Communication
Effective Change Agent Senior Capstone
  • Home
  • About
  • Terms
    • Fall 2019 >
      • Dr. Strongin Research Lab
      • Two Broke College Kids Podcast
      • TRIO Talent Search Program
      • Eco-Systems Sustainable Exhibits
      • Lines for Life (Senior Loneliness Line)
      • Lines for Life (Youth Line)
      • Tuality Community Hospital
      • Potluck in the Park
      • Oregon Recovers
      • An Evergreen Development; A Work in Progress
      • Community Engagement Outreach
      • Dr. Stedman Research Lab
    • Summer 2019 >
      • Cape Town Summer Community Development and Social Justice: Theory + Practice
      • Influence Music Hall
      • Call to Safety
      • Oregon Health Authority
      • Biophysics Research: Portland State University
      • Critical Discourse Analysis
      • "Mal & Friends" Art Show
      • Tutor Workshop
      • Community Sustainable Business Coalition
      • Brain Health and CBPR
      • Post Consumer Plastic Recycling Research
    • Spring 2019 >
      • Dougy Center
      • PSU Orchestra
      • Hands on Greater Portland
      • Conflict Resolution: Artist in Residence
      • Strategic Mediation
      • Transformation Through Healing
      • Legacy Meridian Park
      • Camp Harmon
      • Bloom Beauty Collective
      • AMIGOS de las Americas
      • C.U.R.E. Labs PSU
      • Communal Composting: Lents Neighborhood
      • King School of Contemporary Art
      • Edwards Center
      • Northeast Community Childhood Development Center
      • Japanese International Baptist Church
    • Winter 2019 >
      • Potluck in the Park
      • Eclectronics: Artist Collective and Community Organization
      • Potluck in the Park
      • Legacy Research Institute
      • Harvest Share/PSU Food Pantry
      • King School of Contemporary Art
      • Carpe Mundi
      • Boys and Girls Club of SW Washington
      • Rise: Refugee & Immigrant Services and Empowerment
      • Helen Gordon Child Development Center
      • Walnut Park Shelter
    • Fall 2018 >
      • SAVA - Sexual Assault Victim Advocacy Program
      • Innovation Law Lab
      • Skaters for Portland Skate Parks
      • County CROPS
      • Operation Night Watch
      • Fircrest Elementary
      • Portland Winter Lights Festival
      • Maybelle Center for Community
      • Green Monday - Sustainability Program Coordinator Internship
      • Heart Mantra
      • Junior Youth Spiritual Empowerment Program
      • NW Noggin
      • ASEPALECO
      • OMSI - Early Childhood Education Program
      • OSA - Oregon Society of Artists
      • Aloha Huber Park K-8
    • Summer 2018 >
      • Columbia Land Trust
      • Free Geek
      • Universal Design Lab
      • Matt Dishman Community Center
      • Providence (School Outreach)
      • WIC
      • The Rebuilding Center
      • ESY (Extended School Year)
      • Young Life
    • Spring 2018 >
      • DKMS (Deleting Blood Cancer)
      • Oregon Criminal Justice Reform
      • Portland Rescue Mission
      • Inclusive Summer Camps
      • Cares Northwest
      • CHAP (Children's Healing Art Project)
      • CHAP (Children's Healing Art Project)
      • NW Noggin
      • Grant Research
      • Outside In
      • PDX Commons
      • Blanchet House
      • The Canby Center
      • Space Matters: Race, Equity and The PCC Landscape
      • Chicano Leadership Summer Institute
      • Everybody Sing: Youth Choir Programs
    • Winter 2018 >
      • Wallace Medical Concern
      • p:ear
      • Dexter McCarty Middle School
      • Rockwood Center
      • Ladd Acres Elementary School
      • NAMI (National Alliance on Mental Illness)
      • Jumpstart Humanity
      • Stand for Children
    • Fall 2017 >
      • El Tour de las Sonrisas (Tour of Smiles)
      • Hands on Portland (Cultural Art With Low Income Youth)
      • Church Choir (Piano Accompaniment)
      • Russian Flagship - PSU (Classroom Assistant and Tutor)
      • Echo Theater
      • Pot Luck in the Park
      • Building Bird Houses (Philanthropy)
      • Women Artisans of Plomo
      • Forest Park Conservancy
      • Gladstone High School (Classroom Assistant)
      • Educate Ya
      • Oregon Food Bank
      • Chicano Lesbian Digital Literacy
      • Children's Healing Art Project
      • Zemyra Soap Company (Philanthropy)
    • Summer 2017 >
      • Inukai Boys and Girls Club
      • Randall Children's Hospital
      • Ministry Intern
      • Salvation Army/White Shield
      • PSU/IELP (Intensive English Language Program)
      • Oregon Food Bank
      • Women in Aviation/Willamette Vally Wings
      • Camp Erin
