UCC1: New Course Transmittal Form - University of Floridafora.aa.ufl.edu/docs/47//20Nov12//UCC_20Nov12... · Introductory Intermediate Advanced Department Contact College Contact

UCC1: New Course Transmittal FormDepartment Name and Number

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Environmental Microbiology MCB4934 Spring 2013 – 3 credits On Campus Class Schedule: M 10th and 11th period 5:10pm – 7:05 pm; mandatory Weekly Online Podcasting Lecture – 50 min; mandatory Distance Learning students only: All classes are available as podcasts through the course website (see below). Class Location: For On-campus students Monday class will be held in NEB 0202 Instructor: Dr. Jamie Foster, Associate Professor, Microbiology and Cell Science Course Website: Login available through Sakai (http://lss.at.ufl.edu/). Contact Information: I am located off-campus at the UF Space Life Sciences Lab, Kennedy Space Center My contact information is: Tel: 321-861-2900; Email: [email protected]; Skype: jamief94086. Office Hours: Gainesville Campus: Monday 2:00 pm – 3:30 pm in the Microbiology and Cell Science Building room 1044 Virtual Office Hours: Skype Video Chats Wednesday 7 - 8PM or by appointment Course Description for Environmental Microbiology: Overview of microorganisms in the environment including: occurrence, abundance, and distribution; processes of microbial interaction with the environment and practices of applied environmental microbiology. Learning Objectives for Environmental microbiology: By the end of this course students should be able to: 1) Describe and comprehend the fundamental concepts of environmental microbiology 2) Analyze primary literature articles in the field of environmental microbiology to develop critical thinking skills; and 3) Develop essential writing and verbal communication skills through essays and oral presentations that target the field of environmental microbiology. Prerequisites: MCB3020, MCB 3023 or an equivalent introductory microbiology course Required Texts: 1. Reading Primary Literature by Christopher Gillen ISBN 978-08053-4599-5

2. Environmental Microbiology: From Genomes to Biogeochemistry by Eugene Madsen ISBN-13 978-1405136471 3. Headset microphone; (example: www.rosettastone.com) Grading: 1. One Topical Oral Presentation (10% of your final grade; 100 points) - You will be expected to give a three-minute oral presentation with two additional minutes for questions. I will discuss the appropriate elements to structuring and developing an oral presentation. You MUST consult with me before starting work on this presentation to ensure your selected topic is appropriate. The presentation will be graded using a combination of peer review and instructor evaluation. Your fellow classmates will anonymously evaluate your slides, presentation skills, and information content. Their comments and perceptions of your presentation will account for 20 points of your presentation grade. Another 20 points will be dependent on your evaluation of other students. The objective is for you to develop your critical evaluation skills and ability to constructively critique your peers. The remaining 60 points will be assessed by myself, and will be dependent on your presentation skills, accuracy of the scientific content, and knowledge of the presented material. 2. Discussion and class participation (5% of your final grade; 50 points) - It is important that you each take an active role in your own education. Just showing up isn’t enough. I expect each of you to be prepared for class and involve yourself in the lectures by asking questions and participating in the group discussions. Be prepared to discuss the merits (if any) of the experimental approach and results. 3. Primary Literature Writing Assignment (10% of your final grade; 50 points each; total of 100 points) - You will receive two peer-reviewed literature articles on one or more aspects of environmental microbiology. You will be expected to write a 400-word abstract for each research article. Write your summaries in 12 font Ariel, Helvetica, or Times New Roman. You must not plagiarize text from the papers given to you, nor should you cut and paste text from websites. Plagiarizing will result in an automatic zero on the assignment. The rational behind this assignment is that as a future scientist or doctor you are often required to write abstracts (i.e., summaries) or reviews of large pieces of work into succinct accounts for colleagues, publication, or professors. Your objective is to evaluate and summarize the objectives and conclusions of the paper. The assignment will be graded based on your understanding of the scientific content, ability to analyze the author’s conclusions, and quality of writing. You will have one week to complete each assignment.

