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What is the most genetically simple organism except viruses?

What is the most genetically simple organism except viruses?


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What is the most genetically simple organism (except viruses) on this planet?

By simple I mean the least number of genes.


Mycoplasma genitalium was one of the first full bacterium genomes sequenced and since its a symbiotic organism that lives on the moist and warm genital skin surface it doesn't need as many genes as many bacteria. It has a 582 kbp genome sequence with only 521 genes.

But that is so 1995.

The 159 kbp genome of Candidatus carsonella was published in 2006. It is thought to only contain 182 genes. Its an endosymbiont of some sap eating insects.

But the current record holder, published this year, is Nasuia deltocephalinicola, discovered survey of insect endosymbionts, has only 112 kbp in its genome. Smaller than some viruses. It's thought to contain 137 protein coding genes with 29 tRNA genes, so its not a lot smaller than Carsonella in terms of gene count.

There's no reason to expect that this is the minimal viable genome by any means. I'm sure this response will need revision in a year or two.

M. genitalium has become the model system for minimal genome work. Many of these other bacteria might be difficult to culture, molecular biology lab techniques might have to be developed, so hopping onto newly discovered bacteria isn't always the best idea from a standpoint of producing science. It does suggest that M gentalium doesn't need all of its genes! A possible cause for these extra genes might be a more complex immune response in human beings where its found. It might also be because of the symbiotic requirements of insects is simpler.


Anatomy and Structure of Viruses

Scientists have long sought to uncover the structure and function of viruses. Viruses are unique in that they have been classified as both living and nonliving at various points in the history of biology. Viruses are not cells but non-living, infectious particles. They are capable of causing a number of diseases, including cancer, in various different types of organisms.

Viral pathogens not only infect humans and animals, but also plants, bacteria, protists, and archaeans. These extremely tiny particles are about 1,000 times smaller than bacteria and can be found in almost any environment. Viruses can not exist independently of other organisms as they must take over a living cell in order to reproduce.


List of Viruses Found in Animals | Microbiology

Here is a list of viruses that are found in animals: 1. Papovaviruses 2. Simian Virus-40 3. Adenoviruses 4. Herpesviruses 5. Pox Viruses 6. Picornavirus 7. Togaviruses 8. Rabies Viruses 9. Influenza Viruses 10. Reoviruses.

1. Papovaviruses:

Papovaviruses are one of the four important dsDNA viruses (e.g. papovaviruses, adenoviruses, herpes viruses and pox viruses) which produce tumour in many animals.

The term papova is derived from the first two letters of the three prototypes, papilloma virus, polyoma virus and simian vacuolating virus-40 (SV40). The other important viruses of this group are JC virus (associated with neurological degeneration), BX virus (which suppresses immune system of humans), K virus of mice, etc.

Capsid is of 45-55 nm, naked, icosahedral virion consists of dsDNA and protein. Capsid is made up of 72 capsomers which are built by 420 subunits. Capsid contains one major polypeptide (VP1) and two identical minor polypeptide (VP2 and VP3). Virus enters the cell and migrates to the nucleus where it replicates. The dsDNA encodes the early proteins and capsid proteins.

2. Simian Virus-40 (SV40):

S V40 is an oncogenic virus. It is naked and icosahedral in morphology with a diameter of 45 nm. (Fig. 17.4). Capsid consists of 72 capsomers. SV40 is similar to polyoma virus in size and structure. Polyoma is associated with tumour in mice.

The dsDNA in its native form is supercoiled (i.e. covalently closed circle) helix having the sedimentation coefficient of 21S. Total G+C content of nucleic acid is 41 %. After breaking the phosphodiester bond, single stranded DNA helix is converted into a relaxed circular form. This form has the sedimentation coefficient of 16S. A linear form (of 14S) is formed after double stranded break in the supercoil.

Virus enters the cell and directly migrates to the nucleus. Replication of the viral RNA takes place inside the nucleus. Before the replication begins, early proteins are synthesized in the nucleus of the infected cells.

The mechanism of DNA replication can be divided into the following four stages:

DNA replication begins at a site known as origin of replication as the ori genes are present at this site. Initiation requires a gene product A which is a globular protein. The ori region is rich in adenine and thymine.

Replication in two direction starts from the point of ori region. The RNA polymerase acts at this region and an RNA polymer of about 10 nucleotide in length is formed. Using (+) DNA as template a complementary (-) DNA strand develops on the RNA primer.

The chain elongates discontinuously on both the strands and form short fragements of DNA which is known as Okazaki fragements. In turn the Okazaki fragements are covalently sealed to form a continuous strand. DNA polymerase and DNA ligase are required for the complementary chain.

(c) Segregation of complementary DNA:

Until the two complementary strands reach the termination, chain elongation continues. Both the strands are terminated at about 180° from the ori region. Each duplex contains an original strand and a linear strand.

During maturation the two ends of the linear strand is sealed by the ligase and two complete circular DNA molecules are formed. The histone proteins get attached to DNA and results in super coiled form through winding of the DNA strands.

Within 12h of infection and before start of DNA replication, there begins early protein synthesis. The synthesis of antigen (i.e. tumour antigen) occurs by viral DNA which results in increased DNA metabolism in the infected host cell. Late proteins are synthesized when DNA replication is over. Polyadenylation (addition of poly A) takes place at 3′ end of mRNA which is not coded by the mRNAs.

3. Adenoviruses:

Adenoviruses were first isolated in human adenoids (tonsils) from which its name is derived. The adenoviruses are common pathogens of humans and animals. More than 100 serologically distinct types of adenovirus have been identified including 49 types that infect humans. Moreover, several strains have been the subject of intensive research and are used as tools in mammalian molecular biology.

Several adenoviruses cause respiratory and conjunctival diseases such as pneumonia, acute follicular conjunctivitis, epidemic keratoconjunctivitis, cystitis and gastroenteritis. In infants, pharyngitis and pharyngeal-conjunctival fever are common. In addition, a few types of human adenoviruses induce undifferentiated sarcomas in newborn hamsters and other rodents and can transform certain rodent and human cell cultures.

Adenoviruses are unusually stable to chemical or physical agents and adverse pH conditions. This ability helps in its prolonged survival outside of the body and water. Adenoviruses are primarily spread via respiratory droplets however, they can also be spread by fecal routes as well.

Adenoviruses are classified as group I under the Baltimore classification scheme. Adenoviruses are put iii the family Adenoviridae which is divided into two genera: mastadenoviruses (the mammalian adenoviruses) and aviadenoviruses (the avian adenoviruses). However, more than 100 antigenic types of adenoviruses e.g. mastadenoviruses and aviadenoviruses have been identified that infect mammals and birds.

Since adenoviruses readily infect human and other mammalian cells, their genomes have been developed into vectors in experimental therapy. Vector genomes carry deletions in the E1 and E3 regions the gaps in the genome are used to take up foreign genes, e.g. the gene for the cystic fibrosis trans-membrane conductance regulator (CFTR).

Deletions in E1 minimize the potential of these vector genomes to elicit an infection cycle in human cells. The first clinical applications in patients suffering from the genetic disease cystic fibrosis have been reported but problems with adenovirus toxicity remain.

4. Herpesviruses:

The name ‘herpes’ comes from the Greek word herpein which means ‘to creep’. These viruses cause chronic/latent/recurrent infections. Epidemiology of the common herpesvirus infections puzzled clinicians for many years. In 1950, Burnet and Buddingh showed that herpes simplex virus (HSV) could become latent after a primary infection, becoming reactivated after later provocation.

In 1954, Weller isolated varicella zoster VZV (HHV-3) from chicken pox and zoster, indicating the same causal agent. So far, about 100 herpesviruses have been isolated from many animal species.

Herpesviruses belong to the family Herpesviridae (viruses with double stranded DNA genomes) (Class 1), which have envelope with spikes on icosahedral virion. To date, there are eight known human herpesviruses some of them are oncogenic such as Simplex virus (herpes simples virus, HSV), Varicellovirus (caricella Zoster virus, CZV), Lymphocryptovirus (Epstein-Barr virus).

5. Pox Viruses:

The family Poxviridae is a legacy of the original grouping of viruses associated with diseases that produced poxs in the skin. Modem viral classification is based on the shape and molecular features of viruses and the smallpox virus remains as the most notable member of the family. It has two sub-families: Chordopoxvirinae and Entomopoxvirinae.

Some of the important genera are:

Orthopoxvirus (type species: Vaccinia virus diseases-cowpox, vaccinia, smallpox), Para poxvirus, Avipoxvirus, Capri poxvirus, Leporipoxvirus, Suipoxvirus, Swinepox virus, Molluscipoxvirus (type species: Molluscum contagiosum virus),Yatapoxvirus, Entomopoxvirus A, Entomopoxvirus B, Entomopoxvirus C. Poxviruses can infect both vertebrate and invertebrate animals.

There are four genera of poxviruses that may infect humans e.g. orthopox (variola virus, vaccinia virus, cowpox virus, monkeypox virus, smallpox), Parapox (orf virus, pseudo cowpox, bovine papular stomatitis vims), yatapox (tanapox virus, yaba monkey tumor virus), and molluscipox contagiosum virus (MCV).

The most common viruses are vaccinia (found in Indian subcontinent) and molluscum contagiousum but monkeypox infections are gradually increasing in west and central African rainforest countries.

An example of such a group and the problems of complexity are shown by the members of the poxvirus family. These viruses have oval or brick-shaped 200-400 nm long particles. These particles are so large that they were first observed using high resolution optical microscopes in 1886. At that time they were thought to be ‘the spores of micrococci’.

6. Picornavirus:

Picornaviruses are among the most diverse (more than 200 serotypes) and ‘oldest’ known viruses. A temple record of from Egypt (1400 B.C.) shows a picture of poliomyelitis in a Priest, Ruma. In 1898, Loeffler and Frosch first recognized foot and mouth disease virus (FMDV).

Picornaviruses belong to the family Picornaviridae which is one of the largest of the viral families. Under Baltimore’s viral classification system picornaviruses are classified as Group IV Viruses because they contain a single stranded, positive sense RNA genome of 7.2 – 9.0 Kb in length.

As the term denotes (pico=small, rna=RNA) picorna viruses are the smallest in size (18-30 nm). They are icosaherdal and contain a (+) ssRNA because it acts as mRNA.

There are five groups of picorna viruses:

(i) Human enterovirus which are found in alimentary canal e.g. poliovirus, ECHO (enteric cytoplasmic human orphan) virus causing paralysis, diarrhoea,

(ii) Cardio-viruses of rodent e.g. encephalomyocarditis virus,

(iii) Rhinovirus which causes respiratory infection like common cold, bronchitis and foot and mouth disease virus e.g. FMD virus in catties,

(v) Hepato-viruses (cause of hepatitis A).

The viruses that generally replicate in the intestine are called ‘enterovirus’. The most important pathogens from the genus entero-viruses include: poliovirus and Coxsackie A and B viruses.

7. Togaviruses:

Togaviruses belong to the family Togaviridae, which falls into the group IV of the Baltimore classification of viruses. Some examples Alphavirus (type species- Sindbis virus, eastern equine encephalitis virus, western equine encephalitis virus, Venezuelan equine encephalitis virus, Ross River virus) and Rubivirus (type species Rubella virus). Only Alphaviruses are arthropod-borne. Rubella virus has one species, which is quite distinct from Alphaviruses.

Togaviridae is classified as in Table 17.6:

Rubella was first recognized as a distinct disease in 1814. During 1938, Venezuelan Equine Encephalitis was isolated. Rubella vaccine was licensed in 1969. Large epidemic of the chikungunya virus was reported on the island of La Reunion and the surrounding islands in the Indian Ocean. During 2005-2006 in India, the major epidemic of the chikungunya virus was reported in over 1.5 million cases.

It grows in both mammalian and insect cell lines. Transmission of virus takes place from salivary glands of the mosquito to the bloodstream of the vertebrate host. Thereafter, virus particles travel to the skin and reticuloendothelial sys­tem (spleen and lymph nodes), where the pri­mary infection occurs.

8. Rabies Viruses:

Rabies (Latin: rabies, madness, rage, fury also called ‘hydrophobia’) is a viral zoonotic neuro-invasive disease that causes acute encephalitis (inflammation of the brain) in mammals (Fig. 17.31). It is most commonly caused by a bite from an infected animal or by other contact. Rabies has been known for more than 20,000 years.

The first description dates from the 23rd century BC in the Mesopotamia. During 1880s, Pasteur carried out the serial passage of Rabies virus in rabbits, and eventually succeeded in isolating an attenuated preparation which was used to treat patients bitten by mad dogs. There are over 200 Rhabdo-viruses known, which infect man, other mammals, fish, insects and plants.

