Seminar Notes

Winter Biology

Hope St. John: Odegaard Writing & Research Center, Peer Review

Navigate

• What is the OWRC?
• Services OWRC Provides
• Peer Review as Conversation
• Past Experiences with Peer Review
• Establishing a Community Agreement
• A Question Based Approach

What is the OWRC?

• A free resource open to anyone on campus.
• How can asking the right questions get researchers and writers further?
• Asking questions can be a generative thing for those asking and recieving them.

Services OWRC Provides

• One-on-one apointments - 45-minute meetings with a peer writing tutor
• Targeted learning communities - small group sessions with a peer writing tutor to build writing, language, and cultural skills
• Satellite site appointments - specialized writing appointments for students in the College of Education and Health Sciences.
• All free!

Peer Review as Conversation

• What is peer review?
• How can we think of peer review as a conversational process?
  • Exchanging ideas and feedback - the whole dynamic of asking questions.
  • You are not bound to your reviewer, but it is an oppurtunity to think about the choices you make in your writing, and to be able to approach those conciously.
  • Audience is a very important component.
  • Conversation with literature - your peer reviewer will have some familiarity, but there is a dynamic of conversation with the literature.
    • Who are you in conversation with?
• Peer review is a dialogue between writers and reviewers.
  • Discussion of the ideas being presented and how they are presented.

Past Experiences with Peer Review

• What has been your past experience with peer review?
• Challenges of past peer review experiences?
• Successes of past peer review experiences?

Establishing a Community Agreement

• A document that oulines your group’s mutually agreed-upon goals and expectations for an activity or process.
• For peer review, consdier:
  • How would you like feedback to be conveyed?
  • As a writer, what are your expectations from your peer reviewers?
  • As a peer reviewer, what can you do to provide helpful feedback?

A Question Based Approach

• Understand why questions help the reviewer and the writer.
• Explore kinds of questions you can ask.
• Generate example quesitons to ask writers.

Julie Mathieu: Pluripotent Stem Cells, Regenerative Medicine, and Genome Editing

Navigate

• Introduction
• Stem Cells
  • Stem Cell Potency
  • From Zygote to Newborn
  • Human Embryo Development
• Why study/use pluripotent stem cells?
  • Regenerative Medicine
• Embyronic Development
  • Embyronic Diapause in Mice
• Ellison Stem Cell Core
  • Research
• Genome Editing
  • CRISPR Technology
  • CRISPR gRNA/enzyme complex
• Example of a Project: Study of a Mutation Causing Cardiac Disease
• Regulatory and Ethical Questions
  • Use of Embyronic Stem Cells
  • UW GIM36
  • Gene Editing of Human Embryos

Introduction

• Juie Mathieu, PhD; Assistant Professor, UW
• PhD in Paris at Saint Louis Hospital; worked on apoptosis.
• Post-doctoral worker at UW - work on stem cells and early steps of human development.
• Assistant Professor and Director at Stem Cell Core.
• ISCRM: Institute for Stem Cells and Regenerative Medicine.
  • People work on animal models, stem cells, embryos, differentiating pluripotent stem cells into different lineages.
  • 3-d printing and bioengineering work.

Stem Cells

• Characteristics of stem cells: self renewal (can divide for very long times) and differentiation (into different lineages)
• Two types of stem cells:
  • Adult stem cells (can be found in almost every organ)
  • Embryonic stem cells (blastocyst containing pluripotent stem cell)

Stem Cell Potency

• Can be divided iby their potency, what they can give rise to.
  • Totipotent embryonic stem cell, can give rise to ~80 cells
  • Pluripotent embyronic stem cells
  • multipotent stem cells, much more restricted in specialization
• Yamanaka generate iPS pluripotent cells from somatic cells.
• Main focus of the Ellison stem cell core - pluripoptent embyronic stem cells.

From Zygote to Newborn

• Cells begin dividing to form the blastocyst; inner cell mass divides into all sorts of other cells in the body.
• More than 50% of all fertilized eggs fail to develop.
  • A big issue for couples trying to conceive.
  • In Vitro fertilization success rate is 12% - very low, still.
• Understanding early steps and the rise of a human being is very interesting to study.

