109-630: Sir Michael George Parke Stoker (4 July 1918 – 13 August 2013) was a British physician and medical researcher in virology . Stoker studied medicine at Clare College, Cambridge and St Thomas' Hospital in London, gaining his MD in 1947, after serving in the Royal Army Medical Corps during World War II. On return to civilian life he became a Fellow of Clare College from 1948 and an assistant tutor and director of medical studies from 1949 to 1958. Between 1953 and 1956, he researched
218-424: A bacterial nor a fungal infection , but something completely different. Beijerinck used the word "virus" to describe the mysterious agent in his ' contagium vivum fluidum ' ('contagious living fluid'). Rosalind Franklin proposed the full structure of the tobacco mosaic virus in 1955. One main motivation for the study of viruses is because they cause many infectious diseases of plants and animals. The study of
327-489: A 1993 Nobel to Philip Sharp and Richard Roberts . Catalytic RNA molecules ( ribozymes ) were discovered in the early 1980s, leading to a 1989 Nobel award to Thomas Cech and Sidney Altman . In 1990, it was found in Petunia that introduced genes can silence similar genes of the plant's own, now known to be a result of RNA interference . At about the same time, 22 nt long RNAs, now called microRNAs , were found to have
436-425: A certain amount of time, the message degrades into its component nucleotides with the assistance of ribonucleases . Transfer RNA (tRNA) is a small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and an anticodon region for codon recognition that binds to
545-554: A disadvantage in that it does not differentiate infectious and non-infectious viruses and "tests of cure" have to be delayed for up to 21 days to allow for residual viral nucleic acid to clear from the site of the infection. In laboratories many of the diagnostic test for detecting viruses are nucleic acid amplification methods such as PCR. Some tests detect the viruses or their components as these include electron microscopy and enzyme-immunoassays . The so-called "home" or "self"-testing gadgets are usually lateral flow tests , which detect
654-405: A fellow student at University of Cambridge; the couple had 5 children. Virology Virology is the scientific study of biological viruses . It is a subfield of microbiology that focuses on their detection, structure, classification and evolution, their methods of infection and exploitation of host cells for reproduction, their interaction with host organism physiology and immunity,
763-441: A greater weight on certain virus properties to maintain family uniformity. A unified taxonomy (a universal system for classifying viruses) has been established. Only a small part of the total diversity of viruses has been studied. As of 2021, 6 realms, 10 kingdoms, 17 phyla, 2 subphyla, 39 classes, 65 orders, 8 suborders, 233 families, 168 subfamilies , 2,606 genera, 84 subgenera , and 10,434 species of viruses have been defined by
872-522: A light microscope, sequencing is one of the main tools in virology to identify and study the virus. Traditional Sanger sequencing and next-generation sequencing (NGS) are used to sequence viruses in basic and clinical research, as well as for the diagnosis of emerging viral infections, molecular epidemiology of viral pathogens, and drug-resistance testing. There are more than 2.3 million unique viral sequences in GenBank. NGS has surpassed traditional Sanger as
981-686: A negative charge each, making RNA a charged molecule (polyanion). 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. The chemical structure of RNA is very similar to that of DNA , but differs in three primary ways: Like DNA, most biologically active RNAs, including mRNA , tRNA , rRNA , snRNAs , and other non-coding RNAs , contain self-complementary sequences that allow parts of
1090-647: A nucleoprotein called a ribosome. The ribosome binds mRNA and carries out protein synthesis. Several ribosomes may be attached to a single mRNA at any time. Nearly all the RNA found in a typical eukaryotic cell is rRNA. Transfer-messenger RNA (tmRNA) is found in many bacteria and plastids . It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling. The earliest known regulators of gene expression were proteins known as repressors and activators – regulators with specific short binding sites within enhancer regions near
1199-552: A nucleus, also contain nucleic acids. The role of RNA in protein synthesis was suspected already in 1939. Severo Ochoa won the 1959 Nobel Prize in Medicine (shared with Arthur Kornberg ) after he discovered an enzyme that can synthesize RNA in the laboratory. However, the enzyme discovered by Ochoa ( polynucleotide phosphorylase ) was later shown to be responsible for RNA degradation, not RNA synthesis. In 1956 Alex Rich and David Davies hybridized two separate strands of RNA to form
SECTION 10
#17327913604761308-547: A number of RNA-dependent RNA polymerases that use RNA as their template for synthesis of a new strand of RNA. For instance, a number of RNA viruses (such as poliovirus) use this type of enzyme to replicate their genetic material. Also, RNA-dependent RNA polymerase is part of the RNA interference pathway in many organisms. Many RNAs are involved in modifying other RNAs. Introns are spliced out of pre-mRNA by spliceosomes , which contain several small nuclear RNAs (snRNA), or
1417-457: A pathogen and determine which molecular parts to extract, inactivate, and use in a vaccine. Small molecules with conventional therapeutic properties can target RNA and DNA structures, thereby treating novel diseases. However, research is scarce on small molecules targeting RNA and approved drugs for human illness. Ribavirin, branaplam, and ataluren are currently available medications that stabilize double-stranded RNA structures and control splicing in
1526-472: A role in the development of C. elegans . Studies on RNA interference earned a Nobel Prize for Andrew Fire and Craig Mello in 2006, and another Nobel for studies on the transcription of RNA to Roger Kornberg in the same year. The discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, such as siRNA , to silence genes. Adding to the Nobel prizes for research on RNA, in 2009 it
