a microscope did not appear until 1644, in Giambattista Odiernas Locchio della mosca. It was not until the 1660s and 1670s that the microscope was used extensively for research in Italy, marcello Malpighi in Italy began the analysis of biological structures, beginning with the lungs. Robert Hookes Micrographia had an impact, largely because of its impressive illustrations. A significant contribution came from Antonie van Leeuwenhoek who achieved up to 300 times magnification using a single lens microscope. He sandwiched a very small glass ball lens between the holes in two metal plates riveted together, and with a needle attached to mount the specimen. Then, Van Leeuwenhoek re-discovered red blood cells and spermatozoa, on 9 October 1676, he reported the discovery of micro-organisms. The performance of light microscopy depends as much on how the sample is illuminated as on how it is observed, early instruments were limited until this principle was fully appreciated and developed, and until electric lamps were available as light sources. In 1893 August Köhler developed a key principle of sample illumination, Köhler illumination and this method of sample illumination produces even lighting and overcomes the limited contrast and resolution imposed by early techniques of sample illumination. In the early 20th century a significant alternative to light microscopy was developed, ernst Ruska started development of the first electron microscope in 1931 which was the transmission electron microscope. The transmission electron microscope works on the principle as an optical microscope but uses electrons in the place of light
14.
Agar
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Agar or agar-agar is a jelly-like substance, equivalent to vegan gelatin, obtained from algae. It was discovered in the late 1650s or early 1660s, by Mino Tarōzaemon in Japan, where it is called kanten. Agar is derived from the polysaccharide agarose, which forms the structure in the cell walls of certain species of algae. These algae are known as agarophytes and belong to the Rhodophyta phylum, Agar is actually the resulting mixture of two components, the linear polysaccharide agarose, and a heterogeneous mixture of smaller molecules called agaropectin. Throughout history into modern times, agar has been used as an ingredient in desserts throughout Asia. The gelling agent in agar is an unbranched polysaccharide obtained from the walls of some species of red algae, primarily from the genera Gelidium. For commercial purposes, it is derived primarily from Gelidium amansii, in chemical terms, agar is a polymer made up of subunits of the sugar galactose. Agar was discovered in Japan in 1658 by Mino Tarōzaemon, an innkeeper who was said to have discarded surplus seaweed soup, over the following centuries, agar became a common gelling agent in several Southeast Asian cuisines. Agar was first subjected to analysis in 1859 by the French chemist Anselme Payen. Beginning in the late 19th century, agar began to be used heavily as a medium for growing various microbes. Agar was first described for use in microbiology in 1882 by the German microbiologist Walther Hesse, Agar quickly supplanted gelatin as the base of microbiological media, due to its higher melting temperature, allowing microbes to be grown at higher temperatures without the media liquefying. With its newfound use in microbiology, agar production quickly increased and this production centered on Japan which produced most of the worlds agar until World War II. However, with the outbreak of World War II many nations were forced to establish domestic agar industries in order to continue microbiological research, around the time of World War II, approximately 2,500 tons of agar were produced annually. By the mid-1970s, production worldwide had increased dramatically to approximately 10,000 tons each year, since then, production of agar has fluctuated due to unstable and sometimes over-utilized seaweed populations. The word agar comes from agar-agar, the Malay name for red algae from which the jelly is produced and it is also known as Kanten, Japanese isinglass, Ceylon moss or Jaffna moss. Gracilaria lichenoides is specifically referred to as agal-agal or Ceylon agar, Agar consists of a mixture of two polysaccharides, agarose and agaropectin, with agarose making up about 70% of the mixture. Agarose is a polymer, made up of repeating units of agarobiose. Agar exhibits hysteresis, melting at 85 °C and solidifying from 32–40 °C and this property lends a suitable balance between easy melting and good gel stability at relatively high temperatures
15.
