Difference between revisions of "Team:UCSC/Breakdown"

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<h1> Breakdown </h1>
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<br />
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<!-- Nina Table -->
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<div>
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<div class="col-md-12">
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<b>Background:</b>
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<p style="text-align:left;">Cellulose is the most abundant carbon source on the planet and consequently, cellulolysis is an essential part to the carbon cycle as it replenishes atmospheric carbon. However, the rate of atmospheric carbon accumulation has been increasing exponentially since the onset of industrial age combustion of fossil fuels. Significant changes in global climate can be attributed to increased atmospheric carbon levels, calling an action to start using renewable carbon energy sources. We aim to use waste cellulosic biomass from paper and crop waste as a source of renewable energy by harnessing the catalytic activity of the enzymes responsible for cellulolysis, a class of enzymes known as cellulases, and engineering these cellulases to be tolerant to high saline solutions to reduce the energy cost of the cellulose pretreatment process.
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There are three main types of cellulases: endocellulases, exocellulases, and beta-glucosidases; each play a vital role in cellulose degradation. Endocellulases cleave the hydrogen bonds between crystalline cellulose polymers, exposing the free beta-linked polysaccharide chains. Exocellulases then bind the ends of  loose cellulose strands and cleave the beta-1,4 glycosidic bonds between every two or three glucose subunits producing either cellobiose or cellotriose. Beta-glucosidase finally converts cellobiose into glucose, concluding the cellulose degradation pathway.
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</p>
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</div>
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<div class="col-md-6">
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<b>Methods:</b>
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<p style="text-align: left;">
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We chose to transform Haloferax Volcanii with a B-glucosidase. Our pipeline was to collect data from different cellulases across various organisms, determine which are secreted, and decide which to try to codon optimize to transform into Hvo.
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</p>
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</div>
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<div class="col-md-6">
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<b>Future Goals:</b>
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<p style="text-align:left;">
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Transform Hvo with our - glucosidase(WT) - pTA963C constructs. Then, test each for expression and enzymatic activity.
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</p>
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</div>
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<table style="width: 1230px; text-align: center;">
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<tr>
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<td>
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<br>
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View our <a href="https://2015.igem.org/Team:UCSC/Logs">Notebook</a> for our methodology that lead to our results.
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</td>
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 +
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 +
            <div class="gear-node a" data-node="5" style="top: 405px; left: 105px;">
 +
                <img class="gear" src="https://static.igem.org/mediawiki/2015/9/9c/UCSC_Profile_Gear.png" />
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            <div class="gear-node" data-node="6" style="top: 470px; left: 270px;">
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                <img class="gear c" src="https://static.igem.org/mediawiki/2015/9/9c/UCSC_Profile_Gear.png" />
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            <div class="gear-node a" data-node="7" style="top: 630px; left: 340px;">
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                <img class="gear" src="https://static.igem.org/mediawiki/2015/9/9c/UCSC_Profile_Gear.png" />
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                <img class="profile-picture" src="https://static.igem.org/mediawiki/2015/c/c7/Roger.png" />
 +
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            <div class="profile-cont" data-node="1">
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 +
                <tr>
 +
                <td>
 +
                <p>
 +
                <b>Swathi Balaji</b>
 +
                </p>
 +
                <img src="https://static.igem.org/mediawiki/2015/2/22/ZSMERya.jpg" style=" width: 236px; height: 355px;" />
 +
                </td>
 +
                <td>
 +
                <ul class="list-unstyled">
 +
                <li>Biomolecular Engineering</li>
 +
                <li>Bioinformatics minor</li>
 +
                <li>College Nine (UCSC)</li>
 +
                <li>4th Year</li>
 +
                <li>Grant & Web Team</li>
 +
                <li>From: Pleasanton, CA</li>
 +
                </ul>
 +
                </td>
 +
                </tr>
 +
                </table>
 +
<table style=" width: 500px; padding: 0px; margin: auto;">
 +
                <tr>
 +
                <td style=" padding: 0px;">
 +
                <p class="left">
 +
<i>"Being a part of the UCSC iGEM team this summer has provided me with a valuble life experience
 +
to say the vey least. Not only was I able to
 +
refine my existing lab techniques and develop new ones, but I was also able to
 +
learn how to efficienty work and communicate with my own team to assure maximum success.
 +
Over the course of the summer I can say that I have grown both as a person and as
 +
a researcher. I am truly glad to have taken on such an opportunity and to have been
 +
able to contribute to the scientific community in some way. The amount of experiences and knowledge
 +
that I was able to obtain in the past couple of months is definitely something that will remain with me far beyond my undergraduate
 +
years."</i>
 +
                </p>
 +
               
