BIOM-360 Lecture Notes - Lecture 10: Extremophile, Archaea, Phylogenetic Tree
2 May 2018
School
Department
Course
Professor
Viruses and Viral Research @ MSU
Prokaryotic viruses: viruses that affect bacteria and archaea
The most abundant biological entities on the planet.
Outnumber bacteria by an order of magnitude in the oceans.
Estimated 1031 viral particles on Earth.
More than the # of stars in the known universe.
Responsible for the lysis of 20% of the ocean’s microbial biomass every day.
Large role in nutrient cycling.
Archaeal Viruses
Generally extremophiles.
Viruses = obligate parasites, must have a host.
Extremely understudied.
Remarkable particle diversity.
There is a coke bottle virus--looks like a glass coke bottle.
Viral lineages infecting all three domains of life.
Single Cell Genome Sequencing
Isolate individual cells from environment
Extract DNA
Sequence that DNA
Ubiquitous virus host interactions
Believe every single cell in these environments is interacting with a virus.
**Quiz due today had one question with no correct answer.
Correct answer was chemolithoheterotroph.
Phylogenetic Trees
(continued from Lecture 8)
Can add time on the y-axis to indicate time of splits in the tree.
Building phylogenetic trees: aligning DNA sequences (mathematical algorithms).
DNA = the most widely used data source.
Each line in sequence is a different organism.
Use alignment to measure distance between samples.
Less complicated way of building a tree.
Compile a distance matrix and complete phylogenetic tree using sequence differences.
Changing an A for a T or a G for a C = same weight in this difference.
AT → AA AT → AG
How did we end up with three domains?
Difficult to infer the oldest relationships.
Archaea much closer to Eukaryotes!
Can’t infer time, can
infer distance.
Last Universal Common Ancestor = LUCA
Document Summary
Prokaryotic viruses: viruses that affect bacteria and archaea. The most abundant biological entities on the planet. Outnumber bacteria by an order of magnitude in the oceans. Responsible for the lysis of 20% of the ocean"s microbial biomass every day. More than the # of stars in the known universe. Viruses = obligate parasites, must have a host. There is a coke bottle virus--looks like a glass coke bottle. Viral lineages infecting all three domains of life. Believe every single cell in these environments is interacting with a virus. **quiz due today had one question with no correct answer. Can add time on the y-axis to indicate time of splits in the tree. Building phylogenetic trees: aligning dna sequences (mathematical algorithms). Dna = the most widely used data source. Each line in sequence is a different organism. Compile a distance matrix and complete phylogenetic tree using sequence differences.