Human Embryo Development

• Uterus implants; before it implants, it is a “blastocyst”.
  • Inner cell mass is where embryonic stem cells are developed.
• Done in 1998 - Human ESC (hESC) established.
• Inner cell mass from blastocysts have properties:
  • self renewal
  • virtually unlimited cell division
  • pluripotent
  • express a specific set of markers

Why study/use pluripotent stem cells?

• Basic biology - to understand early steps fo development
• Improvement of In Vitro fertilization
• Disease modelling
• Drug therapy

Regenerative Medicine

• Replacing or “regenerating” human cells, tissues, or organs to restore normal function.
• Potential use of stem cells for lots od fiferent diseases.
• Focus of Mathieu’s research is on basic biology and improvement of in-vitro fertilization.

Embyronic Development

• Naive hESC and primed hESC; even if they are very close to each other in terms of time and development, they are very different.
• In terms of epigenetic regulation, metabolism, DNA repair; there is a lto of difference between naive and primed ESCs.
• CRISPR screen to uncover genes/pathways to go from naive to primed.

Embyronic Diapause in Mice

• Embyronic diapause is arrested development or delayed implementation; a reproductive strategy used by over 100 mammalian species.
• If there is not enough food or will not be able to take care of new animals, they have the ability to arrest development before implantation; it develops into the blastocyst but then stops.
• Determine genes and pathways activated, as well as metabolic state.

Ellison Stem Cell Core

• Located in South Lake Union - Mathieu, Cavanaugh, Hesson.
• Goals:
  1. Facilitate human pluripotent stem cell research
     • Work with many institutions in Seattle.
     • Sources of pluripotent stem cells
     • Shared laboratory sapce
     • Pre-tested reagents
     • Training in culture and iPSC generation
     • Gene editing in pluripotent stem cells (Main focus)
     • Addition of services as needed
  2. Research relevant to quality of pluripotency

Research

1. Cryopreservation - how to best freeze cells?
2. Stages of pluripotency
3. Human embyros for research - patient consent, maintain quality stocks for generative medicine and improving IVF
4. Understanding DNA repair mechanisms in stem cells to improve genome editing techniques
5. Generation of new iPSC models - dogs, whales, rhinos, etc.

Genome Editing

• Exploded very recently.
• New tools that make it efficient to modify the DNA of cells.
• Applications:
  • Basic research: knock out genes to study their function, generate reporter lines to follow some proteins
  • Disease modelling: try to correct genes causing disease

CRISPR Technology

• Based on natural immunity of bacteria to protect themselves from infections by viruses.
  • Immune system of the bacteria.
  • Doudna and Charpentier repurposed this system for genome editing.
    • Nobel Prize 2020
    • First time two women get the Nobel Prize; very early after their discovery.
• CRISPR can be used everywhere from plants, cell lines in culutre, clinical trials, animals, and human embryos.

CRISPR gRNA/enzyme complex

• gRNA - guide RNA, have a PAM sequence (NGG).
• Cas9 - loop in gRNA allows Cas9 to bind; gRNA will bring Cas9 to a specific place in the genome and cuts exactly where it is brought.
• Induces a double-stranded break.
• Two methods of DNA repair:
  • Non-Homologous End Joining. Introduces InDels.
  • Homology Directory Repair. Based on long-sequence flanking homology.

Example of a Project: Study of a Mutation Causing Cardiac Disease

Patient with mutation believed to cause cardiomyopathy.

1. Generation of iPSC from the patient. Reprogram into iPSCs; extract DNA and perform PCR to see where mutations are.
   • Sanger sequencing: differences mean that one allele has a mutation.
   • iPSCs can be differentiated into cardiac cells.
2. Correction of mutation using CRISPR Cas9
   • gRNA recognizes this region.
   • Donor DNA contains correction to be introduced. Corrected mutations; cells can be used not only to look at phenotype but to test new drugs in patient iPS cells.

Regulatory and Ethical Questions

Use of Embyronic Stem Cells

Generation and use of embyronic stem cells regulated at various levels.

UW GIM36

• No UW personnel shall engage in and no UW facilities, equipment, or other resources shall be utilized for any of the following:
  • Human reproductive cloning
  • In vitro culture of an intact human embryo for more than 12 days of development or until formation of the primitive streak, whichever occurs first
  • Payment of a donor solely for the purpose of creating a human embryo to be used in hESC research
  • Implanting a chimeric embryo containing non-human cells into the uterus of a human
  • Implanting a chimeric embryo containing hESCs into the uterus of any vertebrate animal
  • Using federal funds to engage in ineligible hESC research
  • Engaging in hESC research in a manner contrary to federal, state, or local laws and regulations.
• A new GIM36 will include iPSC; old policy about embyronic stem cells completed about 10 years ago.

