{"id":559,"date":"2018-08-08T18:51:37","date_gmt":"2018-08-08T18:51:37","guid":{"rendered":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/?page_id=559"},"modified":"2020-08-21T06:58:48","modified_gmt":"2020-08-21T06:58:48","slug":"biofuels-and-algae","status":"publish","type":"page","link":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/biofuels-and-algae\/","title":{"rendered":"Green Algae Biofuels"},"content":{"rendered":"<div id=\"pl-559\"  class=\"panel-layout\" ><div id=\"pg-559-0\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-559-0-0\"  class=\"panel-grid-cell panel-grid-cell-mobile-last\" ><div id=\"panel-559-0-0-0\" class=\"so-panel widget widget_text panel-first-child panel-last-child\" data-index=\"0\" >\t\t\t<div class=\"textwidget\"><p><a href=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/laura-ludena\/\">LAURA LUDENA<\/a> &amp; <a href=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/audrey-clay-streib\/\">AUDREY CLAY-STREIB<\/a><\/p>\n<\/div>\n\t\t<\/div><\/div><div id=\"pgc-559-0-1\"  class=\"panel-grid-cell panel-grid-cell-empty\" ><\/div><\/div><div id=\"pg-559-1\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-559-1-0\"  class=\"panel-grid-cell panel-grid-cell-mobile-last\" ><div id=\"panel-559-1-0-0\" class=\"so-panel widget widget_metaslider_widget panel-first-child panel-last-child\" data-index=\"1\" ><div id=\"metaslider-id-1162\" style=\"max-width: 900px;\" class=\"ml-slider-3-102-0 metaslider metaslider-flex metaslider-1162 ml-slider has-dots-nav ms-theme-default\" role=\"region\" aria-label=\"Biofuels and Algae\" data-height=\"651\" data-width=\"900\">\n    <div id=\"metaslider_container_1162\">\n        <div id=\"metaslider_1162\">\n            <ul class='slides'>\n                <li style=\"display: block; width: 100%;\" class=\"slide-1163 ms-image \" aria-roledescription=\"slide\" data-date=\"2018-08-22 17:06:02\" data-slide-type=\"image\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/DSC_5446-900x651.jpg\" height=\"651\" width=\"900\" alt=\"\" class=\"slider-1162 slide-1163 msDefaultImage\" \/><div class=\"caption-wrap\"><div class=\"caption\">Laura and Audrey with their final poster<\/div><\/div><\/li>\n                <li style=\"display: none; width: 100%;\" class=\"slide-1166 ms-image \" aria-roledescription=\"slide\" data-date=\"2018-08-22 17:08:37\" data-slide-type=\"image\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/DSC_4065-1-900x651.jpg\" height=\"651\" width=\"900\" alt=\"\" class=\"slider-1162 slide-1166 msDefaultImage\" \/><\/li>\n                <li style=\"display: none; width: 100%;\" class=\"slide-1165 ms-image \" aria-roledescription=\"slide\" data-date=\"2018-08-22 17:08:01\" data-slide-type=\"image\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/DSC_3616-900x651.jpg\" height=\"651\" width=\"900\" alt=\"\" class=\"slider-1162 slide-1165 msDefaultImage\" \/><\/li>\n                <li style=\"display: none; width: 100%;\" class=\"slide-1226 ms-image \" aria-roledescription=\"slide\" data-date=\"2018-08-22 18:59:15\" data-slide-type=\"image\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/C2F055A7-838A-4F85-A8CE-181B52A104BC-900x651.jpeg\" height=\"651\" width=\"900\" alt=\"\" class=\"slider-1162 slide-1226 msDefaultImage\" \/><\/li>\n                <li style=\"display: none; width: 100%;\" class=\"slide-1587 ms-image \" aria-roledescription=\"slide\" data-date=\"2018-08-24 22:33:52\" data-slide-type=\"image\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/1D36CF0D-AA49-46C0-B613-A8CB01C43F70-1-e1535150002426-900x651.jpeg\" height=\"651\" width=\"900\" alt=\"\" class=\"slider-1162 slide-1587 msDefaultImage\" title=\"1D36CF0D-AA49-46C0-B613-A8CB01C43F70 (1)\" \/><div class=\"caption-wrap\"><div class=\"caption\">The Chlamy team and Claudia!