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4.3: Viruses Lab (Instructor Materials Preparation) - Biology

4.3: Viruses Lab (Instructor Materials Preparation) - Biology


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Lab Materials

This is the prep for one section of 24 students.

Sharing Bodily Fluids

Students will do this part in table teams (groups of 4).

MaterialsQuantityNotes
Vials labeled 1-2424randomly choose 1 vial to be infected. This should be a number less than 10 in case there is a small # of students in the class. Let instructor know which vial is infected in advance
Plastic pipets
Reagent

Virology

Virology: A Laboratory Manual is designed for a one-semester virology laboratory course, although more than one semester of exercises are included. Choices of experiments allow for flexibility within a sequentially organized framework. The text features detailed experimental
protocols with comprehensive sections on materials and preparations for all exercises, plus introductory material, discussion questions, and further reading. the use of few viruses and cell lines provides continuity and simplifies preparation of the laboratory exercises. An Instructor's Manual is available to give alternative and assistance in laboratory set-up.

Virology: A Laboratory Manual is designed for a one-semester virology laboratory course, although more than one semester of exercises are included. Choices of experiments allow for flexibility within a sequentially organized framework. The text features detailed experimental
protocols with comprehensive sections on materials and preparations for all exercises, plus introductory material, discussion questions, and further reading. the use of few viruses and cell lines provides continuity and simplifies preparation of the laboratory exercises. An Instructor's Manual is available to give alternative and assistance in laboratory set-up.

Key Features

n Methods for studying viral properties and quantification
n Assays for viral antibodies and interferons
n Techniques in cell culture for viral research
n Experiments to accommodate a bi-weekly laboratory schedule
n Experiments designed to minimize need for extensive preparation or sophisticated instrumentation

n Methods for studying viral properties and quantification
n Assays for viral antibodies and interferons
n Techniques in cell culture for viral research
n Experiments to accommodate a bi-weekly laboratory schedule
n Experiments designed to minimize need for extensive preparation or sophisticated instrumentation


Ecosystem Science and Management

ESSM 102 Introduction to Natural Resources and Ecosystem Management

Credit 1. 1 Lecture Hour.

Introduction to natural resources including range and forest and ecosystem system approach to wildland management survey of the field of natural resources and related industries.

ESSM 201 Exploring Ecosystem Science and Management

Credit 1. 1 Lecture Hour.

Exploration of knowledge, skills and abilities required for varied careers within ecosystem science and management development of a professional portfolio and résumé exploration of career options through team approach conduct one service project.

ESSM 203 Forest Trees of North America

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Taxonomy, phylogeny, and identification of the important forest trees of North America and their ecological and social uses and benefits.
Prerequisites: BIOL 101, BIOL 107, BIOL 111 or BIOL 113 and BIOL 123 or equivalent.

ESSM 281 Seminar in Ecosystem Science and Management

Credit 1. 1 Other Hour.

Writing intensive, focused on writing and formatting technical documents relevant to ecosystem sciences and management includes memos, short synthesis papers and one longer review paper.
Prerequisites: RENR, FORS, RLEM, ECOR and SPSA majors only.

ESSM 291 Research

Credits 0 to 4. 0 to 4 Other Hours.

Research conducted under the direction of faculty member in ecosystem science and management. May be repeated 2 times for credit.
Prerequisites: Freshman or sophomore classification and approval of instructor.

ESSM 300 Field Studies in Forest Ecosystems

Credits 3. 1 Lecture Hour. 6 Lab Hours.

Field-oriented focus on forest ecosystem science and management problem-solve management questions through data collection and team-based research investigate the relationships between landowner objectives, mensuration, silviculture, ecology, soils, and regeneration-focused harvesting systems foster the development of student-faculty relationships enhance professional knowledge and skills.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 301 Wildland Watershed Management

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Elements of watershed management including range, forest and other natural resources and principles and practices of wildland management for protection, maintenance and improvement of water resource values.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 302 Wildland Plants of North America

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Familiarization with the distribution and economic value of important wildland plants including range, forest and other natural resources in Texas and North America and fundamentals of sight identification of these plants plant collection required.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 303 Agrostology

Credits 3. 1 Lecture Hour. 6 Lab Hours.

Classification and identification of grasses based on macro- and micromorphological variations of spikelets interpretation of spikelet variation and use of diagnostic keys to identify important species of North America including range, forest and other natural resources a grass collection required.
Prerequisites: Junior or senior classification or approval of instructor.

ESSM 304 Rangeland Plant Taxonomy

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Interpretation of plant morphology for keying and identification of important flowering rangeland plants vegetative and floral characters for important plant families including toxic compounds affecting domestic livestock. Plant collection required.

ESSM 305 Watershed Analysis and Planning

Credits 3. 3 Lecture Hours.

Provide an integrated framework for watershed planning that addresses the related biophysical, social and economic issues comprehensive in scope and approach giving students the tools and techniques for developing sound watershed management policy and practice water issues, problems and regulations for Texas.
Prerequisite: Junior or senior classification.

ESSM 306 Plant Functional Ecology and Adaptation

Credits 3. 3 Lecture Hours.

Investigation of physiological mechanisms influencing ecological patterns and processes, including plant acclimation and adaptation in contrasting habitats abiotic controls on species productivity and distribution underlying genetic and evolutionary mechanisms contributing to the occurrence of specific genotypes and phenotypes in unique environments.
Prerequisites: RENR 205, any BIOL course, junior or senior classification or approval of instructor.

ESSM 307 Forest Protection

Credits 3. 2 Lecture Hours. 3 Lab Hours.

Destructive agents in forestry as related to importance, identification, cause, extent of losses and protective measures.
Prerequisites: RENR 205, or equivalent, junior or senior classification or approval of instructor.

ESSM 308 Fundamentals of Environmental Decision-Making

Credits 3. 3 Lecture Hours.

Introduction to environmental issues in natural resources management fundamental principles and methods for understanding biosocial interdependencies in complex environmental issues use of computer-aided group decision-making techniques to develop cooperative strategies for resolving local or global environmental issues.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 309 Forest Ecology

Credits 3. 3 Lecture Hours.

Life history and general characteristics of trees structure and function of forest ecosystems fundamental principles of forest tree physiology and ecology applied to an analysis of tree growth in relation to environmental factors and present day forest management global changes and forests.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 310 Forest Tree Improvement and Regeneration

Credits 3. 3 Lecture Hours.

Genetic improvement or manipulation of forest trees through breeding or transformation regeneration of forests including reproduction, nursery production, stand establishment, natural regeneration and problems affecting regeneration.
Prerequisites: BIOL 101, BIOL 113 or equivalent junior or senior classification.

ESSM 311 Biogeochemistry and Global Change

Credits 3. 3 Lecture Hours.

Framework for understanding biogeochemical cycles, their significance at both global and ecosystem levels of organization, and their contemporary relevance to ecosystem science and management.
Prerequisites: RENR 205, RENR 215, any BIOL and/or CHEM course, junior or senior classification or approval of instructor.

ESSM 313 Vegetation Sampling Methods and Designs in Ecosystems

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Basis for vegetation sampling in ecosystems including range, forest and other natural resources methods for conducting sampling selection of sampling unit appropriate for vegetation type sampling statistics mean comparisons regression analysis sampling design principles development of sampling plan presentation and interpretation of sampling data.
Prerequisites: Any MATH course satisfying university core curriculum, junior or senior classification or approval of instructor.

ESSM 314 Principles of Rangeland Management Around the World

Credits 3. 3 Lecture Hours.

Basic knowledge of world rangeland ecosystems, how these systems are managed in diverse cultural settings principles of underlying ecological processes influenced by various land management practices foster understanding of the values that people in different countries place on rangeland resources use of these values to enhance geologically sustainable and socially acceptable rangeland management practices.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 315 Rangeland Inventory and Monitoring

Credit 1. 2 Lab Hours.

Theory and methods to inventory rangeland vegetation sampling design analysis of inventory data interpretation of sampling data preparation of a technical report presentation of inventory data in text, tables, and graphs using the style of the Rangeland Ecology and Management discipline.
Prerequisites: ESSM 313, junior or senior classification or approval of instructor.

ESSM 316 Range Ecology

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Organization and distribution of rangeland ecosystems of the world, with emphasis on North America community dynamics and functions stressed including biotic history, succession, disturbance regimes, competitive interactions, herbivory, energy flow and nutrient cycling conservation of rangeland resources.
Prerequisites: RENR 205, RENR 215, ESSM 302, and ESSM 314, junior or senior classification or approval of instructor.

ESSM 317 Vegetation Management

Credits 3. 3 Lecture Hours.

Familiarization with practices that cause changes in rangeland vegetation composition for multiple uses understanding of criteria for range improvement practices comparison of expected responses of livestock forage production, watershed parameters and wildlife to vegetation changes following range improvements systems concept for planning, analysis and implementation of range improvement practices.
Prerequisites: ESSM 314, junior or senior classification or approval of instructor.

ESSM 318 Coupled Social and Ecological Systems

Credits 3. 3 Lecture Hours.

Resilience-based stewardship of social-ecological systems including range, forest and other natural resources ecological concepts of resilience, sustainability, ecosystem services and vulnerability investigation of linkages among social and ecological system components contribution to sustainability and provisioning of ecosystem services evaluation of multiple knowledge sources as the basis for adaptive ecosystem management.
Prerequisites: RENR 205, AGEC 105 or equivalent, junior or senior classification or approval of instructor.

ESSM 319 Principles of Forestry

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Theory and practice of forestry in controlling forest establishment, composition, structure and growth principles of natural and artificial regeneration intermediate cultural operations silvicultural systems use and control of fire in forests principles of sustainable stand management.
Prerequisite: ESSM 309 or instructor approval.

ESSM 320 Ecosystem Restoration and Management

Credits 3. 3 Lecture Hours.

A basic conceptual framework for restoration ecology and ecological restoration including range, forest and other natural resources major principles of ecology related to practical problems confronting humankind, such as, environmental pollution and degradation, exotic species invasions, land use and management trade-offs and consequences importance of biological diversity.
Prerequisite: RENR 205, RENR 215 or equivalent, junior or senior classification or approval of instructor.

ESSM 324 Forest Measurements

Credits 2. 4 Lab Hours.

Measures and measurement of the dimensions and attributes of forested areas including the diameters, heights, volume and biomass of trees within a well-defined area tools used for forest measurement the conduct of forest inventories summary measures and reports of inventory results remote sensing and related technologies that assist forest measurements.
Prerequisites: ESSM 313 and ESSM 319 or concurrent enrollment junior or senior classification.

ESSM 351/RENR 405 Geographic Information Systems for Resource Management

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Geographic Information Systems (GIS) approach to solving spatial problems and managing natural resources, including the acquisition, management, manipulation, analysis, and mapping of spatial and non-spatial databases identification of natural and relevant features from various data sources integration of relevant technologies and data extensive use of GIS software to solve real-world problems. Only one of the following will satisfy the requirements for a degree: ESSM 351/RENR 405, RENR 405/ESSM 351, ESSM 651, BAEN 651, or RENR 651.
Prerequisite: Junior or senior classification or approval of instructor.
Cross Listing: RENR 405/ESSM 351.

ESSM 398 Interpretation of Aerial Photographs

Credits 3. 2 Lecture Hours. 3 Lab Hours.

Identification and evaluation of natural and cultural features on aerial photographs methods for extracting information concerning land use, vegetative cover, surface and structural features, urban/industrial patterns and archaeological sites.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 404 Changing Natural Resource Policy

Credits 3. 3 Lecture Hours.

Process through which environmental policies are changed study theories of social and political change teams use theories with their original research on environmental policy problems to create and implement plans for changing environmental policies in their own communities.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 405 Forest Resource Assessment and Management

Credits 3. 1 Lecture Hour. 4 Lab Hours.

Integration of biophysical, economic and social factors in forest resource analysis, management planning and decision making applications of interdisciplinary knowledge and multiple-use principles to practical forest management problems.
Prerequisite: Senior classification or approval of instructor.

ESSM 406 Natural Resources Policy

Credits 3. 3 Lecture Hours.

Natural resources and forest policy development in the United States and review of current issues in forest and related natural resource policy.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 415 Range Analysis and Management Planning

Credits 4. 3 Lecture Hours. 2 Lab Hours.

Basic concepts and theories of range management systems. Resource inventory, analysis and management planning.
Prerequisites: AGEC 105 or ECON 202, ESSM 314, ESSM 317 junior or senior classification or approval of instructor.

ESSM 416 Fire Ecology and Natural Resource Management

Credits 3. 3 Lecture Hours.

Behavior and use of fire in the management of natural resources including range, forest and other natural resources principles underlying the role of weather, fuel characteristics and physical features of the environment related to the development and implementation of fire management plans.
Prerequisite: RENR 205 or equivalent, junior or senior classification or approval of instructor.

ESSM 417 Prescribed Fire

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Use of prescribed fire to achieve ecosystem management objectives understanding of how to plan and implement prescribed fires coursework on fire behavior, fuel properties and the social aspects of prescribed fire and wildfire how to safely use fire to achieve multiple outcomes including biodiversity conservation, reduced hazardous fire risk, livestock production and timber management.
Prerequisites: ESSM 416.

ESSM 420 Ecological Restoration of Wetland and Riparian Systems

Credits 3. 2 Lecture Hours. 2 Lab Hours.

How wetland and riparian areas link terrestrial and aquatic systems and function hydrologically and ecologically within watersheds integrated approaches for restoration of degraded wetland and riparian systems improving water resources through vegetation management with a special interest in rangelands.
Prerequisites: RENR 205, junior or senior classification or approval of instructor.

ESSM 430 Advanced Restoration Ecology

Credits 3. 3 Lecture Hours.

A dynamic discipline relying heavily on the fundamentals of ecology practice translating and communicating key ecological concepts to advanced case studies in ecological restoration enhance skills for professional applications.
Prerequisites: RENR 205, ESSM 320, ESSM 420 junior or senior classification.

ESSM 440 Wetland Delineation

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Covers the application of the 1987 Wetland Delineation Manual in use by the Army Corps of Engineers (CORPS) field indicators of hydrophytic vegetation hydric soils, wetland hydrology, methods for making jurisdictional determinations in non-disturbed and disturbed areas, recognition of problem wetlands and technical guidelines for wetlands.
Prerequisite: Junior or senior classification.

ESSM 444 Remote Sensing of the Environment

Credits 3. 2 Lecture Hours. 3 Lab Hours.

Principles and techniques necessary for applying remote sensing to diverse issues in studying and mapping land uses and land covers of the terrestrial environment emphasizes a hands-on learning approach with theoretical foundations and applications in both aerial and satellite remote sensing, using optical and lidar datasets.
Prerequisite: Junior or senior classification or approval of instructor.

ESSM 446 Unmanned Aerial Systems (UAS) for Remote Sensing

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Fundamental components of small unmanned aerial systems (sUAS), sensors and platforms, UAS operational concepts, the principles of UAS data collection, legal framework within which UAS should be operated and applied, data processing software and the generation of orthomosaics and 3D point clouds, emphasizes the use of UAS in a broad spatial sciences, technology and applications context, including vegetated ecosystems.
Prerequisites: ESSM 444 or approval of instructor junior or senior classification.