In additional to the science component to the writing assignments your abstracts will be evaluated with respect to grammar, punctuation, and usage of standard written English, as well as clarity, coherence, and organization. Your writing assignments will be graded using a rubric that will be specific to each writing assignment. Briefly the rubric will include an assessment about the comprehension of the scientific content, your ability to integrate the experimental design and results, your participation in the group discussion, your ability to develop pertinent scientific questions, and the quality of

your writing ability (see previous comment). Each component will account for 20% of your grade on the writing assignments. All critical feedback will be provided to you via track changes in Microsoft Word and Sakai within two weeks of the final due date or prior to the last class meeting. Unless other wise noted all writing assignments are due one week after the assignment is given. Abstracts are limited to 400-words. Note: Off Campus Discussion on the literature papers will occur during the Skype sessions on Wednesdays 7 to 8pm. 5. Personal Statement Assignment (5% of your grade; 50 points) – As each of you graduates and moves into the real world you will need to generate cover letters or personal statements for either your job applications or graduate/medical school applications. This assignment is designed to jump start that process by helping you develop and polish your own personal objectives and statements. You are required to write a one page statement that would be consistent with an application to a post-graduate school. Since this is an important assignment for your future careers you will have as many opportunities as you wish to revise the statement and improve your grade. I will provide feedback to you within one week of your submission. You may correct or revise your statement and resubmit for a new evaluation through Sakai. 6. Weekly quizzes (20% of your final grade; 200 points) – Each week there will be a quiz that needs to be completed on the Sakai course website. The quizzes will include all material covered that week including podcasts. (Approximately 10-15 points each; 200 points total) 7. Written Exams (50% of your final grade; 500 points) - Questions on the exams will take the form of multiple choice and short answers. These exams will allow you to demonstrate your familiarity with the concepts, terminology, and methodologies covered in the course. The first and second exam will be worth 150 points; and the final will be worth 200 points. For the final the majority of the exam will be on the material from the last third of the class, however 50 points of the final will be based on questions from the first two thirds of the class. Make-Up policy – There will be no make up exams unless the following:

• For planned excused absences such as interviews, you must contact the instructor 48 hr in advance of the missed exam and provide adequate documentation.

• For absences due to catastrophic events such as serious illness, accident, or death in the immediate family, proper documented justification is required.

I will require documentation for any missed assignments or exams! Grading: Straight Scale

930 – 1000 points 93% - 100% A 900 – 929 points 90% - 92.9% A- 870 – 899 points 87% - 89.9% B+ 830 – 869 points 83% - 86.9% B 800 – 829 points 80% - 82.9% B- 770 – 799 points 77% - 79.9% C+ 730 – 769 points 73% - 76.9% C 700 – 729 points 70% - 72.9% C- 670 – 699 points 67% - 69.9% D+ 630 – 669 points 63% - 66.9% D 600 – 629 points 60% - 62.9% D- Less than 600 points <60% E

Academic Honesty, Software Use, Campus Helping Resources, Services for Students with Disabilities Academic Honesty In 1995 the UF student body enacted an honor code and voluntarily committed itself to the highest standards of honesty and integrity. When students enroll at the university, they commit themselves to the standard drafted and enacted by students. The Honor Pledge: We, the members of the University of Florida community, pledge to hold ourselves and our peers to the highest standards of honesty and integrity. On all work submitted for credit by students at the university, the following pledge is either required or implied: "On my honor, I have neither given nor received unauthorized aid in doing this assignment." Students should report any condition that facilitates dishonesty to the instructor, department chair, college dean, Student Honor Council, or Student Conduct and Conflict Resolution in the Dean of Students Office. (Source: 2012-2013 Undergraduate Catalog) It is assumed all work will be completed independently unless the assignment is defined as a group project, in writing by the instructor. This policy will be vigorously upheld at all times in this course. Software Use: All faculty, staff and students of the university are required and expected to obey the laws and legal agreements governing software use. Failure to do so can lead to monetary damages and/or criminal penalties for the individual violator. Because such violations are also against university policies and rules, disciplinary action will be taken as appropriate.

Campus Helping Resources Students experiencing crises or personal problems that interfere with their general well-being are encouraged to utilize the university’s counseling resources. The Counseling & Wellness Center provides confidential counseling services at no cost for currently enrolled students. Resources are available on campus for students having personal problems or lacking clear career or academic goals, which interfere with their academic performance.

