- And I'd like to introduce my colleague,
Dr. Thea Popolizio who will introduce our speaker today.
- Good morning, everyone.
It's my pleasure to welcome Dr. Andrea Bodnar
to speak at our 2022 Darwin Festival.
Dr. Bodnar received her bachelor's degree and PhD
from McMaster University in Canada,
followed by postdoctoral work in neurological sciences
at the University of London.
From there, she held senior scientist positions
in the Oncology Department of Hoffman LaRoche,
the Department of Cell Biology and Pharmacology
at Geron Corporation
and the Bioprocessing Technology Institute
at the National University of Singapore.
From 2003 to 2017, Dr. Bodnar was a senior scientist
in the Molecular Discovery Lab
at the Bermuda Institute of Ocean Sciences,
where her research focused on using sea urchins
to understand the cellular and molecular mechanisms
underlying aging and cancer.
In her present position, as Science Director
at the Gloucester Marine Genomics Institute,
Dr. Bodnar brings all this (interference drowns out Thea)
academic and industry experience,
bridging marine biology, human health, and biotechnology.
Dr. Bodnar, I wanna extend a warm welcome to you
from the Salem State Community.
We are so happy to have you and look forward to learning
about the work being done at GMGI.
- Thank you Thea for that nice introduction
and good morning, everybody.
Thanks to the organizers for the opportunity to speak today
as part of the Darwin Festival.
I'm honored and humbled by the invitation.
As you just heard from Thea,
I have a very unusual scientific background
or unconventional scientific background.
The early part of my career was really focused
on studying human aging and cancer cell biology,
but that all changed with a move
to the beautiful island of Bermuda, where I joined
the Bermuda Institute of Ocean Sciences in 2003.
And that was a turning point in my career.
I became incredibly excited and captivated
by the amazing biodiversity that exists
in the world's marine environment,
surprised by how little we know
about the world's marine environments
and really inspired by all the new discoveries
that we could make by applying new technologies to the sea.
So today I'm gonna talk to you
a little bit about the work that we're doing
at the Gloucester Marine Genomics Institute, GMGI.
I joined GMGI in the summer of 2017 as a Science Director.
And really our focus here is bringing
new genetic technologies to the ocean
to really promote sustainable and healthy oceans
and uncover new discoveries
that impact fisheries and human health.
And so I think I can share my screen and get going here.
All righty, I'm gonna start
with this beautiful image from NASA,
which I think beautifully illustrates that the majority
of the surface of our planet is actually covered by water.
The oceans constitute more than 71%
of the surface of our planet,
but when you take into account that on average,
the oceans are about two and a half miles deep,
the oceans actually constitute greater than 90%
of the biosphere or the living space on this planet.
Now, the oceans are incredibly important
in sustaining life on the planet.
More than 50% of the oxygen in the atmosphere is created
by tiny ocean plants called phytoplankton.
The oceans are incredibly important in governing
climate and weather patterns on our planet.
The oceans of course, are important in providing food
to billions of inhabitants of our planet.
And also there's a tremendous array of biodiversity
that exists in the world's marine environments,
and it's this biodiversity
that really excites me about the oceans.
It's estimated that there are more
than a million different species
of plants and animals that live in the ocean.
And today, we probably only know about a quarter of those.
When you think about the microscopic life
that lives in the ocean,
the tiny bacteria and single-cell organisms,
we know a really tiny fraction.
It's estimated that could be between a hundred million
to a billion different species of bacteria in the ocean
of which we know only a tiny fraction.
So this line captures some of my
most favorite creatures in the ocean.
I'm just gotta pick up a pointer.
And starting up at the top corner here, this is the smallest
and most plentiful bacteria on the planet, this is SAR11.
And the combined weight of SAR11 in the oceans is greater
than the combined weight of all the fish in the sea,
and this tiny organism plays a vital role
in scaffolding elements on our planet.
And we go from this tiny, tiny bacteria to the oceans,
being home to the largest animals on the planet,
the largest animal being the blue whale.
The blue whale can attain length of over a hundred feet
and weigh more than 300,000 pounds, which is the equivalent
of more than 30 full grown elephants.
The oceans are also home
to the longest-lived animals on our planet.
And the longevity record goes to this little clam,
with the oldest individual so far
identified being 507 years.
Now, there are animals that are
perfectly adapted to extreme environments,
like the frigid polar regions of our planet,
and also adapted to extreme temperatures and pressures
at deep sea hydrothermal vents in the ocean.
And it's these adaptations that these organisms have
that really fascinate me and we can learn so much from.
And I think that most people appreciate the importance
of the oceans for the provision of food,
but I'm not sure that people really appreciate
the impact that ocean organisms have had
on science and biomedicine as well.
Historically, marine animals have been
really valuable models for scientific research,
and they've helped us to understand
really fundamental biological processes,
including many that are relevant to human health.
So a good way to look at this is to look at the Nobel prizes
that have been given out to work that has been done
using marine animals as models,
and there are seven of those today.
The sea star helped us to understand
the fundamentals of cellular immunology.
The giant axon of the squid helped us
to understand how nerve conduction works,
the eyes of the horseshoe crab were vital
to understand how sensory perception
and how our eyes perceive light and color works.
The the sea hares, little guy up here,
perhaps one of the cutest little animals in the ocean,
but it's also very smart and can exhibit
the three basic forms of learning.
And by coupling the ability to learn
with a very simple nervous system,
it allowed us to elucidate the neural circuitry
associated with learning and memory.
The sea urchin is another vitally important research model,
which attained two Nobel prizes,
one for understanding mitochondrial function
in the respiratory burst
and the other for understanding the proteins
that govern cell cycle and cell division,
which is critically important to understand
if we're gonna understand what happens
when we get cancer and we lose control of cell cycle.
So again, these wonderful biological adaptations
of these animals absolutely facilitated
all these seminal discoveries.
