- Okay, I'd like to welcome you
to this Whitman College Alumni
Association Virtual Event,
Evolution of Color
Pattern in Monkeyflowers:
Undergraduate Research at
Whitman with Dr. Arielle Cooley.
My name's Jennifer Northam.
I'm class of 1991 and I have been a member
of the Alumni Association
staff for almost seven years.
Thank you for being here
today from wherever you are.
As we continue to cancel in-person events
and restrict travel,
the Alumni office staff has been working
to create opportunities
to bring our programs
to a virtual platform
and reach our alumni, our
parents and friends at home.
More content is being created every day
and you can find details
at the Alumni website,
whitman.edu/alumni or in
the Whittie News email
that is delivered to your
inbox the first of every month.
Now, on to our presentation.
Questions about how organisms
are made up, develop,
and evolve have fueled Arielle
Cooley's research for years.
She earned her undergraduate
degree at Pomona,
a combined major in biology
and public policy analysis,
earned her doctorate at Duke University
and did postdoctoral research
at the University of Michigan.
Since coming to Whitman in 2012,
her work has focused on the monkeyflower
or Mimulus, found in
Southeast Asia and Australia,
and along the west coasts
of the Americas from the Bering Straits,
all the way south to Patagonia.
From her lab in the Hall of Science,
she works with numerous
undergraduate students
to explore the genetic mysteries
of how molecular changes in DNA give rise
to striking new flower
colors and patterns.
Today, Dr. Cooley will
talk about her research
and the vital part that our
students play in that research,
as well as how her lab has been impacted
by the COVID-19 pandemic.
Dr. Cooley will share her presentation
and we will have some time
afterwards to answer questions.
Please use the Q&A button
at the bottom of your viewing windows
to submit those questions.
I'll combine things that are similar
and share as many as we
can in the order received.
It's my pleasure now
to turn the screen over
to Dr. Arielle Cooley.
- All right, thanks very much Jennifer
for that introduction
and welcome to everybody who's joining in.
I appreciate your time.
So I am Arielle Cooley,
and I've been in the biology
department at Whitman
for just one year longer
than Jennifer has been here,
for about eight years.
At the moment, as you can see,
I am not in the biology department,
I am in my house as you
probably are as well.
I'm in the midst
of a spring semester
research sabbatical right now
so I have not had the added challenge
that many of my colleagues have faced
of quickly converting
classes to online teaching.
They have been working so hard
to create new ways for
their classes to learn,
and interact and discuss and create.
But a lot of my research
sabbatical consists of,
or was supposed to consist
of doing research in the lab with students
and that obviously
cannot happen right now.
So I have had to adjust my expectations
and face the sense of loss that many
of my colleagues report
feeling in the absence
of the students who are
the reason for our jobs.
I also mourn the loss
of hands-on learning,
both in the classroom and by students
who would normally be
doing mentored research
with their professors right now.
Working with students on
biology research projects is one
of my favorite things at Whitman,
and we are all looking forward
to the day, hopefully sometime this summer
but we'll see, when we
can pick that up again.
So in the meantime, let me go ahead
and share my screen and there we are.
I thought that I would give you all a peek
at the kinds of projects
that my students have been up to lately.
I plan to speak about this
for about half an hour
and then open it up to
any of your questions.
Oh, my slides are not advancing.
Hang on, let me stop the
screen share for a minute
and try again.
All right, and Jennifer,
can you see the next slide here?
- [Jennifer] I am still seeing
you and not your screen.
- Okay, let me try again.
Share screen and PowerPoint.
All right, and how is that?
- [Jennifer] I see your second screen.
- Okay, excellent, good.
So doing research with students
as I said, is rewarding for me
and it is also really
beneficial for the students.
A lot of studies have shown
that doing real research,
that is exploring an unanswered question,
or a relevant topic in their discipline,
has strong positive impacts,
on a student's educational experience.
Discovering new knowledge
for any of us really, helps
us get excited about learning
and it helps us develop our abilities
to work independently and problem-solve.
And for students this
process also helps build,
closer faculty/student interactions,
which is beneficial in a variety of ways.
One of the reasons that I was excited
to join the Whitman faculty
is that Whitman turns out
to be really good at
undergraduate research.
You may be familiar
with the Whitman Undergraduate Conference
which is a pretty neat event
where students from all
disciplines present their work.
And the Whitman Internship
Grants help ensure
that all students have
access to such opportunities,
be it collecting data
or as shown here, conducting an orchestra.
And in the sciences, the newly
completed STEM Hub space,
has helped us build a stronger
student research community.
For example, last semester,
we held a Professor Poster Session
to help students learn about the kinds
of science happening on campus.
So both inside and outside
of the Science Building,
where I work, there are a lot
of opportunities for students
to get involved in meaningful
work with professors.
Importantly, for the sciences,
Whitman has the infrastructure
and institutional support
to foster high level undergraduate
powered research labs.
To give just one example,
our microscopy facilities,
include both confocal microscopy
for looking inside cell-sized structures,
as shown by Professor Coronado here.
