Team:SJTU-BioX-Shanghai/Parts

From 2014.igem.org

(Difference between revisions)
 
(135 intermediate revisions not shown)
Line 3: Line 3:
{{Template:Team:SJTU-BioX-Shanghai/top-nav}}
{{Template:Team:SJTU-BioX-Shanghai/top-nav}}
{{Template:Team:SJTU-BioX-Shanghai/article}}
{{Template:Team:SJTU-BioX-Shanghai/article}}
 +
{{Template:Team:SJTU-BioX-Shanghai/preview}}
<html>
<html>
<style type="text/css">
<style type="text/css">
-
   .header_logo{ background-image:url("https://static.igem.org/mediawiki/2014/7/7c/SJTU14_project.png");}
+
#groupparts {
 +
    width: 100%;
 +
text-align: center; margin-left: auto; margin-right: auto;
 +
background:#FFF;}
 +
#groupparts table{visibility:visible;}
 +
   .header_logo{ background-image:url("/wiki/images/0/01/SJTU14_parts.png");}
 +
.projtile {
 +
    margin-right:1.167%;
 +
    margin-left:1.167%;
 +
    width:31%;}
 +
 
 +
#passage{
 +
    width:100%;}
 +
#passage p{
 +
    padding:4%;}
 +
 
 +
 
 +
 
 +
#subtitleyjn2{
 +
    margin-left:40%;}
 +
 
</style>
</style>
 +
 +
<div class="content">
<div class="content">
-
<div id="overview">
 
-
  <h2>Aims</h2><hr />
 
-
  <ol><li>Flexbox is a new layout mode in CSS3 that is designed for the more sophisticated needs of the modern web. </li><li>This article will describe the newly-stablized Flexbox syntax in technical detail.</li> <li>Browser support is going to grow quickly, so you’ll be ahead of the game when support is wide enough for Flexbox to be practical. </li><li>Read on if you want to know what it does and how it works!</li></ol>
 
-
  <h2>Background</h2><hr />
 
-
  <p>Authors have long been using tables, floats, inline-blocks, and other CSS properties to lay out their site content. However, none of these tools were designed for the complex webpages and webapps we are making nowadays. Simple things like vertical centering require work. Complex things like flexible grid layouts are so hard that it’s considered ambitious to roll your own, hence the success of CSS grid frameworks. Still, if so many projects needs to do these things, why can’t it just be easy? Flexbox aims to change all that.
 
-
  </p>
 
-
  <h2>Results</h2><hr />
 
-
  <p>Though Flexbox makes it trivial to create layouts that would have been difficult or impossible in the past, it takes some time to get used to the Flexbox way of doing things. New terminology and new abstractions can be a barrier to using Flexbox, so let’s discuss them up-front.</p>
 
-
  </div>
 
-
  <article class="post__article">
 
-
<p>Biology is a dynamic, exciting, and important subject. It is dynamic because it is constantly changing, with new discoveries about the living world being made every day. (Although it is impossible to pinpoint an exact number, approximately 1 million new research articles in biology are published each year.) The subject is exciting because life in all of its forms has always fascinated people. As active scientists who have spent our careers teaching and doing research in a wide variety of fields, we know this first hand.<br>
 
-
  Biology has always been important in peoples’ daily lives, if only through the effects of achievements in medicine and agriculture. Today more than ever the science of biology is at the forefront of human concerns as we face challenges raised both by recent advances in genome science and by the rapidly changing environment.<br>
 
-
  Life’s new edition brings a fresh approach to the study of biology while retaining the features that have made the book successful in the past. A new coauthor, the distinguished entomologist May R. Berenbaum (University of Illinois at Urbana-Champaign) has joined our team, and the role of evolutionary biologist David Hillis (University of Texas at Austin) is greatly expanded in this edition. The authors hail from large, medium-sized, and small institutions. Our multiple perspectives and areas of expertise, as well as input from many col- leagues and students who used previous editions, have in- formed our approach to this new edition.</p>
 
-
  <h2>Enduring Features</h2>
 
-
  <p>We remain committed to blending the presentation of core ideas with an emphasis on introducing students to the process of scientific inquiry. Having pioneered the idea of depicting seminal experiments in specially designed figures, we continue to develop this here, with 79 INVESTIGATING LIFE figures. Each of these figures sets the experiment in perspective and relates it to the accompanying text. As in previous editions, these figures employ a structure: Hypothesis, Method, Results, and Conclusion. They often include questions for further research that ask students to conceive an experiment that would explore a related question. Each Investigating Life figure has a reference to BioPortal (yourBioPortal.com), where citations to the original work as well as additional discussion and references to follow-up re- search can be found.<br>
 
-
  A related feature is the TOOLS FOR INVESTIGATING LIFE figures, which depict laboratory and field methods used in biology. These, too, have been expanded to provide more useful context for their importance.<br>
 
-
  Over a decade ago—in Life’s Fifth Edition—the authors and publishers pioneered the much-praised use of BALLOON CAP- TIONS in our figures. We recognized then, and it is even truer today, that many students are visual learners. The balloon captions bring explanations of intricate, complex processes directly into the illustration, allowing students to integrate information without repeatedly going back and forth between the figure, its legend, and the text.<br>
 
-
  Life is the only introductory textbook for biology majors to begin each chapter with a story. These OPENING STORIES pro- vide historical, medical, or social context and are intended to intrigue students while helping them see how the chapter’s biological subject relates to the world around them. In the new edition, all of the opening stories (some 70 percent of which are new) are revisited in the body of the chapter to drive home their relevance.<br>
 
-
  We continue to refine our well-received chapter organization. The chapter-opening story ends with a brief IN THIS CHAPTER preview of the major subjects to follow. A CHAPTER OUTLINE asks questions to emphasize scientific inquiry, each of which is answered in a major section of the chapter. A RECAP at the end of each section asks the student to pause and answer questions to review and test their mastery of the previous material. The end-of-chapter summary continues this inquiry framework and highlights key figures, bolded terms, and activities and animated tutorials available in BioPortal.</p>
 
-
  <h2>New Features</h2>
 
-
  <p>Probably the most important new feature of this edition is new authorship. Like the biological world, the authorship team of Life continues to evolve. While two of us (Craig Heller and David Sadava) continue as coauthors, David Hillis has a greatly expanded role, with full responsibility for the units on evolution and diversity. New coauthor May Berenbaum has rewritten the chapters on ecology. The perspectives of these two ac- claimed experts have invigorated the entire book (as well as their coauthors).<br>
 
-
  Even with the enduring features (see above), this edition has a different look and feel from its predecessor. A fresh new de- sign is more open and, we hope, more accessible to students. The extensively revised art program has a contemporary style and color palette. The information flow of the figures is easier to follow, with numbered balloons as a guide for students. There are new conceptual figures, including a striking visual timeline for the evolution of life on Earth (Figure 25.12) and a single overview figure that summarizes the information in the genome (Figure 17.4).<br>
 
-
  In response to instructors who asked for more real-world data, we have incorporated a feature introduced online in the Eighth Edition, WORKING WITH DATA. There are now 36 of these exercises, most of which relate to an Investigating Life figure. Each is referenced at the end of the relevant chapter and is available online via BioPortal (yourBioPortal.com). In these exercises, we describe in detail the context and approach of there search paper that forms the basis of the figure. We then ask the student to examine the data, to make calculations, and to draw conclusions.<br>
 
-
  We are proud that this edition is a greener Life, with the goal of reducing our environmental impact. This is the first introductory biology text to be printed on paper earning the Forest Steward- ship Council label, the “gold standard” in green paper products, and it is manufactured from wood harvested from sustainable forests. And, of course, we also offer Life as an eBook.</p>
 
