OEB 53 Lecture Notes - J. B. S. Haldane, Effective Population Size, Genetic Drift

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lilaccat118

17 Feb 2014

School

Harvard University

Department

Organismic and Evolutionary Biology

Course

OEB 53

Professor

Andrew Berry

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Document Summary

Shared hardware: all organisms use the same basic biochemical and molecular genetic pathways, implying that these were acquired from an ancient common ancestor. Evolution is disinclined to alter something that works, so once these fundamental processes had evolved, they became a feature of all living organisms. Thus, despite the apparent diversity of life on earth, biological systems are in fact remarkably uniform. >> homology: i. e. derived from a common ancestor. Shared software: 1) about 1. 2% of the human genome encodes proteins; 2) 99% of all human genes are present in the mouse, from which we diverged about 75 million years ago; 3) 61% of fruit fly and. 43% of nematode worm proteins have a clear human homologs despite an evolutionary separation of half a billion years. >> pax 6 = eyeless (different names for the same ancestral gene in different species)

Related Questions

EVOLUTIONARY BIOLOGY HELP!!! Please answer all of them.

1. When k_A>k_S, then:

a. Scientists would reject the null hypothesis of neutral evolution because the number of replacement substitutions is greater than expected.

b. Scientists would reject the hypothesis that natural selection took place millions of years ago and is no longer relevant

c. Scientists would accept the hypothesis that neutral evolution took place millions of years ago and is no longer relevant

2. Consider the following protein-coding genetic regions (shown starting with their first codons). How many amino acids would be different between AUGUCAGACGCGAAA and AUGUCAGAGGCGAAC based on the standard universal genetic code?

a. There would be a difference in 1 amino acid when translated

b. There would be a difference in 2 amino acids when translated

c. none of the above

3. Which of the following statements is true?

a. Some fossil remnants have revealed pigmentation of body structures

b. Carbon-14 is an unstable isotope with a half-life of less than 10,000 years

c. Oxygen-18 is an unstable isotope with a half-life of less than 10,000 years

d. all of the above

e. A and B, but not C

4. Based on current fossil evidence:

a. ancestors of whales were artiodactyls

b. evolution of baleen forced ancestors of land mammals to become aquatic

c. whales and walruses are more recently diverged than whales and dolphins

d. A and C are correct

ochremallard624

Question 1

Evolutionary algorithms are used:

In engineering, to arrive at solutions by going through many permutations of possible solutions and allowing them to evolve.

A genetic feature of complex organisms.

A process undergone by the human brain, which is similar to evolution by natural selection.

Another term used for a computer algorithm in general.

Question 2

Human literature and languages can be studied using methods similar to those used for constructing phylogenies because:

There is no other way of studying these things.

Languages evolve roughly along the lines of species, with mutations (changes in words and pronunciation), descent with modification (languages becoming more different along the way), and branching of languages (languages giving rise to other languages that are similar to them).

Because literature and languages are constructed by organisms (human beings), so what applies to one must apply to the other.

Languages undergo a process of word swapping, which is analogous to horizontal gene transfer.

Question 3

The degree to which horizontal gene transfer occurs in eukaryotes is:

Something upon which the entire validity of evolutionary biology hinges.

A mystery that may or may not disprove evolution, but we simply don't know enough about it at this point.

Something that would overthrow the notion that this phenomenon is important in bacteria.

An interesting and potentially important aspect of biology with relevance for how evolution occurs, but not something that would call it into question one way or the other.

Question 4

Learning about the history of scientific theories and the reasons for why they are initially accepted or rejected is important mostly because:

It makes for exciting story telling, and this is very much needed to get people interested in science.

It teaches us about the process of science as it actually occurs, which is somewhat different to the idealized notion of a purely objective undertaking.

It tells us which theories are definitely true or false.