 +
                </td>
 +
                </tr>
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 +
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 +
                <td>
 +
                <p>
 +
                <b>Anissa Benabbas</b>
 +
                </p>
 +
                <img src="https://static.igem.org/mediawiki/2015/9/9b/B4Xw1uq.jpg" style=" width: 236px; height: 355px;" />
 +
                </td>
 +
                <td>
 +
                <ul class="list-unstyled">
 +
                <li>Biology</li>
 +
                <li>Bioinformatics minor</li>
 +
                <li>Crown College (UCSC)</li>
 +
                <li>Graduate (Post Bac)</li>
 +
                <li>Video Team</li>
 +
                <li>From: Sunnyvale, CA</li>
 +
                </ul>
 +
                </td>
 +
                </tr>
 +
                </table>
 +
<table style=" width: 500px; padding: 0px; margin: auto;">
 +
                <tr>
 +
                <td style=" padding: 0px;">
 +
              <p class="left">
 +
<i>"May name is Anissa, and I am a recent graduate in biology with a bioinformatics minor. I took part in the breakdown portion of the iGEM team, my personal goal being to refine wet lab techniques as well as learn computational skills. Aside from the wet lab work, I also took part in the outreach portion of the team's efforts, such as the crowdfund video. I learned so much in the duration of the summer, and it was a pleasure working in a group of so many bright individuals striving to achieve a common goal. I look forward to taking the skills I've learned in this experience with me to graduate school and beyond."</i>
 +
                </p>
 +
               
 +
                </td>
 +
                </tr>
 +
                </table>
 +
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 +
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 +
                <td>
 +
                <p>
 +
                <b>Cristian Camacho</b>
 +
                </p>
 +
                <img src="https://static.igem.org/mediawiki/2015/7/74/YTbf8tV.jpg" style=" width: 236px; height: 355px;" />
 +
                </td>
 +
                <td>
 +
                <ul class="list-unstyled">
 +
        <li><span>Biomolecular Engineering<br /> </span><em><span>Bioinformatics minor</span></em><span><br /> Crown College (UCSC)<br /> 4th Year<br /> Grant &amp; Video Team<br /> From: La Mirada, CA</span></li>
 +
</ul>
 +
                </td>
 +
                </tr>
 +
                </table>
 +
<table style=" width: 500px; padding: 0px; margin: auto;">
 +
                <tr>
 +
                <td style=" padding: 0px;">
 +
              <p class="left">
 +
<i>"In my opinion, the greatest part of the iGEM experience was being able to witness and take part in the unimaginable amount of success that a random group could produce in such a short period of time.  Being able to operate efficiently as a team on a multi-layered project, raising over $24,000, making new discoveries, and establishing an image for our team and project that we can be proud of. I’ve learned so much because of iGEM, and along the way I’ve been blessed to become friends with a remarkable group of individuals that have helped me become a better leader and a better person."</i>
 +
                </p>
 +
               
 +
                </td>
 +
                </tr>
 +
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            <div class="profile-cont" data-node="4">
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 +
                <tr>
 +
                <td>
 +
                <p>
 +
                <b>Jairo Navarro</b>
 +
                </p>
 +
                <img src="https://static.igem.org/mediawiki/2015/7/7d/CLQ8zNx.jpg" style=" width: 236px; height: 355px;" />
 +
                </td>
 +
                <td>
 +
                <ul class="list-unstyled">
 +
        <li><span>Biomolecular Engineering<br /> </span><em><span>Bioinformatics minor</span></em><span><br /> College Nine (UCSC)<br /> 4th Year<br /> Grant, Programming, Video, &amp; <br /> Web Team<br /> From: Watsonville, CA</span></li>
 +
</ul>
 +
                </td>
 +
                </tr>
 +
                </table>
 +
<table style=" width: 500px; padding: 0px; margin: auto;">
 +
                <tr>
 +
                <td style=" padding: 0px;">
 +
                <p class="left">
 +
<i>"My name is Jairo Navarro and I am currently 22 years old, the youngest in my family. I was born in Santa Clara, and lived in San Jose until my father when to prison when I was about 8 years old. Since then, I have been living in Watsonville with my mother, brother and sister. I am the first in my family to go to college and I could not have picked a better school than UC Santa Cruz to study Biomolecular Engineering and Bioinformatics. Being a part of this year's iGEM team has been the most rewarding and challenging experience during my undergraduate career. Because of iGEM, I have learned how to fund-raise for a research project, conduct my own research experiments, explain my research in layman's terms and has solidified my decision on going to graduate school.  "</i>
 +
                </p>
 +
               