Immunohistochemistry
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IHC takes its name from the roots immuno, in reference to antibodies used in the procedure, and histo, meaning tissue. The procedure was conceptualized and first implemented by Albert Coons in 1941, Immunohistochemical staining is widely used in the diagnosis of abnormal cells such as those found in cancerous tumors. Specific molecular markers are characteristic of cellular events such as proliferation or cell death. Visualising an antibody-antigen interaction can be accomplished in a number of ways, in the most common instance, an antibody is conjugated to an enzyme, such as peroxidase, that can catalyse a colour-producing reaction. Alternatively, the antibody can also be tagged to a fluorophore, preparation of the sample is critical to maintain cell morphology, tissue architecture and the antigenicity of target epitopes. This requires proper tissue collection, fixation and sectioning, a solution of paraformaldehyde is often used to fix tissue, but other methods may be used. The tissue may then be sliced or used whole, dependent upon the purpose of the experiment or the tissue itself, before sectioning, the tissue sample may be embedded in a medium, like paraffin wax or cryomedia. Sections can be sliced on a variety of instruments, most commonly a microtome, cryostat, specimens are typically sliced at a range of 3 µm-50 μm. The slices are then mounted on slides, dehydrated using alcohol washes of increasing concentrations, for formalin-fixed paraffin-embedded tissues, antigen-retrieval is often necessary, and involves pre-treating the sections with heat or protease. These steps may make the difference between the target antigens staining or not staining, depending on the tissue type and the method of antigen detection, endogenous biotin or enzymes may need to be blocked or quenched, respectively, prior to antibody staining. A great amount of non-specific binding causes high background staining which will mask the detection of the target antigen, common blocking buffers include normal serum, non-fat dry milk, BSA, or gelatin. Commercial blocking buffers with proprietary formulations are available for greater efficiency, the antibodies used for specific detection can be polyclonal or monoclonal. Polyclonal antibodies are made by injecting animals with the protein of interest, or a fragment and, after a secondary immune response is stimulated. Thus, polyclonal antibodies are a mix of antibodies that recognize several epitopes. Monoclonal antibodies show specificity for a single epitope, for immunohistochemical detection strategies, antibodies are classified as primary or secondary reagents. Primary antibodies are raised against an antigen of interest and are typically unconjugated, the secondary antibody is usually conjugated to a linker molecule, such as biotin, that then recruits reporter molecules, or the secondary antibody itself is directly bound to the reporter molecule. Reporter molecules vary based on the nature of the detection method, with chromogenic reporters, an enzyme label is reacted with a substrate to yield an intensely colored product that can be analyzed with an ordinary light microscope. While the list of enzyme substrates is extensive, alkaline phosphatase, reaction with DAB can be enhanced using nickel, producing a deep purple/black staining
16.
Alcohol
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In chemistry, an alcohol is any organic compound in which the hydroxyl functional group is bound to a saturated carbon atom. The term alcohol originally referred to the alcohol ethanol, the predominant alcohol in alcoholic beverages. The suffix -ol in non-systematic names also typically indicates that the substance includes a functional group and, so. But many substances, particularly sugars contain hydroxyl functional groups without using the suffix, an important class of alcohols, of which methanol and ethanol are the simplest members is the saturated straight chain alcohols, the general formula for which is CnH2n+1OH. The word alcohol is from the Arabic kohl, a used as an eyeliner. Al- is the Arabic definite article, equivalent to the in English, alcohol was originally used for the very fine powder produced by the sublimation of the natural mineral stibnite to form antimony trisulfide Sb 2S3, hence the essence or spirit of this substance. It was used as an antiseptic, eyeliner, and cosmetic, the meaning of alcohol was extended to distilled substances in general, and then narrowed to ethanol, when spirits as a synonym for hard liquor. Bartholomew Traheron, in his 1543 translation of John of Vigo, Vigo wrote, the barbarous auctours use alcohol, or alcofoll, for moost fine poudre. The 1657 Lexicon Chymicum, by William Johnson glosses the word as antimonium sive stibium, by extension, the word came to refer to any fluid obtained by distillation, including alcohol of wine, the distilled essence of wine. Libavius in Alchymia refers to vini alcohol vel vinum alcalisatum, Johnson glosses alcohol vini as quando omnis superfluitas vini a vino separatur, ita ut accensum ardeat donec totum consumatur, nihilque fæcum aut phlegmatis in fundo remaneat. The words meaning became restricted to spirit of wine in the 18th century and was extended to the class of substances so-called as alcohols in modern chemistry after 1850, the term ethanol was invented 1892, based on combining the word ethane with ol the last part of alcohol. In the IUPAC system, in naming simple alcohols, the name of the alkane chain loses the terminal e and adds ol, e. g. as in methanol and ethanol. When necessary, the position of the group is indicated by a number between the alkane name and the ol, propan-1-ol for CH 3CH 2CH 2OH, propan-2-ol for CH 3CHCH3. If a higher priority group is present, then the prefix hydroxy is used, in other less formal contexts, an alcohol is often called with the name of the corresponding alkyl group followed by the word alcohol, e. g. methyl alcohol, ethyl alcohol. Propyl alcohol may be n-propyl alcohol or isopropyl alcohol, depending on whether the group is bonded to the end or middle carbon on the straight propane chain. As described under systematic naming, if another group on the molecule takes priority, Alcohols are then classified into primary, secondary, and tertiary, based upon the number of carbon atoms connected to the carbon atom that bears the hydroxyl functional group. The primary alcohols have general formulas RCH2OH, the simplest primary alcohol is methanol, for which R=H, and the next is ethanol, for which R=CH3, the methyl group. Secondary alcohols are those of the form RRCHOH, the simplest of which is 2-propanol, for the tertiary alcohols the general form is RRRCOH
17.
