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The Center for Cell Biology and Cancer Research - CCBCR

Curriculum


Ph.D. Program
Students matriculating into the Ph.D. program in the Center for Cell Biology and Cancer Research (CCBCR) are required to complete a total of 26 didactic credits.

All full-time students must be registered for a minimum of 10 credits per semester.

 

Year 1, Fall Semester

CBCR 504 (A,B,C)

Research Rotations (both semesters)

Credits: 1 each
To be arranged

Research laboratory rotations are to be completed during the first year of study. Ph.D. students will complete three rotations in different laboratories as a prerequisite to selecting a mentor. 

AMC 510

Biochemistry

Credits: 2
Dr. Carlos de Noronha

A major challenge to biomedical students is gaining  a better understanding of the structures, functions and interactions of molecular systems used in nature. The elucidation of protein and membrane structure, the role of enzymes in metabolic processes and cell signaling, and the modeling of life processes in the laboratory provide fundamental insights into normal physiological processes and into pathophysiological conditions. This course will provide an integrated exposure to major current concepts in biochemistry including protein structure, enzymology, membrane structure/function, and metabolism. This course covers three central themes common to all advanced courses within the various training programs: Protein Structure/Function, Biological Membranes, and Metabolism.  The first block of lectures includes the topics primarily on bioenergetics and metabolism. It will include a set of three conferences to integrate and review the material taught in each section.  AMC-510-Biochemistry, was carefully planned to integrate with "AMC-511-Molecular Cell Biology" and "AMC-515-Foundations of Biomedical Research." Together these three courses will provide MS and PhD students at AMC with the fundamentals that they will need to begin their research careers.

AMC 511

Molecular Cell Biology

Credits: 3
Dr. Susan LaFlamme

The overall goal of this course is to provide students with a basic understanding of molecular and cell biology and the relevance of these topics to normal and pathophysiology. This course is part of a new integrated core curriculum for all first year graduate students designated to give students the fundamentals needed for upper level graduate courses, to read primary literature, and to understand the health relevance of the basic sciences. The Learning Objectives of this course are to provide students with an understanding of the following:

  1. Mechanisms and regulation of the flow of genetic information from DNA to protein.
  2. Genetics and its role in disease.
  3. How cells interact with each other and their extracellular environment.
  4. Basic signaling cascades and the regulation of cell proliferation and survival.
  5. The structural components of cells and the regulation of these components, including the cytoskeleton, intracellular compartments and vesticular trafficking.

AMC 515

Foundations in Biomedical Research

Credits: 4
Dr. Richard Keller

Biomedical research builds on molecular, biochemical, cellular, and whole animal studies to understand the workings of cells, tissues, and organ systems. This course introduces students to experimental approaches using biomedical research. The goal of this course is to provide first-year graduate students with an understanding of basic experimental approaches used in biomedical research in order to jumpstart their ability to understand the primary literature and to plan and execute their own research. To this end, the course will cover the principles and theory behind currently used experimental approaches and their applications, practical details for those that are commonly used, as well as examples from the primary literature.

AMC 502

Research Topics in the Biomedical Sciences

Credits: 1
Dr. Mark Fleck

This literature-based colloquium will introduce students to the current research in the biomedical sciences with an emphasis on the primary literature. This course will involve student presentations and round table discussions in topical areas that are being covered in AMC 515. This course is required of all first year students. 

AMC 507

Introduction to Scientific Integrity

Credits: 0
Dr. John Kaplan

Students attend a total of three, two-hour class meetings and participate in workshops and discussions. Short readings will be assigned. Sessions will address current issues in scientific integrity, ethical principles and theory, introduction to ethics case analysis, an ethical skills workshop, and considerations in selecting a mentor. At the end of this course students will have a basic appreciation of ethical principles in relation to standards of professional conduct in science. Students will also develop their skills and confidence in their ability to analyze and discuss ethical and professional standards as they apply to specific aspects of scientific research. This course is required of all first year students.