1635-417: A role in the activation of the innate immune system against viral infections. In the late 1970s, it was shown that there is a single stranded covalently closed, i.e. circular form of RNA expressed throughout the animal and plant kingdom (see circRNA ). circRNAs are thought to arise via a "back-splice" reaction where the spliceosome joins a upstream 3' acceptor to a downstream 5' donor splice site. So far
1744-551: A similar filter. In the early 20th century, the English bacteriologist Frederick Twort discovered a group of viruses that infect bacteria, now called bacteriophages (or commonly 'phages'), and the French-Canadian microbiologist Félix d'Herelle described viruses that, when added to bacteria on an agar plate , would produce areas of dead bacteria. He accurately diluted a suspension of these viruses and discovered that
1853-456: A solution passed through it. In 1892, the Russian biologist Dmitri Ivanovsky used this filter to study what is now known as the tobacco mosaic virus : crushed leaf extracts from infected tobacco plants remained infectious even after filtration to remove bacteria. Ivanovsky suggested the infection might be caused by a toxin produced by bacteria, but he did not pursue the idea. At the time it
1962-455: A specific sequence on the messenger RNA chain through hydrogen bonding. Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. The rRNA is the component of the ribosome that hosts translation. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5.8S, 28S and 5S rRNA. Three of the rRNA molecules are synthesized in the nucleolus , and one is synthesized elsewhere. In the cytoplasm, ribosomal RNA and protein combine to form
2071-431: A specific spatial tertiary structure . The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops , bulges, and internal loops . In order to create, i.e., design, RNA for any given secondary structure, two or three bases would not be enough, but four bases are enough. This
2180-401: A statistical probability such as the volume of the test sample needed to ensure 50% of the hosts cells, plants or animals are infected. This is called the median infectious dose or ID 50 . Infective bacteriophages can be counted by seeding them onto "lawns" of bacteria in culture dishes. When at low concentrations, the viruses form holes in the lawn that can be counted. The number of viruses
2289-460: A top speed of around 100,000 rpm, are and this difference is used in a method called differential centrifugation . In this method the larger and heavier contaminants are removed from a virus mixture by low speed centrifugation. The viruses, which are small and light and are left in suspension, are then concentrated by high speed centrifugation. Following differential centrifugation, virus suspensions often remain contaminated with debris that has
SECTION 20
#17327913604762398-809: A variety of disorders. Protein-coding mRNAs have emerged as new therapeutic candidates, with RNA replacement being particularly beneficial for brief but torrential protein expression. In vitro transcribed mRNAs (IVT-mRNA) have been used to deliver proteins for bone regeneration, pluripotency, and heart function in animal models. SiRNAs, short RNA molecules, play a crucial role in innate defense against viruses and chromatin structure. They can be artificially introduced to silence specific genes, making them valuable for gene function studies, therapeutic target validation, and drug development. mRNA vaccines have emerged as an important new class of vaccines, using mRNA to manufacture proteins which provoke an immune response. Their first successful large-scale application came in
2507-402: Is protein synthesis , a universal function in which RNA molecules direct the synthesis of proteins on ribosomes . This process uses transfer RNA ( tRNA ) molecules to deliver amino acids to the ribosome , where ribosomal RNA ( rRNA ) then links amino acids together to form coded proteins. It has become widely accepted in science that early in the history of life on Earth , prior to
2616-675: Is virus classification . It is artificial in that it is not based on evolutionary phylogenetics but it is based shared or distinguishing properties of viruses. It seeks to describe the diversity of viruses by naming and grouping them on the basis of similarities. In 1962, André Lwoff , Robert Horne , and Paul Tournier were the first to develop a means of virus classification, based on the Linnaean hierarchical system. This system based classification on phylum , class , order , family , genus , and species . Viruses were grouped according to their shared properties (not those of their hosts) and
2725-510: Is a polymeric molecule that is essential for most biological functions, either by performing the function itself ( non-coding RNA ) or by forming a template for the production of proteins ( messenger RNA ). RNA and deoxyribonucleic acid (DNA) are nucleic acids . The nucleic acids constitute one of the four major macromolecules essential for all known forms of life . RNA is assembled as a chain of nucleotides . Cellular organisms use messenger RNA ( mRNA ) to convey genetic information (using
2834-423: Is a ribozyme . Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general, adenine (A), cytosine (C), guanine (G), or uracil (U). Adenine and guanine are purines , and cytosine and uracil are pyrimidines . A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have
2943-516: Is a broad subject covering biology, health, animal welfare, agriculture and ecology. Louis Pasteur was unable to find a causative agent for rabies and speculated about a pathogen too small to be detected by microscopes. In 1884, the French microbiologist Charles Chamberland invented the Chamberland filter (or Pasteur-Chamberland filter) with pores small enough to remove all bacteria from
3052-472: Is also dependent on the size of area that the user is counting. A larger area will require more time but can provide a more accurate representation of the sample. Results of the FFA are expressed as focus forming units per milliliter, or FFU/ When an assay for measuring the infective virus particle is done (Plaque assay, Focus assay), viral titre often refers to the concentration of infectious viral particles, which
