What is Stellite DNA

Satellite DNA consists of highly repetitive DNA, and is so called because repetitions of a short DNA sequence tend to produce a different frequency of the nucleotides adenine, cytosine, guanine and thymine, and thus have a different density from bulk DNA - such that they form a second or 'satellite' band when genomic DNA is separated on a density gradient.
Length


A repeated pattern can be between 1 base pair long (a mononucleotide repeat) to several thousand base pairs long, and the total size of a satellite DNA block can be several megabases without interruption. Most satellite DNA is localized to the telomeric or the centromeric region of the chromosome. The nucleotide sequence of the repeats is fairly well conserved across a species. However, variation in the length of the repeat is common. For example, minisatellite DNA is a short region (1-5kb) of 20-50 repeats. The difference in length of the minisatellites is the basis for DNA fingerprinting.

Satellite DNA, at least the microsatellite variety, is thought to have originated by slippage of a replicated chromosome against its template.

Microsatellites are often found in transcription units. Often the base pair repetition will disrupt proper protein synthesis, leading to diseases such as myotonic dystrophy.

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What is Selfish DNA

Selfish DNA refers to those sequences of DNA which, in their purest form, have two distinct properties:

(1) the DNA sequence spreads by forming additional copies of itself within the genome; and

(2) it makes no specific contribution to the reproductive success of its host organism. This idea was sketched briefly by Richard Dawkins in his 1976 book The Selfish Gene and was explicitly exposed in two 1980 articles in Nature magazine. According to one of these articles:

So, the selfish DNA can be considered an efficient replicator that follows another way of increasing in number.

Examples

• Transposons copy themselves to different loci inside the genome. These elements constitute a large fraction of eukaryotic genome sizes (C-values): about 45% of the human genome is composed of transposons and their defunct remnants.
• Homing endonuclease genes cleave DNA at its own site on the homologous chromosome, triggering the DNA double-stranded break repair system, which "repairs" the break by copying the HEG onto the homologous chromosome. HEGs have been characterized in yeast, and can only survive by passing between multiple isolated populations or species. Supernumerary B chromosomes are nonessential chromosomes that are transmitted in higher-than-expected frequencies, which leads to their accumulation in progenies.

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What is Junk DNA

In molecular biology, "junk" DNA is a provisional label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. Scientists fully expect to find functions for some, but definitely not all, of this provisionally classified collection. About 80-90% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. While much of this sequence may be an evolutionary artifact that serves no present-day purpose, some is believed to function in ways that are not currently understood. Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function. Some consider the "junk" label as something of a misnomer, but others consider it apposite as junk is stored away for possible new uses, rather than thrown out; others prefer the term "noncoding DNA" (although junk DNA often includes transposons that encode proteins with no clear value to their host genome). However it now appears that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be transcribed, but transcription by itself does not necessarily imply function.

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Broadly, the science of functional genomics has developed widely accepted techniques to characterize protein-coding genes, RNA genes, and regulatory regions. In the genomes of most plants and animals, however, these together constitute only a small percentage of genomic DNA (less than 2% in the case of humans). The function, if any, of the remainder remains under investigation. Most of it can be identified as repetitive elements that have no known biological function for their host (although they are useful to geneticists for analyzing lineage and phylogeny). Still, a large amount of sequence in these genomes falls under no existing classification other than "junk".
Overall genome size, and by extension the amount of junk DNA, appears to have little relationship to organism complexity: the genome of the unicellular Amoeba dubia has been reported to contain more than 200 times the amount of DNA in humans".
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Hypotheses of origin and function
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There are some hypotheses, none conclusively established, from the most academic to the less expected, for how junk DNA arose and why it persists in the genome:

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  These chromosomal regions could be composed of the now-defunct remains of ancient genes, known as pseudogenes, which were once functional copies of genes but have since lost their protein-coding ability (and, presumably, their biological function). After non-functionalization, pseudogenes are free to acquire genetic noise in the form of random mutations.
• 8% of human junk DNA has been shown to be formed by retrotransposons of Human Endogenous Retroviruses (HERVs), although as much as 25% is recognisably formed of retrotransposons. This is a lower limit on how much of the genome is retrotransposons because older remains might not be recognizable having accumulated too much mutation. New research suggests that genome size variation in at least two kinds of plants is mostly because of retrotransposons.
• In 1997, Steven Sparks proposed that "The end purpose of this "excess DNA" must be to reduce the probability of transcribable genes being cut by chromosomal crossover. Gametes can survive only when their important, transcribed genes are saved from meiotic cutting by being surrounded with "buffer DNA".
• Junk DNA might provide a reservoir of sequences from which potentially advantageous new genes can emerge. In this way, it may be an important genetic basis for evolution.
• Some junk DNA could simply be spacer material that allows enzyme complexes to form around functional elements more easily. In this way, the junk DNA could serve an important function even though the actual sequence information it contains is irrelevant.
• Some portions of junk DNA could serve presently unknown regulatory functions, controlling the expression of certain genes, the development of an organism from embryo to adult, and/or development of certain organs/organelles.
• More and more scientists believe that in fact regulatory layer(s) in the "junk DNA", such as through non-coding RNAs, altogether contain genetic programming at least on par with, and possibly much more important than protein coding genes. But still how much of the 98% would be involved in such activity is unknown.

