RNA Splicing

In molecular biology, splicing is a modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation. For many eukaryotic introns, splicing is done in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs), but there are also self-splicing introns.

How Is Dna Testing Done

DNA testing is done for many different reasons. DNA evidence can link an alleged criminal to a crime scene. DNA paternity and maternity testing can identify a child's father or mother. DNA relationship testing can determine if two individuals are full or half siblings. DNA ancestry testing can determine ethnic origins and genealogical roots. How DNA testing is done depends on the results desired and the samples available. DNA fingerprinting (or profiling as it's also known) is the process of analyzing and comparing two DNA samples. Only identical twins have the exact same DNA sequence, everyone else's DNA is unique. This makes DNA the perfect way to link individuals to each other or to locations where they have been. The entire DNA chain is incredibly long, much to long to examine all of it. Human DNA is made up of about 3.3 billion base pairs. The differences between DNA samples occur only in small segments of the DNA--the rest of the DNA is pretty much the same. DNA testing focuses on those segments that are known to differ from person to person. As DNA testing has evolved over time, the testing methods have become more precise and are able to work with much smaller DNA samples. Early DNA testing was done using dime-size drops of blood. Today's tests can extract DNA from the back of a licked stamp. The DNA must be extracted from whatever sample is provided. DNA must be isolated and purified before it can be compared. In essence, it has to be "unlocked" from the cell in which it exists. The cell walls are usually dissolved with a detergent. Proteins in the cell are digested by enzymes. After this process, the DNA is purified, concentrated, and tested. DNA testing is done most often today using a process called "short tandem repeats," or STR. Human DNA has several regions of repeated sequences. These regions are found in the same place on the DNA chain, but the repeated sequences are different for each individual. The "short" tandem repeats (repeated sequences of two to five base pairs in length) have been proven to provide excellent DNA profiling results. STR is highly accurate--the chance of misidentification being one in several billion. source:articlebase

Dna Testing to Find Your Ancestors

The use of DNA testing for determining a person’s ancestry is becoming more and common. By linking your maternal DNA (mitochondrial DNA) and your paternal DNA (the y-chromosome), these ancestry databases are effectively able to link you to other people to whom you may be related and thereby determining to some degree your ancestral lineage and where your ancestors came from. DNA Ancestry Testing – Y-Chromosome and Mitochondial DNA The first thing that genealogists look for is a father-to-son linkage, tracked down the Y chromosome which only men posses. Therefore, they are able to observe the Y chromosome that appears in other people and compare them, to determine where a paternal link may be present. This comparison, in essence, allows for the genealogist to try and find paternal linkages amongst people. The other thing that can be done is to link maternal DNA. This in particular is a very powerful testing method that allows for accurate tracking back over many generations because of the mitochondria. Unlike DNA found in the nucleus, which can be altered and changes as environments change, mitochondrial DNA is a direct connection from child to mother that can’t be altered along the way. By taking a sample of the mitochondrial DNA, which is different than the DNA found in the nucleus, the genealogist can determine a maternal linkage. By taking this information, they can, once again, find, perhaps those long lost cousins or celebrity ancestors. DNA Ancestry Testing – Matching to a DNA Database However, can this really be effective at tracing family lines? How can they tell you who you’re related to throughout history? Some online ancestry websites create a database of DNA against which your can be matched. By taking a simple mouth swab and run the DNA tests, they then save the DNA profile that is collected. However, the key is for them to continuously compare other people’s DNA profiles to what your profile is. In essence, this will create a massive database that will determine instantly if a piece of code is a direct comparison to yours. So, as the database grows more and more, more and more relatives and ancestors can be discovered for more and more people.DNA Ancestry Testing – Determine geographical ancestry Furthermore, these DNA tests are able to help you find out where you come from. It’s argued that 170,000 years ago, humans left Africa and migrated elsewhere across the globe. Some went to Europe, some went to southern Africa, while others went to Asia to settle. By comparing the DNA profile of a person to that of researched ethnic groups, it is possible to provide information about where people are from. DNA testing has become a very useful method for people to find long lost relatives. Furthermore, the argument of the true nature of one’s ethnic origins can finally be resolved by DNA testing processes. Of course, as the databases grow and more research is conducted on, the usefulness of these types of tests will increase greatly.