3161-498: Is called enhancer RNAs . It is not clear at present whether they are a unique category of RNAs of various lengths or constitute a distinct subset of lncRNAs. In any case, they are transcribed from enhancers , which are known regulatory sites in the DNA near genes they regulate. They up-regulate the transcription of the gene(s) under control of the enhancer from which they are transcribed. At first, regulatory RNA
3270-634: Is different from the total viral particles. Viral load assays usually count the number of viral genomes present rather than the number of particles and use methods similar to PCR . Viral load tests are an important in the control of infections by HIV. This versatile method can be used for plant viruses. Molecular virology is the study of viruses at the level of nucleic acids and proteins. The methods invented by molecular biologists have all proven useful in virology. Their small sizes and relatively simple structures make viruses an ideal candidate for study by these techniques. For further study, viruses grown in
3379-406: Is formed. The FFA is particularly useful for quantifying classes of viruses that do not lyse the cell membranes, as these viruses would not be amenable to the plaque assay. Like the plaque assay, host cell monolayers are infected with various dilutions of the virus sample and allowed to incubate for a relatively brief incubation period (e.g., 24–72 hours) under a semisolid overlay medium that restricts
Michael Stoker - Misplaced Pages Continue
3488-419: Is likely why nature has "chosen" a four base alphabet: fewer than four would not allow the creation of all structures, while more than four bases are not necessary to do so. Since RNA is charged, metal ions such as Mg are needed to stabilise many secondary and tertiary structures . The naturally occurring enantiomer of RNA is D -RNA composed of D -ribonucleotides. All chirality centers are located in
3597-435: Is particularly useful when studying the genetics of viruses that have segmented genomes (fragmented into two or more nucleic acid molecules) such as influenza viruses and rotaviruses . The genes that encode properties such as serotype can be identified in this way. Often confused with reassortment, recombination is also the mixing of genes but the mechanism differs in that stretches of DNA or RNA molecules, as opposed to
3706-413: Is processed to mature mRNA. This removes its introns —non-coding sections of the pre-mRNA. The mRNA is then exported from the nucleus to the cytoplasm , where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA . In prokaryotic cells, which do not have nucleus and cytoplasm compartments, mRNA can bind to ribosomes while it is being transcribed from DNA. After
3815-411: Is relatively inert but easily self-forms a gradient when centrifuged at high speed in an ultracentrifuge. Buoyant density centrifugation can also be used to purify the components of viruses such as their nucleic acids or proteins. The separation of molecules based on their electric charge is called electrophoresis . Viruses and all their components can be separated and purified using this method. This
3924-500: Is then expressed as plaque forming units . For the bacteriophages that reproduce in bacteria that cannot be grown in cultures, viral load assays are used. The focus forming assay (FFA) is a variation of the plaque assay, but instead of relying on cell lysis in order to detect plaque formation, the FFA employs immunostaining techniques using fluorescently labeled antibodies specific for a viral antigen to detect infected host cells and infectious virus particles before an actual plaque
4033-550: Is used as template for building the ends of eukaryotic chromosomes . Double-stranded RNA (dsRNA) is RNA with two complementary strands, similar to the DNA found in all cells, but with the replacement of thymine by uracil and the adding of one oxygen atom. dsRNA forms the genetic material of some viruses ( double-stranded RNA viruses ). Double-stranded RNA, such as viral RNA or siRNA , can trigger RNA interference in eukaryotes , as well as interferon response in vertebrates . In eukaryotes, double-stranded RNA (dsRNA) plays
4142-429: Is usually done in a supporting medium such as agarose and polyacrylamide gels . The separated molecules are revealed using stains such as coomasie blue , for proteins, or ethidium bromide for nucleic acids. In some instances the viral components are rendered radioactive before electrophoresis and are revealed using photographic film in a process known as autoradiography . As most viruses are too small to be seen by
4251-571: Is very sensitive and specific, but can be easily compromised by contamination. Most of the tests used in veterinary virology and medical virology are based on PCR or similar methods such as transcription mediated amplification . When a novel virus emerges, such as the covid coronavirus, a specific test can be devised quickly so long as the viral genome has been sequenced and unique regions of the viral DNA or RNA identified. The invention of microfluidic tests as allowed for most of these tests to be automated, Despite its specificity and sensitivity, PCR has
4360-547: The D -ribose. By the use of L -ribose or rather L -ribonucleotides, L -RNA can be synthesized. L -RNA is much more stable against degradation by RNase . Like other structured biopolymers such as proteins, one can define topology of a folded RNA molecule. This is often done based on arrangement of intra-chain contacts within a folded RNA, termed as circuit topology . RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil), but these bases and attached sugars can be modified in numerous ways as
4469-498: The RNA World theory. There are indications that the enterobacterial sRNAs are involved in various cellular processes and seem to have significant role in stress responses such as membrane stress, starvation stress, phosphosugar stress and DNA damage. Also, it has been suggested that sRNAs have been evolved to have important role in stress responses because of their kinetic properties that allow for rapid response and stabilisation of
