DNA Barcoding and the BOLD Database

Recently, DNA testing has been employed to create a genetic database of endangered animal species. Using this information, scientists have even cloned animals.

The Human Genome Project is a worldwide research effort with the goal of analyzing the structure of human DNA and determining the location of the estimated 100,000 human genes. In parallel with this effort, the DNA of a set of model organisms will be studied to provide the comparative information necessary for understanding the

By using DNA sequencing software and using comparative DNA alignment programs, scientists can piece together where the differences and similarities align and the percentage of identical DNA between two species. Another method of classifying these gene-swapping organisms is to alter the method of vertical genomics and shift to a new form of lateral genomics (Koonin et al. 2001). A method using vertical, linear genomics alone will not provide enough resources to clearly assign an organism to a taxonomic group. Also, scientists can look at gene loss over time as a method to group these organisms (Koonin et al. 2001). If scientists would rather stick with similarities to define a taxonomic group, the use of genomic instruments can provide a better picture of which genes are highly conserved between organisms of the same group (Doolittle 1999). Researchers have begun to employ this method as the means for best completing a phylogenetic tree. Using alignments of single copy genes conserved in the genome allows for scientists to achieve that vertical pattern of phylogeny that can be lost when focusing on the amount of transferred genes between groups (Lang et al. 2013).

Mitochondria are small organelles found in eukaryotic cells which respire aerobically. They are responsible for generating energy from food to ‘power the cell’. They contain their own DNA, reproducing by dividing in 2. As they closely resemble bacteria, it gave the idea that they were derived from bacteria (which were engulfed by ancestors of the eukaryotes we know today). This idea has since been confirmed from further investigations, and it is now widely accepted. (Alberts et al., 2010a)

Introduction: Almost every place on Earth, from the surface of your skin to the bottom of the ocean, is teeming with living things. To keep track of the vast diversity of life, biologists historically named and classified organisms according to their appearance. The system of categorizing organisms is

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.

Indeed DNA profiling has rapidly transform the field of forensics. DNA profiling is the scientific analysis of evidence for crime scene investigation and other legal proceedings. DNA profiling is mostly used by forensic scientists and crime lab technicians. To identify criminals and victims using trace evidence like hair or skin samples. To produce a DNA profile, scientists compare sequences in the genome that vary from person to person. The typical steps in DNA profiling are DNA samples are isolated from the crime scene, suspect, victims, or other evidence. The next selected sequences from each DNA sample are amplified (copied many times) to produce a large sample of DNA fragments. Finally the amplified DNA regions are compared using a gel. All together, these steps provide data about which samples are from the same individual and which sample is unique.

In order to extract DNA from any living thing, we needed to first gather the materials. Then we began the experiment. Step 1, put in a blender 1/2 cup of split peas (100ml), 1/8 teaspoon table salt (less than 1ml), and 1 cup cold water (200ml). Next, we blended the materials on high for 15 seconds. This allowed the pea cells to separate from each other, so we now had a really thin pea-cell soup. Step 2, poured our thin pea-cell soup through a strainer into another container. Added 2 tablespoons of liquid detergent (about 30ml) and swirled to mix. We then let the mixture incubate for 7 minutes. Poured the mixture into test tubes containers, and filled each about 1/3 full. Step 3, added a pinch of meat tenderizer to each test tube and stirred gently to make sure we didn’t break up the DNA. Step 4, tilted our test tube and slowly poured rubbing alcohol (70-95% isopropyl or ethyl alcohol) into the tube down the side so that it forms a layer on top of the pea mixture. Poured until we had about the same amount of alcohol in the tube as pea mixture. Alcohol is less dense than water, so it floats on top. From there we looked for clumps of white stringy stuff where the water and alcohol layers meet. The white stringy stuff was tangled DNA molecules. Thus, we completed DNA extraction. As we performed the experiment we made no changes to the original protocol.

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The Bayesian inference analysis of the COI barcode sequences included 45 L. sericata sequences and 42 L. cuprina sequences. Despite the number of sequences, L. sericata was poorly resolved, which explains the poor node support (0.61) of the L. sericata + L. cuprina + L. taiyuanensis clade. Lucilia taiyuanensis is represented by only one sequence

Bacteria have an intrinsic role to humans thriving commensally in and outside the body, despite their evolutionary and structural differences from us. Their prokaryotic classification gives insight to methods used in identification and observation. Researchers can pinpoint certain genes they know are vital across their phylogeny. An example of this would include autosomal genes, like those that encode for structural proteins used in translation. Particularly, the 16s rRNA gene is highly conserved across prokaryotic species, but unlike many conserved genes, it also includes small variable regions specific to each species. This makes the 16s gene useful as an identification signature for prokaryotes, and it is the most common genetic marker used today (Janda). This is not only due to its presence in nearly all prokaryotes, but because it has been genetically unchanged over time, for the most part. However a flaw to using the 16s rRNA gene is that it cannot be a definite identification

The researchers used shot-gun sequencing which is a technique that uses smaller fragments of deoxyribonucleic acid (DNA) sequences that are reassembled into one sequence by looking for regions of overlap. All of the 3.6M reads, were first trimmed for 99% accuracy for all known organisms then characterized with Sequence-based

Nearly everyone feels some desire to learn about their past and the origin of their ancestors. In Bryan Sykes’ novel, The Seven Daughters of Eve, he takes his readers through the experiences he faced and obstacles he overcame while piecing together the ancestral past of Europe. Ninety-five percent of living native Europeans can trace their past back to one of seven women, whom Sykes named Ursula, Xenia, Helena, Velda, Tara, Katrine and Jasmine. He discovered these clan mothers by studying the mutations found in the control region of mitochondrial DNA. People who had the same or very similar mitochondrial DNA sequences were grouped together and in the end Sykes was left with seven groups. The purpose and benefit of comparing mitochondrial DNA is that every person receives their mitochondrial DNA from their mother. While recombination shuffles and changes the genes in chromosomes, mitochondrial only changes through mutation, making it a reliable source for genetic study. With mitochondrial DNA by his side, Sykes began to look for answers to some of the world’s greatests questions concerning ancestral origin and human colonization throughout the world.

DNA fingerprinting is a scientific technology involving the extraction, replication and arrangement of strands of an organism’s DNA. This results in the formation of a genetically distinctive fingerprint that is unique to the organism which the DNA sample was originally extracted from. Because of the specificity of a DNA fingerprint, the application of this technology can have a substantial influence on many aspects of society. Accessibility to a DNA database allows for higher efficiency in forensic investigations, personal identification, maternal and paternal testing. The availability of a national database to police officers and forensic scientists would equate to increased productivity in investigations and prosecution of suspects in a