The Dna Testing Process

DNA testing is becoming increasingly used to determine genetic links between individuals as a highly accurate and individual way of identifying people and their relationships with one another. The process itself is one carried out in advanced laboratories under the strictest of lab conditions to ensure no cross-contamination and improve result accuracy. As such DNA testing can be said to present with a high degree of accuracy any particular biological relationship that may exist, particularly in paternity disputes where samples of both the mother and the father are provided. Preparing For the DNA Test and Collecting Samples Normally a DNA testing kit is sent to the person who ordered the test by the company from whom the order was made. The test begins with samples being collected from everyone preparing to undertake the test. In most cases, that will mean the mother, the father (alleged) and the child concerned. Samples are taken by the way of oral swabs, which collect cheek cells which are then dried and passed on for testing. In order to prepare the sample, it is first important to make sure that the cotton of the swab never touches any other surface including your hands, and that you have a number of swabs for each person taking the test to ensure reliability in the end results. Press the swab into the inside of the cheek and behind the lips, as well as the tongue area in order to get as good as possible a sample from the mouth. Having left to dry for around an hour, the swab should be carefully sealed off before the collation and mailing process. Testing the Samples After all the samples have been collected and labelled accordingly, they should be sent off to the laboratory for the DNA testing analysis. At this stage, the samples will be individually examined and DNA will be extracted from within the cells present in the sample. The same will be done for both the other two parties to the test and the results of the DNA profiles will be compared. The person analysing your results will be looking for a 50/50 split between your alleles, contained within the DNA, between those found on your mother and father. As you can only inherit genes already carried by one or both parents, no alleles can be present in the child's DNA that are not present in that of either parent. Naturally, this is where it becomes obvious when there is and is not a genetic link between those taking the DNA test. Further to that, the results are processed through the appropriate systems and a conclusion is reached, having covered 16 of the locus which are used as the template by which samples are matched. Receiving the DNA Test Results Once the DNA test is completed, the result will be sent to the participants via email, letter, fax or as otherwise agreed. The DNA test report should show the individual profile of each person that submitted a sample for the paternity test. Also the result should show the percentage probability of the stated relationship, for example in a DNA paternity test this is normally in excess of 99.99%. There's no doubt about it - DNA testing is here to stay. Whilst most people are not very knowledgeable on how DNA paternity testing works, it is probably a good idea to gain some level of understanding given the way in which DNA testing is likely to continue to affect our lives over the coming decades. With growing calls for more extensive DNA databases and records for crime prevention, DNA testing and analysis looks set to remain at the forefront of the civil liberties/state interests debate.

RNA - Transcription

Introduction:

The differences in the composition of RNA and DNA have already been noted. In addition, RNA is not usually found as a double helix but as a single strand. However, the single polynucleotide strand may fold back on itself to form portions which have a double helix structure like the tertiary structure of proteins.

The biosynthesis of RNA, called transcription, proceeds in much the same fashion as the replication of DNA and also follows the base pairing principle. Again, a section of DNA double helix is uncoiled and only one of the DNA strands serves as a template for RNA polymerase enzyme to guide the synthesis of RNA. After the synthesis is complete, the RNA separates from the DNA and the DNA recoils into its helix.

The transcription of a single RNA strand is illustrated in the graphic on the left. One major difference is that the heterocyclic amine, adenine, on DNA codes for the incorporation of uracil in RNA rather than thymine as in DNA. Remember that thymine is not found in RNA and do not confuse the replacement of uracil in RNA for thymine in DNA in the transcription process. For example, thymine in DNA still codes for adenine on RNA not uracil, while the adenine on DNA codes for uracil in RNA.

Note that the new RNA (red) is identical to non coding DNA with the exception of uracil where thymine was located in DNA.

There are three major types of RNA which will be fully explained in a later section. Although RNA is synthesized in the nucleus, it migrates out of the nucleus into the cytoplasm where it is used in the synthesis of proteins.

RNA Transcription Process:

The RNA transcription process occurs in three stages: initiation, chain elongation, and termination.

The first stage occurs when the RNA Polymerase-Promoter Complex binds to the promoter gene in the DNA. This also allows for the finding of the start sequence for the RNA polymerase. The promoter enzyme will not work unless the sigma protein is present (shown in blue in graphic). Specific sequences on the non coding strand of DNA are recognized as the signal to start the unwinding process.

Abamectin

INTRODUCTION

Abamectin is a mixture of avermectins containing > 80% avermectin B1a and <>

Use

Abamectin is used to control insect and mite pests of a range of agronomic, fruit, vegetable and ornamental crops, and it is used by homeowners for control of fire ants. Abamectin is also used as a veterinary antihelmintic. Resistance to abamectin based antihelmintics, although a growing problem, is not as common as to other classes of veterinary antihelmintics.

ACUTE TOXICITY

Abamectin is a highly toxic material, however most formulated products containing abamectin are of low toxicity to mammals. Emulsifiable concentrate formulations may cause moderate eye irritation and mild skin irritation. Symptoms of poisoning observed in laboratory animals include pupil dilation, vomiting, convulsions and/or tremors, and coma .