In addition to these biological adaptations,
marine organisms have amazing chemical adaptations.
They use a really unique chemicals for communication,
for defense against predators,
for defense against infection and disease,
and many of these molecules are becoming
very useful therapeutics in human disease.
There are now nine FDA-approved,
marine-derived drugs on the market.
Four of those are anti-cancer drugs.
Three are for lowering serum triglycerides.
One's an anti-infective and one is a medication for pain.
There are more than two dozen molecules from the sea
in clinical trials for various disease indication
and thousands of molecules in preclinical development.
So we're really finding a rich source of chemical diversity
that can have a tremendous impact on human health.
Now, of course, we're all for familiar
with the important role of the ocean in provision of food
and the United Nations Food and Agriculture Organization
estimates that anywhere between one to three billion people
on this planet depend on the ocean
as their primary source of food.
So the oceans are critically important,
but this is also a really critical time for our oceans.
So the United Nations monitors about 600 different species
of fish and seafood that are consumed by humans
and they estimate that more than 50% of them
are considered fully exploited
and another 24% are over exploited or completely depleted.
So overfishing is taking its toll on our oceans.
That, combined with the impacts of climate change,
where we have increasing temperature
and acidification of our oceans
are having a devastating effect on marine organisms.
In addition, we have the impacts
of pollution and plastics in particular.
So it's a really critical time for us
to start to think about building new tools,
to better understand the diversity that exists
in the world's marine environments
and tools to really help to mitigate some of the impacts
that we're having on the marine environment.
And so this is part of what we're trying to do at GMGI is
to bring new genetic and genomic technologies to the ocean
to better understand this amazing biodiversity,
to promote sustainable and healthy oceans
and to uncover new discoveries
that impact fisheries and human health
and we're doing this really using genomics as a foundation.
So genomics is really the study
of the genetic material or the DNA of any organism
and DNA is made up of these four
basic building blocks, G, A, T and C.
And it's really the order in which these building blocks
are arranged that determine all
the characteristics of an organism.
And so by sequencing the genome or determining the order
of these building blocks, really,
we can start to understand all of the capabilities,
all of the characteristics
and all of the adaptations of any organism.
Now, over the last several decades, we've really been going
through something of a genomics revolution.
And this is because the efficiency
at which we can read the sequence of the genome
is really increasing dramatically,
as well as the cost of doing so is decreasing dramatically.
So to give you an example,
the very first human genome that was sequenced
was a project that was started in 1990.
It took 13 years to accomplish.
Hundreds of scientists around the world
participated in this project.
It costs nearly three billion to complete.
Now with the technology that we have available,
we can sequence that same human genome
in about 48 hours for less than $1,000.
And so this has really opened up the field of genomics,
such that the genomes of every organism are available to us.
And we can use this technology to really understand
the full scope of biodiversity in any environment,
and really understand the characteristics
of the animals that live there,
and from that we can learn a lot that can benefit humankind.
And so today I'm speaking to you from GMGI's facility,
our research facility in Gloucester
on the Gloucester Harbor.
I'm sure many of you are familiar
that Gloucester is the oldest seaport in the country,
coming up to its 400th anniversary in year 2023.
And really the culture and the economy of the region has
really been inextricably linked to the sea.
Principally dependent on capture fisheries industry
and with the decline in capture fisheries
over recent decades,
it's really had a negative impact on the region.
And so the founders of GMGI really wanted to do something,
to build on this 400 years of maritime history,
to bring new technologies to the sea
and really promote sustainable use of ocean resources
and spark a new era of marine innovation
and marine commerce for the region.
And so the established GMGI and our mission
is to address critical challenges
facing our oceans, human health and the environment
through innovative scientific research in education.
And in order to achieve this mission,
we have a strategy that has three parts.
The first part is to establish a world class
marine research institute powered by genomics.
The second part is to create
a vibrant science community here in Gloucester.
By that, I mean, we'd like to promote
doing highly collaborative research,
attract scientists to come out
to Gloucester to attend conferences
and really to attract other scientific entities
to consider Gloucester as a great place to do science.
The third part of the strategy is to create
a vibrant science learning environment
to provide new STEM career opportunities
for the young people of our community.
So the flagship program there is called
the Gloucester Biotechnology Academy.
This is a 10-month intensive program.
It's a lab immersion, hands-on program
in which the students learn all of the techniques
to work in a modern genomics molecular biology lab,
either in biotech or in academic research.
It's been incredibly successful program
with 85% of the graduates going on
to full-time employment in the biotech industry.
And some of the graduates have actually gone
on to higher education as well,
including several students at Salem State University.
So it's been a wonderful program to provide new opportunity,
and it's been terrific to see these young people
get excited about science and to find themself able
to participate in the wonderful STEM economy
and STEM community in Massachusetts.
Now, my focus has really been on the Research Institute
and over the last 40 years at GMGI,
my role has been to devise our science strategy
to hire our science staff
and to oversee the building of our research facility.
So our science strategy is really based
on a platform of oceans and human health
and we have three focus areas:
biomedicine and biotechnology,
ecosystem function and health,
and fisheries and aquaculture.
So in the fisheries and aquaculture program, really there,
we're using genetic and genomic approaches
to promote sustainable fisheries in aquaculture
to ensure global food security.
In the ecosystem function and health program,
we're using genetic and genomic technologies
to really understand the full scope
of biodiversity of marine ecosystems,
how they function, how resilient they are,
and their ability to adapt to environmental change,
which is particularly important in light of climate change.
In our biomedicine and biotechnology program,
we have a number of different programs,
but we're principally interested in studying
the long-lived animals in the ocean
to gain a better understanding
of healthy aging, longevity and resistance to cancer.
So this slide captures some of the projects
that we have ongoing,
and they range from studying
the health of individual animals
to the health of whole ecosystems.