-
  <h2>The Ten Parts</h2>
 
-
  <p>We have reorganized the book into ten parts. Part One, The Science of Life and Its Chemical Basis, sets the stage for the book: the opening chapter focuses on biology as an exciting science. We begin with a startling observation: the recent, dramatic de- cline of amphibian species throughout the world. We then show how biologists have formed hypotheses for the causes of this environmental problem and are testing them by carefully de- signed experiments, with a view not only to understanding the decline, but reversing it. This leads to an outline of the basic principles of biology that are the foundation for the rest of the book: the unity of life at the cellular level and how evolution unites the living world. This is followed by chapters on the basic chemical building blocks that underlie life. We have added a new chapter on nucleic acids and the origin of life, introducing the concepts of genes and gene expression early and expanding our coverage of the major ideas on how life began and evolved at its earliest stages.<br>
 
-
  In Part Two, Cells, we describe the view of life as seen through cells, its structural units. In response to comments by users of our previous edition, we have moved the chapter on cell signal- ing and communication from the genetics section to this part of the book, with a change in emphasis from genes to cells. There is an updated discussion of ideas on the origin of cells and organelles, as well as expanded treatment of water transport across membranes.<br>
 
-
  Part Three, Cells and Energy, presents an integrated view of bio- chemistry. For this edition, we have worked to clarify such challenging concepts as energy transfer, allosteric enzymes, and bio- chemical pathways. There is extensive revision of the discussions of alternate pathways of photosynthetic carbon fixation, as well as a greater emphasis on applications throughout these chapters.<br>
 
-
  Part Four, Genes and Heredity, is extensively revised and reorganized to improve clarity, link related concepts, and provide updates from recent research results. Separate chapters on prokaryotic genetics and molecular medicine have been re- moved and their material woven into relevant chapters. For ex- ample, our chapter on cell reproduction now includes a discus- sion of how the basic mechanisms of cell division are altered in cancer cells. The chapter on transmission genetics now includes coverage of this phenomenon in prokaryotes. New chapters on gene expression and gene regulation compare prokaryotic and eukaryotic mechanisms and include a discussion ofPREFACE xi epigenetics. A new chapter on mutation describes updated applications of medical genetics.<br>
 
-
  In Part Five, Genomes, we reinforce the concepts of the previous part, beginning with a new chapter on genomes—how they are analyzed and what they tell us about the biology of prokaryotes and eukaryotes, including humans. This leads to a chapter describing how our knowledge of molecular biology and genetics underpins biotechnology (the application of this knowledge to practical problems). We discuss some of the latest uses of biotechnology, including environmental cleanup. Part Five finishes with two chapters on development that explore the themes of molecular biology and evolution, linking these two parts of the book.<br>
 
-
  Part Six, The Patterns and Processes of Evolution, emphasizes the importance of evolutionary biology as a basis for comparing and understanding all aspects of biology. These chapters have been extensively reorganized and revised, as well as updated with the latest thinking of biologists in this rapidly changing field. This part now begins with the evidence and mechanisms of evolution, moves into a discussion of phylogenetic trees, then covers speciation and molecular evolution, and concludes with the evolutionary history of life on Earth. An integrated time- line of evolutionary history shows the timing of major events of biological evolution, the movements of the continents, floral and faunal reconstructions of major time periods, and depicts some of the fossils that form the basis of the reconstructions.<br>
 
-
  In Part Seven, The Evolution of Diversity, we describe the latest views on biodiversity and evolutionary relationships. Each chapter has been revised to make it easier for the reader to appreciate the major changes that have evolved within the various groups of organisms. We emphasize understanding the big picture of organismal diversity, as opposed to memorizing a taxonomic hierarchy and names (although these are certainly important). Throughout the book, the tree of life is emphasized as a way of understanding and organizing biological information. A Tree of Life Appendix allows students to place any group of organisms mentioned in the text of our book into the context of the rest of life. The web-based version of this appendix provides links to photos, keys, species lists, distribution maps, and other information to help students explore biodiversity of specific groups in greater detail.<br>
 
-
  After modest revisions in the past two editions, Part Eight, Flowering Plants: Form and Function, has been extensively reorganized and updated with the help of Sue Wessler, to include both classical and more recent approaches to plant physiology. Our emphasis is not only on the basic findings that led to the elucidation of mechanisms for plant growth and reproduction, but also on the use of genetics of model organisms. There is expanded coverage of the cell signaling events that regulate gene expression in plants, integrating concepts introduced earlier in the book. New material on how plants respond to their environment is included, along with links to both the book’s earlier descriptions of plant diversity and later discussions of ecology.<br>
 
-
  Part Nine, Animals: Form and Function, continues to provide a solid foundation in physiology through comprehensive coverage of basic principles of function of each organ system and then emphasis on mechanisms of control and integration. An important reorganization has been moving the chapter on immunology from earlier in the book, where its emphasis was on molecular genetics, to this part, where it is more closely allied to the information systems of the body. In addition, we have added a number of new experiments and made considerable effort to clarify the sometimes complex phenomena shown in the illustrations.<br>
 
-
  Part Ten, Ecology, has been significantly revised by our new coauthor, May Berenbaum. A new chapter of biological interactions has been added (a topic formerly covered in the community ecology chapter). Full of interesting anecdotes and discus- sions of field studies not previously described in biology texts, this new ecology unit offers practical insights into how ecologists acquire, interpret, and apply real data. This brings the book full circle, drawing upon and reinforcing prior topics of energy, evolution, phylogenetics, Earth history, and animal and plant physiology.</p>
 
-
  <h2>Exceptional Value Formats</h2>
 
-
  <p>We again provide Life both as the full book and as a cluster of paperbacks. Thus, instructors who want to use less than the whole book can choose from these split volumes, each with the book’s front matter, appendices, glossary, and index.<br>
 
-
  Volume I, The Cell and Heredity, includes: Part One, The Science of Life and Its Chemical Basis (Chapters 1–4); Part Two, Cells (Chapters 5–7); Part Three, Cells and Energy (Chapters 8–10); Part Four, Genes and Heredity (Chapters 11–16); and Part Five, Genomes (Chapters 17–20).<br>
 
-
  Volume II, Evolution, Diversity, and Ecology, includes: Chapter 1, Studying Life; Part Six, The Patterns and Processes of Evolution (Chapters 21–25); Part Seven, The Evolution of Diversity (Chapters 26–33); and Part Ten, Ecology (Chapters 54–59).<br>
 
-
  Volume III, Plants and Animals, includes: Chapter 1, Study- ing Life; Part Eight, Flowering Plants: Form and Function (Chapters 34–39); and Part Nine, Animals: Form and Function (Chapters 40–53).<br>
 
-
  Responding to student concerns, we offer two options of the entire book at a significantly reduced cost. After it was so well received in the previous edition, we again provide Life as a loose- leaf version. This shrink-wrapped, unbound, 3-hole punched ver- sion fits into a 3-ring binder. Students take only what they need to class and can easily integrate any instructor handouts or other resources.<br>
 
-
  Life was the first comprehensive biology text to offer the en- tire book as a truly robust eBook. For this edition, we continue to offer a flexible, interactive ebook that gives students a new way to read the text and learn the material. The ebook integrates the student media resources (animations, quizzes, activities, etc.) and offers instructors a powerful way to customize the textbook with their own text, images, Web links, documents, and more.</p>
 