      • PSU Invertebrate Museum/Student Sustainability Center Bee Task Force Coordinator
      • International Socialist Organization/ Where We Stand
    • Spring 2017 >
      • Grant High School: College Success Program
      • PSU Museum of Natural History/Living Cully
      • Poetry in the classroom
      • City Repair: T-Crab
      • St. Johns Food Share
      • Olympia Provisions: Supporting local and sustainable food options
      • NAMI: Multnomah
      • Capernaum: Young Life for kids with special needs
      • Teaching Social Justice to 4th and 5th Graders
      • Living Cully
      • Engaging Imagination: Human Solutions
      • Sound Equine Options
    • Winter 2017 >
      • Matt Dishman Community Center
      • School From Home Learning Coach and Advocate
      • Hillsboro High School Math Mentor
      • OHSU Research Volunteer
      • Portland Menstrual Society
      • Africa House Services
      • Beaverton High School Strength and Conditioning Mentor
      • p:ear
      • Art for Justice
      • Zenger Farm
      • Bloomin' Boutique
      • Portland Tenants United
    • Fall 2016 >
      • 4th Dimmension
      • MRG Foundation
      • Environmental Performance Workshop
      • Forward Stride
      • TherapyWorks NW
      • Thailand
      • Teen Comics/Manga Club East Portland Community Center
      • New Avenues for Youth
      • World Comics Network
      • MAPS (Alder Elementary)
      • Todos Juntos (All Together)
    • Summer 2016 >
      • Cascade Aids Project
      • Squirrel Refuge
      • Call to Safety
      • Asian Health and Service Center
      • Civil Air Patrol
      • Free Geek
      • Write Around Portland
    • Spring 2016 >
      • Dream Builders Alliance
      • Habitat for Humanity
      • Tomorrow's Hope and Can We Help?
      • Portland City Rescue Mission and Intwon Church
      • Portland Sister City with France
      • Free Geek
      • Kelly Elementary, PTA President
      • Sunshine Division
      • Young Life, Capernaum
      • Mercy Corps Action Center
      • Alder Elementary
      • Drive Oregon
      • Clowning and Social Justice in Nicaragua
      • Northwest Behavioral Health Services
      • GABRIELA Portland
    • Winter 2016 >
      • Albertina Kerr's Cook for a Cause and Kinship House
      • HEYA: Health Equity Youth Advocates
      • Food Trucks and Equity Opportunity
      • Oregon Public Broadcasting: "State of Wonder" Intern
      • Exploring Civil Rights and Social Change with 5th-8th Graders >
        • Our Civil Rights History: Revisited
        • Civil Rights History: Through Our Eyes
        • Social Change In Our Communities
      • Chiron Studies: Burning Man and Social Change
      • Sunshine Division
      • Albertina Kerr: Project Grow >
        • Responsibilities
        • Archiving Project
        • Social Action
        • Reflection
      • Vita Program: Income Tax Assistance
      • Oregon Partnership: Lines for Life
      • German Saturday School
    • Fall 2015 >
      • Portland Community College (ESOL Program)
      • Church Choir (Piano Accompaniment)
      • Northwest Noggin
      • NAMI Multnomah
      • East County Basketball Academy
      • Malden Court Community Orchard
      • Wanderlust Circus
      • Optimist Club of Gresham
      • Portland City Blessing Church
      • Teaching/Coaching Physical Activity
      • Pride Northwest, Inc.
      • De-Partitioned Housing
    • Summer 2015 >
      • Dress for Success
      • OHSU Acute Care Volunteer
      • Poetry Press Week
      • NW Noggin: Neuroscience Outreach Group >
        • Boys and Girls Club: Vancouver
        • WSU, Mesa
      • Pushfins
      • French Sister City
      • FLOCK Creative Dance for Kids
      • Northwest Institute for Community Enrichment
    • Spring 2015 >
      • Methodology for Conducting Street Tree Survey
      • Volunteer Firefighter
      • Bicycle Transportation Alliance
      • Sam Barlow High School Math Tutor
      • Russian Language for Bilingual Students
      • Community Gardens and Food Shares, Domestic Violence and Sexual Assault Prevention Program, Two Spirit Support Group
      • Community Supported Everything
      • 4th Dimension Recovery Center
      • BRAVO
      • Human Solutions
      • Oregon Student Association >
        • Organize for Change
      • Pure Life Alliance
      • Mobile App Tool Kit - Critical Thinking
      • Applied Psych Lab - Research Assistant >
        • NeuroGeeks
      • Clackamas River Water Analysis
    • Winter 2015 >
      • Metro
      • SnowCap Community Charities
      • Students for Sensible Drug Policy
      • SMART (Woodland Elementary)
      • ChickTech
      • Carpe Diem Education (Gap Year Experience)