ESSM 459 Programming for Spatial Data Applications

Credits 3. 2 Lecture Hours. 3 Lab Hours.

Programming for spatial data applications in general and for natural resources application in particular basic programming concepts and constructs for the creation and manipulation of spatial data automating of processes programming behind spreadsheet and GIS applications.
Prerequisites: ESSM 351/RENR 405 or equivalent, junior or senior classification or approval of instructor.

ESSM 461 Spatial Databases for Data Storage, Manipulation and Analysis

Credits 3. 1 Lecture Hour. 4 Lab Hours.

Relational databases and advanced geodatabase capabilities types of geodatabases Structured Query Language including join-types and subqueries ArcGIS Desktop Advanced.
Prerequisites: ESSM 459 junior or senior classification or approval of instructor.

ESSM 462/GEOG 462 Advanced GIS Analysis for Natural Resources Management

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Advanced topics in geographic information systems (GIS) to solve natural resource problems manipulation of raster data types three-dimensional modeling emphasis on geoprocessing as it relates to applied projects particularly with habitat suitability models field and lab use of global positioning systems (GPS) internet-based GIS modeling.
Prerequisites: ESSM 351/RENR 405 or AGSM 461 or equivalent or approval of instructor junior or senior classification.
Cross Listing: GEOG 462/ESSM 462.

ESSM 464 Spatial Project Management

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Integration of key components of spatial project management to ensure a successful project implementation using life-cycle methodology and spatial project management strategy and planning, requirements analysis, design, development, deployment, and operations and maintenance term project working with real world data to develop and manage a spatial project for practical applications.
Prerequisites: ESSM 351/RENR 405 and ESSM 444, junior or senior classification or approval of instructor.

ESSM 480 Plant Identification and Undergraduate Range Management Exam Team Competitions

Credits 0 to 3. 0 to 3 Other Hours.

Knowledge of plants morphology, identification and distribution for the profession of range management knowledge of range management across the world weekly tests to train on plant and range management knowledge. May be repeated for credit.
Prerequisites: Junior or senior classification or approval of instructor.

ESSM 481 Senior Seminar

Credit 1. 1 Lecture Hour.

Completion of professional e-portfolio, résumé and job application exploration of job search, application, and interview discipline competency exams program evaluation.
Prerequisite: Senior classification in ESSM degree program.

ESSM 484 Internship

Credits 0 to 4. 0 to 4 Other Hours.

Supervised experience program conducted in the student's area of specialization.
Prerequisite: Approval of student's advisor.

ESSM 485 Directed Studies

Credits 0 to 3. 0 to 3 Other Hours.

Individual study and research upon a selected range problem.
Prerequisite: Approval of student's advisor.

ESSM 489 Special Topics in.

Credits 1 to 4. 1 to 4 Lecture Hours. 0 to 4 Lab Hours.

Selected topics in an identified area of rangeland ecology and management. May be repeated for credit.
Prerequisite: Approval of instructor.

ESSM 491 Research

Credits 0 to 4. 0 to 4 Other Hours.

Research conducted under the direction of faculty member in ecosystem science and management. May be repeated for credit.
Prerequisites: Junior or senior classification and approval of instructor.


Preparing Figures, Schemes and Tables

  • File for Figures and Schemes must be provided during submission in a single zip archive and at a sufficiently high resolution (minimum 1000 pixels width/height, or a resolution of 300 dpi or higher). Common formats are accepted, however, TIFF, JPEG, EPS and PDF are preferred.
  • Viruses can publish multimedia files in articles or as supplementary materials. Please contact the editorial office for further information.
  • All Figures, Schemes and Tables should be inserted into the main text close to their first citation and must be numbered following their number of appearance (Figure 1, Scheme I, Figure 2, Scheme II, Table 1, etc.).
  • All Figures, Schemes and Tables should have a short explanatory title and caption.
  • All table columns should have an explanatory heading. To facilitate the copy-editing of larger tables, smaller fonts may be used, but no less than 8 pt. in size. Authors should use the Table option of Microsoft Word to create tables.
  • Authors are encouraged to prepare figures and schemes in color (RGB at 8-bit per channel). There is no additional cost for publishing full color graphics.

Common Body of Knowledge

To assure that students have sufficient prerequisite training for advanced courses, Biology majors must complete a series of courses comprising a Common Body of Knowledge (CBK) prior to their junior year (5th full semester) and enrollment in upper level BIOL courses. A Biology student will be admitted into upper level Biology classes when he or she has met the following criteria:

Completion of a set of CBK courses (37-38 hours) before the student's 5th full semester to include:


BIOL - Biology (BIOL)

Introduction to the study of biology at Texas A&M University gain knowledge of departmental and campus resources to assist and enhance the pursuit of a degree in biology, microbiology, molecular and cellular biology or zoology.
Prerequisites: First-year and first-time-in-college freshman majoring in BIOL, MBIO, BMCB and ZOOL.

BIOL 101 Botany

Credits 4. 3 Lecture Hours. 3 Lab Hours.

(BIOL 1311 and 1111, BIOL 1411) Botany. Structure, physiology and development of plants with an emphasis on seed plants. (Not open to students who have taken BIOL 111 and BIOL 112 or BIOL 113.) includes laboratory that reinforces and provides supplemental information related to the lecture topics.

BIOL 102 Neuroscience Overview

Credit 1. 1 Lecture Hour.

An introductory survey of neuroscience for freshmen undergraduate students on the basic neuroscience core ideas and neurological disorders.
Cross Listing: NRSC 101, PSYC 101 and VIBS 101.

BIOL 107 Zoology

Credits 4. 3 Lecture Hours. 3 Lab Hours.

(BIOL 1313 and 1113, 1413) Zoology. Survey of animal life with respect to cell organization, genetics, evolution, diversity of invertebrates/vertebrates, anatomy/physiology, and interaction of animals with their environment includes laboratory that reinforces and provides supplemental information related to lecture topics. (Not open to students who have taken BIOL 111 and BIOL 112 or BIOL 113).

BIOL 111 Introductory Biology I

Credits 4. 3 Lecture Hours. 3 Lab Hours.

(BIOL 1306 and 1106, 1406) Introductory Biology I. First half of an introdutory two-semester survey of contemporary biology that covers the chemical basis of life, structure and biology of the cell, molecular biology and genetics includes laboratory that reinforces and provides supplemental information related to the lecture topics also taught at Galveston campus.

BIOL 112 Introductory Biology II

Credits 4. 3 Lecture Hours. 3 Lab Hours.

(BIOL 1307 and 1107, 1407) Introductory Biology II. The second half of an introductory two-semester survey of contemporary biology that covers evolution, history of life, diveristy and form and function of organisms includes laboratory that reinforces and provides supplemental information related to the lecture topics.
Prerequisite: BIOL 111 also taught at Galveston campus.

BIOL 113 Essentials in Biology

Credits 3. 3 Lecture Hours.

(BIOL 1308, BIOL 1408) Essentials in Biology. One-semester biology for non-majors overview of essential biological concepts and their application to real world and contemporary issues topics include evolution, biodiversity, cellular, molecular and forensic biology, genetics and heredity to scientific literacy, human impact on the environment, genetically modified organisms and emerging diseases.

BIOL 206 Introductory Microbiology

Credits 4. 3 Lecture Hours. 4 Lab Hours.

(BIOL 2320 and 2120, BIOL 2321 and 2121, BIOL 2420, BIOL 2421) Introductory Microbiology. Basic microbiology of prokaryotes and eukaryotes main topics include morphology, physiology, genetics, taxonomy, ecology, medically important species and immunology mandatory laboratory designed to give hands-on experience and to reinforce basic principles.
Prerequisites: BIOL 101, BIOL 107, BIOL 111, or BIOL 113 CHEM 119. May not be used for credit by biology, molecular and cell biology, microbiology, zoology, predentistry or premedicine majors.

BIOL 213 Molecular Cell Biology

Credits 3. 3 Lecture Hours.

Explores the molecular basis of cell structure, function and evolution gene regulation, cell division cycle, cancer, immunity, differentiation, multicellularity and photosynthesis may not take concurrently with, or after the completion of, BIOL 413.
Prerequisites: BIOL 112 CHEM 120.

BIOL 214 Genes, Ecology and Evolution

Credits 3. 3 Lecture Hours.

A genetically-based introduction to the study of ecology and evolution emphasis on the interactions of organisms with each other and with their environment.
Prerequisite: BIOL 112.

BIOL 285 Directed Studies

Credits 1 to 4. 1 to 4 Other Hours.

Problems in various phases of plant, animal and microbial science.
Prerequisites: Freshman or sophomore classification approval of ranking professor in field chosen and Undergraduate Advising Office.

BIOL 289 Special Topics in.

Credits 1 to 4. 1 to 4 Lecture Hours.

Selected topics in an identified area of biology. May be repeated for credit.
Prerequisite: Approval of instructor.

BIOL 291 Research

Credits 0 to 4. 0 to 4 Other Hours.

Active research of basic nature under the supervision of a Department of Biology faculty member. May be repeated for credit.
Prerequisites: Freshman or sophomore classification and approval of faculty member.

BIOL 302 Careers in Biology

Credit 1. 1 Lecture Hour.

Development of job search skills utilization of career resources self-assessment of career interests and career objectives strategies for professional correspondence and networking business etiquette and interviewing techniques insight into life science career opportunities.
Prerequisites: Junior or senior classification department of biology majors only or approval of instructor.

BIOL 318 Chordate Anatomy

Credits 4. 3 Lecture Hours. 3 Lab Hours.

Classification, phylogeny, comparative anatomy, and biology of chordates diversity, protochordates, vertebrate skeletons, shark and cat anatomy studied in laboratory.
Prerequisite: BIOL 214 or approval of instructor.

BIOL 319 Integrated Human Anatomy and Physiology I

Credits 4. 3 Lecture Hours. 3 Lab Hours.

Integrated approach to cellular, neural, skeletal, muscular anatomy and physiology includes some histology, histopathology, radiology and clinical correlations.
Prerequisite: BIOL 111 and BIOL 112, or BIOL 107.

BIOL 320 Integrated Human Anatomy and Physiology II

Credits 4. 3 Lecture Hours. 3 Lab Hours.

Continuation of BIOL 319. Integrated approach to endocrine, cardiovascular, respiratory, digestive, urinary, reproductive and developmental anatomy and physiology includes some histology, histopathology, radiology and clinical correlations.
Prerequisite: BIOL 319 or approval of instructor.

BIOL 335 Invertebrate Zoology

Credits 4. 3 Lecture Hours. 3 Lab Hours.

Morphology, taxonomy, natual history and phylogeny of invertebrate animals, with emphasis on biodiversity class includes both lecture and lab. Labs include study of preserved material and demonstration of living animals in aquaria and terraria.
Prerequisite: BIOL 214 or approval of instructor.

BIOL 344 Embryology

Credits 4. 3 Lecture Hours. 3 Lab Hours.

Introduction to general and comparative embryology molecular and cellular mechanisms of development genetics and early development of selected invertebrates (C. elegans, Drosophila and sea urchin) and emphasis on vertebrates (frog, fish, chick and mouse).
Prerequisite: BIOL 213 or GENE 302.

BIOL 350 Computational Genomics

Credits 3. 2 Lecture Hours. 2 Lab Hours.

Hands-on approach to obtaining, organizing and analyzing genome-related data emphasis on asking and answering biologically relevant questions by designing and performing experiments using computers understanding biology from a computational perspective.
Prerequisite: Junior or senior classification in life sciences, engineering, mathematics, chemistry.

BIOL 351 Fundamentals of Microbiology

Credits 4. 3 Lecture Hours. 4 Lab Hours.

Introduction to modern microbiology with emphasis on prokaryotes includes microbial cell structure, function, and physiology genetics, evolution, and taxonomy bacteriophage and viruses pathogenesis and immunity and ecology and biotechnology includes laboratory experience with microbial growth and identification.
Prerequisites: BIOL 112 CHEM 227, and CHEM 237 or CHEM 231 or approval of instructor also taught at Galveston campus.

BIOL 352 Diagnostic Bacteriology

Credits 4. 2 Lecture Hours. 6 Lab Hours.

Practical experience in handling, isolation and identification of pathogenic microorganisms using biochemical tests and rapid identification techniques.
Prerequisite: BIOL 351 or approval of instructor.

BIOL 357 Ecology

Credits 3. 3 Lecture Hours.

Analysis of ecosystems at organismal, population, interspecific and community levels. BIOL 358 is the laboratory for this lecture course.
Prerequisite: BIOL 214 or approval of instructor.

BIOL 358 Ecology Laboratory

Credit 1. 3 Lab Hours.

Quantitative analyses of freshwater and terrestrial ecosystems includes data sampling and presentation of results in written and oral formats required fieldtrips analysis of competition and predator-prey interactions using ecological models.
Prerequisite: BIOL 357 or concurrent enrollment junior or senior classification.

BIOL 388 Principles of Animal Physiology

Credits 4. 3 Lecture Hours. 3 Lab Hours.

Introduction to how animals function, including basics of neurophysiology, endocrinology, muscular, cardiovascular, respiratory, ormoregulatory, and metabolic physiology broadly comparative in scope and encompassing adaptation of physiological systems to diverse environments the laboratory stresses techniques used for monitoring and investigating physiological mechanisms and responses to environmental changes.
Prerequisites: BIOL 214 or CHEM 228 or approval of instructor.

BIOL 401 Critical Writing in Biology

Credit 1. 1 Lecture Hour.

Reading scientific papers and writing short synopses of papers with a focus on learning how to think and write like a scientist fills the current Writing Intensive "W" course requirement for biology.
Prerequisites: BIOL 213 and BIOL 214 junior or senior classification.

BIOL 402 Communicating Biological Research to the Public

Credit 1. 1 Lecture Hour.

Interpret scientific papers analyze how research findings are communicated to lay audiences write synopses of research findings for the general public.
Prerequisites: BIOL 213 and BIOL 214 junior or senior classification.

BIOL 405 Comparative Endocrinology

Credits 3. 3 Lecture Hours.

Basic principles of endocrinology including structure and functions of hormones in vertebrates hormonal control of growth, metabolism, osmoregulation, and reproduction endocrine techniques and mechanism of hormone action.
Prerequisites: BIOL 214 and CHEM 227.

BIOL 406/GENE 406 Bacterial Genetics

Credits 3. 3 Lecture Hours.

A problem oriented course surveying the manipulation and mechanisms of genetic systems in bacteria recombination, structure and regulation of bacterial genes, plasmids and phages.
Prerequisites: BIOL 351 GENE 302.
Cross Listing: GENE 406/BIOL 406.

BIOL 413 Cell Biology

Credits 3. 3 Lecture Hours.

Structure, function, and biogenesis of cells and their components interpretation of dynamic processes of cells, including protein trafficking, motility, signaling and proliferation.
Prerequisites: BIOL 213 or GENE 302 BICH 410 or BICH 440.

BIOL 414 Developmental Biology

Credits 3. 3 Lecture Hours.