 +
                </td>
 +
                </tr>
 +
                </table>
 +
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            <div class="profile-cont" data-node="5">
 +
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 +
                <tr>
 +
                <td>
 +
                <p>
 +
                <b>John Poncini</b>
 +
                </p>
 +
                <img src="https://static.igem.org/mediawiki/2015/5/55/QyX9v4a.jpg" style=" width: 236px; height: 355px;" />
 +
                </td>
 +
                <td>
 +
                <ul class="list-unstyled">
 +
        <li><span>Biomolecular Engineering<br /> </span><em><span>Bioinformatics minor</span></em><span><br /> College 8 (UCSC)<br /> 4th Year<br /> Grant &amp; Video Team<br /> From: Stockton, CA&nbsp;</span></li>
 +
</ul>
 +
                </td>
 +
                </tr>
 +
                </table>
 +
<table style=" width: 500px; padding: 0px; margin: auto;">
 +
                <tr>
 +
                <td style=" padding: 0px;">
 +
                <p class="left">
 +
<i>"I started on the Field Team with an interest in finding and identifying Haloferax species that contain cellulases, enzymes that break down cellulose. The process of screening archaea for cellulases took the majority of the summer so I promptly  switched towards developing a synthetic halophilic cellulase. Using a vast array of computational tools, I developed a pipeline for determining a model cellulase which we will test for expression in Haloferax volcanii. My computational work culminated in the discovery of conserved rare codons in specific gene regions across domains of life, leading towards the development of F.O.C.U.S, our computational strategy for determining rare codons in gene sequences. I hope to soon publish my work as well as continue developing useful computational tools for researchers and future iGEM teams."</i>
 +
                </p>
 +
               
 +
                </td>
 +
                </tr>
 +
                </table>
 +
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 +
            <div class="profile-cont" data-node="6">
 +
                <table style=" width: 500px; margin: auto;">
 +
                <tr>
 +
                <td>
 +
                <p>
 +
                <b>Tanvir Saini</b>
 +
                </p>
 +
                <img src="https://static.igem.org/mediawiki/2015/7/75/Amq0zXv.jpg" style=" width: 236px; height: 355px;" />
 +
                </td>
 +
                <td>
 +
                <ul class="list-unstyled">
 +
        <li><span>Molecular, Cell, &amp; </li><li>Developmental Biology<br /> </li></span><li><em><span>Bioinformatics minor</span></em></li><span><li> Oakes College (UCSC)</li><li>5th Year</li><li> Webmaster, Graphic Design, <br />Grant,Social Media&nbsp;&amp; Video Team</li> <li>From: Simi Valley, CA</span></li>
 +
</ul>
 +
                </td>
 +
                </tr>
 +
                </table>
 +
<table style=" width: 500px; padding: 0px; margin: auto;">
 +
                <tr>
 +
                <td style=" padding: 0px;">
 +
                <p class="left">
 +
<i><i>"Saying that the iGEM experience was simply amazing would be the understatement of the year. As a transfer student from a community college, I was able to utilize and refine my lab techniques. As the summer rolled on I gradually learned far more advanced techniques along the way. I can confidently say that this is the highlight of my undergraduate carrer. Besides lab techniques, I was able to use business techniques and tricks I had learned from leadership positions from my former part-time jobs. With these skills I was able to give it my all on every front. Myself and a few others decided to split our efforts between lab work and fundraising. Together we were able to fund about $23,000, and during this time, these very same colleagues along with the rest of the team, have become my second family. The laughs, discoveries, and frustrations from this experience will follow me into the future. The hands on work I have done here has left me wanting more."</i></i>
 +
                </p>
 +
               
