(A) TEM of activation of autophagy in cortical neurons with different concentrations of cocaine.

A marker for apoptosis Treatment

A control protein found Cell type: Neuron consistently in all cells

Prasun Guha et al. PNAS 2016;113:1417-1422 ©2016 by National Academy of Sciences Thursday February 16th, 2017 Class 27 Learning Goals

Abiotic Parasites

• After this class, you should be able to: • Describe the important roles for genes and mechanisms in SINES, LINES, viruses and retroviruses

• Predict the effect on viral survival of human mutations

• Compare the timescales of abiotic parasite evolution, viral evolution, anti-viral human evolution, viral infection and viral entrance into a host cell Clicker Question #0 Each DNA sequence can be millions of base pairs long. DNA sequences have been on this planet for billions of years. A single tiny species can represent many trillions of cells.

1. DNA will never randomly mutate to form new genes. 2. DNA will frequently mutate to form new genes. 3. DNA will rarely mutate to form random new genes, but it has had many, many opportunities. 4. DNA will likely form random new genes, but usually in a few species instead of randomly.

Peer Instruction Transposons are small regions of a chromosome that happen to code for proteins that move that DNA to other regions of the chromosome.

A mutation in a transposon causes increased production of similar transposons. Will evolution select for or against this mutation?

How do transposons increase their population?

Can transposons cause harmful mutations for the host?

Peer Instruction How do Long Interspersed Nuclear Elements make new copies?

Gene for reverse transcriptase Cytoplasm Gene for integrase

“Parent” LINE Translation Transcription

LINE protein LINE mRNA RNA polymerase

Ribosome LINE mRNA and LINE proteins Reverse transcriptase Integrase

cDNA Reverse transcriptase mRNA Integrase Insertion of “Daughter” LINE

Original “parent” copy New copy Clicker Question #1

Gene for reverse transcriptase Gene for integrase

“Parent” LINE Translation Transcription LINE protein LINE mRNA RNA polymerase

Ribosome LINE mRNA and LINE proteins Reverse transcriptase Integrase cDNA

Cytoplasm mRNA Reverse Integrase Insertion of transcriptase “Daughter” LINE

Original copy New copy Both LINE protein products are necessary for 1. True going from 1 copy to 2 copies in a chromosome. 2. False Clicker Question #2

Gene for reverse transcriptase Gene for integrase

“Parent” LINE Translation Transcription LINE protein LINE mRNA RNA polymerase

Ribosome LINE mRNA and LINE proteins Reverse transcriptase Integrase cDNA

Cytoplasm mRNA Reverse Integrase Insertion of transcriptase “Daughter” LINE

Original copy New copy If there are already 45 copies of the LINE DNA in the 1. Yes cell, are new proteins needed for the 46th LINE? 2. No How many of them are there? 98% similar Fracon of the genome made of transposons (or remnants of them): • Maize: 49-78% • Wheat: 68%

90% similar

75% similar How many of them are there? 98% similar Fracon of the genome made of transposons (or remnants of them): • Maize: 49-78% • Wheat: 68%

90% similar

75% similar How many of them are there? 98% similar Fracon of the genome made of transposons (or remnants of them): • Maize: 49-78% • Wheat: 68% • Mammals: 45% to 48% • Humans: 44-45% 90% similar

75% similar Clicker Question #3 Imagine that a mutation gives a transposon a new protein-coding region. This new mutation allows the transposon to survive outside of the host cell and possibly move into a new cell.

This new mutation: 1. Is a disadvantage over other similar transposons and will be removed by evolution

2. Is an advantage over other similar transposons and will be favored by evolution

3. Will have no effect on the evolution of these transposons • What does it means to say that viruses are: – Acellular

– Obligate parasites

– Diverse A bacterial cell (E. coli) How many genes does a circovirus have? Peer Instruction

DNA polymerase gene

Circovirus ssDNA Capsid gene genome (1700 bp)

What does the circovirus capsid gene encode?

This bacteriophage has more genes than a circovirus. Every virion is heavier and more expensive. What advantage does this phage get from these genes? Bacteriophage T4 Video Peer Instruction Why is it worth it to the Ebola virus to spend energy to create envelope, matrix and nucleocapsid proteins?

What parts of the Ebola virion give it the ability to specifically target human cells? Peer Instruction Peer Instruction Explain how HIV infects a cell. Enveloped virus Viral protein Host protein Envelope (lipid bilayer)

Genome (in this case, RNA)

Capsid (protein)

…about 10 billion virions produced daily HIV Life Cycle Video Peer Instruction HIV has virion proteins that interact specifically with T-cell membrane proteins. Why is this advantageous for HIV?

HIV increases transcription when T-cells are most active. Why is this advantageous for HIV?

T-cell DNA: Activation TF P

HIV Genome: Gag, Pol, Env P Clicker Question #4 Why would it benefit the HIV genome to activate when given the same set of signals that activate the T-cell?

1. T-cells will increase metabolism, making more energy available 2. T-cells will undergo more transcription, making transcriptional machinery more available 3. T-cells will synthesize more proteins, making translational machinery more available 4. T-cells may be more mobile when activated, allowing a free ride for virions to spread quickly 5. All of these reasons are likely to be helpful for the survival of the HIV genome Possible HIV Treatments Video Clicker Question #5 What innovation will help stop the spread of HIV the most effectively?

1. Increase funding to start new HIV laboratories to develop new cures 2. Make a protease inhibitor that is 10% more effective 3. Create cheaper versions of the treatment drugs we already have for widespread inexpensive use in poor countries 4. Increase education and contraceptive supply in the United States 5. Increase education and contraceptive supply in poorer countries Key Concepts

• Why is reverse transcriptase vital for viruses to infect hosts over the long term? • Why are SINES able to increase copy number without an integrase? • Why do need to bring both protein and DNA back into the cell?

• What set of mutations would need to happen to allow a LINE to target particular areas of the genome for insertion?

• Which mutation would be most likely to stop HIV infection: • A mutation that allows human enzymes to destroy some viral multi-protein chains • A mutation that destroys some plasma membrane phosopholipids • A mutation that blocks the binding side of CD4 and CCR5 receptors • A mutation that blocks the binding site of the integrase

• Is this order correct? If not, why not? • Longest: viral infection, • viral evolution, • abiotic parasite evolution, • anti-viral human evolution and • Shortest: viral entrance into a host cell Viruses: Disease history

• The last 1,000 years: – Smallpox and measles: High lethality destroyed colonized nave cultures worthwide. – Influenza and common rhinoviral colds are likely to have killed more humans than any other cause • The past 100 years: – 1906: Viruses can cause cancer? – 1918: a new strain of influenza • killed >50 million people • was the most lethal combatant of WWI • reached almost every populaon in the world – 1930s (and again in 2010s): polio outbreaks – 1970s: HIV • The past 10 years: – SARS, avian flu and swine flu viruses threaten to make the jump from animals to humans to pandemic acvity – Ebola • Current outbreak is largest on record & first North American case