Concepts of development in systems ranging from bacteriophage to the mammalian embryo use of recombinant DNA technology and embryo engineering to unravel the relationships between growth and differentiation, morphogenesis and commitment, aging and cancer.
Prerequisite: BIOL 213 or GENE 302 BICH 410 or BICH 440.

BIOL 423 Cell Biology Laboratory

Credits 2. 1 Lecture Hour. 3 Lab Hours.

Modern methods of study of cell structure and cell function.
Prerequisites: BICH 410 and BIOL 413, or concurrent enrollment or approval of instructor.

BIOL 430 Biological Imaging

Credits 4. 3 Lecture Hours. 3 Lab Hours.

Still and video photography and photomicrography, computerbased digital image analysis and processing of biological images theory and principles of light and electron microscopy including transmission and scanning electron microscopy optical contrast methods for light microscopy including phase contrast, DIC, polarizing light and confocal laser scanning microscopy.
Prerequisite: Junior classification or approval of instructor.

BIOL 434/NRSC 434 Regulatory and Behavioral Neuroscience

Credits 3. 3 Lecture Hours.

Cell biology and biophysics of neurons functional organization of the vertebrate nervous system physiological basis of behavior.
Prerequisites: BIOL 213 BIOL 319, BIOL 320, BIOL 388, BIOL 413, NRSC 235/PSYC 235, or PSYC 235/NRSC 235, or approval of instructor.
Cross Listing: NRSC 434/BIOL 434.

BIOL 435 Laboratory for Regulatory and Behavioral Neuroscience

Credit 1. 3 Lab Hours.

Study of modern methods and tools used to investigate nervous system structure and function.
Prerequisite: BIOL 213 BIOL 319, BIOL 320, BIOL 388, BIOL 413, BIOL 434/NRSC 434, NRSC 434/BIOL 434, NRSC 235/PSYC 235, or PSYC 235/NRSC 235, or approval of instructor.

BIOL 437 Molecular and Human Medical Mycology

Credits 3. 3 Lecture Hours.

Principles of fungal pathogenesis, diagnosis and antifungal therapies, and relevant genetic and molecular tools for studying human pathogens and drug delivery.
Prerequisites: BIOL 351 junior or senior classification or approval of instructor.

BIOL 438 Bacterial Physiology

Credits 3. 3 Lecture Hours.

Structure and function of prokaryotic cells, with emphasis on evolutionary adaptations to different environmental, developmental, and pathogenic selections pressures formation of teamsa and preparation of presentations on specific topics in microbiology.
Prerequisites: BIOL 351 BIOL 406/GENE 406 or concurrent enrollment BICH 410, BICH 431/GENE 431 and GENE 302 strongly recommended.

BIOL 440 Marine Biology

Credits 4. 3 Lecture Hours. 3 Lab Hours.

Introduction to biology of common organisms inhabiting bays, beaches and near-shore oceanic waters with special reference to Gulf of Mexico biota emphasis on classification, distribution, history, ecology, physiology, mutualism, predation, major community types and economic aspects of marine organisms.
Prerequisite: BIOL 214 or approval of instructor.

BIOL 444/NRSC 444 Neural Development

Credits 3. 3 Lecture Hours.

Cellular and molecular mechanisms of nervous system development including neural induction and the basis of complex behaviors use of a wide range of model organisms with a specific emphasis on vertebrate nervous system development.
Prerequisites: BIOL 213, BIOL 319, BIOL 320, BIOL 413, BIOL 388, NRSC 235/PSYC 235 or PSYC 235/NRSC 235.
Cross Listing: NRSC 444.

BIOL 445 Biology of Viruses

Credits 3. 3 Lecture Hours.

Structure, composition and life cycles of viruses methods used to study viruses their interaction with host cells mechanisms of pathogenicity and cellular transformation responses of the host to viral infection, and vaccine applications in-depth study of the life cycles of the major classes of viruses and discussion of emerging viruses.
Prerequisite: BIOL 213 or BIOL 351 or approval of instructor.

BIOL 450/BICH 450 Genomics

Credits 4. 3 Lecture Hours. 3 Lab Hours.

The study of genomic data includes consideration of the logic behind the most important genomic approaches, as well as their capabilities and limitations in investigating biological processes the science of accessing and manipulating genomic data and practical applications, including development of an hypotheses-driven datamining experiment.
Prerequisites: BIOL 213, GENE 301 or GENE 302, BICH 431/GENE 431 or GENE 431/BICH 431, or BIOL 351 junior or senior classification or approval of instructor.
Cross Listing: BICH 450/BIOL 450.

BIOL 451 Bioinformatics

Credits 3. 3 Lecture Hours.

Introduction to the entire field of bioinformatics theoretical background of computational algorithms, with an emphasis on application of computational tools related to modern molecular biological research.
Prerequisite: BIOL 213, GENE 301, or GENE 302, or BIMS 320/GENE 320 or GENE 320/BIMS 320 and junior or senior classification, or approval of instructor.

BIOL 454 Immunology

Credits 3. 3 Lecture Hours.

Introduction to basic immunological concepts and principles of serology.
Prerequisite: BIOL 351 or equivalent or approval of instructor.

BIOL 455 Laboratory in Immunology

Credits 2. 6 Lab Hours.

Practical application of serological principles which include precipitation, agglutination and blood banking principles techniques in tissue culture and hybridoma technology also included.
Prerequisite: BIOL 454 or registration therein.

BIOL 456 Medical Microbiology

Credits 3. 3 Lecture Hours.

Microbiology, epidemiology and pathology of human pathogens with an emphasis on bacterial agents.
Prerequisite: BIOL 351 or approval of instructor.

BIOL 461 Antimicrobial Agents

Credit 1. 1 Lecture Hour.

Understanding of antimicrobial agents, limitations of use, biosynthesis and regulation, and challenges in development as new therapeutics.
Prerequisites: BICH 410 or BICH 440 and BIOL 351 or VTPB 405.

BIOL 462/WFSC 462 Amazon River Tropical Biology

Credits 3. 3 Lecture Hours.

History, ecology, evolutionary-biology, geography and culture of the Amazon River and Rio Negro exploration of the world’s most bio-diverse river during a 10-day expedition from Manaus, Brazil survey biota, record observations about the ecosystem, select research topics, development of presentations.
Prerequisites: BIOL 107, BIOL 112, BIOL 113, BIOL 357 or RENR 205 or approval of instructor.
Cross Listing: WFSC 462/BIOL 462.

BIOL 466 Principles of Evolution

Credits 3. 3 Lecture Hours.

Evolutionary patterns, mechanisms and processes at the organismal, chromosomal and molecular levels modes of adaptation and the behavior of genes in populations.
Prerequisite: GENE 302 or approval of instructor.

BIOL 467 Integrative Animal Behavior

Credits 3. 3 Lecture Hours.

Examines how behavior contributes to survival and reproduction, and how evolutionary history and ecological circumstance interact to shape the expression of behavior focus on integrative nature of behavior how the interaction of evolutionary processes, mechanistic constraints, and ecological demands determine behavioral strategies.
Prerequisite: BIOL 214, BIOL 357, BIOL 388, BIOL 405, BIOL 434/NRSC 434, or BIOL 466, or approval of instructor.

BIOL 480 Departmental Colloquium

Credit 1. 1 Lecture Hour.

Attend presentations given by renowned scientists from various fields of biology learn about new developments in science stay abreast of current and trending research topics.
Prerequisites: Senior classification majors in BIOL, MICRO, BMCB and ZOOL.

BIOL 481 Seminar in Biology

Credit 1. 1 Lecture Hour.

Recent advances. Restricted to senior undergraduate majors in biology, microbiology, botany or zoology.

BIOL 484 Internship

Credits 0 to 4. 0-1 Other Hours.

Directed internship in a private firm or public agency to provide research experience appropriate to the student's degree program and career objectives. May be taken two times.
Prerequisite: Approval of internship agency and advising office.

BIOL 485 Directed Studies

Credits 1 to 12. 1 to 12 Other Hours.

Problems in various phases of plant, animal and bacteriological science.
Prerequisites: Junior classification approval of ranking professor in field chosen and Undergraduate Advising Office.

BIOL 487/VTPB 487 Biomedical Parasitology

Credits 4. 3 Lecture Hours. 2 Lab Hours.

Helminth and protozoan parasites of medical and veterinary importance life cycles, morphology, taxonomic classification, economic and public health aspects and current topics in parasitic diseases.
Prerequisites: BIOL 107 or BIOL 114 junior classification or approval of instructor.
Cross Listing: VTPB 487/BIOL 487.

BIOL 489 Special Topics in.

Credits 1 to 4. 1 to 4 Lecture Hours. 0 to 10 Lab Hours.

Selected topics in an identified area of biology. May be repeated once for credit.

BIOL 491 Research

Credits 0 to 4. 0 to 4 Other Hours.

Active research of basic nature under the supervision of a Department of Biology faculty member. May be taken two times. Registration in multiple sections of this course is possible within a given semester provided that the per semester credit hour limit is not exceeded.
Prerequisite: Approval of departmental faculty member.

BIOL 492 Biomedical Therapeutics Development

Credit 1. 1 Lecture Hour.

Basic aspects of the biotechnology business includes key aspects of biotechnology patents, the main steps in preclinical drug development and company structure and funding.
Prerequisites: BIOL 213 or equivalent CHEM 227 and CHEM 228.

BIOL 495 Biology Capstone: Research Communication in the Life Sciences

Credits 2. 2 Lecture Hours.

Culmination of capstone research experience formalization of research results in written and oral forms introduction to primary genres or scientific writing apply principles of rhetoric and composition to diverse methods of professional communication.
Prerequisite: BIOL 452, BICH 464/GENE 464, BIOL 400, BIOL 493 or BIOL 491 or approval of instructor.

BIOL 496 Ethics in Biological Research

Credit 1. 1 Lecture Hour.

Fraud in science, how to recognize it, and how to avoid committing fraud includes the basis of ethics and plagiarism, negotiation techniques and conflict management, the regulations and ethics covering animal and human experiments, record-keeping, data management and peer review.
Prerequisites: BIOL 491, NRSC, 491, BICH 491, GENE 491, BIMS 491, or CHEM 491, or concurrent enrollment, or approval of instructor.

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Assessment

A 90-100 A Clearly stands out as excellent performance and, exhibits mastery of learning outcomes.
B 80-89 B Grasps subject matter at a level considered to be good to very good, and exhibits partial mastery of learning outcomes.
C 70-79 C Demonstrates a satisfactory comprehension of the subject matter, and exhibits sufficient understanding and skills to progress in continued sequential learning.
D 60-69 D Quality and quantity of work is below average and exhibits only partial understanding and skills to progress in continued sequential learning.
F 0-59 F Quality and quantity of work is below average and not sufficient to progress.


Notes

The drop deadline for this course is subject to change depending on the term offered. Please visit the Section Notes below for the specific drop deadline date for the current term.

Departmental contact for academic questions: [email protected] | (510) 643-6901

English Language Proficiency Requirements

All of our courses are taught in English. For you to be successful, you should be able to demonstrate your English proficiency by speaking at the following testing levels:

  • TOEFL: 90
  • IELTS Academic Format: 7
  • DAAD: C1
  • TEM-4 or TEM-8: Level 70
  • iBT Special Home Edition and myBest scores are accepted. Scores must be from the past two years.

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Biology Courses

Topics in biology that are especially relevant to current issues and problems in modern society. For each semester hour of credit earned, one lecture hour a week for one semester. Some topics require one additional discussion hour or three or four additional laboratory hours a week. May not be counted toward a degree in biology. May be repeated for credit when the topics vary. Prerequisite: Varies with the topic.

Topic 1: The Biology of Being Human. Introductory biology course that covers human evolution, genetics and genomics, behavior, population growth and environmental issues. May not be counted toward a degree in the College of Natural Sciences.

BIO𧈭E. Problems in Modern Biology.

An introduction to major concepts in biology, with emphasis on topics, such as genetics, that are relevant to current issues in the field. Three lecture hours and one discussion hour a week for one semester. Biology 301E and 301L may not both be counted Biology 301E and 301M may not both be counted. May not be counted toward a degree in biology. Prerequisite: Admission to the Plan II Honors Program.

BIO𧅦C, 202C, 302C, 402C. Conference Course.

Supervised study of selected subjects in biology, by individual arrangement with the instructor. Conference course. May be repeated for credit. Prerequisite: Varies with instructor.

BIO𧈮D (TCCN: BIOL 1309). Science Literacy and Numeracy: Ecology and Evolution.

Explore science literacy and numeracy skills through methods of inquiry dealing with quantitative data and correcting common misconceptions regarding rational and quantitative thought. Examine these skills in the context of news events that include reference to some or all of the following: Mendelian genetics microevolution macroevolution population ecology community ecology ecosystem ecology. Three lecture hours and one discussion hour a week for one semester.

BIO𧈮E (TCCN: BIOL 1308). Science Literacy and Numeracy: Genetics and Genomics.

Explore science literacy and numeracy skills through methods of inquiry, dealing with quantitative data and correcting common misconceptions regarding rational and quantitative thought. Examine these skills in the context of news events that include reference to some or all of the following: human genetics analysis and manipulation of DNA genetic testing assisted reproductive technology human ancestry personalized medicine forensic genetics. Three lecture hours and one discussion hour a week per semester

BIO𧈮F. Science Literacy and Numeracy: Human Health and Disease.

Explore science literacy and numeracy skills through methods of inquiry, dealing with quantitative data and correcting common misconceptions regarding rational and quantitative thought. Examine these skills in the context of news events that include reference to some or all of the following: metabolic diseases, infectious diseases, genetic diseases - causes, prevention, and treatments. Three lecture hours and one discussion hour a week for one semester.

BIO𧈮G. Science Literacy and Numeracy: Biotechnology and the Future.

Explore science literacy and numeracy skills through methods of inquiry, dealing with quantitative data and correcting common misconceptions regarding rational and quantitative thought. Examine these skills in the context of news events that include reference to some or all of the following: climate change genetically modified organisms biomedical technology. Three lecture hours and one discussion hour a week for one semester

BIO𧇎L. Introductory Laboratory Experiments in Biology.

The organizing principles of biology (such as molecular and cellular functions, reproduction, development, homeostatic mechanisms, and organismal physiology and behavior) are used within a comparative and evolutionary framework to train students in modern laboratory techniques, bioinformatics, experimental design, and interpretation of results. One lecture hour and four laboratory hours a week for one semester. Prerequisite: Credit or registration for Biology 311C or 311D.

BIO𧇐L. Field Biology.

Field projects, laboratory exercises, field trips, and computer simulation exercises to acquaint students with the principles and applications of ecology and some of the experimental and descriptive methods of ecological investigations. One lecture hour and four laboratory hours a week for one semester. Prerequisite: Credit or registration for Biology 311D.

BIO𧈷C (TCCN: BIOL 1306). Introductory Biology I.

Introduction to biological energy transformation, cell structure and physiology, and gene expression. Three lecture hours and one discussion hour a week for one semester. Only one of the following may be counted: Biology 301L, 211, 311C. Biology 311C and 212 may not both be counted. Prerequisite: Credit or registration for Chemistry 301 or 301H.