And they range from studying the smallest creatures
in the ocean, tiny little marine bacteria,
to some of the largest creatures in the ocean, like whales.
And so today I thought I'd just talk about a few
of these programs just to give you a flavor
of the work we're doing at GMGI
and how genomics really can help us
to better understand the world's oceans.
And I'll start right in our own backyard
in the Gulf of Maine.
And so the Gulf of Maine historically has been one
of the world's most productive fishing grounds.
It's an important whale feeding ground,
and it's home to a great array of biodiversity,
as shown over here.
In 2015, a paper was published,
and this is a figure from that paper
in which they measured sea surface
temperatures in decadal time scales
and this is a figure showing the sea surface
temperature change over the last decade
with the red color indicating
increasing warming of the ocean.
And you can see from this,
the Gulf of Maine is outlined in this little box here,
that it's an intensely red part of the ocean
indicating that the Gulf of Maine is actually warming
faster than 99% of the world's oceans.
So it's a pretty critical time for us to understand
what's going on in the Gulf of Maine
and how this changing conditions are going
to impact the organisms that live there.
We're really already seeing
some changes in distribution patterns
of some of the animals that live there.
And certainly, there'll be other effects as well
in terms of not just distribution,
but also timing of reproduction
and great impacts on this community.
So we really wanna start to understand
this part of the ocean to provide baseline of what's there
so that we can understand the impacts of climate change
and mitigate some of those impacts going forward.
So at GMGI, we focused our attention
on one part of the Gulf of Maine,
the Stellwagen Bank National Marine Sanctuary,
which is shown outlined by the red on this map over here.
To orientate you to where we are,
we're setting up here on the north shore,
right where this star is.
So Stellwagen Bank National Marine Sanctuary is part
of the national sanctuary network throughout the U.S.
It's one of 14 sanctuaries, and it was established in 1992.
NOAA oversees the sanctuary and they're responsible for it
for managing everything that happens in the sanctuary.
Now, if you look at this map,
this is the topological map showing you
the bottom of the sea floor,
you see that it's very unique part of the ocean,
where you have a lot of deep valleys,
as well as these plateaus.
And this is what creates
this really unique environment here,
'cause what happens is very nutrient-rich waters
from the Atlantic are really forced up
to the surface, the sunlit surface,
where you really get a flourish of plankton,
which then attracts and supports a lot of other animals,
and this is historically why this is
such a productive part of the ocean.
Now I mentioned NOAA oversees the sanctuary
and biodiversity conservation is one
of their key management objectives.
NOAA has recorded the presence of 72 different species
of fish in the sanctuary and more than 17 species
of cetaceans, whales and dolphins,
and a vast array of invertebrates,
but the technology NOAA uses to assess the biodiversity
are really traditional technologies
using cameras or (indistinct)
to see what's present in these waters.
Now, although this gives you a great view
of some of the macro flora and fauna,
it's missing a lot of the smaller organisms,
the microscopic organisms.
And really we wanted to see if we could use
a genetic approach to try and enhance our understanding
of the full scale of biodiversity
in this unique marine environment.
And so we did this using a technique
called environmental DNA
and environmental DNA is really based on the premise
that anytime any organism interacts with its environment,
it's always leaving a trail of DNA behind.
So as you're sitting in your chair right now
or standing where you are,
you will drop some skin cells
and maybe a few hair follicles.
You will leave a signature that you have been in that space
and that occurs in the ocean as well.
As the fish is swimming through the water,
it's shedding cells, it's excreting into the seawater,
it's leaving a trail of DNA behind it.
And so you don't actually have to catch the fish
or see the whale to know it's been there.
You can just take a sample of seawater,
filter out all the cells and DNA, sequence that,
and then you know what's been present in that body of water.
And we can look at both the water
as well as the sediment to get an idea
of the diversity of organisms, both living there,
the bacteria and other things that are present living there,
or the animals and plants that have passed by.
So sediment is collected with a device
like this one called a grab, which has a jaw open
when it's lowered to the bottom of the ocean,
and then the jaw snaps shut to collect sediment
and water is collected through this device
called a Niskin bottle, which is really just an open tube
that has a trap door on the top and bottom.
And it's lowered to the depth that you wanna collect water,
and then you send a trigger down,
which snaps the top and the bottom shut
and captures a parcel of water.
And you can bring the sediment and the water into the lab.
For the water, to process it,
you put it through a filter to collect all the cells and DNA
on the filter so that you can extract them.
And for this sediment, we just simply take a little scoop
full of sediment and extract DNA from it.
So we can extract the DNA, amplify gene regions
that we can use to identify different species,
we can then sequence those regions of the genome,
we can then analyze the sequences,
and then that tells us a picture of the biodiversity
that is present in those samples.
Now the power of eDNA is that you can answer
a lot of different questions.
You can actually look at the full scale of biodiversity,
so you can see all of the organisms
that are present in those samples.
You can just focus on certain taxonomic groups.
So you may only wanna know all of the fishes
that are there, or all of the bacteria,
or you can just ask the question,
is there a particular species present?
So for example, you may wanna know,
is there a signal from a white whale
that has passed through this water in recent few days?
And so you can just target that species.
So very, very powerful way to look
at what's present in the water,
which provides an alternative to the traditional approaches
and augments the traditional approaches
that we use like (indistinct) and cameras.
So in our first studies at GMGI,
we took some sediment samples from the northwest corner
of the Stellwagen Bank National Marine Sanctuary.
These are the three sites we collected samples from.
We collected them over a couple of seasons.
We brought those back to the lab, extracted DNA,
and then sequenced the DNA that was present.
And we looked basically at two groups.
We amplified the 16S ribosomal RNA section of the genome
to give an indication of all
the prokaryotes that are present
and we amplified the 18S ribosomal RNA
sequence of the genome to give us an indication
of all the eukaryotes that are present.