The family Rhabdoviridae includes the genera Lyssavirus, Ephemerovirus and Vesiculo-virus. The rabies virus is a member of the genus lyssavirus. It is classified under Group V of Baltimore’s classification. Genetically, these viruses have non-segmented (-) sense RNA genome reminiscent of Paramyxoviruses. The family includes six genera.

9. Influenza Viruses:

In a phylogenetic-based taxonomy the RNA viruses includes the negative-sense ssRNA viruses which includes the Order Mononegavirales, and the family Orthomyxoviridae (Greek orthos – straight myxa = mucus). The family Orthomyxoviridae includes five genera: Influenza virus A, Influenza virus B, Influenza virus C, Thogotovirus and Isavirus.

The first three genera contain viruses that cause influenza in vertebrates, including birds, humans, and other mammals. Isaviruses infect salmon thogotoviruses infect vertebrates and invertebrates (e.g. mosquitoes and sea lice).

Orthomyxoviridae consists of 7 to 8 segments of linear negative-sense single stranded RNA. The total length of the genome is 12,000-15,000 nucleotides (nt). The sequence of genome has terminal repeats which are repeated at both ends. At 5′-end the terminal repeats are 12-13 nucleotides long, whereas nucleotide sequences of 3′-terminus are identical.

In most on all RNA species, the terminal repeats at 3′-end, are 9-11 nucleotides long. The 5′ and 3′ terminal sequences of all the genome segments are highly conserved. The nucleic acid is completely genomic in nature. However, each virion may contain defective interfering copies as well.

10. Reoviruses:

The family reoviridae falls under Group III (ds RNA) of Baltimore classification. It is a family of viruses that can affect the gastrointestinal system (such as Rotavirus) and respiratory tract. Viruses of this family have genome consisting of segmented dsRNA. The name Reoviridae is derived from respiratory, enteric and orphan viruses. The orphan virus are either non-Pathogenic or of low virulence.

The virus can be readily detected in feces, and may also be recovered from pharyngeal or nasal secretions, urine, cerebrospinal fluid, and blood. So far, the role of Reovirus in human disease or treatment is not clear.

There are more than 150 species in the family Reoviridae. Examples of reoviruses are: Aquareovirus, Coltivirus, Cypovirus, Fijivirus, Idnoreovirus, Mycoreovirus, Orbivirus, Orthoreovirus, Oryzavirus, Phytoreovirus, Rotavirus, and Seadornavirus.

Some genera and species of reoviridae are given in Table 17.10:


Contents

The word is from the Latin neuter vīrus referring to poison and other noxious liquids, from the same Indo-European base as Sanskrit viṣa, Avestan vīša, and ancient Greek ἰός (all meaning "poison"), first attested in English in 1398 in John Trevisa's translation of Bartholomeus Anglicus's De Proprietatibus Rerum. [14] [15] Virulent, from Latin virulentus (poisonous), dates to c. 1400. [16] [17] A meaning of "agent that causes infectious disease" is first recorded in 1728, [15] long before the discovery of viruses by Dmitri Ivanovsky in 1892. The English plural is viruses (sometimes also vira), [18] whereas the Latin word is a mass noun, which has no classically attested plural (vīra is used in Neo-Latin [19] ). The adjective viral dates to 1948. [20] The term virion (plural virions), which dates from 1959, [21] is also used to refer to a single viral particle that is released from the cell and is capable of infecting other cells of the same type. [22]

Louis Pasteur was unable to find a causative agent for rabies and speculated about a pathogen too small to be detected by microscopes. [23] In 1884, the French microbiologist Charles Chamberland invented the Chamberland filter (or Pasteur-Chamberland filter) with pores small enough to remove all bacteria from a solution passed through it. [24] 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. [25] At the time it 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. [4] In 1898, the Dutch microbiologist Martinus Beijerinck repeated the experiments and became convinced that the filtered solution contained a new form of infectious agent. [26] He observed that the agent multiplied only in cells that were dividing, but as his experiments did not show that it 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. [25] In the same year, Friedrich Loeffler and Paul Frosch passed the first animal virus, aphthovirus (the agent of foot-and-mouth disease), through a similar filter. [27]

In the early 20th century, the English bacteriologist Frederick Twort discovered a group of viruses that infect bacteria, now called bacteriophages [28] (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 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. [29] 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 the therapeutic use of bacteriophages. [30]

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. [31] In 1928, H. B. Maitland and M. C. Maitland grew vaccinia virus in suspensions of minced hens' kidneys. Their method was not widely adopted until the 1950s when poliovirus was grown on a large scale for vaccine production. [32]

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. [33] In 1949, John Franklin Enders, Thomas Weller, and Frederick Robbins grew poliovirus in cultured cells from aborted human embryonic tissue, [34] 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. [35]

The first images of viruses were obtained upon the invention of electron microscopy in 1931 by the German engineers Ernst Ruska and Max Knoll. [36] In 1935, American biochemist and virologist Wendell Meredith Stanley examined the tobacco mosaic virus and found it was mostly made of protein. [37] A short time later, this virus was separated into protein and RNA parts. [38] 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 the full structure of the virus in 1955. [39] 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. [40]

The second half of the 20th century was the golden age of virus discovery, and most of the documented species of animal, plant, and bacterial viruses were discovered during these years. [41] 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, [42] and in 1965 Howard Temin described the first retrovirus. Reverse transcriptase, the enzyme that retroviruses use to make DNA copies of their RNA, was first described in 1970 by Temin and David Baltimore independently. [43] In 1983 Luc Montagnier's team at the Pasteur Institute in France, first isolated the retrovirus now called HIV. [44] In 1989 Michael Houghton's team at Chiron Corporation discovered Hepatitis C. [45] [46]

Viruses are found wherever there is life and have probably existed since living cells first evolved. [47] The origin of viruses is unclear because they do not form fossils, so molecular techniques are used to investigate how they arose. [48] In addition, viral genetic material occasionally integrates into the germline of the host organisms, by which they can be passed on vertically to the offspring of the host for many generations. This provides an invaluable source of information for paleovirologists to trace back ancient viruses that have existed up to millions of years ago. There are three main hypotheses that aim to explain the origins of viruses: [49] [50]

Regressive hypothesis Viruses may have once been small cells that parasitised larger cells. Over time, genes not required by their parasitism were lost. The bacteria rickettsia and chlamydia are living cells that, like viruses, can reproduce only inside host cells. They lend support to this hypothesis, as their dependence on parasitism is likely to have caused the loss of genes that enabled them to survive outside a cell. This is also called the 'degeneracy hypothesis', [51] [52] or 'reduction hypothesis'. [53] Cellular origin hypothesis Some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger organism. The escaped DNA could have come from plasmids (pieces of naked DNA that can move between cells) or transposons (molecules of DNA that replicate and move around to different positions within the genes of the cell). [54] Once called "jumping genes", transposons are examples of mobile genetic elements and could be the origin of some viruses. They were discovered in maize by Barbara McClintock in 1950. [55] This is sometimes called the 'vagrancy hypothesis', [51] [56] or the 'escape hypothesis'. [53] Co-evolution hypothesis This is also called the 'virus-first hypothesis' [53] and proposes that viruses may have evolved from complex molecules of protein and nucleic acid at the same time that cells first appeared on Earth and would have been dependent on cellular life for billions of years. Viroids are molecules of RNA that are not classified as viruses because they lack a protein coat. They have characteristics that are common to several viruses and are often called subviral agents. [57] Viroids are important pathogens of plants. [58] They do not code for proteins but interact with the host cell and use the host machinery for their replication. [59] The hepatitis delta virus of humans has an RNA genome similar to viroids but has a protein coat derived from hepatitis B virus and cannot produce one of its own. It is, therefore, a defective virus. Although hepatitis delta virus genome may replicate independently once inside a host cell, it requires the help of hepatitis B virus to provide a protein coat so that it can be transmitted to new cells. [60] In similar manner, the sputnik virophage is dependent on mimivirus, which infects the protozoan Acanthamoeba castellanii. [61] These viruses, which are dependent on the presence of other virus species in the host cell, are called 'satellites' and may represent evolutionary intermediates of viroids and viruses. [62] [63]

In the past, there were problems with all of these hypotheses: the regressive hypothesis did not explain why even the smallest of cellular parasites do not resemble viruses in any way. The escape hypothesis did not explain the complex capsids and other structures on virus particles. The virus-first hypothesis contravened the definition of viruses in that they require host cells. [53] Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into the three domains. [64] This discovery has led modern virologists to reconsider and re-evaluate these three classical hypotheses. [64]

The evidence for an ancestral world of RNA cells [65] and computer analysis of viral and host DNA sequences are giving a better understanding of the evolutionary relationships between different viruses and may help identify the ancestors of modern viruses. To date, such analyses have not proved which of these hypotheses is correct. [65] It seems unlikely that all currently known viruses have a common ancestor, and viruses have probably arisen numerous times in the past by one or more mechanisms. [66]

Life properties

Scientific opinions differ on whether viruses are a form of life or organic structures that interact with living organisms. [11] They have been described as "organisms at the edge of life", [10] since they resemble organisms in that they possess genes, evolve by natural selection, [67] and reproduce by creating multiple copies of themselves through self-assembly. Although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life. Viruses do not have their own metabolism and require a host cell to make new products. They therefore cannot naturally reproduce outside a host cell [68] —although some bacteria such as rickettsia and chlamydia are considered living organisms despite the same limitation. [69] [70] Accepted forms of life use cell division to reproduce, whereas viruses spontaneously assemble within cells. They differ from autonomous growth of crystals as they inherit genetic mutations while being subject to natural selection. Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules. [2]

Structure

Viruses display a wide diversity of shapes and sizes, called 'morphologies'. In general, viruses are much smaller than bacteria. Most viruses that have been studied have a diameter between 20 and 300 nanometres. Some filoviruses have a total length of up to 1400 nm their diameters are only about 80 nm. [71] Most viruses cannot be seen with an optical microscope, so scanning and transmission electron microscopes are used to visualise them. [72] To increase the contrast between viruses and the background, electron-dense "stains" are used. These are solutions of salts of heavy metals, such as tungsten, that scatter the electrons from regions covered with the stain. When virions are coated with stain (positive staining), fine detail is obscured. Negative staining overcomes this problem by staining the background only. [73]

A complete virus particle, known as a virion, consists of nucleic acid surrounded by a protective coat of protein called a capsid. These are formed from protein subunits called capsomeres. [74] Viruses can have a lipid "envelope" derived from the host cell membrane. The capsid is made from proteins encoded by the viral genome and its shape serves as the basis for morphological distinction. [75] [76] Virally-coded protein subunits will self-assemble to form a capsid, in general requiring the presence of the virus genome. Complex viruses code for proteins that assist in the construction of their capsid. Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid. The capsid and entire virus structure can be mechanically (physically) probed through atomic force microscopy. [77] [78] In general, there are five main morphological virus types:

Helical These viruses are composed of a single type of capsomere stacked around a central axis to form a helical structure, which may have a central cavity, or tube. This arrangement results in virions which can be short and highly rigid rods, or long and very flexible filaments. The genetic material (typically single-stranded RNA, but single-stranded DNA in some cases) is bound into the protein helix by interactions between the negatively charged nucleic acid and positive charges on the protein. Overall, the length of a helical capsid is related to the length of the nucleic acid contained within it, and the diameter is dependent on the size and arrangement of capsomeres. The well-studied tobacco mosaic virus [79] and inovirus [80] are examples of helical viruses. Icosahedral Most animal viruses are icosahedral or near-spherical with chiral icosahedral symmetry. A regular icosahedron is the optimum way of forming a closed shell from identical subunits. The minimum number of capsomeres required for each triangular face is 3, which gives 60 for the icosahedron. Many viruses, such as rotavirus, have more than 60 capsomers and appear spherical but they retain this symmetry. To achieve this, the capsomeres at the apices are surrounded by five other capsomeres and are called pentons. Capsomeres on the triangular faces are surrounded by six others and are called hexons. [81] Hexons are in essence flat and pentons, which form the 12 vertices, are curved. The same protein may act as the subunit of both the pentamers and hexamers or they may be composed of different proteins. [82] Prolate This is an icosahedron elongated along the fivefold axis and is a common arrangement of the heads of bacteriophages. This structure is composed of a cylinder with a cap at either end. [83] Enveloped Some species of virus envelop themselves in a modified form of one of the cell membranes, either the outer membrane surrounding an infected host cell or internal membranes such as a nuclear membrane or endoplasmic reticulum, thus gaining an outer lipid bilayer known as a viral envelope. This membrane is studded with proteins coded for by the viral genome and host genome the lipid membrane itself and any carbohydrates present originate entirely from the host. Influenza virus, HIV (which causes AIDS), and severe acute respiratory syndrome coronavirus 2 (which causes COVID-19) [84] use this strategy. Most enveloped viruses are dependent on the envelope for their infectivity. [85] Complex These viruses possess a capsid that is neither purely helical nor purely icosahedral, and that may possess extra structures such as protein tails or a complex outer wall. Some bacteriophages, such as Enterobacteria phage T4, have a complex structure consisting of an icosahedral head bound to a helical tail, which may have a hexagonal base plate with protruding protein tail fibres. This tail structure acts like a molecular syringe, attaching to the bacterial host and then injecting the viral genome into the cell. [86]