BIO𧈷D (TCCN: BIOL 1307). Introductory Biology II.

Introduction to mechanisms of inheritance, evolution, physiology, and species interactions. Three lecture hours and one discussion hour a week for one semester. Biology 301L and 311D may not both be counted. Biology 301M and 311D may not both be counted. Prerequisite: Biology 311C with a grade of at least C-.

BIO𧈻H. Advanced Introduction to Genetics: Honors.

Basic principles of genetics and cell biology. Emphasis on gene structure and regulation transmission of heritable traits structure and function of cells bacterial and viral genetics and recombinant DNA technology. Three lecture hours and one discussion hour a week for one semester. Prerequisite: A score of 5 on the College Board Advanced Placement Examination in Biology and credit or registration for Chemistry 301 or 301H.

BIO𧅷S, 219S, 319S, 419S, 519S, 619S, 719S, 819S, 919S. Topics in Biology.

This course is used to record credit the student earns while enrolled at another institution in a program administered by the University's Study Abroad Office. Credit is recorded as assigned by the study abroad adviser in the Biology Instructional Office. University credit is awarded for work in an exchange program it may be counted as coursework taken in residence. Transfer credit is awarded for work in an affiliated studies program. . May be repeated for credit when the topics vary.

Upper-Division Courses

BIO𧉀. Cell Biology.

Principles of eukaryotic cell structure and function macromolecules, membranes, organelles, cytoskeleton, signaling, cell division, differentiation, motility, and experimental methodologies. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉀L. Cell Biology Laboratory.

Explores the complex structures and functions of cells through direct observation and experimentation. Subjects may include regulation of gene transcription and translation, protein sorting, organelles and membrane trafficking, cytoskeletal dynamics, and cell division. Use a combination of modern molecular biology, biochemistry, and microscopy techniques, with a strong emphasis placed on hypothesis-driven approaches, proper experimental design, and clear scientific writing and presentation. One lecture hour and five laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Sciences 311.

BIO𧉁G. Principles of Computational Biology.

Introduces computational methods for the analysis of nucleic acid and protein sequences, with applications towards biological problems. Performance assessment will be based on experiential learning methods. Three lecture hours and two computer laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H Statistics and Data Sciences 328M and Mathematics 408C, 408S, or 408R.

BIO𧉁L. Aquatic Entomology.

The taxonomy of aquatic insects the use of aquatic insects in biomonitoring. Two lecture hours and three laboratory hours a week for one semester. Only one of the following may be counted: Biology 321L, 370C (Topic: Applied Aquatic Entomology), 384K (Topic 13). Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉂. Structure, Physiology, and Reproduction of Seed Plants.

The principles of structure and functioning of higher plants special attention to the dynamics of growth and development and reproduction. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-, Chemistry 302 or 302H, and concurrent enrollment in Biology 122L.

BIO𧅺L. Structure, Physiology, and Reproduction of Seed Plants Laboratory.

Observation of structure and reproduction in seed plants and employment of experimental techniques that demonstrate physiological processes, especially processes of growth and development. Two laboratory hours a week for one semester. Prerequisite: Concurrent enrollment in Biology 322 and the following with a grade of at least C-: Biology 206L, 208L, 226L or Environmental Sciences 311.

BIO𧉃L. Laboratory Studies in Cell Biology.

Research exercises involving light/electron microscopy, image processing, autoradiography, chromatography, fractionation, flow cytometry, spectroscopy, diffraction, antibody labeling, cell growth, and kinetics. One lecture hour and four laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Sciences 311 and credit or registration for Biology 320.

BIO𧉄. Survey of the Plant Kingdom.

Survey of the groups of living and fossil plants, comparing organization and reproduction to understand major shifts in the evolution of plant life. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-, and concurrent enrollment in Biology 124L.

BIO𧅼L. Survey of the Plant Kingdom Laboratory.

Hands-on exploration of major plant groups emphasizing organization, reproduction and evolution. Cultures, prepared and living material examined. Local field trips. Designed to pair with Biology 324 lectures. Two laboratory hours a week for one semester. Prerequisite: Concurrent enrollment in Biology 324 and the following with a grade of at least C-: Biology 206L, 208L, 226L or Environmental Sciences 311.

BIO𧉅. Genetics.

Basic principles of Mendelism, molecular genetics, structure and function of genes and chromosomes, populations and evolution. Three lecture hours and one discussion hour a week for one semester. Biology 325 and 325H may not both be counted. Prerequisite: Biology 311C and 311D with a grade of at least C- in each.

BIO𧉅H. Genetics: Honors.

Basic principles of genetics and evolution. Emphasis on population genetics and natural selection structure and function of organ systems behavioral ecology and mutational analysis of organismal development. Three lecture hours and one discussion hour a week for one semester. Biology 325 and 325H may not both be counted. Prerequisite: Biology 315H with a grade of at least C-.

BIO𧉅L. Laboratory Experience in Genetics.

Experimentation and direct observation in fundamental aspects of transmission genetics. One lecture hour and four laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Sciences 311.

BIO𧉅T. Human Genetics.

Genomics, cancer genetics, identification and analysis of human disease genes, and monogenic and multifactorial traits in humans. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧇢L. General Microbiology Laboratory.

Introduction to microbiology laboratory techniques and experimental demonstration of principles of microbiology. One lecture and three laboratory hours a week for one semester. Prerequisite: Credit with a grade of at least C- or registration for Biology 326M or 326R.

BIO𧉆M. Introductory Medical Microbiology and Immunology.

Designed primarily for nursing and prepharmacy students. Overview of the structure, function, and genetics of bacteria, viruses, and fungi, with emphasis on the interactions between micro-organisms and the human host. Includes principles of microbial pathogenesis, the host's innate and adaptive immune responses to infection, epidemiology, laboratory diagnosis, and antimicrobial chemotherapy and vaccines. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 311C Biology 325 or 325H with a grade of at least C- Chemistry 301 with a grade of at least C- and one of the following with a grade of at least C-: Mathematics 408C, 408K, 408N, 408R.

BIO𧉆R. General Microbiology.

Overview of the major areas of microbiological study, including cell structure and function, genetics, host-microbe interactions, physiology, ecology, diversity, and virology. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Credit with a grade of at least C- or registration for Biology 325 or 325H, and Chemistry 302 or 302H with a grade of at least C-.

BIO𧉇. General Phycology.

A general survey of the algae and of their biology. Three lecture hours a week for one semester. Biology 327 and 388J may not both be counted. Prerequisite: Biology 324, 124L, and 325 or 325H, with a grade of at least C- in each, and concurrent enrollment in Biology 127L.

BIO𧉇D. Emerging Infectious Diseases.

Genomic and proteomic tools used to understand the causes of human infectious diseases. Covers genome sequencing, community sequencing, proteomics, microarrays, and human polymorphism analysis and how these technologies have been applied to the study of important human viral diseases. Also includes extensive coverage of the molecular and clinical biology of these diseases. Three lecture hours a week for one semester. Biology 327D and 337 (Topic: Emerging Infectious Diseases) may not both be counted. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉇E. Epigenetics.

A study of epigenetic modifications, the covalent modifications of DNA or histones that cause changes in gene expression. Particular attention is given to how experience or environmental factors epigenetically modify health or behavior in animals. Three lecture hours a week for one semester. Biology 327E and 337 (Topic: Epigenetics) may not both be counted. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉇G. Genomics.

Genome structure, organization, and function of model organisms theory and methodology of genetic and physical mapping sequencing analysis and annotation genome duplication and evolution and ethics for biotechnology and cloning. Three lecture hours a week for one semester. Biology 327G and 337 (Topic: Genomics) may not both be counted. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧅿L. Laboratory in General Phycology.

Survey of various algal groups, including direct observations of their biology, exposure to research techniques, and instruction in culture procedures. Three laboratory hours a week for one semester. Prerequisite: Credit with a grade of at least C- or registration for Biology 327 and the following with a grade of at least C-: Biology 206L, 208L, 226L, or Environmental Sciences 311.

BIO𧉈. Introductory Plant Physiology.

General principles of the mineral nutrition, water relations, metabolic activities, growth and development of green plants. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-, and Chemistry 302 or 302H.

BIO𧉈D. Discovery Laboratory in Plant Biology.

Learning methods of experimental design, data gathering, data interpretation, and data presentation, including original experiments relating to questions of current interest in plant physiology. Five laboratory hours a week for one semester. Biology 328D and 337 (Topic: Discovery Laboratory in Plant Biology) may not both be counted. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Sciences 311.

BIO𧆀L. Laboratory Experiments in Plant Physiology.

Introduction to experimental techniques used in the study of the mineral nutrition, water relations, metabolic activities, growth, and development of green plants. Three laboratory hours a week for one semester. Prerequisite: Credit with a grade of at least C- or registration for Biology 328 and the following with a grade of at least C-: Biology 206L, 208L, 226L, or Environmental Sciences 311.

BIO𧉉. Medical Mycology.

A basic introduction to medical mycology and an overview of research involving both the fungal zoopathogen and its host. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-, and Biology 326R with a grade of at least C-.

BIO𧆁L. Medical Mycology Laboratory.

Basic techniques for the identification and manipulation of fungi of medical importance. Three laboratory hours a week for one semester. Prerequisite: Biology 226L with a grade of at least C- and credit with a grade of at least C- or registration for Biology 329.

BIO𧆁S, 229S, 329S, 429S, 529S, 629S, 729S, 829S, 929S. Topics in Biology.

This course is used to record credit the student earns while enrolled at another institution in a program administered by the University's Study Abroad Office. Credit is recorded as assigned by the study abroad adviser in the Biology Instructional Office. University credit is awarded for work in an exchange program it may be counted as coursework taken in residence. Transfer credit is awarded for work in an affiliated studies program. May be repeated for credit when the topics vary.

BIO𧉊. Molecular Biology of Animal Viruses.

Mechanisms by which viruses replicate and kill or transform cells. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧇦L. Virology Laboratory.

Basic experimental techniques applied to selected bacteriophages and animal viruses. Four laboratory hours and one discussion hour a week for one semester. Prerequisite: Biology 226L with a grade of at least C-, and credit with a grade of at least C- or registration for Biology 330.

BIO𧉋L. Laboratory Studies in Molecular Biology.

Explores molecular biology methods, experimental design, and analyses applicable to both research and fields such as healthcare, biotechnology, and genetic analyses. Conducts experiments in a research project format. One lecture hour and four and one-half laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Sciences 311.

BIO𧉏. Introduction to Biochemical Engineering.

Microorganisms in chemical and biochemical synthesis genetic manipulation of cells by classical and recombinant DNA techniques. Enzyme technology design of bioreactors and microbial fermentations separations of biological products. Three lecture hours a week for one semester. Only one of the following may be counted: Biology 335, Biomedical Engineering 339, Chemical Engineering 339, 379 (Topic: Introduction to Biochemical Engineering). Prerequisite: Biochemistry 339F or 369, and Biology 311C with a grade of at least C-.

BIO𧉐. Tumor Biology.

Covers core aspects of cancer pathology, treatment, epidemiology, the discovery of oncogenes and tumor suppressors, and the molecular genetics underlying the characteristic features of malignant tumors (including metastatic behavior, genomic instability, angiogenesis, cell cycle regulation, and apoptosis). Strong emphasis on the biochemical functions of cancer-related proteins and enzymes and therapeutic approaches based on our understanding of these proteins. Important experimental approaches that have influenced our current understanding of cancer will also be stressed. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C- and one of the following with a grade of at least C-: Biochemistry 339F, 369, Biology 330, 360K.

BIO𧆉, 237, 337, 437. Selected Topics in Biology.

Recent developments and research methods in the biological sciences. For each semester hour of credit earned, one lecture hour a week for one semester. Some topics may require additional hours. May be repeated for credit when the topics vary. Prerequisite: Biology 325 or 325H with a grade of at least C- additional prerequisites vary with the topic.

Topic 1: Seminar in Human Biology. One lecture hour a week for one semester. Only offered as Biology 137. Prerequisite: Biology 346 with a grade of at least C-.
Topic 2: Research Methods: UTeach. Restricted to students in the UTeach-Natural Sciences program. Students perform independent inquiries and use skills from mathematics and science to solve research problems.
Topic 3: Natural History of Protists. A study of protista, a wide variety of eukaryotic organisms which are either unicellular or phylogenetically closely allied to unicellular organisms. Description of the basic taxonomic and ecological groups, and description of the natural history of the major groups of organisms.
Topic 4: Computational Neuroscience and Neural Networks.
Topic 5: Grant Writing and Research Skills. Explores skills required of research scientists, and specifically prepares students to submit a NSF Graduate Research Fellowship Proposal (NSF-GRFP) grant proposal during the semester (deadline for GRFP submission is typically during the last week of October). There are weekly writing milestones to complete an NSF-GRFP proposal by the submission deadline. Additional prerequisite: Upper-division standing and Statistics and Data Sciences 328M with a grade of at least C-.
Topic 6: Practical Ethics for Biologists. Incorporates weekly case studies to introduce common ethical issues faced by biologists in the field and the lab. Employs the Systematic Moral Analysis framework to critically examine ethical issues in scientific inquiry in general (data integrity, who pays for science) as well as issues specific to biologists in the field and laboratory (questionable research practices, conflicts of interest, expertise vs advocacy). Explores issues of personal values, implicit bias and environmental justice.
Topic 7: Sleep Science. Explores the basics of sleep science, current research questions and novel approaches, and the range of sleep disorders and their diagnoses. Additional prerequisite: Neuroscience 330 with at least a grade of C-.
Topic 9: The Emergence of Modern Biology. Explore biology through an analysis of classic texts from the age of Darwin to the present day. Survey the theory of evolution by natural selection, genetics and the Modern Synthesis, population and community ecology, molecular biology and genomics.
Topic 10: Renewable Resources: Environment and Future. Greenhouse gases and their effect on climate and the oceans, renewable energy and materials such as biofuels, bioplastics, and green chemistry: minimizing the generation of chemical waste in manufacturing processes. Biology 337 (Topic: Renewable Rsrcs: Envir/Future) and 137, 237, 337, and 437 (Topic 10) may not both be counted.

BIO𧉑J. Computational Biology Laboratory.

Overview of computational biology, with emphasis on nucleic acid sequence analysis and databases. Class projects and self-learning exercises. Two lecture hours and three computer laboratory hours a week for one semester. Prerequisite: Biology 325 or 325H, and Statistics and Data Sciences 328M with a grade of at least C- in each.

BIO𧊶L. Animal Communication.

Animal communication from a multidisciplinary perspective, with emphasis on quantitative analysis, sensory processing, and evolution of signals. Three lecture hours and three laboratory hours a week for one semester, with computer laboratory hours as required. Prerequisite: Biology 325 or 325H with a grade of at least C-, and Biology 359K or 370 with a grade of at least C-.

BIO𧉓. Metabolism and Biochemistry of Microorganisms.

A study of the metabolic processes of microorganisms, using a biochemical approach. Three lecture hours a week for one semester. Biology 339 and 391R may not both be counted. Prerequisite: Biology 326R with a grade of at least C-.

