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Course Descriptions

Courses are listed in numerical order
BIOL. 70005 – Genetics: Lecture 
Note: this course is given at several different campuses; the content varies slightly, but all campus versions of the course are appropriate for preparation for the First Exam in the MCD subprogram.
Prokaryotic and eukaryotic genetics; organization of DNA, replication repair, mutagenesis, recombination, control of gene expression, genetic engineering, and molecular techniques
4 credits

BIOL. 70007 – Conservation Biology
Conservation biology is the applied, integrative, and multidisciplinary science of maintaining the earth's biological diversity. This course will focus on the science and practice of conservation biology at the graduate level for students with a strong undergraduate background in environmental biology. We will cover the value of, threats to, and strategies for maintaining the earth’s biodiversity, focusing on biological aspects while also considering issues in social science.
3 credits

BIOL. 70503 – Evolution
Study of mechanisms and processes of evolution. Theory, laboratory experimental results and the phenomena found in natural populations are described and discussed in relation to population genetics, speciation and mega evolution.

3 credits

BIOL. 70605 – Taxonomy Vascular Plants: Lecture
This course reviews the basic morphological structures of vascular plants and provides students with a basic understanding of the phylogenetic relationships among vascular plants and within angiosperms.  Students will become conversant in the language of systematics and taxonomy. (must be taken concurrently with Biol 70606 = lab)

3 credits

BIOL. 70606 – Taxonomy Vascular Plants: Lab
Laboratory associated with the lectures of Biol 70605 (must be taken concurrently with Biol. 70605 = lecture)

2 credits

BIOL. 70610 – Biological Systematics

4 credits

BIOL. 70901 – Population Genetics
This course reviews the theoretical foundations of population genetics, introduces the statistical tools of population genetic analyses (e.g. Hardy-Weinberg, F-statistics, and evolutionary clustering), and provides a full description of the techniques in molecular biology currently being applied to population genetics (e.g. PCR, microsatellites, and next-generation sequencing).  The course consists of both lectures and in-depth student readings/interpretations of current literature in the field of population genetics.

3 credits

BIOL. 71013 – Molecular Biology: Lecture
Note: This course (or 71015, see below) is given at several different campuses; all campus versions of either 71013 or 71015 are appropriate for preparation for the First Exam in the MCD subprogram
Structure and function of bio-molecules; enzyme mechanisms; replication, transcription, translation; regulation of macromolecular biosynthesis; energy transformations

5 credits

BIOL. 71015 – Molecular Biology: Lecture
Similar to Biol 71013, see note above

4 credits

BIOL. 71101 – Lab Rotation
Primary goal is to introduce entering students to the science and the scientific methods in individual faculty labs. Students are expected to learn about one or more research projects taking place in the laboratory (e.g. read relevant publications), participate in some of the work being done (undertake a short independent project or work with an experienced lab member), and write a summary report of their experience in the lab (background/significance, experimental approach, results, interpretation and discussion).

2 to 6 credits

BIOL. 71401 – Cell Biology: Lecture
Note: this course is given at several different campuses; the content varies slightly, but all campus versions of the course are appropriate for preparation for the First Exam in the MCD subprogram.
An in-depth examination of cellular and sub-cellular organization and activity. Topics include membrane structure, biogenesis, transport, excitability, cell-surface interactions, cell in culture, the cell cycle; organelle structure, function and assembly, cell motility, modern experimental tools and techniques.

4 credits

BIOL. 71404 – Cell Biology: Laboratory
Training in the investigative procedures of cellular biology in the context of selected experiments. The students will learn how to prepare cells to image various cellular structures using a range of illumination techniques: light, fluorescence, laser scanning and spinning disc confocal mocroscopy.  Lab projects involve immunofluorescence: fixation methods and immunocytochemestry.  Illuminatino methods including multi-channel 3D rendering, image processing and visualizatin software.