-
  <h2>Media and Supplements for the Ninth Edition</h2>
 
-
  <p>The wide range of media and supplements that accompany Life, Ninth Edition have all been created with the dual goal of help- ing students learn the material presented in the textbook more efficiently and helping instructors teach their courses more effectively. Students in majors introductory biology are faced with learning a tremendous number of new concepts, facts, and terms, and the more different ways they can study this mate- rial, the more efficiently they can master it.<br>
 
-
  All of the Life media and supplemental resources have been developed specifically for this textbook. This provides strong consistency between text and media, which in turn helps students learn more efficiently. For example, the animated tutorials and activities found in BioPortal were built using textbook art, so that the manner in which structures are illustrated, the colors used to identify objects, and the terms and abbreviations used are all consistent.<br>
 
-
  For the Ninth Edition, a new set of Interactive Tutorials gives students a new way to explore many key topics across the text- book. These new modules allow the student to learn by doing, including solving problem scenarios, working with experimental techniques, and exploring model systems. All new copies of the Ninth Edition include access to the robust new version of BioPortal, which brings together all of Life’s student and instructor resources, powerful assessment tools, and new integration with Prep-U adaptive quizzing.<br>
 
-
  The rich collection of visual resources in the Instructor’s Media Library provides instructors with a wide range of options for enhancing lectures, course websites, and assignments. High- lights include: layered art PowerPoint® presentations that break down complex figures into detailed, step-by-step presentations; a collection of approximately 200 video segments that can help capture the attention and imagination of students; and Power- Point slides of textbook art with editable labels and leaders that allow easy customization of the figures.<br>
 
-
  For a detailed description of all the media and supplements available for the Ninth Edition, please turn to “Life’s Media and Supplements,” on page xvii.</p>
 
-
  <h2>Many People to Thank</h2>
 
-
  <p>“If I have seen farther, it is by standing on the shoulders of giants.” The great scientist Isaac Newton wrote these words over 330 years ago and, while we certainly don’t put ourselves in his lofty place in science, the words apply to us as coauthors of this text. This is the first edition that does not bear the names of Bill Purves and Gordon Orians. As they enjoy their “retirements,” we are humbled by their examples as biologists, educators, and writers.<br>
 
-
  One of the wisest pieces of advice ever given to a textbook author is to “be passionate about your subject, but don’t put your ego on the page.” Considering all the people who looked over our shoulders throughout the process of creating this book, this advice could not be more apt. We are indebted to many people who gave invaluable help to make this book what it is. First and foremost are our colleagues, biologists from over 100 institutions. Some were users of the previous edition, who suggested many improvements. Others reviewed our chapter drafts in detail, including advice on how to improve the illustrations. Still others acted as accuracy reviewers when the book was al- most completed. All of these biologists are listed in the Reviewer credits.<br>
 
-
  Of special note is Sue Wessler, a distinguished plant biologist and textbook author from the University of Georgia. Sue looked critically at Part Eight, Flowering Plants: Form and Function, wrote three of the chapters (34–36), and was important in the revision of the other three (37–39). The new approach to plant biology in this edition owes a lot to her.<br>
 
-
  The pace of change in biology and the complexities of preparing a book as broad as this one necessitated having two developmental editors. James Funston coordinated Parts 1–5, and Carol Pritchard-Martinez coordinated Parts 6–10. We benefit- ted from the wide experience, knowledge, and wisdom of both of them. As the chapter drafts progressed, we were fortunate to have experienced biologist Laura Green lending her critical eye as in-house editor. Elizabeth Morales, our artist, was on her third edition with us. As we have noted, she extensively revised al- most all of the prior art and translated our crude sketches into beautiful new art. We hope you agree that our art program remains superbly clear and elegant. Our copy editors, Norma Roche, Liz Pierson, and Jane Murfett, went far beyond what such people usually do. Their knowledge and encyclopedic recall of our book’s chapters made our prose sharper and more accurate. Diane Kelly, Susan McGlew, and Shannon Howard effectively coordinated the hundreds of reviews that we described above. David McIntyre was a terrific photo editor, finding over 550 new photographs, including many new ones of his own, that enrich the book’s content and visual statement. Jefferson Johnson is responsible for the design elements that make this edition of Life not just clear and easy to learn from, but beautiful as well. Christopher Small headed the production department—Joanne Delphia, Joan Gemme, Janice Holabird, and Jefferson Johnson—who contributed in innumerable ways to bringing Life to its final form. Jason Dirks once again coordinated the creation of our array of media and supplements, including our superb new Web resources. Carol Wigg, for the ninth time in nine editions, oversaw the editorial process; her influence pervades the entire book.<br>
 
-
  W. H. Freeman continues to bring Life to a wider audience. Associate Director of Marketing Debbie Clare, the Regional Specialists, Regional Managers, and experienced sales force are effective ambassadors and skillful transmitters of the features and unique strengths of our book. We depend on their expertise and energy to keep us in touch with how Life is perceived by its users. And thanks also to the Freeman media group for eBook and BioPortal production.<br>
 
-
  Finally, we are indebted to Andy Sinauer. Like ours, his name is on the cover of the book, and he truly cares deeply about what goes into it. Combining decades of professionalism, high standards, and kindness to all who work with him, he is truly our mentor and friend.</p>
 
-
  <p>DAVID SADAVA DAVID HILLIS CRAIG HELLER MAY BERENBAUM</p>
 
-
  </article>
 
-
  </div>
 
 +
<div class="jiao" >
-
<style type="text/css">
+
<div class="projtile_only">
-
#groupparts {text-align: center; margin-left: auto; margin-right: auto;}
+
      <center><h2>Parts</h2></br></center>
-
</style>
+
<center>
-
<!--main content -->
+
<p>We have characterized and submitted 25 BioBricks which could either be used directly or serve as a universal tool ready for potential scientific or engineering use.<br>
-
<table width="70%" align="center">
+
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Those BioBricks are divided into four groups.</br>
-
<!--welcome box -->
+
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1. BioBricks in Basic Parts are all basic components of the whole project. They can be assembled to carry out different tasks.</br>
-
<tr>
+
 
-
<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
+
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2. BioBricks in USB are our designed sequences. They can help us easily and quickly insert our target sequence and make a whole part.</br>
-
<h1 >WELCOME TO iGEM 2014! </h1>
+
 
-
<p>Your team has been approved and you are ready to start the iGEM season!
+
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3. BioBricks in Application are our complete parts. </br>
-
<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
+
 
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;4. BioBricks in New TAL are our newly designed TAL parts, which are robust and perform better in Golden Gate method.</br>
 +
 
 +
</p>
 +
</center>
 +
 
 +
</div>
 +
 
 +
    <div class="projtile" >
 +
  <a href="#dingweidian2" title="Basic Parts">
 +
    <center><h2>Basic Parts</h2></center></a>
 +
    </div>
 +
     
 +
    <div class="projtile">
 +
  <a href="#dianweidian9"  title="USB">
 +
    <center> <h2>USB</h2></center></a>
 +
    </div>
 +
     
 +
    <div class="projtile">
 +
<a href="#dianweidian14" title="Application">
 +
    <center><h2>Application</h2></center></a>
 +
    </div>
 +
    <div class="projtile">
 +
<a href="#dianweidian10" title="New TAL">
 +
    <center><h2>New TAL</h2></center></a>
 +
    </div>
 +
 