Gene Editing of Human Embryos

• “CRISPR babies” - human embryos can be edited in the United States.
  • Dr. He introduced two babies with CRISPR-Cas9 edited gene.
• The ethics of editing human genomes.
• He introduced a mutation in a gene that would help babies be less susceptible to HIV infection.
  • It is not known if this would work.
  • CRISPR field, even though is moving very fast, is not there yet.
  • Cas9 can cut in other places of the genome by accident.
  • Mosaicism; not all the cells will have the same edits.
• Should we introduce mutations into the embryos of humans?
  • Something important to discuss; not only safety but ethical concerns.
  • Which diseases should it be applied to? - which ones should not be prevented?
• No law regulates this yet; people are working on how to control this.

Undergraduate Research Seminar

Navigation

• What is research?
• UW is a Research Institution
  • Why do Undergraduate Research
  • Remote Research
  • Big Moments and Learning
• The Undergraduate Research Program
  • Undergraduate Research Symposium
  • To Learn More
• How to Find Research
  • Where to Find Research Opportunities
  • Do Your Homework
  • Preparing for Research
  • Where to Go Next?

What is research?

• Inquiry or investigation that makes an original intellectual or creative contribution to a discipline.

UW is a Research Institution

• Research at the UW: Faculty in all disciplines do research but approach it in different ways.
• 2018-19, UW received > $1 billion for research grants.

Why do Undergraduate Research

• With research, you can -
  • Learn for a purpose
  • Choose what you want to learn
  • Apply your coursework to real research problems in all fields
  • Get to know your professor
  • Reduce the size of the university

Remote Research

• Research is still happening at the UW
• Less in person, more remote work
• Remote research can include
  • Literature reviews
  • Data analysis
  • Manuscript writing.

Big Moments and Learning

• You have enough expertise to propose your own ideas independently.
  • Not just a researcher; an inventor and a designer.
• To get started:
  • Utilize URP resources
  • Reaching out to peers/TAs about their research
  • Explore research in a variety of fields

The Undergraduate Research Program

Undergraduate Research Symposium

• May 21st, 2021. A good way to share your work and to learn about the work of other students.

To Learn More

• Attend a URP info session; follow up with 1:1 advising to schedule with URP advisors.
  • There to be a resource for you in a more personal environment
• Getting involved through Research Exposed (only available in Fall and Winter)
  • Learn more about the type of research; panels with different faculty from the different fields, a good way to network and know the different faculty members.
• Undergraduate Research Symposium open to the public and a good way to hear about others.

How to Find Research

Where to Find Research Opportunities

• Database - URP website where faculty post opportunities for undergraduate research.
  • Can be visited often; positions opent o students of all backgrounds, not just limited to a particular major or a certain class standing.
  • Faculty are looking for students that are interested and are willing to commit to that work.
• You don’t have to have prior experience - these are experiences.
• Ask questions, be curious, be fully present and willing to learn.
• Course faculty speakers - maybe speakers or your own professors and graduate students may share their work with you; you can ask and network, potentially find an oppurtunity.
• Summer Research Programs are designed to be very immersive; there are many in all areas, 6-8 full-time and often paid.
  • A good feel for what it is like to be a researcher, to continue that work into the year should you decide that is what you want to do.
• Symposium is good to get a feel for what undergraduates are doing.
  • Abstracts are stored on the website and can be filtered by major.
• Faculty do not always put out a call.
  • Put out a call to learn about researchers on campus; enquire and ask around, talk to people, department advisors; just schedule an appointment with an advisor and talk to them about research in this department.
• Let people know what you are looking for; you do not need to wait that one faculty that is doing work of interest to you.
  • Talk to faculty about what it is that they are doing and you may find someone that yo ucan connect to.
• Visit and check out the website.

Do Your Homework

• Identify 2-3 positions or faculty whose work piques your curiosity
• Dig further than a brief description or general subject area
  • Google potential mentors on the UW homepage
  • Check out department & lab websites for description
  • See if their students have presented at the research symposium

Preparing for Research

• Have a strong interest, passion, and enthusiasm.
• A brief email of interest (cover letter email) - convey interest and passion.
• A resume.
• An unofficial transcript - downloaded from MyUW.