<\/div><\/div><\/li>\n            <\/ul>\n        <\/div>\n        \n    <\/div>\n<\/div><\/div><\/div><div id=\"pgc-559-1-1\"  class=\"panel-grid-cell panel-grid-cell-empty\" ><\/div><\/div><div id=\"pg-559-2\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-559-2-0\"  class=\"panel-grid-cell\" ><div id=\"panel-559-2-0-0\" class=\"so-panel widget widget_text panel-first-child panel-last-child\" data-index=\"2\" ><h3 class=\"widget-title\">Background<\/h3>\t\t\t<div class=\"textwidget\"><p><span style=\"font-weight: 400\">Currently, one of the biggest environmental issues we are facing is climate change. The combustion of fossil fuels has rapidly increased the concentration of the greenhouse gas, (CO<\/span><span style=\"font-weight: 400\">2<\/span><span style=\"font-weight: 400\">) in the atmosphere. Unchecked use of fossil fuel consumption has adverse effects on the environment, but they are also a finite resource. To combat the issues presented by fossil fuels, researchers have turned to algal biofuels. Algae accumulate oil that can be extracted and converted to fuel. Production of bio-oil can be carbon neutral, harmless to the environment, grown fast and is renewable. <\/span><\/p>\n<\/div>\n\t\t<\/div><\/div><\/div><div id=\"pg-559-3\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-559-3-0\"  class=\"panel-grid-cell\" ><div id=\"panel-559-3-0-0\" class=\"so-panel widget widget_text panel-first-child panel-last-child\" data-index=\"3\" ><h3 class=\"widget-title\">Our Projects this Summer<\/h3>\t\t\t<div class=\"textwidget\"><p><span style=\"font-weight: 400\">This summer our team focused on three main projects in regards to manipulating green algae. First, we worked with high school teachers to test laboratory activities assessing how the environment influences phenotype. We did this by growing algae in different light conditions and comparing their growth rates and physical appearance, i.e., phenotype. In addition, we researched, wrote and executed an electroporation protocol in <\/span><i><span style=\"font-weight: 400\">Chlamydomonas<\/span><\/i> <i><span style=\"font-weight: 400\">reinhardtii<\/span><\/i><span style=\"font-weight: 400\">. We also grew large quantities of algal biomass to test scaling effects of biofuel generation. Thought this summer internship, we learned a lot of new skills and lab techniques such as: how to do our own custom codes in R. for the data we collected, how to write our own protocol, how to inoculate algae, make media, and how to streak plates. We also learned how to use machines like a centrifuge, a nanodrop, and an incubator. Two very useful skills we were taught that we used throughout the entire internship are how to properly use a pipette and how to read scientific journals.\u00a0<\/span><\/p>\n<\/div>\n\t\t<\/div><\/div><\/div><div id=\"pg-559-4\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-559-4-0\"  class=\"panel-grid-cell\" ><div id=\"panel-559-4-0-0\" class=\"so-panel widget widget_text panel-first-child panel-last-child\" data-index=\"4\" ><h3 class=\"widget-title\">Genotype to Phenotype<\/h3>\t\t\t<div class=\"textwidget\"><p><span style=\"font-weight: 400\">This summer, we conducted the same experiment twice to evaluate how the environment affects the phenotype i.e., growth rate of <\/span><i><span style=\"font-weight: 400\">Chlamydomonas reinhardtii.<\/span><\/i><span style=\"font-weight: 400\"> We did this by creating a light intensity gradient, each condition received either 300 uE, 150 uE, 25 uE and 0 uE (i.e., no light). Both experiments had two replicates for each intensity of light resulting in 4 total replicates. To test and see growth we used qualitative and quantitative data. For qualitative data, we could see the color (phenotype) of each tube and inferred if the cells were growing. For quantitative data, we used an AquaPen (photosynthesis measuring device) to measure the Optical Density at 680 and 720, Quantum Yield, and cell counts. We calculated growth rate from cell counts of each light condition and calculated the carrying capacity for each flask. Once we had all our quantitative data we analyzed and visualized the results using a custom code in R.<\/span><\/p>\n<\/div>\n\t\t<\/div><\/div><\/div><div id=\"pg-559-5\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-559-5-0\"  class=\"panel-grid-cell panel-grid-cell-mobile-last\" ><div id=\"panel-559-5-0-0\" class=\"so-panel widget widget_metaslider_widget panel-first-child panel-last-child\" data-index=\"5\" ><div id=\"metaslider-id-1210\" style=\"max-width: 750px;\" class=\"ml-slider-3-102-0 metaslider metaslider-flex metaslider-1210 ml-slider has-dots-nav ms-theme-default\" role=\"region\" aria-label=\"Algae\" data-height=\"500\" data-width=\"750\">\n    <div id=\"metaslider_container_1210\">\n        <div id=\"metaslider_1210\">\n            <ul class='slides'>\n                <li style=\"display: block; width: 100%;\" class=\"slide-1211 ms-image \" aria-roledescription=\"slide\" data-date=\"2018-08-22 