Students using microscopes

Biological Sciences Graduate Course Descriptions

502. Research Skills. 2-3 cr.

This advanced course provides students with practical knowledge of computer programs and web sites used in molecular biology for the in silico analysis of DNA and proteins. It also teaches presentation of scientific data and ideas. Topics covered will include: PowerPoint presentations, effective poster design, photography with digital cameras, capturing microscope images, finding sequences in Genbank, DNA and protein sequence analysis, choosing primers for PCR, and engineering gene constructs. Lecture and Laboratory.

503. Light/Electron Microscopy. 3 cr.

This course includes an introduction to light microscopy (phase, differential interference contrast, brightfield, darkfield, and fluorescence microscopy), transmission electron microscopy and scanning electron microscopy. It covers specimen preparation (fixation, embedding, sectioning), photomicroscopy and darkroom techniques (film developing and printing), in addition to image analysis, enhancement and interpretation. Students are required to do a project outside of class hours. Lecture and Laboratory.

505. Microbial Genetics. 3 cr.

A course providing the fundamentals to the rapidly growing field of microbial genetics. Emphasis is on gene structure and function. Areas to be discussed are DNA replication, transcription, translation, control of gene expression, transformation, conjugation, transduction, genetic fine structure and colinearity, mapping methods, mutation, DNA repair, plasmids and their properties. Genetic engineering, gene cloning and in vitro recombination are described. Prerequisite: a course in Microbiology. Lecture.

507. Recombinant DNA Techniques. 4 crs.

This course provides a broad hands-on introduction to contemporary techniques in molecular biology. Manipulation of cloned DNA using restriction endonucleases, ligases, and phosphatases will be carried out. Molecular cloning using both plasmid and bateriophage vectors will be done. Nucleotide sequencing and sequence analysis will be discussed. The student will carry out a nucleic acid hybridization in the form of a Southern blot. Cloned DNA will be transposon mutagenized. Analysis of cloned DNA using a reporter gene will be carried out. DNA amplification using the Polymerase Chain reaction will be done.

513. Developmental Biology. 3 cr.

This course is a study of the progression through time and space from a single cell, the fertilized egg, to a complex multi-cellular organism. The powerful tools of molecular and cellular biology have linked the fields of embryology, morphology, genetics, and evolutionary biology to reveal how cells, tissues, organs, and organisms develop. This course explores the processes of morphogenesis, differentiation, pattern formation, growth, and reproduction at the molecular, cellular, and organismal levels to provide a current overview of development in a wide variety of organisms. Lecture.

515. Mammalian Physiology. 3 cr.

Examination of the molecular and cellular mechanisms of mammalian body function, including consideration of the basic components of biological control systems and the manner in which various tissues and organ systems contribute toward the maintenance of physiological homeostasis in health and disease. Lecture.

516. Comparative and Environmental Physiology. 3 cr.

This course focuses on the diversity of physiological mechanisms that different animals employ, including the high level of physiological and biochemical adaptation and specialization found in animals that live in diverse and challenging environments, or possess other exceptional physiological abilities. Lecture.

517. Invertebrate Biology. 3 cr.

Of the nearly 1.5 million described species of animals, the vast majority are invertebrates. This course will survey the biology, evolutionary history, and relationships of invertebrate organisms from protozoa through invertebrate chordates. An emphasis will be placed on phylogenetic relationships of these organisms, in particular the adaptations and characteristics that identify them as unique groups. A formal understanding of modern phylogenetic techniques will be developed. A collection of invertebrates is required as part of the course and guided field trips will be undertaken to help assemble the collection. Approximately 15% of the course will be devoted to the uses of invertebrates in scientific study (especially Drosophila and C. elegans) and the impact of invertebrates on human life, especially as food, pollinators, disease-causing agents, disease vectors, and agricultural pests. Lecture.

519: Bioinformatics: Analysis of Molecular and Genomic Data. 3 cr.

Bioinformatics is the statistical analysis of biological data. This course will cover the theory, approaches, and methods for interpreting DNA, RNA, protein, and genomic data. Topics covered will include DNA, RNA, and protein analysis, functional genomics, genome assembly and annotation, variant detection and population studies, and transcriptome analysis using RNAseq. The application bioinformatics to understanding phenotypes, diseases, evolution, demography, and population history will be explored. Lecture.

