Extrachromosomal array

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An extrachromosomal array is a method for mosaic analysis in genetics. It is a cosmid, and contains two functioning (wild-type) closely linked genes: a gene of interest and a mosaic marker. Such an array is injected into germ line cells, which already contain mutant (specifically, loss of function) alleles of all three genes in their chromosomal DNA. The cosmid, which is not packed correctly during mitosis, is occasionally present in only one daughter cell following cell division. The daughter cell containing the array expresses the gene of interest; the cell lacking the array does not.

Genetics Science of genes, heredity, and variation in living organisms

Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.

A cosmid is a type of hybrid plasmid that contains a Lambda phage cos sequence . Cosmids DNA sequences are originally from the lambda phage. They are often used as a cloning vector 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 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.

Chromosome DNA molecule containing genetic material of a cell

A chromosome is a deoxyribonucleic acid (DNA) molecule with part or all of the genetic material (genome) of an organism. Most eukaryotic chromosomes include packaging proteins which, aided by chaperone proteins, bind to and condense the DNA molecule to prevent it from becoming an unmanageable tangle.

The mosaic marker is a gene which exhibits a visible phenotype change between the functioning and non-functioning alleles. For example, ncl-1, located in chromosomal DNA, exhibits a larger nucleolus than the wild-type allele, which is in the array. Thus, cells which exhibit larger nucleoli have usually not retained the extrachromosomal array.

Phenotype classification system used to categorize organisms based on their appearance

The phenotype of an organism is the composite of the organism's observable characteristics or traits, including its morphology or physical form and structure; its developmental processes; its biochemical and physiological properties; its behavior, and the products of behavior, for example, a bird's nest. An organism's phenotype results from two basic factors: the expression of an organism's genetic code, or its genotype, and the influence of environmental factors, which may interact, further affecting phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black and brown. Richard Dawkins in 1978 and then again in his 1982 book The Extended Phenotype suggested that bird nests and other built structures such as caddis fly larvae cases and beaver dams can be considered as "extended phenotypes".

Nucleolus A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane. Its prime function is the transcription of the nucleolar DNA

The nucleolus is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis. Nucleoli also participate in the formation of signal recognition particles and play a role in the cell's response to stress. Nucleoli are made of proteins, DNA and RNA and form around specific chromosomal regions called nucleolar organizing regions. Malfunction of nucleoli can be the cause of several human conditions called "nucleolopathies" and the nucleolus is being investigated as a target for cancer chemotherapy.

The gene of interest is the target of the mosaic analysis. Cells lacking the extrachromosomal array also lack the functional gene of interest. Cells which develop normally without the array do not require the gene of interest for normal function. Cells which do not develop normally are said to require the gene. In this way, those cell lineages which require a specific gene can be identified.

Extrachromosomal arrays replace an earlier technique involving a duplicated piece of chromosome called a free duplication. The latter technique required that the gene of interest and the mosaic marker be closely linked on the duplication; the former allows free choice of mosaic marker and target gene.

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Autosome Any chromosome other than a sex chromosome.

An autosome is a chromosome that is not an allosome. The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosome pairs which may have different structures. The DNA in autosomes is collectively known as atDNA or auDNA.

Genotype classification system used to categorize organisms based on their genetic characteristics; organisms full hereditary information, part (DNA sequence) of the genetic makeup of a cell, one of three factors that determine phenotype

The genotype is the part of the genetic makeup of a cell, and therefore of any individual, which determines one of its characteristics (phenotype). The term was coined by the Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1903.

Plasmid small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently

A plasmid is a small DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that benefit the survival of the organism, such as by providing antibiotic resistance. While the chromosomes are big and contain all the essential genetic information for living under normal conditions, plasmids usually are very small and contain only additional genes that may be useful in certain situations or conditions. Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation.

Dominance (genetics) relationship between alleles of a gene, in which the phenotypic effect of one allele masks the phenotypic effect (phenotype) of another allele at the same locus

Dominance in genetics is a relationship between alleles of one gene, in which the effect on phenotype of one allele masks the contribution of a second allele at the same locus. The first allele is dominant and the second allele is recessive. For genes on an autosome, the alleles and their associated traits are autosomal dominant or autosomal recessive. Dominance is a key concept in Mendelian inheritance and classical genetics. Often the dominant allele codes for a functional protein whereas the recessive allele does not.

Homologous chromosome

A couple of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during meiosis. Homologs have the same genes in the same loci where they provide points along each chromosome which enable a pair of chromosomes to align correctly with each other before separating during meiosis. This is the basis for Mendelian inheritance which characterizes inheritance patterns of genetic material from an organism to its offspring parent developmental cell at the given time and area.

Cloning vector

A cloning vector is a small piece of DNA, taken from a virus, a plasmid, or the cell of a higher organism, that can be stably maintained in an organism, and into which a foreign DNA fragment can be inserted for cloning purposes. The vector therefore contains features that allow for the convenient insertion or removal of a DNA fragment to or from vector, for example by treating the vector and the foreign DNA with a restriction enzyme that cuts the DNA. DNA fragments thus generated contain either blunt ends or overhangs known as sticky ends, and vector DNA and foreign DNA with compatible ends can then be joined together by molecular ligation. After a DNA fragment has been cloned into a cloning vector, it may be further subcloned into another vector designed for more specific use.