And the scanning electron
microscope facilities
for looking at the surfaces
of tiny little things
in incredible detail,
like this single grain of pollen.
Faculty at Whitman have
been quite successful,
in obtaining external
funding, including funding
for these microscopy facilities,
and more recently, a
Beckman Scholars grant
to support intensive research
and leadership experiences
for a handful of biology and
BBMB and chemistry majors.
Similarly, the humanities
and social sciences were
recently awarded a major grant,
from the Mellon Foundation
to pursue research projects
that focus on engagement
with the surrounding community.
So we have a great track record
of providing our students
with the resources and
facilities that they need
to seek answers to unanswered questions.
And every professor
at Whitman has a favorite
unanswered question,
one that we find especially fascinating
and mine is, how does the
extraordinary diversity
of life on Earth evolve?
I work primarily in the
monkeyflower genus Mimulus.
Here I'm showing you the
monkeyflower family tree,
you can see a picture about
each of the different species
and that lines show how they
are related to one another.
And although I'm only showing
you the flowers, other parts
of the plant are also
very diverse in height,
whether it's woody or soft
or adapted to the desert or to the ocean.
So there's just a striking amount
of trait variation in this genus
and not the least is trait
variation in flower color.
Most of the research students in my lab,
are studying some aspect of
how monkeyflower pigment evolved?
And I'll give you just a
couple of examples here.
So example one is in the
realm of molecular biology
where I first used genetic mapping
to identify a region of
the monkeyflower genome
that is responsible for the evolution
of orange petals in Mimulus cupreus.
And a second genomic region
that is separately responsible
for the evolution of purple
pigment in variegatus,
the second species shown here.
Interestingly, all of the
candidate flower color genes,
in these two genomic regions
are the same kind of gene.
There are many kinds of
genes that work together
to build the anthocyanin
or reddish pigment
that you see in these photos
but of all those different
kinds the only candidate genes,
in our two genomic
regions are the MYB genes.
In other words they all belong
to the same gene family
called the MYB gene family,
that's why all their name starts with MYB.
And what these are, are regulatory genes,
they encode a protein
that works together in a protein complex
to active the biosynthetic pathway.
They turn on the genes
that produce the enzymes
that actually build the pigment molecules.
So in each case the plants
evolved their new petal colors,
not by inventing a new kind of pigment
but through a regulatory change altering
where and when and how much of the pigment
that they make is produced.
So that helps us kind of think about
how do traits evolve at one level.
An ongoing question in
evolutionary biology is
what's the relative importance
of these enzyme encoding genes
that actually build stuff
versus the regulatory genes
that turn things on and off.
Another level of biological
organization from
which we can think about
this question is well,
what is the particular
gene used in each case?
And can we find any patterns
or tendencies there?
In this situation there are a lot
of MYB genes all
clustered together in each
of these genomic regions
and that's because of gene duplication.
The genes have been copied
through random mutational errors over time
and that's a really neat thing.
That gene duplication is something
that creates new material
for evolution to work with.
So it's nice to see an example
of gene duplication contributing
to evolutionary diversity.
The next question that
we'd like to answer is,
which of these genes
is doing the changing?
Which of these genes
is actually responsible
for flower color and what
kinds of mutations in
that gene are causing it?
To answer this sort of question one tool
that we use is called
RNA interference or RNAi.
This is something that turns
down the product of the genes.
So each gene in the genome
produces usually some RNA,
that's those little purple squiggles
and RNA interference gets rid of that RNA,
essentially turning down the
level of gene expression.
If a gene is responsible
for the evolutionary gain
of a color then turning
that gene down should alter
or remove the color.
This technique is widely used in biology
and biomedical research
for finding the genes
that are responsible for
all kinds of interesting
or important traits from
flower color to human disease
which is why I get a
fair number of pre-med
or pre-health students
in my flower color lab.
They're just using a lot
of the same techniques.
We recently used RNAi
to turn down this gene,
MYB5, in variegatus.
The species that normally
makes purple pigments,
in its petal loops.
As a brief aside I'll
just give you the overview
of how we actually do it.
The way you do RNAi along with a number
of other similar types
of gene manipulations is
to design, build and test transgenes.
So we start by isolating
or creating in the lab
sometimes isolating from a plant
through a technique called
PCR a bit of the gene
that we are working with.
So an RNAi transgene and we
put that into a circular piece
of DNA that's called a plasmid.
This is just like a little
holder, a little holding device
and it holds our transgene
so that the transgene
doesn't get degraded.
In this case the transgene is something
that cues the plant to turn down MYB5.
We can take that plasmid
containing our transgene
and put it into a naturally occurring,
soil bacterium called agrobacterium.
Rachel and Ellen pictured
here are growing bacteria,
even though we're a plant lab
because we do molecular
biology we do a lot
of growing bacteria on
those little agar plates.
So what agrobacterium does in the wild is,
seeks out plants preferably ones
that have nicks or cuts or
some kind of wound in them,
sneaks into the plant,
incorporates part of its
genome into the plants genome.