Xylene
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Xylene, xylol or dimethylbenzene is any one of three isomers of dimethylbenzene, or a combination thereof. With the formula 2C6H4, each of the three compounds has a benzene ring with two methyl groups attached at substituents. They are all colorless, flammable liquids, some of which are of great industrial value, the mixture is referred to as both xylene and, more precisely, xylenes. Xylenes are an important petrochemical produced by reforming and also by coal carbonisation in the manufacture of coke fuel. They also occur in oil in concentrations of about 0. 5–1%. Small quantities occur in gasoline and aircraft fuels, xylenes are produced mainly as part of the BTX aromatics extracted from the product of catalytic reforming known as reformate. The xylene mixture is a greasy, colorless liquid commonly encountered as a solvent. Several million tons are produced annually, in 2011, a global consortium began construction of one of the world’s largest xylene plants in Singapore. Xylene was first isolated and named in 1850 by the French chemist Auguste Cahours, Xylene exists in three isomeric forms. The isomers can be distinguished by the designations ortho-, meta-, and para-, of the three isomers, the p-isomer is the most industrially sought after since it can be oxidized to terephthalic acid. Xylenes are produced by the methylation of toluene and benzene, commercial or laboratory grade xylene produced usually contains about 40-65% of m-xylene and up to 20% each of o-xylene, p-xylene and ethylbenzene. The ratio of isomers can be shifted to favor the highly valued p-xylene via the patented UOP-Isomar process or by transalkylation of xylene with itself or trimethylbenzene and these conversions are catalyzed by zeolites. The chemical and physical properties of xylene differ according to the respective isomers, the melting point ranges from −47.87 °C to 13.26 °C. The boiling point for each isomer is around 140 °C, the density of each isomer is around 0.87 g/mL and thus is less dense than water. Xylene in air can be smelled at concentrations as low as 0.08 to 3.7 ppm, xylenes form azeotropes with water and a variety of alcohols. With water the azeotrope consists of 60% xylenes and boils at 94.5 °C, as with many alkylbenzene compounds, xylenes form complexes with various halocarbons. The complexes of different isomers often have different properties from each other. P-Xylene is the precursor to terephthalic acid and dimethyl terephthalate
18.
Microtome
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A microtome is a tool used to cut extremely thin slices of material, known as sections. Important in science, microtomes are used in microscopy, allowing for the preparation of samples for observation under transmitted light or electron radiation, microtomes use steel, glass, or diamond blades depending upon the specimen being sliced and the desired thickness of the sections being cut. Steel blades are used to prepare sections of animal or plant tissues for light microscopy histology, glass knives are used to slice sections for light microscopy and to slice very thin sections for electron microscopy. Industrial grade diamond knives are used to slice hard materials such as bone, teeth, gem quality diamond knives are used for slicing thin sections for electron microscopy. Microtomy is a method for the preparation of thin sections for such as bones, minerals and teeth. Microtome sections can be thin enough to section a human hair across its breadth, with section thickness between 50 nm and 100 µm. In the beginnings of light development, sections from plants. It was found that to observe the structure of the specimen under observation it was important to make clean reproducible cuts on the order of 100 µm and this allowed for the observation of samples using light microscopes in a transmission mode. One of the first devices for the preparation of such cuts was invented in 1770 by George Adams, Jr. the device was hand operated, and the sample held in a cylinder and sections created from the top of the sample using a hand crank. In 1835, Andrew Prichard developed a table based model which allowed for the vibration to be isolated by affixing the device to the table, occasionally, attribution for the invention of the microtome is given to the anatomist Wilhelm His, Sr. In his Beschreibung eines Mikrotoms, Wilhelm wrote, The apparatus has enabled a precision in work by which I can achieve sections that by hand I cannot possibly create, namely it has enabled the possibility of achieving unbroken sections of objects in the course of research. Other sources further attribute the development to a Czech physiologist Jan Evangelista Purkyně, several sources describe the Purkyne model as the first in practical use. The obscurities in the origins of the microtome are due to the fact that the first microtomes were simply cutting apparatuses, today, the majority of microtomes are a knife-block design with a changeable knife, a specimen holder and an advancement mechanism. The section thickness is controlled by an adjustment mechanism, allowing for precise control, the most common applications of microtomes are, Traditional Histology Technique, tissues are hardened by replacing water with paraffin. The tissue is cut in the microtome at thicknesses varying from 2 to 50 µm. From there the tissue can be mounted on a slide, stained with appropriate aqueous dye after prior removal of the paraffin. This technique is faster than traditional histology and is used in conjunction with medical procedures to achieve a quick diagnosis. Cryosections can also be used in immunohistochemistry as freezing tissue stops degradation of tissue faster than using a fixative, Electron Microscopy Technique, after embedding tissues in epoxy resin, a microtome equipped with a glass or gem grade diamond knife is used to cut very thin sections
19.