BIO𧉓M. Bacterial Behavior and Signaling Mechanisms.

Advanced studies in how bacteria perceive their environment and communicate with each other. Subjects may include chemotaxis and motility, morphogenesis and development, and secretion and virulence. Taught entirely through reading and discussion of original articles. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-, and Biology 326R with a grade of at least C-.

BIO𧉔L. Biology of Birds.

Anatomy, physiology, classification, and ecology of birds. Two lecture hours and three laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Sciences 311.

BIO𧉘. Molecular Biology.

Molecular basis of cellular processes: gene structure and function, DNA replication, RNA and protein synthesis, viruses, molecular aspects of immunology and cancer, and recombinant DNA. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 325 or 325H, and Biochemistry 369 or 339F with a grade of at least a C-.

BIO𧉙E. Endocrinology.

Vertebrate endocrinology (primarily mammalian), with a focus on human pathophysiology. Three lecture hours and one discussion hour a week for one semester. Biology 337 (Topic: Endocrinology) and 345E may not both be counted. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉚. Human Biology.

Introduction to human evolution, genetics, sexuality, senescence, and population growth. Three lecture hours and one discussion hour a week for one semester. Only one of the following may be counted: Biology 301G, 309F, 346. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧊾L. Human Microscopic and Gross Anatomy.

Designed for students preparing for biomedical research and the health professions. Focuses on microscopic and gross anatomy of human tissues and organs, with an emphasis on structure function relationships. Subjects include the effects of disease and aging in addition to normal human anatomy. Three lecture hours and four laboratory hours a week for one semester. Prerequisite: The following courses with a grade of at least C-: Biology 325 or 325H Chemistry 301 and Mathematics 408C, 408K, 408N, 408R, Statistics and Data Sciences 302, or 328M.

BIO𧋀L. Invertebrate Biology.

A study of the diversity and evolution of multicellular invertebrate animals, with emphasis on common themes in animal body construction and function. Three lecture hours and three laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉝. Developmental Biology.

Principles of animal development, with emphasis on developmental mechanisms. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉝L. Experiments in Developmental Biology.

An investigation of methods and principles of developmental biology in a laboratory context, with emphasis on animal embryology using molecular techniques and microscopy. One lecture hour and six laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉞M. Plant Molecular Biology.

Fundamentals of plant molecular biology, including structure and expression of the chloroplast and mitochondrial genomes. Three lecture hours a week for one semester. Biology 350M and 388M may not both be counted. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉟. Economic Botany.

An in-depth analysis of the origin of domesticated plant species, the role in nature of plant products, and the ways natural products have been altered through artificial selection. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉠. Reproductive Biology of Flowering Plants.

Pollination biology, breeding systems, reproductive strategies, and fruit and seed dispersal from evolutionary and ecological vantage points. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉡F. Field Entomology.

A field course on insects, with emphasis on field study techniques, visual identification of species, collecting techniques, and curation in the field. Meets five days a week for one hour a day during a summer-session term additional fieldwork to be arranged, including extended field trips. Biology 337 (Topic: Field Entomology) and 353F may not both be counted. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧋅L. Entomology.

Characteristics, importance, and biology of the major groups of insects. Two lecture hours and three laboratory hours a week for one semester, with additional fieldwork hours to be arranged. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉢C. Cell Biology of Human Birth Defects.

Explores the link between basic cell biology, human genetics, and human birth defects using current scientific literature exposing students to critical thinking and the scientific method, as well as the application of these tools to the study of biology. Three lecture hours a week for one semester. Biology 337 (Topic: Developing Biology) and Biology 354C may not both be counted. Prerequisite: Biology 349 with a grade of at least C-.

BIO𧉢L. Ichthyology.

Overview of the evolution, biology, and ecology of fishes, emphasizing freshwater fishes. Three lecture hours and three hours of laboratory or fieldwork a week for one semester, with field trips to be arranged. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧋇L. Vertebrate Natural History.

Phylogeny, taxonomy, life histories, habits, and distribution. Two lecture hours and three hours of laboratory or fieldwork a week for one semester, with field trips to be arranged. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧋈L. Limnology and Oceanography.

Same as Marine Sciences 440. An introduction to the study of the interactions between aquatic organisms and their environments. Two lecture hours and six laboratory hours a week for one semester. Prerequisite: Chemistry 302 or 302H and the following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉥. Evolutionary Ecology.

Principles of modern ecology, particularly as they relate to natural selection and evolutionary theory. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉧J. Behavioral Ecology.

Advanced topics in behavioral ecology, with detailed consideration of animal communication, altruism, sexual selection, plant-animal interactions. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-, and Biology 359K or 370 with a grade of at least C-.

BIO𧉧K. Principles of Animal Behavior.

An introduction to the study of animal behavior: descriptive analysis of behavior physiological basis of behavior development of behavior adaptive significance and evolution of behavior communication and social behavior. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉧R. Animal Sexuality.

The biology of sexuality, including genetics, morphology, physiology, and psychology of sex. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉨K. Immunology.

The basic concepts of humoral and cell-associated immune phenomena, including innate immunity, the molecular basis of T cell and B cell antigen recognition, hematopoiesis and the development of lymphocytes, cellular and humoral immune responses and the basics of immunodeficiency, autoimmunity, immunotherapy and vaccination. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧈄L. Immunology Laboratory.

Current techniques in experimental cellular and humoral immunology. One hour lecture and four laboratory hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C- Biology 206L, 208L, 226L, or Environmental Science 311 with a grade of at least C- and credit or registration for Biology 360K.

BIO𧉨M. Molecular Immunology.

An advanced immunology course with an emphasis on molecular models and medical relevance. Three lecture hours a week for one semester. Biology 337 (Topic: Molecular Immunology) and 360M may not both be counted. Prerequisite: Biology 325 or 325H with a grade of at least C-, and Biology 360K with a grade of at least B-.

BIO𧉩. Human Infectious Diseases.

Etiology, pathogenesis, diagnosis, and immunobiology of the major microbial diseases, with emphasis on their prevention. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H, and Biology 326M or 326R with a grade of at least C- in each.

BIO𧉩L. Clinical Bacteriology Laboratory.

Training in techniques required for independent work in diagnostic and epidemiological bacteriology. Two lecture hours and five laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C- in each: Biology 325 or 325H 226L and 326R or 326M.

BIO𧉩T. Comparative Animal Physiology.

Physiology of organ systems in animal phyla, with special emphasis on physiological adaptations of organisms to their environment. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧋏L. Plant Systematics.

Principles of plant classification, phylogeny, and diversity as exemplified by families and species of flowering plants found seasonally in Texas with an emphasis on the local flora. Two lecture hours and three laboratory hours a week for one semester, with additional field trips to be arranged. Biology 262 and 262L, and 463L may not both be counted. Prerequisite: The following with grades of at least C-: Biology 325 or 325H and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉬. Microbial Ecology.

Population, community, and ecosystem ecology of microbes and microbiomes. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉭S. Human Systems Physiology.

Overview of human physiology, including the cardiovascular, respiratory, and renal systems, with an emphasis on critical thinking, integration, and application. Additional subjects include membrane movement, osmolarity and tonicity, endocrinology, and neurophysiology. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 311C Biology 325 or 325H, and Chemistry 301 or 301H with a grade of at least C- in each and one of the following with a grade of at least C-: Mathematics 408C, 408K, 408N, 408R, or Statistics and Data Sciences 302.

BIO𧆥U. Human Systems Physiology Laboratory.

Offers hands-on experience in human physiology and encourages critical thinking via case study application. Explores the scientific method through the reading of scientific journal articles writing protocols for basic physiological experiments and collecting, analyzing, and presenting data. Three laboratory hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-, and credit or registration for Biology 365S.

BIO𧉮. Microbial Genetics.

Molecular biology of nucleic acids biosynthesis of macromolecules, transfer of genetic material from cell to cell, recombination, mutagenesis, and regulatory mechanisms. Three lecture hours a week for one semester. Biology 366 and 391S may not both be counted. Prerequisite: Biology 325 or 325H with a grade of at least C-, and Biology 326R with a grade of at least C-.

BIO𧉮R. Molecular Genetics and Medicine.

Implementation of molecular genetics techniques in medicine. Includes application of diagnostic and therapeutic techniques for several genetic disorders and infectious diseases. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉯C. Cellular and Molecular Bases of Neural Development.

An introduction to the principles by which the neural tube (brain and spinal cord) forms during embryonic development. Subjects include the cellular and molecular mechanisms underlying the formation of a three-dimensional neural tube and its division into forebrain, midbrain, hindbrain, and spinal cord. Three lecture hours a week for one semester. Biology 365N and Biology 367C may not both be counted. Prerequisite: One of the following with a grade of at least C-: Biology 325, Neuroscience 330, 365R.

BIO𧅄. Peer Assistant.

May be repeated for credit. Offered on the pass/fail basis only.

BIO𧉱F. Field Herpetology.

Species identification by sight and sound, and research techniques such as sampling populations, data collection, and analysis. One lecture hour and five laboratory hours a week for one semester, with additional field hours to be arranged. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉱L. Herpetology.

Biology of amphibians and reptiles, including evolution, ecology, behavior, physiology, life history, and identification. Three lecture hours and three laboratory hours a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉲. Evolution.

Introduction to modern evolutionary biology, focusing on the evolution of molecular, developmental, morphological, and behavioral traits. Genetic and ecological bases of evolutionary changes within populations and of evolutionary divergence in animals and plants. Three lecture hours and one discussion hour a week for one semester. Biology 370 and 385K (Topic 2: Evolution) may not both be counted. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧆪C, 270C, 370C, 470C. Conference Course.

Supervised study of selected topics in biology, by individual arrangement with the instructor. Conference course. May be repeated for credit when the topics vary. Prerequisite: Biology 325 or 325H with a grade of at least C- additional prerequisites vary with the topic.

BIO𧋗. Introduction to Systematics.

Study of diversification of living and fossil organisms, including speciation, biogeography, taxonomy, and phylogeny of genes, species, and higher taxa. The lecture and laboratory include a significant amount of computational molecular phylogenetics. Three lecture hours and three laboratory hours a week for one semester. Prerequisite: Biology 325 or 325H, and 370 with a grade of at least C-.

BIO𧋗G. Natural History Museum Science.

An introduction to curatorial practices in natural history museums. Three lecture hours and one discussion hour a week for one semester students also complete a twenty- to thirty-hour curatorial project. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉳L. Experimental Physiology.

Experimental approach to physiological mechanisms by which animals adapt to their environment. One lecture hour, four laboratory hours, and two hours of computer work a week for one semester. Prerequisite: The following with a grade of at least C-: Biology 325 or 325H, and Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉴C. Biology Peer Mentors in Research/Teaching.

Students work as peer mentors and assistants in the teaching of biology, with emphasis on developing instructional materials that teach fundamental biology with real world data. Students mentor students for at least three hours a week in addition to other weekly meetings. Biology 372C and Chemistry 372C may not both be counted. Prerequisite: Biology 311C, 311D, and 325, or Biology 315H and 325H, with a grade of at least B in each and consent of the undergraduate adviser.

BIO𧉵. Ecology.

An introduction to ecology, the study of relationships among organisms and between organisms and their environment adaptations, population, communities, and ecosystems. Includes both plants and animals and both terrestrial and aquatic ecosystems. Three lecture hours and one discussion hour a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉵L. Ecology Laboratory.

Intensive field ecology. Includes group field experiment and observation, independent projects, and field trips to other vegetation zones. Students complete weekly write-ups of observation and data analysis, reports of independent projects, and an oral presentation on an independent project. Four laboratory hours and two workshop/lecture hours a week for one semester. Prerequisite: Credit with a grade of at least C- or registration for Biology 373 and the following with a grade of at least C-: Biology 206L, 208L, 226L, or Environmental Science 311.

BIO𧉶. Plant Anatomy with Histological Techniques.

Tissue organization and cellular details of stems, roots, and leaves of seed plants, with emphasis on development and function. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-, and concurrent enrollment in Biology 174L.

BIO𧆮L. Laboratory in Plant Anatomy and Histological Techniques.

Demonstration of cellular details and tissue systems of plant organs instruction in the preparation of plant materials for histological examination. Three laboratory hours a week for one semester. Prerequisite: Credit with a grade of at least C- or registration for Biology 374 and the following with a grade of at least C-: 206L , 208L , 226L , or Environmental Sciences 311 .

BIO𧉷. Conservation Biology.

Application of principles of ecology to the preservation of wild plant and animal species and to the preservation, management, and restoration of natural and seminatural ecosystems. Emphasis on scientific, biological aspects of issues such as endangered species protection, preserve design, and forest management. Three lecture hours a week for one semester. Prerequisite: Biology 325 or 325H with a grade of at least C-, and Biology 357, 359J, or 373 with a grade of at least C-.

BIO𧆱, 277, 377. Undergraduate Research.

Laboratory or field research in the various fields of biological science under the supervision of one or more faculty members. Supervised individual research. Up to three semester hours may be counted toward the major requirement for the Bachelor of Arts degree with a major in biology. May be repeated for credit. Prerequisite: Biology 325 or 325H with a grade of at least C-, and written consent of instructor.

BIO𧋞L. Comparative Vertebrate Anatomy.

Study of vertebrate morphology from developmental anatomy to the function, biomechanics, and phylogenetic relationships of living and fossil taxa. Three lecture hours and four laboratory hours a week for one semester. Biology 478L and Kinesiology 324K, 424K may not both be counted. Prerequisite: Biology 325 or 325H with a grade of at least C-.

BIO𧉻H, 679H. Honors Tutorial Course.

Original laboratory or field research project under the direction of a faculty mentor, leading to a thesis or research presentation for students in the honors program in biology. The equivalent of three or six lecture hours a week for one semester. May be repeated for credit, but no more than six hours may be counted toward a degree in biology. Prerequisite: Consent of the student's research supervisor and the departmental honors adviser.

Graduate Courses

BIO𧉼C. Advanced Conservation Biology.

Application of principles and concepts of ecology to the preservation of wild plant and animal species and to the preservation, management, and restoration of natural and semi-natural ecosystems. Emphasis on biological aspects of issues such as endangered species protection, invasive species, preserve design, and forest management, via a set of case studies. Three lecture hours a week for one semester. Biology 380C and 384K (Topic: Advanced Topics in Conservation Biology) may not both be counted. Prerequisite: Graduate standing.

BIO𧉼E. Advanced Microbial Ecology.

Examines microbial population, community, and ecosystem ecology. Three lecture hours a week for one semester. Only one of the following may be counted: Biology 380E, 384K (Topic 22), and 384K (Topic: Advanced Topics in Microbial Ecology). Prerequisite: Graduate standing.

BIO𧉼F. Biology of Birds.

Anatomy, physiology, classification, and ecology of birds. Three lecture and two laboratory hours a week for one semester. Includes optional weekly, half-day field trips and two optional full-weekend trips. Biology 384K (Topic: Biology of Birds) and 380F may not both be counted.

BIO𧉼G. Methods in Ecological Genomics.