So these pie charts are just showing you a distribution
of all the different bacteria and archaea phyla
that were unearthed in the study
and all the different of eukaryotes.
So what was remarkable about the study was
that (Andrea clears throat) just by looking at the sediment
samples from this tiny part of the sanctuary,
we identified 127 different phyla organisms.
This was remarkable because using traditional approaches,
the standard way that NOAA has been assessing the sanctuary,
the biodiversity assessment before this genetic assessment
only contained 12 phyla.
So by doing this small genetic study,
we added 115 new phyla to the biodiversity assessment
of Stellwagen, and this included organisms
across many different areas of life,
bacteria, archaea, animals, chromista,
protozoa, plantae and fungi.
So it was really showing the power of genomics and genetics
to really understand the full scale of diversity
of what was present in the sanctuary.
So NOAA was excited by these initial results
and invited us back this summer to accompany them
on their annual survey, in which we collected surface water,
bottom water and sediment in 30 sites
in the southern part of the sanctuary.
So we're just analyzing those now,
but the hope is that we can really build a framework
for integrating genetic information
into their biodiversity assessment
to better understand the full scale
of biodiversity that's in the sanctuary,
provide a baseline so that we can understand and monitor
changes that are occurring with the changing climate
and the changing conditions with climate change.
Now at GMGI, we're not limited to studying our own backyard.
Through collaborations, we can get out
into the broader ocean and ask questions
throughout the global oceans.
We have a wonderful collaboration with a group called OceanX
and OceanX have this wonderful ship,
which is designed for ocean exploration,
ocean resource and documentary filmmaking.
So GMGI had the great pleasure of joining an expedition
with OceanX that started in the Azores,
summer in July, and ended up in Norway.
And there were two components to this cruise that GMGI led.
One was an education component and one was research.
The education component was really providing an opportunity
for undergraduate students from underrepresented groups
to experience life at sea and to really experience
what it would be like to be an oceanography,
for a marine biology, or participating in the marine trades.
The research part of this component was
a really unique opportunity to collect some genetic samples
from an extreme environment in the ocean.
The Moytirra hydrothermal vent lies north
of the Azores on the North Atlantic Ridge.
These hydrothermal vents are
really unique parts of the ocean.
They typically occur in areas
where tectonic plates come together,
and there are cracks within the Earth's crust
where seawater can seep below the crust, mix with magma,
and then you see this plume of seawater that's carrying
a lot of minerals and other things into the ocean.
This is a really extreme environment.
The temperature of the water that comes out of the deep sea
hydrothermal bed can reach as hot as 400 degrees Celsius.
It's very, very rich in minerals and heavy metals.
The pH is about two, and there's enormous pressure.
This particular hydrothermal is at 2,900 meters
below the surface of the sea.
So under these conditions,
and there are many biology students
in the audience today, you're thinking,
how can anything survive under these conditions?
We know that proteins and nucleic acids will denature
if you expose them to acidic conditions or temperature.
So this is a part of the ocean where you wouldn't expect
any life to occur, and yet life thrives
at these deep sea hydrothermal vents.
And so really it's a really cool opportunity to understand
what are the organisms that live there
and how are they adapted to living
under these extreme conditions.
And so we were able to collect water samples
around the deep sea hydrothermal vent,
bringing them back to the ship and filter them.
And we've now have them in the lab where we've extracted
all the DNA and RNA in these samples
so that we can see not only what's there,
what are the organisms present in this extreme environment,
but by looking at gene expression in RNA,
we can look at what they're doing there.
And so we have this tremendous opportunity to apply
our genetic skills to questions in the global oceans.
Now, in addition to looking at health of ecosystems,
we can also apply our genetic and genomic approaches
to look at the health of individual animals.
And we have this wonderful collaboration
with a group called Ocean Alliance,
in which we're looking at the microbiome
of the whale respiratory track
as a way of judging the health of individual whales.
Now, Ocean Alliance is an organization
that's been around since 1971,
and they're committed to preserving
and conserving whales in the ocean.
And in 2014, they using drones
as a noninvasive technology to monitor whale populations.
So they can use the drones to capture images
and videos of the whales,
but they can also collect biological samples with the drones
by attaching Petri dishes to the drones,
and then flying it through the blow when the whale surfaces.
And so this is a project that we're collaborating
with Ocean Alliance to look at the microbes,
the bacteria that live within the respiratory tract
of the whale to see if we can get an indication
of what would be a healthy microbiome
or when a whale's health may be compromised.
So this drone with the Petri dishes attached has been named
the SnotBot for collecting whale snot.
And the way this works from a genetic perspective is
the snot is collected onto the Petri dishes,
and then we can collect the snot
with a sterile swab, a Q-Tip,
and then put that into a preservative,
bring it back to the lab, extract DNA from that,
amplify regions of the DNA,
in this case, we're interested in all
the microbes present in the samples,
and then we can sequence them to look the diversity
of the microbes that exist in the whale blow.
And so this is a chart that's showing,
(Andrea clears throat) excuse me,
the relative abundance of various classes of bacteria
and this is in a number of humpback whale samples
that we collected the first summer
we worked with Ocean Alliance
and it was compared to the first two bars,
which are the microbes that are present just in seawater.
So you can see many of the microbes present in seawater,
of course, are also present in the blow samples,
but there are some unique bacteria that are present
in the blow samples that are characteristics
of mammalian respiratory tract.
So for example,
these light orange bars here are actinobacteria,
The bright pink bars are fusobacteria,
and the bright blue bars here are bacilli.
And that represents organisms that are
very common to us in our respiratory tracts,
such as staphylococcus and streptococcus.
So this is representing a pattern from humpback whales.
We've now collected or Ocean Alliance has now collected
(indistinct) with samples from blue whales.
This is a beautiful image of a blue whale mother and calf.