      • Multnomah County Health Department
      • Sexual Assault Resource Center
      • Kairos Learning Academy
      • ESL Conversation Group Leader
      • Catholic Charities
      • Senior Community Center (Documentary, PSA)
      • Wallace Medical Concern
      • CASA (Clackamas County)
      • Assistant Coach, Sandy Swim Team
    • Fall 2014 >
      • Hollywood Senior Center
      • Human Rights Commission
      • Shepherd's Door Family Life Center
      • Scappoose Share and Care
      • Outside In: Hep C Education
      • Portland Solidarity Network
      • US Dept of the Interior Office Environmental Policy and Compliance
      • Photography and Marketing for Non Profits
      • Sunnyside Environmental School
      • Lines for Life (Suicide Prevention)
      • Good Clean Fun
      • Kaiser Permanente Sunnyside
      • Portland Center for Human Rights
    • Summer 2014 >
      • Girl Scouts OSW
      • Youth Yoga Instructor
      • Oregon Humane Society
      • Camp Starlight
      • Neuroscience Outreach Programs
      • Immigrant and Refugee Community Organization
      • Teacher's Assistant, Summer Program (Riverside Elementary)
      • Neurofeedback
      • Rogue Agent of Change
      • Echo Ranch
    • Spring 2014 >
      • Sex Re-Education for Elderly Community >
        • Unit Plan for Sex Re-Education >
          • Survey
      • Quantom Dots: Energy Harvesting
      • Photo Project of Undocumented Immigrants
      • Family Relief Nursery: Abuse and neglect prevention program
      • Empowerment Through: Workshops designed to empower through action
      • OHSU Dental Clinic
      • OMSI Volunteer: Life Sciences Lab
      • VocoForm: Grant writing for urban farm vocational outreach and mentorship
      • "Community Front Porch" Creating community support for the Brentwood-Darlington Neighborhood
      • SOMETIMES WHEN I SPEAK: CONNECTING TO INCARCERATED YOUTH IN PORTLAND >
        • Writings
        • Collages
      • PSU Athletics: Career Development
      • Elementary School Outreach/Creston's Childrens Clinic
      • BIRC: Brain Injury Rehabilitation Center
      • Yellow Brick Road: Street Outreach >
        • Em's Extra Page
  • Community Class Projects
    • Call to Safety
    • NE Community Child Development Center
    • Potluck in the Park
    • Casting A Line.....
    • Rebuilding Center
    • Helen Gordon Child Center, Little Vikings
    • Gratitude Day and College Connection
    • Clackamas Service Center and Stump Town Dance
    • PSU Orchard
    • Human Solutions
    • Blanchet House
    • 4th Dimension and Card Making for Incarcerated Individuals
    • Squirrel Refuge
    • Free Geek and MAPS (PSU and Alder Elementary)
    • Albertina Kerr: Project Grow
    • Malden Court Community Orchard Work Party
    • Recycled Journals for p:ear
    • Parkrose High School Community Closet Organization and Website Development
    • Senior Citizen Dance
    • St. Francis of Assisi Dining Hall
    • Echo Ranch Horse Rescue
    • Measure 11 Awareness Event
  • Contact
  • UNST Goals
    • Fall 2019 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Summer 2019 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Spring 2019 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Winter 2019 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Fall 2018 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Summer 2018 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Spring 2018 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Winter 2018 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Fall 2017 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Summer 2017 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Spring 2017 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Winter 2017 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Fall 2016 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Summer 2016 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Spring 2016 >
      • Diversity
      • Critical Thinking
      • Social Responsibility
      • Communication
    • Winter 2016 >
      • Diversity
      • Critical Thinking
      • Social and Ethical Responsbility
      • Communication
    • Fall 2015 >
      • Diversity
      • Critical Thinking
      • Social and Ethical Responsibility
      • Communication
    • Summer 2015 >
      • Diversity
      • Critical Thinking
      • Social and Ethical Responsibility
      • Communication
    • Spring 2015 >
      • Diversity
      • Critical Thinking
      • Social and Ethical Responsibility
      • Communication
  • Resources
  • University Studies Vision and Mission Statements