Explores state-of-the-art methodologies for: genomics-based demographic and population structure analysis detection of genomic signatures of natural selection analyzing gene expression in the ecology, evolution, and behavior context quantification of complex communities using metabarcoding. Three lecture hours a week for one semester. Biology 380G and 384K (Topic: Methods in Ecological Genomics) may not both be counted. Prerequisite: Graduate standing.

BIO𧉼L. Advanced Systematics.

Explores biodiversity, phylogeny, species concepts, historical biogeography, phylogeography, molecular clocks, phylogenomics, comparative methods, fossils, morphometrics, taxonomy, ontogeny, homology, computational methods, and phylogenetic statistics. Three lecture hours and three laboratory hours a week for one semester. Biology 384K (Topic 14) and 380L may not both be counted. Prerequisite: Graduate standing.

BIO𧉼M. Topics in Biology (Cooperative Programs).

Formal, organized courses taught at institutions other than the University of Texas at Austin. Three lecture hours a week for one semester. Not all topics are offered every year. May be repeated for credit when the topics vary. Prerequisite: Graduate standing, consent of the student's graduate adviser or department chair and the University's graduate dean, and consent of the graduate dean at the host institution additional prerequisites vary with the topic.

BIO𧉼P. Population Genetics.

Introduces students to population genetics. The emphasis is on a quantitative understanding of evolutionary change caused by selection, drift, mutation, and migration. Both phenotypic and molecular evolution will be covered. Three lecture hours a week for one semester. Biology 380P and 385K (Topic 4) may not both be counted.

BIO𧆴R, 280R, 380R. Advanced Readings in the Biological Sciences.

For each semester hour of credit earned, the equivalent of one class hour a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧉼S. Animal Sexuality.

Examines how hormones shape the development of the body, regulate physiological processes, and influence how individuals behave. Three lecture hours a week for one semester. Meets requirements for non-seminar graduate courses in the Ecology, Evolution, and Behavior Graduate Program. Only one of the following may be counted: Biology 380S, 383K (Topic: Animal Sexuality), 383K (Topic: Studies in Animal Sexuality). Prerequisite: Graduate standing.

BIO𧉼T. Current Concepts in Biology.

Designed for beginning graduate students seeking a review of modern biological concepts. Three lecture hours a week for one semester. With consent of instructor, may be repeated for credit when the topics vary. Prerequisite: Graduate standing in the School of Biological Sciences, and consent of instructor and the graduate adviser.

BIO𧉼U. Brain, Behavior, and Evolution.

Same as Neuroscience 380U. Integrative approaches to the study of brain and behavior within an evolutionary and comparative framework. Specifically, the integration of neuroscience, organismal behavior and physiology, behavioral ecology, evolutionary development, experimental evolution, molecular biology, genetics, genomics, systems biology, and bioinformatics. Three lecture hours a week for one semester. Only one of the following may be counted: Biology 380U, 384K (Topic: Brain, Behavior, and Evolution), Neuroscience 380U, 385L (Topic: Brain, Behavior, and Evolution). Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧉼V. Biological Foundations of Decision Making.

Same as Neuroscience 380V. Explores the mechanisms biological organisms use to make decisions and how these mechanisms evolved. Defines a conceptual framework for decision making that can be applied across levels of biological organization. Surveys current research on how animals make decisions using genetic, neurobiological, and evolutionary approaches. Three lecture hours a week for one semester. Only one of the following may be counted: Biology 380V, 384K (Topic: Biological Foundations of Decision Making), Neuroscience 380V, 385L (Topic: Biological Foundations of Decision Making). Prerequisite: Graduate standing.

BIO𧉽. Advanced Plant Physiology.

Concepts in the broad field of plant physiology. Includes aspects of plant growth, development, cell signaling, and stress responses that are very similar to these processes in animals, but will also illustrate unique aspects of plants that exemplify the diversity of life strategies on earth. Explores the critical skills needed to evaluate the current literature, data interpretation, and methods for solving key questions in the field. Three lecture hours a week for one semester. Only one of the following may be counted: Biology 381, 389 (Topic: Advanced Plant Physiology), and 389 (Topic 12). Prerequisite: Graduate standing.

BIO𧉽K. Ecology, Evolution, and Behavior: Physiology and Biophysics.

Lectures, conference discussion, and laboratory projects, depending on topic. Not all topics are offered every year. May be repeated for credit when the topics vary. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser additional prerequisites vary with the topic.

Topic 1: Topics in Biophysics. Irritability of living systems and the principles of energy transformation and transfer in organisms emphasis on bioelectrical processes and electrical energy changes. Three lecture hours a week for one semester.
Topic 2: Comparative Neurophysiology. General treatment of the physiology of neurons, synapses, sensory and motor systems neural basis of behavior emphasis on invertebrates. Three lecture hours a week for one semester.
Topic 3: Sensory Physiology. Physiology and biophysics of the transduction and peripheral processes of the major sensory systems. Three lecture hours a week for one semester.
Topic 4: Current Concepts in Neurobiology. A series of seminars designed to give students a broad background in neurobiology. Three lecture hours a week for one semester.
Topic 5: Laboratory in Neurophysiology. Training in research techniques useful for the neurophysiological study of vertebrate and invertebrate nervous systems. Three lecture hours a week for one semester.
Topic 6: Insect Physiology. An in-depth study of the physiology of insect organ systems, development, and behavior. Three lecture hours a week for one semester.
Topic 7: Developmental Neurobiology. Neuronal cell lineage and differentiation, neuronal migration, axon guidance, neural cell death, synapse formation and maintenance. Three lecture hours a week for one semester.
Topic 8: Addiction Biology. Three lecture hours a week for one semester. Biology 381K (Topic 8) and Neuroscience 385L (Topic 3: Addiction Biology) may not both be counted.
Topic 11: Current Concepts in Neurophysiology. Three lecture hours a week for one semester.

BIO𧉽N. Basic Processes of Nerve Cells.

Same as Neuroscience 381N. Degeneration and regeneration in nervous systems following traumatic injury invertebrate versus vertebrate, peripheral nervous system versus central nervous system, axonal versus cell body, role of glia versus neurons. Three lecture hours a week for one semester. Only one of the following may be counted: Biology 381K (Topic 10), 381N, Neuroscience 381N, 385L (Topic 1). Prerequisite: Graduate standing.

BIO𧉽P. Advanced Plant Physiology.

General principles of mineral nutrition, water relations, metabolic activities, growth and development of green plants. Biology 381P and 389 (Topic 12) may not both be counted.

BIO𧆶, 282, 382, 682, 982. Advanced Study and Research.

For each semester hour of credit earned, the equivalent of one class hour a week for one semester. May be repeated for credit. Prerequisite: Graduate standing and consent of instructor and the graduate adviser.

BIO𧉾E. Epigenetics.

Same as Neuroscience 382E. Study of how epigenetic modifications are covalent modifications of DNA or histones that cause changes in gene expression and how epigenetic modifications appear to be a method through which nurture or the environment can influence nature. Emphasis on how experience or environmental factors epigenetically modify health or behavior of animals. Three lecture hours a week for one semester. Only one of the following may be counted: Biology 381K (Topic: Epigenetics), 382E, Neuroscience 382E. Offered on the letter-grade basis only. Prerequisite: Graduate standing and consent of instructor.

BIO𧉾K. Computational and Statistical Biology.

Three lecture hours a week for one semester. May be repeated for credit when the topics vary.

Topic 1: Recent Advances in Computational Biology. Discussion of current scientific papers, methods, and ideas in computational biology and bioinformatics.
Topic 2: Network Modeling in Biology.
Topic 3: Modeling Infectious Disease Dynamics.
Topic 4: Current Subjects in Biological Statistics. Emphasis on the practical aspects of data management and analysis, including programming in R and related tools. Subjects may include general linear models, multivariate statistics, Bayesian statistics, model selection, and graphical presentation of data. The equivalent of three lecture hours a week for one semester. Additional prerequisite: At least one prior course in probability or statistics, at the undergraduate level or above.
Topic 5: Informatics and Data Analysis in Life Sciences. Introduction to concepts and methods of data-driven life science. Three lecture hours a week for one semester.
Topic 6: Programming for Biology. Explores programming skills that are relevant to research in the biological sciences, including but not limited to programming in Python, R, Perl, C++. Three lecture hours a week for one semester.
Topic 7: Ecological Theory and Modeling. Explores concepts and methods of modeling ecological systems including populations, communities and ecosystems. Focus on the methodology and utility of ecological theory and modeling. Examines the basic techniques and classic insights derived from differential equation, statistical, and individual based models. The ability to interpret and evaluate models in the literature will be emphasized.
Topic 8: Introduction to Biology for Data Science. Explore biological concepts and methods (including its assumptions and limitations), particularly in the areas of systems biology, medical and evolutionary genomics, and neuroscience. Focus on approaches that produce a lot of data but are analysis-challenged. Biology 382K (Topic: Intro to Bio for Data Science) and 382K (Topic 8) may not both be counted.

BIO𧉿K. Ecology, Evolution, and Behavior: Development and Reproduction.

Three lecture hours a week for one semester, or as required by the topic. Not all topics are offered every year. May be repeated for credit when the topics vary. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

Topic 1: Hormonal Control of Development and Reproduction. Three lecture hours a week for one semester.
Topic 2: Techniques in the Study of Development and Reproduction. Eight laboratory hours a week for one semester.
Topic 3: Comparative Endocrinology. Structure, function, and interrelationships of endocrine glands, with emphasis on the control of hormone synthesis and secretion and mechanisms of hormone action. Three lecture hours a week for one semester.
Topic 4: Recent Advances in Development and Reproduction. Discussion of recent scientific papers and their contribution to modern work in development and reproduction. Three lecture hours a week for one semester.
Topic 5: Molecular Analysis of Development. Lectures and discussion concerning the principles of animal development at the molecular level. Three lecture hours a week for one semester.
Topic 8: Development and Evolution. Three lecture hours a week for one semester.
Topic 9: Survey of Animal Development. Three lecture hours a week for one semester.

BIO𧊀C. Subjects and Skills in Ecology, Evolution, and Behavior I.

Designed for first-year graduate students in ecology, evolution, and behavior. Study of why animals behave the ways they do. Study of the proximate and ultimate issues of animal behavior, how it is acquired and regulated, and how it evolved. Emphasis on integration of proximate and ultimate analyses in the various domains in which animals behave. First part of a two-semester sequence. Three lecture hours and one discussion hour a week for one semester. Biology 384C and 389D may not both be counted. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊀D. Subjects and Skills in Ecology, Evolution, and Behavior II.

Designed for first-year graduate students in ecology, evolution, and behavior. Continuation of the study of why animals behave the way they do. Continued overview of both the proximate and ultimate issues of animal behavior, how it is acquired and regulated, and how it evolved. Emphasis on integration of proximate and ultimate analyses in the various domains in which animals behave. Second part of a two-semester sequence. Three lecture hours and one discussion hour a week for one semester. Biology 384D and 389E may not both be counted. Prerequisite: Graduate standing, Biology 384C, and consent of instructor and the graduate adviser.

BIO𧊀K. Ecology, Evolution, and Behavior.

Basic concepts and methods of laboratory and field analysis in various fields of biology systematics and ecology of natural populations. Lectures, conference discussions, and laboratory work, depending on topic. May be repeated for credit when the topics vary. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser additional prerequisites vary with the topic.

Topic 29: Recent Advances in Population Ecology. Seminar course some written assignments required. Faculty- and student-led discussions of current subjects in population ecology. Three lecture hours a week for one semester. Additional prerequisite: Undergraduate upper-division ecology course (Biology 373 or similar course).
Topic 30: Recent Advances in Community Ecology. Seminar course. Faculty- and student-led lectures and discussions of current topics in community ecology. Some written assignments required. Three lecture hours a week for one semester. Additional prerequisite: Undergraduate upper-division ecology course (Biology 373 or similar course) required.
Topic 31: Recent Advances in Ecosystem Ecology. Seminar course. Faculty- and student-led lectures and discussions of current topics in ecosystem ecology. Some written assignments required. Three lecture hours a week for one semester. Additional prerequisite: Undergraduate upper-division ecology course (Biology 373 or similar course).
Topic 32: Recent Advances in Macroecology. Examines recent ideas and new findings in the fields of Macroecology, Biogeography, and Ecosystem Science. Three lecture hours a week for one semester.
Topic 33: Recent Advances in Conservation Biology. Seminar course. Faculty- and student-led discussions of current topics in population ecology. Some written assignments may be required. Three lecture hours a week for one semester. Additional prerequisite: Undergraduate upper-division ecology course (Biology 373 or similar course) undergraduate upper-division evolution course recommended.
Topic 34: Recent Advances in Microbial Ecology. Explores current subjects and controversies in microbial ecology, including community and ecosystem perspectives. Includes faculty- and student-led discussions of primary literature. Some written assignments required. Three lecture hours a week for one semester.
Topic 35: Global Environmental Change. Explores the knowledge of current environmental change and biological responses, efforts to understand and predict changes in the future through both experimental manipulations and models. Discussion of the scientific philosophy behind this work. Three lecture hours a week for one semester. Additional prerequisite: Undergraduate upper-division ecology course (Biology 373 or similar course) undergraduate upper-division evolution course recommended.
Topic 36: Recent Advances in Evolution. Examines recent and classic research and primary literature concerning general subjects within evolutionary biology. Three lecture hours a week for one semester. Additional prerequisite: Undergraduate upper-division evolution course (Biology 370 or similar course).
Topic 37: Recent Advances in Coevolution. Examines current and classic literature related to the coevolution of interacting species, including but not limited to host-parasite interactions, and mutualistic interactions. Three lecture hours a week for one semester.
Topic 38: Recent Advances in Ecological and Evolutionary Genetics. Discussion and analysis of current and classic literature related to ecological and evolutionary genetics. Three lecture hours a week for one semester.
Topic 39: Phylogenetic Perspectives in Ecology, Evolution, and Behavior. Theory, methods, and applications of phylogenetics in ecology, evolution, and behavior. The development of phylogenetics the various phylogenetic optimality criteria and their advantages and disadvantages (include non-parametric, semi-parametric, and parametric methods) models of evolution for molecular and morphological data algorithms and heuristics for searching solution space, including discussion of Bayesian Markov chain Monte Carlo approaches phylogenetic simulation statistical assessment of phylogenetic results molecular clocks and major applications of phylogenetics. Three lecture hours a week for one semester.
Topic 40: Recent Advances in Biogeography and Phylogeography. Reviews concepts and recent literature in Biogeography, Phylogeography, or Macroecology. Three lecture hours a week for one semester.
Topic 41: Recent Advances in Molecular and Genomic Evolution. Three lecture hours a week for one semester. Additional prerequisite: Undergraduate upper-division evolution course (Biology 370 or similar course).
Topic 42: Human and Primate Evolutionary Genetics. Three lecture hours a week for one semester. Anthropology 388 (Topic: Human/Primate Evolut Genetics) and Biology 384K (Topic 42) may not both be counted.
Topic 43: Ancient and Environmental DNA. Explores the prospects and challenges of ancient/environmental DNA research, and considers the applications in evolutionary biology, paleontology, and anthropology. Three lecture hours a week for one semester. Only one of the following may be counted: Anthropology 388 (Topic: Ancient DNA) Biology 384K (Topic: Ancient DNA), 384K (Topic 43).
Topic 44: Recent Advances in Behavior. Explores recent and classic research and primary literature concerning general topics within behavioral ecology, and the evolution of behavior. Three lecture hours a week for one semester.
Topic 45: Seminars in Brain Behavior and Evolution. Explores how to give a seminar and/or writing a grant proposal. Preparation for job talks, paper presentations, or writing grants.