Frozen section
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The frozen section procedure is a pathological laboratory procedure to perform rapid microscopic analysis of a specimen. It is used most often in oncological surgery, the technical name for this procedure is cryosection. The quality of the produced by frozen section is of lower quality than formalin fixed paraffin embedded tissue processing. While diagnosis can be rendered in many cases, fixed tissue processing is preferred in many conditions for accurate diagnosis. The report given by the pathologist is usually limited to a benign or malignant diagnosis, the method of processing is usually done with the bread loafing technique. But margin controlled surgery can be performed using a variety of cutting and mounting methods. The frozen section procedure as practiced today in medical laboratories is based on the description by Dr Louis B. Wilson in 1905, the key instrument for cryosection is the cryostat, which is essentially a microtome inside a freezer. The microtome can be compared to a very accurate deli slicer, the usual histology slice is cut at 5 to 10 micrometres. The surgical specimen is placed on a metal disc which is then secured in a chuck. At this temperature, most tissues become rock-hard, usually a lower temperature is required for fat or lipid rich tissue. Each tissue has a temperature for processing. Subsequently it is cut frozen with the portion of the cryostat. The preparation of the sample is more rapid than with traditional histology technique. However, the quality of the sections is much lower. The entire laboratory can occupy a space less than 9-square-foot, the principal use of the frozen section procedure is the examination of tissue while surgery is taking place. This may be for reasons, In the performance of Mohs surgery – a simple method for real-time margin control of a surgical specimen. If a tumor appears to have metastasized, a sample of the metastasis is sent for cryosection to confirm its identity. This will help the surgeon decide whether there is any point in continuing the operation, usually, aggressive surgery is performed only if there is a chance to cure the patient
20.
Cryostat
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A cryostat is a device used to maintain low cryogenic temperatures of samples or devices mounted within the cryostat. Low temperatures may be maintained within a cryostat by using various refrigeration methods, hence it is usually assembled into a vessel, similar in construction to a vacuum flask or Dewar. Cryostats have numerous applications within science, engineering, and medicine, closed-cycle cryostats consist of a chamber through which cold helium vapour is pumped. An external mechanical refrigerator extracts the warmer helium exhaust vapour, which is cooled and recycled, closed-cycle cryostats consume a relatively large amount of electrical power, but need not be refilled with helium and can run continuously for an indefinite period. Objects may be cooled by attaching them to a metallic coldplate inside a chamber which is in thermal contact with the helium vapour chamber. Continuous-flow cryostats are cooled by liquid cryogens from a storage dewar, as the cryogen boils within the cryostat, it is continuously replenished by a steady flow from the storage dewar. The length of time over which cooling may be maintained is dictated by the volume of cryogens available, owing to the scarcity of liquid helium, some laboratories have facilities to capture and recover helium as it escapes from the cryostat, although these facilities are also costly to operate. Bath cryostats are similar in construction to vacuum flasks filled with liquid helium, a coldplate is placed in thermal contact with the liquid helium bath. The liquid helium may be replenished as it boils away, at intervals between a few hours and several months, depending on the volume and construction of the cryostat. The boil-off rate is minimised by shielding the bath with cold helium vapour. The helium vapour which boils away from the bath very effectively cools thermal shields around the outside of the bath, in the older designs there may be additional liquid nitrogen bath, or several concentric layers of shielding, with gradually increasing temperatures. However, the invention of super insulator materials has made this technology obsolete, in order to achieve temperature lower than liquid helium additional cooler stages may be added to the cryostat. Temperatures down to 1K can be reached by attaching the coldplate to a 1-K pot, temperatures down to 1mK can be reached by employing dilution refrigerator or dry dilution refrigerator typically in addition to the main stage and 1K pot. Temperatures below that can be reached using magnetic refrigeration, cryostats used in MRI machines are designed to hold a cryogen, typically helium, in a liquid state with minimal evaporation. The liquid helium bath is designed to keep the superconducting magnets bobbin of superconductive wire in its superconductive state, in this state the wire has no electrical resistance and very large currents are maintained with a low power input. To maintain superconductivity, the bobbin must be kept below its transition temperature by being immersed in the liquid helium. If, for any reason, the wire becomes resistive, i. e. loses superconductivity, a known as a quench. A burst disk, usually made of carbon, is placed within the chimney or vent pipe so that during a pressure excursion, modern MRI cryostats use a mechanical refrigerator to re-condense the helium gas and return it to the bath, to maintain cryogenic conditions and to conserve helium
21.
Resection margin
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A resection margin is the margin of apparently non-tumerous tissue around a tumor that has been surgically removed, called resected, in surgical oncology. The resection is an attempt to remove a tumor so that no portion of the malignant growth extends past the edges or margin of the removed tumor. These are retained after the surgery and examined microscopically by a pathologist, if cancerous cells are found at the edges the operation is much less likely to achieve the desired results. R0 is also called clean, tumor negative or negative margin, R1, the size of the margin is an important issue in areas that are functionally important, or in areas for which the extent of surgery is minimized due to aesthetic concerns. The desired size of margin around the tumor can vary, in resections for breast cancer there appears to be a difference between European and American radiation oncologists, with the former preferring larger margins of over 5 mm. Emmadi, R, Wiley, EL. Evaluation of resection margins in breast conservation therapy, the pathology perspective-past, present, and future
22.
