575.703.81 - Environmental Biotechnology

Course Structure

The course materials are divided into modules. The modules can be accessed by clicking Modules on the menu in Canvas. A module will have several sections including the overview, content, readings, discussions, and assignments. Students are encouraged to preview all sections of the module before starting your work. Most modules run for a period of seven (7) days, exceptions are noted on the Course Outline page. Students should regularly check the Calendar and Announcements for assignment due dates. 

Course Topics

N/A

Course Goals

To identify methods to exploit microorganisms for use in applications of biotechnology to environmental quality evaluation, monitoring, and remediation of contaminated environments. To identify environmental conditions where specific environmental biotechnologies may be applied to improve the quality of the environment or enhance energy efficiency.

Course Learning Outcomes (CLOs)

• Categorize how microbial structure dictates their function in the environment.
• Explain the biochemical bases for microbial metabolism of environmental contaminants.
• Describe techniques to modify and augment microorganisms in the laboratory and environment.
• Compare several methods of facilitating the bioremediation of contaminants in the environment.
• Given a category of environmental pollutants develop a basic bioremediation scheme.
• Identify applications for biosensors to environmental analysis and monitoring.
• Clarify contamination scenarios when phytoremediation may be appropriate/applicable.
• Explain the basic design and application of microbial fuel cells.
• Defines role of bioplastics in environment.
• Climate change and Biotechnology part in climate change.
• Expresses the importance of Sustainability and Sustainable development goals.
• Describes Biosafety positive and negative effects to the environment.

Textbooks

 Required

 1. Vallero, D.,(2015). Environmental Biotechnology, A Biosystems Approach (2nd ed.).

Academic Press.

• • Pradeep Verma.(2022), Industrial Microbiology and Biotechnology.
  • Madigan, M.T., Bender, S., Buckley, D.H., Sattley, W.M., Stahl, D.A., Brock, T.D.(February 25th, 2020- Copyright © 2021)), Brock Biology of Microorganism (16h ed.), Pearson. ISBN-13: 9780134874401.

 3. Anoop Singh, (December 2021). Environmental Microbiology and Biotechnology. ISBN:9811574952, ISBN13:9789811574955.

Required Software

MS Office (or equivalent) including presentation software such as PowerPoint is required.

Student Coursework Requirements

It is expected that each module will take approximately 4–7 hours per week to complete. Here is an approximate breakdown: reading the assigned sections of the texts or assigned journal articles (approximately 2–3 hours per week), listening to the audio annotated slide presentations, and assigned videos and pod casts (approximately 1–2 hours per week), and self-assessment quizzes, problem sets and writing assignments (approximately 1–2 hours per week). 

This course will consist of five basic student requirements: 

1. Preparation and Participation (Module Discussions) (15% of Final Grade Calculation) 
2. Quizzes (10% of Final Grade Calculation) 
3. Written Assignments and Problem Sets (15% of Final Grade Calculation) 
4. Technical Research Presentation Project (35% of Final Grade Calculation) 
5. Midterm Exam (20% of Final Grade Calculation) 
   

Discussion (15% of Final Grade Calculation)

Preparation and Participation emphasis on module discussions- Each module will contain assigned material. Students should prepare for discussion. student are responsible for carefully reading all assigned material and being prepared for discussion and post their initial response to the discussion questions by the evening of day 3 for that module week.

Posting a response to the discussion question is part one of the grade for module discussions (i.e., Timeliness). Part two of the grade for module discussion is students’ interaction (i.e., responding to classmate postings with thoughtful responses) with at least two classmates (i.e., Critical Thinking). Weekly assignments will vary depending on module learning objectives. 

Additional guidelines

1. Avoid postings that are limited to 'I agree' or 'great idea', etc. If you agree (or disagree) with a posting then say why you agree by supporting your statement with concepts from the readings or by bringing in a related example or experience. 
2. Address the questions as much as possible (don't let the discussion stray). 
3. Try to use quotes from the articles that support your postings. Include page numbers when you do that. o Build on others’ responses to create threads. 
4. Bring in related prior knowledge (work experience, prior coursework, readings, etc.)
5. Use proper etiquette (proper language, typing, etc.). 