• University Counseling & Wellness Center, 3190 Radio Road, 352-392-1575, www.counseling.ufl.edu/cwc/

Counseling Services Groups and Workshops Outreach and Consultation Self-Help Library Training Programs Community Provider Database

• Career Resource Center, First Floor JWRU, 392-1601, www.crc.ufl.edu/ Services for Students with Disabilities The Disability Resource Center coordinates the needed accommodations of students with disabilities. This includes registering disabilities, recommending academic accommodations within the classroom, accessing special adaptive computer equipment, providing interpretation services and mediating faculty-student disability related issues. 0001 Reid Hall, 352-392-8565, www.dso.ufl.edu/drc/

MCB 4XXX - Environmental Microbiology Spring 2013 Format Due Date Assisgnment Date Lecture Topic

7"Jan

Introduction.to.Environmental.Microbiology.and.the.Nature.of.Science.(How.do.we.know.what.we.know?) In.person

Environmental.Microbiology:.from.genomes.to.biogeochemistry.textbook.(EM).".Chapter.

1Quiz.1 7"Jan Formation.of.the.Biosphere.".Origin.of.the.Earth In.person EM.textbook.Chapter.2

podcastFormation.of.the.Biosphere.".Origin.of.Life.".Where.did.the.raw.materials.come.from? podcast

Online.Quiz.1.due.1/13/13 Gilmour.and.Sephon.(PDF.at.Sakai)

14"JanFormation.of.the.Biosphere.".Origin.of.Life."Role.of.minerals In.person

First.Draft.of..Personal.Statement.Due.

1/28/13 EM.textbook.Chapter.2

Quiz.2 14"JanFormation.of.the.Biosphere.".Origin.of.Life."Its.an.RNA.world! In.person

Origin.of.DNA.genomes.".Forterre.(PDF.at.Sakai)

podcastFormation.of.the.Biosphere.".Origin.of.Life.".Last.Universal.Comman.Ancestor.".origin.of.the.genome podcast

Online.Quiz.2.due.1/20/13 EM.textbook.Chapter.2

21"Jan no.class.Dr..King.Holiday

28"Jan

Introduction to the Primary Literature and Environmental Microbiology Paper 1 - Group Discussion In.person

Reading.Primary.Literature.pp..1"40.and.Ferris.paper.(PDF.in.Sakai).

Quiz.3 28"Jan Rise.of.Oxygen.and.origin.of.eukaryotes in.person Kasting.nature.PDF.(Sakai)

podcastClimate.and.the.environment:.the.impact.on.microbes podcast


Exam.1 4"Feb Exam.1."Multiple.Choice,.Short.Answer in.person

11"FebDarwin's.birthday.celebration.".Evolution.and.the.Origin.of.Species.".The.arguments.and.the.evidence In.person

Quiz.4 11"Feb Interplanetary.Transport.of.Microbes.".Panspermia. In.person Nicholson.et.al.,.review.(PDF.at.Sakai)

podcastPhysiological.Ecology:.microbial.responses.to.resource.limitations podcast


18"FebMicrobial.Diversity.on.Earth."The.microbial.tree.of.life In.person EM.textbook.Chapter.5

Quiz.5 18"FebMicrobial.Diversity.".Meta"advances.in.meta"omics.and.the.tools.of.environmental.microbiology. In.person

EM.textbook.Chapter.5;.Primer.on.Metagenomics.(see.PDF.in.Sakai)

podcastMicrobial.Diversity.".a.practical.tutorial.of.16S.rRNA.gene.analysis podcast

Online.Quiz.5.due.2/17/13

complete.online.learning.module.of.community.data.set

25"FebEnvironmental Microbiology Paper 2 - Group Discussion Group.Disc

Abstract.write"up.due.3/11/13

.Mobberley.et.al.,.2012.Environmental.Microbiology.(Sakai)

Quiz.6 25"FebMicrobial.Life.in.Extreme.environments.I."Thermophilic.adaptation In.person

EM.textbook.Chapter.4........................Rothschild.Nature.paper.(PDF.Sakai)

podcastMicrobial.Life.in.Extreme.environments.II."Salt,.UV.radiation.pH,.pressure podcast