So it genetically modified the plant,
this is just a natural
version of GMO thing.
And then that GMO plant gets reprogrammed
to produce a little habitat
that is suitable for agrobacterium.
And scientists have
simply tweaked that system
so this agrobacterium instead
of putting bacteria home
making instructions,
into the plants genome, will
put this RNAi transgene,
into the plant's genome.
So we grow up the bacteria
make a little mixture of it
and then spray it onto some plants.
In my lab and with this kind of plant
that we work with,
we then use a step called
vacuum infiltration,
being demonstrated here by Kenny Stanton.
We just lower this little glass bell
that's covered in a wire mesh,
lower that over the plants
and apply a vacuum that
squeezes the air out
and when we release the vacuum air
and agrobacteria we hope will
rush into the plant's cells.
And this a lovely machine
that you see here was
formerly a carbon coder
at the University of
Washington geology department,
in the 1970s and I'm not sure
why our building engineer,
Larry North had it just
laying around his shop.
But when I mentioned to
him that I was looking
for a larger sort of a
vacuum he threw the magic
of engineering, turned that device into,
the vacuum infiltrator
that you see before you.
So thanks to Larry for that.
Here is student Kuenzang
Om preparing a plant
for infiltration in Larry's shop
and here is the text
that Kuenzang sent me
reporting the first ever,
RNAi phenotype in my lab.
This was very exciting
text to get on my phone
and it turned what was about
to be a slightly dull faculty meeting,
into a really exciting faculty meeting.
And it's exciting because it shows
that turning down just
one single gene made five,
is sufficient to eliminate the
pigment from the petal lobes.
And that in turn together
with the previous genetic
mapping results tells us
that the way variegatus,
evolved its purple color
in the first place was
through changes in the MYB5 gene.
In contrast, pigment elsewhere
in the plant was unaffected
by RNAi against MYB5
and that's you can see here the stems
of the untreated plant
and the stems of the RNAi
plant are both equally purple
and that's because of
that same kind of pigment
that we call anthocyanin.
And that shows that the action
of MYB5 is really quite
spatially specific.
Experiments like this
help highlight the ways in
which new traits evolve
answering questions like,
what kind of gene tends to get used?
How specific is the action of that gene?
And our next step is going to be to ask
which is more important, the coding region
of that gene or the regulatory
region of that gene?
There are still plenty
of unanswered questions,
both in the molecular biology direction
and just in terms of thinking about
what this flower color means
for plants in the wild.
For example a lot of flower
color changes have been thought
to be driven by pollinators.
You may know or have heard
that hummingbirds often
prefer red flowers,
bees often prefer yellow flowers
and in this species group that
does not seem to be the case.
Based on some field work
that I did in Chile three
of the Chilean Mimulus taxa
that differ in flower color
were abundantly visited
by a single native Chilean
bumblebee pollinator.
The fourth, Mimulus cupreus,
had a very low visitation rate.
It hardly ever got visited by pollinators
but when it did it was again
that same Bombus dahlbomii.
So it doesn't seem
that the differing flower
colors are associated
with differences in pollinator preference.
If anything there has been an evolution
of self-fertilization in
this orange flowered cupreus.
It self-fertilizes really well,
completely in the absence of pollinators,
much better than the other taxa.
And that is surprising
given that it went off
to all the trouble
of evolving this very showy orange flower.
So why did it evolve these
bright striking flower colors,
if not to catch the
attention of a pollinator?
As with much of science,
we don't really know.
I can make you a speculation.
Oh, I'll first mention I also
found a hybrid population
of monkeyflowers in Chile
where different flower colors
were all mixed together
so I was able to track
individual bumblebees thinking
that perhaps there was sort of separation
at the level of one individual
bee preferring redder flowers
and another preferring yellower flowers.
But that also did not seem to be the case
that these colors switched,
within a single pollination
bout very readily.
One interesting thing about
this anthocyanin pigment,
pathway is that it helps
protect the plants against a lot
of environmental stressors.
The pathway itself produces
the cyanidin pigment
and there are a lot of
side branches coming off
of this pathway that produce other kinds
of really important plant compounds.
Many of these compounds
have a bitter taste
that's thought to protect plants,
against insect or herbivore.
The pigments themselves
absorb excess UV radiation
which can protect,
the plant against damage especially
to its photosystems from
getting too much sunlight.
And the pigments and many
of the precursors act
as antioxidants, helping to
protect against cellular damage
that can occur in places
where there are extremes
of drought or temperature,
hot or cold temperature.
So we're not sure why more
anthocyanins are produced,
in variegatus and cupreus
but we're interested in the idea of this,
some sort of environmental protection.
Now in addition to studying
each species individually,
we're also investigating
a surprising thing
that happens when they cross
two species to one another.
Each of these parent species appears
to be solidly pigmented.
Your orange flowered cupreus
and your purple flowered variegatus.
But when you cross pollinate them, the F1
or first-generation hybrid
that you get is not
solidly pigmented at all.
It has this really
intricate magenta speckling,
on a cream-colored background.