522. Animal Behavior. 3 cr.

An evolutionary approach will be undertaken to study the behavior of animals. Using the Darwinian framework, one can understand basic life history events such as natal dispersal or seasonal migrations. Moreover intra-sexual selection and inter-sexual selection (mate choice) will be examined in several taxa. Finally intra-specific variation (or culture) will be explored among several animal populations, with special emphasis on chimpanzees. Lecture.

524. Immunology. 3 cr.

This is a course in the fundamental mechanisms of the immune system with applications in basic research, medicine and public health. Topics include the mechanisms of induction, regulation, and expression of the cellular and humoral immune responses, immunochemistry, antigen-antibody reactions, immunogenetics, hypersensitivity, and immunopathology. Lecture.

526. Pathogenic Microbiology. 3 cr.

This course will study the infectious agents of human disease with emphasis on host-parasite relationships, unique aspects of bacterial activities and organization, metabolism, regulation and genetics which contribute to pathogenicity, including identification of bacteria and principles of prevention, treatment, and laboratory diagnosis.

527. Microbial Ecology. 3 cr.

In this course the interaction of microorganisms, primarily prokaryotes, with each other, plants, animals, and fungi, and the environment is explored. The course takes a systematic approach, examining these interactions at the ecosystem, organismal, subcellular, and historical level. Topics include microbial primary production and photosynthesis, biogeochemical cycling, the structure of microbial communities, modeling, symbiosis, and microbial evolution.

529. Microbial Physiology. 3 cr.

This is a course which focuses on microbial energy metabolism, biosynthesis, metabolic regulation, and cell structure. Energy metabolism includes organotrophy (aerobic and anaerobic respiration, fermentation), chemolithotrophy, and phototrophy. Selected topics of microbial biosynthesis, including cell envelope biosynthesis, will be covered. Regulation of energy metabolism and biosynthesis at the levels of gene expression and enzyme activity will be a major topic in this course. Lecture.

530W. DNA Methods Population Genetics. 4 cr.

This combined laboratory and lecture course examines the biology underlying the most common genetic marker systems used in the forensic community. The basics of population genetics and DNA analysis methodologies will be covered, including the CODIS database. Techniques include extraction protocols, quantification using both uv-vis spec and qPCR, amplification of DNA, methods for labeling DNA, primer design and genotyping via an ABI 3130 Avant Genetic Analyzer. A semester-long project involves processing non-human DNA tissue samples that mimics the techniques employed in a forensic laboratory. True Allele, an Expert System used in analyzing genotyping data will also be examined. Prerequisites: BIOL 579 and permission of the instructor if not in Forensic track.

532. Applied and Environmental Microbiology. 3 cr.

This course takes an in-depth look at microbial biogeochemical cycling and the application of microbial processes (both prokaryotic and eukaryotic) for biotechnology and bioremediation. Topics include biogeochemistry, the design and application of genetically engineered microbes (GEMS), natural attenuation, fermentation, and water treatment, in addition to current issues in environmental science.

534. Medical Microbiology. 3 cr.

A systematic coverage of medical microbiology and its role in clinical medicine. Emphasis is based on current concepts of infectious disease and microbial genetics as it pertains to pathogenicity. Special attention is given to host-parasite interactions and to the interpretation and significance of laboratory findings in the diagnosis and treatment of human microbial disease. Lecture.

535. Vertebrate Anatomy, Development and Evolution. 3 cr.

This course emphasizes comparative development, functional anatomy and macroevolution of vertebrate body plans. Topics include the diversity and phylogenetic history of fossil and local forms, development and comparative embryology of each organ system, and comparative functional anatomy of the major clades of living vertebrates within an evolutionary framework. Lecture and Laboratory.

537. Virology. 3 cr.

An introductory course emphasizing basic understanding of the biochemical, replication, host-parasite relationships and pathogenesis of plant, animal, and microbial viruses. Medical virology and human viral pathogenesis are emphasized. Prerequisite: A course in introductory microbiology or permission of the instructor.