 +
 
 +
 
 +
 
 +
</div>
 +
 
 +
<div style="clear:both;"></div></html>
 +
<groupparts>iGEM014 SJTU-BioX-Shanghai</groupparts><p id="dingweidian2"></p>
 +
<html><div class="content"><article class="post__article">
 +
</br></br>
 +
<h2>Basic Parts</h2>
 +
<h3>Review previous parts</h3>
 +
<p>
 +
ssDsbA: SsDsbA is the signal recognition particle (SRP)-dependent signaling sequence of DsbA. SsDsbA-tagged proteins are exported to the periplasm through the SRP pathway. With ssDsbA fused to the N-terminus, fusion proteins with Lgt are expected to be anchored onto inner membrane of E.coli.<br><a name="#dianweidian2"></a>
 +
From: ssDsbA-PDZ Ligand-LGT-SH3 Ligand ( (<a href="http://parts.igem.org/Part:BBa_K771002" target="_blank">BBa_K771002</a>, SJTU-BioX-Shanghai)
 +
</p>
 +
<p>
 +
Lgt: Phosphatidylglycerol:: prolipoprotein diacylglyceryl transferase (Lgt) is an inner membrane protein act as an membrane anchor of E.coli with seven transmembrane segments and has been successfully overexpressed in E. coli without causing harm to cells.<br>
 +
From: ssDsbA-PDZ Ligand-LGT-SH3 Ligand (<a href="http://parts.igem.org/Part:BBa_K771002" target="_blank">BBa_K771002</a>, SJTU-BioX-Shanghai)
 +
</p>
 +
<p>
 +
mRFP: Red Fluorescent Protein. To visualize the localization of fusion protein with fluorescence test , we added mRFP in the Connectee1 and placed it just after the ssDsbA.<br>
 +
From: Highly engineered mutant of red fluorescent protein from Discosoma striata (<a href="http://parts.igem.org/Part:BBa_E1010" target="_blank">BBa_E1010</a>, Antiquity )
 +
<h3>FL3-TALE<a href="http://parts.igem.org/Part:BBa_K1453300" target="_blank">(BBa_K1453300)</a></h3>
 +
<center><img src="https://static.igem.org/mediawiki/parts/7/73/Fl3tal.png" width=400px></img></center>
 +
</br><center><small><strong>Figure 2.3.1 Diagram of FL3-TALE</strong></small></center></br>
 +
<p>
 +
This is a TALE protein with a flexible linker 3 before it. <br>
 +
</p>
 +
<p>
 +
Since we cannot connect TALE by Golden Gate method designed by 2012 Freiburg, so the sequence was synthesized by Genwize company. This TALE can recognize the DNA sequence TTGGTCATGAGA(12bp). Moreover, we use this part with our part BBa_K14530000 to make our composite part BBa_K1453305.<br>
 +
 
 +
</p>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<h3>Connector</h3>
 +
<p>
 +
We have four types of connector.
<br>
<br>
-
<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:SJTU-BioX-Shanghai/Parts&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
+
<center><img src="https://static.igem.org/mediawiki/2014/f/fb/4plasmid.png" width= 800px></img></center>
-
</td>
+
</br><center><small><strong>Figure 2.3.2 Diagram of four types of connector: pBluescript II KS(+) ScaI deletion, </strong></small></center>
-
</tr>
+
</br><center><small><strong>pBluescript II KS(+) EcoRV deletion, pBluescript II KS(+)_3_copy and pBluescript II KS(+)_5_copy</strong></small></center></br>
 +
<p>
 +
pBluescript II KS(+) ScaI deletion <a href="http://parts.igem.org/Part:BBa_K1453901" target="_blank">(BBa_K1453901)</a>
 +
</p>
 +
<p>
 +
pBluescript II KS(+) EcoRV deletion <a href="http://parts.igem.org/Part:BBa_K1453001" target="_blank">(BBa_K1453001)</a>
 +
</p>
 +
<p>
 +
pBluescript II KS(+)_3_copy <a href="http://parts.igem.org/Part:BBa_K1453003" target="_blank">(BBa_K1453003)</a>  
 +
</p>
 +
<p>
 +
pBluescript II KS(+)_5_copy <a href="http://parts.igem.org/Part:BBa_K1453004" target="_blank">(BBa_K1453004)</a>  
 +
</p>
-
<tr> <td colspan="3"  height="5px"> </td></tr>
+
<p>
-
<!-- end welcome box -->
+
Each type of connector has its own function. If you want to know the details, please click it. We have introduction on our part's main page.<br>
-
<tr>  
+
<br>
 +
</p>
-
<!--navigation menu -->
+
<h3>ssDsbA-mRFP-Lgt-TAL1-His Tag<a href="http://parts.igem.org/Part:BBa_K1453005" target="_blank">(BBa_K1453005)</a></h3>
-
<td align="center" colspan="3">
+
-
<table  width="100%">
+
<center><img src="https://static.igem.org/mediawiki/2014/4/41/Membrane_TAL1.png" width=800px></img></center>
-
<tr heigth="15px"></tr>
+
</br><center><small><strong>Figure 2.3.3 Diagram of ssDsbA-mRFP-Lgt-TAL1-His Tag</strong></small></center></br>
-
<tr heigth="75px">  
+
<p>
 +
The structure is based on the BBa_1453000 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats
 +
protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089.
 +
<br>
 +
</p>
 +
<br>
 +
<br>
 +
<h3>TAL1-His Tag<a href="http://parts.igem.org/Part:BBa_K1453007" target="_blank">(BBa_K1453007)</a></h3>
 +
<center><img src="https://static.igem.org/mediawiki/2014/e/e6/Free_TAL1.png" width=400px></img></center>
 +
</br><center  id="dianweidian9"><small><strong>Figure 2.3.4 Diagram of TAL1-His Tag</strong></small></center></br>
 +
<p>
 +
This part is a first second of connectee, which we used to check the connection between connectee and connector in our basic test.
 +
</p>
 +
<p>
 +
The structure is based on the BBa_K1453006 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089.
 +
<br>
 +
</p>
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
 
-
<a href="https://2014.igem.org/Team:SJTU-BioX-Shanghai"style="color:#000000">Home </a> </td>
 
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
 
-
<a href="https://2014.igem.org/Team:SJTU-BioX-Shanghai/Team"style="color:#000000"> Team </a> </td>
 
-
<td style="border:1px solid black;" align="center"  height ="45px"  onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
 
-
<a href="https://igem.org/Team.cgi?year=2014&team_name=SJTU-BioX-Shanghai"style="color:#000000"> Official Team Profile </a></td>
 
