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Viewing: BIT 477/BIT 577 : Metagenomics

Last approved: Sat, 14 Jan 2017 09:01:29 GMT

Last edit: Mon, 28 Nov 2016 19:40:43 GMT

Catalog Pages referencing this course
Change Type
Major
BIT (Biotechnology)
477
032356
Dual-Level Course
Yes
577
Cross-listed Course
No
Metagenomics
Metagenomics
College of Agriculture and Life Sciences
Biotechnology (11BIT)
Term Offering
Fall Only
Offered Every Year
Spring 2016
Previously taught as Special Topics?
Yes
3
 
Course Prefix/NumberSemester/Term OfferedEnrollment
BIT495/595Fall 201310
BIT495/595Fall 201413
BIT495/595Fall 201518
Course Delivery
Face-to-Face (On Campus)

Grading Method
Letter Grade Only
2
8
Contact Hours
(Per Week)
Component TypeContact Hours
Lecture1.8
Laboratory5
Course Attribute(s)


If your course includes any of the following competencies, check all that apply.
University Competencies

Course Is Repeatable for Credit
No
 
 
Carlos Goller
Teaching Assistant Professor
Assoc

Open when course_delivery = campus OR course_delivery = blended OR course_delivery = flip
Enrollment ComponentPer SemesterPer SectionMultiple Sections?Comments
Lecture1616NoEnrollment is capped at 16 due to laboratory space
Laboratory1616NoEnrollment is capped at 16 due to laboratory space
Open when course_delivery = distance OR course_delivery = online OR course_delivery = remote
Prerequisite: BIT 410 or 510
Is the course required or an elective for a Curriculum?
Yes
SIS Program CodeProgram TitleRequired or Elective?
11BIMBiotechnology Minor (undergraduate)Elective
Molecular Biotechnology CertificateMolecular Biotechnology Certificate ProgramElective
Graduate Biotechnology MinorGraduate Biotechnology MinorElective
Participants will be introduced to a variety of methods for studying the complex microbial populations that surround us, including theory, applications, limitations, and health and legal implications. Students will apply deep sequencing techniques to mine the genetic diversity of complex microbial populations such as the rhizosphere, a swine lagoon sample, or even the communities of microbes growing happily inside your kitchen sink drain. This course will provide hands-on experience with molecular and computational tools that can be used to study the relationships between microbial communities and ecosystems or hosts.

Undergraduate and graduate students pursuing the BIT minor or certificate are interested in this course as an elective to fulfill the minor or certificate requirements.  There is also a significant population of microbiology orientated students across many disciplines at NC State University that have the potential to benefit from this course. 


No

Is this a GEP Course?
No
GEP Categories

Humanities Open when gep_category = HUM
Each course in the Humanities category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
 

 
 

Mathematical Sciences Open when gep_category = MATH
Each course in the Mathematial Sciences category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

Natural Sciences Open when gep_category = NATSCI
Each course in the Natural Sciences category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

Social Sciences Open when gep_category = SOCSCI
Each course in the Social Sciences category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
 

 
 

Interdisciplinary Perspectives Open when gep_category = INTERDISC
Each course in the Interdisciplinary Perspectives category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
 

 
 

 
 

 
 

Visual & Performing Arts Open when gep_category = VPA
Each course in the Visual and Performing Arts category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
 

 
 

Health and Exercise Studies Open when gep_category = HES
Each course in the Health and Exercise Studies category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
&
 

 
 

 
 

 
 

Global Knowledge Open when gep_category = GLOBAL
Each course in the Global Knowledge category of the General Education Program will provide instruction and guidance that help students to achieve objective #1 plus at least one of objectives 2, 3, and 4:
 
 

 
 

 
Please complete at least 1 of the following student objectives.
 

 
 

 
 

 
 

 
 

 
 

US Diversity Open when gep_category = USDIV
Each course in the US Diversity category of the General Education Program will provide instruction and guidance that help students to achieve at least 2 of the following objectives:
Please complete at least 2 of the following student objectives.
 