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0


 

Year 1, Spring Semester

CBCR 604

Tissue Remodeling and Cell Motility

Credits: 3
Dr. Paula McKeown-Longo , Dr. C. Michael DiPersio , Dr. Livingston Van De Water

This course is designed to provide the student with a basic understanding of the molecular mechanisms which regulate cell adhesion, migration and extracellular matrix remodeling. Sessions will consist of a one hour lecture followed by a one hour discussion of a related article from the primary literature. Students will also be required to present and lead the discussion of selected papers which support and extend key concepts presented in the lecture topics.

CBCR 502A

Journal Club

Credits: 1
CBCR Faculty

Students and faculty present papers on current research in Cell Biology & Cancer Research for review and discussion.

CBCR 603

Signal Transduction

Credits: 3
Dr. Michelle Lennartz

The is an upper-level, literature-driven course that begins with 5 didactic sessions covering the major components of cell signaling cascades. The remainder of the course is divided into 13 x 2 session modules focusing on specific signaling paradigms including signaling through lipid rafts, integrins, growth factors, hormones and catenins, and for apoptosis, inflammation, and gene regulation, among others. The modules consist of 1 didactic lecture and 1 session discussing the current literature. The course assumes a basic knowledge of biochemistry, molecular and cell biology. Discussions are student-led. Students are required to write one in-depth review article on a signaling system of their choice. There will be three non-comprehensive exams. In addition to the exams (60%), grades will be based on leading and participating in the discussions (10%), and the review paper (30%).

Elective

(Selected from list below)

Credits: 2 or 3                                                                                          Electives are selected from a list of courses consistent with the CCBCR Program.

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0


 

Year 2, Fall Semester

CBCR 601

Molecular Mechanisms of Cell Growth and Differentiation    (alternate years)

Credits: 2
Dr. Paul Higgins, Dr. Susan LaFlamme

This is an advanced course designed to detail molecular mechanisms which underlie cellular responses to growth factors and adhesion (cell-ECM and cell-cell) receptors. Focus will be placed on signaling pathways and transcriptional control mechanisms which culminate in the activation (and repression) of genes that determine cellular phenotype. Course will be subdivided into individual modules that will consist of a didactic component followed by student-led evaluation of selected papers from the current literature. Modules are constructed so that each student will present, in a critical manner, a paper selected to compliment and amplify key concepts developed in the didactic portion of the course. Grades will be determined on the basis of the quality of class participation, literature presentations, and a detailed paper that highlights any modular topic covered in the course, the selection of which can be determined by the student.  [Taken once during 2nd or 3rd year]

CBCR 605

Cancer Cell Biology (alternate years)

Credits: 3
Dr. Kevin Pumiglia

This course will survey the cellular changes associated with the development of neoplastic disease. In particular, topical areas will focus on disruptions in the cellular regulation of proliferation, survival, tumor angiogenesis, development of the metastatic phenotype, and modern approaches to therapeutically modulate cancer progression. Sessions covering each of these areas will be taught through use of data derived from the primary literature to reinforce didactic principals relevant to each session. A series of independent readings relevant to the topical area will also be assigned. At the conclusion of each section each student will have the opportunity to formally present a selection of these readings, which reinforce and extend the key concepts of these topical areas. These discussion periods are open to discussion and clarification of the other independent readings as well.

AMC 612/613

Discussions in Scientific Integrity

Credits: 1                                                                                                            Dr. John Kaplan

This course will utilize a case study based discussion format to provide a vehicle for students to learn and reflect upon the responsible conduct of research.  Topics to be covered include an overview of ethical theory, conducting research, reporting research, peer review, handling research materials and information, mentoring and laboratory supervision, misconduct in research, conflict of interest, human subjects and clinical research, animals in research and genetic research.  This course will also familiarize students with both internal and national policies regulating research conduct.  (This program fulfills the NIH requisite for predoctoral students and postdoctoral fellows on National Research Service Award Training Grants.)   [Prerequisite:  AMC 507]

CBCR 501

Thesis Research

Credits: To be arranged
To be arranged

These credits are earned during thesis research in the laboratory. The number of credits is determined by the mentor.

