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Undergraduate Research
BMB 488: Communities of Practice
Student and mentor working in the lab

Overview:

BMB 488 (Communities of Practice) is a 2 cr. course that integrates the practice of primary research with the acquisition of key concepts of biochemistry and molecular biology, including the philosophy of science, central concepts and details of experimental systems, ethics, and the societal implications of research. Students in BMB 488 join a research laboratory and pursue an independent project that relates to the major goals of the lab. Students from different labs investigating similar research questions meet once per week in a seminar setting to discuss critical issues surrounding the research topic. Students engaging in research through BMB 488 have two support networks: scientists at different career stages in the research laboratory, and a peer group of other students in the seminar. Because students in the course are from different labs, they learn from each other about different research perspectives and methods and provide each other with support and advice. Students continue their independent projects and remain in BMB 488 over multiple semesters, allowing them to strengthen this network and build skills over time.

 

How do I get involved in BMB 488?

Some faculty prefer for students to first be accepted into their lab for independent research, and then they encourage students to enroll in a corresponding BMB 488 section.  Other faculty will consider students that apply directly to a BMB 488 section. So, if you are interested in a BMB 488 section, you are encourage to apply through the 488 application as well as reach out to the faculty member through email, expressing interest in their lab.

Section 001:  Antibiotics: Development and Resistance

Is a section that integrates primary research in antibiotic discovery with a student-driven seminar investigating scientific, societal, and ethical issues associated with antibiotic development and the spread of antibiotic resistance. Participation in section 001 of B M B 488 is application based.  Applications are taken the start of every semester.  Instructor approval is required for enrollment in this section.

Submit Your Application

ANTIBIOTICS: DEVELOPMENT AND RESISTANCE

BMB 488, Section 001 integrates primary research in antibiotic discovery with a student-driven seminar investigating scientific, societal, and ethical issues associated with antibiotic development and the spread of antibiotic resistance.

Research: Students will be fully integrated into a research team in one of the participating laboratories and perform research (5 hours/week) designed to identify novel antibiotics.

Seminar: Students in this section will meet as a group on a weekly basis for discussions with the participating faculty. Students will read and discuss articles from the primary literature related to antibiotic resistance and explore the broader implications of the research. Topics for discussion will be selected by the class members in consultation with the faculty. Possible topics include the drug development process from the bench to the pharmacy, the use and misuse of antibiotics, and the threat of multiple drug-resistant bacterial pathogens. In addition, students will learn how to develop research proposals and how to present their findings.

BMB 488 is a 2-credit section for freshmen, sophomore, and juniors with a record of academic achievement and an interest in research.  This section will be offered on an ongoing basis and students are encouraged to enroll in the section each semester that they are involved in the research project with approval of the instructors. Research times will be arranged with the individual faculty. The meeting time for the seminar will be determined after enrollment is complete.

For more information about this section, contact Dr. Ken Keiler.

Section 002:  Genetic Control of Organogenesis

The goal of section 002 of B M B 488 is to provide authentic research experiences to students who are entering the major and to engage students in a community of practice, a group of scientists with varying levels of experience working toward a shared scientific objective. The scientific objective is to identify genes that direct morphogenesis of biological tubes by using RNAi and DIC microscopy to screen a selection of candidate genes for those with defects in morphogenesis of the C. elegans vulva.  Applications are taken the start of every semester.  Instructor approval is required for enrollment in this section.

Submit Your Application

GENETIC CONTROL OF ORGANOGENESIS

Instructors:

  • Dr. Wendy Hanna-Rose
    • 104D Life Science Building
  • Dr. Melissa Rolls
    • 118 Life Science Building

Goals: The goal of BMB/MICRB 488 section 002 is to provide authentic research experiences to students who are entering the major and to engage students in a community of practice, a group of scientists with varying levels of experience working toward a shared scientific objective.Seminar: 1 hour per week,128 LSB plus 5 hours of lab work per week

Scientific Objective: To identify genes that direct morphogenesis of biological tubes by using RNAi and DIC microscopy to screen a selection of candidate genes for those with defects in morphogenesis of the C. elegans vulva.