 

 
 

 
 

 
 

 
 

 
 

 
 

 
 

Requisites and Scheduling
 
a. If seats are restricted, describe the restrictions being applied.
 

 
b. Is this restriction listed in the course catalog description for the course?
 

 
List all course pre-requisites, co-requisites, and restrictive statements (ex: Jr standing; Chemistry majors only). If none, state none.
 

 
List any discipline specific background or skills that a student is expected to have prior to taking this course. If none, state none. (ex: ability to analyze historical text; prepare a lesson plan)
 

Additional Information
Complete the following 3 questions or attach a syllabus that includes this information. If a 400-level or dual level course, a syllabus is required.
 
Title and author of any required text or publications.
 

 
Major topics to be covered and required readings including laboratory and studio topics.
 

 
List any required field trips, out of class activities, and/or guest speakers.
 

College(s)Contact NameStatement Summary
College of SciencesEric StoneConsultation with Functional Genomics DGP Eric Stone

Hi Sabrina,

Thanks for consulting with us. I don't see any issue of overlap with this course, and indeed I've already recommended it to several functional genomics students.

Best,

Eric
College of SciencesJames MahaffeyAs far a I can tell there is limited overlap with current Genetics courses. There could be overlap with some of the Genomics courses or Bioinformatics courses, but I don’t think they would be major. Jose Alonso would be a good contact for Genomics, and perhaps Eric Stone or David Reif for the bioinformatics side.
The professor will be teaching this as part of his teaching semester requirements. The course has an in-lab section, which requires use of instrumentation in the biotechnology program. In addition, it will require the purchase of reagents to perform such experiments that are covered by BIT and a dedicated classroom and lab space.

Course Goals: Upon completion of the course, participants will be able to:



  • Demonstrate laboratory skills required of a modern-day molecular biologist in the era of next generation sequencing. This includes keeping detailed and accurate laboratory notes (e.g., electronic records for sequence analyses) and choosing and using an appropriate sequence analysis tool.

  • Design and troubleshoot metagenomics experiments.

  • Prepare genomic DNA for deep sequencing and metagenomic analyses.

  • Identify and analyze the function of sequences with potential industrial applications or public health implications from a complex sample or metagenomic dataset.

  • Interpret data and identify limitations related to metagenomic surveys. 


Student Learning Outcomes

Specific Learning Outcomes:



  • Given a complex genomic DNA sample, the participant will be able to list the steps for creating an amplicon library (e.g., 16S), sequencing the sample, pre-processing the reads, and inferring taxonomic representation.

  • Given a formatted metagenomics dataset and access to online databases/portals and software, the participant will be able to apply appropriate bioinformatics gene prediction and annotation tools.

  • Given a formatted dataset and an appropriate visualization tool, the participant will be able to accurately summarize the output for different measures of diversity.

  • Given a specific source of DNA, the participant will be able to design an appropriate experiment to obtain metagenomic data from a sample for experiments involving extraction of environmental DNA.


Specific Learning Outcome for BIT577 (Graduate) Students:



  • Given workflows followed during the course, the participant will be able to design future experiments and analyses for hypothesis testing of metagenomic data.


Evaluation MethodWeighting/Points for EachDetails
Lab Report10Lab Report 1
Lab Report15Lab Report 2
Lab Report10Electronic Lab notebook
Readings assignments15Journal club readings (3) and assignments
Written Assignment5In-class assignments: Throughout the course, we will engage in activities including short assigned readings from eBooks available via the NCSU Libraries (http://www.lib.ncsu.edu/), class discussions, and writing opportunities. Written assignments will be collected at random and graded (see “Assignments” grade item) to assess your understanding of the material covered in lectures, lab sessions, guest lectures, and posted readings.
Quizzes10Quizzes
presentation15Final Presentation and data analysis
*note different weight for graduate students 10%*
Exam20Final exam
*note different weight for graduate students 25%*