It tells us that science is actually a totally subjective process that tries to present itself as objective. In reality, personal subjective factors are the only relevant factors that really matter in science.

mauvemammoth554

HELP ASAP;

Please help me understand my lab results, so be detailed to clearly understand . INclude answers to these questions what role does ampicilin (amp) and arabinose (ara) play in the experiment. Because GFP was isolated from jelly fisht, what modification to the GFP DNA had to be made to result in expression in E. coli?

BACKGROUND INFORMATION

Transformation of GFP and the pGLO Plasmid

GFP is a commonly used reporter protein in research labs, as the fluorescence creates a marker protein that can be used in many types of cell biology and biochemical studies. In basic research, GFP is often fused to a specific target protein of interest, creating a chimeric reporter protein. GFP has been used as a reporter protein to study blood vessel and tumor progression in mice, brain activity in mice, and malaria eradication in mosquitoes for instance (see website mentioned in notes).

In the first week you will use a procedure to genetically transform bacteria with the gene that codes for Green Fluorescent Protein. Following the transformation procedure, the bacteria express their newly acquired jellyfish gene and produce the fluorescent protein, which causes them to glow a brilliant green color under ultraviolet light. During the second week you will purify the protein away from all of the other proteins produced by the bacteria using chromatography, and during the third week you will evaluate the success of the purification procedure and estimate the size (molecular weight) of GFP by using sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE).

Fundamental to the process of genetic transformation of bacteria are plasmids. In addition to one large chromosome, bacteria naturally contain one or more small circular pieces of DNA called plasmids. Plasmid DNA usually contains genes for one or more traits that may be beneficial to bacterial survival. In nature, bacteria can transfer plasmids back and forth allowing them to share these beneficial genes. This natural mechanism allows bacteria to adapt to new environments. The occurrence of bacterial resistance to antibiotics is due in large part to the transmission of plasmids which contain antibiotic resistance genes.

The pGLO plasmid (Fig. 5, not a naturally occurring plasmid) contains the gene for GFP, and also contains the gene for the enzyme Î²-lactamase (bla), which provides resistance to the antibiotic ampicillin. The Î²-lactamase protein is produced and secreted by bacteria that contain the plasmid. Î²-Lactamase inactivates the ampicillin present in the LB nutrient agar, allowing bacterial growth. Only transformed bacteria that contain the plasmid and express Î²-lactamase can survive on plates that contain ampicillin. Only a very small percentage of the cells take up the plasmid DNA and are transformed. Untransformed cells cannot grow on the ampicillin selection plates. pGLO also incorporates a special gene regulation system, which can be used to control expression of the fluorescent protein in transformed cells. The gene for GFP can be switched on in transformed cells by adding the sugar arabinose to the cellsâ nutrient medium. Selection for cells that have been transformed with pGLO DNA is accomplished by growth on antibiotic plates. Transformed cells will appear white (wild-type phenotype) on plates not containing arabinose, and fluorescent green when arabinose is included in the nutrient agar medium.

for the first week section of lab

To each of two microfuge tubes, add 250ul of transformation buffer. Keep these tubes on ice.

Using a sterile loop, pick one colony of bacteria from the LB plate.

Transfer this colony to one of the microfuge tubes. Gently vortex the tube until the colony is dispersed. Repeat for the second tube.

Add 0.08ug of DNA to one of these tubes (+DNA tube).

Incubate both tubes on ice for 10 minutes.

Incubate both tubes at 42Â°C for 50 seconds.

Incubate both tubes on ice for 2 minutes.

Add 250ul of LB broth to each tube and incubate at room temperature for 10 minutes.

Flick each tube gently. Add 100ul of this transformation mix to the appropriate plates.

Results:

+DNA: LB/amp--> 1 colony, Glow: uncertain

+DNA: LB/amp/ara--> 9 colonies, Glow: yes

-DNA: LB/amp--> 7 colonies, GLow: no

-DNA: LB--> many colonies, Glow: no

OEB 53 Lecture Notes - J. B. S. Haldane, Effective Population Size, Genetic Drift

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