The poxviruses are large, complex viruses that have an unusual morphology. The viral genome is associated with proteins within a central disc structure known as a nucleoid. The nucleoid is surrounded by a membrane and two lateral bodies of unknown function. The virus has an outer envelope with a thick layer of protein studded over its surface. The whole virion is slightly pleomorphic, ranging from ovoid to brick-shaped. [87]

Giant viruses

Mimivirus is one of the largest characterised viruses, with a capsid diameter of 400 nm. Protein filaments measuring 100 nm project from the surface. The capsid appears hexagonal under an electron microscope, therefore the capsid is probably icosahedral. [88] In 2011, researchers discovered the largest then known virus in samples of water collected from the ocean floor off the coast of Las Cruces, Chile. Provisionally named Megavirus chilensis, it can be seen with a basic optical microscope. [89] In 2013, the Pandoravirus genus was discovered in Chile and Australia, and has genomes about twice as large as Megavirus and Mimivirus. [90] All giant viruses have dsDNA genomes and they are classified into several families: Mimiviridae, Pithoviridae, Pandoraviridae, Phycodnaviridae, and the Mollivirus genus. [91]

Some viruses that infect Archaea have complex structures unrelated to any other form of virus, with a wide variety of unusual shapes, ranging from spindle-shaped structures to viruses that resemble hooked rods, teardrops or even bottles. Other archaeal viruses resemble the tailed bacteriophages, and can have multiple tail structures. [92]

Genome

  • DNA
  • RNA
  • Both DNA and RNA (at different stages in the life cycle)
  • Linear
  • Circular
  • Segmented
  • Single-stranded (ss)
  • Double-stranded (ds)
  • Double-stranded with regions of single-strandedness
  • Positive sense (+)
  • Negative sense (−)
  • Ambisense (+/−)

An enormous variety of genomic structures can be seen among viral species as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. There are millions of different types of viruses, [6] although fewer than 7,000 types have been described in detail. [93] As of January 2021, the NCBI Virus genome database has more than 193,000 complete genome sequences, [94] but there are doubtlessly many more to be discovered. [95] [96]

A virus has either a DNA or an RNA genome and is called a DNA virus or an RNA virus, respectively. The vast majority of viruses have RNA genomes. Plant viruses tend to have single-stranded RNA genomes and bacteriophages tend to have double-stranded DNA genomes. [97]

Viral genomes are circular, as in the polyomaviruses, or linear, as in the adenoviruses. The type of nucleic acid is irrelevant to the shape of the genome. Among RNA viruses and certain DNA viruses, the genome is often divided up into separate parts, in which case it is called segmented. For RNA viruses, each segment often codes for only one protein and they are usually found together in one capsid. All segments are not required to be in the same virion for the virus to be infectious, as demonstrated by brome mosaic virus and several other plant viruses. [71]

A viral genome, irrespective of nucleic acid type, is almost always either single-stranded (ss) or double-stranded (ds). Single-stranded genomes consist of an unpaired nucleic acid, analogous to one-half of a ladder split down the middle. Double-stranded genomes consist of two complementary paired nucleic acids, analogous to a ladder. The virus particles of some virus families, such as those belonging to the Hepadnaviridae, contain a genome that is partially double-stranded and partially single-stranded. [97]

For most viruses with RNA genomes and some with single-stranded DNA (ssDNA) genomes, the single strands are said to be either positive-sense (called the 'plus-strand') or negative-sense (called the 'minus-strand'), depending on if they are complementary to the viral messenger RNA (mRNA). Positive-sense viral RNA is in the same sense as viral mRNA and thus at least a part of it can be immediately translated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA-dependent RNA polymerase before translation. DNA nomenclature for viruses with genomic ssDNA is similar to RNA nomenclature, in that positive-strand viral ssDNA is identical in sequence to the viral mRNA and is thus a coding strand, while negative-sense viral ssDNA is complementary to the viral mRNA and is thus a template strand. [97] Several types of ssDNA and ssRNA viruses have genomes that are ambisense in that transcription can occur off both strands in a double-stranded replicative intermediate. Examples include geminiviruses, which are ssDNA plant viruses and arenaviruses, which are ssRNA viruses of animals. [98]

Genome size

Genome size varies greatly between species. The smallest—the ssDNA circoviruses, family Circoviridae—code for only two proteins and have a genome size of only two kilobases [99] the largest—the pandoraviruses—have genome sizes of around two megabases which code for about 2500 proteins. [90] Virus genes rarely have introns and often are arranged in the genome so that they overlap. [100]

In general, RNA viruses have smaller genome sizes than DNA viruses because of a higher error-rate when replicating, and have a maximum upper size limit. [48] Beyond this, errors when replicating render the virus useless or uncompetitive. To compensate, RNA viruses often have segmented genomes—the genome is split into smaller molecules—thus reducing the chance that an error in a single-component genome will incapacitate the entire genome. In contrast, DNA viruses generally have larger genomes because of the high fidelity of their replication enzymes. [101] Single-strand DNA viruses are an exception to this rule, as mutation rates for these genomes can approach the extreme of the ssRNA virus case. [102]

Genetic mutation

Viruses undergo genetic change by several mechanisms. These include a process called antigenic drift where individual bases in the DNA or RNA mutate to other bases. Most of these point mutations are "silent"—they do not change the protein that the gene encodes—but others can confer evolutionary advantages such as resistance to antiviral drugs. [103] [104] Antigenic shift occurs when there is a major change in the genome of the virus. This can be a result of recombination or reassortment. When this happens with influenza viruses, pandemics might result. [105] RNA viruses often exist as quasispecies or swarms of viruses of the same species but with slightly different genome nucleoside sequences. Such quasispecies are a prime target for natural selection. [106]

Segmented genomes confer evolutionary advantages different strains of a virus with a segmented genome can shuffle and combine genes and produce progeny viruses (or offspring) that have unique characteristics. This is called reassortment or 'viral sex'. [107]

Genetic recombination is the process by which a strand of DNA is broken and then joined to the end of a different DNA molecule. This can occur when viruses infect cells simultaneously and studies of viral evolution have shown that recombination has been rampant in the species studied. [108] Recombination is common to both RNA and DNA viruses. [109] [110]

Replication cycle

Viral populations do not grow through cell division, because they are acellular. Instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble in the cell. [111] When infected, the host cell is forced to rapidly produce thousands of copies of the original virus. [112]

Their life cycle differs greatly between species, but there are six basic stages in their life cycle: [113]

Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface. This specificity determines the host range and type of host cell of a virus. For example, HIV infects a limited range of human leucocytes. This is because its surface protein, gp120, specifically interacts with the CD4 molecule—a chemokine receptor—which is most commonly found on the surface of CD4+ T-Cells. This mechanism has evolved to favour those viruses that infect only cells in which they are capable of replication. Attachment to the receptor can induce the viral envelope protein to undergo changes that result in the fusion of viral and cellular membranes, or changes of non-enveloped virus surface proteins that allow the virus to enter. [114]

Penetration or viral entry follows attachment: Virions enter the host cell through receptor-mediated endocytosis or membrane fusion. The infection of plant and fungal cells is different from that of animal cells. Plants have a rigid cell wall made of cellulose, and fungi one of chitin, so most viruses can get inside these cells only after trauma to the cell wall. [115] Nearly all plant viruses (such as tobacco mosaic virus) can also move directly from cell to cell, in the form of single-stranded nucleoprotein complexes, through pores called plasmodesmata. [116] Bacteria, like plants, have strong cell walls that a virus must breach to infect the cell. Given that bacterial cell walls are much thinner than plant cell walls due to their much smaller size, some viruses have evolved mechanisms that inject their genome into the bacterial cell across the cell wall, while the viral capsid remains outside. [117]

Uncoating is a process in which the viral capsid is removed: This may be by degradation by viral enzymes or host enzymes or by simple dissociation the end-result is the releasing of the viral genomic nucleic acid. [118]

Replication of viruses involves primarily multiplication of the genome. Replication involves the synthesis of viral messenger RNA (mRNA) from "early" genes (with exceptions for positive-sense RNA viruses), viral protein synthesis, possible assembly of viral proteins, then viral genome replication mediated by early or regulatory protein expression. This may be followed, for complex viruses with larger genomes, by one or more further rounds of mRNA synthesis: "late" gene expression is, in general, of structural or virion proteins. [119]

Assembly – Following the structure-mediated self-assembly of the virus particles, some modification of the proteins often occurs. In viruses such as HIV, this modification (sometimes called maturation) occurs after the virus has been released from the host cell. [120]

Release – Viruses can be released from the host cell by lysis, a process that kills the cell by bursting its membrane and cell wall if present: this is a feature of many bacterial and some animal viruses. Some viruses undergo a lysogenic cycle where the viral genome is incorporated by genetic recombination into a specific place in the host's chromosome. The viral genome is then known as a "provirus" or, in the case of bacteriophages a "prophage". [121] Whenever the host divides, the viral genome is also replicated. The viral genome is mostly silent within the host. At some point, the provirus or prophage may give rise to the active virus, which may lyse the host cells. [122] Enveloped viruses (e.g., HIV) typically are released from the host cell by budding. During this process, the virus acquires its envelope, which is a modified piece of the host's plasma or other, internal membrane. [123]

Genome replication

The genetic material within virus particles, and the method by which the material is replicated, varies considerably between different types of viruses.

DNA viruses The genome replication of most DNA viruses takes place in the cell's nucleus. If the cell has the appropriate receptor on its surface, these viruses enter the cell either by direct fusion with the cell membrane (e.g., herpesviruses) or—more usually—by receptor-mediated endocytosis. Most DNA viruses are entirely dependent on the host cell's DNA and RNA synthesising machinery and RNA processing machinery. Viruses with larger genomes may encode much of this machinery themselves. In eukaryotes, the viral genome must cross the cell's nuclear membrane to access this machinery, while in bacteria it need only enter the cell. [124] RNA viruses Replication of RNA viruses usually takes place in the cytoplasm. RNA viruses can be placed into four different groups depending on their modes of replication. The polarity (whether or not it can be used directly by ribosomes to make proteins) of single-stranded RNA viruses largely determines the replicative mechanism the other major criterion is whether the genetic material is single-stranded or double-stranded. All RNA viruses use their own RNA replicase enzymes to create copies of their genomes. [125] Reverse transcribing viruses Reverse transcribing viruses have ssRNA (Retroviridae, Metaviridae, Pseudoviridae) or dsDNA (Caulimoviridae, and Hepadnaviridae) in their particles. Reverse transcribing viruses with RNA genomes (retroviruses) use a DNA intermediate to replicate, whereas those with DNA genomes (pararetroviruses) use an RNA intermediate during genome replication. Both types use a reverse transcriptase, or RNA-dependent DNA polymerase enzyme, to carry out the nucleic acid conversion. Retroviruses integrate the DNA produced by reverse transcription into the host genome as a provirus as a part of the replication process pararetroviruses do not, although integrated genome copies of especially plant pararetroviruses can give rise to infectious virus. [126] They are susceptible to antiviral drugs that inhibit the reverse transcriptase enzyme, e.g. zidovudine and lamivudine. An example of the first type is HIV, which is a retrovirus. Examples of the second type are the Hepadnaviridae, which includes Hepatitis B virus. [127]

Cytopathic effects on the host cell

The range of structural and biochemical effects that viruses have on the host cell is extensive. [128] These are called 'cytopathic effects'. [129] Most virus infections eventually result in the death of the host cell. The causes of death include cell lysis, alterations to the cell's surface membrane and apoptosis. [130] Often cell death is caused by cessation of its normal activities because of suppression by virus-specific proteins, not all of which are components of the virus particle. [131] The distinction between cytopathic and harmless is gradual. Some viruses, such as Epstein–Barr virus, can cause cells to proliferate without causing malignancy, [132] while others, such as papillomaviruses, are established causes of cancer. [133]

Dormant and latent infections

Some viruses cause no apparent changes to the infected cell. Cells in which the virus is latent and inactive show few signs of infection and often function normally. [134] This causes persistent infections and the virus is often dormant for many months or years. This is often the case with herpes viruses. [135] [136]

Host range

Viruses are by far the most abundant biological entities on Earth and they outnumber all the others put together. [137] They infect all types of cellular life including animals, plants, bacteria and fungi. [93] Different types of viruses can infect only a limited range of hosts and many are species-specific. Some, such as smallpox virus for example, can infect only one species—in this case humans, [138] and are said to have a narrow host range. Other viruses, such as rabies virus, can infect different species of mammals and are said to have a broad range. [139] The viruses that infect plants are harmless to animals, and most viruses that infect other animals are harmless to humans. [140] The host range of some bacteriophages is limited to a single strain of bacteria and they can be used to trace the source of outbreaks of infections by a method called phage typing. [141] The complete set of viruses in an organism or habitat is called the virome for example, all human viruses constitute the human virome. [142]

Classification 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. [143] 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 the type of nucleic acid forming their genomes. [144] 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 the more traditional hierarchy. [145] 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. [146]

ICTV classification

The ICTV developed the current classification system and wrote guidelines that put 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. [147] As of 2020, 6 realms, 10 kingdoms, 17 phyla, 2 subphyla, 39 classes, 59 orders, 8 suborders, 189 families, 136 subfamilies, 2,224 genera, 70 subgenera, and 9,110 species of viruses have been defined by the ICTV. [5]

The general taxonomic structure of taxon ranges and the suffixes used in taxonomic names are shown hereafter. As of 2020, the ranks of subrealm, subkingdom, and subclass are unused, whereas all other ranks are in use.