538. Environmental Biology. 3 cr.

The course provides an overview of life and the environment. Basic biological principles are examined in the context of the impact humans have on the biosphere. Topics include: ecological principles at the population, community and ecosystems levels; climate; biogeochemical cycles; human population growth; sources and effects of pollution; deforestation and habitat loss; loss of species richness; extinction; global warming; disease; biomarkers; biotechnology; and bioremediation. The course is appropriate for science majors and for non-majors with a strong science background. Lecture.

540. Evolution. 3 cr.

Evolution is the single most important concept uniting the many fields of biology. This course covers the theory of evolution and the various levels at which evolution works in living systems. Topics to be addressed include evolutionary genetics (including molecular evolution), adaptation and natural selection, evolution and diversity (including phylogeny reconstruction), and paleobiology and macroevolution. Lecture.

544. Plant Biology, Biotechnology, and Genomics. 3 cr.

This course is a merger of basic plant biology, molecular biology, and biotechnology. In it, we will discuss plant biochemistry, physiology, genetics, and development. The emphasis is placed upon linking basic plant systems to current research problems and developments in biotechnology and genomics. Typical topics will include applications of plant molecular biology to understand cellular structure and function, genomics, developmental genetics, and methods to develop tools for plant biotechnology. The course will also discuss the issue of plant biology as it pertains to world economics and food production.

557. Reproductive Physiology. 3 cr.

This course offers a broad overview of mammalian reproductive physiology. The major emphasis will be on human/primate biology, but other mammalian species will be included for comparison. The application of modern techniques of cellular and molecular biology to answer central questions of reproductive physiology will be explored in more detail. Lecture.

560. Endocrinology. 3 cr.

This advanced integrative physiology course investigates the role of the endocrine system in coordination and regulation of body activities. Topics include homeostasis, reflex arcs, hormone synthesis, hormone action and signal transduction, hypothalamic/pituitary axis, regulation of salt, mineral and water balances, regulation of energy metabolism, reproduction, growth and development. This course is appropriate for biology and biochemistry majors interested in physiology, as well as for pre-health profession students. Lecture.

566. Terrestrial Field Biology. 3 cr.

This applied ecology course is designed to present an overview of field and laboratory methods used by ecologists to describe and analyze plant and animal aggregations and their environments. The course focus is on the principles and practice of various ecological procedures with explanation of how to collect, record and analyze data. The course reviews the basic concepts of ecology that are needed to understand the various methods and their significance. The course material is presented as a combination of lecture, laboratory and field sessions. Lecture and Laboratory.

567. Genomics. 3 cr.

This course examines the structure, function, and evolution of genomes, including both prokaryotes and eukaryotes. Topics covered will include genome sequencing methods and analysis, gene expression, chromosome structure, proteomics, bioinformatics, and genome evolution.

568. Human Genetics. 3 cr.

This is an advanced course in human genetics focusing on principles of inheritance, structure and function of the human genome, genetic mapping of diseases, and patterns of human genetic diversity. We will examine both theoretical concepts as well as practical applications to a variety of fields. The emphasis of applications will be on the logic of the approach rather than on technical experimental details.

569. Signal Transduction. 3 cr.

This advanced cell biology course addresses the question of how the messages from various chemical signaling molecules are "transduced" into biological responses. Topics include: modes of cell communication, types of chemical signals, steroid hormone action, transduction by cell-surface receptor proteins, channel-linked receptors, G-protein-linked receptors, catalytic receptors, second messengers, cAMP, calcium, calmodulin, inositol trisphosphate pathway, diacylglycerol pathway, protein kinases and growth factors. Lecture.

570. Lab I: Experimental Biology. 3 cr.

This lab course sequence is designed to provide students with a multidisciplinary lab that reflects the integration among different disciplines in the broad areas of cellular and molecular biology. The course emphasizes techniques and approaches in the molecular, biochemical, and cellular biology of organisms from bacteria to mammals. Included are an introduction to research skills (computer use, library resources), characterizations and manipulations of cellular macromolecules including proteins and nucleic acids, and microscopy. Laboratory.

571. Lab II: Cell and Molecular Biology. 3 cr.

The second semester continues to build on BIOL 570 through investigative labs in cellular and molecular biology including cell culture, genetic mapping, constructing transgenic organisms, and microscopy of cellular structures. Laboratory and recitation.