-
<td style="border:1px solid black" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
<br>
-
<a href="https://2014.igem.org/Team:SJTU-BioX-Shanghai/Project"style="color:#000000"> Project</a></td>
+
<h2>USB</h2>
 +
<p>We make two kinds of USB. One is TAL USB, the other is Enzyme USB. They can help us easily and quickly insert our target TALE or Enzyme, respectively.</p>
 +
<h3>TAL USB<a href="http://parts.igem.org/Part:BBa_K1453000" target="_blank">(BBa_K1453000)</a></h3>
 +
<center><img src="https://static.igem.org/mediawiki/2014/9/9b/Part%EF%BC%9ABBa_K1453000.png" width= 800px></img></center>
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
</br><center><small><strong>Figure 2.3.5 Diagram of TAL USB</strong></small></center></br>
-
<a href="https://2014.igem.org/Team:SJTU-BioX-Shanghai/Parts"style="color:#000000"> Parts</a></td>
+
<p>
 +
We design a sequence which can be used together with 2012 Freiburg's part. The TAL USB can make two specific sticky ends. The two ends are the same as the first part and the last part of Freiburg design. So when we digest and ligate them together, we can get a whole TALE. But unluckily, since the sticky ends designed by Freiburg are too similar, we can just have some mismatch sequence by using these TAL USB.
 +
</p>
 +
<h3>Enzyme USB<a href="http://parts.igem.org/Part:BBa_K1453400" target="_blank">(BBa_K1453400)</a><a href="http://parts.igem.org/Part:BBa_K1453401" target="_blank">(BBa_K1453401)</a></h3>
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
<br>
-
<a href="https://2014.igem.org/Team:SJTU-BioX-Shanghai/Modeling"style="color:#000000"> Modeling</a></td>
+
<p>
 +
In order to easily and quickly insert the target function enzyme into our system, we design two enzyme-USBs. The enzyme USB have three fundamental components, flexible linker- enzyme adaptor-flexible linker. </p>
 +
<center><img src="https://static.igem.org/mediawiki/parts/5/5c/Aari.png" width=400px></img></center>
 +
<center><img src="https://static.igem.org/mediawiki/parts/9/91/Bsmai.png" width=400px></img></center>
 +
</br><center><small><strong>Figure 2.3.6 Diagram of two kinds of enzyme USB: AarI and BsmBI</strong></small></center></br>
 +
<p>
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
The first flexible linker has deleted the PstI recognition site. And at the beginning of the sequence there is a Bsu36I recognition site. The second flexible linker we replace the original PstI site with a isocaudamer SduI, since our part can not have a PstI recognition site. </p><p>
-
<a href="https://2014.igem.org/Team:SJTU-BioX-Shanghai/Notebook"style="color:#000000"> Notebook</a></td>
+
On the other hand, the enzyme adaptor has two same restriction enzyme recognition sites. In one of our enzyme-USB, it is the AarI recognition site; The other enzyme-USB is the BsmAI recognition site. The AarI and BsmAI are similar to BsmBI which all can make a 4bp sticky end designed by ourselves.</p><p>
 +
When we want to insert a functional enzyme into our fusion protein, first we need to have a PCR experiment to add a head and a tail around our enzyme. After that, the enzyme product also has the restriction enzyme recognition site. When digested by the specific restriction enzyme, it can generate the same sticky ends, so our enzyme can be inserted into our part.</p>
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
<br>
-
<a href="https://2014.igem.org/Team:SJTU-BioX-Shanghai/Safety"style=" color:#000000"> Safety </a></td>
+
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
<h3>TAL_USB-His Tag<a href="http://parts.igem.org/Part:BBa_K1453006" target="_blank">(BBa_K1453006)</a></h3>
-
<a href="https://2014.igem.org/Team:SJTU-BioX-Shanghai/Attributions"style="color:#000000"> Attributions </a></td>
+
 +
<center><img src="https://static.igem.org/mediawiki/2014/0/0d/FL-TAL_USB-His_Tag.png" width=400px></img></center>
 +
</br><center><small><strong>Figure 2.3.7 Diagram of TAL_USB-His Tag</strong></small></center></br>
 +
<p>
 +
In order to bind TAL protein designed by 2012 Freiburg iGEM team, the TAL USB also consists of T1 sequence, T14 sequence and two sites for type II restriction enzyme BsmBI.
 +
<p>
 +
When digested with BsmBI, this part can produce two sticky-ends that can bind TAL-Protein DiRepeat (Bba_K747000 to Bba_K747095)
 +
<br>
 +
</p>
-
<td align ="center"> <a href="https://2014.igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px"></a> </td>
+
<br>
-
</tr>
+
-
</table>
+
-
<!--end navigation menu -->
+
<h3>ssDsbA-Lgt-Enzyme USB(BsmAI)-TAL_USB-His Tag<a href="http://parts.igem.org/Part:BBa_K1453402" target="_blank">(BBa_K1453402)</a></h3>
-
</tr>
+
 +
<center><img src="https://static.igem.org/mediawiki/2014/f/fe/3402.png" width=800px></img></center>
 +
</br><center><small><strong>Figure 2.3.8 Diagram of ssDsbA-Lgt-Enzyme USB(BsmAI)-TAL_USB-His Tag</strong></small></center></br>
 +
<p>
 +
This part is the combination of BBa_K1453401 BBa_K1453006 and BBa_K1453000.See more details please search these two parts of iGEM14_SJTU_BioX_Shanghai.
 +
<br>
 +
</p>
-
</tr>
+
<br>
-
+
 +
<h3>ssDsbA-Lgt-Enzyme USB(AarI)-TAL_USB-His Tag<a href="http://parts.igem.org/Part:BBa_K1453403" target="_blank">(BBa_K1453403)</a></h3>
 +
<center><img src="https://static.igem.org/mediawiki/2014/2/29/3403.png" width=800px></img></center>
 +
</br><center><small><strong>Figure 2.3.9 Diagram of ssDsbA-Lgt-Enzyme USB(AarI)-TAL_USB-His Tag</strong></small></center></br>
 +
<p>
 +
This part is the combination of BBa_K1453400 BBa_K1453006 and BBa_K1453000.See more details please search these two parts of iGEM14_SJTU_BioX_Shanghai.
 +
<br>
 +
</p>
-
</td>
+
<br>
-
<tr> <td colspan="3"  height="15px"> </td></tr>
 
-
<tr><td bgColor="#e7e7e7" colspan="3" height="1px"> </tr>
 
-
<tr> <td colspan="3"  height="5px"> </td></tr>
 
-
<!--Parts Submitted to the Registry  -->
+
<h3>Enzyme USB(BsmAI)-TAL_USB-His Tag<a href="http://parts.igem.org/Part:BBa_K1453406" target="_blank">(BBa_K1453406)</a></h3>
-
<tr><td > <h3> Parts Submitted to the Registry </h3></td>
+
 
-
<td ></td >
+
<center><img src="https://static.igem.org/mediawiki/2014/4/4a/3406.png" width=400px></img></center>
-
<td > <h3>What information do I need to start putting my parts on the Registry? </h3></td>
+
</br><center><small><strong>Figure 2.3.10 Diagram of Enzyme USB(BsmAI)-TAL_USB-His Tag</strong></small></center></br>
-
</tr>
+
-
<tr>
+
-
<td width="45%"  valign="top">  
+
<p>
<p>
-
An important aspect of the iGEM competition is the use and creation of standard  biological parts. Each team will make new parts during iGEM and will submit them to the <a href="http://partsregistry.org"> Registry of Standard Biological Parts</a>. The iGEM software provides an easy way to present the parts your team has created. The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. 
+
This part is the combination of BBa_K1453401 and BBa_K1453006.
 +
<br>
 +
</p>
 +
<br>
 +
 +
 +
<h3 id="dianweidian14">Enzyme USB(AarI)-TAL_USB-His Tag<a href="http://parts.igem.org/Part:BBa_K1453407" target="_blank">(BBa_K1453407)</a></h3>
 +
 +
<center><img src="https://static.igem.org/mediawiki/2014/0/09/3407.png" width=400px></img></center>
 +
</br><center><small><strong>Figure 2.3.11 Diagram of Enzyme USB(AarI)-TAL_USB-His Tag</strong></small></center></br>
<p>
<p>
-
<strong>Note that if you want to document a part you need to document it on the <a href="http://partsregistry.org Registry"> Registry</a>, not on your team wiki.</strong> Future teams and other users and are much more likely to find parts on the Registry than on your team wiki.
+
This part is the combination of BBa_K1453400 and BBa_K1453006.See more details please search these two parts of iGEM14_SJTU_BioX_Shanghai.
 +
<br>
</p>
</p>
 +
<br>
 +
 +
<h2>Application</h2>
<p>
<p>
-
Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without a need to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.
+
We chose some functional enzymes and inserted them into <strong><em>connectees</em></strong>
 +
<br>
 +
We want to prove that our <strong><em>connectees and connectors</em></strong> system can successfully achieve our designed function in the end.
 +
<br>
</p>
</p>
 +
<h3>ssDsbA-Lgt-pykF-TAL1-His Tag<a href="http://parts.igem.org/Part:BBa_K1453404" target="_blank">(BBa_K1453404)</a></h3>
 +
<center><img src="https://static.igem.org/mediawiki/2014/9/93/3404.png" width=800px></img></center>
 +
</br><center><small><strong>Figure 2.3.12 Diagram of ssDsbA-Lgt-pykF-TAL1-His Tag</strong></small></center></br>
 +
<p>
 +
This part is based on the BBa_K1453402 or BBa_K1453403 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089. The enzyme we used here is the pyruvate kinase (EC:2.7.1.40) or pykF.
 +
<br>
 +
</p>
-
<h3>When should you put parts into the Registry?</h3>
+
<br>
 +
<h3>ssDsbA-Lgt-poxB-TAL1-His Tag<a href="http://parts.igem.org/Part:BBa_K1453405" target="_blank">(BBa_K1453405)</a></h3>
 +
 +
<center><img src="https://static.igem.org/mediawiki/2014/a/ab/3405.png" width=800px></img></center>
 +
</br><center><small><strong>Figure 2.3.13 Diagram of ssDsbA-Lgt-poxB-TAL1-His Tag</strong></small></center></br>
<p>
<p>
-
As soon as possible! We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better recall you will have of all details surrounding your parts. Remember you don't need to send us the DNA to create an entry for a part on the Registry. However, you must send us the sample/DNA before the Jamboree. Only parts for which you have sent us samples/DNA are eligible for awards and medal requirements.  
+
This part is based on the BBa_K1453402 or BBa_K1453403 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089. The enzyme we used here is the pyruvate dehydrogenase (quinone) [EC:1.2.5.1] or poxB
 +
<br>
</p>
</p>
-
</td>
 