BIO𧊀L. Issues in Population Biology.

Analysis at an advanced level of currently active areas of research in population biology. Three lecture hours a week for one semester. Offered on the credit/no credit basis only. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊂. Topics in Plant Science: Ecology and Evolution.

Three lecture hours a week for one semester. May be repeated for credit when the topics vary. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser additional prerequisites vary with the topic.

Topic 10: Recent Advances in Plant Systematics. Basic concepts and methods of laboratory and field analysis in various fields of biology systematics and ecology of natural populations.
Topic 11: Advanced Subjects in Plant Ecology.
Topic 12: Advanced Subjects in Plant Evolution.
Topic 13: Advanced Subjects in Plant Molecular Biology.

BIO𧊂K. Plant Sciences.

Three lecture hours a week for one semester. May be repeated for credit when the topics vary. Prerequisite: Graduate standing.

Topic 1: Advanced Subjects in Plant Ecology. Seminar course with faculty- and student-led lectures and discussions of current subjects in plant ecology. Additional prerequisite: Undergraduate upper-division ecology course (Biology 373 or similar course).
Topic 2: Advanced Subjects in Plant Evolution. Seminar course with faculty- and student-led lectures and discussions of current subjects in plant evolution. Additional prerequisite: Undergraduate upper-division evolution course (Biology 370 or similar course).
Topic 3: Advanced Subjects in Plant Systematics.
Topic 4: Advanced Subjects in Plant Molecular Biology. Seminar course with faculty- and student-led lectures and discussions of current subjects in plant molecular biology. Additional prerequisite: Undergraduate upper-division ecology course (Biology 373 or similar course).

BIO𧊂P. Foundations of Plant Biology.

Restricted to students in the plant biology graduate program. Study of foundational ideas across the breadth of plant biology. Three lecture hours a week for one semester. Offered on the credit/no credit basis only. Prerequisite: Graduate standing, and consent of the instructor and the graduate adviser.

BIO𧈟F. Plant Systematics.

Principles of plant taxonomy, as exemplified by families of flowering plants found seasonally around Austin. Two lecture hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧋧G. Taxonomic Plant Anatomy.

An advanced course that emphasizes those aspects of plant anatomy that are most reliable and useful for systematic purposes. Three lecture hours and two laboratory hours a week for one semester. Biology 472L and 487G may not both be counted. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊃J. Advanced Plant Anatomy.

Plant anatomy in relation to development and differentiation, systematics, and evolution. Three lecture hours a week for one semester. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and concurrent enrollment in Biology 187L.

BIO𧊃K. Plant Evolution.

The properties of plant populations, considered from genetic and ecological perspectives mechanisms of evolution within and among populations. Three lecture hours a week for one semester. May be repeated for credit. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧆻L. Laboratory in Advanced Plant Anatomy.

Demonstration of cellular details and tissue systems of plant organs, and instruction on the preparation of plant materials for histological examination. Three laboratory hours a week for one semester. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and concurrent enrollment in Biology 387J.

BIO𧊃M. Reproductive Biology of Flowering Plants.

Pollination biology, breeding systems, and fruit and seed dispersal from evolutionary and ecological vantage points. Three lecture hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊃N. Plant Ecology.

Advanced topics in plant ecology, including evaluation of ecological concepts, aspects of experimental ecology, and the principles of plant distribution. Three lecture hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧆻P. Plant Ecology Laboratory.

Demonstrations and experiments stressing plant ecological principles, including laboratory and field exercises. Three laboratory hours a week for one semester. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and credit or registration for Biology 387N.

BIO𧊃R. Population Ecology of Plants.

A combination of lectures and student-led discussions covering major concepts and current literature in plant population ecology. Three lecture hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊃S. Laboratory Methods in Molecular Ecology and Systematics.

An introduction to DNA methods in the study of molecular ecology, systematics, and evolution: DNA isolation and purification DNA quantification polymerase chain reaction restriction fragment length polymorphism random amplified polymorphic DNA amplified fragment length polymorphism cloning simple sequence repeat (microsatellite) marker development DNA sequencing automated sequencing automated genotyping phylogenetic and population genetic analyses. Seven laboratory hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧈟T. Angiosperm Diversity Laboratory.

Practical experience in recognizing, identifying, and classifying families of flowering plants. Four laboratory hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊄C. Transmembrane Signaling Mechanisms.

Mechanisms by which hormones, light, and other stimuli trigger changes in plant and animal cell metabolism. Three lecture hours a week for one semester. Biology 343M and 388C may not both be counted. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊄D. Research Topics in Plant Biology.

An introduction to various fields of plant biology. Students attend seminars, faculty research presentations, and other meetings. Three lecture hours a week for one semester, with additional meeting times to be arranged. Prerequisite: Graduate standing in the School of Biological Sciences.

BIO𧊄E. Plant Growth and Development.

Emphasis on whole plant physiology, especially growth and development, water relations, and mineral nutrition of vascular plants. Three lecture hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊄J. General Phycology.

Survey of the algae, including significant biological aspects of selected genera, research techniques, and readings in the literature. Three lecture hours a week for one semester. Biology 327 and 388J may not both be counted. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and concurrent enrollment in Biology 188K.

BIO𧆼K. Laboratory in General Phycology.

Survey of various algal groups, including direct observations of their biology, exposure to research techniques, and instruction in cultural procedures. Three laboratory hours a week for one semester. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and concurrent enrollment in Biology 388J.

BIO𧊄L. Laboratory Studies in Cell Biology: Plant Biology.

Research exercises involving light microscopy, including polarization, phase contrast, Nomarski interference, dark field, fluorescence, and bright-field optics. High-resolution transmission electron microscopy. Hands-on experience with atomic and molecular imaging, including digital image processing and time-lapse video microscopy. One lecture hour and four laboratory hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊄M. Plant Molecular Biology.

Fundamentals of plant molecular biology, including structure and expression of the chloroplast and mitochondrial genomes. Three lecture hours a week for one semester. Biology 350M and 388M may not both be counted. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊅C. Chemistry and Biology of Membranes.

Consideration of the origin and structure of biological membranes at the microscopic and molecular levels describes membrane function, especially with regard to transport properties. Three lecture hours a week for one semester. Prerequisite: Graduate standing and consent of instructor and the graduate adviser.

BIO𧊅D. Subjects and Skills for Graduate Students in the Biological Sciences.

Designed for first-year graduate students in ecology, evolution, and behavior. Provides training in many of the skills required of research scientists. Introduction to the writing, presentation and appraisal skills needed to excel in all fields of biological research. Three lecture hours a week for one semester. Biology 384C and 389D may not both be counted. Prerequisite: Graduate standing, and consent of instructor and graduate adviser.

BIO𧊅E. Subjects and Skills for Graduate Students in the Biological Sciences II.

Explores the general subjects and skills required of research scientists, with an emphasis on the research, teaching, and service skills needed by professional biologists, as well as on the major research themes and questions in ecology, evolution, and behavior. Builds on the writing skills developed in Biology 389D to include issues of ethical behavior in research, effective presentation of results, oral presentation skills, interacting with the media, work-life balance, and public outreach. Three lecture hours a week for one semester. Biology 384D and 389E may not both be counted. Prerequisite: Graduate standing, Biology 389D, and consent of instructor and graduate adviser.

BIO𧊅K. Advanced Cell Biology.

Three lecture hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊆C. Fundamentals of Evolution.

Introduction to major principles and questions in evolutionary biology. Subjects include population genetics, genetic diversity, adaptation, origin of species, phylogenetics, molecular evolution, and macroevolution. Emphasis on identifying open questions, analysis and interpretation of data, and gaining familiarity with the primary scientific literature. Three lecture hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊆D. Fundamentals of Integrative Animal Behavior.

Introduction to major principles and questions in animal behavior with emphasis on why animals behave the way they do. Study of both the proximate and ultimate issues of animal behavior, how it is acquired and regulated, and how it evolved. Emphasis on integration of proximate and ultimate analyses in the various domains in which animals behave. Three lecture hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊆E. Fundamentals of Ecology.

Fundamentals of ecology, ranging from organism physiology to population, species, community, and ecosystem-level processes across landscapes and biomes. Three lecture hours a week for one semester. Prerequisite: Graduate standing and consent of instructor.

BIO𧑺G. Applied Public Health and Medical Microbiology.

One semester (or one summer session) of full-time training in the Texas Department of Health Laboratories, with rotation in the divisions of medical microbiology, mycology, parasitology, virology, sanitary bacteriology, and biologics. Assigned reading and regular meetings with the Department of Health Laboratories staff and the molecular genetics and microbiology faculty. Forty hours of supervised fieldwork a week for one semester. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and courses in immunology, public health bacteriology, and virology.

BIO𧈢K. Scanning Electron Microscopy, Theory and Practice.

Theory of scanning electron microscopy and basic principles of instrument design basic procedures in specimen preparation hands-on experience. Two lecture hours and six laboratory hours a week for six weeks. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧋪M. Electron Microscopy I: Theory and Practice.

An introduction to electron optics emphasis on basic operation and maintenance of the transmission microscope theory and practice of basic preparative techniques. Two lecture hours and six laboratory hours a week for one semester. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊆P. Techniques in Molecular Genetics.

Laboratory training in modern molecular genetics, with emphasis on the manipulation of bacterial plasmid DNA as a model system. DNA purification, gene mapping and cloning, site-directed mutagenesis, polymerase chain reaction, and DNA sequencing. One lecture hour and seven laboratory hours a week for one semester. Biology 368L and 390P may not both be counted. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and Biology 366.

BIO𧊇. Grant Writing and Presentation Skills.

Restricted to second-year graduate students in the microbiology and cell and microbiology programs. Preparation of a detailed proposal of the dissertation research goals of each student with a presentation in the form of a short talk. Emphasis on critical evaluation of research aims, methodology, and communication skills. Designed for second-year doctoral students in biology. Three lecture hours a week for one semester. Biology 391 and 394 (Topic: Grant Writing and Presentation Skills) may not both be counted. Offered on the letter-grade basis only. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser.

BIO𧊇K. Cellular Immunology.

Cell-associated immune responses, with emphasis on transplantation, immunity, tumor immunology, delayed hypersensitivity, and acquired cellular resistance. Three lecture hours a week for one semester. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and Biology 360K and 260L.

BIO𧊇P. Advanced Virology.

Replication of and transformation by DNA and RNA animal viruses. Three lecture hours a week for one semester. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and Biology 330.

BIO𧊇R. Advanced Metabolism and Biochemistry of Microorganisms.

Study of the metabolic processes of microorganisms, using a biochemical approach. Three lecture hours a week for one semester. Biology 339 and 391R may not both be counted. Prerequisite: Graduate standing and consent of instructor and the graduate adviser.

BIO𧊇S. Microbial Genetics.

Molecular biology of nucleic acids biosynthesis of macromolecules, transfer of genetic material from cell to cell, recombination, mutagenesis, and regulatory mechanisms. Three lecture hours a week for one semester. Biology 366 and 391S may not both be counted. Prerequisite: Graduate standing and consent of instructor and the graduate adviser.

BIO𧊈. Problems in Host-Parasite Biology.

Three lecture hours a week for one semester. May be repeated for credit when the topics vary. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser additional prerequisites vary with the topic.

Topic 1: Current Topics in Virology and Immunology.
Topic 2: Current Topics in Pathogenic Mechanisms.

BIO𧊈D. DNA Repair.

Broad overview of the repair of DNA in archae, prokaryotes, eukaryotes, and viruses, focusing on the primary research literature, and developing critical thinking and presentation skills. Three lecture hours a week for one semester. Biology 392D and Biology 393 (Topic: DNA Repair) may not both be counted. Prerequisite: Graduate standing.

BIO𧊉. Problems in Molecular Genetics.

Three lecture hours a week for one semester. May be repeated for credit when the topics vary. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser additional prerequisites vary with the topic.

Topic 1: Current Topics in DNA Transactions.
Topic 2: Current Topics in Fungal and Cell Molecular Biology.
Topic 3: Current Topics in Gene Regulation.

BIO𧊊. Problems in Microbial Physiology.

Three lecture hours a week for one semester. May be repeated for credit when the topics vary. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser additional prerequisites vary with the topic.

Topic 1: Current Topics in Cell Envelope Structure and Functions.
Topic 2: Current Topics in Microbial Signal Transduction.

BIO𧊊L. Immunology.

Introduction to the immune system for graduate students without prior coursework in immunology. Discuss innate immunity, the molecular basis of T cell and B cell antigen recognition, hematopoiesis and the development of lymphocytes, and cellular and humoral immune responses. Touch on immunodeficiency, autoimmunity, immunotherapy and vaccination. Explore current primary literature on select immunological topics in greater depth. Three lecture hours a week for one semester. Biology 394L and 394M (Topic 1) may not both be counted. Prerequisite: Graduate standing, consent of instructor, and consent of the graduate adviser.

BIO𧊊M. Advanced Studies in Microbiology.

In-depth study of microbiology topics. Students read original research papers in addition to text assignments. Three lecture hours a week for one semester. May be repeated for credit when the topics vary. Prerequisite: Graduate standing, and consent of instructor and the graduate adviser additional prerequisites vary with the topic.

Topic 2: Advanced Microbial Signal Transduction. Studies in molecular and cellular biology of a wide variety of signal transduction systems in diverse microorganisms the role of signal transduction across biological membranes in allowing cells to recognize and respond to their environment.
Topic 3: Advanced Medical Mycology. Studies in medical mycology and an overview of research involving both the fungal zoopathogen and its host.
Topic 4: Advanced Fungal Cell and Molecular Biology. Studies of the structure, function, and biological activities of fungi, with emphasis on recent advances in research.

BIO𧊊T. Tumor Biology.

Explore core aspects of cancer pathology, treatment, epidemiology, the discovery of oncogenes and tumor suppressors, and the molecular genetics underlying the characteristic features of malignant tumors (including metastatic behavior, genomic instability, angiogenesis, cell cycle regulation, and apoptosis). Emphasize the biochemical functions of cancer-related proteins and enzymes and therapeutic approaches based on understanding of these proteins. Examine important experimental approaches that have influenced the current understanding of cancer. Three lecture hours a week for one semester. Biology 384M (Topic: Tumor Biology) and 394T may not both be counted. Prerequisite: Graduate standing consent of instructor and the graduate adviser

BIO𧊋F. Genetics.

Same as Chemistry 395F and Molecular Biology 395F. Basic principles of Mendelian and molecular genetics, and an exploration of the genetic toolbox using examples of analytic methods and modern genetic manipulations. Focus on the genetic analysis of model organisms. Use of genetic tools in dissecting complex biological pathways, developmental processes, and regulatory systems. Three lecture hours a week for one semester. Prerequisite: Graduate standing. An introductory course in genetics, such as Biology 325, is strongly recommended.

