1. Bruce Blumberg (blumberg@uci.edu)
BioSci D145 Lecture #1
Bruce Blumberg
4103 Nat Sci 2 - office hours Tu, Th 3:30-5:00 (or by appointment)
phone
TA – Riann Egusquiza
4351 Nat Sci 2– office hours TBA
Phone
check and noteboard daily for announcements, etc..
Please use the course noteboard for discussions of the material
Updated lectures will be posted on web pages after lecture
BioSci D145 lecture 1 page 1 ©copyright Bruce Blumberg All rights reserved

2. Introductions and Goals
Let’s introduce each other -
Name
Major
Favorite thing about UCI
Least favorite thing about UCI
BioSci D145 lecture 1 page 2 ©copyright Bruce Blumberg All rights reserved

3. Class requirements Grading Midterm 35% Final exam 35% Presentation 10%
Term paper 10%
Participation 10% (attendance, class discussion)
How are grades determined?
20 minute presentation and discussion of a journal article is required
These will be randomly assigned unless you volunteer – Riann will schedule yours
Presentations will be done as teams for most papers (depending on class size)
Volunteers for 1/18 and 1/25? See Riann.
Attendance and participation is important
Please come to class having read assigned material
Final examination will not be cumulative, however, understanding of concepts and techniques from first part of course is required.
BioSci D145 lecture 1 page 3 ©copyright Bruce Blumberg All rights reserved

4. Focus will be on research problems
General comments
Overall philosophy
This class is about understanding genomic and proteomic (i.e. whole genome) approaches to problems of biological interest
Focus will be on research problems
Intended to be informative and cutting edge but also interesting and relevant, even fun.
Office hours are after class but I am always around
Questions are welcome
Please stop me and ask questions if something is unclear
I am going to ask you questions
Answers get participation creditcredit
Memorizing vs. understanding
I am not concerned with your memory
This course is about problem solving – how to address interesting biological problems using modern, whole-genome approaches
BioSci D145 lecture 1 page 4 ©copyright Bruce Blumberg All rights reserved

5. Letters of recommendation
General comments
Letters of recommendation
If you want a letter from me, I need to know you as more than a student number and grade
come to office hours
participate in class discussions
make your interest in the subject apparent
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6. Neither text book is absolutely required
About the texts
Bookstore vs. online?
Neither text book is absolutely required
Brown has lots of introductory material that will help to fill in background between BioSci 99 and this class
Reading noted in text books are intended to supplement lecture material
Source of material for this class will be lectures and assigned papers.
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7. Requirements for the term paper
Goals
Analytical thinking
Improved writing
Select a topic related of interest to you and then propose a whole genome approach to address the problem (not necessarily your 199 research!)
Talk with me about your topic (so that I can help you focus it on something do-able and rewarding to you)
Write a short paper (5 pages) in the style of a predoctoral fellowship describing how you will attack this problem (examples posted).
Specific aims (1/2 page)
Hypotheses to be tested
How will you test hypotheses?
Background and significance (1-2 pages)
What is known, what remains to be learned
why should someone give you money to study this problem?
Research plan (~3 pages)
specific experiments to answer the questions posed in specific aims
How will you handle expected vs. unexpected results
BioSci D145 lecture 1 page 7 ©copyright Bruce Blumberg All rights reserved

8. Requirements for the term paper (contd)
Outline (due Friday February 2)
Title and topic
Introductory paragraph telling why the problem is important
What is the hypothesis that your proposed research will address?
Enumerate 1-3 specific aims in the form of questions that will test aspects of your hypothesis
Topic can be changed later, if necessary
What is a hypothesis?
A supposition or conjecture put forth to account for known facts; esp. in the sciences, a provisional supposition from which to draw conclusions that shall be in accordance with known facts, and which serves as a starting-point for further investigation by which it may be proved or disproved and the true theory arrived at.
What is a theory ?
An analytical framework that explains a set of observations
A comprehensive explanation of an important feature of nature that is supported by facts that have been repeatedly confirmed through observation and experiment
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9. Requirements for the oral presentation
Goal – again to get you to think more analytically
Exposure to literature (classic and current)
Learn critical reading
Discuss practical applications of what we are learning
Powerpoint (“journal club”) presentation – as a presenter
15-20 minutes with time allowed for discussion (max of 15 – 20 slides)
Frame the problem – what is the big picture question?
What was known before they started? What was unknown?
Present background (not more than 5 slides)
What are specific questions asked or hypotheses tested
Discuss figures
What is the question being asked in each figure or panel?
What experiments did the authors do to answer questions?
Do the data support the conclusions drawn?
What did they conclude overall?
What could have been improved?
Point out a few papers for further reading (reviews, follow-ups, etc)
Summarize main points and key techniques used at the end
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10. Requirements for the oral presentation (contd)
Powerpoint presentation – as a listener
READ THE PAPERS – you are responsible for the material covered
Study the figures
What points don’t you understand?
Make notations, ask the speaker to clarify these
Listen to the speaker
If presentation is unclear, ask the speaker to elaborate
Always feel free to ask questions – we want an open discussion
Papers are posted on the web sites listed
Logistics
Prepare presentation in Powerpoint or PDF (not Keynote) and either to me or bring it on a USB stick.
BioSci D145 lecture 1 page 10 ©copyright Bruce Blumberg All rights reserved

