Biology 2581B Lecture Notes - Lecture 12: Ethidium Bromide, Restriction Enzyme, Dna Profiling

15 views3 pages

apricotsea-lion820

18 Apr 2016

School

Department

Course

Professor

For unlimited access to Class Notes, a Class+ subscription is required.

Document Summary

A polymorphic locus is one with two or more alleles, where each allele is present in more than 1% of the populations. The alleles of polymorphic loci are called genetic variations rather than wild types or mutants. Advanced sequence technologies allow the sequencing of complete genomes from individuals (e. g. single nucleotide substitutions and amino acid changes). Every individual within a species has genetic changes which are unique to them and those that they share with others. For example, most of the single nucleotide substitutions in the genomic region for the cystic fibrosis gene do not have any effect on function (only about 2% of the nucleotides in this region are part of coding sequences). The overall lengths of genomes differ as much as 1% between healthy individuals. The locus (plural loci) is any location within the genome that has a defined chromosomal location, irrespective of any function (includes coding and non-coding regions, whether short or long).

Related Questions

1. Humans and chimpanzees share several polymorphic loci. Which is the LEAST plausible explanation for this fact?

A. Balancing selection has maintained polymorphism in both species

B. Incomplete lineage sorting left polymorphic loci and those have persisted since the speciation event.

C. Interbreeding has allowed introgression of alleles at theses loci in both directions.

D. Genetic variation provided by the polymorphic alleles enhances resistance to pathogens.

2. According to the social brain hypothesis, we should expect primates living in larger social groups to have:

A. Larger brains, specifically, a neocortex of relatively larger size

B. Lager incisors and canines, to defend against more social competitors

C. Smaller brains, because many individuals can work together to solve problems

D. Great variation in brain and neocortex size, with the dominant individuals having the largest

3. You extract DNA from human bones in an ancient village buried by volcanic ash. You discover that there is an extremely high frequency of the LCT allele for lactase persistence. What might you reasonably conclude about the population?

A. This population is likely the source of the high frequency of the LCT gene in Northern Europe

B. The village could not be more than 4,500 years old

C. The members of this population likely used domesticated livestock for their milk

D. villagers had a diet rich in wheat or another domesticated crop

4. Why do populations father from Africa have more deleterious mutations in their genome?

A. Repeated bottlenecks and founder effects made drift more intense more often

B. Populations farther from Africa have been exposed to more mutagens in the environment

C. As people migrated over the globe they interbred with Neanderthals and Denisovans

D. The populations are younger, so purifying selection has not had time to purge delirious mutations from the populations.

yelloweel732

For years we have been able to analyze the fossils of extincthumans like those of Neanderthals. Their bones gave us clues to howthey looked, how they lived, and how they might be related to us.In the last few years, we have been able to get a better view intothese extinct species and their relationship to our species. Thanksto next generation genomic sequencing technologies, we have beenable to obtain genetic data on Neanderthals, Denisovans and othersthat have allowed us to make direct comparisons between our speciesand theirs. In addition, we have been able to observe the presenceof DNA from these extinct species within our own genomes which tellus that we had kids with these now extinct humans.

If we take Neanderthal DNA as an example, we find that we share99.5 percent of our DNA with them. Which means that we andNeanderthals were separated from each other for more than 500,000years. This also means that we were genetically similar enough tobe able to have offspring with each other. We see evidence of thisgenetic introgression between us and Neanderthals when we look atour DNA. Interestingly, if we obtain one thousand DNA samples fromGrossmont College students, we estimate that we would be able toextract at least 20% of the Neanderthal genome from them. Thismeans that 20% of our collective nucleotide sequences are sharedwith Neanderthals but this doesnât mean that 20% of our genes areNeanderthal specific genes. Of the twenty-one thousand genes thatNeanderthals had, only a few dozen of their genes survive withinour genome. The same holds true for Denisovans. What is moreinteresting is that older versions of ourselves have a tendency tohave higher levels of DNA from extinct humans compared toourselves. In other words, over the course of thousands of years wehave been slowly weeding out the DNA of the other humans from ourgenome in favor of our genes.

One basic question that we might like to ask is why have we beenlosing Neanderthal and Denisovan genes over time? Also, why do westill have a significant amount of DNA segments that donât seem tobe going anywhere? The answer to this has to do with selection.

The answer to the first part of the question has to do with thefact that we were not fully genetically compatible with the otherhuman species to begin with. Basically, to have had Neanderthal orDenisovan genes in the past meant that an individual's level offitness was reduced. To get rid of their genes in favor of our ownwould mean that the relative fitness of individuals would increaseovertime.

The answer to the second question has to do with the fact thatDNA segments from Neanderthals and Denisovans that did not code forproteins remained because there was little selective pressureagainst them. As far as genes are concerned, the only Neanderthaland Denisovan genes that remain only exist because they had aselective advantage or at least have been neutral to ourspecies.