Realm (-viria) Subrealm (-vira) Kingdom (-virae) Subkingdom (-virites) Phylum (-viricota) Subphylum (-viricotina) Class (-viricetes) Subclass (-viricetidae) Order (-virales) Suborder (-virineae) Family (-viridae) Subfamily (-virinae) Genus (-virus) Subgenus (-virus) Species

Baltimore classification

The Nobel Prize-winning biologist David Baltimore devised the Baltimore classification system. [43] [148] The ICTV classification system is used in conjunction with the Baltimore classification system in modern virus classification. [149] [150] [151]

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:

  • I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)
  • II: ssDNA viruses (+ strand or "sense") DNA (e.g. Parvoviruses)
  • III: dsRNA viruses (e.g. Reoviruses)
  • IV: (+)ssRNA viruses (+ strand or sense) RNA (e.g. Coronaviruses, Picornaviruses, Togaviruses)
  • V: (−)ssRNA viruses (− strand or antisense) RNA (e.g. Orthomyxoviruses, Rhabdoviruses)
  • VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses)
  • VII: dsDNA-RT viruses DNA with RNA intermediate in life-cycle (e.g. Hepadnaviruses)

Examples of common human diseases caused by viruses include the common cold, influenza, chickenpox, and cold sores. Many serious diseases such as rabies, Ebola virus disease, AIDS (HIV), avian influenza, and SARS are caused by viruses. The relative ability of viruses to cause disease is described in terms of virulence. Other diseases are under investigation to discover if they have a virus as the causative agent, such as the possible connection between human herpesvirus 6 (HHV6) and neurological diseases such as multiple sclerosis and chronic fatigue syndrome. [153] There is controversy over whether the bornavirus, previously thought to cause neurological diseases in horses, could be responsible for psychiatric illnesses in humans. [154]

Viruses have different mechanisms by which they produce disease in an organism, which depends largely on the viral species. Mechanisms at the cellular level primarily include cell lysis, the breaking open and subsequent death of the cell. In multicellular organisms, if enough cells die, the whole organism will start to suffer the effects. Although viruses cause disruption of healthy homeostasis, resulting in disease, they may exist relatively harmlessly within an organism. An example would include the ability of the herpes simplex virus, which causes cold sores, to remain in a dormant state within the human body. This is called latency [155] and is a characteristic of the herpes viruses, including Epstein–Barr virus, which causes glandular fever, and varicella zoster virus, which causes chickenpox and shingles. Most people have been infected with at least one of these types of herpes virus. [156] These latent viruses might sometimes be beneficial, as the presence of the virus can increase immunity against bacterial pathogens, such as Yersinia pestis. [157]

Some viruses can cause lifelong or chronic infections, where the viruses continue to replicate in the body despite the host's defence mechanisms. [158] This is common in hepatitis B virus and hepatitis C virus infections. People chronically infected are known as carriers, as they serve as reservoirs of infectious virus. [159] In populations with a high proportion of carriers, the disease is said to be endemic. [160]

Epidemiology

Viral epidemiology is the branch of medical science that deals with the transmission and control of virus infections in humans. Transmission of viruses can be vertical, which means from mother to child, or horizontal, which means from person to person. Examples of vertical transmission include hepatitis B virus and HIV, where the baby is born already infected with the virus. [161] Another, more rare, example is the varicella zoster virus, which, although causing relatively mild infections in children and adults, can be fatal to the foetus and newborn baby. [162]

Horizontal transmission is the most common mechanism of spread of viruses in populations. [163] Horizontal transmission can occur when body fluids are exchanged during sexual activity, by exchange of saliva or when contaminated food or water is ingested. It can also occur when aerosols containing viruses are inhaled or by insect vectors such as when infected mosquitoes penetrate the skin of a host. [163] Most types of viruses are restricted to just one or two of these mechanisms and they are referred to as "respiratory viruses" or "enteric viruses" and so forth. The rate or speed of transmission of viral infections depends on factors that include population density, the number of susceptible individuals, (i.e., those not immune), [164] the quality of healthcare and the weather. [165]

Epidemiology is used to break the chain of infection in populations during outbreaks of viral diseases. [166] Control measures are used that are based on knowledge of how the virus is transmitted. It is important to find the source, or sources, of the outbreak and to identify the virus. Once the virus has been identified, the chain of transmission can sometimes be broken by vaccines. When vaccines are not available, sanitation and disinfection can be effective. Often, infected people are isolated from the rest of the community, and those that have been exposed to the virus are placed in quarantine. [167] To control the outbreak of foot-and-mouth disease in cattle in Britain in 2001, thousands of cattle were slaughtered. [168] Most viral infections of humans and other animals have incubation periods during which the infection causes no signs or symptoms. [169] Incubation periods for viral diseases range from a few days to weeks, but are known for most infections. [170] Somewhat overlapping, but mainly following the incubation period, there is a period of communicability—a time when an infected individual or animal is contagious and can infect another person or animal. [170] This, too, is known for many viral infections, and knowledge of the length of both periods is important in the control of outbreaks. [171] When outbreaks cause an unusually high proportion of cases in a population, community, or region, they are called epidemics. If outbreaks spread worldwide, they are called pandemics. [172]

Epidemics and pandemics

A pandemic is a worldwide epidemic. The 1918 flu pandemic, which lasted until 1919, was a category 5 influenza pandemic caused by an unusually severe and deadly influenza A virus. The victims were often healthy young adults, in contrast to most influenza outbreaks, which predominantly affect juvenile, elderly, or otherwise-weakened patients. [173] Older estimates say it killed 40–50 million people, [174] while more recent research suggests that it may have killed as many as 100 million people, or 5% of the world's population in 1918. [175]

Although viral pandemics are rare events, HIV—which evolved from viruses found in monkeys and chimpanzees—has been pandemic since at least the 1980s. [176] During the 20th century there were four pandemics caused by influenza virus and those that occurred in 1918, 1957 and 1968 were severe. [177] Most researchers believe that HIV originated in sub-Saharan Africa during the 20th century [178] it is now a pandemic, with an estimated 37.9 million people now living with the disease worldwide. [179] There were about 770,000 deaths from AIDS in 2018. [180] The Joint United Nations Programme on HIV/AIDS (UNAIDS) and the World Health Organization (WHO) estimate that AIDS has killed more than 25 million people since it was first recognised on 5 June 1981, making it one of the most destructive epidemics in recorded history. [181] In 2007 there were 2.7 million new HIV infections and 2 million HIV-related deaths. [182]

Several highly lethal viral pathogens are members of the Filoviridae. Filoviruses are filament-like viruses that cause viral hemorrhagic fever, and include ebolaviruses and marburgviruses. Marburg virus, first discovered in 1967, attracted widespread press attention in April 2005 for an outbreak in Angola. [183] Ebola virus disease has also caused intermittent outbreaks with high mortality rates since 1976 when it was first identified. The worst and most recent one is the 2013–2016 West Africa epidemic. [184]

Except for smallpox, most pandemics are caused by newly evolved viruses. These "emergent" viruses are usually mutants of less harmful viruses that have circulated previously either in humans or other animals. [185]

Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) are caused by new types of coronaviruses. Other coronaviruses are known to cause mild infections in humans, [186] so the virulence and rapid spread of SARS infections—that by July 2003 had caused around 8,000 cases and 800 deaths—was unexpected and most countries were not prepared. [187]

A related coronavirus emerged in Wuhan, China in November 2019 and spread rapidly around the world. Thought to have originated in bats and subsequently named severe acute respiratory syndrome coronavirus 2, infections with the virus caused a pandemic in 2020. [188] [189] [190] Unprecedented restrictions in peacetime have been placed on international travel, [191] and curfews imposed in several major cities worldwide. [192]

Cancer

Viruses are an established cause of cancer in humans and other species. Viral cancers occur only in a minority of infected persons (or animals). Cancer viruses come from a range of virus families, including both RNA and DNA viruses, and so there is no single type of "oncovirus" (an obsolete term originally used for acutely transforming retroviruses). The development of cancer is determined by a variety of factors such as host immunity [193] and mutations in the host. [194] Viruses accepted to cause human cancers include some genotypes of human papillomavirus, hepatitis B virus, hepatitis C virus, Epstein–Barr virus, Kaposi's sarcoma-associated herpesvirus and human T-lymphotropic virus. The most recently discovered human cancer virus is a polyomavirus (Merkel cell polyomavirus) that causes most cases of a rare form of skin cancer called Merkel cell carcinoma. [195] Hepatitis viruses can develop into a chronic viral infection that leads to liver cancer. [196] [197] Infection by human T-lymphotropic virus can lead to tropical spastic paraparesis and adult T-cell leukaemia. [198] Human papillomaviruses are an established cause of cancers of cervix, skin, anus, and penis. [199] Within the Herpesviridae, Kaposi's sarcoma-associated herpesvirus causes Kaposi's sarcoma and body-cavity lymphoma, and Epstein–Barr virus causes Burkitt's lymphoma, Hodgkin's lymphoma, B lymphoproliferative disorder, and nasopharyngeal carcinoma. [200] Merkel cell polyomavirus closely related to SV40 and mouse polyomaviruses that have been used as animal models for cancer viruses for over 50 years. [201]

Host defence mechanisms

The body's first line of defence against viruses is the innate immune system. This comprises cells and other mechanisms that defend the host from infection in a non-specific manner. This means that the cells of the innate system recognise, and respond to, pathogens in a generic way, but, unlike the adaptive immune system, it does not confer long-lasting or protective immunity to the host. [202]

RNA interference is an important innate defence against viruses. [203] Many viruses have a replication strategy that involves double-stranded RNA (dsRNA). When such a virus infects a cell, it releases its RNA molecule or molecules, which immediately bind to a protein complex called a dicer that cuts the RNA into smaller pieces. A biochemical pathway—the RISC complex—is activated, which ensures cell survival by degrading the viral mRNA. Rotaviruses have evolved to avoid this defence mechanism by not uncoating fully inside the cell, and releasing newly produced mRNA through pores in the particle's inner capsid. Their genomic dsRNA remains protected inside the core of the virion. [204] [205]

When the adaptive immune system of a vertebrate encounters a virus, it produces specific antibodies that bind to the virus and often render it non-infectious. This is called humoral immunity. Two types of antibodies are important. The first, called IgM, is highly effective at neutralising viruses but is produced by the cells of the immune system only for a few weeks. The second, called IgG, is produced indefinitely. The presence of IgM in the blood of the host is used to test for acute infection, whereas IgG indicates an infection sometime in the past. [206] IgG antibody is measured when tests for immunity are carried out. [207]

Antibodies can continue to be an effective defence mechanism even after viruses have managed to gain entry to the host cell. A protein that is in cells, called TRIM21, can attach to the antibodies on the surface of the virus particle. This primes the subsequent destruction of the virus by the enzymes of the cell's proteosome system. [208]

A second defence of vertebrates against viruses is called cell-mediated immunity and involves immune cells known as T cells. The body's cells constantly display short fragments of their proteins on the cell's surface, and, if a T cell recognises a suspicious viral fragment there, the host cell is destroyed by 'killer T' cells and the virus-specific T-cells proliferate. Cells such as the macrophage are specialists at this antigen presentation. [209] The production of interferon is an important host defence mechanism. This is a hormone produced by the body when viruses are present. Its role in immunity is complex it eventually stops the viruses from reproducing by killing the infected cell and its close neighbours. [210]

Not all virus infections produce a protective immune response in this way. HIV evades the immune system by constantly changing the amino acid sequence of the proteins on the surface of the virion. This is known as "escape mutation" as the viral epitopes escape recognition by the host immune response. These persistent viruses evade immune control by sequestration, blockade of antigen presentation, cytokine resistance, evasion of natural killer cell activities, escape from apoptosis, and antigenic shift. [211] Other viruses, called 'neurotropic viruses', are disseminated by neural spread where the immune system may be unable to reach them.