11. Presentation schedule
Week 1 – Dear and Cook, 1993, Jiang et al, 2011 (Riann)
Week 2 – (1) Geisler et al., 1999 (2) Redon et al., 2006 (3)  Myers et al., 2000
Week 3 – (4) Iyer et al., 1999 (5) Venter et al., 2004, (6) Bentley et al., 2008
Week 4 – (7) RIKEN, 2005 (8) Kapranov et al., 2007 (9) Lindblad-Toh et al., 2011 
Week 5 – Midterm, no presentations
Week 6 – (10) Horak et al., 2002 (11) Chen et al., 2012 (12) Dewey et al., 2016
Week 7 – (13)  Seisenberger et al, 2012 (14)  Siklenka et al., 2015 (15) Donkin et al., 2016
Week 8 – (16) Gilbert et al., 2014 (17) Liu et al., 2017 (18) Luo et al., 2009
Week 9 – (19) Ito et al., 2001 (20) Dejardin and Kingston, 2009 (21) Gavin et al., 2002
Week 10 - (22) David et al., 2014 (23)  Breton et al., 2016 (24) Rampelli et al., 2015 
BioSci D145 lecture 1 page 11 ©copyright Bruce Blumberg All rights reserved

12. Lecture Outline – Organization and Structure of Genomes
Today’s topics
Genome complexity
Implications of split genes for protein diversity
Repetitive elements and gene evolution
The big picture for the next 2 lectures
How are genomes similar and different?
How do we find out this information?
Why do we care?
What is genomics? Proteomics?
‘omics is the study of a property using “whole genome” approach
Genomics – study of genes and gene function
Proteomics – study of all the proteins
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13. The -omics revolution of science
The rise of -omics
The -omics revolution of science
What does it all mean?
Transcriptomics –
Proteomics –
Functional genomics –
Structural genomics –
Pharmacogenomics –
Toxicogenomics –
Metabolomics –
Interactomics –
Bibliomics –
large scale profiling of gene expression
study of complement of expressed proteins
vague term, typically encompasses many others
prediction of structure and interactions from sequence (Rick Lathrop, Pierre Baldi)
transcriptional profiling of response to drug treatment – often looking for genetic basis of differences
transcriptional profiling of response to toxicants (often includes pharmacogenomics
Seeks mechanistic understanding of toxic response
analysis of total metabolite pool ("metabolome") to reveal novel aspects of cellular metabolism and global regulation
genome wide study of macromolecular interactions, physical and genetic are included
identifying words that occur together in papers
Sadly, usually just abstracts
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14. Organization and Structure of Genomes (contd)
Genome size
i.e. total number of DNA bp
Varies widely - WHY?
i.e., what is the source of the differences?
Do the number of genes required vary so much?
Phylum Chordata
Phylum Arthropoda
Mixed bag
C- paradox
unlikely
(how many “phyla” are represented at the right?)
BioSci D145 lecture 1 page 14 ©copyright Bruce Blumberg All rights reserved