CBCR 502B

Journal Club

Credits: 1
CBCR Faculty

Students and faculty present papers on current research in Cell Biology & Cancer Research for review and discussion.

Elective

(Selected from list below)

Credits: 2 or 3

Electives are selected from a list of courses consistent with the CCBCR Program.

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0


 

Year 2, Spring Semester

CBCR 501

Thesis Research

Credits: To be arranged
To be arranged

These credits are earned during thesis research in the laboratory. The number of credits is determined by the mentor.

CBCR502B

Journal Club

Credits: 1
CBCR Faculty

Students and faculty present papers on current research in Cell Biology & Cancer Research for review and discussion.

Elective

(Selected from list below)

Credits: 2 or 3

Electives are selected from a list of courses consistent with the CCBCR Program.

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0

Written Exam (comprehensive)

Must be completed by the end of Summer, Year 2

Credits: 0


 

Year 3 and Beyond, Fall Semester

CBCR 501

Thesis Research

Credits: To be arranged
To be arranged

These credits are earned during thesis research in the laboratory. The number of credits is determined by the mentor.

CBCR 502B

Journal Club

Credits: 1
CBCR Faculty

Students and faculty present papers on current research in Cell Biology & Cancer Research for review and discussion.

Elective

(As needed)

Credits: varies

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0


 

Year 3 and Beyond, Spring Semester

CBCR 501

Thesis Research

Credits: To be arranged
To be arranged

These credits are earned during thesis research in the laboratory. The number of credits is determined by the mentor.

CBCR 502B

Journal Club

Credits: 1
CBCR Faculty

Students and faculty present papers on current research in Cell Biology & Cancer Research for review and discussion.

Elective

(As needed)

Credits: varies

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0

Ph.D.
Qualifying Exam

Must be taken by the end of Summer, Year 3

Credits: 0


 

Electives

CBCR 602

Model Systems in Cell Biology (Spring)

Credits: 2
To be arranged

This course will survey the recent literature with yearly emphasis in a specific topic area and reflecting current trends in cell biology. Discussions will focus on certain model systems including: Tissue repair and remodeling; Tumor growth and metastasis; Inflammation and monocyte response; Cytoskeleton and cell function; Nuclear structure and gene expression; Cell growth and differentiation; Growth factor signaling. Basic knowledge of cell biology and biochemistry is required. CMB courses in Signal Transduction and Tissue Remodeling and Cell Motility are strongly recommended. The course will center around faculty-organized discussions and student presentations. Each student will be required to present papers from the current literature (to be selected by the Faculty Course Director) and lead a group discussion. Grades will reflect student performance as both discussion leader and participant. The subject covered in CMB602 will change during each year offered and will likely reflect the research interests of the Course Director. At the time of registration, students will be informed of the subject matter to be addressed and the name of the responsible faculty member. Exams will not be part of the grading system, however a paper may be required by particular faculty, and, if so, students will be made aware of this prior to registration. Evaluations of any such required paper will be a consideration in the final grade.

CBCR606

Transcriptional Control in Cancer, Infflammation and Cardiovascular Diseases

Credits:  3                                                                                                           Dr. Dorina Avram

This is an upper level literature-driven course on transcriptional regulation processes, with main emphasis on transcription factors with role in cancer, immune diseases and cardiovascular diseases.  This course requires a basic knowledge of biochemistry, molecular and cell biology.

BIO 539

Comparative Functional Genomics (Fall) *

Credits: 3
To be arranged

This graduate level course is required for students participating in the Functional Genomics training program. This course consists of several modules that represent an integrated, comprehensive review of concepts, goals and methods of genome analysis at several levels, encompassing both classical and molecular approaches. (1) Review of classical genetics: the basics of Mendelian inheritance, unusual genetic and epigenetic phenomena; (2) Review of molecular genetics: recombinant DNA technology; principles and mechanisms of gene expression: transcription and its regulation, posttranscriptional events, translational and posttranslational control; (3) Model organisms and model genomes (bacteria, yeast, Drosophila, C. elegans, zebrafish, Arabidopsis, mouse, human), life cycles, genome structure and peculiarities; (4) Comparative analyses: gene and protein families, phylogenetic reconstructions, computational support of the genome-wide scale sequence analysis; (5) Large scale genome analysis and genome sequencing: physical and genetic mapping, expressed sequence tags, large scale sequencing strategies; (6) Map based cloning and application to human genetic disease; and (7) Transgenic technologies: principles and applications.