And if you take that F1
hybrid and self-fertilize it
so take out its own pollen and use that
to pollinate that plant you get the F2
or second generation hybrids
which are stunningly gorgeous
and show a huge range
of color and pattern variations.
And the reason this is happening
by the way in the F2 is
that the F1 has a copy of cupreus genome
and a copy of the variegatus genome
and within the body of the F1 plant,
those chromosomes are crossing
over and mixing and matching
and creating all different
kinds of gene combinations
that then get passed on
to the next generation.
So the next generation is
where we get the scrambled up
many different combinations
of variegatus and cupreus.
Now, surprisingly little is known about
how spatially complex
patterns arise in development,
particularly in plants.
And it's a hard question to tackle
because one of the first things we'd like
to do is genetic mapping to find the genes
that are responsible.
But to do genetic mapping
you have to be able
to measure variation in
your trait of interest
and just looking at this stuff
it's not immediately clear
how to slap numbers on
that kind of a thing.
Fortunately for us, Whitman
recently established,
an outstanding new
computer science department
and one of their many
teaching innovations is
to have a senior capstone research project
that is done as a group
under the direction
of a computer science professor.
This group works together
with a local individual
or program or company
to help them solve some kind of a problem.
So my lab particularly,
lab member Dan Thomas
have been working on,
building a computational approach
to analyzing phenotypes.
And we decided to volunteer our problems
to the computer science departments.
And since then my lab has
been working with this team
of computer science seniors shown here,
Jack, Owen and Abbey together
with Professor John Stratton
to find and improve our abilities
to quantify the complex
color pattern variation
that is observed in the F2 hybrids.
So the basic idea which was
initiated by folks in my lab
and expanded and improved
by the computer science students is
to take photos of the
petals, convert those petals
to two color images
and then use traditional
computer vision techniques
to identify the placement of anthocyanin
and spots across the petals.
And I've also been
collaborating with a professor
at the College of William
& Mary, Dr. Joshua Puzey.
We have now used results
from a first pass version
of our digital image analysis pipeline
to find six genomic
regions that contribute
to color pattern variation
in our monkeyflower hybrids.
What you're seeing in this slide,
is the monkeyflower genome
spread out across the bottom,
each number corresponds to a chromosome
and then the six vertical bars
that are sort of a salmon color correspond
to genomic regions
where it matters whether
you have a cupreus version
or a variegatus version
that affects the color
pattern of the hybrid.
And Dr. Puzey and I are
additionally collaborating
with a mathematician at the
College of William & Mary
to build and test some mathematical models
that could help explain how networks
of gene expression involving
the genomic regions
that we have found
through genetic mapping,
could create these speckling patterns.
This idea comes from
kind of a classic notion
by British mathematician
Alan Turing in the 1950s.
He was really curious about
kind of a broader problem,
in development how do
you go from a circular,
spherically symmetrical ball of cells
to something like a horse
that is not symmetrical,
in specific or two patterns?
So how do you break
symmetry during development?
And he was particularly interested in the,
semi-random looking
patterns that often pop up.
Like the spots on a cheetah
or stripes on a zebra
and he proposed that a
reaction diffusion model
which is a kind of a
self-organizing molecular system,
might be able to explain the appearance
of these more or less periodic patterns.
And back to the 21st century
and monkeyflower world,
my colleague Yaowu Yuan,
recently published an article showing
that one kind of spot
patterning in Mimulus
that is the nectar guide
spots found in the throat
of a lot of the flowers
seems to be operating
by a reaction diffusion
model that is consistent
with Alan Turing's idea.
And at the same time
that Dr. Yuan has been working on,
the nectar guide spotting in
his species of monkeyflower,
we have been really interested in the idea
that this same system,
could perhaps explain
spotting in our hybrids.
The fundamental mechanism is
that you have two components,
an activator and a repressor.
In this diagram here the
activator is called Megan,
that's another name for that MYB5 gene
that I showed you earlier.
That gene, the model posits that gene,
has random fluctuations in expression,
eventually it gets expressed
at a high enough level
that it can start to turn its own self on,
in a positive feedback loop.
Eventually it gets
expressed strongly enough
that it turns on pigment production
and pigment starts getting made,
in an ever increasingly large spot
and then it gets turned on so high
that it eventually crosses a threshold
to be able to activate its own represser
which is labeled RTO in this diagram here.
That repressor rushes rapidly
upward creating a zone
of inhibition and that's what
limits the size of the spot.
What we think is going
on in our hybrids is
that there actually is a spot
determining system in cupreus
that makes it look orange
because it's actually
tons and tons and tons
of tiny little red spots
on a yellow background.
And meanwhile there's a separate,
spot determination system in variegatus
that creates one big large blotch
that covers the entire petal.
And when you combine these two different,
reaction diffusion systems together
and force them to interact in the body
of an F1 hybrid you get all kinds
of interesting combinations
and mis-regulations
that we think could explain a lot
of this sort of hybrid novelty
and intricate patterning that we see.
National Geographic just this past week,
published a story about
monkeyflower patterning.