They've also brought us in some samples of sperm whales
that they've collected from the Azores.
(Andrea clears throat)
And so the idea here is to look at the profile of microbes
that are present in the blow of individual whales,
look at how they change over time in individuals,
so from season to season,
and how it differs from different species.
And then can we look at these data in determining
what a healthy microbiome looks like
and what a microbiome looks like
in a whale whose health is compromised
by comparing the genetic data with the other data
that's collected with the drones.
And so we hope to continue to expand this project,
to create this noninvasive tool,
to provide an indication of whale health.
Now, switching over to fisheries,
I wanted to talk a little bit about some
of the iconic species of New England
and one of those is Atlantic cod.
Cod has a pretty wide range,
ranging from North Carolina up through the Sea of Labrador,
around the coast of Greenland and Iceland
throughout the North Sea and into the Arctic Ocean here.
And of course it's been fished for thousands of years.
In fact, Northern European fishers
have followed cod over to North America.
Now because it's been so intensely fished,
there are tremendous records dating back to the 1800s.
And this is a graph showing the amount of cod landed in tons
from 1850 all the way to year 2000.
What you can see from this is when you look
from the year 1850 to year 1960,
you can see that the amount of cod landed oscillates
between about 100,000 to 300,000 tons.
And really there's sort of a slow increase
in the amount of cod that's caught over time.
But something quite remarkable happens in 1960,
where you'd see this tremendous increase
in the number of cods landed in a very short period of time.
Now, this is a result of technology boom
in the fishing industry.
This is where we started using sonar and radar.
There was the introduction of factory trollers,
which had the ability to process
and freeze fish while they were at sea
so they could stay out at sea longer
and catch larger amounts of fish.
And so it really had a tremendous ability
to bring in more fish than historically was possible.
Unfortunately for cod, this resulted in a tragic collapse
of the population from overfishing.
And because of this, the government stepped in
to pass the Magnuson-Stevens Act,
which really was a law to really introduce
new fishery management strategies,
to try and prevent overfishing,
and also to try and rebuild these collapsed fishery stocks.
A couple of the things that Magnuson and Stevens Act did
were one, was to extend the fishing boundaries in the U.S.
from 12 nautical miles to 200 nautical miles,
meaning that foreign fishing vessels could not fish
within 200 miles of the U.S. coast.
The other thing was to introduce science-based catch limits
to try and prevent overfishing.
Unfortunately, it was a little bit too late for cod
and the population continued to decrease
and collapse to an all-time low in 1992,
and still has not recovered
(Andrea clears throat) from this collapse.
And so there's intense effort by fishers
and fisheries managers to really understand
the current populations of cod
and anything that can be done to sustain
and help to rebuild the population.
So recently there was a large group called
the Atlantic Cod Stock Structure Working Group
who got together and created a large collection of data
with all of the data they have on cod in the Gulf of Maine
and from the data they established that there were
about five different subpopulations of cod.
Three of these populations were geographically isolated,
so they could follow the progress of them,
but two of these populations were a little more problematic,
'cause they share the same area of the Gulf of Maine.
In fact, they spawn in the same area of Gulf of Maine.
The only thing that separates them
is that they spawn at different times of year.
So the winter spawners spawn between November and December
and the spring spawners spawn between May and June.
So these are genetically distinct populations of fish,
but they're possible to tell apart by looking at them
and they share the same area.
So there's no way to know how these two
individual populations are doing.
So together with the Division of Marine Fisheries,
our fisheries team decided to take a genetics approach
to try and devise a small panel of genetic markers
that would allow the fisheries manager
to tell the difference between these two populations.
So Division of Marine Fisheries went out
to collect samples, hundreds of samples of cod,
from these two different spawning grounds.
So they'd go out in the spring spawning season
and collect fish that were in spawning condition
from the spring spawning group
and they went out in the winter spawning season
and collect fish in spawning condition in the winter group.
And they provided fin clips
of these hundreds of animals to GMGI.
So our fisheries team extracted the DNA
from these fin clips and sequenced the full genome
of more than 200 individual cod.
Then they took these genome sequences
and aligned them together
and looked for variations across the genome.
They found there were more than 3,000 areas
of the genome that showed variation.
These are called single nucleotide polymorphisms.
And then with some mathematical computational work,
they could reduce these three million variations
down to a panel of only just 25 sites in the genome.
So 25 variations which would allow them to distinguish
spring from winter spawners, with an 88.5% assignment rate.
So by looking at just 25 variants in the genome,
the fisheries managers can tell the difference
between these two populations of fish.
And at the same time, they found that it was quite easy
to devise a panel that could distinguish males from females.
And so they've now created these two wonderful tools
that fisheries managers can use
to take any fish cod anytime, anywhere,
and assign it back to these spawning grounds
so that they can really understand the contributions
of these two spawning grounds to the overall population.
And this is actually pretty critically important
because what's been realized is
that spring spawning group is in decline
and they're contributing
very little fish to the overall population.
So understanding why that's happening
and protecting the spring spawners is
really a priority for fisheries management.
Another iconic species that we're
interested in is American Lobster.
The lobster is the most valuable single species
fisheries in the United States.
In 2019, 126 million pounds of lobster were landed,
representing $630 million in value.
The lobster lives for a long time.
This is one of the things I'm really fascinated about.
Of course, the lobster grows by stepwise process of molting.
So it sheds its hard parts,
which makes it very high, hard to age a lobster,
but it's estimated that lobsters live
for greater than 50 years, perhaps as long as 100 years.
And even though they're long lived,
there are very few reported cases of cancer.
It's a very interesting animal to understand how it lives
so long and avoids getting cancer in its long life.
Historically, the lobster has been
a classic model for neuroscience.
And so it's been really important for understanding
processes like repetitive motion,
like the beating of the heart, walking, chewing,
and also the sensory nervous system.
