Graduate Biology Courses
5101 Evolution (3 s.h.)
A lecture and discussion course for upper-level science majors and graduate students. Topics covered include Darwinism and neo-Darwinian theory, including adaptation, natural selection, sexual selection, and speciation.
5111 Genomics in Medicine. (3 s.h.)
The completion of the Human Genome Project in 2003 began a revolution in the treatment of human disease. More than 10 years later, the promise of personalized genome-guided medical treatment is becoming reality. This course will explore how genomic information has enhanced our understanding of human genetic variation and disease susceptibility. Students will become familiar with current research as presented by researchers currently working in relevant fields. Students will complete an independent project focused on a particular disease topic, integrating literature review with new analyses of published data.
5112 Fundamentals of Genomic and Evolutionary Medicine (3 s.h.)
Modern evolutionary theory offers a conceptual framework for understanding human health and disease. In this course we will examine human disease in evolutionary contexts with a focus on modern techniques and genome-scale datasets. We ask: What can evolution teach us about human populations? How can we understand disease from molecular evolutionary perspectives? What are the relative roles of negative and positive selection in disease? How do we apply evolutionary principles in to diagnose diseases and develop better treatments? Students will develop familiarity with primary literature relevant to genomic medicine, and use computational tools to interpret genomic data in case studies and problem sets based on disease diagnosis, prevention, and treatment.
5225 Evolutionary Genetics
This class covers fundamental principles of population genetics and comparative genomics. The scope of the class ranges from understanding variation at the population level to addressing species-level questions. Topics covered include classical population genetics, quantitative genetics, molecular evolution, phylogenomics and speciation. Lectures will explore recent theoretical and empirical advances in these exciting fields. Students will be introduced to computational resources, tools and algorithms during tutorials.
5232 Behavioral Genetics (3 s.h.)
This course is an introduction to the interdisciplinary field – behavioral genetics – that combines behavioral sciences and genetics and unifies the long-standing debate on what underlies complex human behavior: “nurture” or “nature.” This course will discuss the genetic approaches used to dissect out the genetic determinant of complex human traits. For example, students will learn about genes that influence learning and memory, intelligence (IQ), cognitive disabilities, personality disorders, psychopathology, antisocial behavior, substance abuse, and sexual orientation. In addition, the interplay of environment and genetic factors that create individual differences in behavior will be explored. Because this field represents the intersection between what is known and what might be known in the future about complex and potentially controversial behaviors and characteristics, students will be encouraged to discuss contemporary ethical issues regarding human behavior in realm of the scientific evidence presented.
5248 Virology (3 s.h.)
The role of viruses in human diseases, and their potential as tools for research and clinical interventions. The course will focus on virus-induced diseases in man including (polio, rabies, hepatitis, herpes, and influenza); recently discovered viruses such as HIV and HTLV-1 will also be studied. Virus-host interactions and the mechanisms involved in disease progression, therapeutic strategies, and vaccines, strategies for viral entry, evasion of the immune system, transmission, and the subversion of host-cell machinery will be emphasized. Potential uses of viruses as vector for gene therapy of genetic disorders, cancers, and infectious diseases will also be discussed.
5254 Animal Behavior (4 s.h.)
Animals exhibit a wide diversity of behaviors that enable successful feeding, habitat selection, navigation, communication, social interactions, reproduction, and rearing of young. Why do animals behave in these ways, and why do animals differ in their behaviors? In this course, we will investigate the proximate (developmental and mechanistic) and ultimate (functional and evolutionary) explanations for these behaviors. We will study how ecological and evolutionary processes shape animal behavior. We will study classic theories and major principles of animal behavior, weighing the experimental and observational evidence for each idea. We will illustrate concepts with examples from a wide range of taxonomic groups of animals in diverse ecosystems. We will also discuss some emerging theories in animal behavior, and some applications of animal behavior for conservation and human behavior.