DNA segments that that were neutral or that had a selectiveadvantage, whether genes or not, simply remained because they wereadvantages or there was little selective pressure against them.

Your task for this week is to look for information about oneNeanderthal or Denisovan gene that survive within our species andto tell me what function that gene has and how that gene mayincrease the fitness of modern human populations.

In your post, discussONE Neanderthal orDenisovan gene that is currently found within our species.
- Tell us about the gene and its function. Explain what it doesfor us. (Make sure you give a citation.)
- Explain in your own words any possible advantages that yourNeanderthal or Denisovan gene might have. Make sure you give ininformed opinion that is grounded in your research.

azurecrow764

In a small paragraph, compare and summarize these two articles.

Article 1 Description

This article is an observational study, which discusses how frequency dependent selection affects two phenotypes of a predator through differential guarding response. The researcher examines the ratio of handedness of two samples of P. microlepis collected from two adjacent sites along Lake Tanganyikaâs northwestern shoreline for a period of eleven years. The process of observations includes observing the correspondence between the handedness of P. microlepis and their targeted prey (Hori, 1993). The researcher carried observations to identify the direction from which P. microlepis attacked the flank of their prey. Moreover, the researcher used a gill net to catch each P. microlepis that attacked the lure. Catching the P. microbes made it possible for the researcher to observe its features and determine its handedness. The researcher determined the handedness of the scales of P. microlepis by observing the fish under a microscope.

During the period of study, Hori (1993) established that the ratio of handedness of P. microbes remained at 0.5 for each one-to-two year intervals throughout the eleven years of the study. Further investigations on temporal changes in handedness ratio showed that the ratio oscillated with amplitude of 0.15 within a five-year period (Hori, 1993). These observations were made for the two species of P. microlepis under investigation. The researcher concludes that the direction of mouth opening of scale eating cichlid fish in Lake Tanganyika is determined by the genetics of the fish. The researcher demonstrates that frequency-dependent natural selection determines the number of left-handedness or right-handedness fish. Based on researcherâs observations, when right-handed fish attack from behind, they snatch the scales from their prey from the left flank (Hori, 1993). On the other hand, when left-handed fish attack their prey from behind, they attack the right flank (Hori, 1993). Therefore, fish with rare phenotypes are more successful as predators than ones that have the more predominant phenotype. This study can be used to guide researchers who are interested in seeking ways of increasing the population of different species of fish. It can also be used as a basis for investigations on how fish type determines its survival tactics or predator tactics.

Article 2 Description

The study was an experimental analysis which sought to quantify phosphoglucose isomerase (Pgi) frequency change over a period of time and compare Pgi genotypes based on physiological responses to high temperatures and subzero thermal extremes encountered by beetles in nature. The research seeks to establish how the local climate in Bishop relates to changes in allele frequency at Pgi and other allozyme loci. It also seeks to establish if ambient temperature of beetle habitants rise to levels that expose beetles to stressful temperature. The researcher also seeks to establish how Pgi genotypes differ physiologically when exposed to subzero temperatures. By answering these questions, the researcher will establish the relationship between changes in enzyme genotype frequency and regional climate changes in addition to investigating major physiological mechanisms through which animals respond to change in climate.

To answer research questions and test research hypothesis, the researchers carried out several experiments and analyses of data. The experimental study involved collecting adult beetles that had emergent recently from pupae for a period of one year between August 1988 and August 1989 (Rank & Dahlhoff, 2002). Their genotype was determined at five different polymorphic enzyme loci. Some of the things analyzed during the study include fluctuations in climate and allele frequency change; daily and annual mean values of air temperature, Effects of Pgi genotype on HSP70 expression, and quantification of Pgi genotype on HSP70 expression among other things (Rank & Dahlhoff, 2002). The study results revealed that although beetle populations were genetically different the FST-values for 1996 were greater for each enzyme locus than those for 1998 (Rank & Dahlhoff, 2002). Moreover, researchers established that the frequency of Pgi allele had increased by 11 percent, a trend that was not observed for all the other loci investigated. Therefore, the researchers conclude that Pgi genotype differences in thermal physiology account for Pgi allele frequency change in nature. Contrary to selected hypothesis that the frequency of Pgi allele should increase with decrease in temperature, the study established that the frequency of Pgi allele decrease with decrease in temperature. This work is important because it provides a basis for more research on how variations in temperature affect beetle populations. The study findings can be used to guide researchers who are interested in seeking ways of protecting endangered beetle populations in different climatic conditions.

Biology 2581B Lecture Notes - Lecture 12: Ethidium Bromide, Restriction Enzyme, Dna Profiling

Document Summary

Get access

Related Documents

Biology 2581B Lecture Notes - Lecture 12: Mammalian Genome, Myotonic Dystrophy, Allele-Specific Oligonucleotide

Biology 2581B Study Guide - Midterm Guide: Genetic Variation, Wild Type, Allele

Biology 2581B Study Guide - Restriction Enzyme, Dna Profiling, Autoradiograph

Related Questions