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Hok/sok system

The host killing/suppressor of killing system, it is also known as hok/sok system, in molecular biology, is a postsegregational killing system of the plasmid R1 of Escherichia coli(or is it).

In simple words, the system is controlled by two genes, hok and sok, coding respectively what can be thought of as a long-lived poison and a short-lived antidote. After cell division, daughter cells without a copy of the plasmid die, as the poison is still active from the parent cell, while the short-lived antidote is not stopping the poison anymore. Only cells with a plasmid can produce more antidote and survive. For this reason, the killing system is "postsegregational", since cell death occurs after segregation of the plasmid.

The hok gene codes for a 52 amino acid toxic protein which causes cell death by depolarization of the cell membrane. The translation of hok mRNA is, however, inhibited by the transcript of the sok gene, which is an antisense regulator and binds to the hok mRNA, forming a duplex which is recognized by the RNase III and degraded. The killing mechanism is obtained through differential decay rates of the hok and sok transcripts: while hok mRNA is quite stable, sok-RNA is rapidly degraded, which would allow hok to be expressed; however the higher rate of transcription of sok compensate, leaving hok mRNA untranslated in plasmid-containing cells. The loss of plasmid causes the hok mRNA not to be inhibited anymore by sok antisense, leading to protein expression and cell death.

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El Tor

El Tor is the name given to a particular strain of the bacterium Vibrio cholerae, the causative agent of cholera. Also known as O1, it has been the dominant strain in the seventh global pandemic. It is distinguished from the classic strain at a genetic level, although both are in the O1 serogroup and both contain Inaba, Ogawa and Hikojima serotypes. It was first identified in 1905 at a camp in El-Tor, Egypt.

El Tor was identified again in an outbreak in 1937 but the pandemic did not arise until 1961 in Sulawesi. El Tor spread through Asia (Bangladesh in 1963, India in 1964) and then into the Middle East, Africa and Europe. From North Africa it spread into Italy by 1973. In the late 1970s there were small outbreaks in Japan and in the South Pacific.

The extent of the pandemic has been due to the relative mildness (lower expression level) of El Tor, the disease has many more asymptomatic carriers than is usual, outnumbering active cases by up to 50:1. El Tor also remains in the body for longer and survives better than other known types. The actual infection is also relatively mild, or at least rarely fatal. Additionally El Tor is capable of host-to-host transmission, unlike the classic strain

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Ice-minus bacteria

Ice-minus bacteria is a nickname given to a variant of the common bacterium Pseudomonas syringae (P. syringae). This strain of P. syringae lacks the ability to produce a certain surface protein, usually found on wild-type "ice-plus" P. syringae. The "ice-plus" protein (Ina protein, "Ice nucleation-active" protein) found on the outer bacterial cell wall acts as the nucleating centers for ice crystals. This facilitates ice formation, hence the designation "ice-plus." The ice-minus variant of P. syringae is a mutant, lacking the gene responsible for ice-nucleating surface protein production. This lack of surface protein provides a less favorable environment for ice formation. Both strains of P. syringae occur naturally, but recombinant DNA technology has allowed for the synthetic removal or alteration of specific genes, enabling the creation of the ice-minus strain.

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Economic importance:

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The success of the agricultural world is heavily dependent on the weather. Cold weather conditions are directly responsible for the appearance of frost on plants and most importantly, crops. In the United States alone, it has been estimated that frost accounts for approximately $1 billion in crop damage each year. As P. syringae commonly inhabits plant surfaces, its ice nucleating nature incites frost development, freezing the buds of the plant and destroying the occurring crop. The introduction of an ice-minus strain of P. syringae to the surface of plants would incur competition between the strains. Should the ice-minus strain win out, the ice nucleate provided by P. syringae would no longer be present, lowering the level of frost development on plant surfaces at normal water freezing temperature (0oC). Even if the ice-minus strain does not win out, the amount of ice nucleate present from ice-plus P. syringae would be reduced due to competition. Decreased levels of frost generation at normal water freezing temperature would translate into a lowered quantity of crops lost due to frost damage, rendering higher crop yields overall.

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Controversy

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At the time of Dr. Lindow's work on ice-minus P. syringae, genetic engineering was considered to be very controversial. The controversy primarily revolved around fears of introducing new organisms that may permanently disrupt the ecosystem. The fear was that the introduction of ice-minus bacteria to the environment would eliminate bacterial and plant varieties. This was true in the case of the gypsy moth's accidental introduction into the U.S. Without a predator in the U.S., the gypsy moth is still causing overwhelming destruction to the hardwood forests of northeastern U.S.

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Naked DNA

Naked DNA is histone-free DNA that is passed from cell to cell during a gene transfer process called transformation or transfection. In transformation , purified or naked DNA is taken up by the recipient cell which will give the recipient cell a new characteristic or phenotype. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed.

In the field of DNA vaccines or genetic immunization, the term "naked DNA" was coined by Vical to mean DNA delivered free from agents which promote transfection. Research on the use of naked DNA for DNA vaccinations and gene therapy has shown some initial success, but have not yet resulted in any generally available therapy.