3 credits

BIOL. 71710 – Virology
Viruses use common strategies to replicate and propagate within their hosts. This course is designed to provide graduate and advanced undergraduate students with a foundation from which to examine and analyze the molecular biology of viruses, including their classification, structure, pathogenesis, interactions with their hosts, and mechanisms of propagation.

3 credits

BIOL. 71800 – Immunology
HC: Study of the immune system from a molecular perspective.  Subjects include molecular genetics of antibody and T cell receptor diversity, hematopoiesis and lymphocyte development, humoral and cellular immunity, histocompatibility.  Course will consist of lectures, together with readings and discussion of the primary literature underlying current concepts. Learning goals: The two primary goals of this course are for students to demonstrate a) an understanding of the vertebrate immune system and how it functions and b) an understanding of how this information has been obtained through experimental research.

4 credits

BIOL. 72301 – Neurosciences I: Lecture
Neuronal cell biology (structure and trophic functions), cellular neurophysiology (membrane physiology, action potentials), synapses (neurotransmitters and physiology), neuroendocrine mechanisms, local neuronal circuits (integrative properties and ontogeny, function in simple invertebrate nervous systems), and anatomical organization of the vertebrate nervous system

4 credits (Cross-listed with PSYC 71000)

BIOL. 72302 – Neurosciences II: Lecture
(Sequel to Neurosciences I) Sensory and motor systems; neurochemical pathways; receptor physiology and information processing in somatosensory. visual and auditory systems; vertebrate motor systems with respect to spinal, supraspinal and cortical mechanisms; psychopharmacology

4 credits (Cross listed with PSYC 71100)

BIOL. 72403 – Animal Behavior I: Lecture
Lectures and discussions of selected major areas in modern animal behavior research.  Included among the topics are conceptual issues in methodology, behavior and genetics, evolution and development of behavior. A modern eclectic approach is emphasized. Students read and lead discussion of papers from the original literature.

3 credits (Cross listed with PSYC 71600)

BIOL 72406 – Behavior and Evolution
In this advanced graduate seminar course, students will study current research addressing the mechanisms by which behavior evolves.  Behavior by its very definition is highly condition- dependent, meaning that its expression relies heavily on cues from an organism’s environment, so there can always be multiple behavioral phenotypes for a given genotype at a given time.
Recently, careful field research, phylogenetic analyses, and investigations of behavioral control at physiological and molecular levels have resulted in an exponential rise in our understanding of the mechanisms of behavioral evolution. The primary goal of this course is to integrate the various conclusions from this new research with insights from thinkers throughout the history of evolutionary biology, in an effort to address fundamental questions about behavioral evolution.

3 credits

BIOL. 72407 – Animal Behavior II
Mechanisms of animal behavior, behavioral physiology, hormonal aspects of behavior, orientation, communication, space usage, the functions of territorial behavior, habitant selection, feeding strategies, predator-prey relationships, reproductive strategies, moral and ethical concerns in animal behavior research.

3 credits (Cross listed with PSYC 71800)

BIOL. 72605 – Human Neuroanatomy Lab

2 credits
BIOL. 73001 – Plant Physiology: Lecture
Physiological phenomena of plants, with an emphasis on growth and development

3 credits

BIOL. 73002 – Plant Physiology: Laboratory
Physiological phenomena of plants, with emphasis on growth and development

2 credits

BIOL. 74501 – Phytochemistry: Lecture
Biochemical activities of plants, including photosynthesis, respiratory pathways, sulfate and nitrate reduction, and cell-wall metabolism; biosynthesis by plants of drugs of pharmacological significance such as alkaloids and vitamins