And also the lobster is susceptible
to the impacts of climate change.
So it's a pretty important time to start understanding more
about the biology of this animal.
When you look at lobster landings since 1982 to present day,
there are two stocks, the Southern New England stock,
which is shown with the red line,
and the Gulf of Maine or Georges Bank stock,
which is shown by the blue line.
And what you see over the last decade or couple decades
is that the Southern New England stock
has reached an all-time low.
Whereas the Gulf of Maine and Georges Bank stock
has reached an all-time high.
And this is thought to be because of the changing conditions
in the Gulf of Maine and the lobster migrating northward,
to stay in the cooler waters.
In addition to this northward migration of lobsters
with warming waters in Southern New England,
we're also seeing an increase incidence
of shell disease in lobster.
And this is a devastating bacterial infection,
degrades the shell of the lobster,
ultimately causing its mortality because it fails to molt.
And so this is a critical time to start understanding
and providing tools that we can better understand
the interesting biology of these animals
and create tools for the fisheries to better manage it
as it is undergoing changes with respect to climate change.
So we undertook the project
to sequence a genome of the American Lobster.
This was a collaborative project that took place
between GMGI and scientists from Tufts University,
Harvard, Johns Hopkins, University of Florida,
Dalhousie University in Nova Scotia
and the University of Prince Edward Island
in Canada as well.
It was a project that took us years to accomplish
and that's because this lobster genome turned out
to be much more challenging than we anticipated.
The size of the lobster genome is
about the same size as the human genome.
That means it has about three billion building blocks
or nucleotides or base pairs.
And the problem isn't the size of the genome.
The problem is the lobster genome
is full of repetitive sequences.
So there are certain sequences of nucleotides that are
repeated over and over and over again in the genome.
In fact, 80% of the genome is
made up of repetitive sequences.
So this posed a lot of technical problems for sequencing
through these repetitive regions,
but it also caused tremendous challenges
for assembling the genome
and putting the genome pieces back together again.
You can imagine it was like doing a puzzle
with three billion pieces where 80% of the pieces
were exactly the same color and exactly the same shape,
really hard to know how to fit those pieces together.
So after years of effort, we finally assembled
a reasonably good genome of the lobster.
And this now provides a great resource
for the scientific community, the research community,
the fisheries community to build upon.
From my perspective, I'm particularly interested
in the longevity of this animal.
And so I wanted to see if we could look at the genes
and get a hint as to why the lobster
has such a long and healthy life.
In its genome we could predict
more than 25,000 individual genes.
What was interesting about that is
when we look at those genes and infer their function
by comparison to known genes,
we find that more than a third of the genomes
in the genome are completely uncharacterized.
They have novel functions.
They don't match anything that exists
in a characterized database.
So there's a lot of biology of these animals
that we just don't understand and so much more to learn.
But when we looked at the genes of this animal,
what we did was to look at what gene families were expanded
and contracted compared to closely related crustaceans,
crayfish, shrimp, and daphnia
(Andrea clears throat) as example.
Now all these other crustaceans are very short lived.
They live for anywhere from 54 days to 3 years
and the lobster of course lives for more than 50 years.
So a nice comparison to see what parts of the genome
are responsible for this longevity,
and there were some tremendous clues here.
So these numbers on this biogenetic tree here
are showing that 821 gene families were expanded
in the lobster relative to its closest neighbor
and 2,445 gene families were contracted
in the lobster genome relative to its neighbors.
Now, we didn't get much information
about the genes that were contracted
because many of them had unknown function,
but within the genes that were expanded,
there was a tremendous amount of interesting opportunity,
which indicated the lobster has really invested a lot
in physical, biological and chemical defense mechanisms.
There was a tremendous expansion of genes
involved in its shell formation,
so giving it a tremendous physical defense,
an expansion of genes involved in innate immunity,
allowing the lobster to defend itself
against bacterial infections,
and also an expansion of genes
that involved in chemical defense
to protect this animal from chemicals
that it might encounter in the environment.
There was an increase in genes
associated with genome stability.
And this may be part of the reason
we don't see cancer in lobsters
and also some very interesting expansion
of its nervous system,
including expansion of its sensory nervous system.
So really all of these characteristics are part and parcel
why this animal lives so long and its ecological success
in the benthic marine environment.
So the lobster is not the only long-lived animal
that I'm interested in.
In fact, the oceans are home to all
of the longest living animals on the planet.
The longest living mammal on the planet is the bowhead whale
estimated to live for more than 200 years.
The Greenland shark is the longest lived vertebrate
on the planet living for nearly 400 years
and the quahog clam is the longest lived invertebrate
on the planet living for more than 500 years.
This is only outdone by this little jellyfish up here,
which is reported to be
the only immortal animal on the planet,
going from this fully formed adult stage
to reverting to an embryonic stage
and back to an adult continuously.
And so it's the only organism we know
of that's achieved immortality.
Now these in animals are really interesting
and I'd love to look at their genomes
to understand the secrets they hold,
but these animals are really
also very challenging to study in the lab,
very difficult to study big marine animals
or a colony of shark or clams burying in the sea bottom.
So I've turned my attention to sea urchins
and the red sea urchin is among one
of the Earth's longest living animals
living for more than 200 years.
And sea urchins are an interesting model
because they've been a model
for scientific research for centuries.
There's lots of labs that study them,
there are a lot of tools available to study them
and they're really easy to keep and handle in the lab.
And so I'm gonna, in the interest of time,
I'm just gonna go through the last slides
a little bit more quickly
so that there's time for questions,
but what I focused in on the sea urchins
is a very closely related species
at very different natural life spans.
Where some species of sea urchins
only live for a short time, 4 to 10 years in the wild,
other species can live for more than 200 years in the wild.