Pigment
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A pigment is a material that changes the color of reflected or transmitted light as the result of wavelength-selective absorption. This physical process differs from fluorescence, phosphorescence, and other forms of luminescence, many materials selectively absorb certain wavelengths of light. Materials that humans have chosen and developed for use as pigments usually have properties that make them ideal for coloring other materials. A pigment must have a high tinting strength relative to the materials it colors and it must be stable in solid form at ambient temperatures. For industrial applications, as well as in the arts, permanence, pigments that are not permanent are called fugitive. Fugitive pigments fade over time, or with exposure to light, pigments are used for coloring paint, ink, plastic, fabric, cosmetics, food, and other materials. Most pigments used in manufacturing and the arts are dry colorants. This powder is added to a binder, a neutral or colorless material that suspends the pigment. A distinction is made between a pigment, which is insoluble in its vehicle, and a dye, which either is itself a liquid or is soluble in its vehicle. A colorant can act as either a pigment or a dye depending on the vehicle involved, in some cases, a pigment can be manufactured from a dye by precipitating a soluble dye with a metallic salt. The resulting pigment is called a lake pigment, the term biological pigment is used for all colored substances independent of their solubility. In 2006, around 7.4 million tons of inorganic, organic, asia has the highest rate on a quantity basis followed by Europe and North America. By 2020, revenues will have risen to approx, the global demand on pigments was roughly US$20.5 billion in 2009, around 1. 5-2% up from the previous year. It is predicted to increase in a growth rate in the coming years. The worldwide sales are said to increase up to US$24.5 billion in 2015, pigments appear the colors they are because they selectively reflect and absorb certain wavelengths of visible light. White light is an equal mixture of the entire spectrum of visible light with a wavelength in a range from about 375 or 400 nanometers to about 760 or 780 nm. When this light encounters a pigment, parts of the spectrum are absorbed by the molecules or ions of the pigment, in organic pigments such as diazo or phthalocyanine compounds the light is absorbed by the conjugated systems of double bonds in the molecule. Some of the inorganic pigments such as vermilion or cadmium yellow absorb light by transferring an electron from the ion to the positive ion
23.
Eosin
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In addition to staining proteins in the cytoplasm, it can be used to stain collagen and muscle fibers for examination under the microscope. Structures that stain readily with eosin are termed eosinophilic, the name Eosin comes from Eos, the Ancient Greek word for dawn and the name of the Ancient Greek goddess of the dawn. There are actually two closely related compounds commonly referred to as eosin. Most often used is Eosin Y, it has a slightly yellowish cast. The other eosin compound is eosin B, it has a faint bluish cast. The two dyes are interchangeable, and the use of one or the other is a matter of preference, Eosin Y is a tetrabromo derivative of fluorescein. Eosin B is a dibromo dinitro derivative of fluorescein, Eosin is most often used as a counterstain to hematoxylin in H&E staining. H&E staining is one of the most commonly used techniques in histology, tissue stained with haematoxylin and eosin shows cytoplasm stained pink-orange and nuclei stained darkly, either blue or purple. Eosin also stains red blood cells intensely red, for staining, eosin Y is typically used in concentrations of 1 to 5 percent weight by volume, dissolved in water or ethanol. For prevention of growth in aqueous solutions, thymol is sometimes added. A small concentration of acetic acid gives a deeper red stain to the tissue. It is listed as an IARC class 3 carcinogen, romanowsky stain Merbromin Jocelyn H. Bruce-Gregorios, M. D. Histopathologic Techniques, JMC Press Inc
24.
Cell nucleus
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In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. Eukaryotes usually have a nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei. Cell nuclei contain most of the genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones. The genes within these chromosomes are the nuclear genome and are structured in such a way to promote cell function. The nucleus maintains the integrity of genes and controls the activities of the cell by regulating gene expression—the nucleus is, therefore, because the nuclear membrane is impermeable to large molecules, nuclear pores are required to regulate nuclear transport of molecules across the envelope. The pores cross both nuclear membranes, providing a channel through which larger molecules must be transported by carrier proteins while allowing free movement of small molecules. Movement of large molecules such as proteins and RNA through the pores is required for gene expression and the maintenance of chromosomes. The best-known of these is the nucleolus, which is involved in the assembly of ribosomes. After being produced in the nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA, the nucleus was the first organelle to be discovered. What is most likely the oldest preserved drawing dates back to the early microscopist Antonie van Leeuwenhoek and he observed a lumen, the nucleus, in the red blood cells of salmon. Unlike mammalian red blood cells, those of other vertebrates still contain nuclei, the nucleus was also described by Franz Bauer in 1804 and in more detail in 1831 by Scottish botanist Robert Brown in a talk at the Linnean Society of London. Brown was studying orchids under microscope when he observed an opaque area and he did not suggest a potential function. In 1838, Matthias Schleiden proposed that the plays a role in generating cells. He believed that he had observed new cells assembling around cytoblasts, Franz Meyen was a strong opponent of this view, having already described cells multiplying by division and believing that many cells would have no nuclei. The function of the nucleus remained unclear, between 1877 and 1878, Oscar Hertwig published several studies on the fertilization of sea urchin eggs, showing that the nucleus of the sperm enters the oocyte and fuses with its nucleus. This was the first time it was suggested that an individual develops from a nucleated cell, therefore, the necessity of the sperm nucleus for fertilization was discussed for quite some time. However, Hertwig confirmed his observation in other groups, including amphibians. Eduard Strasburger produced the results for plants in 1884
25.