A genetic screen or mutagenesis screen is an experimental technique used to identify and select for individuals who possess a phenotype of interest in a mutagenized population. Hence a genetic screen is a type of phenotypic screen. Genetic screens can provide important information on gene function as well as the molecular events that underlie a biological process or pathway. While genome projects have identified an extensive inventory of genes in many different organisms, genetic screens can provide valuable insight as to how those genes function.

In genetics, a mosaic, or mosaicism, involves the presence of two or more populations of cells with different genotypes in one individual who has developed from a single fertilized egg. Mosaicism has been reported to be present in as high as 70% of cleavage stage embryos and 90% of blastocyst-stage embryos derived from in vitro fertilization.

Non-Mendelian inheritance

Non-Mendelian inheritance is any pattern of inheritance in which traits do not segregate in accordance with Mendel's laws. These laws describe the inheritance of traits linked to single genes on chromosomes in the nucleus. In Mendelian inheritance, each parent contributes one of two possible alleles for a trait. If the genotypes of both parents in a genetic cross are known, Mendel’s laws can be used to determine the distribution of phenotypes expected for the population of offspring. There are several situations in which the proportions of phenotypes observed in the progeny do not match the predicted values. Non-Mendelian Inheritance is applicable in co-dominance and incomplete dominace.

Genetics, a discipline of biology, is the science of heredity and variation in living organisms.

Loss of heterozygosity

Loss of heterozygosity (LOH) is a cross chromosomal event that results in loss of the entire gene and the surrounding chromosomal region.

Genetic marker Gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species

A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change, or a long one, like minisatellites.

Medical genetics medical specialty that involves the diagnosis and management of hereditary disorders

Medical genetics is the branch of medicine that involves the diagnosis and management of hereditary disorders. Medical genetics differs from human genetics in that human genetics is a field of scientific research that may or may not apply to medicine, while medical genetics refers to the application of genetics to medical care. For example, research on the causes and inheritance of genetic disorders would be considered within both human genetics and medical genetics, while the diagnosis, management, and counselling people with genetic disorders would be considered part of medical genetics.

In molecular biology, SNP array is a type of DNA microarray which is used to detect polymorphisms within a population. A single nucleotide polymorphism (SNP), a variation at a single site in DNA, is the most frequent type of variation in the genome. Around 325 million SNPs have been identified in the human genome, 15 million of which are present at frequencies of 1% or higher across different populations worldwide.

Gene cluster

A gene family is a set of homologous genes within one organism. A gene cluster is part of a gene family. A gene cluster is a group of two or more genes found within an organism's DNA that encode for similar polypeptides, or proteins, which collectively share a generalized function and are often located within a few thousand base pairs of each other. The size of gene clusters can vary significantly, from a few genes to several hundred genes. Portions of the DNA sequence of each gene within a gene cluster are found to be identical; however, the resulting protein of each gene is distinctive from the resulting protein of another gene within the cluster. Genes found in a gene cluster may be observed near one another on the same chromosome or on different, but homologous chromosomes. An example of a gene cluster is the Hox gene, which is made up of eight genes and is part of the Homeobox gene family.

This glossary of genetics is a list of definitions of terms and concepts commonly used in the study of genetics and related disciplines in biology, including molecular biology and evolutionary biology. It is intended as introductory material for novices; for more specific and technical detail, see the article corresponding to each term.

Balancer chromosomes are special, modified chromosomes used for genetically screening a population of organisms to select for heterozygotes. Balancer chromosomes can be used as a genetic tool to prevent crossing over between homologous chromosomes during meiosis. Balancers are most often used in Drosophila melanogaster genetics to allow populations of flies carrying heterozygous mutations to be maintained without constantly screening for the mutations but can also be used in mice. Balancer chromosomes have three important properties: they suppress recombination with their homologs, carry dominant markers, and negatively affect reproductive fitness when carried homozygously.

In molecular cloning, a vector is a DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell, where it can be replicated and/or expressed. A vector containing foreign DNA is termed recombinant DNA. The four major types of vectors are plasmids, viral vectors, cosmids, and artificial chromosomes. Of these, the most commonly used vectors are plasmids. Common to all engineered vectors are an origin of replication, a multicloning site, and a selectable marker.

A knockout mouse or knock-out mouse is a genetically modified mouse in which researchers have inactivated, or "knocked out", an existing gene by replacing it or disrupting it with an artificial piece of DNA. They are important animal models for studying the role of genes which have been sequenced but whose functions have not been determined. By causing a specific gene to be inactive in the mouse, and observing any differences from normal behaviour or physiology, researchers can infer its probable function.

References

Miller LM, Waring DA, Kim SK (1996). Mosaic analysis using a ncl-1 (+) extrachromosomal array reveals that lin-31 acts in the Pn.p cells during Caenorhabditis elegans vulval development. Genetics 143 (3): 1181-1191.