BIO 540

Principles of Bioinformatics (Spring) *

Credits: 3
Dr. George Berg

This course will provide hands-on training in methods of computer-assisted bioinformatics, with specific application to biological research. Topics include: data mining, sequence retrieval, DNA and protein sequence alignment, molecular evolution and phylogenetic analysis, population genetics and analysis of genetic variation within species, comparative genomics of model organisms, and computer-based visualization and analysis of macromolecular structures.

BMS 601A

Introduction to Biomedical Sciences (Fall)

Credits: 3

BMS 601B

Introduction to Biomedical Sciences (Spring)

Credits: 3

BMS 665T

Mammalian Genetics (Fall)

Credits: 1

CS 601

Molecular Control of Vascular Cell Cytoskeletal Proteins (Fall)

Credits: 2
Dr. Harold Singer , Dr. Peter Vincent

This course addresses the actin cytoskeleton and actin-myosin interactions during smooth muscle contraction/relaxation and in endothelial cells during shape changes leading to altered vascular permeability. The signal transduction pathways responsible for regulating cytoskeletal interactions in these cells are compared. The course first focuses on the contractile and structural cytoskeleton in smooth muscle. This is followed by discussions of the regulation of actin-myosin interactions by kinases, phosphatases, and thin filament regulatory proteins during smooth muscle contraction. The focus of the course then shifts to non-muscle cells with emphasis on the regulation of endothelial cell shape. Topics of discussion with respect to non-muscle cells include: comparison of the cortical actin cytoskeleton versus stress fibers, the role of small GTPases, and regulation of actin assembly by thin filament binding proteins. Control of endothelial cell shape is discussed in the context of the association of cell-cell and cell-matrix junctions with the actin cytoskeleton. Classes combine didactic presentations and student-lead discussions of current publications. Grades for this course are based on the quality of the student-led discussions and on a paper to be handed in two weeks after the last lecture.

CS 608

Cardiovascular Physiology (Spring)

Credits: 3
Dr. Daniel Loegering

This course provides a solid foundation in the basic physiology of the cardiovascular system. The fundamentals of cardiac mechanics, hemodynamics, electrocardiography, and cardiovascular reflexes are integrated into understanding the control of cardiac output and tissue blood flow. The importance of these parameters is illustrated by discussion of exercise and the pathophysiological changes associated with valve defects and heart failure. Classes consist of lectures, laboratories, clinical presentations, and problem-solving conferences. Grades for this course are based upon a final examination.

CS 609

Respiratory and Renal Physiology (Spring)

Credits: 4
Dr. Donald Bell

This course provides a solid foundation in basic physiology of the respiratory and renal systems. Basic concepts in gas exchange, pulmonary mechanics, ion transport processes, and nephron function are integrated into understanding the control of breathing and acid-base disorders. Basic concepts are extended into understanding the pathophysiology of abnormalities in ventilation perfusion and tissue oxygen delivery. The multiple transport processes within the kidney and their control are used to gain an understanding of a number of fluid and electrolyte disorders. There is a special emphasis on the quantitative analysis of clinical problems. Course format: Classes consist of lectures, laboratories, clinical presentations, and problem solving conferences. Grades for this course are based upon a final examination.

IMD 608

Immunology (Spring)

Credits: 3
Dr. James Drake

The course provides an introductory overview of immunology. Student evaluation will be based on exams and student presentations. Required of ALL IMD theme students. Taught every year.

IMD 609

Microbial Disease (Spring)

Credits: 3
Dr. Lisa Petti , Dr. Jing-Ren Zhang

The course provides an introductory overview of immunology. Student evaluation will be based on exams. Required of all IMD theme students during their first year. Taught every year.