So nature's provided a lovely model system
to do comparative genomics to understand
why this animal is living only a short life span
where this closely related cousin
can live for more than 200 years.
The other thing that's interesting about these animals is
not just their difference in longevity,
but they appear to show no signs of aging,
and what I mean by that is they grow
and reproduce throughout their lifespan.
There's no increase in mortality rate
associated with getting older,
no increase incidence of disease
associated with getting older,
and that includes no reported cases of cancer.
And so we're doing comparative studies to try and understand
what's the difference between these animals
that defines their different lifespans
and how do they remain healthy throughout their lives?
How do they avoid cancer throughout their lives?
And so we've been working on the genome
for the red sea urchin,
which is proving to be much more easy than the lobster.
We now have the genome assembled into 24 pieces,
which equal to 24 chromosomes.
So we have chromosome length assembly of this animal,
which allows us to now compare it
to other sea urchin species.
And we also wanna do comparison between animals
that are resistant to cancer,
like the long-lived sea urchin, lobsters and bowhead whales,
and compare their genomics to marine animals
that are highly susceptible to cancer,
like some species of bivalve, like the soft-shell clam,
some fish and some marine mammals.
In addition to (Andrea clears throat) neoplastic disease,
we're also interested in building tools
to understand infectious disease in the marine environment.
Infectious disease is increasing with warming waters,
as I mentioned already for the lobster,
but infectious disease is also a problem in agriculture
where animals are grown in hot density
and diseases spread rapidly.
And so just very quickly,
we're building new next-generation tools
together with collaborators at MIT and University of Arizona
using CRISPR technology to create diagnostic tools.
CRISPR, it's something that I'm sure
most people have heard about now.
It's a ribonucleoprotein,
it's part of a bacterial defense mechanism against viruses,
and it has the ability to hone in on specific sequences
of nucleic acids and then cleave them.
And so we can create diagnostic tools
that when a certain sequence is detected,
it can cleave a reporter and give a very sensitive output.
So we've been focusing our attention
on diseases that impact aquaculture
to viral diseases in shrimp,
white spot syndrome virus being one of them,
and have designed an assay
that can detect down to one viral copy
and is very specific to detecting this.
But the beautiful thing about these CRISPR-based diagnostics
is not just their sensitivity and specificity,
but they can be adopted to very simple assays,
like the lateral flow assays.
I think people are becoming very familiar with these
'cause these are similar type of assays
you do with the at-home COVID test.
And this actually is very powerful because it would allow
resource managers and fisheries managers
to have a very simple test in which they can
quickly detect the presence of pathogens
and quickly respond to mitigate the impacts
on their ecosystems and in aquaculture scenarios.
So with that, I'm gonna just acknowledge all of the people
at GMGI who contributed to the work that we're doing.
There are 11 members of our research team at the moment.
So we're a small group, a very talented group of scientists.
And so I wanted to thank all of our researchers
for all of the work that that we're doing at GMGI.
In addition, I wanna thank all of our collaborators.
We have wonderful collaborators
and all of our supporters who provide us
with the financial support to do
the work that we're doing at GMGI.
And with that, I'd be happy to take any questions
from the audience and welcome you to visit our facility
in Gloucester at sometime in the future.
Sorry, I realize I covered a lot of ground there,
but hopefully everyone found something interesting
and there's some questions from the audience.
- Thank you so much, Dr. Bodnar. That was fascinating.
And there are lots of questions
and I'm gonna start off with a question from a student.
"What is the length of time in which eDNA measures?
Is it hours, days, et cetera?"
- That's a wonderful question
and it's actually quite variable.
It depends on the conditions of the ocean.
So because the oceans are so dynamic,
the signal can last from anywhere from hours,
or hours to days, but typically not longer than days.
So it does give you a very recent snapshot
of what's been present.
The things that we have to take into account are currents,
which will carry the eDNA away,
also the depth at which we're collecting water.
So in the surface waters,
UV radiation will help to degrade DNA quicker.
And if in deeper waters, the cold will help to preserve DNA.
So we really have to take in the environmental conditions
into account when we're interpreting data,
but generally speaking, it's generally in the order of days.
And so we're really seeing a recent snapshot
of what's present in the marine environment.
- Thank you, Dr. Bodnar.
This is Ethel Gordon,
also from the Darwin Festival committee.
I'm gonna ask a question from one of our colleagues.
"Do you look for any viruses in whale blow
or other metagenomic analyses and what gene is targeted?"
- Yeah, so so far all we've looked
at are the bacterial profile.
So we've been targeting the 16S ribosomal RNA gene for that.
We are really interested in looking at viruses
and I think everybody's thinking
about respiratory viruses over the last few years,
but we haven't yet designed our primers yet
to look at viral sequences,
but we've connected with a lab that does a lot
of looking at viruses throughout the ocean
and we hope to add that to that analysis
so we can start to look at the viral profiles
that are present in the respiratory tract of whales.
- [Ethel] Thank you.
- There's another question from a student.
"Have you done similar work in fresh water areas in Maine?
There are some pretty remote bodies of water
in northern Maine, and I'd love to know if there is any sort
of genetic variability due to their seclusion."
- Yeah, that's an excellent question
and eDNA technologies are being used
in both marine and freshwater environments.
We haven't done much work in freshwater environments,
but there are groups that are looking at that.
And it's a wonderful way to look at the full diversity
of those unique ecosystems and really to understand
what's there and what they're doing there.
It's a great way to look at that question.
(Andrea clears throat)
- I have another question from a student.
"How does finding these organisms from sediments
in water samples connect to evolution?"
- Oh, that's another great question.
And so again, we can, by looking at the genetic sequence,
we can infer the relationship between the organisms
and draft those wonderful trees,
which help us look back in time.
And so it is possible to get an idea
of sort of the rate of evolution of different organisms
and the scope of evolution
by looking at the genetic patterns.