572. Lab III: Cell and Systems Physiology. 3 cr.

The second semester continues to build on BIOL 570 through investigative labs in cardiovascular/respiratory physiology, muscle and neurophysiology, and endocrinology. Experiments in many cases employ MacLab hardware and Apple Macintosh computers for data acquisition. The course is laboratory project based. Laboratory.

573. Lab IV Microbiology. 3 cr.

The second semester continues to build on BIOL 570 through investigative labs in microbial physiology, ecology and genetics. This laboratory also examines cell culture, virology and immunological techniques used in microbiology and virology. Laboratory.

574. Ethics in Biotechnology. 1 cr.

In this course, students consider the ethical issues such as fraud in science, bias in interpretation, the use of animals in research, the use of human embryos, human cells, genetic engineering and therapy, protection of human subjects and patient care. This course will also discuss ethical issues found in commercial R&D including technology ownership, use of intellectual property, confidentiality, and business ethics. Weekly discussions are led by various professionals in the medical, scientific, and ethics fields.

575. Neurobiology. 3 cr.

This course will survey topics found in the science of neurobiology. Neurobiology is the study of the nervous system, its development, its function and its diseases. Topics will include evolution and development of the nervous system, electrophysiology of neurons, human neuroanatomy, anatomy and functioning of the sensory systems and molecular genetics of the nervous system. The focus of the course is on how a scientist discovers the inner workings of the brain. Science has shown that the study of "simple" brains can tell us a great deal about how all brains function, including human brains. As such, in this class, we will study aspects of the neurobiology of many different organisms.

576. Lab VI: Microscopy. 3 cr.

Microscopy can provide a unique glimpse at cell morphology and intracellular form and function. The purpose of this course is to introduce the theory and practice in the various types of microscopy including light (bright field, dark field, phase contrast, differential interference contrast), fluorescence, and confocal scanning laser, as well as scanning and transmission electron microscopy. It focuses on experimental design where microscopy provides the answer (conceptualization), determination of microscopy/technique that will provide the answer (instrumentation), and producing the micrograph with digital photography and image processing (documentation). Graduate students will work on a project that directly relates to their research, imaging in confocal and TEM and SEM cells related to their research projects. Graduate students will also prepare a manuscript-style report of their finding.

579. Forensic Molecular Biology. 3 cr.

This is a graduate Level Laboratory/ Lecture course that will introduce the student to molecular techniques that are germane to Forensics. Topics include restriction fragment length polymorphism (RFLP); recombinant DNA technology and sequencing nuclear DNA, via cloning ; working with Bi-Allelic Markers systems (ALUs and Amelogenin), and mtDNA sequencing. Students will also work with BLAST and mtDNA databases. Permission of Instructor.

580. Readings in Cell & Molecular Biology. 1 cr.

Discussion and critical evaluation by faculty and students of significant papers from the recent research literature.

581. Readings in Cellular & Systems Physiology. 1 cr.

Discussion and critical evaluation by faculty and students of significant papers from the recent research literature.

582. Readings in Microbiology. 1 cr.

Discussion and critical evaluation by faculty and students of significant papers from the recent research literature.

592W. Stream Field Biology. 3 cr.

This course is the study of the functional relationships and productivity of fresh water streams as they are affected by their physical, chemical and biotic environment. The course material is presented as a combination of lecture, laboratory and field sessions. Prerequisites: There are no specific course prerequisites; however, students should have knowledge of basic biology, chemistry and fundamental algebra.

594. Environmental Sampling and Analyses. 3 cr.

Explores the fundamentals of sample collection from experimental design and chain of custody, to methods used for obtaining environmental samples from air, water, and sediment in addition to biological sampling. The class lectures are augmented with trips to field research stations and a river excursion with RiverQuest to obtain environmental samples. Sample analysis includes microscopy and spectrometry, as well as biological and molecular techniques. Prerequisites: Biology 111/111L, 112/112L; CHEM 121/121L, 122/122L; MATH 225 or enrollment in graduate program.