Online.Quiz.6.due.3/10/13

EM.textbook.Chapter.4........................Rothschild.Nature.paper.(PDF.Sakai)

5"Mar spring.break

11"MarMicrobial.Life.in.Extreme.environments.III."Mechanisms.of.Cold.Adaptation In.person

EM.textbook.Chapter.4..........................Madigan.and.Oren.paper.(PDF.in.Sakai)

Quiz.7 11"Mar

Microbial.Life.in.Extreme.environments.IV".desiccation.and.potential.habitability.beyond.the.biosphere In.person

EM.textbook.Chapter.4...............................Feller.et.al.,.paper.(PDF.in.Sakai)

podcastIntroduction.to.Microbial.Biogeochemistry.".Methodologies.and.Tools.of.the.trade podcast

Online.Quiz.7.due.3/17/13 EM.textook.Chapter.7

Exam.2 18"Mar Exam.2.".Multiple.Choice.and.short.Answer In.person

25"MarMicrobial.Biogeochemistry.".Carbon.and.Nitrogen.Cycle In.person EM.textook.Chapter.7

Quiz.8 25"MarEnvironmental Microbiology Paper 3 - Group Discussion Group.Disc

Abstract.write"up.due.4/1/13

Bebout.et.al.,.2004.Geobiology.See.Sakai.for.paper

podcastMicrobial.Biogeochemistry."Sulfur.and.Phosphorus.cycle podcast


1"Apr Host"microbe.Interactions.".Animals In.person McFall"Ngai.paper.(PDF.Sakai)Quiz.9 1"Apr Host"microbe.interactions.".Plants In.person Brencic.and.Winans.paper.(PDF.Sakai)

podcast Microbial.Communities.".Introduction.to.Biofilms podcastOnline.Quiz.9.due.

4/7/13 Stoodley.et.al.,.2002.(PDF.Sakai)

Quiz.10 8"AprStudent.Oral.Presentations.".The.FAME.lab.(famelab.org)

peer.evaluation.of.student.presentations.".inclass.assignment

podcastApplied.Enviromental.Microbiology.".biotechnology/antibiotic.resistance podcast


Quiz.11 15"Apr Student.Oral.Presentations.".The.FAME.labpeer.evaluation.of.student.presentations.".

inclass.assignment

podcastApplied.Enviromental.Microbiology.".bioenergy/biofuels Podcast.13

Online.Quiz.11.due.4/15/13 Antoni.et.al.,.2007.paper.(PDF.Sakai)

23"Apr

Applied.Enviromental.Microbiology."Biodegradation.and.Remediation.".case.study.International.Space.Station In.person Madsen.paper.(PDF.Sakai)

Quiz.12 23"AprFuture.Frontiers.of.Environmental.Microbiology"part.1 In.person

Final.Submission.Personal.Satement.

4/24/2013 EM.textook.Chapter.9

podcastFuture.Frontiers.of.Environmental.Microbiology"part.2 podcast


Final.Exam TBD Final.Exam.".Multiple.Choice.and.short.Answer. TBD

Lecture Schedule – Spring 2013

UCC: External Consultations

Rev. 10/10

External Consultation Results (departments with potential overlap or interest in proposed course, if any)

Department Name and Title

E-mailPhone Number

Comments


E-mailPhone Number

Comments


E-mailPhone Number

Comments

Ramesh,

Thanks for taking the time to look this over I do appreciate it.

cheersJamie

On Jun 24, 2012, at 10:15 AM, Reddy, K. Ramesh wrote:

Jamie: It sounds like an interesting course. I am not too concerned minor overlap. Good luck with your course. Ramesh_____________________________________________________________________________ K. Ramesh Reddy | Graduate Research Professor and Chair | Distance Education CoordinatorUniversity of Florida | IFAS | Soil and Water Science Department |

