Cell & Molecular Biology Graduate Group

CAMB Home» Program » Developmental, Stem Cell, and Regenerative Biology

Developmental, Stem Cell and Regenerative Biology

Overview | Research, Communication & Outreach| Program Course Requirements

Program Overview
Faculty labs affiliated with DSRB are addressing key questions in developmental biology, stem cell/niche interactions, and regenerative biology. The thread that unites these areas is the compelling drive to understand how tissues are formed, maintained and repaired. The primary mission of the DSRB program is the training of students in hypothesis-driven research at the forefront of these areas. Emphasizing that it is essential that we scientists communicate “what we do” and “why” to both our scientific peers and to the community at large, our program also emphasizes intellectual exchange and outreach, with activities geared to collective student participation.

Research
DSRB Students will be exposed to interdisciplinary training in gametogenesis; embryonic and fetal development; nervous system development and its wiring; the genesis of tissues and organ systems as well as their homeostasis, metabolism and repair. Exciting work is unraveling the basic biology of these processes, as well as understanding the consequences of and working toward the amelioration of diseases affecting their function. Complementing these areas is work on Embryonic Stem Cells (ESCs) and Induced Pluripotent Stem Cells (iPSCs; patient-derived iPSCs), using genome-scale approaches to understand disease processes in vitro in order to develop cell replacement strategies for therapy. The proximity of the University of Pennsylvania Health System, a world-renowned academic medical center, provides unparalleled opportunity for translational research.

DSRB Students have at their disposal all the tools of the modern genomic era. For example, some students have been developing high-throughput and genomic-scale screens, using deep sequencing, ChIP-SEQ, RNAi tools or small molecule libraries, while others are capitalizing on classical genetic analyses and screens. Some have been utilizing high-resolution microscopy techniques, including liveimaging of cells, organs and tissues in vivo, while others have adapted novel biochemical, epigenetic and cell biological approaches to their questions. Some students are actively isolating and manipulating ESCs and iPSCs, as well as characterizing the nuclear reprogramming events required to coax these cells into distinct neuroepithelial, mesodermal or endodermal lineages, an essential step in taking these powerful, biomedically promising entities into the clinic. Facilitating this work, is access to world-class cores, including those for Next Generation Sequencing, Proteomics, the Zebrafish faclity, Stem cell & Xenografting, and Microscopy, to name but a few (http://www.med.upenn.edu/cores/).

A wide variety of experimental model systems are accessible to the student within DSRB. This situation not only facilitates comparative and collaborative work, but can significantly speed that work. For example, progress might be begun in one system highly adapted to a particular approach, and then work might shift to another system more amenable for addressing the next part of the problem. The systems used in DSRB labs include plants, such as Arabidopsis; the yeasts; several invertebrate organisms, such as the nematode worm, fruitfly and ant; various vertebrate models, such as zebra fish, the frog, chick, rat and mouse.

Click on the links below to see a list of Faculty working in particular areas:

Gametogenesis
Embryo & Fetal development
Cell Migration, Polarity and Morphogenesis
 Neurogenesis and Axonogenesis
Tissue & Organ Formation
Stem Cell/Niche Interactions
Regenerative Biology
Epigenetics, gene regulatory networks & signal integration

Communication:
An important facet of each student’s training is the ability to communicate effectively and interact productively with scientific peers. For this reason, the DSRB program uses several mechanisms to guide students in communicating their research. This includes a popular biweekly student research lunch - - a very successful forum, fostering cohesion among the students in DSRB. Communication skills are also sharpened by opportunities to host student-invited seminar speakers; to give presentations at various symposia, such as the CAMB Graduate Symposium, and various Departmental or Institute symposia; and finally, opportunities to present at national and international meetings.

Outreach
The students we train have an important responsibility to enhance scientific and technological understanding within our communities. We want our students to convey to diverse audiences the general excitement about DSRB research as well as of their own specific accomplishments. For these reasons, DSRB supports and encourages the participation of interested students in any one of several proven outreach activities. Opportunities range from a semester as a teaching assistant to participation in a nationally renowned outreach program, or mentoring an intern in a research project for a summer. Encouraging outreach aligns the DSRB program track with the Penn Compact, "Engaging Locally" (http:// www.upenn.edu/president/penn-compact/engaging-locally). An appropriate time for our graduate students to participate in outreach would be in the middle-to-out years of their work, when coursework is complete and a thesis project is solidly underway.

Example opportunities
-- Participate in the renowned outreach programs, “BioEYES” or “ReBIO”: with over 12 years in area public schools, these programs are managed by Dr. Jamie Shuda, an experienced educator who develops university-community partnerships in science. She will provide training, help establish relationships with students and teachers, and serve as a mentor to help assess impact and effectiveness. Students are encouraged to adapt the existing programs to best communicate their research focus to the most appropriate audience. http://bioeyes.org/index.html, http://irm.upenn.edu/BridgetoReBIO.