 +
                </td>
 +
                </tr>
 +
                </table>
 +
            </div>
 +
            <div class="profile-cont" data-node="7">
 +
                <table style=" width: 500px;">
 +
                <tr>
 +
                <td>
 +
                <p>
 +
                <b>Roger Volden</b>
 +
                </p>
 +
                <img src="https://static.igem.org/mediawiki/2015/8/86/Ec2n2bM.jpg" style=" width: 236px; height: 355px;" />
 +
                </td>
 +
                <td>
 +
                <ul class="list-unstyled">
 +
        <li><span>Biomolecular Engineering<br /> </span><em><span>Bioinformatics minor</span></em><span><br /> College Eight (UCSC)<br /> 3rd Year<br /> From: San Jose, CA</span></li>
 +
</ul>
 +
                </td>
 +
                </tr>
 +
                </table>
 +
<table style=" width: 500px; padding: 0px; margin: auto;">
 +
                <tr>
 +
                <td style=" padding: 0px;">
 +
                <p class="left">
 +
<i>"I would undoubtedly say that I have gotten much more comfortable with the people I work with in lab, and it has definitely made me more productive and contribute more to everything that happens. I have definitely grown as a person because of iGEM, and I feel like I have become a better researcher, teammate, and friend because of it. Between all of the lunches, coffee runs, socials, and lab time, I would say that the UCSC iGEM team is like a second family to me. I know I'll always cherish the work that we've been doing and that I'll look back and know how it influenced me as a person."</i>
 +
                </p>
 +
               
 +
                </td>
 +
                </tr>
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Latest revision as of 03:15, 19 September 2015

Breakdown


Background:

Cellulose is the most abundant carbon source on the planet and consequently, cellulolysis is an essential part to the carbon cycle as it replenishes atmospheric carbon. However, the rate of atmospheric carbon accumulation has been increasing exponentially since the onset of industrial age combustion of fossil fuels. Significant changes in global climate can be attributed to increased atmospheric carbon levels, calling an action to start using renewable carbon energy sources. We aim to use waste cellulosic biomass from paper and crop waste as a source of renewable energy by harnessing the catalytic activity of the enzymes responsible for cellulolysis, a class of enzymes known as cellulases, and engineering these cellulases to be tolerant to high saline solutions to reduce the energy cost of the cellulose pretreatment process. There are three main types of cellulases: endocellulases, exocellulases, and beta-glucosidases; each play a vital role in cellulose degradation. Endocellulases cleave the hydrogen bonds between crystalline cellulose polymers, exposing the free beta-linked polysaccharide chains. Exocellulases then bind the ends of loose cellulose strands and cleave the beta-1,4 glycosidic bonds between every two or three glucose subunits producing either cellobiose or cellotriose. Beta-glucosidase finally converts cellobiose into glucose, concluding the cellulose degradation pathway.

Methods:

We chose to transform Haloferax Volcanii with a B-glucosidase. Our pipeline was to collect data from different cellulases across various organisms, determine which are secreted, and decide which to try to codon optimize to transform into Hvo.

Future Goals:

Transform Hvo with our - glucosidase(WT) - pTA963C constructs. Then, test each for expression and enzymatic activity.


View our Notebook for our methodology that lead to our results.


Swathi Balaji

  • Biomolecular Engineering
  • Bioinformatics minor
  • College Nine (UCSC)
  • 4th Year
  • Grant & Web Team
  • From: Pleasanton, CA

"Being a part of the UCSC iGEM team this summer has provided me with a valuble life experience to say the vey least. Not only was I able to refine my existing lab techniques and develop new ones, but I was also able to learn how to efficienty work and communicate with my own team to assure maximum success. Over the course of the summer I can say that I have grown both as a person and as a researcher. I am truly glad to have taken on such an opportunity and to have been able to contribute to the scientific community in some way. The amount of experiences and knowledge that I was able to obtain in the past couple of months is definitely something that will remain with me far beyond my undergraduate years."