15. Organization and Structure of Genomes (contd)
How to measure genome complexity?
Hybridization kinetics
Shear and melt DNA
Allow to hybridize and measure double-stranded vs. single-stranded by spectrophotometry
Cot½ - measures genome size and complexity
What does a large value (longer to hybridize) mean?
k is smaller (rate constant slower)
Longer to hybridize – more unique sequences, larger genome
Much of what we knew about genome size and complexity (until advent of genome sequencing) comes from these studies
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16. Organization and Structure of Genomes (contd)
Assumptions
Cot½ measures rate of association of sequences
Simple curves at right suggest simple composition
No repetitive sequences
What would a more complex genome look like?
Would it be just shifted further to the right?
Or ?
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17. Organization and Structure of Genomes (contd)
Measure eukaryotic DNA
Multiple components
Can calculate more than 1 Cot½ value
Either means starting material is not pure (i.e., multiple types of DNA)
Or means different frequency classes of DNA
Highly repetitive
Moderately repetitive
Unique
Very big surprise
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18. Organization and Structure of Genomes (contd)
What can we conclude from great variation in genome size ?
Genetic complexity is not directly proportional to genome size!
Increase in C is not always accompanied by proportional increase in number of genes
Gene number is controversial
Depends on what is a “gene”
Are we no more complicated than a weed (Arabidopsis) ?
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19. Organization and Structure of Genomes (contd)
What can we learn by hybridizing RNA back to the genomic DNA?
Label RNA and hybridize with excess DNA – measure formation of hybrids over time
Rot½ analysis shows that RNA does not hybridize with highly repetitive DNA
What does this mean?
Most of mRNA is transcribed from non-repetitive DNA
Moderately repetitive DNA is transcribed
Much of highly repetitive DNA is probably not transcribed into mRNA
Key argument why genome sequencers do not bother with “difficult” regions of repetitive DNA
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20. Organization and Structure of Genomes (contd) stopped here
Gene content is proportional to single copy DNA
Amount of non-repetitive DNA has a maximum,total genome size does not
What is all the extra DNA, i.e., what is it good for?
Repetitive DNA
Telomeres
Centromeres
Transposons
Junk of all sorts
Where did all this junk come from and why is it still around?
DNA replication is very accurate
Selective advantage? OR
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21. Organization and Structure of Genomes (contd)
What is this highly repetitive DNA?
Selfish DNA?
Parasitic sequences that exist solely to replicate themselves?
Or evolutionary relics?
Produced by recombination, duplication, unequal crossing over
Probably both
Transposons exemplify “selfish DNA”
Akin to viruses?
Crossing over and other recombination lead to large scale duplications
ENCODE (encyclopedia of DNA elements) considers > 80% of genome to be functional.
But see Grauer et al, Genome Biol Evol 5: On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE
BioSci D145 lecture 1 page 21 ©copyright Bruce Blumberg All rights reserved

22. Transcription of Prokaryotic vs Eukaryotic genomes (stopped here)
Prokaryotic genes are expressed in linear order on chromosome
mRNA corresponds directly to gDNA
Most eukaryotic genes are interrupted by non-coding sequences
Introns (Gilbert 1978)
These are spliced out after transcription and prior to transport out of nucleus
Post-transcriptional processing in an important feature of eukaryotic gene regulation
Why do eukaryotes have introns, i.e., what are they good for?
Main function may be to generate protein diversity
Harbor regulatory sequences
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23. Alternative splicing can generate protein diversity
Introns and splicing
Alternative splicing can generate protein diversity
Many forms of alternative splicing seen
Some genes have numerous alternatively spliced forms
Dozens are not uncommon, e.g., cytochrome P450s
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24. Alternative splicing can generate protein diversity (contd)
Introns and splicing
Alternative splicing can generate protein diversity (contd)
Others show sexual dimorphisms
Sex-determining genes
Classic chicken/egg paradox
how do you determine sex if sex determines which splicing occurs and spliced form determines sex?
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25. Origins of intron/exon organization
Introns and exons tend to be short but can vary considerably
“Higher” organisms tend to have longer lengths in both
First introns tend to be much larger than others – WHY?
Often contain regulatory elements
Enhancers
Alternative promoters
etc
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26. Origins of intron/exon organization
Exon number tends to increase with increasing organismal complexity
Possible reasons?
Longer time to accumulate introns?
Genomes are more recombinogenic due to repeated sequences?
Selection for increased protein complexity
Gene number does not correlate with complexity
therefore, it must come from somewhere
BioSci D145 lecture 1 page 26 ©copyright Bruce Blumberg All rights reserved

27. Origins of intron/exon organization
When did introns arise
Introns early – Walter Gilbert
There from the beginning, lost in bacteria and many simpler organisms
Introns late – Cavalier-Smith, Ford Doolittle, Russell Doolittle
Introns acquired over time as a result of transposable elements, aberrant splicing, etc
If introns benefit protein evolution – why would they be lost?
Which is it?
Actin
Introns “late” (at the moment)
But late = ~580 million years ago
What is common factor among animals that share intron locations?
All deuterostomes (echinoderms, chordates, hemichordates, xenoturbellids – diverged about 580 x 106 years ago
BioSci D145 lecture 1 page 27 ©copyright Bruce Blumberg All rights reserved