 

OBJECTIVE

Students will become familiar with the practice of science

Learning Outcomes

  • Students will be able to design and execute experiments
  • Students will be able to communicate experimental results using both oral and written formats
  • Students will efficiently work as part of a team to manage a project.

OBJECTIVE

Students will gain familiarity with the scientific literature

Learning Outcomes

  • Students will be able to distinguish between primary and secondary literature sources
  • Students will be able to find primary literature and secondary literature sources on a topic of interest
  • Students will begin to build a vocabulary appropriate to a molecular and developmental biologist.

OBJECTIVE

Students will acquire specific laboratory skills

Learning Outcomes

  • Students will become proficient at culturing and manipulating C. elegans.
  • Students will recognize normal and abnormal C. elegans vulval anatomy.
  • Students will be able to acquire DIC images from live C. elegans samples.
  • Students will keep a detailed research notebook.

OBJECTIVE

Students will gain familiarity with genetics as a research tool

Learning Outcomes

  • Students will be able to articulate the purpose of genetic screens
  • Students will begin to build a vocabulary appropriate to a geneticist
  • Students will be able to broadly outline the mechanism of RNAi
  • Students will be able to differentiate between forward and reverse genetics
  • Students will be able to differentiate between different types of genetic alleles and manipulations (e.g., null, loss of function, gain of function, hypomorph, reduction of function, etc)

 

REQUIREMENTS

Research: A minimum of 5 hours/week doing primary research in the laboratory is required.

Seminar: (1 hour a week)

  • The seminar will focus on introductory material such as:
  • The practice of Science
  • Model system biology
  • C. elegans anatomy and vulval development
  • Mechanisms of tube formation
  • Genetics and RNAi as a tool

 

  • The seminar will focus on presentations of research progress by enrolled students and other advanced students from the Hanna-Rose lab. We will discuss research progress, trouble shoot experiments and learn how to present findings.
  • The seminar will focus on topical discussions from “The Everyday Practice of Science: Where Intuition and Passion meet Objectivity and Logic” by Frederick Grinnell

Written Assignments:

  • At the beginning of the semester, students will write a 1-page paper describing the goal of their research project, the hypothesis to be tested, and the experimental approach to be used.
  • Students will keep a laboratory notebook.
  • At the end of the semester students will write a summary of research progress, including recommended future directions.
  • Other assignments as directed by the instructors

GRADING

  • 50% Laboratory research
  • 25% Seminar

The seminar grade will be based on the student’s preparation for and participation in the discussions. Since this part of the grade is based on participation, attendance is critical. If you cannot come to a meeting of the seminar due to a valid excuse such as a documented illness, you must contact one of the instructors as soon as possible, preferably before the missed class.

  • 25% Written assignments

Section 003: Genetics and genomics: principles and practice

Is a section that integrates primary research in genetics and genomics with a student-driven seminar investigating scientific, societal, and ethical issues associated with gene discovery and the molecular genetic basis of human diseases.  Applications are currently not being accepted.

Currently not accepting applications

GENETICS AND GENOMICS: PRINCIPLES AND PRACTICE

BMB 488, Section 003 integrates primary research in genetics and genomics with a student-driven seminar investigating scientific, societal, and ethical issues associated with gene discovery and the molecular genetic basis of human diseases.

Research: Students will be fully integrated into a research team in one of the participating laboratories and learn experimental and analytical techniques (upto 5 hours/week) designed to understand the principles and applications of genomics.

Seminar: Students in this section will meet as a group on a weekly basis for discussions with the participating faculty. Students will read and discuss articles from the primary literature related to genomics and explore the broader implications of the research. Topics for discussion will be selected by the class members in consultation with the faculty. Possible topics include the practice of science, hypothesis generation and design of experiments, fundamentals of conducting research, grant writing, and presentation of research findings to peers and public.

BMB 488 is a 2-credit section for freshmen, sophomore, and juniors with a record of academic achievement and an interest in research. There are no prerequisites for this course.  All interested students will have to obtain approval of the instructors. Research times will be arranged with the individual faculty. The meeting time for the seminar will be determined after enrollment is complete.

For more information about this section, contact Dr. Ross Hardison.