Prevention and treatment

Because viruses use vital metabolic pathways within host cells to replicate, they are difficult to eliminate without using drugs that cause toxic effects to host cells in general. The most effective medical approaches to viral diseases are vaccinations to provide immunity to infection, and antiviral drugs that selectively interfere with viral replication.

Vaccines

Vaccination is a cheap and effective way of preventing infections by viruses. Vaccines were used to prevent viral infections long before the discovery of the actual viruses. Their use has resulted in a dramatic decline in morbidity (illness) and mortality (death) associated with viral infections such as polio, measles, mumps and rubella. [212] Smallpox infections have been eradicated. [213] Vaccines are available to prevent over thirteen viral infections of humans, [214] and more are used to prevent viral infections of animals. [215] Vaccines can consist of live-attenuated or killed viruses, or viral proteins (antigens). [216] Live vaccines contain weakened forms of the virus, which do not cause the disease but, nonetheless, confer immunity. Such viruses are called attenuated. Live vaccines can be dangerous when given to people with a weak immunity (who are described as immunocompromised), because in these people, the weakened virus can cause the original disease. [217] Biotechnology and genetic engineering techniques are used to produce subunit vaccines. These vaccines use only the capsid proteins of the virus. Hepatitis B vaccine is an example of this type of vaccine. [218] Subunit vaccines are safe for immunocompromised patients because they cannot cause the disease. [219] The yellow fever virus vaccine, a live-attenuated strain called 17D, is probably the safest and most effective vaccine ever generated. [220]

Antiviral drugs

Antiviral drugs are often nucleoside analogues (fake DNA building-blocks), which viruses mistakenly incorporate into their genomes during replication. The life-cycle of the virus is then halted because the newly synthesised DNA is inactive. This is because these analogues lack the hydroxyl groups, which, along with phosphorus atoms, link together to form the strong "backbone" of the DNA molecule. This is called DNA chain termination. [221] Examples of nucleoside analogues are aciclovir for Herpes simplex virus infections and lamivudine for HIV and hepatitis B virus infections. Aciclovir is one of the oldest and most frequently prescribed antiviral drugs. [222] Other antiviral drugs in use target different stages of the viral life cycle. HIV is dependent on a proteolytic enzyme called the HIV-1 protease for it to become fully infectious. There is a large class of drugs called protease inhibitors that inactivate this enzyme. [223]

Hepatitis C is caused by an RNA virus. In 80% of people infected, the disease is chronic, and without treatment, they are infected for the remainder of their lives. There is now an effective treatment that uses the nucleoside analogue drug ribavirin combined with interferon. [224] The treatment of chronic carriers of the hepatitis B virus by using a similar strategy using lamivudine has been developed. [225]

Viruses infect all cellular life and, although viruses occur universally, each cellular species has its own specific range that often infects only that species. [226] Some viruses, called satellites, can replicate only within cells that have already been infected by another virus. [61]

Animal viruses

Viruses are important pathogens of livestock. Diseases such as foot-and-mouth disease and bluetongue are caused by viruses. [227] Companion animals such as cats, dogs, and horses, if not vaccinated, are susceptible to serious viral infections. Canine parvovirus is caused by a small DNA virus and infections are often fatal in pups. [228] Like all invertebrates, the honey bee is susceptible to many viral infections. [229] Most viruses co-exist harmlessly in their host and cause no signs or symptoms of disease. [4]

Plant viruses

There are many types of plant viruses, but often they cause only a loss of yield, and it is not economically viable to try to control them. Plant viruses are often spread from plant to plant by organisms, known as vectors. These are usually insects, but some fungi, nematode worms, and single-celled organisms are vectors. When control of plant virus infections is considered economical, for perennial fruits, for example, efforts are concentrated on killing the vectors and removing alternate hosts such as weeds. [230] Plant viruses cannot infect humans and other animals because they can reproduce only in living plant cells. [231]

Originally from Peru, the potato has become a staple crop worldwide. [232] The potato virus Y causes disease in potatoes and related species including tomatoes and peppers. In the 1980s, this virus acquired economical importance when it proved difficult to control in seed potato crops. Transmitted by aphids, this virus can reduce crop yields by up to 80 per cent, causing significant losses to potato yields. [233]

Plants have elaborate and effective defence mechanisms against viruses. One of the most effective is the presence of so-called resistance (R) genes. Each R gene confers resistance to a particular virus by triggering localised areas of cell death around the infected cell, which can often be seen with the unaided eye as large spots. This stops the infection from spreading. [234] RNA interference is also an effective defence in plants. [235] When they are infected, plants often produce natural disinfectants that kill viruses, such as salicylic acid, nitric oxide, and reactive oxygen molecules. [236]

Plant virus particles or virus-like particles (VLPs) have applications in both biotechnology and nanotechnology. The capsids of most plant viruses are simple and robust structures and can be produced in large quantities either by the infection of plants or by expression in a variety of heterologous systems. Plant virus particles can be modified genetically and chemically to encapsulate foreign material and can be incorporated into supramolecular structures for use in biotechnology. [237]

Bacterial viruses

Bacteriophages are a common and diverse group of viruses and are the most abundant biological entity in aquatic environments—there are up to ten times more of these viruses in the oceans than there are bacteria, [238] reaching levels of 250,000,000 bacteriophages per millilitre of seawater. [239] These viruses infect specific bacteria by binding to surface receptor molecules and then entering the cell. Within a short amount of time, in some cases, just minutes, bacterial polymerase starts translating viral mRNA into protein. These proteins go on to become either new virions within the cell, helper proteins, which help assembly of new virions, or proteins involved in cell lysis. Viral enzymes aid in the breakdown of the cell membrane, and, in the case of the T4 phage, in just over twenty minutes after injection over three hundred phages could be released. [240]

The major way bacteria defend themselves from bacteriophages is by producing enzymes that destroy foreign DNA. These enzymes, called restriction endonucleases, cut up the viral DNA that bacteriophages inject into bacterial cells. [241] Bacteria also contain a system that uses CRISPR sequences to retain fragments of the genomes of viruses that the bacteria have come into contact with in the past, which allows them to block the virus's replication through a form of RNA interference. [242] [243] This genetic system provides bacteria with acquired immunity to infection. [244]

Archaeal viruses

Some viruses replicate within archaea: these are DNA viruses with unusual and sometimes unique shapes. [7] [92] These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales. [245] Defences against these viruses involve RNA interference from repetitive DNA sequences within archaean genomes that are related to the genes of the viruses. [246] [247] Most archaea have CRISPR–Cas systems as an adaptive defence against viruses. These enable archaea to retain sections of viral DNA, which are then used to target and eliminate subsequent infections by the virus using a process similar to RNA interference. [248]

Viruses are the most abundant biological entity in aquatic environments. [2] There are about ten million of them in a teaspoon of seawater. [249] Most of these viruses are bacteriophages infecting heterotrophic bacteria and cyanophages infecting cyanobacteria and they are essential to the regulation of saltwater and freshwater ecosystems. [250] Bacteriophages are harmless to plants and animals, and are essential to the regulation of marine and freshwater ecosystems [251] are important mortality agents of phytoplankton, the base of the foodchain in aquatic environments. [252] They infect and destroy bacteria in aquatic microbial communities, and are one of the most important mechanisms of recycling carbon and nutrient cycling in marine environments. The organic molecules released from the dead bacterial cells stimulate fresh bacterial and algal growth, in a process known as the viral shunt. [253] In particular, lysis of bacteria by viruses has been shown to enhance nitrogen cycling and stimulate phytoplankton growth. [254] Viral activity may also affect the biological pump, the process whereby carbon is sequestered in the deep ocean. [255]

Microorganisms constitute more than 90% of the biomass in the sea. It is estimated that viruses kill approximately 20% of this biomass each day and that there are 10 to 15 times as many viruses in the oceans as there are bacteria and archaea. [256] Viruses are also major agents responsible for the destruction of phytoplankton including harmful algal blooms, [257] The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms. [255]

In January 2018, scientists reported that 800 million viruses, mainly of marine origin, are deposited daily from the Earth 's atmosphere onto every square meter of the planet's surface, as the result of a global atmospheric stream of viruses, circulating above the weather system but below the altitude of usual airline travel, distributing viruses around the planet. [258] [259]

Like any organism, marine mammals are susceptible to viral infections. In 1988 and 2002, thousands of harbour seals were killed in Europe by phocine distemper virus. [260] Many other viruses, including caliciviruses, herpesviruses, adenoviruses and parvoviruses, circulate in marine mammal populations. [255]

Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution. [9] [261] It is thought that viruses played a central role in early evolution, before the diversification of the last universal common ancestor into bacteria, archaea and eukaryotes. [262] Viruses are still one of the largest reservoirs of unexplored genetic diversity on Earth. [255]

Life sciences and medicine

Viruses are important to the study of molecular and cell biology as they provide simple systems that can be used to manipulate and investigate the functions of cells. [263] The study and use of viruses have provided valuable information about aspects of cell biology. [264] For example, viruses have been useful in the study of genetics and helped our understanding of the basic mechanisms of molecular genetics, such as DNA replication, transcription, RNA processing, translation, protein transport, and immunology.

Geneticists often use viruses as vectors to introduce genes into cells that they are studying. This is useful for making the cell produce a foreign substance, or to study the effect of introducing a new gene into the genome. Similarly, virotherapy uses viruses as vectors to treat various diseases, as they can specifically target cells and DNA. It shows promising use in the treatment of cancer and in gene therapy. Eastern European scientists have used phage therapy as an alternative to antibiotics for some time, and interest in this approach is increasing, because of the high level of antibiotic resistance now found in some pathogenic bacteria. [265] The expression of heterologous proteins by viruses is the basis of several manufacturing processes that are currently being used for the production of various proteins such as vaccine antigens and antibodies. Industrial processes have been recently developed using viral vectors and several pharmaceutical proteins are currently in pre-clinical and clinical trials. [266]

Virotherapy

Virotherapy involves the use of genetically modified viruses to treat diseases. [267] Viruses have been modified by scientists to reproduce in cancer cells and destroy them but not infect healthy cells. Talimogene laherparepvec (T-VEC), for example, is a modified herpes simplex virus that has had a gene, which is required for viruses to replicate in healthy cells, deleted and replaced with a human gene (GM-CSF) that stimulates immunity. When this virus infects cancer cells, it destroys them and in doing so the presence the GM-CSF gene attracts dendritic cells from the surrounding tissues of the body. The dendritic cells process the dead cancer cells and present components of them to other cells of the immune system. [268] Having completed successful clinical trials, the virus gained approval for the treatment of melanoma in late 2015. [269] Viruses that have been reprogrammed to kill cancer cells are called oncolytic viruses. [270]

Materials science and nanotechnology

Current trends in nanotechnology promise to make much more versatile use of viruses. [271] From the viewpoint of a materials scientist, viruses can be regarded as organic nanoparticles. Their surface carries specific tools that enable them to cross the barriers of their host cells. The size and shape of viruses and the number and nature of the functional groups on their surface are precisely defined. As such, viruses are commonly used in materials science as scaffolds for covalently linked surface modifications. A particular quality of viruses is that they can be tailored by directed evolution. The powerful techniques developed by life sciences are becoming the basis of engineering approaches towards nanomaterials, opening a wide range of applications far beyond biology and medicine. [272]

Because of their size, shape, and well-defined chemical structures, viruses have been used as templates for organising materials on the nanoscale. Recent examples include work at the Naval Research Laboratory in Washington, D.C., using Cowpea mosaic virus (CPMV) particles to amplify signals in DNA microarray based sensors. In this application, the virus particles separate the fluorescent dyes used for signalling to prevent the formation of non-fluorescent dimers that act as quenchers. [273] Another example is the use of CPMV as a nanoscale breadboard for molecular electronics. [274]

Synthetic viruses

Many viruses can be synthesised de novo ("from scratch") and the first synthetic virus was created in 2002. [275] Although somewhat of a misconception, it is not the actual virus that is synthesised, but rather its DNA genome (in case of a DNA virus), or a cDNA copy of its genome (in case of RNA viruses). For many virus families the naked synthetic DNA or RNA (once enzymatically converted back from the synthetic cDNA) is infectious when introduced into a cell. That is, they contain all the necessary information to produce new viruses. This technology is now being used to investigate novel vaccine strategies. [276] The ability to synthesise viruses has far-reaching consequences, since viruses can no longer be regarded as extinct, as long as the information of their genome sequence is known and permissive cells are available. As of February 2021 [update] , the full-length genome sequences of 10462 different viruses, including smallpox, are publicly available in an online database maintained by the National Institutes of Health. [277]

Weapons

The ability of viruses to cause devastating epidemics in human societies has led to the concern that viruses could be weaponised for biological warfare. Further concern was raised by the successful recreation of the infamous 1918 influenza virus in a laboratory. [278] The smallpox virus devastated numerous societies throughout history before its eradication. There are only two centres in the world authorised by the WHO to keep stocks of smallpox virus: the State Research Center of Virology and Biotechnology VECTOR in Russia and the Centers for Disease Control and Prevention in the United States. [279] It may be used as a weapon, [279] as the vaccine for smallpox sometimes had severe side-effects, it is no longer used routinely in any country. Thus, much of the modern human population has almost no established resistance to smallpox and would be vulnerable to the virus. [279]

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240 ms 12.1% ? 220 ms 11.1% Scribunto_LuaSandboxCallback::gsub 200 ms 10.1% dataWrapper 140 ms 7.1% Scribunto_LuaSandboxCallback::match 140 ms 7.1% Scribunto_LuaSandboxCallback::getExpandedArgument 140 ms 7.1% Scribunto_LuaSandboxCallback::find 100 ms 5.1% Scribunto_LuaSandboxCallback::callParserFunction 80 ms 4.0% 60 ms 3.0% citation0 60 ms 3.0% [others] 600 ms 30.3% Number of Wikibase entities loaded: 6/400 -->


How are bacteria used in genetic engineering?

