Difference between revisions of "BIN-MYSPE"

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<div id="BIO">
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<div id="ABC">
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
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YFO (Your Favourite Organism)
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MYSPE (My Species)
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  </div>
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Scenario: Yeast cell-cycle; Model organism, MYSPE)
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  {{Vspace}}
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Scenario: Yeast cell-cycle; Model organism, YFO
 
 
</div>
 
</div>
  
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{{Vspace}}
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{{Smallvspace}}
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__TOC__
 
  
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{{Vspace}}
 
  
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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{{LIVE}}
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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{{Vspace}}
 
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</div>
 
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "../components/BIN-YFO.components.wtxt", section: "abstract" -->
+
This unit discusses a scenario for model-organism based inference in a (possibly) uncharacterized species and selects a "MYSPE" (My Species), a genome-sequenced fungus that is specific to your explorations in the course.
−
This unit discusses a scenario for model-organism based inference in a (possibly) uncharacterized organism and selects a "YFO" (Your Favourite Organism), a genome-sequenced fungus that is specific to you. You will investigate aspects of this organism throughout the course.
 
 
<section end=abstract />
 
<section end=abstract />
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</div>
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{{Vspace}}
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<!-- ============================ -->
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<hr>
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<table>
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== This unit ... ==
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<tr>
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "../components/BIN-YFO.components.wtxt", section: "prerequisites" -->
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<b>Objectives:</b><br />
−
<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
 
−
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:
 
−
<!-- included from "FND-prerequisites.wtxt", section: "biomolecules" -->
 
−
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
 
−
You need to complete the following units before beginning this one:
 
−
*[[FND-CSC-Data_models|FND-CSC-Data_models (Relational Data Models)]]
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
=== Objectives ===
 
−
<!-- included from "../components/BIN-YFO.components.wtxt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
 
* Introduce the concept of "model organisms";
 
* Introduce the concept of "model organisms";
−
* Present an R exercise to choose an organism from a list;
+
* Work through an R exercise to assign a MYSPE species from a list;
 
* Demonstrate code that downloads and uses files from two public databases.
 
* Demonstrate code that downloads and uses files from two public databases.
 +
</td>
 +
<td style="padding:10px;">
 +
<b>Outcomes:</b><br />
 +
After working through this unit you ...
 +
* have chosen a "MYSPE" species for this course;
 +
* have examined code that implements a typical bioinformatics workflow;
 +
* are familiar with MYSPE and the reasons it was sequenced.
 +
</td>
 +
</tr>
 +
</table>
 +
<!-- ============================  -->
 +
<hr>
 +
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 +
<u>
 +
<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
 +
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
 +
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 +
</u>
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:<br />
 +
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
 +
This unit builds on material covered in the following prerequisite units:<br />
 +
*[[FND-CSC-Data_models|FND-CSC-Data_models (Relational Data Models)]]
 +
<section end=prerequisites />
 +
<!-- ============================  -->
 +
</div>
  
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{{Vspace}}
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{{Smallvspace}}
  
  
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=== Outcomes ===
 
−
<!-- included from "../components/BIN-YFO.components.wtxt", section: "outcomes" -->
 
−
After working through this unit you ...
 
−
* have chosen a "YFO" species for this course and recorded it in your R profile file;
 
−
* have had a look at code that implements a typical bioinformatics workflow;
 
−
* are familiar with YFO and the reasons it was sequenced.
 
  
−
{{Vspace}}
+
{{Smallvspace}}
  
  
−
=== Deliverables ===
+
__TOC__
−
<!-- included from "../components/BIN-YFO.components.wtxt", section: "deliverables" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
−
*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
−
*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
−
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
  
 
{{Vspace}}
 
{{Vspace}}
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=== Evaluation ===
 
=== Evaluation ===
−
<!-- included from "../components/BIN-YFO.components.wtxt", section: "evaluation" -->
 
−
<!-- included from "ABC-unit_components.wtxt", section: "eval-none" -->
 
 
<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
−
:This unit is not evaluated for course marks.
+
<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
−
 
 
−
{{Vspace}}
 
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−
 
 
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</div>
 
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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
−
<!-- included from "../components/BIN-YFO.components.wtxt", section: "contents" -->
 