This is based on the
nectar guide spotting paper
that I just showed you and
also has a lot of pictures
of the Chilean monkeyflowers
that I am working on.
And it's a really beautiful
story, you can read it for free
and I thought it was really interesting
that the cover photo they
chose was actually not,
my monkeyflowers or the
ones that Dr. Yuan works on
but this very interesting other species,
called Mimulus pictus.
And Mimulus pictus does
something else yet again.
This is not hybrid spots,
it is not the nectar guides
of Dr. Yuan's paper, this is pigment
that is produced along
the veins of the petals.
So it's getting these lines
are sort of showing you
where a number of the major
petal veins are located.
And we think in our
hybrids we have observed,
almost the exact inverse of that.
That the spots as they are formed tend
to have their spot centers
or their origins in between the veins
as though veins were inhibiting,
rather than promoting pigment production.
And this is again something
that the computer science team,
has helped us be able to investigate.
So one new question that we're starting
to ask is, do petal veins
influence where spots form?
And here on the left you
can see a two color version
of a photograph of some petals
and after we take our color
photo, we can then clear out,
we can remove the pigment
through chemical treatment
and take another picture of the petals
that shows just the underlying veins.
And then through our newly enhanced,
digital image analysis pipeline,
we can overlay those two
images and then quantify
where is the origin or
the center of each spot
and where are the locations
of the veins in order
to assess whether there is any kind
of inverse correlation
between veins and spots.
This is all really new work,
we just submitted a grant proposal for it
to the National Science Foundation
so we're very excited to see
how it unfolds in the future.
All right, lastly not all
of my research originates
in my monkeyflower lab.
This last project began
when three students,
in my EvoDevo class,
evolution and development
that's Qingsong, Mitch
and Max shown here decided
to study these two flower species,
Drosophila novamexicana
and Drosophila americana
for their independent project.
The genes that make these
species different colors,
also function in the fly's visual system.
And so Qingsong, Mitch
and Max were curious
whether the different colors
of flies would also have
different preferences
with respect to light,
to their visual habitats.
They created a habitat cage similar
to this one where the flies can crawl
through the little holes back and forth
and choose whether to be on
the light side of the cage
or the dark side of the cage.
with a little food dish on each side
and plenty of opportunities
to move back and forth.
Their question and their
approach were intriguing enough
that I had the whole class to the project
at a larger scale for the next two years.
And so far it looks like
the light bodied species,
that's this Drosophila novamexicana,
shown in the gray line does in fact tend
to prefer the lighter or brighter habitat.
What you're seeing here is the mean
of a whole bunch of trials
and for each trial we looked
at it across six different days.
And then on the y-axis you can see well
what proportion of the
flies, ten flies per trial,
what proportion of the flies,
are found on the light side of the cage?
And there are slightly
but significantly more
novamexicana on the light side
of the cage, whether you look at noon
or 4:00 p.m. same flies just
checking (mumbles) of day.
So this is an association
that has not been demonstrated before
and I think it is really evolutionarily
and developmentally intriguing.
In my class last spring wrote a manuscript
that we submitted to a
scientific journal called,
"Histology and Evolution".
And up till the whole COVID-19 situation,
a couple of these students,
Shantel, Vincent and Sophie
(mumbles) we're working hard
to collect some additional data
to address reviewers requests
with a plan to resubmit our manuscript
at the end of the next permissible
chunk of research time.
So the question of whether pigmentation
and vision are related in these species,
is a real unanswered
question for a species pair
that has interested Drosophila researchers
for quite some time.
And I think it's really
neat that a biology class
at Whitman is coming up with
the ideas for investigating.
So to conclude that part of my talk,
I guess I would just say
that one of the things
that makes Whitman special
is being there on campus
where students and faculty
can work closely together
to discover new knowledge.
With this next phase of COVID-19
and with the higher frequency
of pandemics expected
to be associated
with climate change there
is gonna be a huge demand
for people working in
the public health sector.
And I just wanna say that does not mean
that everyone should rush out
and major in the sciences.
I totally recommend
being a biology major if
that's what you love to do.
But every major at Whitman
College does an outstanding job
of preparing students to
think carefully and critically
and creatively about complicated problems
and to communicate in clear and effective
and compelling ways.
To manage our public health
crisis like COVID-19,
to manage the unknown future challenges
that are definitely coming our way,
we'll need storytellers and translators
and visual thinkers and
creators both within
and outside the sciences.
And having advised plenty
of pre-health students I can confirm
that a good liberal arts education
for example science
classes paired with a music
or language major can be very competitive
and even help students stand
out from amongst upon ranks
of biology major applicants.
So if you know a college
student who is inspired
to help defend the world
against the next pandemic,
being a science major is a great choice
and it is just one of many
many routes to that end.
The most important thing
I think is to find a place
where you can dive deeply into hard stuff,
while being both challenged
and supported by your professors.
Doing an authentic research project
as an undergraduate is an amazing
way to build your creative
and analytical and organizational skills.
And I may have mentioned this before
but I am really looking
forward to getting back to it.
