Influenza

The Blame GameThe greatly feared pandemic flu virus has finally broken out. Millions are sick and thousands have already died. It is almost impossible for the Centers for Disease Control (CDC) to keep track of the new cases reported each day. Contrary to everyone's expectations, the first reported cases appeared in San Francisco and not in Asia or Eastern Europe. From an anonymous source the New York Times is reporting that there was mishandling of the recently reconstituted and extremely dangerous 1918 influenza virus at several labs. Apparently, there was unauthorized shipping of the virus to a Biosafety Level 3 (BSL-3) lab at UC San Francisco and it …

The Blame Gameappears that the package might have been damaged en route to the lab or potentially mishandled onsite at UCSF. In immediate reaction to the newspaper's report all related parties at UCSF have been arrested for the illegal dissemination of a biological agent to the public. Several of the arrested parties are researchers without US citizenship (but with appropriate visas) and some members of congress are calling for immediate deportation or even reclassification of their status to 'Enemy Combatants' and trying them as terrorists. In other related news, the virus strain from San Francisco has been fully sequenced and, just today, released to the public.

PBS video

http://www.pbs.org/wgbh/nova/body/1918-flu.html

Influenza Virus (flu)Small genome—8 RNA molecules

Antigenic glycoproteins

16 Hemagglutinins:Attachement to host

9 Neuraminidases: Passage through mucin, budding

- E.g., H1N1

Influenza A, B, and C

A: the one that can cause pandemics, broad host range (humans, birds, swine, horses…)

B: infects only seals and humans, ~ 1/3 of all influenza cases in US

C: infects humans and swine, causes only mild infections

Influenza Virus (flu)Sequencing

Reverse Transcriptase

DNASequencing

Genomic Nucleotide Sequence

Influenza Pandemics

1918 Flu Killed from 50-100 Mil. people worldwide Considered to be one of the most deadly pandemics Killed many of the young and healthy Influenza A, Type H1N1 Thought to have derived from Avian Influenza Recently reconstituted from recovered human samples Considerable ethical debate

Avian Influenza

Fear of pandemic High mortality rate (including young and healthy) Current concern is Influenza A, Type H5N1 Limited human-human transmission (2 cases as of

2009) in avian flu

Confirmed cases

Swine virus, the fear of viral reassortment

HHMI animation

Post-pandemic stage of swine flu

Antiviral drugs

Amantadine + Rimantadine inhibit one of the matrix proteins and thus passage into the cytosol. By 2008-2009 season, virtually all H3N2 were resistant. .

Kimball’s Biology Pages

Antiviral drugs

Relenza and Tamiflublock neraminidase and thus inhibit the attachment of virions. By 2008-2009, all H1N1 strains circulating in the US were resistant.

.

Kimball’s Biology Pages

Introduction to Bioinformatics

Alexandra M Schnoes

Univ. California San Francisco

Alexandra.Schnoes@ucsf.edu

What is Bioinformatics?

Intersection of Biology and Computers Broad field

Often means different things to different people

Personal Definition: The utilization of computation for biological

investigation and discovery—the process by which you unlock the biological world through the use of computers.

What does one do in Bioinformatics?

(a small sample)

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Our Lab: Understanding Protein (Enzyme) Function

What does one do in Bioinformatics?

(a small sample) Discover new drug targets—computational docking

Atreya, C. E. et al. J. Biol. Chem. 2003;278:14092-14100Shoichet, B. K. Nature. 2004;432:862-865

What does one do in Bioinformatics?

(a small sample) Systems Biology

sbw.kgi.edu/ www.sbi.uni-rostock.de/ research.html

This lab: Nucleotide & Protein Informatics

Sequence analysis Finding similar sequences Multiple sequence alignment Phylogenetic analysis

SequenceStructureFunction

Process of Evolution

Sequences change due to Mutation Insertion Deletion

Use Evolutionary Principles to Analyze Sequences

If sequence A and sequence B are similar A and B evolutionarily related

If sequence A, B and C are all similar but A and B are more similar than A and C and B and C. A and B are more closely evolutionarily related to each

other than to C

Extremely Powerful Idea

1. Start with unknown sequence

2. Find what the unknown is similar to

3. Use information about the known to make predictions about the unknown

How do you know when sequences are similar?

Align two sequences together and score their similarity

TASSWSYIVE

TATSFSYLVG

Use substitution matrices to score the alignment

Substitution Matrices Give a Score for Each Mutation

Many different matrices available Blosum matrices standard in the field

Blosum 62 Scoring matrix

http://www.carverlab.org/images/

Scoring: Add up the positional Scores

Score of 30

TASSWSYIVE

TATSFSYLVG

TASSWSYIVE

TATSFSYLVG

Score of 1

Additional issues…

Gaps (insertions/deletions) Have scoring penalties for opening and continuing a

gap

TASSWSYIVE TASSWSYIVE

TATSFLVG TATSF--LVG

How do we find similar sequences?

Start at the National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/

How do we find similar sequences?

Nucleotide Sequence Databases

How do we find similar sequences?

Protein Sequence Databases

How do we find similar sequences?

Similarity Search: BLAST Basic Local Alignment Search Tool

BLAST is very quick but … Only local alignments Alignments aren’t great Only pair-wise alignments

Want better alignments … Multiple alignment

Multiple sequences Better signal to noise

More Sequences = Better alignment More accurate reflection of evolution

ClustalW Commonly used Easy to use

Visualize the Multiple Alignment

Use the Alignment to Calculate Evolutionary Distances See ‘how close’ sequences are to each other Best way to tell what is ‘most similar’ Can calculate simple tree from clustalW

Taubenberger et al., Nature: 437, 889-893, 2005

Caveats!

In reality Sequences (even parts of sequences) can evolve at

different rates Don’t have a good understanding of sequence and

function High sequence identity does not always mean the same

function Getting good alignments and good trees can be very

hard

Bioinformatics: Sequence Analysis

1. Start with unknown sequence

2. Find similar sequences

3. Create alignment

4. Create phylogenetic tree

5. Use information about knowns to make predictions about unknown