DNA Barcoding Project

The sticky end DNA fragments are subject to fluorescent probes, having separate colours for a single base. The labeled DNA fragments are fed into an automatic sequencing machine that reads the base sequence according to the colours of the bases. A computer then uses this piece of information to read the sequence into a continuous DNA sequence by finding overlaps and matching

The following results helped obtain the haplogroup that in which the sequence of mtDNA would identify. The PCR reaction worked, and this can be determined by looking at the agarose gel in figure 1. If the PCR reaction was successful, than a band should appear around 550bp. Individual AC displays a band around 550bp, this means the PCR reaction was successful. The band for individual AC, depicts a low concentration of product, because the band faint. After the purification process the concentration, A260/280 ratio, and A260/A230 ratio were determined by using the nanodrop. The concentration of mtDNA in the product was 60.9 ng/uL. The ratio for A260/280 was 1.79 and the ratio for A260/230 was 0.77. The A260 and 280 are a spectrometer measurement that measure absorbance at wavelengths of

The number of repeat on Genomic DNA fragment #1 is 22 and on Genomic DNA fragment #2 is 26.

Each human being has something called DNA. DNA is described as genetics and an extremely long macromolecule that is the main component of chromosomes and is the material that transfers genetic characteristics in all life forms. DNA constructs of two nucleotide strands coiled around each other in a ladder like arrangement with the sidepieces composed of alternating phosphate and deoxyribose units and the rungs composed of the purine and pyrimidine bases adenine, guanine, cytosine, and thymine. Each chromosome consist of one continuous thread-like molecule of DNA coiled tightly around proteins and contains a portion of the 6,400,000,000 basepairs that make up your DNA.

In the essay, “DNA fingerprinting: Cracking Our Genetic ‘Barcode’,” by Elaine Marieb, illustrates how significant DNA fingerprinting is today. She initiates a candid example of how New York City’s World Trade Center massacre killed more than 3, 000, left millions of bodies distorted, charred, and decayed. It was the staple for the ever-increasing need for DNA fingerprinting.

DNA collection is a good thing not only can it help catch the person responsible for an illegal crime, but it can also clear up a suspect’s name. In the case of Maryland v. King on April 2009 Alonzo Jay King was charged for first and second degree assault for scarring a crowd of people with a shotgun, he was arrested and as a part of their booking procedure, they swabbed Alonzo Jay King for his DNA. Kings DNA sample later resulted to be a match of a DNA sample in the system “CODIS” of a rape victim by the name of Vonette W.’s Salisbury. Vonnette was raped on September 2003 but had not gotten justice for the crime against her since the only evidence was the DNA sample of the semen that was swabbed. No matches were found in the data base until Alonzo Jay King was arrested. By collecting DNA, it can help lead to an arrest of a suspect and to be able to close cases.

When I first started reading the article I could not believe in the idea of DNA barcoding. As I continued reading I was even more upset with the measure people would go to sale fake goods. I thought that I really do not want anyone missing with my food. The article allowed me to see the bigger picture of DNA Barcoding. People have found ways to made foods look as if we are eating fish, chicken and other goods. I think the DNA Barcoding is a step in the right direction because a lot of are foods are filled with hormones and things that should not go into are body. If DNA Barcoding cuts down on this why not try to find ways to improve and crack down on the fake goods.

-DNA purification is an important method that involved in many areas of molecular biology, genomics, biotechnology and clinical research. Purification will reduce the chance of contaminations happen during the experiments and extract amount of DNA sample from limited source to satisfy the requirements of research. The whole procedure of DNA purification involves many different techniques, such as anion exchange, affinity, and so on.

Let the agarose powder sit in the buffer for a few minutes. The beaker is covered with plastic wrap an placed in the microwave. Microwave the solution slowly with boiling it. As soon as the solution starts to boil, take it out and carefully mix it with the hot gloves on and continue to heat the solution until it is completely clear. Once the solution is cooled, add 3µL of ethidium bromide stock to the solution and mix it by swirling it. The gel is poured into the prepared mould that is taped on the ends and eliminate any bubbles. Place the comb on the negatively (-) charged side. After the gel solidifies, remove the comb and tape and place the gel into the chamber. Gently pour TAE buffer over the gel as the gel should be completely covered by 2-3 mm of buffer. If air bubbles form, gently displace them with a disposable micropipette tip. Droplets of prepared loading buffer are placed on a piece of parafilm paper. The ladder will consists of only the buffer because it will work as a measuring device to compare the DNA samples. 10 µL from each of the DNA samples will be mixed with the loading buffer using the micropipette tip. The positive control will be consist of 10 µL of water and the droplet of loading buffer. The samples including the ladder and positive control are added to a separate well in the gel. Once all of the samples are loaded into their own