So as an example of how different
and not obviously practical perspectives,
can help address a complex
problem like COVID-19,
my work is about flower evolution.
I am no epidemiologist
but my training in evolution provides one
of the many perspectives
that we need to have in
the conversation right now.
Understanding how evolution works
and how our own actions,
can alter the evolutionary trajectories
of other organisms can be a powerful tool
for changing the future.
Lemme give you a super
quick primer on evolution.
The basic mechanism
of evolution can be
described pretty simply.
It starts with mutation.
Mutation is random
changes in the DNA genome
or if we're talking about
SARS-CoV-2, the RNA genome.
And these are not mutations
on-demand, you can't come up
with the mutation that you need,
these are just mistakes that happen.
Once a mutation arises it will either fail
to get transmitted to the next generation
or it will get transmitted
to the next generation
and it's frequency in the
population depends on two things.
One is simply what we call drift
that is chance.
Mutation that does nothing
for you whatsoever,
what we call a neutral mutation,
could become more abundant by chance alone
or could disappear by chance alone.
And the more famous aspect
of evolution is Darwin's
Natural Selection.
This is the idea that if
a mutation helps its owner
to survive and reproduce that gives
that mutation a reproductive advantage.
It's gonna become more
common in the population.
So beneficial mutations will tend
to spread through selection.
And here's one of the few cool things,
about the SARS-CoV-2 virus.
Since it's utterly dependent
on us for it's ability
to reproduce and spread,
we have some power
to shape the selective
pressure that it experiences.
We can't control the
mutations, those are random,
we can't prevent drift but we can help
to favor certain kinds of mutations.
For example if we're all
going to COVID-19 parties
which apparently did not
actually happen in Walla Walla
and signing up for cruises right now,
we are creating an environment
where it is really easy for the virus
to jump to a new host.
In this kind of environment,
mutations that make the
virus more virulent,
faster to reproduce even at the cost
of damaging its host, these will tend
to dominate in the population.
Those mutations will tend to spread
and if in the process
of spreading the virus kills
its host that's not a big deal
to the virus because a new
host is readily available.
In contrast if we all stay at home
and rarely go out, we're
creating an environment
where there is a really long
time in between opportunities
for new hosts.
And this creates selective
pressure to favor viruses
that are less virulent.
So this is definitely
something that we want to do.
This physical distancing
doesn't create selection
to be less transmissible,
just to be less harmful
to the hosts.
There's an article linked here
that gives a little primer on
sort of evolutionary theory
and how various conditions
should impact viral evolution.
And one other thing that
this article points out is
that there is something
we can do to evolve
to create selective pressure on the virus
to become less transmissible
and that is to get vaccinated.
As more and more hosts
are vaccinated the benefit
of host jumping becomes less on average
and the risk becomes greater.
So when a vaccine does become
available that's another way
to shape the evolution of this virus.
Right now social isolation
is what we've got
and interestingly a mutation,
has recently been discovered in Arizona
that may well be a mutation
that reduces the virulence of the virus.
This is a massive deletion,
it's an 81 base-pair deletion,
it removes 27 amino acids from a protein
that is not required for the virus
to survive and reproduce but
it is something the virus uses
to kill host cells, so
it promotes virulence.
This new mutation presumably
disrupts the ability
of that protein to promotes
the death of host cells
and that's something we wanna encourage.
So to end this part of my presentation,
I'll just say research experiences,
I think are really
unfortunate for undergraduates
and Whitman is a great
place to be doing that.
I've shown you, I hope that
our research projects here,
can span the spectrum from
basic science questions
to interdisciplinary collaboration
to course-based research
and that you personally can
help shape the evolution
of the SARS-CoV-2 virus by avoiding crowds
and washing your hands.
So thanks very much
to Jennifer Northam, Charles
Marr, Tristan Rupert,
the other staff of Whitman College
who have helped make this event happen.
I'd like to thank all of my students
for being wonderful people
as well as my collaborators,
my funding sources
and all of you for your
time and attention.
And I will get out of
the screenshare mode now
and I would love to take your thoughts
or questions at this time.
- Well, that was fascinating
and now I want to grow a
whole bunch of monkeyflowers.
- They're surprisingly
hard to grow at home
but they do quite well
in the United Kingdom
where they have become
slightly naturalized,
they're not aggressive
but they have managed
to get out and they grow
in the scenic byways,
in the United Kingdom.
- Good to know.
We have a handful questions
and I don't know if I'm
gonna say this right
but if I have to spell it, I will.
Are your Chilean monkeyflowers
very far phylogenically,
from the Erythranthe?
- Oh, my goodness, this is somebody
who knows something about monkeyflowers.
So the monkey flower genus Mimulus used
to be one large glorious genus
and then a few years
ago a lovely scientist,
a lovely person who is also a
scientist wrote a paper saying
that we should split the
genus into two parts,
Mimulus and Erythranthe
and there are good reasons for doing that.
It kind of is tidy and makes sense.
