Capsid in the context of Realm (virology)

Marine viruses are defined by their habitat as viruses that are found in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Viruses are small infectious agents that can only replicate inside the living cells of a host organism, because they need the replication machinery of the host to do so. They can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.

When not inside a cell or in the process of infecting a cell, viruses exist in the form of independent particles called virions. A virion contains a genome (a long molecule that carries genetic information in the form of either DNA or RNA) surrounded by a capsid (a protein coat protecting the genetic material). The shapes of these virus particles range from simple helical and icosahedral forms for some virus species to more complex structures for others. Most virus species have virions that are too small to be seen with an optical microscope. The average virion is about one one-hundredth the linear size of the average bacterium.

A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 16,000 of the millions of virus species have been described in detail. The study of viruses is known as virology, a subspeciality of microbiology.

When infected, a host cell is often forced to rapidly produce thousands of copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent viral particles, or virions, consisting of (i) genetic material, i.e., long molecules of DNA or RNA that encode the structure of the proteins by which the virus acts; (ii) a protein coat, the capsid, which surrounds and protects the genetic material; and in some cases (iii) an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope and are one-hundredth the size of most bacteria.

A bacteriophage (/bækˈtɪrioʊfeɪdʒ/), also known informally as a phage (/ˈfeɪdʒ/), is a virus that infects and replicates within bacteria. The term is derived from Ancient Greek φαγεῖν (phagein) 'to devour' and bacteria. Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes (e.g. MS2) and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm.

Bacteriophages are among the most common and diverse entities in the biosphere. Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 10 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined. Viruses are the most abundant biological entity in the water column of the world's oceans, and the second largest component of biomass after prokaryotes, where up to 9x10 virions per millilitre have been found in microbial mats at the surface, and up to 70% of marine bacteria may be infected by bacteriophages.

A virion (plural, viria or virions) is an inert virus particle capable of invading a cell. Upon entering the cell, the virion disassembles and the genetic material from the virus takes control of the cell infrastructure, thus enabling the virus to replicate. The genetic material (core, either DNA or RNA, along with occasionally present virus core protein) inside the virion is usually enclosed in a protection shell, known as the capsid.

While the terms "virus" and "virion" are occasionally confused, recently "virion" is used solely to describe the virus structure outside of cells, while the terms "virus/viral" are broader and also include biological properties such as the infectivity of a virion.

Poliovirus, the causative agent of polio (also known as poliomyelitis), is a serotype of the species Enterovirus C, in the family of Picornaviridae. There are three poliovirus serotypes, numbered 1, 2, and 3.

Poliovirus is composed of an RNA genome and a protein capsid. The genome is a single-stranded positive-sense RNA (+ssRNA) genome that is about 7500 nucleotides long. The viral particle is about 30 nm in diameter with icosahedral symmetry. Because of its short genome and its simple composition—only a strand of RNA and a nonenveloped icosahedral protein coat encapsulating it—poliovirus is widely regarded as the simplest significant virus.

A viral envelope is the outermost layer of many types of viruses. It protects the genetic material in their life cycle when traveling between host cells. Not all viruses have envelopes. A viral envelope protein or E protein is a protein in the envelope, which may be acquired by the capsid from an infected host cell.

Lambda phage (coliphage λ, scientific name Lambdavirus lambda) is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli (E. coli). It was discovered by Esther Lederberg in 1950. The wild type of this virus has a temperate life cycle that allows it to either reside within the genome of its host through lysogeny or enter into a lytic phase, during which it kills and lyses the cell to produce offspring. Lambda strains, mutated at specific sites, are unable to lysogenize cells; instead, they grow and enter the lytic cycle after superinfecting an already lysogenized cell.

The phage particle consists of a head (also known as a capsid), a tail, and tail fibers (see image of virus below). The head contains the phage's double-strand linear DNA genome. During infections, the phage particle recognizes and binds to its host, E. coli, causing DNA in the head of the phage to be ejected through the tail into the cytoplasm of the bacterial cell. Usually, a "lytic cycle" ensues, where the lambda DNA is replicated and new phage particles are produced within the cell. This is followed by cell lysis, releasing the cell contents, including virions that have been assembled, into the environment. However, under certain conditions, the phage DNA may integrate itself into the host cell chromosome in the lysogenic pathway. In this state, the λ DNA is called a prophage and stays resident within the host's genome without apparent harm to the host. The host is termed a lysogen when a prophage is present. This prophage may enter the lytic cycle when the lysogen enters a stressed condition.

The capsomere is a subunit of the capsid, an outer covering of protein that protects the genetic material of a virus. Capsomeres self-assemble to form the capsid.