Michael Stoker - Misplaced Pages Continue
4578-536: The Royal Army Medical Corps and was sent to India. He worked in Lucknow, Hydrabad and finally Pune. In Pune, he became involved in studying typhus and bush typhus which led to his life-long work in virology, since at the time it was thought that the Rickettsia that caused these diseases were a type of virus. In 1947 he returned to civilian life. He married Veronica English (died 2004) in 1942, whom he met as
4687-453: The amino acid sequence in the protein that is produced. However, many RNAs do not code for protein (about 97% of the transcriptional output is non-protein-coding in eukaryotes ). These so-called non-coding RNAs ("ncRNA") can be encoded by their own genes (RNA genes), but can also derive from mRNA introns . The most prominent examples of non-coding RNAs are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in
4796-583: The galactic center of the Milky Way Galaxy . RNA, initially deemed unsuitable for therapeutics due to its short half-life, has been made useful through advances in stabilization. Therapeutic applications arise as RNA folds into complex conformations and binds proteins, nucleic acids, and small molecules to form catalytic centers. RNA-based vaccines are thought to be easier to produce than traditional vaccines derived from killed or altered pathogens, because it can take months or years to grow and study
4905-414: The genetic code . There are more than 100 other naturally occurring modified nucleosides. The greatest structural diversity of modifications can be found in tRNA , while pseudouridine and nucleosides with 2'-O-methylribose often present in rRNA are the most common. The specific roles of many of these modifications in RNA are not fully understood. However, it is notable that, in ribosomal RNA, many of
5014-440: The nitrogenous bases of guanine , uracil , adenine , and cytosine , denoted by the letters G, U, A, and C) 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 active processes
5123-475: The 2006 Nobel Prize in Physiology or Medicine for discovering microRNAs (miRNAs), specific short RNA molecules that can base-pair with mRNAs. Post-transcriptional expression levels of many genes can be controlled by RNA interference , in which miRNAs , specific short RNA molecules, pair with mRNA regions and target them for degradation. This antisense -based process involves steps that first process
5232-423: The 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occurring in the 5’ to 3’ direction. The DNA sequence also dictates where termination of RNA synthesis will occur. Primary transcript RNAs are often modified by enzymes after transcription. For example, a poly(A) tail and a 5' cap are added to eukaryotic pre-mRNA and introns are removed by the spliceosome . There are also
5341-562: The B-form most commonly observed in DNA. The A-form geometry results in a very deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone. The functional form of single-stranded RNA molecules, just like proteins, frequently requires
5450-994: The ICTV. The general taxonomic structure of taxon ranges and the suffixes used in taxonomic names are shown hereafter. As of 2021, the ranks of subrealm, subkingdom, and subclass are unused, whereas all other ranks are in use. The Nobel Prize-winning biologist David Baltimore devised the Baltimore classification system. The Baltimore classification of viruses is based on the mechanism of mRNA production. Viruses must generate mRNAs from their genomes to produce proteins and replicate themselves, but different mechanisms are used to achieve this in each virus family. Viral genomes may be single-stranded (ss) or double-stranded (ds), RNA or DNA, and may or may not use reverse transcriptase (RT). In addition, ssRNA viruses may be either sense (+) or antisense (−). This classification places viruses into seven groups: RNA Ribonucleic acid ( RNA )
5559-768: The RNA so that it can base-pair with a region of its target mRNAs. Once the base pairing occurs, other proteins direct the mRNA to be destroyed by nucleases . Next to be linked to regulation were Xist and other long noncoding RNAs associated with X chromosome inactivation . Their roles, at first mysterious, were shown by Jeannie T. Lee and others to be the silencing of blocks of chromatin via recruitment of Polycomb complex so that messenger RNA could not be transcribed from them. Additional lncRNAs, currently defined as RNAs of more than 200 base pairs that do not appear to have coding potential, have been found associated with regulation of stem cell pluripotency and cell division . The third major group of regulatory RNAs
SECTION 50
#17327913604765668-410: The RNA to fold and pair with itself to form double helices. Analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis (like enzymes). For instance, determination of the structure of
5777-507: The RNAs mature. Pseudouridine (Ψ), in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine (T) are found in various places (the most notable ones being in the TΨC loop of tRNA ). Another notable modified base is hypoxanthine , a deaminated adenine base whose nucleoside is called inosine (I). Inosine plays a key role in the wobble hypothesis of
5886-416: The antibodies they react with. The use of the antibodies which were once exclusively derived from the serum (blood fluid) of animals is called serology . Once an antibody–reaction has taken place in a test, other methods are needed to confirm this. Older methods included complement fixation tests , hemagglutination inhibition and virus neutralisation . Newer methods use enzyme immunoassays (EIA). In
5995-445: The case of the 5S rRNA of the members of the genus Halococcus ( Archaea ), which have an insertion, thus increasing its size. Messenger RNA (mRNA) carries information about a protein sequence to the ribosomes , the protein synthesis factories in the cell. It is coded so that every three nucleotides (a codon ) corresponds to one amino acid. In eukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it