Unfortunately almost
all of the monkeyflowers
that have been studied since
the dawn of about 1970 go
by the name Mimulus and there's
a whole sort of Mimulus,
there's a love Mimulus
in the science community.
We love to be Mimulus people,
we have Mimulus meetings,
we like the letter M and we
don't wanna be Erythranthe.
So we drew on a few examples,
Drosophila melanogaster
you may have heard of,
technically it's supposed to be,
have its name changed to Sophophora
and the Drosophila folks were
like, nah, not gonna do it.
So the Mimulus folks
said, nah, not gonna do it
so technically Mimulus luteus
and Mimulus cupreus should
be Erythranthe luteus
and Erythranthe cupreau but they're not.
There's been a bit of
a hullabaloo about that
but you can kind of mentally
equate Mimulus and Erythranthe.
- Thank you, one of our other questions,
a very interesting
presentation and thanks to you.
How did you get interested in studying,
monkeyflower evolution and
where is your research
headed in the future?
- Sure, so when I was an undergraduate,
I was interested in
different aspects of biology.
I wanted to find a system
where I could do evolution
and ecology and genetics and
I also wasn't sure if I wanted
to go with plants or animals.
But one thing I really like about plants,
is you can pick them up and put them down
and they stay there.
So that sounds a little trite
but it makes a huge
difference for fieldwork,
you can move stuff around
and the plants are still
there when you come back,
there's just a whole lot
that you can do with plants
that is a lot easier in
some ways than trying
to do similar sorts of
things with animals.
So then I kind of scanned
the graduate school world
of plant labs who were
working across the boundaries
of ecology and evolution and genetics.
And John Willis' is lab at
Duke University was a lab
that was doing this really effectively
and really cheerfully,
supposedly monkeyflowers
are an herbal remedy
to promote cheerfulness.
So I don't know if the
Willis lab was so cheerful
because they studied monkeyflowers
or the causation lend the other way.
But it was definitely a wonderful
place to do my PhD work,
to spend six years of my life
and then I went and did
a postdoc in Drosophila
which was wonderful and
educational and they are lovely
and charming but they're
not quite the same.
So for my main body of work
I came back to these plants.
The reason I got into the South
American group in particular
is that some scientists from Santiago
and Chile emailed my advisor Mitt saying,
"Hey we've got these really amazing colors
"of monkeyflowers down here,
"is there anyone in your lab
"who's interested in
coming down to take a look?
"Maybe do some genetics on them."
And fortunately I spoke
Spanish much better,
then than I do now and so I was the one
who spoke the best Spanish at the moment
and the one who lacked a research project
at the moment.
So those two happy things
coincided to send me to Chile
to do my first round of
looking at the populations.
Oh, and next steps.
Right now we're really
excited to pursue the idea
of reaction diffusion systems
that could underlie spot
developments in monkeyflowers.
That's a really relatively new area,
not a ton of work has been done on it
and monkeyflowers are a wonderful system
for getting some traction on it.
Pigment is a great trait for
looking at developmental models
'cause you can see
where the underlying biosynthetic
pathway is turned on.
If there's a spot that means
the genes were turned on there.
If there's not a spot
that means the genes
were not turned on there.
So it's sort of like an automatic readout
and that makes things a lot
simpler in some ways than some
of the other developmental
traits that could arise
through a reaction diffusion system.
So we think this is a great opportunity
to try and understand something about,
how spatial complexity develops.
- Thank you, do you know the
transcriptional targets of MYB
and how those downstream genes
change the pigment color?
- There are a lot of science
savvy people in the audience.
Yeah, so the MYB transcription
factor is a protein
that works together with two
co-factors, they form a complex
and they target a handful of genes
that are the downstream parts
of the anthocyanin and
biosynthetic pathways.
So the MYB protein is the
one that physically connects
to the DNA of the target
gene and turns that gene on.
In other words it's a direct
activator of the genes
that are needed to build pigment.
When we did our RNAi experiment,
we also did some transcriptomics work
and looked at sort of genome-wide changes,
in gene expression that
occurred after we did RNAi.
We found that, first of
all our RNAi was effective
at turning down MYB5
and not any of the other flower color MYBs
so it was really specific
to that one gene.
We found that it turned
down the anthocyanin
and biosynthetic pathway
genes, those enzyme genes
that it's supposed to be targeting,
so that was really reassuring.
And what was really
interesting is we found
that it also turned down
all of the other regulators,
the two cofactors and that
repressor that I showed you
that was labeled RTO,
basically turned down its own repressor.
And that is consistent
with emerging research
that the regulatory interactions amongst,
the transcription factor
proteins are really quite complex
and we don't completely
understand all of them
but we know there's a
lot of feedback loops.
So tweaking one player in this
system causes the expression
of many different genes to change.
Not just the genes that we
think of as being downstream
or direct targets of MYB5
but even MYB5 partners
and the things that regulate MYB5 in turn.
- All right, here's someone.
I'm interested in your breeding experiment
and the explosion of variation
in F2s, do you have any idea
what natural selection would favor?
Would you expect or have
you observed heterosis,
that is not word (mumbles)
it's not a science person.