Cytoplasm
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In cell biology, the cytoplasm is the material within a living cell, excluding the cell nucleus. It comprises cytosol and the organelles – the cells internal sub-structures, all of the contents of the cells of prokaryotic organisms are contained within the cytoplasm. Within the cells of organisms the contents of the cell nucleus are separated from the cytoplasm. The cytoplasm is about 80% water and usually colorless, the submicroscopic ground cell substance or cytoplasmatic matrix which remains after exclusion the cell organelles and particles is groundplasm. It is within the cytoplasm that most cellular activities occur, such as many metabolic pathways including glycolysis, the concentrated inner area is called the endoplasm and the outer layer is called the cell cortex or the ectoplasm. Movement of calcium ions in and out of the cytoplasm is an activity for metabolic processes. In plants, movement of the cytoplasm around vacuoles is known as cytoplasmic streaming, the term was introduced by Rudolf von Kölliker in 1863, originally as a synonym for protoplasm, but later it has come to mean the cell substance and organelles outside the nucleus. There has been disagreement on the definition of cytoplasm, as some authors prefer to exclude from it some organelles. The physical properties of the cytoplasm have been contested in recent years and it remains uncertain how the varied components of the cytoplasm interact to allow movement of particles and organelles while maintaining the cell’s structure. The flow of cytoplasmic components plays an important role in cellular functions which are dependent on the permeability of the cytoplasm. An example of function is cell signalling, a process which is dependent on the manner in which signaling molecules are allowed to diffuse across the cell. While small signaling molecules like calcium ions are able to diffuse with ease, larger molecules, the irregular dynamics of such particles have given rise to various theories on the nature of the cytoplasm. There has long been evidence that the cytoplasm behaves like a sol-gel and it is thought that the component molecules and structures of the cytoplasm behave at times like a disordered colloidal solution and at other times like an integrated network, forming a solid mass. Recently it has proposed that the cytoplasm behaves like a glass-forming liquid approaching the glass transition. A cells ability to vitrify in the absence of activity, as in dormant periods. There has been examining the motion of cytoplasmic particles independent of the nature of the cytoplasm. In such an approach, the aggregate random forces within the cell caused by motor proteins explain the non-Brownian motion of cytoplasmic constituents. The three major elements of the cytoplasm are the cytosol, organelles and inclusions, the cytosol is the portion of the cytoplasm not contained within membrane-bound organelles
26.
Safranin
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Safranin is a biological stain used in histology and cytology. Safranin is used as a counterstain in some staining protocols, colouring all cell nuclei red and this is the classic counterstain in both Gram stains, and endospore staining. It can also be used for the detection of cartilage, mucin, safranin typically has the chemical structure shown at right. There is also trimethyl safranin, which has a methyl group in the ortho- position of the lower ring. Both compounds behave essentially identically in biological staining applications, and most manufacturers of safranin do not distinguish between the two, commercial safranin preparations often contain a blend of both types. Safranin is also used as indicator in analytical chemistry. Safranines are the compounds of symmetrical 2, 8-dimethyl-3, 7-diamino-phenazine. They are crystalline solids showing a green metallic lustre, they are readily soluble in water. They are strong bases and form stable monacid salts and their alcoholic solution shows a yellow-red fluorescence. Phenosafranine is not very stable in the state, its chloride forms green plates. It can be readily diazotized, and the salt when boiled with alcohol yields aposafranine or benzene induline. F. Kehrmann showed that aposafranine could be diazotized in the presence of concentrated sulfuric acid. Aposafranone, C18H12N2O, is formed by heating aposafranine with concentrated hydrochloric acid and these three compounds are perhaps to be represented as ortho- or as para-quinones. The safranine of commerce is an ortho-tolusafranine, the first aniline dye-stuff to be prepared on a manufacturing scale was mauveine, which was obtained by Sir William Henry Perkin by heating crude aniline with potassium bichromate and sulfuric acid. Mauveine was converted to parasafranine by Perkin in 1878 by oxidative/reductive loss of the 7-N-para-tolyl group, another well known safranin is phenosafranine widely used as histological dye, photosensitizer and redox probe. This article incorporates text from a now in the public domain, Chisholm, Hugh
27.