6104-402: The cell nucleus and is usually catalyzed by an enzyme— RNA polymerase —using DNA as a template, a process known as transcription . Initiation of transcription begins with the binding of the enzyme to a promoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the helicase activity of the enzyme. The enzyme then progresses along the template strand in
6213-489: The centrifugation. In some cases, preformed gradients are used where solutions of steadily decreasing density are carefully overlaid on each other. Like an object in the Dead Sea , despite the centrifugal force the virus particles cannot sink into solutions that are more dense than they are and they form discrete layers of, often visible, concentrated viruses in the tube. Caesium chloride is often used for these solutions as it
6322-405: The determination of the structure of viruses. Viruses are obligate intracellular parasites and because they only reproduce inside the living cells of a host these cells are needed to grow them in the laboratory. For viruses that infect animals (usually called "animal viruses") cells grown in laboratory cell cultures are used. In the past, fertile hens' eggs were used and the viruses were grown on
6431-543: The detrimental effect they have on the host cell. These cytopathic effects are often characteristic of the type of virus. For instance, herpes simplex viruses produce a characteristic "ballooning" of the cells, typically human fibroblasts . Some viruses, such as mumps virus cause red blood cells from chickens to firmly attach to the infected cells. This is called "haemadsorption" or "hemadsorption". Some viruses produce localised "lesions" in cell layers called plaques , which are useful in quantitation assays and in identifying
6540-399: The diseases they cause, the techniques to isolate and culture them, and their use in research and therapy. The identification of the causative agent of tobacco mosaic disease (TMV) as a novel pathogen by Martinus Beijerinck (1898) is now acknowledged as being the official beginning of the field of virology as a discipline distinct from bacteriology . He realized the source was neither
6649-428: The documented species of animal, plant, and bacterial viruses were discovered during these years. In 1957 equine arterivirus and the cause of bovine virus diarrhoea (a pestivirus ) were discovered. In 1963 the hepatitis B virus was discovered by Baruch Blumberg , and in 1965 Howard Temin described the first retrovirus . Reverse transcriptase , the enzyme that retroviruses use to make DNA copies of their RNA,
SECTION 60
#17327913604766758-444: The earliest forms of life (self-replicating molecules) could have relied on RNA both to carry genetic information and to catalyze biochemical reactions—an RNA world . In May 2022, scientists discovered that RNA can form spontaneously on prebiotic basalt lava glass , presumed to have been abundant on the early Earth . In March 2015, DNA and RNA nucleobases , including uracil , cytosine and thymine , were reportedly formed in
6867-405: The environment, are used in phage display techniques for screening proteins DNA sequences. They are a powerful tool in molecular biology. All viruses have genes which are studied using genetics . All the techniques used in molecular biology, such as cloning, creating mutations RNA silencing are used in viral genetics. Reassortment is the switching of genes from different parents and it
6976-414: The evolution of DNA and possibly of protein-based enzymes as well, an " RNA world " existed in which RNA served as both living organisms' storage method for genetic information —a role fulfilled today by DNA, except in the case of RNA viruses —and potentially performed catalytic functions in cells—a function performed today by protein enzymes, with the notable and important exception of the ribosome, which
7085-456: The first crystal of RNA whose structure could be determined by X-ray crystallography. The sequence of the 77 nucleotides of a yeast tRNA was found by Robert W. Holley in 1965, winning Holley the 1968 Nobel Prize in Medicine (shared with Har Gobind Khorana and Marshall Nirenberg ). In the early 1970s, retroviruses and reverse transcriptase were discovered, showing for the first time that enzymes could copy RNA into DNA (the opposite of
7194-469: The first time in the 1930s when electron microscopes were invented. These microscopes use beams of electrons instead of light, which have a much shorter wavelength and can detect objects that cannot be seen using light microscopes. The highest magnification obtainable by electron microscopes is up to 10,000,000 times whereas for light microscopes it is around 1,500 times. Virologists often use negative staining to help visualise viruses. In this procedure,
7303-455: The first virus to be grown without using solid animal tissue or eggs. This work enabled Hilary Koprowski , and then Jonas Salk , to make an effective polio vaccine . The first images of viruses were obtained upon the invention of electron microscopy in 1931 by the German engineers Ernst Ruska and Max Knoll . In 1935, American biochemist and virologist Wendell Meredith Stanley examined
7412-541: The full molecules, are joined during the RNA or DNA replication cycle. Recombination is not as common as reassortment in nature but it is a powerful tool in laboratories for studying the structure and functions of viral genes. Reverse genetics is a powerful research method in virology. In this procedure complementary DNA (cDNA) copies of virus genomes called "infectious clones" are used to produce genetically modified viruses that can be then tested for changes in say, virulence or transmissibility. A major branch of virology
7521-438: The full structure of the virus in 1955. In the same year, Heinz Fraenkel-Conrat and Robley Williams showed that purified tobacco mosaic virus RNA and its protein coat can assemble by themselves to form functional viruses, suggesting that this simple mechanism was probably the means through which viruses were created within their host cells. The second half of the 20th century was the golden age of virus discovery, and most of