2 credits

BIOL. 75003 – Developmental Biology: Lecture
Note: This course is given at several different campuses; the content and credits earned vary, but all campus versions of the course are appropriate for preparation for the First Exam in the MCD subprogram.
B:   4 credits. An analysis of animal development based on normal embryogenesis, experimental embryology and molecular biology of selected invertebrate embryos. The principle area of consideration is the determinative events of embryogeny as explicable by defect, isolation and transplantation experiments and the role of gene transcription in embryonic determination. The latter will be approached from our knowledge of DNA-DNA and DNA-RNA interactions and the synthesis of specific proteins.
C:  3 credits. Interaction of egg and sperm; theories of induction; model of tissue interaction: Wolffian lens regeneration, mechanisms involved in induction of epithelial structures; Genes in development. Genetic coding and the origin of cell, tissue and organ specificity.
H,Q, GC:   4 credits.  Analysis of problems of embryonic development, including gametogenesis, fertilization, early development, induction, selected examples of later cell differentiation and organization, and neoplasia.

BIOL. 75401 – Comparative Morphology Vascular Plants: Lecture

2 credits (Course meets at New York Botanical Garden)

BIOL. 76003 – Community Ecology: Lecture
This course concentrates on the major generalizations in community ecology for energy flow, material cycling, species diversities, ecosystem development, and managed ecosystems.

3 credits


BIOL. 76005 – Population Ecology: Lecture
An analysis of the structure and dynamics of plant and animal populations. Topics include density, growth, regulation, fluctuation of numbers, niche, dispersal systems, dispersion patterns, demographic techniques, and interactions between populations.

3 credits (Course meets at American Museum of Natural History)

BIOL. 76501 – Paleobotany: Lecture

2 credits (Course meets at New York Botanical Gardens)

BIOL. 78001 – Mathematical Biology: Lecture
This course will serve to introduce the principles of experimental design and statistical analyses as applied to biological systems. The content will range from descriptive to inferential statistics and hypothesis testing. Considerable emphasis will be placed on the analysis of variance and its application to various experimental designs. Some attention will be given to non-parametric methods and randomization procedures.

3 credits

BIOL. 78002 – Mathematical Biology: Lab
The laboratory work consists of individual student projects and of introduction to computer programming.

3 credits

BIOL. 78201 – Biostatistics I
The lecture portion of the course will introduce the principles of experimental design and statistical analyses as applied to biological systems, in both parametric and non-parametric contexts. The content will range from descriptive to inferential statistics and hypothesis testing. Additional topics covered include exploratory data analysis, ANOVA and post-hoc tests, contingency analysis, analysis of grouped data, correlation and regression. The lab part of the course will allow students to analyze data and apply the methods learned in lecture using freely-available R software.  This course will thus also introduce students to using R, including reading tables (into R) and writing tables (to be read by other programs, e.g., Excel), conducting statistical analyses and making publication-ready graphics.
BIOL. 79001 – Seminar in Evolution: Frontiers in Phylogeography
This seminar class will concentrate on phylogeography papers that: 1) go beyond using data from a handful of loci but instead make use of data on the scale of genomic sampling or 2) make use of a fully integrative approach thereby using of data types in conjunction with genetic data. Emphasis will be on studies that expand the role of phylogeography in evolutionary and ecological research by making use of recent molecular and methodological advances.

3 credits


BIOL. 79002 – Seminar in Genetics

3 credits

BIOL. 79004 – Seminar in Molecular Genetics

3 credits

BIOL. 79011 – Seminar in Systematics

3 credits

BIOL. 79100 – Colloquium
Weekly research talks presented by speakers from around the world (independent series take place at each college)

1 credit

BIOL. 79301 -  Journal Club
CSI: EEB Journal Club
CSI: Neuroscience Journal Club
CSI: Core Principles Neurobiology – a prep course for the First Exam in NS.  Critical analysis of concepts learned from Kandel’s “Principles of Neuroscience”; capacitance, membrane resistance versus conductance; leakage channels; action potentials; Neurotransmitter release, pre- and postsynaptic processes; neuronal pathways and systems biology; Regulation of gene expression; Critical analysis of research articles and reviews.
GC: Research: Ecology, Evolutionary Biology, Behavior. For First-year EEB students only; research presentations by CUNY faculty
H:  Seminar Current Biological Research. Weekly seminars from outside speakers in multiple areas of biology; paper required
L:  Seminar in R
Q: MCD Journal Club; cross-listed with BICM 81000