Silver
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Silver is a metallic element with symbol Ag and atomic number 47. The symbol Ag stems from Latin argentum, derived from the Greek ὰργὀς, a soft, white, lustrous transition metal, it exhibits the highest electrical conductivity, thermal conductivity, and reflectivity of any metal. The metal is found in the Earths crust in the pure, free form, as an alloy with gold and other metals. Most silver is produced as a byproduct of copper, gold, lead, Silver is more abundant than gold, but it is much less abundant as a native metal. Its purity is measured on a per mille basis, a 94%-pure alloy is described as 0.940 fine. As one of the seven metals of antiquity, silver has had a role in most human cultures. Silver has long valued as a precious metal. Silver metal is used in many premodern monetary systems in bullion coins, Silver is used in numerous applications other than currency, such as solar panels, water filtration, jewelry, ornaments, high-value tableware and utensils, and as an investment medium. Silver is used industrially in electrical contacts and conductors, in specialized mirrors, window coatings, Silver compounds are used in photographic film and X-rays. Dilute silver nitrate solutions and other compounds are used as disinfectants and microbiocides, added to bandages and wound-dressings, catheters. Silver is similar in its physical and chemical properties to its two neighbours in group 11 of the periodic table, copper and gold. This distinctive electron configuration, with an electron in the highest occupied s subshell over a filled d subshell. Silver is a soft, ductile and malleable transition metal. Silver crystallizes in a cubic lattice with bulk coordination number 12. Unlike metals with incomplete d-shells, metallic bonds in silver are lacking a covalent character and are relatively weak and this observation explains the low hardness and high ductility of single crystals of silver. Silver has a brilliant white metallic luster that can take a polish. Protected silver has greater optical reflectivity than aluminium at all wavelengths longer than ~450 nm, at wavelengths shorter than 450 nm, silvers reflectivity is inferior to that of aluminium and drops to zero near 310 nm. The electrical conductivity of silver is the greatest of all metals, greater even than copper, during World War II in the US,13540 tons of silver were used in electromagnets for enriching uranium, mainly because of the wartime shortage of copper
28.
Antibody
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An antibody, also known as an immunoglobulin, is a large, Y-shaped protein produced mainly by plasma cells that is used by the immune system to neutralize pathogens such as bacteria and viruses. The antibody recognizes a molecule of the harmful agent, called an antigen. Each tip of the Y of an antibody contains a paratope that is specific for one particular epitope on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can tag a microbe or a cell for attack by other parts of the immune system. Depending on the antigen, the binding may impede the process causing the disease or may activate macrophages to destroy the foreign substance. The ability of an antibody to communicate with the components of the immune system is mediated via its Fc region. The production of antibodies is the function of the humoral immune system. Antibodies are secreted by B cells of the immune system. In most cases, interaction of the B cell with a T helper cell is necessary to produce full activation of the B cell and, therefore, soluble antibodies are released into the blood and tissue fluids, as well as many secretions to continue to survey for invading microorganisms. Antibodies are glycoproteins belonging to the immunoglobulin superfamily and they constitute most of the gamma globulin fraction of the blood proteins. They are typically made of basic structural units—each with two heavy chains and two small light chains. There are several different types of heavy chains that define the five different types of crystallisable fragments that may be attached to the antigen-binding fragments. The five different types of Fc regions allow antibodies to be grouped into five isotypes, each Fc region of a particular antibody isotype is able to bind to its specific Fc Receptor, thus allowing the antigen-antibody complex to mediate different roles depending on which FcR it binds. The ability of an antibody to bind to its corresponding FcR is further modulated by the structure of the present at conserved sites within its Fc region. The ability of antibodies to bind to FcRs helps to direct the immune response for each different type of foreign object they encounter. For example, IgE is responsible for an allergic response consisting of mast cell degranulation, igEs Fab paratope binds to allergic antigen, for example house dust mite particles, while its Fc region binds to Fc receptor ε. The allergen-IgE-FcRε interaction mediates allergic signal transduction to induce conditions such as asthma and this region is known as the hypervariable region. Each of these variants can bind to a different antigen and this enormous diversity of antibody paratopes on the antigen-binding fragments allows the immune system to recognize an equally wide variety of antigens
29.
Protein
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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
30.
Lipid
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In biology, lipids comprise a group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins, monoglycerides, diglycerides, triglycerides, phospholipids, and others. The main biological functions of lipids include storing energy, signaling, lipids have applications in the cosmetic and food industries as well as in nanotechnology. Biological lipids originate entirely or in part from two types of biochemical subunits or building-blocks, ketoacyl and isoprene groups. Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids called triglycerides, lipids also encompass molecules such as fatty acids and their derivatives, as well as other sterol-containing metabolites such as cholesterol. Although humans and other mammals use various biosynthetic pathways both to break down and to synthesize lipids, some essential lipids cannot be made this way, the word lipid stems etymologically from the Greek lipos. The fatty acid structure is one of the most fundamental categories of biological lipids, the carbon chain, typically between four and 24 carbons long, may be saturated or unsaturated, and may be attached to functional groups containing oxygen, halogens, nitrogen, and sulfur. If a fatty acid contains a double bond, there is the possibility of either a cis or trans geometric isomerism, cis-double bonds cause the fatty acid chain to bend, an effect that is compounded with more double bonds in the chain. This in turn plays an important role in the structure and function of cell membranes, most naturally occurring fatty acids are of the cis configuration, although the trans form does exist in some natural and partially hydrogenated fats and oils. Examples of biologically important fatty acids include the eicosanoids, derived primarily from arachidonic acid and eicosapentaenoic acid, that include prostaglandins, leukotrienes, docosahexaenoic acid is also important in biological systems, particularly with respect to sight. Other major lipid classes in the fatty acid category are the fatty esters, fatty esters include important biochemical intermediates such as wax esters, fatty acid