18:44:39\" data-slide-type=\"image\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Poster_cellcounts_final-e1535130953682-650x433.png\" height=\"500\" width=\"750\" alt=\"\" class=\"slider-1210 slide-1211 msDefaultImage\" title=\"Poster_cellcounts_final\" \/><div class=\"caption-wrap\"><div class=\"caption\">Figure 1. Increasing cell density over time for all replicates and light conditions <\/div><\/div><\/li>\n                <li style=\"display: none; width: 100%;\" class=\"slide-1212 ms-image \" aria-roledescription=\"slide\" data-date=\"2018-08-22 18:44:43\" data-slide-type=\"image\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Poster_growth_rate-e1535130989570-650x433.png\" height=\"500\" width=\"750\" alt=\"\" class=\"slider-1210 slide-1212 msDefaultImage\" title=\"Poster_growth_rate\" \/><div class=\"caption-wrap\"><div class=\"caption\">Figure 2. Growth rate for all replicates at each light condition<\/div><\/div><\/li>\n                <li style=\"display: none; width: 100%;\" class=\"slide-1213 ms-image \" aria-roledescription=\"slide\" data-date=\"2018-08-22 18:44:48\" data-slide-type=\"image\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Poster_QY-e1535131007566-650x433.png\" height=\"500\" width=\"750\" alt=\"\" class=\"slider-1210 slide-1213 msDefaultImage\" title=\"Poster_QY\" \/><div class=\"caption-wrap\"><div class=\"caption\">Figure 3. Quantum Yield Over time for each light condition<\/div><\/div><\/li>\n            <\/ul>\n        <\/div>\n        \n    <\/div>\n<\/div><\/div><\/div><div id=\"pgc-559-5-1\"  class=\"panel-grid-cell panel-grid-cell-empty\" ><\/div><\/div><div id=\"pg-559-6\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-559-6-0\"  class=\"panel-grid-cell\" ><div id=\"panel-559-6-0-0\" class=\"so-panel widget widget_text panel-first-child panel-last-child\" data-index=\"6\" ><h3 class=\"widget-title\">Electroporation of Chlamydomonas reinhardtii<\/h3>\t\t\t<div class=\"textwidget\"><p><span style=\"font-weight: 400\">CRISPR\/Cas9 is a defense mechanism in many bacterial cells that scientists have been able to manipulate to successfully edit genes in other organisms. Electroporation is the process of applying an electrical field to cells, which temporarily creates pores in the cell membrane, allowing for DNA, chromosomes, drugs and other chemicals to be introduced into the cell. <\/span><i><span style=\"font-weight: 400\">C. reinhardtii<\/span><\/i><span style=\"font-weight: 400\"> is a micro-eukaryote with a cell wall and lipid bilayer, they are inherently difficult to bioengineer relative to other systems like <\/span><i><span style=\"font-weight: 400\">E. coli<\/span><\/i><span style=\"font-weight: 400\"> or mammalian cells. <\/span><\/p>\n<p><span style=\"font-weight: 400\">Our goal was to create a protocol using electroporation to successfully insert a selection vector and a Cas9 + sgRNA ribonucleoprotein (RNP) complex into <\/span><i><span style=\"font-weight: 400\">C. reinhardtii<\/span><\/i><span style=\"font-weight: 400\">. The overall goal of creating this protocol was to eventually edit their genes to attempt to make them produce more biofuel. <\/span><\/p>\n<\/div>\n\t\t<\/div><\/div><\/div><div id=\"pg-559-7\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-559-7-0\"  class=\"panel-grid-cell\" ><div id=\"panel-559-7-0-0\" class=\"so-panel widget widget_media_image panel-first-child panel-last-child\" data-index=\"7\" ><figure style=\"width: 1024px\" class=\"wp-caption alignnone\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"312\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/MolecularWorkflowhorizontal_v3-1-1024x312.png\" class=\"image wp-image-1253  attachment-large size-large\" alt=\"\" style=\"max-width: 100%; height: auto;\" srcset=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/MolecularWorkflowhorizontal_v3-1-1024x312.png 1024w, https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/MolecularWorkflowhorizontal_v3-1-300x91.png 300w, https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/MolecularWorkflowhorizontal_v3-1-768x234.png 768w, https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/MolecularWorkflowhorizontal_v3-1-e1534966115534.png 780w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"wp-caption-text\">Figure 4. Explains the four main steps needed to insert the pOpt vector and Cas9 enzyme into Chlamy as well as the gene editing step. The check marks represent the steps we were able to complete and include in our