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Ecology and EvolutionHerpAIDS

Cancio, Fosgate, Ramos, de Castro, Gatchalian, Serrano

DNA Probe● application of nucleic acid hybridization● homologous strands of DNA hybridize to one another● used to locate a specific nucleotide sequence due

to high specificity of base pair interactions

Polymerase Chain Reaction

● amplifies a DNA template to produce specific DNA fragments● PCR can be used to analyze extremely small amounts of sample● Quantitative PCR measures the accumulation of DNA product

after each round of PCR amplification● PCR also permits identification of non-cultivable or slow-

growing microorganisms

DNA Probes, PCR and Ecology● an amplified DNA sequence results from DNA undergoes probing

and PCR● the amplified product is then quantified to give an assessment of

how many microorganisms are present in an area● quantification of nucleic acids includes response to treatments

(e.g. measurement of HIV RNA)

Membrane-Impermeative Fluorescent Probes● can passively diffuse through the cell

wall of a bacterium, which can then act as an indicator of a loss in membrane integrity

● loss in membrane integrity = cell viability = degradation of nucleic acids

● DNA degradation is used to quantify dead cells

● limitation: DNA damage can be misinterpreted due to changes in the coiling status of DNA and/or permeability

DNA Barcoding● technique for characterizing species of organisms using a short DNA sequence from a standard

and agreed-upon position in the genome. ● DNA barcode sequences are very short relative to the entire genome● Works for all stages of life, Unmasks look-alikes ● Barcoding newly discovered species will help show where they belong among known species● use of nucleotide sequence variations

C = blueA = greenT = redG= black

Molecular Paleontology● the recovery of DNA from ancient human,

animal, and plant remains● one can quantify the level of relatedness

between any two organisms for which DNA has been recovered.

❖ Mitochondrial DNA (mtDNA) vs Nuclear DNA-far smaller mutation rate thannuclear DNA-thousands of copies of it exist in every cell

Molecular Paleontology❖ Isolation

-what it is and where it is considered- DNA extraction from fossils is a very popular method- taken from small samples and mixed with different substances, centrifuged, incubated, and centrifuged again- undergoes Amplification

❖ Amplification-Polymerase Chain Reaction (PCR)

Molecular Paleontology❖ Sequencing

- done to determine the order of nucleotides and genes, and used to build evolutionary trees

- mtDNA for animals, chloroplasts for plants

Using various biotechnological techniques, scientists have been able to gain expanded new insights into the divergence and evolutionary history of countless organisms.

Tracing Human Population Movement

● DNA analysis through mitochondrial DNA and the Y-chromosome● use of the polymerase chain reaction (PCR) and the successful

recovery of DNA from preserved hard tissues

Mitochondrial DNA (mtDNA)● DNA passed on from

mothers to offspring● can be used to trace

family lines● findings: DNA gathered

from people in Europe, Asia and Africa are fairly similar despite mutations

Y-Chromosome● passed on from father to son● without any variations, except for

the occasional mutation● a more accurate way to trace

human population movement● 1988: Mike Hammer observed that

almost all Y chromosomes can be traced back to a male African ancestor

Cloning of Extinct Animals● At present, scientists have already discovered ways

to resurrect extinct species, which led to the rise of issues regarding de-extinction

● three ways of bringing back extinct species:>backbreeding>genetic engineering>cloning

Benefits● scientific knowledge● technological advancement● environmental benefits - threatened or damaged

ecosystems can be restored● justice - bring back species that humanity has

pushed to extinction● wonder

Objections● animal welfare - animals could be exploited for human

purposes● health - species could carry retroviruses● environment - species may disrupt the ecosystem● political - may change priorities in other fields of science

such as medical research

Ethical Issue“Is de-extinction playing god, or just plain wrong?”

De-extinction:● is antithetical to animal

welfare● ignores the current mass

extinction problem● is not conservation● promotes risky human

attitudes

SOURCES● http://highered.mheducation.

com/sites/9834092339/student_view0/chapter17/dna_probe__dna_hybridization_.html● http://barcoding.si.edu/PDF/TenReasonsBarcoding.pdf● http://aem.asm.org/content/64/7/2697.full● http://www.sciencemuseum.org.

uk/WhoAmI/FindOutMore/Yourgenes/Wheredidwecomefrom/Whowerethefirsthumans/Onebirthplace.aspx

● http://archive.archaeology.org/9609/abstracts/dna.html● http://blogs.discovermagazine.com/d-brief/2013/04/04/5-reasons-to-bring-back-extinct-

animals-and-5-reasons-not-to/#.VPrpH_mUeSo● http://www.earthintransition.org/2013/04/four-reasons-why-cloning-extinct-animals-is-wrong/● http://www.slideshare.net/JessicaKabigting/group-5-dna-tech-ecology-envt● http://en.wikipedia.org/wiki/Molecular_paleontology