Abamectin acts on insects by interfering with neural and neuromuscular transmission. It acts on a specific type of synapse located only within the brain and is protected by the blood-brain barrier. However, at very high doses, the mammalian blood-brain barrier can be penetrated, causing symptoms of CNS depression such as incoordination, tremors, lethargy, excitation and pupil dilation. Very high doses have caused death from respiratory failure.

Abamectin is not readily absorbed through skin. Tests with monkeys show that less than 1% of dermally applied abamectin was absorbed into the bloodstream through the skin . Abamectin does not cause allergic skin reactions.

The amount of a chemical that is lethal to one-half (50%) of experimental animals fed the material is referred to as its acute oral lethal dose fifty, or LD50. The oral LD50 for abamectin in rats is 11 mg/kg, and in mice range from 14 to > 80 mg/kg. The dermal LD50 for technical abamectin on rats and rabbits is > 330 mg/kg. The oral LD50 for the product Affirm 0.011% Fire Ant Bait in rats is > 5,000 mg/kg, and its dermal LD50 on rabbits is > 2,000 mg/kg. The oral LD50 for the 1.8% w/v Abamectin EC product in rats is 300 mg/kg, and the dermal LD50 for this product on rabbits is > 2,000 mg/kg .

CHRONIC TOXICITY

In a 1-year study with dogs given oral doses of 0, 0.25, 0.5, or 1 mg/kg/day, there were no changes in tissue at any dose level. However, some dogs at the 0.5 and 1 mg/kg/day levels had pupillary dilation, weight loss, lethargy, tremors and recumbency. The NOEL for this study was 0.25 mg/kg/day. Similar results were seen in a 2-year study with rats fed 0, 0.75, 1.5, or 2 mg/kg/day. No changes in the nervous or muscular systems were observed, but rats in all the dosage levels exhibited body weight gains significantly higher than the controls. A few individuals in the high dose group exhibited tremors .

When mice were fed 8 mg/kg/day, the highest dose tested, for 94 weeks, the males developed dermatitis and changes in blood formation in the spleen, while females exhibited tremors and weight loss.

Abietic acid

Abietic acid (also known as abietinic acid or sylvic acid), a resin acid, is the primary irritant in pine wood and resin, isolated from rosin (via isomerization) and is the most abundant of several closely related organic acids that constitute most of rosin, the solid portion of the oleoresin of coniferous trees. Its ester is called an abietate.

Abietic acid is a weak contact allergen, however compounds resulting of its oxidation by air elicit stronger response. It is soluble in alcohols, acetone, and ethers.

Synonym Name:Sylvic acid; abietinic acid; abieta-7,13-dien-18-oic acid; 1-phenanthrenecarboxylic acid, 1,2,3,4,4a,4b,5,6,10,10a-decahydro-1,4a-dimethyl-7-(1-methylethyl)-, (1R,4aR,4bR,10aR)-; (1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydro-phenanthrene-1-carboxylic acid

Commercial abietic acid is usually a glassy or partly crystalline yellowish solid that melts at temperatures as low as 85°C (185°F). It belongs to the diterpene group of organic compounds (compounds derived from four isoprene units). It is used in lacquers, varnishes, and soaps, and for the analysis of resins and the preparation of metal resinates. It is listed in the Toxic Substances Control Act inventory.

Rosin has been used for centuries for caulking ships. It is also rubbed on the bows of musical instruments to make them less slippery. In modern times methods have been developed for improving the properties of the rosin acids, which are soft, tacky, and low-melting and subject to rapid deterioration by oxidation in air. Stability is greatly increased by heat treatment.

Rosin acids are converted into ester gum by reaction with controlled amounts of glycerol or other polyhydric alcohols. Ester gum has drying properties and is used in paints, varnishes, and lacquers.

Acetic acid

Definition of Acetic acid

Acetic acid: The acid most commonly associated with vinegar. Acetic acid is a two-carbon carboxylic acid. Its formula is: CH3COOH. It is the most commercially important organic acid and is used in the manufacture of a broad range of chemical products, such as plastics and insecticides.

Acetic acid, CH3COOH, also known as ethanoic acid, is an organic acid which gives vinegar its sour taste and pungent smell. Pure, water-free acetic acid (glacial acetic acid) is a colourless liquid that absorbs water from the environment (hygroscopy), and freezes at 16.7 °C (62 °F) to a colourless crystalline solid. It is a weak acid, in that it is only partially dissociated acid in aqueous solution.