Section 004:  Gene Regulation

B M B 488 section 004 will enhance laboratory research experience with a community of practice in the Penn State Center for Eukaryotic Gene Regulation.  Participants will perform gene regulation research in the laboratory of Joseph Reese, Song Tan, David Gilmour, Lu Bai and Shaun Mahony and participate in weekly student-driven seminars investigating scientific, societal and ethical issues associated with gene regulation and the molecular basis of human diseases.”  Instructor approval is required for enrollment in this section.

Currently not accepting applications

Gene Regulation

BMB 488, Section 004 integrates primary research in gene regulation with a student-driven seminar investigating scientific, societal, and ethical issues associated with gene regulation and the molecular basis of human diseases.

Research: Students will be fully integrated into a research team in one of the participating laboratories and learn experimental and analytical techniques (5-10 hours/week) designed to understand the principles of gene regulation.

Seminar: Students in this section will meet as a group on a weekly basis for discussions with the participating faculty. Students will read and discuss articles from the primary literature related to gene regulation and explore the broader implications of the research. Possible topics include the practice of science, hypothesis generation and design of experiments, fundamentals of conducting research, grant writing, and presentation of research findings to peers and public.

BMB 488 is a 2-credit section for undergraduates with a record of academic achievement and an interest in research. BMB 251 is a recommended course (but may be waived with permission of the faculty). All interested students will have to obtain approval of the faculty. Research times will be arranged with the individual faculty.

For more information about this section, contact Dr. Pugh

Section 005: Structural Biology: An Integrative Approach

The goal of BMB488 Structural Biology: An Integrative Approach is to achieve a holistic understanding of challenging biological questions through the lens of structures. In the community of integrative structural biology, student researchers critically discuss and apply multiple structure-determination, modeling and bioinformatic methods to piece together and interpret structural information in order to elucidate the three-dimensional cellular context of the macromolecular world. This goal is attained by integrating the practice of primary research with acquisition of key concepts in Structural Biology with a student-driven seminar investigating scientific, societal, and ethical issues associated with molecular basis of human health and diseases.

Submit Your Application

Section 006:  Host-Microbe Interactions

This section of BMB 488 will focus upon how various microbes (bacteria, parasites) can interface with their host, in both pathogenic and beneficial ways. We will discuss how these interactions work, and what their outcomes are for the organism on both sides of the interaction. We will accomplish this through group discussions and presentations of these topics as concepts, but we will also investigate Host-Microbe Interactions by performing original research in the laboratory. Research will be hosted by the laboratories of Drs. Manuel Llinas, and Tim Miyashiro, and will focus on interactions that are new, relevant, and exciting for this field.  Instructor approval is required for enrollment in this section.

Submit Your Application

HOST-MICROBE INTERACTIONS

This section of BMB 488 will focus upon how various microbes (with a focus on bacteria and parasites) can interface with their host, in both pathogenic and beneficial ways. We will discuss how these interactions work, and what their outcomes are for the organism on both sides of the interaction.

Research: Each student will be fully integrated with one of the sponsoring research groups (Lindner, Llinas, Miyashiro) to conduct original research and to learn first-hand how to design and carry out experimental and computational approaches (5-10 hours/week) to understanding Host-Microbe Interactions.

Seminar: We will meet together weekly for discussions of both the beneficial and pathogenic aspects of Host-Microbe Interactions. These discussions will focus upon recent publications and developments in this field, how to design a testable hypothesis and a research experiment that can address it, and how to effectively communicate about your research to others in various formats (presentations, elevator speeches, short grant applications). We will also benefit from guest lectures from other professors who actively conduct research in this field. Above all, we will benefit from one another and develop these skills as a cohort, and apply them to new, relevant, real-world problems.

BMB 488 is a 2 credit section that is designed for undergraduates with a record of strong academic achievement and an interest in pursuing biological research. Interested students should apply to participate in this new section of the course, and will be contacted for a short meeting to discuss placement for this section and the participating laboratories. Research times will be established by each sponsoring faculty member’s laboratory.

For more information about the section, contact Dr. Timothy Miyashiro or  Dr. Manuel Llinas