PO Box 110510 | 106 Newell Hall.Gainesville, FL 32611-0510 | USAPH 352-392-1804 | FAX 352-392-3399EMAIL: [email protected] | http://soils.ifas.ufl.edu______________________________________________________________________________Additional Contacts: Ms. Cheryl Combs [email protected] | Tel: 352-392-1803___________________________________________________________________________________________________The Soil and Water Science Newsletter "MYAKKA" is available at: The Soil and Water Science Spring 2012 Newsletter “MYAKKA” is now available for your reading at: http://soils.ifas.ufl.edu/department/newsletters/Spring_2012_MYAKKA_Newsletter.pdf Please forward this message to your contacts. If you need a hard copy of the newsletter, please contact Mr. Michael Sisk at: [email protected] From: Jamie Foster [mailto:[email protected]] Sent: Saturday, June 23, 2012 1:00 PMTo: Ogram,Andrew VCc: Reddy, K. Ramesh; Teplitski,Max; Inglett,Patrick WSubject: Re: New Environmental Micro Course Dear Andy, Ramesh, and Patrick, This proposed course will be a 4000 level course and will cover the Origin of the Biosphere, Origin of Life, impact of microbes on the climate over Earth's history (i.e., snowball earth), Environmental selection on the genome, Microbial Diversity (mainly tools of the trade, high through put sequencing), Basic Biogeochemistry, Extremophiles, Host-microbe interactions, and some aspects of Applied Environmental Microbiology (e.g. bioremediation on the International Space Station, Bioenergy); I am reattaching the syllabus (the last page has the proposed lecture schedule). The only overlap I see is that I introduce biogeochemistry and give three overview lectures on that subject. I was planning on using my research on stromatolites, the moons of Jupiter and Saturn as examples of potential habitability and biogeochemistry beyond Earth for those lectures. If you think those two lectures are problematic I can replace them with something else. Thank youJamie On Jun 23, 2012, at 9:48 AM, Ogram,Andrew V wrote:

Jamie, I teach SWS4303 Soil Microbial Ecology. I don't see significant overlap with that course. What level will this course be taught (3000 or 4000)? Andy

From: Reddy, K. RameshSent: Saturday, June 23, 2012 9:10 AMTo: Teplitski,Max; Foster,Jamie SCc: Ogram,Andrew V; Inglett,Patrick W

From: Jamie Foster <[email protected]>Subject: Re: New Environmental Micro Course

Date: June 24, 2012 1:03:54 PM EDTTo: "Reddy, K. Ramesh" <[email protected]>

mailto:[email protected]

http://soils.ifas.ufl.edu/


http://soils.ifas.ufl.edu/department/newsletters/Spring_2012_MYAKKA_Newsletter.pdf


Subject: RE: New Environmental Micro Course

Jamie: Also, please make sure the course will not overlap with the topics presented in the following courses. Soil Microbial Ecology – Andy OgramAdvanced Microbial Ecology – Andy OgramEnvironmental Biogeochemistry – Patrick InglettAdvanced Biogeochemistry – Patrick InglettBiogeochemistry of Wetlands -‐ K. Ramesh Reddy We want to make sure your course compliments the existing courses we currently offer in the department. We will be happy to work with you in developing such course. Ramesh_____________________________________________________________________________ K. Ramesh Reddy | Graduate Research Professor and Chair | Distance Education CoordinatorUniversity of Florida | IFAS | Soil and Water Science Department |

PO Box 110510 | 106 Newell Hall.Gainesville, FL 32611-0510 | USAPH 352-392-1804 | FAX 352-392-3399EMAIL: [email protected] | http://soils.ifas.ufl.edu

______________________________________________________________________________Additional Contacts: Ms. Cheryl Combs [email protected] | Tel: 352-392-1803___________________________________________________________________________________________________The Soil and Water Science Newsletter "MYAKKA" is available at: The Soil and Water Science Spring 2012 Newsletter “ MYAKKA” is now available for your reading at: http://soils.ifas.ufl.edu/department/newsletters/Spring_2012_MYAKKA_Newsletter.pdf Please forward this message to your contacts. If you need a hard copy of the newsletter, please contact Mr. Michael Sisk at: [email protected]

From: Teplitski,Max Sent: Saturday, June 23, 2012 9:04 AMTo: Foster,Jamie SCc: Reddy, K. RameshSubject: RE: New Environmental Micro Course Hi Jamie,

I have reviewed the information you supplied for your proposed course Environmental Microbiology. What you proposed does not overlap with my course SWS4307/SWS5308 in terms of the content, we also use different textbooks. Best of luck in developing your course. I have copied Dr. Reddy on this communication.