protocol. <\/figcaption><\/figure><\/div><\/div><\/div><div id=\"pg-559-8\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-559-8-0\"  class=\"panel-grid-cell\" ><div id=\"panel-559-8-0-0\" class=\"so-panel widget widget_text panel-first-child panel-last-child\" data-index=\"8\" ><h3 class=\"widget-title\">Growth and Collection of Biofuel<\/h3>\t\t\t<div class=\"textwidget\"><p><span style=\"font-weight: 400\">In this experiment, we grew <\/span><i><span style=\"font-weight: 400\">C. reinhardtii<\/span><\/i><span style=\"font-weight: 400\"> in a 10L bioreactor and tested its Optical Density (OD), Quantum Yield (QY) and the cell counts. The purpose of this experiment was to grow enough algae to collect biofuel in order to demonstrate the paradigm of scaling up. As shown in the pictures above, this gives us a model to see how much algae needs to be grown in order to produce a small amount of biofuel. The main challenge to switching over to biofuels is that since it takes a lot of algae to extract a small amount of biofuel, the amount you have to grow to get enough fuel is very high, especially if you want to eventually power something like a truck.<\/span><\/p>\n<\/div>\n\t\t<\/div><\/div><div id=\"pgc-559-8-1\"  class=\"panel-grid-cell\" ><div id=\"panel-559-8-1-0\" class=\"so-panel widget widget_media_gallery panel-first-child panel-last-child\" data-index=\"9\" ><div id='gallery-1' class='gallery galleryid-559 gallery-columns-3 gallery-size-large'><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/website\/'><img loading=\"lazy\" decoding=\"async\" width=\"768\" height=\"1024\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Website-768x1024.png\" class=\"attachment-large size-large\" alt=\"\" aria-describedby=\"gallery-1-1276\" srcset=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Website-768x1024.png 768w, https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Website-225x300.png 225w\" sizes=\"auto, (max-width: 768px) 100vw, 768px\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-1276'>\n\t\t\t\tFigure 6. Shows 10 L of algae\n\t\t\t\t<\/figcaption><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/website-2\/'><img loading=\"lazy\" decoding=\"async\" width=\"768\" height=\"1024\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Website-2-768x1024.png\" class=\"attachment-large size-large\" alt=\"\" aria-describedby=\"gallery-1-1280\" srcset=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Website-2-768x1024.png 768w, https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Website-2-225x300.png 225w\" sizes=\"auto, (max-width: 768px) 100vw, 768px\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-1280'>\n\t\t\t\tFigure 7. Shows 500 mL of algae\n\t\t\t\t<\/figcaption><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/website-1\/'><img loading=\"lazy\" decoding=\"async\" width=\"768\" height=\"1024\" src=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Website-1-768x1024.png\" class=\"attachment-large size-large\" alt=\"\" aria-describedby=\"gallery-1-1277\" srcset=\"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Website-1-768x1024.png 768w, https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-content\/uploads\/sites\/6\/2018\/08\/Website-1-225x300.png 225w\" sizes=\"auto, (max-width: 768px) 100vw, 768px\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-1277'>\n\t\t\t\tFigure 8. Shows 15 mL of algae\n\t\t\t\t<\/figcaption><\/figure>\n\t\t<\/div>\n<\/div><\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"<p>LAURA LUDENA &amp; AUDREY CLAY-STREIB<\/p>\n","protected":false},"author":28,"featured_media":479,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-559","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-json\/wp\/v2\/pages\/559","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-json\/wp\/v2\/users\/28"}],"replies":[{"embeddable":true,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-json\/wp\/v2\/comments?post=559"}],"version-history":[{"count":86,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-json\/wp\/v2\/pages\/559\/revisions"}],"predecessor-version":[{"id":1706,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-json\/wp\/v2\/pages\/559\/revisions\/1706"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-json\/wp\/v2\/media\/479"}],"wp:attachment":[{"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2018\/wp-json\/wp\/v2\/media?parent=559"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}