-
<td > </td>
+
<br>
-
<td width="45%" valign="top">
+
 +
<h3>pykF-TAL1-His Tag<a href="http://parts.igem.org/Part:BBa_K1453408" target="_blank">(BBa_K1453408)</a></h3>
 +
 +
<center><img src="https://static.igem.org/mediawiki/2014/f/ff/3408.png" width=400px></img></center>
 +
</br><center><small><strong>Figure 2.3.14 Diagram of pykF-TAL1-His Tag</strong></small></center></br>
<p>
<p>
-
The information needed to initially create a part on the Registry is:
+
This part is used in our application test free in the cytoplasm.
 +
</p>
 +
<p>
 +
This part is based on the BBa_K1453406 or BBa_K1453407 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089. The enzyme we used here is the pyruvate kinase (EC:2.7.1.40) or pykF.
 +
<br>
</p>
</p>
-
<ol>
 
-
<li>Part Name</li>
+
<br>
-
<li>Part type</li>
+
-
<li>Creator</li>
+
-
<li>Sequence</li>
+
-
<li>Short Description (60 characters on what the DNA does)</li>
+
-
<li>Long Description (Longer description of what the DNA does)</li>
+
-
<li>Design considerations</li>
+
-
</ol>
+
 +
 +
<h3>poxB-TAL1-His Tag<a href="http://parts.igem.org/Part:BBa_K1453409" target="_blank">(BBa_K1453409)</a></h3>
 +
 +
<center><img src="https://static.igem.org/mediawiki/2014/7/7e/3409.png" width=400px></img></br><p id="dianweidian10"></p></center>
 +
</br><center><small><strong>Figure 2.3.15 Diagram of poxB-TAL1-His Tag</strong></small></center></br>
 +
<p >
 +
This part is used in our application test free in the cytoplasm.
 +
</p>
<p>
<p>
-
We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. Check out part <a href="http://parts.igem.org/Part:BBa_K404003">BBa_K404003</a> for an excellent example of a highly characterized part.  
+
This part is based on the BBa_1453006 and BBa_K1453406 or BBa_K1453407 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089. The enzyme we used here is the pyruvate dehydrogenase (quinone) [EC:1.2.5.1] or poxB
</p>
</p>
 +
<br>
 +
 +
 +
 +
 +
 +
<h2>New TAL</h2>
 +
<h3>New TAL with better sticky ends<a href="http://parts.igem.org/Part:BBa_K1453500" target="_blank">(BBa_K1453500)</a>
 +
<a href="http://parts.igem.org/Part:BBa_K1453501" target="_blank">(501)</a>
 +
<a href="http://parts.igem.org/Part:BBa_K1453502" target="_blank">(502)</a>
 +
<a href="http://parts.igem.org/Part:BBa_K1453503" target="_blank">(503)</a>
 +
<a href="http://parts.igem.org/Part:BBa_K1453504" target="_blank">(504)</a>
 +
<a href="http://parts.igem.org/Part:BBa_K1453505" target="_blank">(505)</a>
 +
<a href="http://parts.igem.org/Part:BBa_K1453506" target="_blank">(506)</a></h3>
<p>
<p>
-
You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry"> Add a Part to the Registry</a> link.
+
We design seven new sticky ends which get the least score when judging the similarity.<br>
 +
If you want to know how we design these ends, please go to see our  
 +
<a href="https://2014.igem.org/Team:SJTU-BioX-Shanghai/Part3_TAL_Improvement" >project-Part3 TAL improve</a>.<br>
</p>
</p>
-
</td>
+
<p>
-
</tr>
+
<br>
 +
</p>
 +
<p >
 +
<b>PART-left:</b><br>
 +
…CTGACCCCGGAGACG
 +
</p>
 +
<p>
 +
<b>PART1(150bp):</b><br>
 +
CGTCTCGCCCCGGAACAGGTGGTGGCCATTGCAAGCAACGGTGGTGGCAAGCAGG
 +
CCCTGGAGACAGTCCAACGGCTGCTTCCGGTTCTGTGTCAGGCCCACGGCCTGACT
 +
CCAGAACAAGTGGTTGCTATCGTGGCGGAAAATGAGACG</p>
 +
<p>
 +
<b>PART2(219bp):</b><br>
 +
CGTCTCTAAAACAAGCCCTCGAAACCGTGCAGCGCCTGCTTCCGGTGCTGTGTCAG
 +
GCCCACGGGCTCACCCCGGAACAGGTGGTGGCCATCGCATCTAACAATGGCGGTA
 +
AGCAGGCACTGGAAACAGTGCAGCGCCTGCTTCCGGTCCTGTGTCAGGCTCATGG
 +
CCTGACCCCAGAGCAGGTCGTGGCAATTGCCTCCAACATTGGAGGGCGAGACG</p>
 +
<p>
 +
<b>PART3(262bp):</b><br>
 +
CGTCTCTAGGGAAGCAGGCACTGGAGACCGTGCAGCGGCTGCTGCCGGTGCTGTG
 +
TCAGGCCCACGGCTTGACCCCGGAACAGGTGGTGGCCATCGCCTCCAACGGCGGT
 +
GGCAAACAGGCGCTGGAAACAGTTCAACGCCTCCTTCCGGTCCTGTGCCAGGCCC
 +
ATGGTCTGACTCCAGAGCAGGTTGTGGCAATTGCAAGCAACATTGGTGGTAAACA
 +
AGCTTTGGAAACCGTCCAGCGCTTGCTGCCAGTACGGAGACG</p></center>
 +
<p>
-
<tr> <td colspan="3"  height="15px"> </td></tr>
+
<b>PART4(224bp):</b><br>
 +
CGTCTCCGTACTGTGTCAGGCCCACGGGCTTACCCCGGAACAGGTGGTGGCCATT
 +
GCAAGCAACGGTGGTGGCAAGCAGGCCCTGGAGACAGTCCAACGGCTGCTTCCGG
 +
TTCTGTGTCAGGCCCACGGCCTGACTCCAGAACAAGTGGTTGCTATCGCCAGCCA
 +
CGATGGCGGTAAACAAGCCCTCGAAACCGTGCAGCGCCTGCTTCCGGTGCTGGGA<br>
 +
GACG
 +
</p>
 +
<p>
 +
<b>PART5(194bp):</b><br>
 +
CGTCTCCGCTGTGTCAGGCCCACGGACTGACCCCGGAACAGGTGGTGGCCATCGC
 +
CTCCAACATTGGTGGTAAGCAAGCCCTCGAAACTGTGCAGCGGCTGCTTCCAGTC
 +
TTGTGCCAGGCTCACGGCCTGACACCGGAGCAGGTGGTTGCAATCGCGTCTAATA<br>
 +
TCGGCGGCAAACAGGCACTCGATGAGACG
 +
</p>
 +
<p>
 +
<b>PART6(249bp):</b><br>
 +
CGTCTCATCGAGACCGTGCAGCGCTTGCTTCCAGTGCTGTGTCAGGCCCACGGCC
 +
TGACCCCGGAACAGGTGGTGGCCATCGCCTCTAACAATGGCGGCAAACAGGCATT
 +
GGAAACAGTTCAGCGCCTGCTGCCGGTGTTGTGTCAGGCTCACGGCCTGACTCCG
 +
GAGCAGGTTGTGGCCATCGCAAGCCATGATGGCGGTAAACAAGCTCTGGAGACAG<br>
 +
TGCAACGCCTCTTGCCAGTTTTAGAGACG</p>
 +
<p>
-
<tr><td colspan="3" > <h3> Parts Table</h3></td></tr>
+
<b>PART-right:</b><br>
 +
CGTCTCATTTTGTGTCAGGCCCACGGA...</p><br>
-
<tr><td width="45%" colspan="3" valign="top">
+
<p>
-
Any parts your team has created will appear in this table below:</td></tr>
+
The recognition sequence of the TALE protein:
 +
<center><font size="5" color="red">TCGATATCAAGC</font></center></p>
 +
<div class="default" id="default">
 +
<groupparts>iGEM014 SJTU-BioX-Shanghai</groupparts>
 +
</div>
 +
</article>
 +
  </div>
-
</table>
 