Max

From: Jamie Foster [[email protected]]Sent: Friday, June 22, 2012 8:13 PMTo: Teplitski,MaxSubject: Re: New Environmental Micro Course

Hi Max, I am planning on using the book Environmental Microbiology: From Genomes to Biogeochemistry by Eugene Madsen I just need the statement for the approval process. thanksJamie On Jun 22, 2012, at 4:43 PM, Teplitski,Max wrote:

Jamie, I don't think that the topics are even close...

what textbook do you plan to use?

here's the content of my course:Jan Assigned Readings


http://soils.ifas.ufl.edu/


http://soils.ifas.ufl.edu/department/newsletters/Spring_2012_MYAKKA_Newsletter.pdf



11Environmentally Transmitted Pathogens Hrudley et al13Environmentally Transmitted Pathogens Environm Micro Ch 2216NO CLASS. Dr. M. L. King's Day18Emerging and Re-emerging Pathogens Ahmed et al

Detection, enumeration and identification of pathogens20Sample Collection, Microscopy Case Study Begins EM Ch 8, 923Culture-based techniques EM Ch 1025Physiological Methods EM Ch 11.2, 11.7 and 11.927Immunological Methods EM Ch 1230Nucleic acid-based techniques EM Ch 13

Feb1Nucleic acid-based techniques3Source tracking of pathogens SourceTracking Suppl

Habitats Where Pathogens Survive6Soil, Air, Water EM Ch. 4, Ch. 5, Ch.68Plant-associated environments Brandl et all

10Human pathogens in produce Supplem Reading13Global climate change and infectious diseases EM Ch18, Suppl: Lipp 2002, Ford 200915Climate change and disease of aquatic animals Suppl Reading17Pathogens in multicellular communities EM Ch 1620Pre-exam review

Fundamentals of microbial ecology22FIRST EXAM24Biofilms and microbial cell-to-cell signaling Biofilms Suppl27Evolution of antibiotic resistance Antibioitcs Suppl29Evolution of virulence Evolution of Virulence Supp

March2Case Study Presentations Case Study Ends5SPRING BREAK BEGINS9SPRING BREAK ENDS

12Case Study Presentations14Case Study Presentations16Pathogens as prey19Student Presentation

Components of microbiological water safety21What is water quality?23Indicator organisms26Student Presentation28Drinking water treatment and disinfection Pre-exam questions due30Pre-exam Review

April2SECOND EXAM4Reclaimed water treatment6Sustainable control of waterborne pathogens9 Intro to food safety

11Student Presentation13Urban microbiology16Microbes and Bioterrorism18Risk assessment and communication20Careers in microbial ecology23Final review25CLASSES END

From: Jamie Foster [[email protected]]Sent: Friday, June 22, 2012 4:26 PMTo: Teplitski,MaxSubject: New Environmental Micro Course

Dear Max,

I am proposing to develop a new Environmental Microbiology course for the Microbiology and Cell Science Department that will examine aspects of biogeochemistry, environmental evolution, extremophiles, symbiosis and the applications of environmental microbiology in biotechnology.

I am writing to you to make sure you do not see any significant conflict with your SWS 4303C Soil Microbial Ecology course. I will not be discussion soil communities in any detail in this proposed course.

I have attached a syllabus with a proposed lecture schedule on the last page. I was wondering if you do not foresee any conflict perhaps you might write me an email stating that fact. If you do see a potential conflict, however, perhaps we can discuss this over the phone and I can try to revise my course.


Thank you for your attention to this request.

Best RegardsJamie

___________________________________Jamie Foster, Ph.D.Department of Microbiology and Cell ScienceUniversity of FloridaSpace Life Sciences LabKennedy Space Center, FL 32899Tel: 321-861-2900http://jamiefosterscience.com

http://jamiefosterscience.com/

Documents

UCC1: New Course Transmittal Form - University of Floridafora.aa.ufl.edu/docs/47//20Nov12//UCC_20Nov12... · Introductory Intermediate Advanced Department Contact College Contact