Biology 1002B Lecture Notes - Lecture 11: Asymmetric Cell Division, Volvox, Neutral Mutation

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13 Jun 2018

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Lecture 22 Outcomes:

GlsA gene from Volvox versus Chlamydomonas.

- GlsA is a gene that is found in Volvox and Chlamydomonas

- Volvox is multicellcular but otherwise very similar to chlamy… also a green algae

- homologous does not mean identical nucleotide sequence, amino acid sequence, or function

- in Volvox, GlsA is required for asymmetric cell division (plays an important role in cell

development), but in chlamy it’s function is unknown (assumed to be none, because no

effects when mutated)

- ancestral GlsA is thought to have had no function until it was recruited in Volvox

- if you have a volvox mutant in which the gene does not work, to rescue the glsA mutant you

can insert the chlamy glsA gene and it will revert to the wild type

Reasons why one does sequence alignments.

- sequence alignment is an attempt to fit the sequences together such that as many bases as

possible match

- to determine high or low sequence similarity (vertical lines between 2 sequences)

Differences between global versus local (advantages of each).

- Global alignment: (end-to-end) starts at one end and tries to align as many as possible (may

introduce gaps if necessary)

- more time consuming than local alignment,

- Local alignment: not interested in looking for matches from one end to the other… it’s

searching for small areas of high similarity

- computationally faster,

Relationship between E-value and likelihood of homology

- E-value (Blast Statistic): Probability that 2 sequences have the same score simply by chance

- The higher the similarity between 2 sequences the lower the probability that they originated

independently of each other and became similar just by chance

- the probability that they arised separately but developed the same sequence is infinitely low

Lecture 23 Outcomes:

synonymous vs nonsynonymous mutations

- silent (synonymous) mutations: they don’t effect the amino acid sequence

- non-synonymous mutation: the substitutions in the DNA lead to a change at the protein level

characteristics of the neutral theory of molecular evolution

- Natural selection is not the only game in town

- Neutral theory: many mutations have no effect, you don’t see a change in the amino acid

sequence

- the chance of having an advantageous theory is even smaller than in selection theory

- used to have the selection theory: all mutations can effect fitness (either deletrious or

advantageous)

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Document Summary

Glsa is a gene that is found in volvox and chlamydomonas. Volvox is multicellcular but otherwise very similar to chlamy also a green algae. Homologous does not mean identical nucleotide sequence, amino acid sequence, or function. In volvox, glsa is required for asymmetric cell division (plays an important role in cell development), but in chlamy it"s function is unknown (assumed to be none, because no effects when mutated) Ancestral glsa is thought to have had no function until it was recruited in volvox. If you have a volvox mutant in which the gene does not work, to rescue the glsa mutant you can insert the chlamy glsa gene and it will revert to the wild type. Sequence alignment is an attempt to fit the sequences together such that as many bases as possible match. To determine high or low sequence similarity (vertical lines between 2 sequences) Differences between global versus local (advantages of each).

Related Questions

Cystic Fibrosis (CF) is an autosomal recessive genetic disease that is characterized by the secretion of thick, abnormal mucous in the lungs. The mutated gene that leads these symptoms is the CF transmembrane conductance regulator (CFTR gene). The encoded protein is a chloride channel that moves chloride ions out of epithelial cells. In a homozygous individual, the lack of this chloride channel function in a mutant slows the flow of water into extracellular spaces. This lack of water export leads to the heavy mucus in the lungs of CF patients. Although children with CF would die in childhood, current treatments provide life expectancies into the 30âs.