Anissa Benabbas

  • Biology
  • Bioinformatics minor
  • Crown College (UCSC)
  • Graduate (Post Bac)
  • Video Team
  • From: Sunnyvale, CA

"May name is Anissa, and I am a recent graduate in biology with a bioinformatics minor. I took part in the breakdown portion of the iGEM team, my personal goal being to refine wet lab techniques as well as learn computational skills. Aside from the wet lab work, I also took part in the outreach portion of the team's efforts, such as the crowdfund video. I learned so much in the duration of the summer, and it was a pleasure working in a group of so many bright individuals striving to achieve a common goal. I look forward to taking the skills I've learned in this experience with me to graduate school and beyond."

Cristian Camacho

  • Biomolecular Engineering
    Bioinformatics minor
    Crown College (UCSC)
    4th Year
    Grant & Video Team
    From: La Mirada, CA

"In my opinion, the greatest part of the iGEM experience was being able to witness and take part in the unimaginable amount of success that a random group could produce in such a short period of time. Being able to operate efficiently as a team on a multi-layered project, raising over $24,000, making new discoveries, and establishing an image for our team and project that we can be proud of. I’ve learned so much because of iGEM, and along the way I’ve been blessed to become friends with a remarkable group of individuals that have helped me become a better leader and a better person."

Jairo Navarro

  • Biomolecular Engineering
    Bioinformatics minor
    College Nine (UCSC)
    4th Year
    Grant, Programming, Video, &
    Web Team
    From: Watsonville, CA

"My name is Jairo Navarro and I am currently 22 years old, the youngest in my family. I was born in Santa Clara, and lived in San Jose until my father when to prison when I was about 8 years old. Since then, I have been living in Watsonville with my mother, brother and sister. I am the first in my family to go to college and I could not have picked a better school than UC Santa Cruz to study Biomolecular Engineering and Bioinformatics. Being a part of this year's iGEM team has been the most rewarding and challenging experience during my undergraduate career. Because of iGEM, I have learned how to fund-raise for a research project, conduct my own research experiments, explain my research in layman's terms and has solidified my decision on going to graduate school. "

John Poncini

  • Biomolecular Engineering
    Bioinformatics minor
    College 8 (UCSC)
    4th Year
    Grant & Video Team
    From: Stockton, CA 

"I started on the Field Team with an interest in finding and identifying Haloferax species that contain cellulases, enzymes that break down cellulose. The process of screening archaea for cellulases took the majority of the summer so I promptly switched towards developing a synthetic halophilic cellulase. Using a vast array of computational tools, I developed a pipeline for determining a model cellulase which we will test for expression in Haloferax volcanii. My computational work culminated in the discovery of conserved rare codons in specific gene regions across domains of life, leading towards the development of F.O.C.U.S, our computational strategy for determining rare codons in gene sequences. I hope to soon publish my work as well as continue developing useful computational tools for researchers and future iGEM teams."

Tanvir Saini

  • Molecular, Cell, &
  • Developmental Biology
  • Bioinformatics minor
  • Oakes College (UCSC)
  • 5th Year
  • Webmaster, Graphic Design,
    Grant,Social Media & Video Team
  • From: Simi Valley, CA

"Saying that the iGEM experience was simply amazing would be the understatement of the year. As a transfer student from a community college, I was able to utilize and refine my lab techniques. As the summer rolled on I gradually learned far more advanced techniques along the way. I can confidently say that this is the highlight of my undergraduate carrer. Besides lab techniques, I was able to use business techniques and tricks I had learned from leadership positions from my former part-time jobs. With these skills I was able to give it my all on every front. Myself and a few others decided to split our efforts between lab work and fundraising. Together we were able to fund about $23,000, and during this time, these very same colleagues along with the rest of the team, have become my second family. The laughs, discoveries, and frustrations from this experience will follow me into the future. The hands on work I have done here has left me wanting more."

Roger Volden

  • Biomolecular Engineering
    Bioinformatics minor
    College Eight (UCSC)
    3rd Year
    From: San Jose, CA

"I would undoubtedly say that I have gotten much more comfortable with the people I work with in lab, and it has definitely made me more productive and contribute more to everything that happens. I have definitely grown as a person because of iGEM, and I feel like I have become a better researcher, teammate, and friend because of it. Between all of the lunches, coffee runs, socials, and lab time, I would say that the UCSC iGEM team is like a second family to me. I know I'll always cherish the work that we've been doing and that I'll look back and know how it influenced me as a person."