 
==Scenario==
 
==Scenario==
 
You have learned about the concept of "{{WP|cargo cult science}}". The "cargo" in Bioinformatics is to understand biology. This includes understanding how things came to be the way they are, and how they work. Both relate to the concept of '''function''' of biomolecules, and the ''systems''<ref>cf. [[BIN-SYS-Concepts|the Systems Concepts unit]]</ref> they contribute to. But "function" is a rather poorly defined concept and exploring ways to make it rigorous and computable and explore it from the perspective of "collaborating" components is a major objective of this course. For this, we will work with an example: a {{WP|Transcription factor|transcription factor}} that plays an important role in the regulation of the cell cycle. This is a relatively well-characterized protein that is part of a relatively well-characterized process. The genetic regulation of budding- and fission yeast cell-cycles has been lucidly described in a highly recommended review by McInerny (2011)<ref>{{#pmid: 21310294}}</ref> (see also the short, recent introduction to cell-cycle regulated transcription by McInerny (2016)<ref>{{#pmid: 27239285}}</ref>). One transcription factor, '''Mbp1''' is a key component of the MBF complex (Mbp1/Swi6) in yeast. This complex regulates gene expression at the crucial G1/S-phase transition of the mitotic cell cycle and has been shown to bind to the regulatory regions of more than a hundred target genes. It is therefore a DNA binding protein that acts as a control switch for a key cellular process, it is highly conserved across species, and its human homologue plays a role in human disease.
 
You have learned about the concept of "{{WP|cargo cult science}}". The "cargo" in Bioinformatics is to understand biology. This includes understanding how things came to be the way they are, and how they work. Both relate to the concept of '''function''' of biomolecules, and the ''systems''<ref>cf. [[BIN-SYS-Concepts|the Systems Concepts unit]]</ref> they contribute to. But "function" is a rather poorly defined concept and exploring ways to make it rigorous and computable and explore it from the perspective of "collaborating" components is a major objective of this course. For this, we will work with an example: a {{WP|Transcription factor|transcription factor}} that plays an important role in the regulation of the cell cycle. This is a relatively well-characterized protein that is part of a relatively well-characterized process. The genetic regulation of budding- and fission yeast cell-cycles has been lucidly described in a highly recommended review by McInerny (2011)<ref>{{#pmid: 21310294}}</ref> (see also the short, recent introduction to cell-cycle regulated transcription by McInerny (2016)<ref>{{#pmid: 27239285}}</ref>). One transcription factor, '''Mbp1''' is a key component of the MBF complex (Mbp1/Swi6) in yeast. This complex regulates gene expression at the crucial G1/S-phase transition of the mitotic cell cycle and has been shown to bind to the regulatory regions of more than a hundred target genes. It is therefore a DNA binding protein that acts as a control switch for a key cellular process, it is highly conserved across species, and its human homologue plays a role in human disease.
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{{Vspace}}
 
{{Vspace}}
  
−
==Model organism and YFO==
+
==Model organism and MYSPE==
  
−
Baker's yeast, ''Saccharomyces cerevisiae'' is one of the most important {{WP|Model_organism|model organisms}}, a eukaryote that has been studied genetically and biochemically in great detail for many decades, and is easily manipulated with high-throughput experimental methods. But model organisms are studied for their value in inferring biology in other, less-well characterized or less experimentally tractable organisms through computational inference. To implement such a process, you will adopt a different genome-sequenced fungus in which to make discoveries based on knowledge about yeast.
+
Baker's yeast, ''Saccharomyces cerevisiae'' is one of the most important {{WP|Model_organism|model organisms}}, a eukaryote that has been studied genetically and biochemically in great detail for many decades, and is easily manipulated with high-throughput experimental methods. But model organisms are studied for their value in inferring biology in other, less-well characterized or less experimentally tractable species through computational inference. To implement such a process, you will adopt a different genome-sequenced fungus in which to make discoveries based on knowledge about yeast.
  
−
In this unit we will set out on our exploration of the system that regulates the G1/S transition by focussing first on the Mbp1 protein in selected species from the {{WP|Kingdom_(biology)|kingdom}} of fungi, whose genome has been completely sequenced; our quest is thus also an exercise in ''model-organism reasoning'': the transfer of knowledge from one, well-studied organism to others.  It's reasonable to hypothesize that such central control machinery is conserved in most if not all fungi. But we don't know. Many of the species that we will be working with have not been characterized in great detail, and some of them are new to our class this year. And while we know a fair bit about Mbp1, we probably don't know very much at all about the related genes in other organisms: whether they exist, whether they have similar functional features and whether they might contribute to the ''G1/S checkpoint system'' in a similar way. Thus we might discover things that are new and interesting. This is a quest of discovery.
+
In this unit we will set out on our exploration of the system that regulates the G1/S transition by focussing first on the Mbp1 protein in selected species from the {{WP|Kingdom_(biology)|kingdom}} of fungi, whose genome has been completely sequenced; our quest is thus also an exercise in ''model-organism reasoning'': the transfer of knowledge from one, well-studied species to others.  It's reasonable to hypothesize that such central control machinery is conserved in most if not all fungi. But we don't know. Many of the species that we will be working with have not been characterized in great detail, and some of them are new to our class this year. And while we know a fair bit about Mbp1, we probably don't know very much at all about the related genes in other species: whether they exist, whether they have similar functional features and whether they might contribute to the ''G1/S checkpoint system'' in a similar way. Thus we might discover things that are new and interesting. This is a quest of discovery.
  