1 credit

Note: 79302-79304 are special topics courses.  They are not offered every year, and they are offered at specific campuses (or at the Graduate Center), and often only by specific faculty members, as indicated below each description.
BIOL. 79302 – Seminar in Ecological and Population Genomics
This seminar is aimed at students that do not necessarily have a strong background in molecular biology, but are conducting ecological or evolutionary research that may benefit from genomic approaches.  The course will begin with discussions of the basic molecular biology and techniques needed to understand the primary literature.  In the second part of the course, students will lead discussions of recent papers on selected topics from the growing ecological & population genomics literature.

Bar:  2 credits

BIOL. 79302 – MCD Seminar (Molec/Cell/Develop)
For First-year MCD students; seminars by CUNY faculty; professional development activities; student presentations; paper required

GC:   2 credits (MCD subprogram chair)

BIOL. 79302 – Seminar in Virology

B:    2 credits (Studamire)

BIOL. 79302 – Tumor Suppressor Pathways

B:    2 credits (Saxena)

BIOL. 79302 – Gene Regulation Sys/Development/Evolution
The course emphasizes the understanding of the regulatory entities that control gene expression and their evolutionary dynamics.

GC: 2 credits (Arenas-Mena)

BIOL. 79302 – Grantsmanship/Sci Writing
This course will take on the format of an interactive workshop to introduce students to the art of proposal development, grant writing, and grant proposal review. The course will provide useful techniques for developing hypothesis-driven grant proposals for submission to funding sources or to develop a hypothesis-driven second level exam proposal.

L: 2 credits (Wurtzel)
BIOL 79303 – Advanced Statistical Ecology
This course presents statistical methods not covered in a basic stats course, but very useful to ecologists and evolutionary biologists.  While this course cannot comprehensively cover all methods that all students might want to learn, it is meant to treat the most commonly encountered methods in the (EEB) literature, and so should be useful to a wide spectrum of EEB students. For every topic, motivating examples from the literature will be presented.  Analyses will be conducted with R, and each class meeting will include a lecture portion and a computer lab portion.

GC: 3 credits (Manne)

BIOL 79303 – Applied Microbiology

B:    3 credits (Muth)

BIOL 79303 – Behavioral Neuroendocrinology

GC: 3 credits (Forlano/Walder) (cross-listed with PSYC 80103)

BIOL 79303 – BioMed Informatics/Translational Genomics

H:  3 credits (Dottin)

BIOL 79303 – Cancer Biology
This course will focus on the mechanisms involved in forming a tumor cell, the progression to metastasis, and the roles tumor-suppressor genes play in killing cancer cells.  Course objectives are for students to a) achieve an understanding of cancer formation and progression b) achieve an understanding of tumor suppressor genes and their operational pathways c) read some of the current research literature on cancer and thereby understand the relationship between research and progress in medicine.

BC: 3 credits (Saxena)

BIOL 79303 – Cell Biology of Myelination

H:  3 credits (Melendez-Vasquez)

BIOL 79303 – Cell Bio of the Nervous System

H:  3 credits (Goldfarb)

BIOL 79303 – Cognitive Neuroscience
This course will provide students with an overview of behavioral and cognitive neuroscience. Each week, the students will read recent reviews and primary research articles.

GC: 3 credits (Ro) (Cross-listed with PSYC 80103)

BIOL 79303 – Collective Behavior in Biology
Quantitative approaches to understanding collective behavior (e.g. bacterial colonies, bird flocks, insect swarms, fish schools, etc.)  The goal is to provide Biology students with quantitative tools that may be used (and understood) in studying group behaviors.  Students will receive instruction in all necessary quantitative tools during the course.  A basic knowledge of math is assumed (e.g. derivatives, integrals, and, to some very little extent, differential equations).