5301 Cell Biology. (3 s.h.)
Advanced knowledge in cell biology will be discussed. Topics include macromolecules, cell structure, cell motility, bio-membrane, endo- and exocytosis, nucleocytoplasmic transport, visualizing cells and macromolecules with advanced microscopy imaging. Current journal articles reporting recent developments in modern cell biology will be also covered.
5307 Conservation Biology (3 s.h.)
The Earth harbors an incredible diversity of species and communities, most still poorly understood by science. This biodiversity is essential to the functioning of natural ecosystems and provides a wide array of priceless services to people today and a treasure of benefits for the future. Yet human threats to biodiversity have led us to the brink of the sixth major extinction event in Earth’s history. Which populations, species, communities, and ecoregions are most diverse? Which are most threatened, and by which human activities? What does the science suggest is needed to conserve biodiversity? How might this best be done given social, economic, and political realities? We will examine all these questions and more in this course, focusing on the key principles of conservation biology and the application of those principles to conservation of terrestrial, freshwater, and marine conservation at local, national, and international scales.
Reptiles and amphibians comprise nearly 7,400 species and can be found on every major and minor landmass in the world except Antarctica. This course will provide a broad, evolutionary survey of the major groups of reptiles and amphibians (“herps”). We will cover topics about their basic biology, including anatomy, physiology, ecology, behavior, and conservation. The laboratory will emphasize taxonomic characters and identification of living and preserved specimens, with emphasis on species found in North America. Additionally several field trips (conducted during lab hours and spring break) will reinforce course material through hands-on experience.
5312 Biostatistics (3 s.h.)
Biostatistics is an important part of the research activities related to biological and medical issues. Statistics is used to analyze phenomena with random properties and is often essential to draw the right conclusions based on a data set. The course will be designed to cover different statistical methods for data analysis mainly applied to medical and biological problems. Advanced undergraduate and graduate students with interests in medicine and biomedical research will benefit most from the course. However statistical methods that can be applied to behavioral science and ecology will also be covered.
5321 Plant Community Ecology
This class focuses on fundamental principles in community ecology as they relate to plant systems. The scope of the class ranges from plant-environment interactions and species interactions, to the relationship among communities at larger spatial scales. Lectures and small group discussions will also highlight theoretical and empirical advances made in ecology through classic and contemporary studies of plant communities.
5322 Plant Genetics (3 s.h.)
Current molecular and genetic analyses of classical problems in the genetics of higher plants.
5358 Cellular & Molecular Neuroscience
5368 Biology of Cancer (3 s.h.)
This course will survey the categories of tumors and their varying natures. Known mechanisms that lead to tumor cell development, multistep tumorigenesis, metastasis, tumor immunology, and cancer treatments will be examined in depth.
5403 Genomics & Proteomics (3 s.h.)
Objectives: To understand structure and function of proteins and how mutations result in disease, to learn modern methods of analyzing proteins, expose students to genomic and proteomic data bases, to introduce data mining and foster experimental design in genomics, to discover basic biology in the context of applied research, to use case study methods to examine genome expression in context, to become proficient with computer tools for proteomics and genomics, to appreciate the benefits of using math to understand biology, to gain practical experience and exposure to “practical” genomics and proteomics.
5416 Tropical Marine Biology: Belize (4 s.h. An Inter-session Course)
An introduction to the largest coral barrier reef in the Atlantic Ocean. Course lectures begin at Temple (Approximately Dec 29-Jan 31; holidays excluded) followed by a week of lectures, field trips and field or laboratory projects in Belize. Lectures include coral biology, reef geology and ecology, coral reef microbiota, food chains and nutrient transfer in coral reefs, reef community organization, the biology of reef fishes, commensal and symbiotic interactions of reef organisms, and other appropriate topics. Group student team projects and lectures are required.