Where to Go Next?

• Schedule an appointment with the URP Staff
• Getting started with research
• Resume and cover letter feedback
• Summer research
• Research funding
• Other questions about the research experience and process

Amina Cesario: Principles of Community Ecology and Virtual Field Trip

Navigation

• Community Ecology
• Species Interaction
• Community Structure
• Species Reintroduction and Trophic Cascade
• What is a Tide?
  • Tides Affect Marine Life
• Species Ecological Niche
• A Virtual Experiment
• Marine Invertebrates
  • Marine Invertibrates Evolutionary Key Innovations
  • Phylum Porifera - Sponges
  • Phylum Cnidaria
  • Phylum Mollusca
  • Phylum Arthropoda - Subphylum Crustacea
  • Phylum Echinodermata
• Ecology of Rocky Intertidal Invertebrates
  • Rocky Intertidal Transect Survey
  • Transect Procedure, Data Observation, Collection, and Entry

Community Ecology

• A biological community consists of all the populations of different species that interact in a certain area.
  • All these species interact in a location.
  • Interactions are not only limited to only two species.
• Community ecology explores how species interact with each other and how they develop and change over time.
  • The goal of exploring how these species interact with each other and how populations change over time.
• Over time, the distributions of the population changes.

Species Interaction

Community Structure

• Four key attributes:
  1. Total number of species
  2. Sum of interactions among all species
  3. Relative abundance of those species - number of individuals over the total
  4. Physical attributes of the community - abiotic (temperature, salinity, etc.) and biotic (food, etc.) factors.
• We are not all created equal.
• Some species have a disproportionate influence on the diversity and abundance of other species in communities due to both direct and indirect effects.
• Bottom-up or top-down effect, having a greater impact on the community as a whole.

Species Reintroduction and Trophic Cascade

• How Wolves Change Rivers.
• Discovery of trophic cascades - an ecological process that starts at the top of the food chain and tumbles to the bottom.
• Yellowstone National Park - wolves reintroduced in 1995.
  • Wolves kill, but also give life to many others.
• Wolves had been absent for 70 years; the amount of deer had built up and reduced much of the vegetation there to nothing.
• The wolves killed some of the doors and radically changed their behavior.
  • They began to avoid certain parts of the park; those places started to regenerate.
• Birds, beavers, come in; the dams they build create habitats for amphibians.
• Coyotes, bald eagles, bears,
• The wolves changed the shape of the river.
• By driving the deer out of some places, there was less soil erosion.
• Wolves transformed not only the ecosystem of the park but also its physical geography.
• The trophic cascade is affecting the ecosystem as a whole - not only species but the biotic factors as well.
• Creating niches.
• A small number of animals could change Yellowstone park - small.

What is a Tide?

• Rise and fall of water due to gravity.
• Gravity of the moon.
• Everything is attracted to everything else - the Earth and the moon are attracted to each other.
  • The gravitational attractions are of equal strength.
• The water bulges outwards in the area closer to the moon.
• There are two high tides a day.
• The strength of gravity is higher when objects are closer.
• There is a partial bulge in the area farthest from the moon and one in the area closest - two high tides and two low tides a day.
• By the time the Earth has rotated once, the moon has moved a little bit - the Earth has to “catch up”, so the next day’s high tide is about 50 minutes.

Tides Affect Marine Life

• Marine life is affected by the tide - especially organisms that live by the shore.
• When there is a low tide, sessile organisms - anchored to a specific substrate - are left outside of the water, which affects their distribution.
  • Need to cope with not drying out completely, but also with other things - presence and absence of predators, etc.
  • Absence of hosts in case they are predators.

Species Ecological Niche

• Ecological niche for each species.
• Fundamental niche - abiotic factors, the total range of environmental conditions that a species could theoretically tolerate.
  • The species had specific resistance to those variables in certain areas.
• Realized niche - considering the competition, hosts, availability, etc. that narrow down the fundamental niche to form the realized niche.