</html>
</html>
-
<groupparts>iGEM013 SJTU-BioX-Shanghai</groupparts>
 
{{Team:SJTU-BioX-Shanghai/footer}}
{{Team:SJTU-BioX-Shanghai/footer}}

Latest revision as of 23:41, 17 October 2014

Parts


We have characterized and submitted 25 BioBricks which could either be used directly or serve as a universal tool ready for potential scientific or engineering use.
      Those BioBricks are divided into four groups.
      1. BioBricks in Basic Parts are all basic components of the whole project. They can be assembled to carry out different tasks.
      2. BioBricks in USB are our designed sequences. They can help us easily and quickly insert our target sequence and make a whole part.
      3. BioBricks in Application are our complete parts.
      4. BioBricks in New TAL are our newly designed TAL parts, which are robust and perform better in Golden Gate method.

<groupparts>iGEM014 SJTU-BioX-Shanghai</groupparts>



Basic Parts

Review previous parts

ssDsbA: SsDsbA is the signal recognition particle (SRP)-dependent signaling sequence of DsbA. SsDsbA-tagged proteins are exported to the periplasm through the SRP pathway. With ssDsbA fused to the N-terminus, fusion proteins with Lgt are expected to be anchored onto inner membrane of E.coli.
From: ssDsbA-PDZ Ligand-LGT-SH3 Ligand ( (BBa_K771002, SJTU-BioX-Shanghai)

Lgt: Phosphatidylglycerol:: prolipoprotein diacylglyceryl transferase (Lgt) is an inner membrane protein act as an membrane anchor of E.coli with seven transmembrane segments and has been successfully overexpressed in E. coli without causing harm to cells.
From: ssDsbA-PDZ Ligand-LGT-SH3 Ligand (BBa_K771002, SJTU-BioX-Shanghai)

mRFP: Red Fluorescent Protein. To visualize the localization of fusion protein with fluorescence test , we added mRFP in the Connectee1 and placed it just after the ssDsbA.
From: Highly engineered mutant of red fluorescent protein from Discosoma striata (BBa_E1010, Antiquity )

FL3-TALE(BBa_K1453300)


Figure 2.3.1 Diagram of FL3-TALE

This is a TALE protein with a flexible linker 3 before it.

Since we cannot connect TALE by Golden Gate method designed by 2012 Freiburg, so the sequence was synthesized by Genwize company. This TALE can recognize the DNA sequence TTGGTCATGAGA(12bp). Moreover, we use this part with our part BBa_K14530000 to make our composite part BBa_K1453305.

Connector

We have four types of connector.


Figure 2.3.2 Diagram of four types of connector: pBluescript II KS(+) ScaI deletion,

pBluescript II KS(+) EcoRV deletion, pBluescript II KS(+)_3_copy and pBluescript II KS(+)_5_copy

pBluescript II KS(+) ScaI deletion (BBa_K1453901)

pBluescript II KS(+) EcoRV deletion (BBa_K1453001)

pBluescript II KS(+)_3_copy (BBa_K1453003)

pBluescript II KS(+)_5_copy (BBa_K1453004)

Each type of connector has its own function. If you want to know the details, please click it. We have introduction on our part's main page.

ssDsbA-mRFP-Lgt-TAL1-His Tag(BBa_K1453005)


Figure 2.3.3 Diagram of ssDsbA-mRFP-Lgt-TAL1-His Tag

The structure is based on the BBa_1453000 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089.



TAL1-His Tag(BBa_K1453007)


Figure 2.3.4 Diagram of TAL1-His Tag

This part is a first second of connectee, which we used to check the connection between connectee and connector in our basic test.

The structure is based on the BBa_K1453006 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089.


USB

We make two kinds of USB. One is TAL USB, the other is Enzyme USB. They can help us easily and quickly insert our target TALE or Enzyme, respectively.

TAL USB(BBa_K1453000)


Figure 2.3.5 Diagram of TAL USB

We design a sequence which can be used together with 2012 Freiburg's part. The TAL USB can make two specific sticky ends. The two ends are the same as the first part and the last part of Freiburg design. So when we digest and ligate them together, we can get a whole TALE. But unluckily, since the sticky ends designed by Freiburg are too similar, we can just have some mismatch sequence by using these TAL USB.

Enzyme USB(BBa_K1453400)(BBa_K1453401)


In order to easily and quickly insert the target function enzyme into our system, we design two enzyme-USBs. The enzyme USB have three fundamental components, flexible linker- enzyme adaptor-flexible linker.


Figure 2.3.6 Diagram of two kinds of enzyme USB: AarI and BsmBI

The first flexible linker has deleted the PstI recognition site. And at the beginning of the sequence there is a Bsu36I recognition site. The second flexible linker we replace the original PstI site with a isocaudamer SduI, since our part can not have a PstI recognition site.

On the other hand, the enzyme adaptor has two same restriction enzyme recognition sites. In one of our enzyme-USB, it is the AarI recognition site; The other enzyme-USB is the BsmAI recognition site. The AarI and BsmAI are similar to BsmBI which all can make a 4bp sticky end designed by ourselves.

