1. How are DNA probes and PCR technology used for monitoring microorganisms in the environment (i.e. water quality tests)? https://www.bcidaho.com/providers/medical_policies/med/mp_20410.asp Recently, the availability of nucleic acid probes has permitted the rapid direct identification of microorganisms’ DNA or RNA. Amplification techniques, including but not limited to the polymerase chain reaction (PCR), results in a doubling of copies of the specified target DNA with each round of amplification, eventually resulting in millionfold levels of amplification. The product of amplification (i.e., DNA) is then detected using a variety of techniques. The amplified product can also be quantified to give an assessment of how many microorganisms are present. Quantification of the amount of nucleic acids permits serial assessments of response to treatment; the most common clinical application of quantification is the serial measurement of HIV RNA (called viral load), which serves as a prognostic factor.

2. How is DNA technology used to break the cycle of disease in nature (i.e. intervention in the life cycle of parasites)? http://aem.asm.org/content/64/7/2697.full Membrane-impermeative fluorescent probes that can passively diffuse through the cell wall of a bacterium can act as an indicator of a loss in membrane integrity, which, in turn, can often act as an indicator of cell viability. Indeed, the loss of membrane integrity results in membrane permeabilization and thus, in the degradation of nucleic acids whose maintenance is at least essential to retain viability. However, such degradation may occur with a delay after the loss of membrane integrity, which may be dependent on both environmental conditions and species. Although DNA integrity is not sufficient to ensure viability of a cell, DNA degradation is sometimes used to quantify dead cells. However, fluorescent probes used to detect the fraction of dead cells with damaged DNA also have limitations. The use of DNA probes for assessment of DNA degradation should be considered with caution since apparent DNA damage can be misinterpreted due to changes in the coiling status of the DNA and/or in the permeability of membranes by these dyes

3. What are applications of DNA technology in taxonomic classification? How is it used to establish that a particular organism is, for example, a separate or a new species? DNA barcoding is a way to identify species using a short sequence of DNA from a standard part of the cell's genome, or genetic material. This system is similar to a supermarket scanner that reads a pattern of lines of different thicknesses to identify a specific item for purchase. Traditionally, biologists identified biological species by looking at specific characteristics of its shape or form--called morphological features, but there are differences in external appearance that aren’t obvious. There are several factors that must be taken into consideration--the smallest details must be observed (fine structural details, minute teeth cusp patterns, etc.) DNA barcoding is a new tool that will supplement taxonomic knowledge and enable non-experts in other fields of study, such as conservation biology, wildlife management, or endangered species protection, to make quick and cost-effective species identifications. The part of the gene used as the standard "barcode" for animal groups is a string of 648 base-pairs from a gene called cytochrome c oxidase 1 (CO1) found in the mitochondrion, or energy-producing part of the cell. This particular region was selected because it had been well studied and was found to be variable enough to distinguish different species. CO1 has proved to be highly efficient in identifying birds, mammals, fish, amphibians, reptiles, butterflies, flies, and many other animal groups. Unfortunately, it is not an effective barcode region for plants.

There are four main components to building a functional system for DNA barcoding. 1. Specimens that have already been identified using traditional taxonomy. (repositories of biological materials are the treasure troves of life, containing tissue samples of known species from which genetic material can be extracted) 2. Labs! Amplification using a technique called the Polymerase Chain Reaction (PCR) makes numerous copies of the target gene to ensure there is enough genetic material for analysis. Sequencing involves using biochemical methods to determine in which order the nucleotide bases--adenine (A), guanine (G), cytosine (C), and thymine (T)--are strung along the strand of DNA. 3. A comprehensive database system. DNA sequences will be managed in a database system, a kind of reference library of identified species. The database will include associated information about the specimen, a photograph of the specimen, and map coordinates indicating where the specimen was found. 4. Sophisticated computational algorithms. Biologists use these programs to compare the newly generated sequence data with samples in the reference database to analyze barcodes. These results can be illustrated in the form of a branching tree, clustering similar sequences together and showing where in the tree of identified species the unknown samples belong or the next closest match.

4. How is DNA technology used in the field of molecular paleontology? What is the value of recovering DNA from fossilized specimens? Molecular paleontology - small amounts of DNA from samples such as fossils can be easily reproduced (amplified?) using PCR, or polymerase chain reaction. Recovered DNA from fossilized specimens can be further processed in order to obtain the sequence of its nucleotides. Researchers will be able to compare this with the nucleotide sequence of present organisms, and will be able to determine if the two organisms are related, or if the fossilized organism is an ancestor of certain organisms.

5. How was DNA technology used to trace the movements of the human population from its African birthplace?

Mitochondrial DNA (mtDNA) is DNA exclusively passed from mothers to daughters, so it can be used as accurate evidence for tracing a family tree, or line. Scientists used this, and they found out that although there may have been some mutations in the mtDNA, DNA gathered from people in Europe, Asia, and Africa are almost similar to each other. For males, the Y chromosome is passed from father to son, without any variations (except when mutations occur.) Mike Hammer, in 1988, observed that almost all the Y chromosomes present in males can be traced back to a male African ancestor. 6. What issues attend the cloning of extinct animals? Cloning extinct animals could disrupt the balance of nature. These animals died for a reason, and that reason was because they were not fit enough to survive. Also, it would be difficult for cloning other animals that would have no surrogate mother. Animals that have become extinct due to human activities, however could be cloned, but with less considerations for ethical issues, as they were cloned in order to preserve their species.