Preparation and participation is evaluated by the following grading elements: 

1. Timeliness (50%) 
2. Critical Thinking (50%) 

Preparation and participation is graded as follows: 

100–90 = A—Timeliness [regularly participates; all required postings; early in discussion; throughout the discussion]; Critical Thinking [rich in content; full of thoughts, insight, and analysis]. 

89–80 = B—Timeliness [frequently participates; all required postings; some not in time for others to read and respond]; Critical Thinking [substantial information; thought, insight, and analysis has taken place].

79–70 = C—Timeliness [infrequently participates; all required postings; most at the last minute without allowing for response time]; Critical Thinking [generally competent; information is thin and commonplace].

<70 = F—Timeliness [rarely participates; some, or all required postings missing]; Critical Thinking [rudimentary and superficial; no analysis or insight is displayed].

Quizzes (10% of Final Grade calculation)

Quizzes will be multiple choice and will be evaluated with full credit or no credit depending on selection of the correct answer. No partial credit will be awarded.

Assignments (15% of Final Grade Calculation)

Assignments will include a mix of qualitative assignments (e.g. written literature reviews, model summaries), and quantitative problem sets. Each problem should include assumptions, computations, and the final answers should be boxed. All assignments are due according to the dates in the Calendar. 

Late assignments will not be accepted and will not be graded and there are no exceptions. This ensures a fair system of evaluation of all students in the course. 

Qualitative assignments are evaluated by the following grading elements:

1. Each part of assignment is addressed (25%) 
2. Writing quality and technical accuracy (20%) (Writing is expected to meet or exceed accepted graduate-level English and scholarship standards. That is, all assignments will be graded on grammar and style as well as content). 
3. Rationale for answer is provided (30%) 
4. Examples are included to illustrate rationale or direct support from readings is provided (25%) (If a student does not have direct experience related to a particular question, then the student is to provide analogies versus examples). 

Qualitative assignments are graded as follows: 

100–90 = A—All parts of question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rich in content; full of thought, insight, and analysis]. 

89–80 = B—All parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [substantial information; thought, insight, and analysis has taken place]. 79–70=C—Majority of parts of the question 

<70 = F—Timeliness [rarely participates; some, or all required postings missing]; Critical Thinking [rudimentary and superficial; no analysis or insight is displayed]. 

Quantitative assignments are evaluated by the following grading elements:

1. Each part of question is answered (20%)
2. Assumptions are clearly stated (20%)
3. Intermediate derivations and calculations are provided (25%)
4. Answer is technically correct and is clearly indicated (25%)
5. Answer precision and units are appropriate (10%)

Quantitative assignments are graded as follows: 

100–90 = A—All parts of question are addressed; All assumptions are clearly stated; All intermediate derivations and calculations are provided; Answer is technically correct and is clearly indicated; Answer precision and units are appropriate. 

89–80 = B—All parts of question are addressed; All assumptions are clearly stated; Some intermediate derivations and calculations are provided; Answer is technically correct and is indicated; Answer precision and units are appropriate. 

79–70=C—Most parts of question are addressed; Assumptions are partially stated; Few intermediate derivations and calculations are provided; Answer is not technically correct but is indicated; Answer precision and units are indicated but inappropriate. 

<70=F—Some parts of the question are addressed; Assumptions are not stated; Intermediate derivations and calculations are not provided; The answer is incorrect or missing; The answer precision and units are inappropriate or missing.

Research Project (35% of Final Grade calculation)

By the third week of the course, students will propose and seek approval from instructor for a research project topic. The topic should represent a novel or application of a novel environmental biotechnology. The last week will be devoted to presentation of each student’s research project. 

Qualitative assignments are evaluated by the following grading elements:

1. Each part of assignment is addressed (25%) 
2. Writing quality and technical accuracy (20%) (Writing is expected to meet or exceed accepted graduate-level English and scholarship standards. That is, all assignments will be graded on grammar and style as well as content.) 
3. Rationale for answer is provided (30%) 
4. Examples are included to illustrate rationale or direct support from readings is provided (25%) (If a student does not have direct experience related to a particular question, then the student is to provide analogies versus examples.) 