Final Exam: The final exam will be a cumulative in-class evaluation held during the last week of class. It may address any concept touched upon in lecture or laboratory. The exam may include multiple choice, true/false, short answer, and essay questions. Studying the lecture notes and assigned articles will be very helpful and worthwhile. ♦ Students registered for BIT 577 will have an additional section on the final exam focusing on the design of a workflow for analyses of a sample metagenomic data set. In preparation for the final exam, we will have a short review after the midpoint of the module.
TopicTime Devoted to Each TopicActivity
Intro to deep sequencing & metagenomicsWeek 1Lecture 1.
Introduction to deep sequencing and metagenomics.

Discussion of Paper #1.
Metagenomic surveysWeek 2 Lab 1.
Safety training.

Overview of lab project (lecture): How will we use metagenomics tools for this study?

Experimental design (during 16S PCR).

Sample preparation day #1: Genomic DNA preparation (provided but discussed), 16S rRNA amplification, PCR clean-up of 16S amplicons, and index PCR.

Thursday 08/27. Lecture 2.
Quiz #1.

Metagenomic surveys: Sargasso Sea, The Human Microbiome Project, Earth Microbiome Project... our own homes.


Processing data and softwareWeek 3 Lab 2.
Sample preparation day #2: Index PCR clean-up and quantification of libraries. Preparation of samples for sequencing submission.

Discussion of considerations for sample preparation.

Thursday 09/03. Lecture 3.
Discussion of Paper #2.

File types and FASTQC. Pre-processing reads. Introduction to Geneious software.

FASTQC/Geneious activity.

MG-RAST and AmphoraNETWeek 4 Lab 3.
Lab report guidelines.

Geneious software for metagenomic sample analyses.

Case study on data visualization/water sanitation using Geneious.


Thursday 09/10. Lecture 4.
Quiz #2.

MG-RAST and AmphoraNet.

AmphoraViz activity.

MothurWeek 5Lecture 4.
Quiz #2.

MG-RAST and AmphoraNet.

AmphoraViz activity.

Thursday 09/17. Lecture 5.

Discussion of Paper #3.

Mothur.

Data VisualizationWeek 6Tuesday 09/22. Lab 5.

Duke chambers project and Qiime

Guest speaker: Dr. Julia Stevens

Lecture 6.
Quiz #3.

Data visualization with R and Phyloseq activity.

Data analysisWeek 7Analyses of our data using the tools we covered.

Work on presentations.

Summary of review due.

Review and feedback.

Exam.

FINAL EXAM!

Final presentation of dataWeek 8 Lab 7.

Final presentations.

Lab notebooks/course binders due.

Thursday 10/08

NO CLASS!

Lab Report 2 due 10/09: Computational analyses of your metagenomic data.

Please complete online survey

NOTE: ♦ Students registered for BIT 577 have an additional learning outcome and will have an additional section on the final exam focusing on the design of a workflow for analyses of a sample metagenomic data set.

mlnosbis 1/26/2016: No directly overlapping courses. Suggest consultation with Genetics DGP (James Mahaffey) and Functional Genomics DGPs (Eric Stone and Spencer Muse).

ghodge 1/26/2016 Agree with request for consultation described above. Comment: Only difference between undergraduate and graduate is final exam question worth 5% of the semester grades. Is this a significant difference. ABGS reviewers should comment.

ghodge 3/22/2016 Ready for ABGS reviewers. Comments: contact hours for lab seem high given only 2 credit hours; the difference in weighting for grad vs undergrad grading seems low

ABGS Reviewer Comments:
- There seems to be very minor difference between the undergraduate and graduate requirements.

ghodge 6/29/2016 Ready for ABGS meeting.
renutt (Mon, 07 Dec 2015 14:10:22 GMT): Rollback: Sabrina Robertson has requested edits from committee.
Key: 8530