GC: 3 credits (GC visiting Professor Cavagna)

BIOL 79303 – Computational Molecular Bio
This course will introduce both bioinformatics theories and practices. Topics include database searching, sequence alignment, molecular phylogenetics, structure predication, and microarray analysis. The course is held in a UNIX-based instructional lab specifically configured for bioinformatics applications. Each session consists of a first-half instruction on bioinformatics theories and a second-half session of hands-on exercises.

H: 3 credits (Qiu)

BIOL 79303 – Game Theory & Decision Making in Biological systems
A course focusing on the development of models to understand collective decision making (e.g. individual behavior to global consensus; independent choices vs interacting individuals).  Biological systems relevant to these issues include quorum sensing, nest site selection in social insects, flocks, swarming, etc.  Students will receive instruction in all necessary quantitative tools during the course.  A basic knowledge of math is assumed (e.g. derivatives, integrals, and, to some very little extent, differential equations).

GC: 3 credits (GC visiting Professor Giardina)

BIOL 79303 – Diseases of the Nervous System
This course will cover the symptoms, etiology and possible remedies of diseases that affect the brain and the nervous system.  Research articles will be assigned for study and analysis and at several class sessions, expert researchers in the field will present their work.

GC:   3 credits (Banerjee; can be attended by videoconference)

BIOL 79303 – Drugs Changing the Brain
Course will center on current research and review articles that concern the neurochemistry of drugs of abuse.

H:    3 credits (Angulo)

BIOL 79303 – Dynamic Org of Nuclear Transport
This course centers on current research and review articles in cell biology that focus on mechanisms of nuclear transport.

H:    3 credits (Zhong)

BIOL 79303 – Fundamentals Developmental Neurobiology
This course will cover the concepts that guide current understanding of how the nervous system is formed from the time of early embryogenesis and how it is continually altered later in adult life.  The molecular processes underlying neural tissue specification, brain region-specific maturation, proper circuit formation and synapse assembly during the development of eukaryotic organisms will be highlighted.  Examples from both invertebrates and vertebrates will be detailed.

H:  3 credits (Dictenberg)

BIOL 79303 – Gene Regulation
This course covers current literature on the mechanisms of gene regulation.  An emphasis in this course is the development of student skills in both oral and written communication of research.

H:    3 credits  (Ortiz)

BIOL 79303 – Hot Topics in Dev Neurobiology
The goals of this weekly course are the critical reading of current research articles in neurobiology; the presentation of a polished, professional summary of a recent article; and, the development of listening and critical skills so that students become active participants in scientific seminars. The intent here is that the student will learn to critically evaluate new information presented in a seminar format and participate in a scientific dialogue.

H:  3 credits (Filbin)

BIOL 79303 – Mechanisms of Aging
Course will cover the current theories of aging and the biological complexity associated with this process.  Assigned research papers will present the newest and most exciting ideas in aging research, with an emphasis on molecular approaches. Lecture topics encompass model systems (yeast, Drosophila and C. elegans); mitochondrial defects, oxidative stress, and the mechanistic, molecular underpinnings of recent research on aging.

Q: 3 credits (Melendez)

BIOL 79303 – Microbial Pathogenesis
The student learning goals for this course are: 1. To develop skills in searching for and critically analyzing primary literature 2. Understand basic methods of experimental design and hypothesis testing 3. Understand the role of experimentation in biology 4. Gain knowledge of the molecular arms race between microbes and host

H: 3 credits (Raper)

BIOL 79303 – MicroRNA and Development

H:  3 credits (Bratu)

BIOL 79303 – Model Systems

B:    2 credits  (Forest)

BIOL 79303 – Modern Concepts in Genomics

B: 3 credits (Polle)

BIOL 79303 – Molecular Evolution
Molecular evolution is the study of the diversification of DNA and protein sequences through time. Theories and techniques of molecular evolution are widely used in species classification, biodiversity studies, comparative genomics, and molecular epidemiology. Contents of the course include:
•           Population genetics, which provides a framework of understanding mechanisms of sequence evolution through mutation, gene duplication, genetic drift, and natural selection;
•           Molecular systematics, which introduces statistical models of sequence evolution and methods of phylogenetic inference;
•           Bioinformatics, which  provides hands-on training on data acquisition and the use of software tools for phylogenetic analyses;
•           Applications of molecular evolution in biological classification, epidemiology, and comparative genomics.