Subunits called protomers aggregate to form capsomeres. Various arrangements of capsomeres are: 1) Icosahedral, 2) Helical, and 3) Complex.

Herpesvirales is an order of dsDNA viruses (Baltimore group I) with animal hosts, characterised by a common morphology consisting of an icosahedral capsid enclosed in a glycoprotein-containing lipid envelope. Common infections in humans caused by members of this order include cold sores, genital herpes, chickenpox, shingles, and glandular fever. Herpesvirales is the sole order in the class Herviviricetes, which is the sole class in the phylum Peploviricota.

Picornaviruses are a group of related nonenveloped RNA viruses which infect vertebrates including fish, mammals, and birds. They are viruses that represent a large family of small, positive-sense, single-stranded RNA viruses with a 30 nm icosahedral capsid. The viruses in this family can cause a range of diseases including the common cold, poliomyelitis, meningitis, hepatitis, and paralysis.

Picornaviruses constitute the family Picornaviridae, order Picornavirales, and realm Riboviria. There are 159 species in this family, assigned to 68 genera, most of which belong to 5 subfamilies. Notable examples are genera Enterovirus (including Rhinovirus and Poliovirus), Aphthovirus, Cardiovirus, and Hepatovirus.

Onasemnogene abeparvovec, sold under the brand name Zolgensma among others, is a gene therapy used to treat spinal muscular atrophy, a disease causing muscle function loss in children. It involves a one-time infusion of the medication into a vein. It works by providing a new copy of the survival of motor neuron (SMN) gene that produces the SMN protein.

Spinal muscular atrophy stems from a mutation in the survival motor neuron 1 (SMN1) gene, causing survival of motor neuron protein deficiency vital for motor neuron survival. Onasemnogene abeparvovec, a biologic medication utilizing adeno-associated virus (AAV9) virus capsids containing an SMN1 transgene, is administered to motor neurons, boosting SMN protein levels. Common side effects include vomiting and elevated liver enzymes, while more severe reactions involve liver issues and low platelet count.

A cosmid is a type of hybrid plasmid that contains a Lambda phage cos sequence. Often used as cloning vectors in genetic engineering, cosmids can be used to build genomic libraries. They were first described by Collins and Hohn in 1978.Cosmids can contain 37 to 52 (normally 45) kb of DNA, limits based on the normal bacteriophage packaging size. They can replicate as plasmids if they have a suitable origin of replication (ori): for example SV40 ori in mammalian cells, ColE1 ori for double-stranded DNA replication, or f1 ori for single-stranded DNA replication in prokaryotes. They frequently also contain a gene for selection such as antibiotic resistance, so that the transformed cells can be identified by plating on a medium containing the antibiotic. Those cells which did not take up the cosmid would be unable to grow.

Unlike plasmids, they can also be packaged in vitro into phage capsids, a step which requires cohesive ends, also known as cos sites also used in cloning with a lambda phage as a vector, however nearly all the lambda genes have been deleted with the exception of the cos sequence. The hybrid cosmid DNA in the capsids can then be transferred into bacterial cells by transduction. Since there is a requirement for in vitro packaging whereby at least 38 kb of DNA is required between the cos sites, the vector without insert DNA will not be packaged (plasmids instability is increased if the novel inserted DNA contains many direct repeats or palindromic (inverted repeats) DNA. This instability can largely be counteracted by using a host bacterium with specific mutations affecting DNA recombination (N.B. Absence of inverted repeats was noted in the first Hohn & Collins publication cited above; see also).

Double-stranded RNA viruses (dsRNA viruses) are a polyphyletic group of viruses that have double-stranded genomes made of ribonucleic acid. The double-stranded genome is used as a template by the viral RNA dependent RNA polymerase (RdRp) to transcribe a positive-strand RNA functioning as messenger RNA (mRNA) for the host cell's ribosomes, which translate it into viral proteins. The positive-strand RNA can also be replicated by the RdRp to create a new double-stranded viral genome.

A distinguishing feature of the dsRNA viruses is their ability to carry out transcription of the dsRNA segments within the capsid, and the required enzymes are part of the virion structure.

In geometry, a pentagonal pyramid is a pyramid with a pentagon base and five triangular faces, having a total of six faces. It is categorized as a Johnson solid if all of the edges are equal in length, forming equilateral triangular faces and a regular pentagonal base.

Pentagonal pyramids occur as pieces and tools in the construction of many polyhedra. They also appear in the field of natural science, as in stereochemistry where the shape can be described as the pentagonal pyramidal molecular geometry, as well as the study of shell assembling in the underlying potential energy surfaces and disclination in fivelings and related shapes such as pyramidal copper and other metal nanowires.