5427 Immunology (3 s.h.)
The purpose of the Immunology course is to provide a comprehensive overview of the immune system that in its normal function protects each of us from the harmful effects of microbial invaders. The lectures will describe the general properties and development of immunity, the condition of being protected from infection by microorganisms or the effects of foreign molecules. They will provide systemic coverage of immune responses to viruses, bacteria, protozoa and roundworms as well as the practical aspects of vaccine development. Additional lectures will include a description of various types of primary immunodeficiencies, most prevalent autoimmune disease and cancer.
5429 Developmental Genetics. (3 s.h.)
Prerequisites: Biology 203. The role of genes in the determination and differentiation of eukaryotes. Emphasis on the regulation of gene function and on the genetic and molecular interactions which control the processes of development
5433 Advanced Techniques in Microscopy (3 s.h.)
A survey of modern techniques in microscopy. Students will acquire a thorough grounding in general principles of optics and conventional microscopy, and learn the theory of many methods current in biology and medicine, fluorescence, confocal microscopy, video microscopy, and digital image processing and analysis.
5436 Freshwater Ecology (3 s.h.)
The interrelationships between biological, chemical, and physical factors in freshwater environments. Lectures, laboratories and evaluation of recent literature address general ecological principles as they apply to microorganisms, plants and animals in lakes, ponds, streams and wetlands. Field trips include sampling Pennsylvania streams and lakes.
5452 Systems Neuroscience. (3 s.h.)
Study of the structure and function of the central nervous system (CNS) with a focus on the functional brain at a systems level. Systems level questions include how circuits are formed and used anatomically and physiologically to produce physiological functions, such as reflexes, sensory integration, motor coordination, emotional responses, learning and memory.
5454 Neurological Basis of Animal Behavior. (3 s.h.)
Prerequisites: One semester neurobiology. An exploration of the relationship of neural activity and connectivity to behavior. Topics include motor control, object recognition and learning. Examples from both vertebrate and invertebrate species. Analytic and synthetic approaches.
5456 Organization and Development of the Nervous System. (3 s.h.)
Prerequisite: Biology 204 or equivalent. This course covers developmental, anatomical and integrative aspects of the nervous system. The relationship of form to function will be studied in a variety of systems both invertebrate and vertebrate. The course is intended to complement Neurobiology 352/452 so that students will have a perspective on neuroscience ranging from the molecular to the systems level.
Prerequisites: Biol. 3096. A study of the process of biochemical differentiation of embryonic cells.
5458 Cellular and Molecular Neuroscience. (3 s.h.)
The course will focus on the molecular and cellular basis of neurological processing. The fundamentals of action potential generation, synaptic and receptor potentials generation and neuron-neuron communication will be discussed. The contemporary understanding of sensory processing will be covered in great detail with a particular focus on molecular sensors of light, sound, odorants, taste and touch and the signal transduction pathways that underlie the five senses.
5464 Biochemical Embryology. (3 s.h.)
This course will compare and contrast key biochemical mechanisms of embryonic development in a variety of model organisms ranging from humans to plants. We will examine the roles of enzymes, peptides, small RNA molecules and chromatin structure during embryogenesis. Topics will include micro RNAs, modification of DNA structure, and effects of mutation on enzyme activity. These basic principles will then be applied to subjects such as cell communication, stem cells, and cloning. Course material will be drawn from the experimental literature.
5465 Concepts in Mammalian Development. (3 s.h.)
Topics include gametogenesis, fertilization and pre- and post- implantation development. Analyses will be based upon experimental, genetic and molecular studies. Primary references will be used.
5467 Endocrinology. (3 s.h.)
Prequisites: General Biology and Organic Chemistry. Broad coverage of “chemical messengers”, occurrence, biochemistry, and physiology. Vertebrate endocrinology with minor treatment of invertebrates and plants.