H: 3 credits (Qiu)

BIOL 79303 – Neuropharmacology

C:  3 credits (Wang)

BIOL 79303 – Topics in Biotechnology
Invited speakers are scheduled to give presentations on their areas of expertise for some of the course sessions. These speakers comprise experts from biotechnology and the private sector. Each presentation will be followed by a class discussion with the speaker. In other class sessions, individual students will give a 45 minute presentation on a published research paper covering a current disease mechanism and its potential as a strategy for therapeutics intervention.

H:  3 credits  (Rockwell)

BIOL 79303 – Theoretical/Computational Neuroscience
This course will develop theoretical and computational approaches to structural and functional organization in the brain. The course will cover: (i) the basic biophysics of neural responses, (ii) neural coding and decoding with an emphasis on sensory systems, (iii) approaches to the study of networks of neurons, (iv) models of adaptation, learning and memory, (v) models of decision making, and (vi) ideas that address why the brain is organized the way that it is. The course is appropriate for beginning and more advanced graduate students.
Mathematics: Knowledge of multi-variable calculus, some linear algebra and some differential equations is necessary for this course. The methods will be developed in class for the benefit of students without much exposure to this material. Students without some prior background must have the permission of the instructor to take this class.  Computation: Prior knowledge of MATLAB will be useful, but students will go through programming exercises to develop their skills.      Neuroscience: Basic knowledge of the architecture of the brain, and of the mechanisms of neural signaling will be very useful. However, for the benefit of students from physics and bioengineering without background in neuroscience, the necessary material will also be developed in class and in tutorial sessions.

GC: 3 credits (Balasubramanian)

BIOL 79303 – Ubiquitin/Proteasome Pathway
Students will learn up to date aspects of the ubiquitin/proteasome pathway (UPP). In the first five weeks the instructor will lecture on different aspects of the UPP. In the following weeks, two students/week will make a 45-min power point presentation (each) based on current research articles relevant to the role of the UPP in neurodegeneration or cancer.

H:  3 credits (Figuereido-Pereira)

BIOL. 79304 – Laboratory in Cell Structure
Students will learn how to prepare cells to image various cellular structures using a range of illumination techniques: light, fluorescence, laser scanning and spinning disc confocal microscopy. Lab projects involve immunofluorescence: fixation methods and immunocytochemistry. Illumination methods including multi-channel 3D rendering, image processing and visualization software.  Each student is given the choice to design a project that will reveal the localization and expression patterns of specific target molecules as well as fluorescent staining of subcellular organelles: ER, Golgi complex, mitochondria.

H: 4 credits (Bratu)

BIOL. 79304 – Physiology of Nervous System

H:  4 credits  (Goldfarb)

BIOL. 79304 – Plant Physiology

Q: 4 credits (Short)

BIOL. 89800 – Advanced Study
This course is taken under individual faculty supervision and consists of field work, laboratory research and/or in-depth study of the research literature. Students present the results of their study/work in either oral (e.g. laboratory meeting presentations) or written form.

1-10 credits (can be taken more than once, but not concurrently with Biol 89900)

BIOL. 89900 – Independent Doctoral Research
Student works on an advisory committee-approved doctoral thesis project under supervision of a faculty thesis mentor.

1-10 credits (10 maximum credits over course of a student’s training; cannot be taken concurrently with Biol 89800)
BIOL. 90000 – Dissertation Supervision
Level 3 students working on thesis project under the supervision of the thesis mentor.

1 credit