Bacteria are the simplest model organism and most of our early understanding of molecular biology comes from studying Escherichia coli. Scientist can easily manipulate and combine genes within the bacteria to create novel or disrupted proteins and observe the effect this has on various molecular systems.

Beside above, how are bacteria used in genetic engineering quizlet? the process where an organism has the exact same genes as the organism from which it was produced. How are bacteria used in genetic engineering? the bacteria is used to inject or make protein in the organism.

Simply so, how do you genetically engineer bacteria?

is extracted from the bacteria or yeast cell. A small section is then cut out of the circular plasmid by restriction enzymes, 'molecular scissors'. The gene for human insulin is inserted into the gap in the plasmid. The more the cells divide, the more insulin is produced.

What does a genetic engineer do?

Genetic engineering or recombinant DNA technology introduces foreign genes into microbes, plant, and animals in order to express new characteristics. The technique has been used in breeding crops and livestock to increase yields in food production, as well as to manufacture pharmaceuticals and industrial chemicals.


Scientists create simple synthetic cell that grows and divides normally

An illustration of the simple synthetic cell JCVI-syn3A. Credit: © Emily Pelletier

Five years ago, scientists created a single-celled synthetic organism that, with only 473 genes, was the simplest living cell ever known. However, this bacteria-like organism behaved strangely when growing and dividing, producing cells with wildly different shapes and sizes.

Now, scientists have identified seven genes that can be added to tame the cells' unruly nature, causing them to neatly divide into uniform orbs. This achievement, a collaboration between the J. Craig Venter Institute (JCVI), the National Institute of Standards and Technology (NIST) and the Massachusetts Institute of Technology (MIT) Center for Bits and Atoms, was described in the journal Cell.

Identifying these genes is an important step toward engineering synthetic cells that do useful things. Such cells could act as small factories that produce drugs, foods and fuels detect disease and produce drugs to treat it while living inside the body and function as tiny computers.

But to design and build a cell that does exactly what you want it to do, it helps to have a list of essential parts and know how they fit together.

"We want to understand the fundamental design rules of life," said Elizabeth Strychalski, a co-author on the study and leader of NIST's Cellular Engineering Group. "If this cell can help us to discover and understand those rules, then we're off to the races."

Scientists at JCVI constructed the first cell with a synthetic genome in 2010. They didn't build that cell completely from scratch. Instead, they started with cells from a very simple type of bacteria called a mycoplasma. They destroyed the DNA in those cells and replaced it with DNA that was designed on a computer and synthesized in a lab. This was the first organism in the history of life on Earth to have an entirely synthetic genome. They called it JCVI-syn1.0.

Since then, scientists have been working to strip that organism down to its minimum genetic components. The super-simple cell they created five years ago, dubbed JCVI-syn3.0, was perhaps too minimalist. The researchers have now added 19 genes back to this cell, including the seven needed for normal cell division, to create the new variant, JCVI-syn3A. This variant has fewer than 500 genes. To put that number in perspective, the E. coli bacteria that live in your gut have about 4,000 genes. A human cell has around 30,000.

Identifying those seven additional genes took years of painstaking effort by JCVI's synthetic biology group, led by co-author John Glass. Co-lead author and JCVI scientist Lijie Sun constructed dozens of variant strains by systematically adding and removing genes. She and the other researchers would then observe how those genetic changes affected cell growth and division.

NIST's role was to measure the resulting changes under a microscope. This was a challenge because the cells had to be alive for observation. Using powerful microscopes to observe dead cells is relatively easy. Imaging live cells is much harder.

Holding these cells in place under a microscope was particularly difficult because they are so small and delicate. A hundred or more would fit inside a single E. coli bacterium. Tiny forces can tear them apart.

To solve this problem, Strychalski and MIT co-authors James Pelletier, Andreas Mershin and Neil Gershenfeld designed a microfluidic chemostat—a sort of mini-aquarium—where the cells could be kept fed and happy under a light microscope. The result was stop-motion video that showed the synthetic cells growing and dividing.

One video shows JCVI-syn3.0 cells—the ones created five years ago—dividing into different shapes and sizes. Some of the cells form filaments. Others appear to not fully separate and line up like beads on a string. Despite the variety, all the cells in that video are genetically identical.

Another video shows the new JCVI-Syn3A cells dividing into cells of more uniform shape and size.

These videos and others like them allowed the researchers to observe how their genetic manipulations affected the cell growth and division. If removing a gene disrupted the normal process, they'd put it back and try another.

"Our goal is to know the function of every gene so we can develop a complete model of how a cell works," Pelletier said.

But that goal has not been reached yet. Of the seven genes added to this organism for normal cell division, scientists know what only two of them do. The roles that the other five play in cell division are not yet known.

"Life is still a black box," Strychalski said. But with this simplified synthetic cell, scientists are getting a good look at what's going on inside.


What is the most genetically simple organism except viruses? - Biology

Examples of Multiple Choice Questions for Exam 1, Biology 250

Letters for correct answers are capitalized. 1. A slippery outer covering in some bacteria that protects them from phagocytosis by host cells is A. capsule b. cell wall c. flagellum d. peptidoglycan 2. When flagella are distributed all around a bacterial cell, the arrangement is called a. polar b. random C. peritrichous d. encapsulated 3. A shiny, sticky colony of Streptococcus pneumoniae is likely to be A. encapsulated and pathogenic c. nonencapsulated and nonpathogenic b. nonencapsulated and pathogenic d. encapsulated and nonpathogenic 4. A bacterial cell wall does all of the following except a. gives shape and rigidity to the cell b. is the site of action for some antibiotics c. is associated with some symptoms of disease D. protects the cell from phagocytosis 5. The minimum distance at which a microscope is capable of distinguishing two points as separate is its a. magnification b. illumination C. resolving power 6. A Gram negative cell wall is __________ than a Gram positive one. a. thicker B. thinner 7. Because penicillin prevents peptidoglycan synthesis, it is more effective on _______________ cells. A. Gram positive b. Gram negative 8. Flagella and pili are made of a. lipids b. carbohydrates c. nucleic acids D. protein 9. The genetic information of bacteria is stored in _______, in one circular chromosome located in the cytoplasm. A. DNA b. protein c. phospholipids d. RNA 10. Differences between eukaryotic and prokaryotic cells include all of the following except a. eukaryotic cells have mitochondria c. prokaryotic cells have more complex cell walls b. eukaryotic cells have cilia and flagella with complex structure D. prokaryotic cells have no genetic material 11. The fact that viruses are obligate intracellular parasites means that they require a ____________________ for reproduction. a. culture dish B. host cell c. phenol red broth d. secondary virus 12. One way to determine the size, cell morphology and grouping of bacterial cells is to use a __________ technique. a. streak plate b. phenol red C. simple stain d. nutrient broth culture 13. Cloudiness is a sign that bacteria have grown in a -_______________ after inoculation and incubation. a. streak plate B. tube of nutrient broth c. Gram stain d. simple stain 14. The bacterial envelope includes all of the following structures except a. capsule b. cell wall c. cell membrane D. endospore 15. All of the following structures of bacteria contain (or are made of) protein except A. plasmids b. ribosomes c. pili d. cell membrane 16. Which of the following contains polysaccharide? A. Gram negative cell wall b. pili c. flagella d. plasmids 17. Which of the following contains DNA? a. Gram positive cell wall b. capsule c. pili D. plasmids 18. In a Gram stain procedure, bacteria with Gram positive cell walls decolorize less easily than those with Gram negative cell walls. A. true b. false 19. The cell wall type that has less peptidoglycan is A. Gram negative b. Gram positive 20. The cell wall type that is most vulnerable to the action of penicillin is a. Gram negative B. Gram positive 21. When flagella are located around the entire bacterial cell, the arrangement is called a. polar b. random c. bipolar D. peritrichous 22. An encapsulated cell will reproduce to form colonies that appear a. nonpathogenic b. translucent c. pink D. smooth 23. Endospore are all of the following except ___________ as compared to vegetative cells. a. more likely to survive treatment with disinfectants c. more resistant to staining B. more likely to die in nutritionally poor conditions d. more resistant to temperature changes 24. Phagocytosis of the bacteria that cause pneumonia is ____ likely if the bacteria are protected by a capsule. A. less b. more 25. If you use a visible light microscope to examine a live culture of a bacterium possessing flagella, you will be able to see the flagella moving the bacteria. a. true B. false 26. In what phase of the growth curve is/does a culture (use letters on phases of growth curve for answers): most sensitive to antibiotics? a, B-exponential growth, c, d have the maximum amount of nutrients? A-initial stationary, b, c, d have the maximum amount of accumulated waste products? a, b, c, D-exponential death have equal #'s of dividing and dying cells? A-initial stationary, b, C-maximum stationary, d 27. Most human pathogens prefer temperatures near that of the human body. They are called a. psychrophiles b. thermophiles C. mesophiles d. halophiles 28. The optimum temperature for an organism is the one at which A. it grows with the shortest generation time b. it has the longest time between cell divisions c. it is near one extreme of its range of tolerated temperatures d. its enzymes begin to denature 29. The breakdown of glucose to pyruvate is called glycolysis and produces most of the ATP available from the glucose molecule. a. true B. false 30. Energy is stored in the ATP (adenosine triphosphate) molecule in its a. sugar portion b. adenine portion C. third phosphate bond 31. Organisms that ferment glucose may produce any of the following end products except a. lactic acid b. propionic acid c. alcohol D. oxygen


Contents

Ancient precursors Edit

The possible existence of microscopic organisms was discussed for many centuries before their discovery in the 17th century. By the fifth century BC, the Jains of present-day India postulated the existence of tiny organisms called nigodas. [6] These nigodas are said to be born in clusters they live everywhere, including the bodies of plants, animals, and people and their life lasts only for a fraction of a second. [7] According to the Jain leader Mahavira, the humans destroy these nigodas on a massive scale, when they eat, breathe, sit, and move. [6] Many modern Jains assert that Mahavira's teachings presage the existence of microorganisms as discovered by modern science. [8]

The earliest known idea to indicate the possibility of diseases spreading by yet unseen organisms was that of the Roman scholar Marcus Terentius Varro in a 1st-century BC book titled On Agriculture in which he called the unseen creatures animalcules, and warns against locating a homestead near a swamp: [9]

… and because there are bred certain minute creatures that cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and they cause serious diseases. [9]

In The Canon of Medicine (1020), Avicenna suggested that tuberculosis and other diseases might be contagious. [10] [11]

Early modern Edit

My work, which I've done for a long time, was not pursued in order to gain the praise I now enjoy, but chiefly from a craving after knowledge, which I notice resides in me more than in most other men. And therewithal, whenever I found out anything remarkable, I have thought it my duty to put down my discovery on paper, so that all ingenious people might be informed thereof.

Antony van Leeuwenhoek remains one of the most imperfectly understood figures in the origins of experimental biology. The popular view is that Leeuwenhoek worked in a manner that was essentially crude and undisciplined, using untried methods of investigation that were lacking in refinement and objectivity. He has often been designated as a 'dilettante.' His microscopes, furthermore, have been described as primitive and doubt has been expressed over his ability to have made many of the observations attributed to him. Recent research shows these views to be erroneous. His work was carried out conscientiously, and the observations were recorded with painstaking diligence. Though we may see evidence of his globulist understanding of organic matter (this view has frequently been cited as evidence of his observational inadequacies), this minor preoccupation cannot detract from two firm principles that underlie his work: (a) a clear ability to construct experimental procedures which were, for their time, rational and repeatable, and (b) a willingness both to fly in the face of received opinion – for example, over the question of spontaneous generation – and to abandon a previously held belief in the light of new evidence. In his method of analysing a problem, Leeuwenhoek was able to lay many of the ground rules of experimentation and did much to found, not only the science of microscopy, but also the philosophy of biological experimentation.