7630-423: The function of circRNAs is largely unknown, although for few examples a microRNA sponging activity has been demonstrated. Research on RNA has led to many important biological discoveries and numerous Nobel Prizes . Nucleic acids were discovered in 1868 by Friedrich Miescher , who called the material 'nuclein' since it was found in the nucleus . It was later discovered that prokaryotic cells, which do not have
7739-551: The genes to be regulated. Later studies have shown that RNAs also regulate genes. There are several kinds of RNA-dependent processes in eukaryotes regulating the expression of genes at various points, such as RNAi repressing genes post-transcriptionally , long non-coding RNAs shutting down blocks of chromatin epigenetically , and enhancer RNAs inducing increased gene expression. Bacteria and archaea have also been shown to use regulatory RNA systems such as bacterial small RNAs and CRISPR . Fire and Mello were awarded
7848-428: The high vacuum inside the electron microscope and the electron beam itself is destructive. In cryogenic electron microscopy the structure of viruses is preserved by embedding them in an environment of vitreous water . This allows the determination of biomolecular structures at near-atomic resolution, and has attracted wide attention to the approach as an alternative to X-ray crystallography or NMR spectroscopy for
7957-510: The highest dilutions (lowest virus concentrations), rather than killing all the bacteria, formed discrete areas of dead organisms. Counting these areas and multiplying by the dilution factor allowed him to calculate the number of viruses in the original suspension. Phages were heralded as a potential treatment for diseases such as typhoid and cholera , but their promise was forgotten with the development of penicillin . The development of bacterial resistance to antibiotics has renewed interest in
8066-461: The introns can be ribozymes that are spliced by themselves. RNA can also be altered by having its nucleotides modified to nucleotides other than A , C , G and U . In eukaryotes, modifications of RNA nucleotides are in general directed by small nucleolar RNAs (snoRNA; 60–300 nt), found in the nucleolus and cajal bodies . snoRNAs associate with enzymes and guide them to a spot on an RNA by basepairing to that RNA. These enzymes then perform
8175-406: The laboratory need purifying to remove contaminants from the host cells. The methods used often have the advantage of concentrating the viruses, which makes it easier to investigate them. Centrifuges are often used to purify viruses. Low speed centrifuges, i.e. those with a top speed of 10,000 revolutions per minute (rpm) are not powerful enough to concentrate viruses, but ultracentrifuges with
8284-472: The laboratory under outer space conditions, using starter chemicals such as pyrimidine , an organic compound commonly found in meteorites . Pyrimidine , like polycyclic aromatic hydrocarbons (PAHs), is one of the most carbon-rich compounds found in the universe and may have been formed in red giants or in interstellar dust and gas clouds. In July 2022, astronomers reported massive amounts of prebiotic molecules , including possible RNA precursors, in
8393-404: The mainstay of virology, did not exist. Now there are many methods for observing the structure and functions of viruses and their component parts. Thousands of different viruses are now known about and virologists often specialize in either the viruses that infect plants, or bacteria and other microorganisms , or animals. Viruses that infect humans are now studied by medical virologists. Virology
8502-463: The manner in which viruses cause disease is viral pathogenesis . The degree to which a virus causes disease is its virulence . These fields of study are called plant virology , animal virology and human or medical virology . Virology began when there were no methods for propagating or visualizing viruses or specific laboratory tests for viral infections. The methods for separating viral nucleic acids ( RNA and DNA ) and proteins , which are now
8611-471: The membranes surrounding the embryo. This method is still used in the manufacture of some vaccines. For the viruses that infect bacteria, the bacteriophages , the bacteria growing in test tubes can be used directly. For plant viruses, the natural host plants can be used or, particularly when the infection is not obvious, so-called indicator plants, which show signs of infection more clearly. Viruses that have grown in cell cultures can be indirectly detected by
8720-410: The more traditional hierarchy. Starting in 2018, the ICTV began to acknowledge deeper evolutionary relationships between viruses that have been discovered over time and adopted a 15-rank classification system ranging from realm to species. Additionally, some species within the same genus are grouped into a genogroup . The ICTV developed the current classification system and wrote guidelines that put
8829-432: The most common ones are laboratory modified plasmids (small circular molecules of DNA produced by bacteria). The viral nucleic acid, or a part of it, is inserted in the plasmid, which is the copied many times over by bacteria. This recombinant DNA can then be used to produce viral components without the need for native viruses. The viruses that reproduce in bacteria, archaea and fungi are informally called "phages", and
8938-405: The most popular approach for generating viral genomes. Viral genome sequencing as become a central method in viral epidemiology and viral classification . Data from the sequencing of viral genomes can be used to determine evolutionary relationships and this is called phylogenetic analysis . Software, such as PHYLIP , is used to draw phylogenetic trees . This analysis is also used in studying
9047-401: The nucleotide modification. rRNAs and tRNAs are extensively modified, but snRNAs and mRNAs can also be the target of base modification. RNA can also be methylated. Like DNA, RNA can carry genetic information. RNA viruses have genomes composed of RNA that encodes a number of proteins. The viral genome is replicated by some of those proteins, while other proteins protect the genome as