-- The “Summer Undergraduate Internship Program (SUIP)”: http://www.med.upenn.edu/bgs/applicants_suip.shtml
Run successfully by Biomedical Graduate Studies for over 15 years, the program serves some 30 college interns each summer, and particularly so, those from underrepresented minority groups or disadvantaged backgrounds, those with disabilities, or who attend small colleges. In this program you will directly oversee the intern’s research in collaboration with your PI, and coach them in their summer’s end presentation to the Leadership Alliance National Symposium.

-- iPraxis Scienteering:
http://www.ipraxis.org/programs
Mentoring local high school students in STEM science fair projects (Science, Technology, Engineering & Math).

DSRB gratefully acknowledges the essential support of:
The CAMB graduate group; The Penn Institute for Regenerative Medicine; The Departments of – Cell and Developmental Biology, and Dermatology; The School of Veterinary Medicine - Animal Biology and the Center for Developmental Biology at CHOP

Overview | Research, Communication & Outreach| Program Course Requirements

Program course requirements

Typical course & research schedule for DSRB students:

First year --
Fall - BIOM 600 Cell Biology
            - CAMB 605 First year seminar (literature readings + discussions)
            - Lab Rotation

Spring - BIOM 555 Gene Expression
            -CAMB 511 Principles of Development (required for DSRB)
            -Elective -
            -Two lab rotations

Summer - Research in prospective thesis lab

Second year --
Fall - CAMB 620 Thematic concepts in Development (required for DSRB)
        -Elective -
        - Research in prospective thesis lab

Spring - Two Electives -
             - CAMB 695 Prelim prep writing course (optional)
             - Research in prospective thesis lab

This semester ends with the successful oral defense of the Prelim Proposal. See the"CAMB Academics" site for more general, detailed information about courses, rotations and the Prelim exam.

Elective choices:

Students have tremendous flexibility, and in consultation with faculty advisors will select electives that fit their research interests and prospective directions.

Suggested electives follow:

CAMB 534: Seminar on Current Genetic Research
CAMB 541: Genetic Systems
CAMB 542: Topics in Molecular Medicine
CAMB 550: Genetic Principles
CAMB 597: Developmental Neurobiology
CAMB 608: Regulation of Eukaryotic Gene Expression
CAMB 630: Topics in Human Genetics
CAMB 632: Cell Control by Signal Transduction Pathways
CAMB 691 / 692: Advanced Topics in Cell Biology and Physiology
CAMB 697: The Biology of Stem Cells
GCB 531: Introduction to Genome Science

CAMB 511: Principles of Development
2012 Syllabus
This graduate course, which will include lectures and readings from the literature, is designed to provide a foundation in the principles of developmental biology.  Topics covered will include: fertilization and cleavage, pattern formation, gastrulation, germ layer formation, tissue specification, morphogenesis, tissue differentiation, organogenesis, stem cell biology, and developmental evolution.  The use of modern molecular biology, genetics, and embryological manipulations will be discussed in the context of the analysis of developmental mechanisms. Offered spring semester. [up]

CAMB 620: Thematic Concepts in Developmental Biology
2012 Syllabus
The goal of this seminar course is to foster discussion about general strategies used by cells and organisms to solve fundamental problems during development. This is not a survey course in Developmental Biology. Rather, we focus on an overarching theme for the semester (see below), enabling us to define the issues central to that theme, and explore attempts to uncover solutions using different model systems. Primary research papers are assigned for discussion, and all students are expected to contribute thoughtfully and energetically to the discussion each week. Prior years' topics have been: "Developmental links to Disease"; "Cell Biology in Development"; "Stem Cells"; "Rulers, Clocks & Oscillators in Development". Offered fall semester. [up]

Suggested Elective Courses:

CAMB 534: Seminar on current genetic research: Modeling Human Disease in Animals.
2010 Syllabus
An advanced seminar course emphasizing genetic research in model organisms and how it informs modern medicine. Each week a student will present background on a specific human disease. This is followed by an intense discussion by the entire class of ~2 recent papers in which model organisms have been used to address the disease mechanism and/or treatment. Offered spring semester. Prerequisites: CAMB 605 or CAMB542 or permission of the instructor. [up]

CAMB 541: Genetic Systems
2011 Syllabus
The genetics of different organisms (mouse, Drosophila, C.elegans, Arabidopsis, etc.) will be considered with an emphasis on the various techniques employed to study the action of genes in these organisms. Offered spring semester. [up]

CAMB 542: Topics in Molecular Medicine
2012 Syllabus
TiMM is planned as a once-weekly seminar course whose goal is to introduce students to the ways in which biomedical research can provide new insights into clinical medicine and, conversely, how knowledge of clinical disease impacts scientific discovery. There are two sections for the course -- 401 and 402. Section 401 is for first year MD/PhD students only and section 402 is for VMD/PhD and PhD students. [up]

CAMB 550: Genetic Principles
2011 Syllabus
TThis is a required course of the Genetics and Gene Regulation Program and is designed to provide students with a comprehensive overview of genetic concepts and methodology. The course is organized into three parts: I Fundamental genetic concepts; II Genetics of model organisms (with a focus on worms, flies and mice); III Human genetics and disease. Each week there will be two lectures and one associated discussion/problem-solving session. Discussions emphasize practical aspects of generating and interpreting genetic data. Offered spring semester. [up]

