Go over possible answers to extra credit question here

Go over example of pairwise alignment ala Needleman Wunsch on blackboard.

If you need yet another view on how this works, check this primer in Nature Biotech (needs a UConn IP address)

 

Dot Plots

Dot Plots are techniques to compare two sequences.

The Swiss Institute for Bioinformatics provides a JAVA applet that perform interactive dot plots. It is called Dotlet. The main use of dot plots is to detect domains, duplications, insertions, deletions, and, if you work at the DNA level, inversions (excellent illustrations of the use of dot plots are given on the examples page). The applet works in Internet Explorer and most of the time in Firebird.

Example sequences: GI:1303679 and 67951

Midterm date October 8 or 10 or 15th ? (vote?)

How to detect an intein/intron in a BLAST comparison?
Use this sequence; (you also can use a gene sequence and blastx, works to detect introns)

ATP synthases



The F1-ATPase as three cylinder three-cycle engine

ATP synthase - the rotary engine in the cell

How old is life on Earth?
Brief review of controversies

  • The Earth is about 4.5 Ga old, but no crustal rocks has survived from that time. The oldest rocks are no older than 4.0 Ga (but their are crystals in younger rock that are older).
Morphological Fossil Evidence:
  • For about a decade the oldest microfossils were considered to be about 3.5 Ga old (see here). The fossils (as interpreted by Bill Schopf) look like "modern" Cyanobacteria. Recently the evidence for these fossils was questioned.
  • 3.2Ga old filamentous fossils, probably of thermophilic chemotrophic prokaryotes (Rasmussen, 2000)
  • 1.8Ga old fossils from Gunflint formation: iron-loving bacteria and cyanobacteria
Biological Signature Evidence (examples):
  • Oldest geological evidence for life - 3.8 Ga ago - is based on 13C discrimination (carbon derived from living systems often have lower delta 13C values than inorganic carbonates) [here]. The rocks are from Akilia island off the coast of Greenland, and severely altered by metamorphism. However, recently the evidence for that was reassessed.
  • 2.7Ga old: probable biomarkers of cyanobacteria and of eukaryotes (Roger Summons, Roger Buick and Jochen Brocks)
  • Bottomline interpreting the early fossil record is very difficult.

Discuss Snowball Earth events. Illustration here

Notes on the TREE of LIFE -
   recent overview tree here
   Powerpoint presentation here

Assignments

Read through the first three items in the dotlet help pages .

Send in a question for take-home-quiz #2

For next Monday:
Next quiz will be posted over the weekend - read through it, so that we can discuss questions on Monday.

Read chapter 4 in the textbook