Difference between revisions of "20.109(S14):Microbial DNA extraction (Day1)"
From Course Wiki
(→Introduction) |
(→Introduction) |
||
Line 7: | Line 7: | ||
Please begin by reading the [[20.109%28S14%29:Module_1 | '''Module 1 overview'''.]] | Please begin by reading the [[20.109%28S14%29:Module_1 | '''Module 1 overview'''.]] | ||
− | Today we'll begin our primary experiment, a phylogenetic analysis of bird gut microbiota. Through birds' stool, their resident microbes can be transferred to the environment and in some cases infect other animals. Perhaps the most well-known pathogenic avian microbe with zoonotic potential (potential for inter-species transmission) is the flu virus. For your safety, all the samples we will work with have been screened to exclude those carrying | + | Today we'll begin our primary experiment, a phylogenetic analysis of bird gut microbiota. Through birds' stool, their resident microbes can be transferred to the environment and in some cases infect other animals. Perhaps the most well-known pathogenic avian microbe with zoonotic potential (potential for inter-species transmission) is the flu virus. For your safety, all the samples we will work with have been screened to exclude those carrying human pathogenic flu strains. However, we will be able to mine much of the same intellectual content that we could were we studying flu directly. |
Investigations in disease ecology, or "the ecological study of host-pathogen interactions within the context of their environment and evolution" ([http://www.nature.com/scitable/knowledge/library/disease-ecology-15947677 '''via Scitable''']), help determine how pathogens transmit and cause disease, persist, and evolve in host organisms as different as humans and birds. Pathogen, host, and environment all play roles in defining the natural history of disease. In studies of pathogens that cause zoonotic disease, researchers are particularly interested in defining major influences on pathogen distribution, transmission, and evolution. The Runstadler lab currently studies the disease ecology of influenza viruses in several groups of birds and other animals (see for example [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115932/ '''this paper'''] and [http://www.ncbi.nlm.nih.gov/pubmed/22192630 '''this one''']), a research area that can provide information useful for predicting the next flu pandemic and designing effective vaccines that will be produced in time. Researchers track viral mutations/evolution, infection of different bird species (including co-infection by multiple strains), and the trafficking patterns of those birds; they often visualize the data by phylogenetic trees and related methods. Your own phylogenetic analysis will consist of comparing bacterial communities in two distinct bird populations. (We admit, not as flashy as studying the flu!) | Investigations in disease ecology, or "the ecological study of host-pathogen interactions within the context of their environment and evolution" ([http://www.nature.com/scitable/knowledge/library/disease-ecology-15947677 '''via Scitable''']), help determine how pathogens transmit and cause disease, persist, and evolve in host organisms as different as humans and birds. Pathogen, host, and environment all play roles in defining the natural history of disease. In studies of pathogens that cause zoonotic disease, researchers are particularly interested in defining major influences on pathogen distribution, transmission, and evolution. The Runstadler lab currently studies the disease ecology of influenza viruses in several groups of birds and other animals (see for example [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115932/ '''this paper'''] and [http://www.ncbi.nlm.nih.gov/pubmed/22192630 '''this one''']), a research area that can provide information useful for predicting the next flu pandemic and designing effective vaccines that will be produced in time. Researchers track viral mutations/evolution, infection of different bird species (including co-infection by multiple strains), and the trafficking patterns of those birds; they often visualize the data by phylogenetic trees and related methods. Your own phylogenetic analysis will consist of comparing bacterial communities in two distinct bird populations. (We admit, not as flashy as studying the flu!) | ||
Line 20: | Line 20: | ||
<br style="clear:both;"/> | <br style="clear:both;"/> | ||
− | Returning to today's specific work, each of you will extract a DNA pool from a single bird cloacal sample using a commercial kit. Unlike most mammals, which have different excretory paths for urine and feces, birds have both their urine and feces excreted through a single opening called the cloaca. The cloacal swab is a somewhat vexing material from which to extract DNA, because many enzyme inhibitors (including materials that inhibit polymerase) are present. As described in the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC167874/pdf/621102.pdf '''paper by Carol Kreader'''], inhibitors in feces include bile salts and environmental inhibitors such as humic compounds present in water and dirt. Chemicals that degrade DNA may be present, which is especially troubling when one wants to amplify a low concentration DNA. The DNA extraction kit contains two reagents that degrade or bind up inhibitors | + | Returning to today's specific work, each of you will extract a DNA pool from a single bird cloacal sample using a commercial kit. Unlike most mammals, which have different excretory paths for urine and feces, birds have both their urine and feces excreted through a single opening called the cloaca. The cloacal swab is a somewhat vexing material from which to extract DNA, because many enzyme inhibitors (including materials that inhibit polymerase) are present. As described in the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC167874/pdf/621102.pdf '''paper by Carol Kreader'''], inhibitors in feces include bile salts and environmental inhibitors such as humic compounds present in water and dirt. Chemicals that degrade DNA may be present, which is especially troubling when one wants to amplify a low concentration DNA. The DNA extraction kit contains two reagents that degrade or bind up inhibitors |