CF is the most frequently inherited genetic disorder among American children. It affects 1 of every 2,500 children; 30,000 currently have the disease. Although its frequency is higher in European populations, it affects all human populations. Heterozygous carrier frequencies in the US are estimated to be 1 out of 29 Caucasians, 1 out of 46 Hispanics, 1 out of 61 African Americans and 1 out of 90 Asians. There are genetic screens for carriers of CF but they are not routinely performed despite this high frequency of carriers. At least all states in the US proscribe testing of newborns to identify children with CF early so that treatment can be started. Newborn tests for CF: http://www.cff.org/AboutCF/Testing/NewbornScreening/ScreeningforCF/ . If CF is such a common genetic disease, and such a simple Mendelian trait, why is genetic screening of parents not done more frequently? Is it just economic, a pain to do, or is it more complex such that the results of genetic testing are not just positive or negative?

Answer the following questions:
1. If two parents are heterozygous carriers of CF, show a pedigree with four children showing the incidence of carriers and afflicted children. If each unafflicted child (carrier or not) mates with another person, who has a 1 out of 30 chance of being a carrier of CF, what is the expected incidence CF disease in the third generation (frequency of CF in any one of grandchildren of the original couple)?

2. Pleiotropy of Cystic Fibrosis. Watch the two videos on the left at:

http://www.cftrscience.com/MOD-animation
or, if you can not view these, read the short NIH Genetics Home Reference for Cystic Fibrosis http://ghr.nlm.nih.gov/condition/cystic-fibrosis

Connect the description with one of the following videos, or related ones (there are many) you see:
video (10 minutes) of daily life of a child with Cystic Fibrosis http://www.youtube.com/watch?v=WUsuGKzdDg8
Lauraâs (20 year old) video diary of life with CF http://www.youtube.com/watch?v=Pgrf8qJXhpc&feature=related

In your own words, describe the range of CF phenotypes. List the other organs besides lungs that are affected and how does it affects those organs.

3.The DNA sequence of the CFTR gene is 170,000 base pairs in length and encodes the CFTR protein that is 1480 amino acids long. Open the accompanying text file (in Canvas/Files/Discussion folder) âCFTR gene DNA sequenceâ. You will see an alignment of the NIH human genome sequence of the CFTR gene â called âReferenceâ rather than âwild-typeâ- against a gene sequence containing a common mutation in CFTR. Look at the alignment and determine how the DNA sequence differs between them. What is the position number where they differ? How many and what nucleotides do they differ in? A â-â mark in one sequence in the alignment means that that base sequence is missing the corresponding bases in the other sequence. The sequence is a long one but the differences are in bolded bright red text. Matching sequence is marked with a | linking the two sequences. Look near the sequence AAATATCATC if you use FIND tool in Word.

In another file, you will an alignment of the reference translated into a protein sequence, compared to the mutant allele translated into protein sequence. The differences are again in red whereas the areas where the proteins match are in black. Look at the alignment. How do these two proteins differ? Again, find the position number and describe how they differ at that location. A â-â mark in the alignment means that amino acid is missing when compared to the other sequence.

4. Given that the CFTR gene can be analyzed for a mutation that causes CF, couples interested in being tested as carriers face several choices given the results.
What could be a consequence of a false positive result (couple is identified as carriers but they would not produce any children with symptoms)?

What could be a consequence of a false negative result (a test indicates the couple is not both carriers but they would produce some children with CF)?

5. The sensitivity of the test can vary with ethnic group. The following is a chart from the NCBI Genetic testing site. A sensitivity less than 100% would be likely to produce false negative results from an inability to determine that someone is carrier.

CF Carrier Test Sensitivity by Ethnic Group http://www.ncbi.nlm.nih.gov/projects/GeneTests/static/concepts/primer/ptscarr5.shtml
Ethnic Group ¹	Population Frequency of CF	Sensitivity of Carrier Detection ²
Caucasian	1 in 29	90%
Ashkenazi Jewish	1 in 29	97%
Native American	1 in 32	94%
Latino	1 in 46	57%
African-American	1 in 60	75%
Asian	1 in 90	30%

Why might different ethnic populations differ in the ability of the genetic test to identify carriers of CF?

Biology 1002B Lecture Notes - Lecture 11: Asymmetric Cell Division, Volvox, Neutral Mutation

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