 
{{Vspace}}
 
{{Vspace}}
  
−
==Choosing YFO (Your Favourite Organism)==
+
==Choosing MYSPE (My Species)==
  
 
Since we were trying to find related proteins in a different species, our first task is to find suitable species. Where do these come from? For the purposes of the course "quest", we need species:
 
Since we were trying to find related proteins in a different species, our first task is to find suitable species. Where do these come from? For the purposes of the course "quest", we need species:
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* for which the sequences have been deposited in the RefSeq database, NCBI's unique sequence collection.
 
* for which the sequences have been deposited in the RefSeq database, NCBI's unique sequence collection.
  
−
Selecting them is a process that is exemplary for other purposes: define properties that you need in a particular organism, and select accordingly. Let's dive into some R scripts for this purpose. This is lengthy code that you probably won't be able to understand in detail (yet). But read through it anyway and make a point of understanding the general workflow of the process in which we retrieve data from choose lists from different databases, and merge it.
+
Selecting them is a process that is exemplary for other purposes: define properties that you need in a particular species, and select accordingly. The R-project contains R scripts for this purpose. This is rather detailed code, read through it anyway and make a point of understanding the general workflow of the process in which we retrieve data from different databases, and merge it.
  
 
{{Vspace}}
 
{{Vspace}}
  
−
{{ABC-unit|BIN-YFO.R}}
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{{ABC-unit|BIN-MYSPE.R}}
−
 
 
  
 
{{Vspace}}
 
{{Vspace}}
  
 
{{task|1=
 
{{task|1=
−
 
+
<ul>
−
* Search for the article on YFO on Wikipedia https://wikipedia.org/wiki/Special:Search to learn more about the organism.
+
* Search for the article on MYSPE on Wikipedia https://wikipedia.org/wiki/Special:Search to learn more about the species.
−
* Navigate to the NCBI genomes database at https://www.ncbi.nlm.nih.gov/genome , search for YFO and read about the status of and motivation for genome work with YFO.
+
* Navigate to the NCBI genomes database at https://www.ncbi.nlm.nih.gov/genome , search for MYSPE and read about the status of and motivation for genome work with MYSPE.
−
 
+
</ul>
 
}}
 
}}
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{{Vspace}}
 
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−
== Further reading, links and resources ==
 
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<!-- {{#pmid: 19957275}} -->
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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{{Vspace}}
 
  
  
 
== Notes ==
 
== Notes ==
−
<!-- included from "../components/BIN-YFO.components.wtxt", section: "notes" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes" -->
 
 
<references />
 
<references />
  
 
{{Vspace}}
 
{{Vspace}}
  
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</div>
 
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<div id="ABC-unit-framework">
 
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== Self-evaluation ==
 
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<!-- included from "../components/BIN-YFO.components.wtxt", section: "self-evaluation" -->
 
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<!--
 
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=== Question 1===
 
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Question ...
 
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Answer ...
 
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Answer ...
 
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----
 
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<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
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:2020-09-20
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:1.0
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:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*1.1 2020 revisions - new workflow
 
*1.0 First live version
 
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 09:26, 25 September 2020

MYSPE (My Species)

(Scenario: Yeast cell-cycle; Model organism, MYSPE)


 


Abstract:

This unit discusses a scenario for model-organism based inference in a (possibly) uncharacterized species and selects a "MYSPE" (My Species), a genome-sequenced fungus that is specific to your explorations in the course.

Objectives:
This unit will ...

  • Introduce the concept of "model organisms";
  • Work through an R exercise to assign a MYSPE species from a list;
  • Demonstrate code that downloads and uses files from two public databases.

Outcomes:
After working through this unit you ...

  • have chosen a "MYSPE" species for this course;
  • have examined code that implements a typical bioinformatics workflow;
  • are familiar with MYSPE and the reasons it was sequenced.

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.
    •

    Prerequisites:
    You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:

    • Biomolecules: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.