5469 Molecular Biology. (3 s.h.)
A background knowledge of biochemistry and basic genetics at the undergraduate level is desirable. Structure, function and interaction of proteins and nucleic acids; building macromolecular complexes; techniques in molecular biology; introduction to molecular genetics and genomics; DNA replication and repair; transcription at the level of both genes and genomes; role of chromatin in gene regulation; non-coding RNAs; RNA processing; RNA interference; protein synthesis and its regulation; introduction to proteomics; transposons; regulatory proteins in eukaryotes.
5471 Cell Proliferation. (3 s.h.)
Prerequisites: Biology 2296 and 3096 or equivalent. Discussion of cell proliferation and its control; assay systems, comparisons of proliferating cells with nonproliferating cells, controls of cell division and how that control is modified in proliferative diseases such as cancer, the relationships between proliferation and differentiation.
5474 Physical Biochemistry. (3 s.h.)
Prerequisites: Chemistry C071-C072, C073-C074, or C091-C092, two semesters of calculus, and one semester of calculus-based physics; Pre or Corequisites: third semester calculus and second semester physics. Permission of instructor required. The course covers those aspects of computer simulation of molecular dynamics, quantum mechanics, and statistical mechanics of use to biochemist and biologist interested in molecular modeling. The course is intended to be computer intensive.
5475 General Biochemistry I. (3 s.h.)
Prerequisites: Biology 2112 or eqivalent. Properties of water (pH and buffers); metabolism of carbohydrates, amino acids, fatty acids, and phospholipids properties of biomacromolecules proteins, and nucleic acids; DNA structure and replication; protein synthesis; energy generation; catalysis and control of enzymatic activity and interrelationships among the metabolic pathways.
5476(476) General Biochemistry II. (3 s.h.)
Prerequisite: Chemistry 4401 or Biology 4375 Emphasis on the biochemical reactions in various metabolic pathways. Biosynthesis and degradation of carbohydrates, lipids, proteins and amino acids. Regulation and integration of metabolic pathways. Bioenergetics and oxidative phosphorylation. Signal transduction. Transcription, translation and their control.
5479. Biotechnology (3 s.h.)
This course is designed to survey current issues in technologies including therapeutics and diagnostics, and to examine consequences of developments in this area. The course is designed in a Problem Based Learning format, where students research critical areas and provide oral and written reports for other members in the class. The course is organized by topics including Concepts in Genetics, Cloning and Ethics, Gene Therapy, Prenatal Diagnosis, Gene Therapy for Cancer, Cell Replacement Therapy, Genomics and Proteomics, Vaccines, Forensics, Plant Biotechnology, and Instrumentation. At the end of the course, each student makes a formal presentation on a specific advance in biotechnology.
8001-8002 Teaching of Biology. (3 s.h.)
Instruction in the art of teaching laboratories and recitations.
8003 Introduction to Biological Research. (3 s.h.)
A laboratory course providing hands-on experience in common techniques of biological research. Topics covered will include laboratory safety, pH buffers, spectroscopy, centrifugation, electrophoresis and chromatography. Instruction will also be given in experimental design, the use of controls and the analysis of data. Limited to graduate students.
8802 Research Techniques. (3 s.h.)
Laboratory instruction in the biochemical and biophysical techniques used to investigate biological problems.
8807 Recombinant DNA Tech. (4 s.h.)
Co- or Prerequisites: Bio. 55469 and undergraduates who have had Bio 3324 or permission of the instructor. Laboratory instruction in molecular biology and recombinant DNA techniques. The course will provide practical experience in modern cloning, hybridization, and DNA sequencing technology.
8210-8820 Seminar. (variable credit.)
Topics will vary.
8250-8260 Seminar. (variable credit.)
Topics will vary.
8450 Seminar. (3 s.h.)
8510 Seminar. Neuroscience(3 s.h.)
Topics will vary.
9283 Directed Reading. (variable credit)
Directed study and discussion of the current research literature.
9991 Graduate Research.
9994 Preliminary Exam Preparation
9998 Pre-Dissertation Research
9999 Dissertation Research