Or outbreeding depression in hybrids,
between wild populations.
- Sure, great question.
So heterosis is when the hybrid
or the intermediate form does
better than its two parents
and that can happen for a lot of reasons.
The plants that I work
with in the greenhouse I
use in bread lines just
to keep the genetics simpler.
So they do suffer from
inbreeding depression
and the hybrids are quite
fertile and vigorous
but I think that's more the release
of the lab induced
inbreeding depression than,
necessarily an intrinsic heterosis.
That was sort of an
answer for a scientist.
Lemme try that again.
So when you cross pollinate
the plants in the wild,
they don't necessarily do any better,
than the parent species.
What I have seen in Chile in the wild is
that hybrids do get formed.
They pop up here and
there around the country,
I found one population where
there are all different colors
of hybrids mixed up,
they looked like an F2
hybrid generation and that's
where I did my individual
pollinator observations.
But what's interesting is
they don't particularly seem
to spread or persist.
Over the hundreds of years
that scientists have been noticing,
since the earliest British
explorers to Chile,
that people have been
noticing these plants.
The species, the luteus,
variegatus, cupreus
and (mumbles) have persisted
as pretty discrete species,
even though they can cross-pollinate,
very easily in the lab
and they clearly do so
at times in nature.
What that most likely means is
that there is something about the hybrids
that doesn't work as well
but is not as well suited
to the local environments
but what that is is swathed in mystery.
- Mystery in the flower world, I love it.
Here's maybe a quick
question, I don't know,
how do you target RNAi to a specific gene?
- Great question.
So RNAi is a naturally
occurring phenomenon
that is found in flowering
plants and mammals (mumbles)
and eukaryotes in general.
And the way it works is the transgene
that we put in has a little fragment,
from our target gene
inserted into the plasmid.
When we turn that gene fragment on,
it creates a little
piece of RNA that matches
with the sequence of the
gene in the genome itself.
So our little gene fragment,
it actually creates a
double-stranded version
of that gene fragment.
It's recognized by the plant cells
and is used by the plant
cells as kind of a template,
one of those gene products
floats around in the cell,
grabs onto the RNA
produced by the MYB5 gene
that's naturally in the genome
and cues cellular machinery
to come and degrade that RNA.
It most likely evolved
as a defense against a
certain type of RNA virus.
Not SARS-CoV-2, that's a
single-stranded RNA virus
and the way RNAi works is against,
double-stranded RNA viruses.
So it's a cellular defense,
against viruses originally perhaps
that is now actually used in our cells,
in plant cells, in all kinds of cells
as a way to get rid of gene products,
after the gene products have been made.
So you can think of it as kind of,
once you've turned on a gene,
made a bunch of gene products
and you suddenly don't need it anymore,
the cell can activate RNAi to clean up
and get rid of the gene products.
So again it's a similar to
the agrobacterium trick,
this is a naturally occurring process
that scientists have co-opted
and tweaked a little bit
to use for our own ends.
So instead of letting the cell,
turn down whatever genes it chooses,
we are additionally creating a situation
where we trick it into turning
down the gene that we choose.
- I think we have time for
just one more question.
- Why did Mimulus become the favorite
for these color pattern studies?
- Well, there's a lot of
plants out there for sure,
the best studied plant
is Arabidopsis thaliana
and that's kind of the
premier system for lab studies
and there's a lot of
great things about it.
It does not have color pattern variation.
There are a lot of
treats in the plant world
that are simply not
present in every species.
So one important thing as
a scientific community is
to have both breadth and depth.
You want to have a model
system like Arabidopsis
or Drosophila where you can
go really deep into mechanisms
and kind of get deeper into questions
by building a lot of
expertise in that one species.
But it's important to remember
that that one species is not necessarily,
a good stand-in for all
the species of the world.
So it's also really good to
diversify out into other groups.
Of the other groups, monkeyflowers
have become a really,
active area for research
because the genus is so diverse,
there's just a ton of
trait variation to look at.
There are monkeyflowers that are adapted
to the hot springs of
Yellowstone, they can grow
where almost no other plants can grow.
There are monkeyflowers that
are adapted to saltwater,
to deserts, to all kinds of different
to toxic copper mine tailings.
There is just a lot of
diversity to look at
and it's of the incredibly
diverse genera plants.
this is one that is
relatively easy to work with.
Under greenhouse conditions
you can grow it pretty easily,
it grows in a modest amount of time
so it's kind of manageable
as a lab organism.
- That's great, well we
are just about out of time
so I wanted to thank Dr. Cooley
for taking the time to do this
with us in pandemic isolation.
Hopefully the youngest member
of your family was not too insistent.
We appreciate it very
much and those questions
that I did not get a chance
to pass on to Dr. Cooley
I will absolutely share
with her afterwards.
We have recorded this session
and it will be available
to view online in the next week or so
and we hope all of you stay safe and well
and we look forward
to hearing your questions
on our next virtual event.
Thanks so much
- All right, thanks very
much Jennifer, my pleasure.