    This unit builds on material covered in the following prerequisite units:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Scenario

    You have learned about the concept of "cargo cult science". The "cargo" in Bioinformatics is to understand biology. This includes understanding how things came to be the way they are, and how they work. Both relate to the concept of function of biomolecules, and the systems[1] they contribute to. But "function" is a rather poorly defined concept and exploring ways to make it rigorous and computable and explore it from the perspective of "collaborating" components is a major objective of this course. For this, we will work with an example: a transcription factor that plays an important role in the regulation of the cell cycle. This is a relatively well-characterized protein that is part of a relatively well-characterized process. The genetic regulation of budding- and fission yeast cell-cycles has been lucidly described in a highly recommended review by McInerny (2011)[2] (see also the short, recent introduction to cell-cycle regulated transcription by McInerny (2016)[3]). One transcription factor, Mbp1 is a key component of the MBF complex (Mbp1/Swi6) in yeast. This complex regulates gene expression at the crucial G1/S-phase transition of the mitotic cell cycle and has been shown to bind to the regulatory regions of more than a hundred target genes. It is therefore a DNA binding protein that acts as a control switch for a key cellular process, it is highly conserved across species, and its human homologue plays a role in human disease.


     

    Model organism and MYSPE

    Baker's yeast, Saccharomyces cerevisiae is one of the most important model organisms, a eukaryote that has been studied genetically and biochemically in great detail for many decades, and is easily manipulated with high-throughput experimental methods. But model organisms are studied for their value in inferring biology in other, less-well characterized or less experimentally tractable species through computational inference. To implement such a process, you will adopt a different genome-sequenced fungus in which to make discoveries based on knowledge about yeast.

    In this unit we will set out on our exploration of the system that regulates the G1/S transition by focussing first on the Mbp1 protein in selected species from the kingdom of fungi, whose genome has been completely sequenced; our quest is thus also an exercise in model-organism reasoning: the transfer of knowledge from one, well-studied species to others. It's reasonable to hypothesize that such central control machinery is conserved in most if not all fungi. But we don't know. Many of the species that we will be working with have not been characterized in great detail, and some of them are new to our class this year. And while we know a fair bit about Mbp1, we probably don't know very much at all about the related genes in other species: whether they exist, whether they have similar functional features and whether they might contribute to the G1/S checkpoint system in a similar way. Thus we might discover things that are new and interesting. This is a quest of discovery.


     

    Choosing MYSPE (My Species)

    Since we were trying to find related proteins in a different species, our first task is to find suitable species. Where do these come from? For the purposes of the course "quest", we need species:

    • that actually have transcription factors that are related to Mbp1;
    • whose genomes have been sequenced; and
    • for which the sequences have been deposited in the RefSeq database, NCBI's unique sequence collection.

    Selecting them is a process that is exemplary for other purposes: define properties that you need in a particular species, and select accordingly. The R-project contains R scripts for this purpose. This is rather detailed code, read through it anyway and make a point of understanding the general workflow of the process in which we retrieve data from different databases, and merge it.


     

    Task:

     
    • Open RStudio and load the ABC-units R project. If you have loaded it before, choose File → Recent projects → ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit.
    • Choose Tools → Version Control → Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included.
    • Type init() if requested.
    • Open the file BIN-MYSPE.R and follow the instructions.


     

    Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.


     


     

    Task:


    Notes

    1. ↑ cf. the Systems Concepts unit
    2. ↑
      McInerny (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73:51-85. (pmid: 21310294)

      [ PubMed ] [ DOI ] The regulation of gene expression through the mitotic cell cycle, so that genes are transcribed at particular cell cycle times, is widespread among eukaryotes. In some cases, it appears to be important for control mechanisms, as deregulated expression results in uncontrolled cell divisions, which can cause cell death, disease, and malignancy. In this review, I describe the current understanding of such regulated gene expression in two established simple eukaryotic model organisms, the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In these two yeasts, the global pattern of cell cycle gene expression has been well described, and most of the transcription factors that control the various waves of gene expression, and how they are in turn themselves regulated, have been characterized. As related mechanisms occur in all other eukaryotes, including humans, yeasts offer an excellent paradigm to understand this important molecular process.

    3. ↑
      McInerny (2016) Cell cycle regulated transcription: from yeast to cancer. F1000Res 5:. (pmid: 27239285)

      [ PubMed ] [ DOI ] Recent studies have revealed exciting new functions for forkhead transcription factors in cell proliferation and development. Cell proliferation is a fundamental process controlled by multiple overlapping mechanisms, and the control of gene expression plays a major role in the orderly and timely division of cells. This occurs through transcription factors regulating the expression of groups of genes at particular phases of the cell division cycle. In this way, the encoded gene products are present when they are required. This review outlines recent advances in our understanding of this process in yeast model systems and describes how this knowledge has informed analysis in more developmentally complex eukaryotes, particularly where it is relevant to human disease.


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-20

    Version:

    1.1

    Version history:

    • 1.1 2020 revisions - new workflow
    • 1.0 First live version
    • 0.1 First stub

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-MYSPE&oldid=11685"