Leeuwenhoek is universally acknowledged as the father of microbiology. He discovered both protists and bacteria. More than being the first to see this unimagined world of ‘animalcules', he was the first even to think of looking—certainly, the first with the power to see. Using his own deceptively simple, single-lensed microscopes, he did not merely observe, but conducted ingenious experiments, exploring and manipulating his microscopic universe with a curiosity that belied his lack of a map or bearings. Leeuwenhoek was a pioneer, a scientist of the highest calibre, yet his reputation suffered at the hands of those who envied his fame or scorned his unschooled origins, as well as through his own mistrustful secrecy of his methods, which opened a world that others could not comprehend.

Akshamsaddin (Turkish scientist) mentioned the microbe in his work Maddat ul-Hayat (The Material of Life) about two centuries prior to Antonie Van Leeuwenhoek's discovery through experimentation:

It is incorrect to assume that diseases appear one by one in humans. Disease infects by spreading from one person to another. This infection occurs through seeds that are so small they cannot be seen but are alive. [13] [14]

In 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or even without contact over long distances. [15]

Antonie Van Leeuwenhoek is considered to be the father of microbiology. He was the first in 1673 to discover and conduct scientific experiments with microorganisms, using simple single-lensed microscopes of his own design. [16] [17] [4] [18] Robert Hooke, a contemporary of Leeuwenhoek, also used microscopy to observe microbial life in the form of the fruiting bodies of moulds. In his 1665 book Micrographia, he made drawings of studies, and he coined the term cell. [19]

19th century Edit

Louis Pasteur (1822–1895) exposed boiled broths to the air, in vessels that contained a filter to prevent particles from passing through to the growth medium, and also in vessels without a filter, but with air allowed in via a curved tube so dust particles would settle and not come in contact with the broth. By boiling the broth beforehand, Pasteur ensured that no microorganisms survived within the broths at the beginning of his experiment. Nothing grew in the broths in the course of Pasteur's experiment. This meant that the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. Thus, Pasteur refuted the theory of spontaneous generation and supported the germ theory of disease. [20]

In 1876, Robert Koch (1843–1910) established that microorganisms can cause disease. He found that the blood of cattle that were infected with anthrax always had large numbers of Bacillus anthracis. Koch found that he could transmit anthrax from one animal to another by taking a small sample of blood from the infected animal and injecting it into a healthy one, and this caused the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, then inject it into a healthy animal, and cause illness. Based on these experiments, he devised criteria for establishing a causal link between a microorganism and a disease and these are now known as Koch's postulates. [21] Although these postulates cannot be applied in all cases, they do retain historical importance to the development of scientific thought and are still being used today. [22]

The discovery of microorganisms such as Euglena that did not fit into either the animal or plant kingdoms, since they were photosynthetic like plants, but motile like animals, led to the naming of a third kingdom in the 1860s. In 1860 John Hogg called this the Protoctista, and in 1866 Ernst Haeckel named it the Protista. [23] [24] [25]

The work of Pasteur and Koch did not accurately reflect the true diversity of the microbial world because of their exclusive focus on microorganisms having direct medical relevance. It was not until the work of Martinus Beijerinck and Sergei Winogradsky late in the 19th century that the true breadth of microbiology was revealed. [26] Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques. [27] While his work on the tobacco mosaic virus established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemolithotrophy and to thereby reveal the essential role played by microorganisms in geochemical processes. [28] He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria. [26] French-Canadian microbiologist Felix d'Herelle co-discovered bacteriophages and was one of the earliest applied microbiologists. [29]

Microorganisms can be found almost anywhere on Earth. Bacteria and archaea are almost always microscopic, while a number of eukaryotes are also microscopic, including most protists, some fungi, as well as some micro-animals and plants. Viruses are generally regarded as not living and therefore not considered as microorganisms, although a subfield of microbiology is virology, the study of viruses. [30] [31] [32]

Evolution Edit

Single-celled microorganisms were the first forms of life to develop on Earth, approximately 3.5 billion years ago. [33] [34] [35] Further evolution was slow, [36] and for about 3 billion years in the Precambrian eon, (much of the history of life on Earth), all organisms were microorganisms. [37] [38] Bacteria, algae and fungi have been identified in amber that is 220 million years old, which shows that the morphology of microorganisms has changed little since at least the Triassic period. [39] The newly discovered biological role played by nickel, however – especially that brought about by volcanic eruptions from the Siberian Traps – may have accelerated the evolution of methanogens towards the end of the Permian–Triassic extinction event. [40]

Microorganisms tend to have a relatively fast rate of evolution. Most microorganisms can reproduce rapidly, and bacteria are also able to freely exchange genes through conjugation, transformation and transduction, even between widely divergent species. [41] This horizontal gene transfer, coupled with a high mutation rate and other means of transformation, allows microorganisms to swiftly evolve (via natural selection) to survive in new environments and respond to environmental stresses. This rapid evolution is important in medicine, as it has led to the development of multidrug resistant pathogenic bacteria, superbugs, that are resistant to antibiotics. [42]

A possible transitional form of microorganism between a prokaryote and a eukaryote was discovered in 2012 by Japanese scientists. Parakaryon myojinensis is a unique microorganism larger than a typical prokaryote, but with nuclear material enclosed in a membrane as in a eukaryote, and the presence of endosymbionts. This is seen to be the first plausible evolutionary form of microorganism, showing a stage of development from the prokaryote to the eukaryote. [43] [44]

Archaea Edit

Archaea are prokaryotic unicellular organisms, and form the first domain of life, in Carl Woese's three-domain system. A prokaryote is defined as having no cell nucleus or other membrane bound-organelle. Archaea share this defining feature with the bacteria with which they were once grouped. In 1990 the microbiologist Woese proposed the three-domain system that divided living things into bacteria, archaea and eukaryotes, [45] and thereby split the prokaryote domain.

Archaea differ from bacteria in both their genetics and biochemistry. For example, while bacterial cell membranes are made from phosphoglycerides with ester bonds, archaean membranes are made of ether lipids. [46] Archaea were originally described as extremophiles living in extreme environments, such as hot springs, but have since been found in all types of habitats. [47] Only now are scientists beginning to realize how common archaea are in the environment, with Crenarchaeota being the most common form of life in the ocean, dominating ecosystems below 150 m in depth. [48] [49] These organisms are also common in soil and play a vital role in ammonia oxidation. [50]

The combined domains of archaea and bacteria make up the most diverse and abundant group of organisms on Earth and inhabit practically all environments where the temperature is below +140 °C. They are found in water, soil, air, as the microbiome of an organism, hot springs and even deep beneath the Earth's crust in rocks. [51] The number of prokaryotes is estimated to be around five nonillion, or 5 × 10 30 , accounting for at least half the biomass on Earth. [52]

The biodiversity of the prokaryotes is unknown, but may be very large. A May 2016 estimate, based on laws of scaling from known numbers of species against the size of organism, gives an estimate of perhaps 1 trillion species on the planet, of which most would be microorganisms. Currently, only one-thousandth of one percent of that total have been described. [53] Archael cells of some species aggregate and transfer DNA from one cell to another through direct contact, particularly under stressful environmental conditions that cause DNA damage. [54] [55]

Bacteria Edit

Bacteria like archaea are prokaryotic – unicellular, and having no cell nucleus or other membrane-bound organelle. Bacteria are microscopic, with a few extremely rare exceptions, such as Thiomargarita namibiensis. [56] Bacteria function and reproduce as individual cells, but they can often aggregate in multicellular colonies. [57] Some species such as myxobacteria can aggregate into complex swarming structures, operating as multicellular groups as part of their life cycle, [58] or form clusters in bacterial colonies such as E.coli.

Their genome is usually a circular bacterial chromosome – a single loop of DNA, although they can also harbor small pieces of DNA called plasmids. These plasmids can be transferred between cells through bacterial conjugation. Bacteria have an enclosing cell wall, which provides strength and rigidity to their cells. They reproduce by binary fission or sometimes by budding, but do not undergo meiotic sexual reproduction. However, many bacterial species can transfer DNA between individual cells by a horizontal gene transfer process referred to as natural transformation. [59] Some species form extraordinarily resilient spores, but for bacteria this is a mechanism for survival, not reproduction. Under optimal conditions bacteria can grow extremely rapidly and their numbers can double as quickly as every 20 minutes. [60]

Eukaryotes Edit

Most living things that are visible to the naked eye in their adult form are eukaryotes, including humans. However, many eukaryotes are also microorganisms. Unlike bacteria and archaea, eukaryotes contain organelles such as the cell nucleus, the Golgi apparatus and mitochondria in their cells. The nucleus is an organelle that houses the DNA that makes up a cell's genome. DNA (Deoxyribonucleic acid) itself is arranged in complex chromosomes. [61] Mitochondria are organelles vital in metabolism as they are the site of the citric acid cycle and oxidative phosphorylation. They evolved from symbiotic bacteria and retain a remnant genome. [62] Like bacteria, plant cells have cell walls, and contain organelles such as chloroplasts in addition to the organelles in other eukaryotes. Chloroplasts produce energy from light by photosynthesis, and were also originally symbiotic bacteria. [62]

Unicellular eukaryotes consist of a single cell throughout their life cycle. This qualification is significant since most multicellular eukaryotes consist of a single cell called a zygote only at the beginning of their life cycles. Microbial eukaryotes can be either haploid or diploid, and some organisms have multiple cell nuclei. [63]

Unicellular eukaryotes usually reproduce asexually by mitosis under favorable conditions. However, under stressful conditions such as nutrient limitations and other conditions associated with DNA damage, they tend to reproduce sexually by meiosis and syngamy. [64]

Protists Edit

Of eukaryotic groups, the protists are most commonly unicellular and microscopic. This is a highly diverse group of organisms that are not easy to classify. [65] [66] Several algae species are multicellular protists, and slime molds have unique life cycles that involve switching between unicellular, colonial, and multicellular forms. [67] The number of species of protists is unknown since only a small proportion has been identified. Protist diversity is high in oceans, deep sea-vents, river sediment and an acidic river, suggesting that many eukaryotic microbial communities may yet be discovered. [68] [69]

Fungi Edit

The fungi have several unicellular species, such as baker's yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe). Some fungi, such as the pathogenic yeast Candida albicans, can undergo phenotypic switching and grow as single cells in some environments, and filamentous hyphae in others. [70]

Plants Edit

The green algae are a large group of photosynthetic eukaryotes that include many microscopic organisms. Although some green algae are classified as protists, others such as charophyta are classified with embryophyte plants, which are the most familiar group of land plants. Algae can grow as single cells, or in long chains of cells. The green algae include unicellular and colonial flagellates, usually but not always with two flagella per cell, as well as various colonial, coccoid, and filamentous forms. In the Charales, which are the algae most closely related to higher plants, cells differentiate into several distinct tissues within the organism. There are about 6000 species of green algae. [71]

Microorganisms are found in almost every habitat present in nature, including hostile environments such as the North and South poles, deserts, geysers, and rocks. They also include all the marine microorganisms of the oceans and deep sea. Some types of microorganisms have adapted to extreme environments and sustained colonies these organisms are known as extremophiles. Extremophiles have been isolated from rocks as much as 7 kilometres below the Earth's surface, [72] and it has been suggested that the amount of organisms living below the Earth's surface is comparable with the amount of life on or above the surface. [51] Extremophiles have been known to survive for a prolonged time in a vacuum, and can be highly resistant to radiation, which may even allow them to survive in space. [73] Many types of microorganisms have intimate symbiotic relationships with other larger organisms some of which are mutually beneficial (mutualism), while others can be damaging to the host organism (parasitism). If microorganisms can cause disease in a host they are known as pathogens and then they are sometimes referred to as microbes. Microorganisms play critical roles in Earth's biogeochemical cycles as they are responsible for decomposition and nitrogen fixation. [74]

Bacteria use regulatory networks that allow them to adapt to almost every environmental niche on earth. [75] [76] A network of interactions among diverse types of molecules including DNA, RNA, proteins and metabolites, is utilised by the bacteria to achieve regulation of gene expression. In bacteria, the principal function of regulatory networks is to control the response to environmental changes, for example nutritional status and environmental stress. [77] A complex organization of networks permits the microorganism to coordinate and integrate multiple environmental signals. [75]

Extremophiles Edit

Extremophiles are microorganisms that have adapted so that they can survive and even thrive in extreme environments that are normally fatal to most life-forms. Thermophiles and hyperthermophiles thrive in high temperatures. Psychrophiles thrive in extremely low temperatures. – Temperatures as high as 130 °C (266 °F), [78] as low as −17 °C (1 °F) [79] Halophiles such as Halobacterium salinarum (an archaean) thrive in high salt conditions, up to saturation. [80] Alkaliphiles thrive in an alkaline pH of about 8.5–11. [81] Acidophiles can thrive in a pH of 2.0 or less. [82] Piezophiles thrive at very high pressures: up to 1,000–2,000 atm, down to 0 atm as in a vacuum of space. [83] A few extremophiles such as Deinococcus radiodurans are radioresistant, [84] resisting radiation exposure of up to 5k Gy. Extremophiles are significant in different ways. They extend terrestrial life into much of the Earth's hydrosphere, crust and atmosphere, their specific evolutionary adaptation mechanisms to their extreme environment can be exploited in biotechnology, and their very existence under such extreme conditions increases the potential for extraterrestrial life. [85]

In soil Edit

The nitrogen cycle in soils depends on the fixation of atmospheric nitrogen. This is achieved by a number of diazotrophs. One way this can occur is in the root nodules of legumes that contain symbiotic bacteria of the genera Rhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Azorhizobium. [86]

The roots of plants create a narrow region known as the rhizosphere that supports many microorganisms known as the root microbiome. [87]

Symbiosis Edit

A lichen is a symbiosis of a macroscopic fungus with photosynthetic microbial algae or cyanobacteria. [88] [89]

Microorganisms are useful in producing foods, treating waste water, creating biofuels and a wide range of chemicals and enzymes. They are invaluable in research as model organisms. They have been weaponised and sometimes used in warfare and bioterrorism. They are vital to agriculture through their roles in maintaining soil fertility and in decomposing organic matter.