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VECTOR

In molecular biology, a vector is any vehicle used to transfer foreign genetic material to another cell.
The vector itself is generally a DNA sequence that consists of an insert (transgene) and a larger sequence that serves of the "backbone" of the vector. The purpose of a vector to transfer genetic information to another cell is typically to isolate, multiply, or express the insert in the target cell. Vectors called expression vectors (expression constructs) specifically are for the expression of the transgene in the target cell, and generally have a promoter sequence that drives expression of the transgene. Simpler vectors called transcription vectors are only capable of being transcribed but not translated: they can be replicated in a target cell but not expressed, unlike expression vectors. Transcription vectors are used to amplify their insert.
Insertion of a vector into the target cell is generally called transfection, although insertion of a viral vector is often called transduction.

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Characteristics:

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Two common vectors are plasmids and viral vectors.

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Plasmids

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Plasmids are double-stranded generally circular DNA sequences that are capable of automatically replicating in a host cell. Plasmid vectors minimalistically consist of an origin of replication that allows for semi-independent replication of the plasmid in the host and also the transgene insert. Modern plasmids generally have many more features, notably including a "multiple cloning site" which includes nucleotide overhangs for insertion of an insert, and multiple restriction enzyme consensus sites to either side of the insert. In the case of plasmids utilized as transcription vectors, incubating bacteria with plasmids generates hundreds or thousands of copies of the vector within the bacteria in hours, and the vectors can be extracted from the bacteria, and the multiple cloning site can be restricted by restriction enzymes to excise the hundredfold or thousandfold amplified insert. These plasmid transcription vectors characteristically lack crucial sequences that code for polyadenylation sequences and translation termination sequences in translated mRNAs, making expression of transcription vectors impossible.

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Viral vectors

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Viral vectors are generally genetically-engineered viruses carrying modified viral DNA or RNA that has been rendered noninfectious, but still contain viral promoters and also the transgene, thus allowing for translation of the transgene through a viral promoter. However, because viral vectors frequently are lacking infectious sequences, they require helper viruses or packaging lines for large-scale transfection. Viral vectors are often designed for permanent incorporation of the insert into the host genome, and thus leave distinct genetic markers in the host genome after incorporating the transgene. For example, retroviruses leave a characteristic retroviral integration pattern after insertion that is detectable and integrates that the viral vector has incorporated into the host genome.

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Transcription

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Transcription is a necessary component in all vectors: the premise of a vector is to multiply the insert (although expression vectors later also drive the translation of the multiplied insert). Thus, even stable expression is determined by stable transcription, which generally depends on promoters in the vector. However, expression vectors have a variety of expression patterns: constituitive (consistent expression) or inducible (expression only under certain conditions or chemicals). This expression is based on different promoter activities, not post-transcriptional activities, thus, these two different types of expression vectors depend on different types of promoters.
Viral promoters are often used for constitutive expression in plasmids and in viral vectors because they normally reliably force constant transcription in many cell lines and types.
Inducible expression depends on promoters that respond to the induction conditions: for example, the murine mammary tumor virus promoter only initiates transcription after dexamethasone application and the Drosphilia heat shock promoter only iniates after high temperatures.

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Expression

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Expression vectors require not only transcription but translation of the vector's insert, thus requiring more components than simpler transcription-only vectors. Expression vectors require sequences that encode for:

• Polyadenylation tail: Creates a polyadenylation tail at the end of the transcribed pre-mRNA that protects the mRNA from exonucleases and ensures transcriptional and translational termination: stabilizes mRNA production.
• Minimal UTR length: UTRs contain specific characteristics that may impede transcription or translation, and thus the shortest UTRs or none at all are encoded for in optimal expression vectors.
• Kozak sequence: Vectors should encode for a Kozak sequence in the mRNA, which assembles the ribosome for translation of the mRNA.

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Features

Modern vectors may encompass additional features besides the transgene insert and a backbone:

• Promoter: Necessary component for all vectors: used to drive transcription of the vector's transgene.
• Genetic markers: Genetic markers for viral vectors allow for confirmation that the vector has integrated with the host genomic DNA.
• Antibiotic resistance: Vectors with antibiotic-resistance open reading frames allow for identification of which cells have uptaken the vector through antibiotic selection.
• Epitope: Vector contains a sequence for a specific epitope that is incorporated into the expressed protein. Allows for antibody identification of cells expressing the vector.
• β-galactosidase: Vector's multiple cloning site contains sequence for β-galactosidase, an enzyme that digests galactose, to either side of the region intended for an insert. If the insert has not successfully ligated into the vector, cells expressing the empty vector will generate β-galactosidase and digest galactose. However, cells that express a vector with a transgene will have the coding sequence for β-galactosidase and be unable to digest galactose, and a subsequent color dye for galactose (X-gal) subsequently identifies cells expressing a vector with an insert, although it is unknown whether the insert is the intended one.
• Targeting sequence: Expression vectors may include encoding for a targeting sequence in the finished protein that directs the expressed protein to a specific organelle in the cell.

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