So really looking at it through the variation
in the various genetic sequences
that you can unearth from these technologies
and looking them from a more
from a phylogenetic point of view.
So putting them in relationship, one to the other.
So you can certainly can infer
evolutionary information from the analysis.
- Here's another question.
"How are animals like Greenland sharks
and urchins able to live so long?
Is it because they have a slower metabolism
that they burn energy at a slower rate
than less stationary animals?"
- Yeah, that's another great question.
And certainly metabolism is a very important part of aging
and things that do slow down their metabolism,
typically slow down the accumulation
of damaging their tissue.
So that's part of the secret of their success,
but I think it's much more complicated than that
and there are many parts (Andrea chuckles) to that question.
We find that they can maintain stability of their genome,
which is a really important part of aging.
So by maintaining, for example,
the caps at the end of the chromosomes' telomeres,
these animals maintain their telomeres.
Whereas aging animals shorten their telomeres.
Some of these animals, sea urchins in particular
have wonderful regenerative properties.
So they can continually regenerate tissues
presumably from stem cell compartments.
So they're constantly removing damaged tissue
and replacing it with healthy new tissue
from this regenerative process.
So there are a lot of different mechanisms
by which these animals are living a long time.
One of the most remarkable studies we did recently
with the red sea urchin was to look
at the gene expression in its nervous system.
And we see that the gene expression in its nervous system
is so completely different from the gene expression
in the aging nervous system of humans and aging animals.
They're really preserving their nervous system
in a very unique way.
And so preservation of the nervous system may also be key
because the nervous system, of course,
innervates the whole body
and preserving the nervous system may systemically preserve
the health of the animal for centuries.
- I'd like to ask another question from the audience.
"Do we see the shell-eating bacteria
in only the American Lobster
or do you see it affecting other crustaceans?
Is it only present in salt water?"
- Yeah, unfortunately I don't know
the answer to that question.
That's a great question.
It's something I'll have to look into more.
Certainly it is in lobsters,
but I don't know if that also transfers
to other crustaceans, for example.
So that's sounds thing I'm afraid I can't answer,
but great question.
- [Ethel] Thank you.
- Another question, "any opportunities for internships,
undergraduate research?"
- Yeah, we're very small still.
We're hoping to establish an internship program
in the summer and in the summer months going forward.
At the moment, it's been a little bit
of an ad hoc (Andrea chuckles) process,
but we're certainly interested in,
when we can and when we have funding,
to have students and to have the opportunity
to train students in the lab.
So if you're interested,
please feel free to send your CV onto us
with a cover letter, expressing your interest in the ocean.
And we'd be happy to consider that
for when opportunities do come up in the future.
- Another question from the audience.
"How is the Turritopsis dohrnii proven immortal?"
- Yeah, I think because it has such a unique mechanism
that when it encounters stress in the environment,
it can revert and essentially de-differentiate
into an embryonic state,
which is a very unique part of its biology.
And then when conditions improve,
it will then progress through the embryonic development
and reform an adult.
And so it's through going through this sort of process
of a fully-formed adult, reverting back to an embryo,
and then going back to an embryo,
this continual process is how it's achieved immortality.
Although I think one caveat to that is
I think we all know it's impossible to achieve immortality
because we can't account for accidents
and eventually these things are eaten
by other things and meet their demise. (Andrea laughs)
So unfortunately, theoretically immortal,
but practically speaking, immortality is quite elusive.
- We have another question.
"Do you have any intention in the future to do
the same research at other countries, such as in Africa,
since a lot of people like to eat seafood in those areas?"
- Yeah. That's another great question.
And we'd love to bring these genetic technologies
to promote sustainable fisheries in aquaculture globally.
And I think we'd love to bring the skills and the talents
that we have to address questions throughout the globe
and I think Africa is a particularly interesting scenario
as the growth of aquaculture is tremendous right now.
And if we can bring tools and techniques
to make that more sustainable, I think that would be
a tremendous contribution to global aquaculture practices.
So that's something that definitely is on our radar.
We'd love to find a way to make an impact globally.
- [Nelson] Cool.
- Another question from the audience is,
"What do you mean by the three forms
of learning in the seahorse?"
- Oh, okay. That's in the sea hare.
And the three basic forms of learning are
classical conditioning, habituation and sensitization.
And so basically the different types of reflexes,
some that are learned (Andrea chuckles)
and some that are more of a reflex.
And so each of them have a different
neurocircuitry associated with them.
And so you can think about sort of classical conditioning.
So studies that they did with the dogs,
where they ring the bell and feed the dogs
so the dog would only have to hear the bell
and then start salivating
'cause they know the food is coming.
The sea hare is capable of that level of learning
and having some kind of stimulus
that actually invokes a response.
And so those sort of sensitization, habituation,
and classical conditioning are the three forms of learning
that this relatively primitive animal
can exhibit all three forms of learning.
- And then I think we'll end with one last question.
"How is the age of a lobster determined?
Just size, since there's no tree rings
when it sheds its skeleton?"
- Yeah, another great question,
'cause it's very, very challenging to do so.
Typically we age these animals through looking
at the hard parts of the animal,
which we do with sea urchins and bivalves and other
because when they grow, they lay down shell
in a seasonal growth pattern.
So you can count growth rings,
similar to counting growth rings on a tree.
The lobster creates a serious problem
because it sheds its hard parts when it molts.
So through growth kinetics,
so looking at the growth characteristics
of these animals over time
and also by looking at the accumulation
of something called lipofuscin in the tissues
are two methods by which people
have assigned age to lobster,
but there's a tremendous error in those estimates.
And so we really don't know for sure how long lobsters live.
And so that's another interesting problem.
If we could find a biological indicator of aging,
it would be a wonderful tool for these animals
where they're challenging to age.
- Wonderful, thank you so much for of your time
and your wonderful talk and presentation.