Acetic acid is one of the simplest carboxylic acids. It is an important chemical reagent and industrial chemical, used in the production of polyethylene terephthalate mainly used in soft drink bottles; cellulose acetate, mainly for photographic film; and polyvinyl acetate for wood glue, as well as synthetic fibres and fabrics. In households, diluted acetic acid is often used in descaling agents. In the food industry acetic acid is used under the food additive code E260 as an acidity regulator.

The global demand of acetic acid is around 6.5 million tonnes per year (Mt/a), of which approximately 1.5 Mt/a is met by recycling; the remainder is manufactured from petrochemical feedstocks or from biological sources.

Use ofAcetic acid

CLINICAL PHARMACOLOGY

Acetic acid is anti-bacterial and anti-fungal; propylene glycol is hydrophilic and provides a low surface tension; benzethonium chloride is a surface active agent that promotes contact of the solution with tissues.

INDICATIONS AND USAGE

For the treatment of superficial infections of the external auditory canal caused by organisms susceptible to the action of the antimicrobial.

CONTRAINDICATIONS

Hypersensitivity to Acetic Acid Otic Solution or any of the ingredients. Perforated tympanic membrane is considered a contraindication to the use of any medication in the external ear canal.

WARNINGS

Discontinue promptly if sensitization or irritation occurs.

PRECAUTIONS

Transient stinging or burning may be noted occasionally when the solution is first instilled into the acutely inflamed ear.

Pediatric Use

Safety and Effectiveness in pediatric patients below the age of 3 years have not been established.

ADVERSE REACTIONS

Stinging or burning may be noted occasionally; local irritation has occurred very rarely.

DOSAGE AND ADMINISTRATION

Carefully remove all cerumen and debris to allow Acetic Acid Otic Solution to contact infected surfaces directly. To promote continuous contact, insert a wick of cotton saturated with the solution into the ear canal; the wick may also be saturated after insertion. Instruct the patient to keep the wick in for at least 24 hours and to keep it moist by adding 3 to 5 drops of the solution every 4 to 6 hours. The wick may be removed after 24 hours but the patient should continue to instill 5 drops of Acetic Acid Otic Solution 3 or 4 times daily thereafter, for as long as indicated. In pediatric patients, 3 to 4 drops may be sufficient due to the smaller capacity of the ear canal.

The Analysis of DNA or RNA

In order to measure DNA content you can use UV Spectrophotometer with the advantages are nondestructive and allows the sample to be recovered for further analysis or manipulation. Spectrophotometry uses the fact that there is a relationship between the absorption of ultraviolet light by DNA/RNA and its concentration in a sample. In this particular posting, I want to give you facts about the relationship between DNA/RNA with the wavelength in the Spectrophotometer assay. 1. The absorption maximum of DNA/RNA is approx 260 nm. This figure is an average of the absorption of the individual nucleotides that vary between 256 and 281 nm. 2. In the case of RNA, the concentration of a sample containing RNA may be calculated following Equation: 40 x OD260 of the sample = concentration of RNA (microgram/mL) And this equation for DNA concentration: 50 x OD260 of the sample =concentration of DNA (microgram/mL) The equation above describe that when the OD-260 of the sample is 1 the concentration of RNA will be approx 40 micrograms/mL (50 micrograms/mL for DNA). 3. We can also assess the degree of purity of the nucleic acids by examining the absorption at other wavelengths in which protein and polysaccharides have known absorption maxima. Proteins are known to absorb strongly at 280 nm and polysaccharides may be identified by their maximum at 230 nm. 4. Therefore, in assessing the purity degree of the nucleic acid sample we use the ratio of measurements of these three wavelengths 230 nm, 260 nm, and 280 nm. 5. For example a sample containing only RNA following an extraction method is judged as being uncontaminated if the ratio is 1 :2 : 1, and for DNA is 1 : 1.8 : 1 (it reflects OD-230 : 260 : 280 ratio). If there is significant deviation from the ratio, then it is evident that contaminants are present and that further purification of the sample is necessary. In many cases, the purity and the concentration may be further obscured by the presence of reagents that are used in the extraction process itself. Some of these have characteristics that are evident on a spectrophotometric scan that includes the three wavelengths indicated. Therefore, when using spectrophotometry in the analysis of DNA or RNA it is necessary to be aware of the potential problems that may result in misleading ratio. Further, when analyzing ratios and concentrations of DNA or RNA spectrophotometrically it is also necessary not only to derive readings at 280,260, and 230 nm but also to scan throughout the range 200-320 nm. Trace amounts of reagents used in the extraction process can influence adversely and provide misleading data that may affect any subsequent manipulation.