thioester coenzyme A derivatives, fatty acid thioester ACP derivatives and fatty acid carnitines. The fatty amides include N-acyl ethanolamines, such as the cannabinoid neurotransmitter anandamide, glycerolipids are composed of mono-, di-, and tri-substituted glycerols, the best-known being the fatty acid triesters of glycerol, called triglycerides. The word triacylglycerol is sometimes used synonymously with triglyceride, in these compounds, the three hydroxyl groups of glycerol are each esterified, typically by different fatty acids. Because they function as a store, these lipids comprise the bulk of storage fat in animal tissues. The hydrolysis of the bonds of triglycerides and the release of glycerol. Additional subclasses of glycerolipids are represented by glycosylglycerols, which are characterized by the presence of one or more sugar residues attached to glycerol via a glycosidic linkage, examples of structures in this category are the digalactosyldiacylglycerols found in plant membranes and seminolipid from mammalian sperm cells. Glycerophospholipids, usually referred to as phospholipids, are ubiquitous in nature and are key components of the bilayer of cells, as well as being involved in metabolism. Neural tissue contains high amounts of glycerophospholipids, and alterations in their composition has been implicated in various neurological disorders. Examples of glycerophospholipids found in biological membranes are phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine, the major sphingoid base of mammals is commonly referred to as sphingosine
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Carbohydrate
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A carbohydrate is a biological molecule consisting of carbon, hydrogen and oxygen atoms, usually with a hydrogen–oxygen atom ratio of 2,1, in other words, with the empirical formula Cmn. This formula holds true for monosaccharides, some exceptions exist, for example, deoxyribose, a sugar component of DNA, has the empirical formula C5H10O4. Carbohydrates are technically hydrates of carbon, structurally it is accurate to view them as polyhydroxy aldehydes and ketones. The term is most common in biochemistry, where it is a synonym of saccharide, a group that includes sugars, starch, the saccharides are divided into four chemical groups, monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Monosaccharides and disaccharides, the smallest carbohydrates, are referred to as sugars. The word saccharide comes from the Greek word σάκχαρον, meaning sugar, while the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix -ose. For example, grape sugar is the glucose, cane sugar is the disaccharide sucrose. Carbohydrates perform numerous roles in living organisms, polysaccharides serve for the storage of energy and as structural components. The 5-carbon monosaccharide ribose is an important component of coenzymes and the backbone of the genetic molecule known as RNA, the related deoxyribose is a component of DNA. Saccharides and their derivatives include many other important biomolecules that play key roles in the system, fertilization, preventing pathogenesis, blood clotting. In food science and in informal contexts, the term carbohydrate often means any food that is particularly rich in the complex carbohydrate starch or simple carbohydrates. Often in lists of information, such as the USDA National Nutrient Database, the term carbohydrate is used for everything other than water, protein, fat, ash. This will include chemical compounds such as acetic or lactic acid, carbohydrates are found in wide variety of foods. The important sources are cereals, potatoes, sugarcane, fruits, table sugar, bread, milk, starch and sugar are the important carbohydrates in our diet. Starch is abundant in potatoes, maize, rice and other cereals, sugar appears in our diet mainly as sucrose which is added to drinks and many prepared foods such as jam, biscuits and cakes. Glucose and fructose are found naturally in fruits and some vegetables. Glycogen is carbohydrate found in the liver and muscles, cellulose in the cell wall of all plant tissue is a carbohydrate. It is important in our diet as fibre which helps to maintain a healthy digestive system, formerly the name carbohydrate was used in chemistry for any compound with the formula Cm n
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DNA
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Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids, alongside proteins, lipids and complex carbohydrates, most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are termed polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases—cytosine, guanine, adenine, or thymine —a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison the total mass of the biosphere has been estimated to be as much as 4 trillion tons of carbon. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information and this information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences, the two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases and it is the sequence of these four nucleobases along the backbone that encodes biological information. RNA strands are created using DNA strands as a template in a process called transcription, under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells DNA is organized into structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, eukaryotic organisms store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast prokaryotes store their DNA only in the cytoplasm, within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed, DNA was first isolated by Friedrich Miescher in 1869. DNA is used by researchers as a tool to explore physical laws and theories, such as the ergodic theorem. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro-, among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a polymer made from repeating units called nucleotides
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RNA
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Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome, some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these processes is protein synthesis, a universal function where RNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA molecules to deliver amino acids to the ribosome, analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, in this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA. Each nucleotide in RNA contains a sugar, with carbons numbered 1 through 5. A base is attached to the 1 position, in general, adenine, cytosine, guanine, adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3 position of one ribose, the phosphate groups have a negative charge each, making RNA a charged molecule. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil, however, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural feature of RNA that distinguishes it from DNA is the presence of a group at the 2 position of the ribose sugar. The A-form geometry results in a deep and narrow major groove. RNA is transcribed with only four bases, but these bases, pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine are found in various places. Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine, inosine plays a key role in the wobble hypothesis of the genetic code. The specific roles of many of these modifications in RNA are not fully understood, the functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule and this leads to several recognizable domains of secondary structure like hairpin loops, bulges, and internal loops