645. Advanced Cell & Molecular Biology I. 3 cr.

This course is intended to be the first semester of a two-semester primary core of study taken by all graduate students in the biological sciences. It offers an in-depth integrated examination of advanced topics in cellular and molecular biology. Topics include structure, function and experimental techniques relating to biological molecules and sub-cullular and extra cellular structures. Emphasis will also be placed on processes such as genomic organization, gene regulation, replication, cell cycle control, translation, vesicular trafficking, and receptor signal transduction. Course materials are drawn from review articles and recent primary research reports.

645W. Advanced Cell & Molecular Biology I. 5 cr.

This course is identical to BIOL 645, but provides an additional in-depth evaluation and interpretation of the primary research literature, focusing on both concepts and experimental design.

646. Advanced Topics in Biology. 1 cr.

This is a discussion-based analysis of selected topics in biology. Students research issues using the current literature and present their findings regularly throughout the course. Topics and faculty vary each semester, and each topic is considered from different viewpoints. Recent topics include: molecular parasitology, pathogenic microbiology, and signal transduction. Pre-requisites: BIOL 645, BIOL 647 or consent of Instructor.

647. Advanced Cell and Molecular Biology II. 3 cr.

This course focuses on the structure, function, and experimental techniques relating to biological molecules, sub-cellular, and extra-cellular structures. Emphasis will also be placed on processes such as genomic organization, replication, mutation, DNA repair mechanisms, and transposable elements. Reading material for this course will include substantial amounts of primary and review literature, in addition to the textbook.

650. Conservation Biology. 3 cr.

This course will provide an overview of the current concepts and issues. Topics that will be covered include threats to biodiversity, life tables and reproductive strategies, population structure and metapopulation dynamics, population viability analysis, gap analysis, conservation genetics, habitat restoration, propagation programs, and recovery plans for imperiled species. Lecture (3 hours) Pre-requisites: Biology 111/111L, 112/112L; CHEM 121/121L, 122/122L; MATH 225 or enrollment in graduate program.

651. Special Topics - Biology. 1-3 cr.

Treatment of topics of current or special interest in biology. Lecture, laboratory or combination.

667. Advanced Molecular Biology. 3 cr.

Molecular biology is the study of the expression, inheritance, function, and maintenance of the genetic material - chromosomes, DNA and genes. Examination of gene regulation using both prokaryotic and eukaryotic systems will be emphasized. Evaluation of experimental design and interpretation of the literature are used to study the structure and function of genes and chromosomes. Medical and agricultural examples are provided in the area of genome manipulation.

674. Ethics in Biology. 1 cr.

In this course, students consider the ethical issues such as fraud in science, bias in interpretation, the use of animals in research, the use of human embryos, genetic engineering, and patient care. Weekly discussions are led by various professionals in the medical, scientific, and ethics fields. This course is required for all graduate students.

Students attend and participate in weekly departmental research presentations and demonstrations by biological scientists from the Department of Biological Sciences, field stations, biotechnology laboratories, and other universities.

680. Graduate Research in Biology. 1-8 cr.

Graduate students register for research as part of the degree curriculum. MS and PhD students both register for this course.

690. Seminar. 0-1 cr.

Students attend and participate in weekly departmental research presentations and demonstrations by biological scientists from the Department of Biological Sciences, and from other universities.

691. Biology Experience in China. 4 cr.

This course provides an in-depth three-week scientific and cultural experience in China facilitated through Duquesne University and the Chinese Association of Science and Technology. Students will travel to a variety of locations in China and work in seminars or small groups with the opportunity to (1) communicate orally and in writing in topics such as environmental science and pollution abatement; (2) acquire appropriate learning skills for collective laboratory work; (3) become familiar with the Chinese scientific issues through actively participating in scientific presentations. Students must participate in pre-trip seminars during the prior spring semester, in the three-week trip (typically in August) including all activities during the trip, in the writing of reports to include in the trip summary document, and in a post-trip presentation to the public. This course is for graduate students in biology.

695. Introduction to Graduate Research I.  3 cr.

This is required of all first year Ph.D. students. Students rotate in a research laboratory. Lecture/Laboratory.

696. Introduction to Graduate Research II.  3 cr.

This is required of all first year Ph.D. students. Students rotate in a research laboratory. Lecture/Laboratory.