Qualitative assignments are graded as follows: 

100–90 = A—All parts of question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rich in content; full of thought, insight, and analysis]. 

89–80 = B—All parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [substantial information; thought, insight, and analysis has taken place]. 79–70=C—Majority of parts of the question 

<70 = F—Timeliness [rarely participates; some, or all required postings missing]; Critical Thinking [rudimentary and superficial; no analysis or insight is displayed]. 

<70 = F—Timeliness [rarely participates; some, or all required postings missing]; Critical Thinking [rudimentary and superficial; no analysis or insight is displayed].

Technical Research Presentation Project (25% of Final Grade Calculation) 

By the third week of the course, students will propose and seek approval from instructors for a research project topic. The topic should represent a novel or application of a novel environmental biotechnology. The last week will be devoted to presentation of each student’s research project. The project details are outlined in Research Presentation Project Guidelines.pdf (see Course Content Folder entitled: Research Presentation Project) 

The course project is evaluated by the following grading elements: 

1. Material is coherent and logical in its presentation (20%)
2. Presentation demonstrates in depth knowledge and critical analysis of subject (30%) Presentation came to a logical conclusion and makes recommendations for future research (15%)
3. Effective use of PowerPoint (Prezi) slides in presentation (10%)
4. Research is conducted using credible sources (include slide of all references) (10%)
5. Public speaking/presentation skill (10%)
6. Presentation falls within specified time limit (5%)

Midterm Exam (25% of Final Grade Calculation)

The midterm exam will be available in Module 8. Students will have one week to complete the exam.

The exams are evaluated by the following grading elements:

1. Each part of question is answered (30%) 
2. Writing quality and technical accuracy (30%) (Writing is expected to meet or exceed accepted graduate-level English and scholarship standards. That is, all assignments will be graded on grammar and style as well as content.) 
3. Rationale for answer is provided (20%) 
4. Examples are included to illustrate rationale (15%) (If a student does not have direct experience related to a particular question, then the student is to provide analogies versus examples.)
5. Outside references are included (5%)

Exams are graded as follows: 

100–90 = A—All parts of question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rich in content; full of thought, insight, and analysis]. 

89–80 = B—All parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [substantial information; thought, insight, and analysis has taken place]. 79–70 = C—Majority of parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [generally competent; information is thin and commonplace]. 

<70 = F—Some parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rudimentary and superficial; no analysis or insight displayed]. 

Grading Policy

Student assignments are due according to the dates in the Calendar and Assignments items in the corresponding modules. The instructors will post grades one week after assignment due dates. 

We generally do not directly grade spelling and grammar. However, egregious violations of the rules of the English language will be noted without comment. Consistently poor performance in either spelling or grammar is taken as an indication of poor written communication ability that may detract from your grade.

A grade of A indicates achievement of consistent excellence and distinction throughout the course, that is, conspicuous excellence in all aspects of assignments and discussion in every week.

A grade of B indicates work that meets all course requirements on a level appropriate for graduate academic work. These criteria apply to both undergraduates and graduate students taking the course. 

Course Policies

Course Website 

The course website is hosted by the JHU Canvas system. The course website will be used for posting announcements, assignments and course materials. Please check the website DAILY as you are responsible for reviewing all material and announcements on this website. 

Student Resources 

Students should refer to Help & Support on the menu for a listing of all the student services and support available to them. 

Missed Assignments 

Please see the course outline for the schedule of the assignments, midterm exam and quizzes. You must submit your documents in WORD format. [I cannot open other document formats.] You are expected to complete all assigned readings prior to next module; these may include materials supplemental to the textbook posted on Canvas. 

You are also responsible for completing all assignments. I will accept only one late or make-up homework. 

Late quizzes and exams will not be accepted or graded and there are no exceptions to this policy. 

Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically. 

For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity. 
 
If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.