Dr. Stedman's Research Lab:
​Archaeal Viruses and their Host

This page is being made for a Portland State University Capstone and is a work in progress by Suzie Wallace. 
All images have links associated to bring you to the paper they originated as well as the bright orange texts.

My Background
I have been working in Dr. Kenneth Stedman's research lab since June of 2019. Before starting here I had taken molecular biology from him where he encouraged everyone to take his Biology C.U.R.E class for Recombinant DNA Laboratory Techniques. In this class I had the opportunity to meet Nichole Procter who was taking this Capstone at the time and was a T.A. for Dr. Stedman's class. She made her own web page explaining C.U.R.E. classes and their purpose. Now, I get to work along side her as I continue to learn how the lab opperates and work on my own projects with her continued support. 
My Goals
In the near future I hope to move into graduate school and earn my PhD. My intentions of working in this lab were to understand if research was the path I wanted to take. However, I ended up wanting to go into research by the time the C.U.R.E. class was over. My next goal was to learn how labs regularly operate and get into my own project to keep learning. My main areas of interest are viruses and microbiology. More specifically, I am very interested in Archaea. This lab is the perfect combination of both so my time here has solidified those interests. I have also gained confidence working on an independent project while still having the support and guidance of others. 
About the Lab
Dr. Stedman's lab is one of the labs associated with the Center for Life in Extreme Environments at Portland State University. The goal of this lab is to study life where most other organisms can't survive. They are extreme in the sense that they are too hot, too cold, too salty, too acidic, too basic, or under too much pressure. The organisms we work with are single cellular microscopic Archaea and the viruses that infect them. Because they live in extreme circumstances we want to know how they are structured and function to not only live but thrive in these harsh environments. 

PictureKhan Academy, 2019

  • Outline:
  • Virus Background
    Sulfolobus Spindle-Shaped Viruses and Sulfolobus

  • Fun Facts about SSVs and Sulfolobus


Virus Background
Viruses are nonliving biological entities that do not have the mechanisms necessary to reproduce themselves. They can, however, hijack the mechanisms of living cells to reproduce themselves to go and infect new cells. As seen above, viruses are made of a capsid, nucleic acid, and sometimes an envelope. The nucleic acid can be DNA or RNA and is the genetic material for the virus. The capsid is made of proteins and is used to protect the genetic material as well as interact with the host of the virus. The envelope is a similar structure but is made of fats and proteins that can also protect the genetic material and mediate interactions between the virus and the host. The envelope can even help the virus evade the host's immune response in some cases.
Sulfolobus Spindle Shaped Viruses and Sulfolobus
PictureStedman et. al. Virology, 2015
Sulfolobus is a genus in the Domain Archaea that includes many species of single celled organisms. These organisms live in hot springs all over the world in temperatures ranging from 75-95°C (167-203 °F) and pH levels ranging from 2-4 (similar to lemon juice!). These cells are hosts for the ever so unique, Sulfolobus Spindle-Shaped Virus. One of the things that makes these viruses so unique is their lemon-shaped capsid. While the virus is not actually these colors, the outside of the virus is split into the green capsid section and the blue tail section on the capsid diagram on the right. The capsid is made of the structural proteins VP1 and VP3 and the tail portion is likely made of the structural protein VP4. On the surface of the host there is a layer of proteins called the S Layer. This is comprised of a single layer of the proteins SlaA and SlaB. The paper I am adapting methods from for my own project is called "Architecture and modular assembly of Sulfolobus S-layers revealed by electron cryo-tomography" . This paper found SlaB to be more of a ruler and a stilt to separate the S Layer from the rest of the cell rather than directly interacting with the virus. 

My Favorite Fun Facts about Sulfolobus and SSVs
SSVs systematically and rapidly reproduce in Sulfolobus under UV induction.
PictureFrols et. al. Virology, 2007
Normally, UV light radiation is damaging to and can kill cells by damaging their genetic material. However, Sulfolobus infected with SSV1 starts to rapidly reproduce the virus after being exposed to UV radiation. The pattern of reproduction is a predictable cycle of up-regulating and down-regulating genes to make proteins at specific time intervals following UV exposure. The image to the left shows this predictable cycle of regulation on the circular genome of the virus. The red to yellow arrows indicate sections of the genes and their timing of regulation where immediate early is right after UV exposure and late is hours after UV exposure. The green arrows are the individual genes that are translated into each protein. When the infected Sulfolobus cells are exposed to UV radiation we can expect to see genes translated into proteins in this predictable order. The exact cause to this pattern is unknown which only makes it more fascinating. 