Food production Edit

Microorganisms are used in a fermentation process to make yoghurt, cheese, curd, kefir, ayran, xynogala, and other types of food. Fermentation cultures provide flavour and aroma, and inhibit undesirable organisms. [90] They are used to leaven bread, and to convert sugars to alcohol in wine and beer. Microorganisms are used in brewing, wine making, baking, pickling and other food-making processes. [91]

Some industrial uses of Microorganisms:

Product Contribution of Microorganisms
Cheese Growth of microorganisms contributes to ripening and flavor. The flavor and appearance of a particular cheese is due in large part to the microorganisms associated with it. Lactobacillus Bulgaricus is one of the microbes used in production of diary products
Alcoholic beverages yeast is used to convert sugar, grape juice, or malt-treated grain into alcohol. other microorganisms may also be used a mold converts starch into sugar to make the Japanese rice wine, sake. Acetobacter Aceti a kind of bacterium is used in production of Alcoholic beverages
Vinegar Certain bacteria are used to convert alcohol into acetic acid, which gives vinegar its acid taste. Acetobacter Aceti is used on production of vinegar which gives vinegar odor of alcohol and alcoholic taste
Citric acid Certain fungi are used to make citric acid, a common ingredient of soft drinks and other foods.
Vitamins Microorganisms are used to make vitamins, including C, B2 , B12.
Antibiotics With only a few exceptions, microorganisms are used to make antibiotics. Penicillin, Amoxicillin, Tetracycline and Erythromycin

Water treatment Edit

These depend for their ability to clean up water contaminated with organic material on microorganisms that can respire dissolved substances. Respiration may be aerobic, with a well-oxygenated filter bed such as a slow sand filter. [92] Anaerobic digestion by methanogens generate useful methane gas as a by-product. [93]

Energy Edit

Microorganisms are used in fermentation to produce ethanol, [94] and in biogas reactors to produce methane. [95] Scientists are researching the use of algae to produce liquid fuels, [96] and bacteria to convert various forms of agricultural and urban waste into usable fuels. [97]

Chemicals, enzymes Edit

Microorganisms are used to produce many commercial and industrial chemicals, enzymes and other bioactive molecules. Organic acids produced on a large industrial scale by microbial fermentation include acetic acid produced by acetic acid bacteria such as Acetobacter aceti, butyric acid made by the bacterium Clostridium butyricum, lactic acid made by Lactobacillus and other lactic acid bacteria, [98] and citric acid produced by the mould fungus Aspergillus niger. [98]

Microorganisms are used to prepare bioactive molecules such as Streptokinase from the bacterium Streptococcus, [99] Cyclosporin A from the ascomycete fungus Tolypocladium inflatum, [100] and statins produced by the yeast Monascus purpureus. [101]

Science Edit

Microorganisms are essential tools in biotechnology, biochemistry, genetics, and molecular biology. The yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe are important model organisms in science, since they are simple eukaryotes that can be grown rapidly in large numbers and are easily manipulated. [102] They are particularly valuable in genetics, genomics and proteomics. [103] [104] Microorganisms can be harnessed for uses such as creating steroids and treating skin diseases. Scientists are also considering using microorganisms for living fuel cells, [105] and as a solution for pollution. [106]

Warfare Edit

In the Middle Ages, as an early example of biological warfare, diseased corpses were thrown into castles during sieges using catapults or other siege engines. Individuals near the corpses were exposed to the pathogen and were likely to spread that pathogen to others. [107]

In modern times, bioterrorism has included the 1984 Rajneeshee bioterror attack [108] and the 1993 release of anthrax by Aum Shinrikyo in Tokyo. [109]

Soil Edit

Microbes can make nutrients and minerals in the soil available to plants, produce hormones that spur growth, stimulate the plant immune system and trigger or dampen stress responses. In general a more diverse set of soil microbes results in fewer plant diseases and higher yield. [110]

Human gut flora Edit

Microorganisms can form an endosymbiotic relationship with other, larger organisms. For example, microbial symbiosis plays a crucial role in the immune system. The microorganisms that make up the gut flora in the gastrointestinal tract contribute to gut immunity, synthesize vitamins such as folic acid and biotin, and ferment complex indigestible carbohydrates. [111] Some microorganisms that are seen to be beneficial to health are termed probiotics and are available as dietary supplements, or food additives. [112]

Disease Edit

Microorganisms are the causative agents (pathogens) in many infectious diseases. The organisms involved include pathogenic bacteria, causing diseases such as plague, tuberculosis and anthrax protozoan parasites, causing diseases such as malaria, sleeping sickness, dysentery and toxoplasmosis and also fungi causing diseases such as ringworm, candidiasis or histoplasmosis. However, other diseases such as influenza, yellow fever or AIDS are caused by pathogenic viruses, which are not usually classified as living organisms and are not, therefore, microorganisms by the strict definition. No clear examples of archaean pathogens are known, [113] although a relationship has been proposed between the presence of some archaean methanogens and human periodontal disease. [114] Numerous microbial pathogens are capable of sexual processes that appear to facilitate their survival in their infected host. [115]

Hygiene Edit

Hygiene is a set of practices to avoid infection or food spoilage by eliminating microorganisms from the surroundings. As microorganisms, in particular bacteria, are found virtually everywhere, harmful microorganisms may be reduced to acceptable levels rather than actually eliminated. In food preparation, microorganisms are reduced by preservation methods such as cooking, cleanliness of utensils, short storage periods, or by low temperatures. If complete sterility is needed, as with surgical equipment, an autoclave is used to kill microorganisms with heat and pressure. [116] [117]


Role in laboratory research

Phages have played an important role in laboratory research. The first phages studied were those designated type 1 (T1) to type 7 (T7). The T-even phages, T2, T4, and T6, were used as model systems for the study of virus multiplication. In 1952 Alfred Day Hershey and Martha Chase used the T2 bacteriophage in a famous experiment in which they demonstrated that only the nucleic acids of phage molecules were required for their replication within bacteria. The results of the experiment supported the theory that DNA is the genetic material. For his work with bacteriophages, Hershey was awarded the Nobel Prize for Physiology or Medicine in 1969. He shared the award with biologists Salvador Luria and Max Delbrück, whose experiments with the T1 phage in 1943 (the fluctuation test) showed that phage resistance in bacteria was the product of spontaneous mutation and not a direct response to environmental factors. Certain phages, such as lambda, Mu, and M13, are used in recombinant DNA technology. The phage ϕX174 was the first organism to have its entire nucleotide sequence determined, a feat that was accomplished by Frederick Sanger and colleagues in 1977.

In the 1980s American biochemist George P. Smith developed a technology known as phage display, which allowed for the generation of engineered proteins. Such proteins were produced by fusing foreign or engineered DNA fragments into phage gene III. Gene III encodes a protein expressed on the phage virion surface. Thus, gene III fusion proteins taken up by phages were displayed on the surfaces of virion particles. Researchers could then use antibodies developed to recognize the foreign protein fragment to purify fusion phage cultures, thereby effectively amplifying the foreign gene sequence for further study. British biochemist Gregory P. Winter subsequently refined phage display technology for the development of human antibody proteins. Such proteins could be used to treat diseases in humans with less risk of inducing potentially dangerous immune reactions compared with previous therapeutic antibodies derived from animals. Adalimumab (Humira), used for the treatment of rheumatoid arthritis, was the first fully human antibody made via phage display to be approved by the U.S. Food and Drug Administration (approved in 2002). For their discoveries relating to phage display, Smith and Winter were awarded a share of the 2018 Nobel Prize in Chemistry.


What is the most genetically simple organism except viruses? - Biology

The genetic information of an organism is stored in DNA molecules. How can one kind of molecule contain all the instructions for making complicated living beings like ourselves? What component or feature of DNA can contain this information? It has to come from the nitrogen bases, because, as you already know, the backbone of all DNA molecules is the same. But there are only four bases found in DNA: G, A, C, and T. The sequence of these four bases can provide all the instructions needed to build any living organism. It might be hard to imagine that 4 different “letters” can communicate so much information. But think about the English language, which can represent a huge amount of information using just 26 letters. Even more profound is the binary code used to write computer programs. This code contains only ones and zeros, and think of all the things your computer can do. The DNA alphabet can encode very complex instructions using just four letters, though the messages end up being really long. For example, the E. coli bacterium carries its genetic instructions in a DNA molecule that contains more than five million nucleotides. The human genome (all the DNA of an organism) consists of around three billion nucleotides divided up between 23 paired DNA molecules, or chromosomes.

The information stored in the order of bases is organized into genes: each gene contains information for making a functional product. The genetic information is first copied to another nucleic acid polymer, RNA (ribonucleic acid), preserving the order of the nucleotide bases. Genes that contain instructions for making proteins are converted to messenger RNA (mRNA). Some specialized genes contain instructions for making functional RNA molecules that don’t make proteins. These RNA molecules function by affecting cellular processes directly for example some of these RNA molecules regulate the expression of mRNA. Other genes produce RNA molecules that are required for protein synthesis, transfer RNA (tRNA), and ribosomal RNA (rRNA).

In order for DNA to function effectively at storing information, two key processes are required. First, information stored in the DNA molecule must be copied, with minimal errors, every time a cell divides. This ensures that both daughter cells inherit the complete set of genetic information from the parent cell. Second, the information stored in the DNA molecule must be translated, or expressed. In order for the stored information to be useful, cells must be able to access the instructions for making specific proteins, so the correct proteins are made in the right place at the right time.

Figure 1. DNA’s double helix. Graphic modified from “DNA chemical structure,” by Madeleine Price Ball, CC-BY-SA-2.0

Both copying and reading the information stored in DNA relies on base pairing between two nucleic acid polymer strands. Recall that DNA structure is a double helix (see Figure 1).

The sugar deoxyribose with the phosphate group forms the scaffold or backbone of the molecule (highlighted in yellow in Figure 1). Bases point inward. Complementary bases form hydrogen bonds with each other within the double helix. See how the bigger bases (purines) pair with the smaller ones (pyrimidines). This keeps the width of the double helix constant. More specifically, A pairs with T and C pairs with G. As we discuss the function of DNA in subsequent sections, keep in mind that there is a chemical reason for specific pairing of bases.

To illustrate the connection between information in DNA and an observable characteristic of an organism, let’s consider a gene that provides the instructions for building the hormone insulin. Insulin is responsible for regulating blood sugar levels. The insulin gene contains instructions for assembling the protein insulin from individual amino acids. Changing the sequence of nucleotides in the DNA molecule can change the amino acids in the final protein, leading to protein malfunction. If insulin does not function correctly, it might be unable to bind to another protein (insulin receptor). On the organismal level of organization, this molecular event (change of DNA sequence) can lead to a disease state—in this case, diabetes.

Practice Questions

The order of nucleotides in a gene (in DNA) is the key to how information is stored. For example, consider these two words: stable and tables. Both words are built from the same letters (subunits), but the different order of these subunits results in very different meanings. In DNA, the information is stored in units of 3 letters. Use the following key to decode the encrypted message. This should help you to see how information can be stored in the linear order of nucleotides in DNA.

ABC = a DEF = d GHI = e JKL = f
MNO = h PQR = i STU = m VWX = n
YZA = o BCD = r EFG = s HIJ = t
KLM = w NOP = j QRS = p TUV = y

Encrypted Message: HIJMNOPQREFG – PQREFG – MNOYZAKLM – DEFVWXABC – EFGHIJYZABCDGHIEFG – PQRVWXJKLYZABCDSTUABCHIJPQRYZAVWX