CAMB 597: Developmental Neurobiology
2011 Syllabus
The goal of this course is to examine the principles underlying nervous system development. This is not a survey course in Developmental Neurobiology. Rather, the course will focus on selected topics, for which we will discuss the molecular and cellular strategies employed in different model organisms. Offered fall semester. [up]

CAMB 608: Seminar in Regulation of Eukaryotic Gene Expression
2012 Syllabus
An advanced seminar course emphasizing the molecular biology and molecular genetics of transcription in eukaryotes. Based on current literature, the presentations and discussions will familiarize the student with present day technology and developing principles. Prerequisites: CAMB 555 and permission of instructors. Offered fall semester. [up]

CAMB 630 : Topics in Human Genetics and Disease
Building on the foundations of the Human GenomeHapMap projects, our understanding of the basic concepts of Mendelian and non-Mendelian human genetic disease is proceeding at an unprecedented pace. This course will provide students with an overview of current problems and technical approaches in human genetics. Areas of focus will be analysis of disease mutations, chromosome rearrangements and disease, epigenetics, gene regulation and disease, human genomic variation and genomic applications to disease susceptibility. The format will be an advanced seminar course, with directed reading and student presentations. Prerequisites: This course is designed for students with previous background in graduate level genetics, i.e., CAMB graduate students having taken CAMB 550, or students in MD/PhD, veterinary, genetic counseling or nursing programs with equivalent courses. Offered fall semester even years. [up]

CAMB 632: Cell Control by Signal Transduction Pathways
2011 Syllabus
How do extracellular signals regulate cells and how do cells respond to these signals? Answers to these questions are crucial for understanding the molecular cascades that control cell function as well as the process of tumorigenesis. This course, "Cell control by signal transduction pathways", will examine how various signal transduction pathways influence cell functions such as gene transcription, protein translation, intracellular protein trafficking, and cell proliferation. The primary signal transduction pathways to be examined will be those mediated by Notch, Wnt, NF- B, Ras and Rho. After taking this course participants will have 1) become familiar with the principle of cellular signal transduction pathways, regulation of cellular behavior by the pathways, and typical approaches to investigation of signaling pathways. and 2) further developed and strengthened skills that are critical for success in scientific research. These include critical analysis of the scientific literature, generation of testable new hypotheses based on the literature, and design of well controlled experiments to test these hypotheses. Additionally, students will strengthen their skills in both oral and written scientific presentations. Offered spring semester. [up]

CAMB 691: Advanced Topics in Cell Biology and Physiology I
This course offers an advanced, in depth analysis of a broad array of topics in cell biology. Two courses, each covering a different selection of topics, will alternate each spring; the courses can be taken in either order, but require BIOM 600 or an equivalent background in basic cell biology. One course will cover channels and transporters, protein trafficking, and cytoskeleton and cell motility. This will alternate with a course considering signal transduction, mitosis, and cell cycle regulation. The style of the course will be a seminar, primarily focusing on representative papers form the current or older literature, which students will read, present and discuss. Offered alternately in the spring semester with CAMB 692. [up]

CAMB 692: Advanced Topics in Cell Biology and Physiology II
An in-depth consideration of the role of signal transduction in cell biology, focusing on signaling as it relates to cancer, immunology and metabolism. The course format will include student-led discussion sessions both providing an overview of a topic as well as focusing on important papers from the primary literature. Students will be evaluated on their presentations and participation, as well as problem sets.  Offered alternately in the spring semester with CAMB 691.[up]

CAMB 697: The Biology of Stem Cells
2012 Syllabus
The goal of this course is to introduce graduate students to the field of stem cell biology through lectures and reviews of important contributions from the literature.  Topics include stem cell niche biology, epigenetics and reprogramming, tissue specific stem cells such as hematopoietic and epithelial stem cells, tissue regeneration, tissue engineering, and ethical and legal issues of stem cell and regeneration biology.  The future potential and challenges in stem cell and regeneration biology will be discussed.  Important aspects of stem cell identification and characterization utilizing multiple model systems will also be a focus.  Offered Spring Semester.  Limited to 14 students. [up]

GCB 531: Introduction to Genome Science
Recent advances in molecular biology, computer science, and engineering have opened up new possibilities for studying the biology of organisms. Biologists now have access to the complete set of cellular instructions encoded in the DNA of specific organisms, including dozens of bacterial species, the yeast Saccharomyces cerevisiae, the nematode C. elegans, and the fruit fly Drosophila melanogaster. The goals of the course are to 1) introduce the basic principles involved in mapping and sequencing genomes, 2) familiarize the students with new instrumentation, informatics tools, and laboratory automation technologies related to genomics; 3) teach the students how to access the information and biological materials that are being developed in genomics, and 4) examine how these new tools and resources are being applied to specific research problems. [up]

[top of page]