once the DNA is received in the form of files, the genealogy needs to be translated from the files labeled “.seq” and “ab1”. The first step is viewing the first file .seq using the desktop application called DNASTAR Lasergene Core Suite 9.0, dragging the DNA sequence file into the SeqBuilder. The DNA is displayed with a grey bar at the top of each nucleotide. The grey bars represent the confidence level that the nucleotide is correct. the grey bars can either be tall or short; the tall bars means that the confidence is very high, while short bars means the confidence level is low and the probability of the Nucleotide below is not the correct one. The DNA sequence can also have mutations such as frameshifts (section of a repeating c’s) causing sections to be highlighted first.Then, the whole DNA sequence can be sequenced, if not, the whole DNA section can be highlighted,

//I organized the signals this way in the hopes ofmaking them easier to read when viewing the waveform

Let the test tube sit undisturbed for 2 - 5 minutes. You should begin to see air bubbles form at the boundary line between the ethanol and the filtered fruit solution. Bubbles will form near the top, and you will eventually see the DNA float to the top of the ethanol. Gently insert the stir stick into the test tube. Slowly raise and lower the tip several times to spool and collect the DNA. If there is an insufficient amount of DNA available, it may not float to the top of the solution in a form that can be easily spooled or removed from the tube. However, the DNA will still be visible as white/clear clusters by gently stirring the solution and pushing the clusters around the top. Post-Lab Questions What is the texture and consistency of the DNA DNA is viscous and greasy. Why did we use a salt in the extraction solution High salt makes DNA less soluble in water. In order to dissolve, the water needs to interact with the DNA. Since DNA is quite large, it needs to interact with lots of water for this purpose. When you add salt, the water preferentially interacts with the salt (its small, and can move around in solution easier than the DNA can). This makes it so there is less water available to interact with the DNA and it becomes less soluble. Is the DNA soluble in the aqueous solution or alcohol DNA is less soluble in an alcohol such as isopropanol than it is in water. This is because alcohols are non-polar, whereas water is polar. The polar

Many technological advancements have been made since the discovery of DNA structure and its function in 1953 by James Watson and Francis Crick. Recently, scientists have developed a process called DNA barcoding. The result of DNA barcoding is a database of barcodes of species, made up of a sequence of nucleotides in specific genes. DNA barcoding is a relatively new process that isolates a section of a mitochondrial gene and amplifies it, allowing scientists to sequence the order of nucleotide bases in a certain gene, the organism’s “barcode.” The mitochondrial cytochrome c oxidase 1 gene (CO1) is used for animals. It codes for a protein that is a part of the electron transport chain, which is used by every species during oxidative phosphorylation in cellular respiration. Every organism has a unique CO1 gene, but organisms that are within the same families will have more similar genes. Thus, by looking at a sequence of nucleotides in the CO1 gene, scientists can identify and categorize species. Each DNA barcode is registered in the Barcode of Life Database (BOLD) under its respective species, and barcodes are being continually added to this database by scientists on the grassroots level. This allows easy and fast identification of species with no expert knowledge of the species required. The old Linnaean system of taxonomy is now outdated, replaced by this revolutionary new way to identify organisms. Today, scientists are utilizing the DNA barcoding process to answer a

The first is to denature dsDNA through heating to ~96 °C. This separates the two strands of DNA. The exact temperature to be used can be calculated with Tm = 4oC x (no. of G & C) + 2oC x (no. of A & T). Tm is the melting point of the strands and to supply the number of G, C, A, & T ‘s the primer is used.

Due to the DNA’s specificity, samples can be utilised for identification. DNA is a nucleic acid composed of deoxyribose sugar bound to a phosphate group and one of four nitrogenous bases (adenine, guanine, cytosine and thymine). Each section of these three components are referred to as nucleotides, which are joined to the phosphate or sugar of another nucleotide by strong covalent bonds to form a backbone. The nitrogenous bases are joined to complimentary bases of another nucleotide (adenine with thymine, guanine with cytosine) to create a double stranded molecule (Figure 2). To complete the double helical structure, the molecule coils to compact it’s contents. DNA molecules can contain up to two million base pairs, with a human genome containing approximately 3 million base pairs. The random assortment of nitrogenous bases as well as the numerous mutations within certain DNA sequences, results in genetically diverese DNA molecules and genomes between individials.