SSVs do not lyse the host cells.
Viruses in general have two primary forms of replication in host cells. The first is the lysogenic cycle where viruses infect the host cell and keep their genes dormant within the hosts cells. That way when the host cell replicates itself and duplicates its' own genetic material, it is also replicating the virus's genetic material and the new cell inherits the infection. The other kind of cycle a virus can have is the lytic cycle. Where the host's molecular replication machinery is actively hijacked to build more viruses. Typically, when the cell has produced enough viruses the cell bursts, or lyses the cell membrane, killing the cell and releasing the newly produced viruses to go on and infect other cells. One of the mysteries of Sulfolobus and some SSVs is that they do not have these relationships. So far, all but two SSVs that infect Sulfolobus have been shown to not lyse the host cell. While viruses are being actively produced the cell does have slowed growth but the host doesn't die. This has raised the question of what, if any, benefit the host cell may be getting from the infection. The virus is clearly getting the benefit of being replicated by the host cell. Maybe the host doesn't benefit from the infection but if it does maybe there is a potentially symbiotic or quasi-symbiotic relationship. 
SSVs can withstand a large amount of mutations and still function.
PictureGoodman & Stedman et al, 2018

Mutated DNA can mean a variety of things like that the chemical structure of the molecule is damaged in some way or that the original sequence of their genes is altered to some degree. The build up of these mutations is what causes cancer in animals. In this context mutations will refer only to the addition a known large sequence of genes. DNA can be thought of as a track that needs to be shaped a specific way for the machinery to ride down and read to produce RNA and then read again to produce a protein. These insertions into the genetic material disrupt how replication machinery would build the proteins from the genes by changing the message being translated. To better explain how these mutations effect replication the following sentence is how a gene would be read if there was an insertion in the genetic material.

" She went to the zoo and had a fun time lookThere is a parking lot over there.ing at the penguins with her children." 

When we read this sentence we can tell that there is a disruption, what both sentences are, and exactly where the insertion is taking place. When a protein is being made from a gene that has been interrupted like this it makes a protein that might not work properly. While we do know what the interrupting sequence is, it takes analysis and preparation to determine where the disrupting gene is in the context of the virus' genome.

​The goal of intentionally interrupting their genes is to determine if the proteins made by those genes are essential for the viruses to function. Only a handful of proteins in this genome are defined. There is room to learn about the functionality of any genetic mutation no matter where it is randomly inserted, even if we find the gene is nonessential. We determine the functionality based on the infection and subsequent observation of Sulfolobus growth. Methods used in this process can tell us if these viruses are behaving chemically how we would expect them to, that the mutation is exactly where we determined it to be, and then ultimately if the virus is capable of infecting Sulfolobus with the particular genetic mutation in question.

If a mutant virus is repeatedly observed to not infect the host cells the mutation is considered to be a nonfunctional mutation and we conclude that the protein that was altered by this mutation is essential for virus activity. If the mutation of this gene does not prevent the virus from infecting a cell and replicating itself in the host as usual then we conclude that the protein coded for by this gene is nonessential for virus activity and that the mutation is functional. Interestingly, genes that code for the same protein can function when mutated at one point but can be nonfunctional when mutated at a slightly different point. 

If a gene is essential we can then ask, why is this gene essential? Why is this other gene not essential? These questions allow us to learn more about how these mostly undefined viruses operate on a molecular level. SSVs are specifically interesting because they can tolerate almost half of their DNA being mutated and still be infective. With all this room for mutation we can keep making more mutant viruses and continue to learn from them.

The image above is another circular virus genome, this time of SSV10. The rainbow colored arrows once again represent the individual genes to make each protein. The red arrows pointing at the colored arrows represent previously shown noninfectious mutation insertions and green arrows represent previously shown infectious mutation insertions. The paper this diagram came from is a detailed look at some of these mutations and some of the genes of SSVs. This image is from a paper published by David Goodman and Dr. Stedman. Other papers from this web page were written by past and present members of the lab. SSVs have been mutated in multiple other ways and their applications, analysis of mutants, and process of mutation is simplified for this web page. The papers linked have a much more detailed explanation of all of the topics I have touched on today and further explore the details of Sulfolobus and Sulfolobus Spindle-Shaped Viruses.

​Thank you for reading everything and I strongly urge you to continue to read about these viruses and their equally as interesting hosts. 

Proudly powered by Weebly