9156-403: The ones that infect bacteria – bacteriophages – in particular are useful in virology and biology in general. Bacteriophages were some of the first viruses to be discovered, early in the twentieth century, and because they are relatively easy to grow quickly in laboratories, much of our understanding of viruses originated by studying them. Bacteriophages, long known for their positive effects in
9265-524: The particles including the defective ones. Infectivity assays measure the amount (concentration) of infective viruses in a sample of known volume. For host cells, plants or cultures of bacterial or animal cells are used. Laboratory animals such as mice have also been used particularly in veterinary virology. These are assays are either quantitative where the results are on a continuous scale or quantal, where an event either occurs or it does not. Quantitative assays give absolute values and quantal assays give
9374-693: The physiological state. Bacterial small RNAs generally act via antisense pairing with mRNA to down-regulate its translation, either by affecting stability or affecting cis-binding ability. Riboswitches have also been discovered. They are cis-acting regulatory RNA sequences acting allosterically . They change shape when they bind metabolites so that they gain or lose the ability to bind chromatin to regulate expression of genes. Archaea also have systems of regulatory RNA. The CRISPR system, recently being used to edit DNA in situ , acts via regulatory RNAs in archaea and bacteria to provide protection against virus invaders. Synthesis of RNA typically occurs in
9483-405: The post-transcriptional modifications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function. Messenger RNA (mRNA) is the type of RNA that carries information from DNA to the ribosome , the sites of protein synthesis ( translation ) in the cell cytoplasm. The coding sequence of the mRNA determines
9592-928: The process of translation. There are also non-coding RNAs involved in gene regulation, RNA processing and other roles. Certain RNAs are able to catalyse chemical reactions such as cutting and ligating other RNA molecules, and the catalysis of peptide bond formation in the ribosome ; these are known as ribozymes . According to the length of RNA chain, RNA includes small RNA and long RNA. Usually, small RNAs are shorter than 200 nt in length, and long RNAs are greater than 200 nt long. Long RNAs, also called large RNAs, mainly include long non-coding RNA (lncRNA) and mRNA . Small RNAs mainly include 5.8S ribosomal RNA (rRNA), 5S rRNA , transfer RNA (tRNA), microRNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNAs), Piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA) and small rDNA-derived RNA (srRNA). There are certain exceptions as in
9701-512: The ribosome—an RNA-protein complex that catalyzes the assembly of proteins—revealed that its active site is composed entirely of RNA. An important structural component of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar . The presence of this functional group causes the helix to mostly take the A-form geometry , although in single strand dinucleotide contexts, RNA can rarely also adopt
9810-407: The same sedimentation coefficient and are not removed by the procedure. In these cases a modification of centrifugation, called buoyant density centrifugation , is used. In this method the viruses recovered from differential centrifugation are centrifuged again at very high speed for several hours in dense solutions of sugars or salts that form a density gradient, from low to high, in the tube during
9919-402: The species of virus by plaque reduction assays . Viruses growing in cell cultures are used to measure their susceptibility to validated and novel antiviral drugs . Viruses are antigens that induce the production of antibodies and these antibodies can be used in laboratories to study viruses. Related viruses often react with each other's antibodies and some viruses can be named based on
10028-489: The spread of infectious virus, creating localized clusters (foci) of infected cells. Plates are subsequently probed with fluorescently labeled antibodies against a viral antigen, and fluorescence microscopy is used to count and quantify the number of foci. The FFA method typically yields results in less time than plaque or fifty-percent-tissue-culture-infective-dose (TCID 50 ) assays, but it can be more expensive in terms of required reagents and equipment. Assay completion time
10137-570: The spread of viral infections in communities ( epidemiology ). When purified viruses or viral components are needed for diagnostic tests or vaccines, cloning can be used instead of growing the viruses. At the start of the COVID-19 pandemic the availability of the severe acute respiratory syndrome coronavirus 2 RNA sequence enabled tests to be manufactured quickly. There are several proven methods for cloning viruses and their components. Small pieces of DNA called cloning vectors are often used and
10246-613: The structure of Coxiella burnetii , the bacteria causing Q fever , with Paul Fiset . Stoker moved to Glasgow University in 1958. There he was the first professor of virology at the university (the first chair of virology to be established at a British university) from 1958 to 1968 and was appointed honorary director of the Medical Research Council Unit in 1959. He was the director of Imperial Cancer Research Fund Laboratories from 1968 to 1979 and president of Clare Hall , Cambridge University 1980–87. He
10355-602: The therapeutic use of bacteriophages. By the end of the 19th century, viruses were defined in terms of their infectivity , their ability to pass filters, and their requirement for living hosts. Viruses had been grown only in plants and animals. In 1906 Ross Granville Harrison invented a method for growing tissue in lymph , and in 1913 E. Steinhardt, C. Israeli, and R.A. Lambert used this method to grow vaccinia virus in fragments of guinea pig corneal tissue. In 1928, H. B. Maitland and M. C. Maitland grew vaccinia virus in suspensions of minced hens' kidneys. Their method