NEU 607

Fundamentals of Pharmacology (Spring)

Credits: 2
Dr. Lindsay Hough

An introduction will be provided to the principles by which drugs and other bioactive substances are absorbed, distributed and metabolized and how they act on biological systems. Topics include drug-receptor interactions, drug-effector interactions and pharmacokinetics.

NEU 608

Biostatistics (Spring)

Credits: 3
Dr. Jeffrey Carlson

This is a course in basic biostatistics, which includes lectures on the mathematics necessary to understand statistical analysis. Integral to the course are instructions for proper experimental design and the appropriate use of statistical tests.

NEU 612

Developmental Neuroscience (Spring)

Credits: 2
Dr. Sally Temple , Dr. Tara Fletcher , Dr. Pamela Swiatek

This course focuses on cellular and molecular mechanisms underlying the development of the central and peripheral nervous system. Lecture topics include neural induction, histogenesis, neuron migration, axon guidance, synaptogenesis and apoptosis. Also included are lectures on the modification of synaptic connections in development and regeneration, coordination of neural development with organogenesis, and the use of genetically modified animal models to probe gene function. In addition, students read and discuss article representative of current research on each lecture topic.

NEU 613

Receptor Pharmacology (Fall)

Credits: 2
Dr. Milt Teitler

The course will cover the molecular biology and pharmacology of receptors. Introductory material will include an in-depth approach to the molecular dynamics of the ligand-receptor interaction. This will be followed by lectures on the three major families of receptors: the G-protein-coupled receptors (GPCR), the tyrosine kinase receptors (TK), and the ligand-gated ion channel receptors. Graduate level biochemistry is a prerequisite.

CCBCR Ph.D. students are expected to complete a minimum of 5 elective credits to meet the programmatic didactic requirement. Electives consistent with the CCBCR Program are listed above. Courses offered as part of the proposed Interdisciplinary Training Program with SUNY Albany are indicated with an asterisk *.

 

M.S. Program
Students matriculating into the M.S. program in the Center for Cell Biology and Cancer Research (CCBCR) are required to complete a total of 16 credits per semester.

All full time students must be registered for a minimum of 10 credits per semester.

 

Year 1, Fall Semester

CBCR 504 (A,B,C)

Research Rotations (both semesters)

Credits: 1 each
To be arranged

Research laboratory rotations are to be completed during the first year of study. M.S. students will complete two rotations in different laboratories as a prerequisite to selecting a mentor. 

AMC 510

Biochemistry

Credits: 2
Dr. Carlos de Noronha

A major challenge to biomedical students is gaining  a better understanding of the structures, functions and interactions of molecular systems used in nature. The elucidation of protein and membrane structure, the role of enzymes in metabolic processes and cell signaling, and the modeling of life processes in the laboratory provide fundamental insights into normal physiological processes and into pathophysiological conditions. This course will provide an integrated exposure to major current concepts in biochemistry including protein structure, enzymology, membrane structure/function, and metabolism. This course covers three central themes common to all advanced courses within the various training programs: Protein Structure/Function, Biological Membranes, and Metabolism.  The first block of lectures includes the topics primarily on bioenergetics and metabolism. It will include a set of three conferences to integrate and review the material taught in each section.  AMC-510-Biochemistry, was carefully planned to integrate with "AMC-511-Molecular Cell Biology" and "AMC-515-Foundations of Biomedical Research." Together these three courses will provide MS and PhD students at AMC with the fundamentals that they will need to begin their research careers.

AMC 511

Molecular Cell BIology

Credits: 3
Dr. Susan LaFlamme

The overall goal of this course is to provide students with a basic understanding of molecular and cell biology and the relevance of these topics to normal and pathophysiology. This course is part of a new integrated core curriculum for all first year graduate students designated to give students the fundamentals needed for upper level graduate courses, to read primary literature, and to understand the health relevance of the basic sciences. The Learning Objectives of this course is to provide students with an understanding of the following:

  1. Mechanisms and regulation of the flow of genetic information    from DNA to protein.
  2. Genetics and its role in disease.
  3. Basic signaling cascades and the regulation of cell proliferation and survival.
  4. The structural components of cells and the regulation of these   components, including the cytoskeleton, intracellular compartments and vesticular trafficking.