Bacteriocin

Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s). They are typically considered to be narrow spectrum antibiotics, though this has been debated They are phenomenologically analogous to yeast and paramecium killing factors, and are structurally, functionally, and ecologically diverse.

Methods of classification

Alternative methods of classification include: method of killing (pore forming, dnase, nuclease, murein production inhibition, etc), genetics (large plasmids, small plasmids, chromosomal), molecular weight and chemistry (large protein, polypeptide, with/without sugar moiety, containing atypical amino acids like lanthionine) and method of production (ribosomal, post ribosomal modifications, non-ribosomal).

Class I bacteriocins

The class I bacteriocins are small peptide inhibitors and include nisin.

Class II bacteriocins

The class II bacteriocins are small heat-stable proteins. The action of Class IIa bacteriocins seems to involve disruption of mannose transport into target cells. Class IIb bacteriocins form pores in the membranes of target cells and disrupt the proton gradient of target cells. Other bacteriocins can be grouped together as Class IIc. These have a wide range of effects on membrane permeability, cell wall formation and pheromone actions of target cells.

Class III bacteriocins

Large, heat-labile protein bacteriocins.

Medical significance

Bacteriocins are of interest in medicine because they are made by non-pathogenic bacteria that normally colonize the human body. Loss of these harmless bacteria following antibiotic use may allow opportunistic pathogenic bacteria to invade the human body.

Bacteriocins have also been suggested as a cancer treatment. They have shown distinct promise as a diagnostic agent for some cancers, , but their status as a form of therapy remains experimental and outside the main thread of cancer research. Partly this is due to questions about their mechanism of action and the presumption that anti-bacterial agents have no obvious connection to killing mammalian tumor cells. Some of these questions have been addressed, at least in part.

In the long quest for medical applications, bacteriocins have also been tested as AIDS drugs.

Production

There are many ways to demonstrate bacteriocin production, depending on the sensitivity and labor intensiveness desired. To demonstrate their production, technicians stab inoculate multiple strains on separate multiple nutrient agar Petri dishes, incubate at 30 °C for 24 h., overlay each plate with one of the strains (in soft agar), incubate again at 30 °C for 24 h. After this process, the presence of bacteriocins can be inferred if there are zones of growth inhibition around stabs. This is the simplest and least sensitive way. It will often mistake phage for bacteriocins. Some methods prompt production with UV radiation, Mitomycin C, or heat shock. UV radiation and Mitomycin C are used because the DNA damage they produce stimulates the SOS response. Cross streaking may be substituted for lawns. Similarly, production in broth may be followed by dripping the broth on a nascent bacterial lawn, or even filtering it. Precipitation (ammonium sulfate) and some purification (e.g. column or HPLC) may help exclude lysogenic and lytic phage from the assay.

Nucleic Acids - DNA - RNA

DNA is composed of four types of molecules known as nucleic acids or nucleotides. The four nucleotides are: adenine (A), guanine (G), cytosine (C), and thymine (T). These molecules are further classified into two families. Adenine (A) and guanine (G) are known as purine and cytosine (C) and thymine (T) are known as pyrimidine. During DNA synthesis, nucleotides are converted into nucleic acids to so that they can be linked to form strands of DNA. The assembled strand of DNA takes on the structure of a double helix.

The two strands of DNA are held together by hydrogen bonds between adjacent complementary nucleotides.

The chemical structures of the four nucleotides are planar due to the delocalized electrons in the five- and six-membered rings, each having a thickness of 3.4 angstroms. When the nucleotides form the double helix structure, A-T and G-C are joined together by a hydrogen bond to form a base pair. The base pairs are then joined together by sugar bonds to form the helix. X-ray data shows that there are 10 base pairs per turn of the helix.

The helical model of DNA also explains the theory of genetic replication. James Watson once described it as the "pretty molecule" because the method of replication is so self evident in this structure. During replication, the hydrogen bonds between nucleotides break and allow each single strand of DNA to serve as a template for replication of the other half. The two identical copies of newly synthesized of DNA are then distributed to two new daughter cells. Because during each cycle of replication half of the old DNA is preserved, DNA replication is said to be semi-conservative.

Although DNA contains the genetic blueprint of life, it requires the assistance of ribonucleic acid (RNA) to be functional. RNA also consists of strands of nucleic acids joined together by sugar-phosphate bonds. Unlike DNA, RNA substitutes the nucleotide thymine (T) with uracil (U) and exists as single strands. After DNA is converted into strands of RNA, the messenger RNA (mRNA) is sent to the ribosome to direct the synthesis of proteins.

genomics

TRANSCRIPTION

DNA

Molecular Biology