10464-450: The tobacco mosaic virus and found it was mostly made of protein. A short time later, this virus was separated into protein and RNA parts. The tobacco mosaic virus was the first to be crystallised and its structure could, therefore, be elucidated in detail. The first X-ray diffraction pictures of the crystallised virus were obtained by Bernal and Fankuchen in 1941. Based on her X-ray crystallographic pictures, Rosalind Franklin discovered
10573-506: The type of nucleic acid forming their genomes. In 1966, the International Committee on Taxonomy of Viruses (ICTV) was formed. The system proposed by Lwoff, Horne and Tournier was initially not accepted by the ICTV because the small genome size of viruses and their high rate of mutation made it difficult to determine their ancestry beyond order. As such, the Baltimore classification system has come to be used to supplement
10682-423: The usual route for transmission of genetic information). For this work, David Baltimore , Renato Dulbecco and Howard Temin were awarded a Nobel Prize in 1975. In 1976, Walter Fiers and his team determined the first complete nucleotide sequence of an RNA virus genome, that of bacteriophage MS2 . In 1977, introns and RNA splicing were discovered in both mammalian viruses and in cellular genes, resulting in
10791-467: The virus particle moves to a new host cell. Viroids are another group of pathogens, but they consist only of RNA, do not encode any protein and are replicated by a host plant cell's polymerase. Reverse transcribing viruses replicate their genomes by reverse transcribing DNA copies from their RNA; these DNA copies are then transcribed to new RNA. Retrotransposons also spread by copying DNA and RNA from one another, and telomerase contains an RNA that
10900-446: The virus using a tagged monoclonal antibody . These are also used in agriculture, food and environmental sciences. Counting viruses (quantitation) has always had an important role in virology and has become central to the control of some infections of humans where the viral load is measured. There are two basic methods: those that count the fully infective virus particles, which are called infectivity assays, and those that count all
11009-487: The viruses are suspended in a solution of metal salts such as uranium acetate. The atoms of metal are opaque to electrons and the viruses are seen as suspended in a dark background of metal atoms. This technique has been in use since the 1950s. Many viruses were discovered using this technique and negative staining electron microscopy is still a valuable weapon in a virologist's arsenal. Traditional electron microscopy has disadvantages in that viruses are damaged by drying in
11118-506: The years before PCR was invented immunofluorescence was used to quickly confirm viral infections. It is an infectivity assay that is virus species specific because antibodies are used. The antibodies are tagged with a dye that is luminescencent and when using an optical microscope with a modified light source, infected cells glow in the dark. PCR is a mainstay method for detecting viruses in all species including plants and animals. It works by detecting traces of virus specific RNA or DNA. It
11227-566: Was awarded for the elucidation of the atomic structure of the ribosome to Venki Ramakrishnan , Thomas A. Steitz , and Ada Yonath . In 2023 the Nobel Prize in Physiology or Medicine was awarded to Katalin Karikó and Drew Weissman for their discoveries concerning modified nucleosides that enabled the development of effective mRNA vaccines against COVID-19. In 1968, Carl Woese hypothesized that RNA might be catalytic and suggested that
11336-664: Was elected a Fellow of the Royal Society in 1968 and delivered their Leeuwenhoek Lecture in 1971. He was made a CBE in 1974 and was knighted in 1980. Stoker was born in Taunton , UK. His father, born in Ireland, was a medical doctor. He attended Oakham School and then medicine at University of Cambridge. At the outbreak of the Second World War he was in training at St Thomas's Hospital, London. He enlisted in
11445-595: Was first described in 1970 by Temin and David Baltimore independently. In 1983 Luc Montagnier 's team at the Pasteur Institute in France, first isolated the retrovirus now called HIV. In 1989 Michael Houghton 's team at Chiron Corporation discovered hepatitis C . There are several approaches to detecting viruses and these include the detection of virus particles (virions) or their antigens or nucleic acids and infectivity assays. Viruses were seen for
11554-413: Was made of particles, he called it a contagium vivum fluidum (soluble living germ) and reintroduced the word virus . Beijerinck maintained that viruses were liquid in nature, a theory later discredited by Wendell Stanley , who proved they were particulate. In the same year, Friedrich Loeffler and Paul Frosch passed the first animal virus, aphthovirus (the agent of foot-and-mouth disease ), through
11663-554: Was not widely adopted until the 1950s when poliovirus was grown on a large scale for vaccine production. Another breakthrough came in 1931 when the American pathologist Ernest William Goodpasture and Alice Miles Woodruff grew influenza and several other viruses in fertilised chicken eggs. In 1949, John Franklin Enders , Thomas Weller , and Frederick Robbins grew poliovirus in cultured cells from aborted human embryonic tissue,
11772-488: Was thought that all infectious agents could be retained by filters and grown on a nutrient medium—this was part of the germ theory of disease . In 1898, the Dutch microbiologist Martinus Beijerinck repeated the experiments and became convinced that the filtered solution contained a new form of infectious agent. He observed that the agent multiplied only in cells that were dividing, but as his experiments did not show that it
11881-405: Was thought to be a eukaryotic phenomenon, a part of the explanation for why so much more transcription in higher organisms was seen than had been predicted. But as soon as researchers began to look for possible RNA regulators in bacteria, they turned up there as well, termed as small RNA (sRNA). Currently, the ubiquitous nature of systems of RNA regulation of genes has been discussed as support for
#475524