AMC 515

Foundations in Biomedical Research

Credits: 4
Dr. Richard Keller 

Biomedical research builds on molecular, biochemical, cellular, and whole animal studies to understand the workings of cells, tissues, and organ systems. This course introduces students to experimental approaches using biomedical research. The goal of this course is to provide first-year graduate students with an understanding of basic experimental approaches used in biomedical research in order to jumpstart their ability to understand the primary literature and to plan and execute their own research. To this end, the course will cover the principles and theory behind currently used experimental approaches and their applications, practical details for those that are commonly used, as well as examples from the primary literature.

AMC 502

Research Topics in the Biomedical Sciences

Credits: 1
Dr. Mark Fleck

This literature based colloquium will introduce students to the current research in the biomedical sciences with an emphasis on the primary literature.  This course will involve student presentations and round table discussions in topical areas that are being covered in AMC 515. This course is required of all first year students.

AMC 507

Introduction to Scientific Integrity

Credits: 0
Dr. John Kaplan

Students attend a total of three, two-hour class meetings and participate in workshops and discussions. Short readings will be assigned. Sessions will address current issues in scientific integrity, ethical principles and theory, introduction to ethics case analysis, an ethical skills workshop, and considerations in selecting a mentor. At the end of this course students will have a basic appreciation of ethical principles in relation to standards of professional conduct in science. Students will also develop their skills and confidence in their ability to analyze and discuss ethical and professional standards as they apply to specific aspects of scientific research. This course is required of all first year students.

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0


 

Year 1, Spring Semester

CBCR 604

Tissue Remodeling and Cell Motility

Credits: 3
Dr. Paula McKeown-Longo , Dr. C. Michael DiPersio , Dr. Livingston Van De Water

This course is designed to provide the student with a basic understanding of the molecular mechanisms which regulate cell adhesion, migration and extracellular matrix remodeling. Sessions will consist of a one hour lecture followed by a one hour discussion of a related article from the primary literature. Students will also be required to present and lead the discussion of selected papers which support and extend key concepts presented in the lecture topics.

CBCR 502A

Journal Club

Credits: 1
CBCR Faculty

Students and faculty present papers on current research in Cell Biology & Cancer Research for review and discussion.

CBCR 603

Signal Transduction

Credits: 3
Dr. Michelle Lennartz

The is an upper-level, literature-driven course that begins with 5 didactic sessions covering the major components of cell signaling cascades. The remainder of the course is divided into 13 x 2 session modules focusing on specific signaling paradigms including signaling through lipid rafts, integrins, growth factors, hormones and catenins, and for apoptosis, inflammation, and gene regulation, among others. The modules consist of 1 didactic lecture and 1 session discussing the current literature. The course assumes a basic knowledge of biochemistry, molecular and cell biology. Discussions are student-led. Students are required to write one in-depth review article on a signaling system of their choice. There will be three non-comprehensive exams. In addition to the exams (60%), grades will be based on leading and participating in the discussions (10%), and the review paper (30%).

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0


 

Years 2 and 3, Fall Semester

CBCR 501

Thesis Research

Credits: To be arranged
To be arranged

These credits are earned during thesis research in the laboratory. The number of credits is determined by the mentor.

CBCR502B

Journal Club

Credits: 1
CBCR Faculty

Students and faculty present papers on current research in Cell Biology & Cancer Research for review and discussion.

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0


 

Years 2 and 3, Spring Semester

CBCR 501

Thesis Research

Credits: To be arranged
To be arranged

These credits are earned during thesis research in the laboratory. The number of credits is determined by the mentor.

CBCR502B

Journal Club

Credits: 1
CBCR Faculty

Students and faculty present papers on current research in Cell Biology & Cancer Research for review and discussion.

CBCR Research Colloquium

Student/Postdoctoral Fellow Presentations

Credits: 0

Y