A Virtual Experiment

• 3 scenarios on the rocky shores:
  • One species: barnacle (Chthamalus).
  • Two species: barnacles (Chthamalus and Balanus)
  • Three species: barnacles (Chthamalus and Balanus) and sea snail (Thais)
    • Sea snails are predators of barnacles.
    • Barnacles are stuck to the rock and can filter feed - will shut close their teeth - will release egg and sperm in mating sequence; the nauplii have a swimming stage and finally attach to a substrate.
• One species scenario.
  • The barnacle can grow on the entire rock.
  • Even distribution.
• Two species scenario.
  • Balanus is added; can only inhabit lower tabs.
  • Some species interaction is occurring - competition.
  • Distribution of Chthamalus is pushed upwards.
• Three species scenario.
  • Thais is added.
  • The distribution of Balanus is reduced from the bottom.

Marine Invertebrates

Marine Invertibrates Evolutionary Key Innovations

1. Tissue / no tissue
   • No tissue: sponges.
2. Tissue > Bilateral / Radial symmetry
   • Radial symmetry: cnidarians
3. Bilateral symmetry > Protosome / Deuterostome
   • Deuterostome: echinoderms (e.g. starfish)
4. Protosome > Acoelomates / Coelomates
   • Coelomates: mollusks (e.g. octopi), arthropods (crustaceans)

Phylum Porifera - Sponges

• Simple multicellular animal (no tissues)
• Benthic and sessile
• Filter feeders
• Each cell individually digests its food
• Marine and freshwater species
• Classified by the spicules they produce

Phylum Cnidaria

• Include the swimming jellyfish, the sessile (corals), all freshwater, and some marine forms.
• Diploblast - two germ layers, two tissue layers separated by a jelly layer.
• Radial symmetry.
• Rudimentary nervous system (nerve net).
• Gastrovascular cavity with one opening - mouth/anus
• Nematocysts - shoot a barbed thread to predate (jellyfish on fish, for instance) or for defense.

Phylum Mollusca

• Cephalopoda - “head-feet”; squid, octopuses, nautiluses, cuttlefishes.
• Bivalvia - two valves, two shells; clams.
• Gastropoda - “belly-feet”; snails, slugs.
• Polyplacophora - “many-plate-bearing”, able to attach to a substrate; chitons.
• Have a muscle or afoot, which can evolve into a complex system of arms and legs.
• Radula - scraping surface for feeding or protection.
  • This can be modified into a beak.
• Mantle - for mollusks that have a shell, the mantle secretes the shell.

Phylum Arthropoda - Subphylum Crustacea

• The largest phylum of the animal kingdom.
• Segmented body.
• Two pairs of antennae, strong mandibles for chewing, hard exoskeleton.
• Paired and jointed appendages.
  • Otherwise could not move such a heavy and hard skeleton.
  • Need to shed the skeleton; grow by molting.
• Crustaceans: shrimp, crab, crayfish, barnacles, prawn, etc.

Phylum Echinodermata

• Sea stars, sea urchins, brittle stars, sea cucumbers, feather stars, sea lilies.
• Have “spiny-skin” in the endoskeleton made of calcium carbonate plates under the skin.
• Bilaterian and Penta-radial symmetry.
• Exclusively marine organisms.
• Water vascular system that forms a hydrostatic skeleton that operates the tube feet (movement, feeding, breathing).
• Sea stars are carnivores - they eat anything, very much into mussels.
  • Eat the body of the mussel and retrieve their stomach.
• Keystone species - a species that has a much greater impact on the distribution and abundance of the surrounding species (i.e. community structure) relative to its abundance.
  • What happens if we remove sea stars from the environment?
• When the sea stars are removed from the environment, the biodiversity fell significantly.
  • When there is no keystone predator, the diversity suffers.

Ecology of Rocky Intertidal Invertebrates

• In the intertidal zone, there are different species; mostly shelled organisms can contain water inside them

Rocky Intertidal Transect Survey

1. Recognize the common physical and chemical factors on the rocky intertidal ecosystem.
2. Recognize dominant inhabitants.
3. Recognize obvious adaptations of marine organisms to desiccation and wave action.
4. Recognize vertical zonation in rocky intertidal communities.
5. Quantify species diversity and abundance.

Transect Procedure, Data Observation, Collection, and Entry

• Have 10 quadrat (1 by 1 meter) lined along a line transect.
• Abiotic data - water temperature, salinity, pH, dissolved oxygen concentration duration of exposure to air.
• Abundance: counts (larger species), percentage, present/absence scales.
• Simpson’s Index of Diversity - from 0 to 1.