When we want to insert a functional enzyme into our fusion protein, first we need to have a PCR experiment to add a head and a tail around our enzyme. After that, the enzyme product also has the restriction enzyme recognition site. When digested by the specific restriction enzyme, it can generate the same sticky ends, so our enzyme can be inserted into our part.


TAL_USB-His Tag(BBa_K1453006)


Figure 2.3.7 Diagram of TAL_USB-His Tag

In order to bind TAL protein designed by 2012 Freiburg iGEM team, the TAL USB also consists of T1 sequence, T14 sequence and two sites for type II restriction enzyme BsmBI.

When digested with BsmBI, this part can produce two sticky-ends that can bind TAL-Protein DiRepeat (Bba_K747000 to Bba_K747095)


ssDsbA-Lgt-Enzyme USB(BsmAI)-TAL_USB-His Tag(BBa_K1453402)


Figure 2.3.8 Diagram of ssDsbA-Lgt-Enzyme USB(BsmAI)-TAL_USB-His Tag

This part is the combination of BBa_K1453401 BBa_K1453006 and BBa_K1453000.See more details please search these two parts of iGEM14_SJTU_BioX_Shanghai.


ssDsbA-Lgt-Enzyme USB(AarI)-TAL_USB-His Tag(BBa_K1453403)


Figure 2.3.9 Diagram of ssDsbA-Lgt-Enzyme USB(AarI)-TAL_USB-His Tag

This part is the combination of BBa_K1453400 BBa_K1453006 and BBa_K1453000.See more details please search these two parts of iGEM14_SJTU_BioX_Shanghai.


Enzyme USB(BsmAI)-TAL_USB-His Tag(BBa_K1453406)


Figure 2.3.10 Diagram of Enzyme USB(BsmAI)-TAL_USB-His Tag

This part is the combination of BBa_K1453401 and BBa_K1453006.


Enzyme USB(AarI)-TAL_USB-His Tag(BBa_K1453407)


Figure 2.3.11 Diagram of Enzyme USB(AarI)-TAL_USB-His Tag

This part is the combination of BBa_K1453400 and BBa_K1453006.See more details please search these two parts of iGEM14_SJTU_BioX_Shanghai.


Application

We chose some functional enzymes and inserted them into connectees
We want to prove that our connectees and connectors system can successfully achieve our designed function in the end.

ssDsbA-Lgt-pykF-TAL1-His Tag(BBa_K1453404)


Figure 2.3.12 Diagram of ssDsbA-Lgt-pykF-TAL1-His Tag

This part is based on the BBa_K1453402 or BBa_K1453403 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089. The enzyme we used here is the pyruvate kinase (EC:2.7.1.40) or pykF.


ssDsbA-Lgt-poxB-TAL1-His Tag(BBa_K1453405)


Figure 2.3.13 Diagram of ssDsbA-Lgt-poxB-TAL1-His Tag

This part is based on the BBa_K1453402 or BBa_K1453403 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089. The enzyme we used here is the pyruvate dehydrogenase (quinone) [EC:1.2.5.1] or poxB


pykF-TAL1-His Tag(BBa_K1453408)


Figure 2.3.14 Diagram of pykF-TAL1-His Tag

This part is used in our application test free in the cytoplasm.

This part is based on the BBa_K1453406 or BBa_K1453407 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089. The enzyme we used here is the pyruvate kinase (EC:2.7.1.40) or pykF.


poxB-TAL1-His Tag(BBa_K1453409)



Figure 2.3.15 Diagram of poxB-TAL1-His Tag

This part is used in our application test free in the cytoplasm.

This part is based on the BBa_1453006 and BBa_K1453406 or BBa_K1453407 and the recognition sequence is T-TCGATATCAAGC-T. Therefore, the TAL-Protein DiRepeats protein we need are BBa_K747013, BBa_K747024, BBa_K747044, BBa_K747061, BBa_K747064 and BBa_K747089. The enzyme we used here is the pyruvate dehydrogenase (quinone) [EC:1.2.5.1] or poxB


New TAL

New TAL with better sticky ends(BBa_K1453500) (501) (502) (503) (504) (505) (506)

We design seven new sticky ends which get the least score when judging the similarity.
If you want to know how we design these ends, please go to see our project-Part3 TAL improve.


PART-left:
…CTGACCCCGGAGACG

PART1(150bp):
CGTCTCGCCCCGGAACAGGTGGTGGCCATTGCAAGCAACGGTGGTGGCAAGCAGG CCCTGGAGACAGTCCAACGGCTGCTTCCGGTTCTGTGTCAGGCCCACGGCCTGACT CCAGAACAAGTGGTTGCTATCGTGGCGGAAAATGAGACG

PART2(219bp):
CGTCTCTAAAACAAGCCCTCGAAACCGTGCAGCGCCTGCTTCCGGTGCTGTGTCAG GCCCACGGGCTCACCCCGGAACAGGTGGTGGCCATCGCATCTAACAATGGCGGTA AGCAGGCACTGGAAACAGTGCAGCGCCTGCTTCCGGTCCTGTGTCAGGCTCATGG CCTGACCCCAGAGCAGGTCGTGGCAATTGCCTCCAACATTGGAGGGCGAGACG

PART3(262bp):
CGTCTCTAGGGAAGCAGGCACTGGAGACCGTGCAGCGGCTGCTGCCGGTGCTGTG TCAGGCCCACGGCTTGACCCCGGAACAGGTGGTGGCCATCGCCTCCAACGGCGGT GGCAAACAGGCGCTGGAAACAGTTCAACGCCTCCTTCCGGTCCTGTGCCAGGCCC ATGGTCTGACTCCAGAGCAGGTTGTGGCAATTGCAAGCAACATTGGTGGTAAACA AGCTTTGGAAACCGTCCAGCGCTTGCTGCCAGTACGGAGACG

PART4(224bp):
CGTCTCCGTACTGTGTCAGGCCCACGGGCTTACCCCGGAACAGGTGGTGGCCATT GCAAGCAACGGTGGTGGCAAGCAGGCCCTGGAGACAGTCCAACGGCTGCTTCCGG TTCTGTGTCAGGCCCACGGCCTGACTCCAGAACAAGTGGTTGCTATCGCCAGCCA CGATGGCGGTAAACAAGCCCTCGAAACCGTGCAGCGCCTGCTTCCGGTGCTGGGA
GACG

PART5(194bp):
CGTCTCCGCTGTGTCAGGCCCACGGACTGACCCCGGAACAGGTGGTGGCCATCGC CTCCAACATTGGTGGTAAGCAAGCCCTCGAAACTGTGCAGCGGCTGCTTCCAGTC TTGTGCCAGGCTCACGGCCTGACACCGGAGCAGGTGGTTGCAATCGCGTCTAATA
TCGGCGGCAAACAGGCACTCGATGAGACG

PART6(249bp):
CGTCTCATCGAGACCGTGCAGCGCTTGCTTCCAGTGCTGTGTCAGGCCCACGGCC TGACCCCGGAACAGGTGGTGGCCATCGCCTCTAACAATGGCGGCAAACAGGCATT GGAAACAGTTCAGCGCCTGCTGCCGGTGTTGTGTCAGGCTCACGGCCTGACTCCG GAGCAGGTTGTGGCCATCGCAAGCCATGATGGCGGTAAACAAGCTCTGGAGACAG
TGCAACGCCTCTTGCCAGTTTTAGAGACG

PART-right:
CGTCTCATTTTGTGTCAGGCCCACGGA...


The recognition sequence of the TALE protein:

TCGATATCAAGC

iGEM014 SJTU-BioX-Shanghai