BIO𧊋G. Structure and Function of Proteins and Membranes.

Same as Biochemistry 395G and Molecular Biology 395G. Detailed consideration of the structure and function of proteins, with discussion of enzyme mechanisms and kinetics, the biochemistry of energy production, and the metabolism of lipids and nucleotides. Three lecture hours a week for one semester. Only one of the following may be counted: Biochemistry 395G, Biology 395G, Molecular Biology 395G. Prerequisite: Graduate standing a one-year undergraduate sequence in biochemistry is strongly recommended.

BIO𧊋H. Cell Biology.

Same as Chemistry 395H and Molecular Biology 395H. Detailed consideration of mechanisms of growth control, cell cycle regulation, mitosis, cell signaling, protein targeting, and the integration of these processes. Three lecture hours a week for one semester. Prerequisite: Graduate standing and consent of instructor or Biology 395F and 395G, Chemistry 395F, Molecular Biology 395F and 395G.

BIO𧊋J. Genes, Genomes, and Gene Expression.

Same as Biochemistry 395J and Molecular Biology 395J. Detailed consideration of prokaryotic and eukaryotic mechanisms of DNA replication and transcription posttranscriptional processing of transcription products and mechanism and regulation of the translation of messenger RNAs. Three lecture hours a week for one semester. Only one of the following may be counted: Biochemistry 395J, Biology 395J, Molecular Biology 395J. Prerequisite: Graduate standing and Biology 395F and 395G, or Chemistry 395F and 395G, or Molecular Biology 395F and 395G, or consent of instructor.

BIO𧊋L. Laboratory Studies in Molecular Biology.

Explore modern molecular biology with a research project focus in a laboratory setting. Use methods such as eukaryotic RNA purification, quantitative PCR, CRISPR or site-directed mutagenesis cloning, cell fractionation, protein purification and Western blotting detection toward experimental goals. One lecture hour and six laboratory hours a week for one semester. Biology 395 and 395L may not both be counted.

BIO𧊋M. Advanced Microbiology.

Restricted to microbiology students. Prokaryotic and lower eukaryote genome organization control of gene/operon/regulon expression chromosome replication and its control signal transduction protein trafficking organelle assembly the cell cycle and its control developmental processes cell to cell communication and DNA polymorphisms and adaption. Three lecture hours a week for one semester. Prerequisite: Graduate standing and consent of instructor and the graduate adviser.

BIO𧊌. Membranes and Walls of Bacteria.

Structure, biosynthesis, and function of bacterial envelopes and walls, including associated optional components. Three lecture hours a week for one semester. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and a course in general microbiology and a course in general biochemistry.

BIO𧊌R. Microbiology Research Seminar.

Students present their research findings and receive feedback from faculty and peers. Designed to help students refine their presentation techniques, practice giving critical feedback, and gain familiarity with a wide variety of research topics. Three lecture hours a week for one semester. Prerequisite: Graduate standing.

BIO𧇅. Seminar in Microbiology.

One lecture hour a week for one semester. Required of all molecular genetics and microbiology majors. May be repeated for credit. Offered on the credit/no credit basis only. Prerequisite: Graduate standing and consent of instructor and the graduate adviser.

BIO𧊍J. Advanced Genetics.

Intended mainly for first- and second-year graduate students. Selected related topics of current interest with an emphasis on molecular developmental genetics, and any needed review of classical genetics. Designed to help the student to read the literature critically, deliver a good seminar, and participate in thoughtful discussion. Three lecture hours a week for one semester. May not be counted toward the doctoral degree in microbiology. Prerequisite: Graduate standing, consent of instructor and the graduate adviser, and a course in genetics.

BIO𧎺. Thesis.

The equivalent of three lecture hours a week for two semesters. Offered on the credit/no credit basis only. Prerequisite: For 698A , graduate standing in the School of Biological Sciences and consent of the graduate adviser for 698B , Biology 698A or the equivalent.

BIO𧊎R. Master's Report.

Preparation of a report to fulfill the requirement for the master's degree under the report option. The equivalent of three lecture hours a week for one semester. Offered on the credit/no credit basis only. Prerequisite: Graduate standing in the School of Biological Sciences and consent of the graduate adviser.

BIO𧊎T. Supervised Teaching in Biological Sciences.

Teaching under the close supervision of course instructors weekly group meetings with the instructor, individual consultations, and reports throughout the teaching period. The equivalent of three lecture hours a week for one semester. Prerequisite: Graduate standing and appointment as a teaching assistant.

BIO𧊏W, 699W, 999W. Dissertation.

May be repeated for credit. Offered on the credit/no credit basis only. Prerequisite: Admission to candidacy for the doctoral degree.


Contents

PCR amplifies a specific region of a DNA strand (the DNA target). Most PCR methods amplify DNA fragments of between 0.1 and 10 kilo base pairs (kbp) in length, although some techniques allow for amplification of fragments up to 40 kbp. [5] The amount of amplified product is determined by the available substrates in the reaction, which becomes limiting as the reaction progresses. [6]

A basic PCR set-up requires several components and reagents, [7] including:

  • a DNA template that contains the DNA target region to amplify
  • a DNA polymerase an enzyme that polymerizes new DNA strands heat-resistant Taq polymerase is especially common, [8] as it is more likely to remain intact during the high-temperature DNA denaturation process
  • two DNA primers that are complementary to the 3′ (three prime) ends of each of the sense and anti-sense strands of the DNA target (DNA polymerase can only bind to and elongate from a double-stranded region of DNA without primers, there is no double-stranded initiation site at which the polymerase can bind) [9] specific primers that are complementary to the DNA target region are selected beforehand, and are often custom-made in a laboratory or purchased from commercial biochemical suppliers
  • deoxynucleoside triphosphates, or dNTPs (sometimes called "deoxynucleotide triphosphates" nucleotides containing triphosphate groups), the building blocks from which the DNA polymerase synthesizes a new DNA strand
  • a buffer solution providing a suitable chemical environment for optimum activity and stability of the DNA polymerase
  • bivalentcations, typically magnesium (Mg) or manganese (Mn) ions Mg 2+ is the most common, but Mn 2+ can be used for PCR-mediated DNA mutagenesis, as a higher Mn 2+ concentration increases the error rate during DNA synthesis [10] and monovalent cations, typically potassium (K) ions [better source needed]

The reaction is commonly carried out in a volume of 10–200 μL in small reaction tubes (0.2–0.5 mL volumes) in a thermal cycler. The thermal cycler heats and cools the reaction tubes to achieve the temperatures required at each step of the reaction (see below). Many modern thermal cyclers make use of the Peltier effect, which permits both heating and cooling of the block holding the PCR tubes simply by reversing the electric current. Thin-walled reaction tubes permit favorable thermal conductivity to allow for rapid thermal equilibrium. Most thermal cyclers have heated lids to prevent condensation at the top of the reaction tube. Older thermal cyclers lacking a heated lid require a layer of oil on top of the reaction mixture or a ball of wax inside the tube.

Procedure Edit

Typically, PCR consists of a series of 20–40 repeated temperature changes, called thermal cycles, with each cycle commonly consisting of two or three discrete temperature steps (see figure below). The cycling is often preceded by a single temperature step at a very high temperature (>90 °C (194 °F)), and followed by one hold at the end for final product extension or brief storage. The temperatures used and the length of time they are applied in each cycle depend on a variety of parameters, including the enzyme used for DNA synthesis, the concentration of bivalent ions and dNTPs in the reaction, and the melting temperature (Tm) of the primers. [11] The individual steps common to most PCR methods are as follows:

  • Initialization: This step is only required for DNA polymerases that require heat activation by hot-start PCR. [12] It consists of heating the reaction chamber to a temperature of 94–96 °C (201–205 °F), or 98 °C (208 °F) if extremely thermostable polymerases are used, which is then held for 1–10 minutes.
  • Denaturation: This step is the first regular cycling event and consists of heating the reaction chamber to 94–98 °C (201–208 °F) for 20–30 seconds. This causes DNA melting, or denaturation, of the double-stranded DNA template by breaking the hydrogen bonds between complementary bases, yielding two single-stranded DNA molecules.
  • Annealing: In the next step, the reaction temperature is lowered to 50–65 °C (122–149 °F) for 20–40 seconds, allowing annealing of the primers to each of the single-stranded DNA templates. Two different primers are typically included in the reaction mixture: one for each of the two single-stranded complements containing the target region. The primers are single-stranded sequences themselves, but are much shorter than the length of the target region, complementing only very short sequences at the 3′ end of each strand.
  • Extension/elongation: The temperature at this step depends on the DNA polymerase used the optimum activity temperature for the thermostable DNA polymerase of Taq polymerase is approximately 75–80 °C (167–176 °F), [13][14] though a temperature of 72 °C (162 °F) is commonly used with this enzyme. In this step, the DNA polymerase synthesizes a new DNA strand complementary to the DNA template strand by adding free dNTPs from the reaction mixture that is complementary to the template in the 5′-to-3′ direction, condensing the 5′-phosphate group of the dNTPs with the 3′-hydroxy group at the end of the nascent (elongating) DNA strand. The precise time required for elongation depends both on the DNA polymerase used and on the length of the DNA target region to amplify. As a rule of thumb, at their optimal temperature, most DNA polymerases polymerize a thousand bases per minute. Under optimal conditions (i.e., if there are no limitations due to limiting substrates or reagents), at each extension/elongation step, the number of DNA target sequences is doubled. With each successive cycle, the original template strands plus all newly generated strands become template strands for the next round of elongation, leading to exponential (geometric) amplification of the specific DNA target region.
  • Final elongation: This single step is optional, but is performed at a temperature of 70–74 °C (158–165 °F) (the temperature range required for optimal activity of most polymerases used in PCR) for 5–15 minutes after the last PCR cycle to ensure that any remaining single-stranded DNA is fully elongated.
  • Final hold: The final step cools the reaction chamber to 4–15 °C (39–59 °F) for an indefinite time, and may be employed for short-term storage of the PCR products.

To check whether the PCR successfully generated the anticipated DNA target region (also sometimes referred to as the amplimer or amplicon), agarose gel electrophoresis may be employed for size separation of the PCR products. The size of the PCR products is determined by comparison with a DNA ladder, a molecular weight marker which contains DNA fragments of known sizes, which runs on the gel alongside the PCR products.

Stages Edit

As with other chemical reactions, the reaction rate and efficiency of PCR are affected by limiting factors. Thus, the entire PCR process can further be divided into three stages based on reaction progress:

  • Exponential amplification: At every cycle, the amount of product is doubled (assuming 100% reaction efficiency). After 30 cycles, a single copy of DNA can be increased up to 1,000,000,000 (one billion) copies. In a sense, then, the replication of a discrete strand of DNA is being manipulated in a tube under controlled conditions. [15] The reaction is very sensitive: only minute quantities of DNA must be present.
  • Leveling off stage: The reaction slows as the DNA polymerase loses activity and as consumption of reagents, such as dNTPs and primers, causes them to become more limited.
  • Plateau: No more product accumulates due to exhaustion of reagents and enzyme.

In practice, PCR can fail for various reasons, in part due to its sensitivity to contamination causing amplification of spurious DNA products. Because of this, a number of techniques and procedures have been developed for optimizing PCR conditions. [16] [17] Contamination with extraneous DNA is addressed with lab protocols and procedures that separate pre-PCR mixtures from potential DNA contaminants. [7] This usually involves spatial separation of PCR-setup areas from areas for analysis or purification of PCR products, use of disposable plasticware, and thoroughly cleaning the work surface between reaction setups. Primer-design techniques are important in improving PCR product yield and in avoiding the formation of spurious products, and the usage of alternate buffer components or polymerase enzymes can help with amplification of long or otherwise problematic regions of DNA. Addition of reagents, such as formamide, in buffer systems may increase the specificity and yield of PCR. [18] Computer simulations of theoretical PCR results (Electronic PCR) may be performed to assist in primer design. [19]

Selective DNA isolation Edit

PCR allows isolation of DNA fragments from genomic DNA by selective amplification of a specific region of DNA. This use of PCR augments many ways, such as generating hybridization probes for Southern or northern hybridization and DNA cloning, which require larger amounts of DNA, representing a specific DNA region. PCR supplies these techniques with high amounts of pure DNA, enabling analysis of DNA samples even from very small amounts of starting material.

Other applications of PCR include DNA sequencing to determine unknown PCR-amplified sequences in which one of the amplification primers may be used in Sanger sequencing, isolation of a DNA sequence to expedite recombinant DNA technologies involving the insertion of a DNA sequence into a plasmid, phage, or cosmid (depending on size) or the genetic material of another organism. Bacterial colonies (such as E. coli) can be rapidly screened by PCR for correct DNA vector constructs. [20] PCR may also be used for genetic fingerprinting a forensic technique used to identify a person or organism by comparing experimental DNAs through different PCR-based methods.

Some PCR fingerprint methods have high discriminative power and can be used to identify genetic relationships between individuals, such as parent-child or between siblings, and are used in paternity testing (Fig. 4). This technique may also be used to determine evolutionary relationships among organisms when certain molecular clocks are used (i.e. the 16S rRNA and recA genes of microorganisms). [21]

Amplification and quantification of DNA Edit

Because PCR amplifies the regions of DNA that it targets, PCR can be used to analyze extremely small amounts of sample. This is often critical for forensic analysis, when only a trace amount of DNA is available as evidence. PCR may also be used in the analysis of ancient DNA that is tens of thousands of years old. These PCR-based techniques have been successfully used on animals, such as a forty-thousand-year-old mammoth, and also on human DNA, in applications ranging from the analysis of Egyptian mummies to the identification of a Russian tsar and the body of English king Richard III. [22]

Quantitative PCR or Real Time PCR (qPCR, [23] not to be confused with RT-PCR) methods allow the estimation of the amount of a given sequence present in a sample—a technique often applied to quantitatively determine levels of gene expression. Quantitative PCR is an established tool for DNA quantification that measures the accumulation of DNA product after each round of PCR amplification.

qPCR allows the quantification and detection of a specific DNA sequence in real time since it measures concentration while the synthesis process is taking place. There are two methods for simultaneous detection and quantification. The first method consists of using fluorescent dyes that are retained nonspecifically in between the double strands. The second method involves probes that code for specific sequences and are fluorescently labeled. Detection of DNA using these methods can only be seen after the hybridization of probes with its complementary DNA takes place. An interesting technique combination is real-time PCR and reverse transcription. This sophisticated technique, called RT-qPCR, allows for the quantification of a small quantity of RNA. Through this combined technique, mRNA is converted to cDNA, which is further quantified using qPCR. This technique lowers the possibility of error at the end point of PCR, [24] increasing chances for detection of genes associated with genetic diseases such as cancer. [4] Laboratories use RT-qPCR for the purpose of sensitively measuring gene regulation. The mathematical foundations for the reliable quantification of the PCR [25] and RT-qPCR [26] facilitate the implementation of accurate fitting procedures of experimental data in research, medical, diagnostic and infectious disease applications. [27] [28] [29] [30]

Medical and diagnostic applications Edit

Prospective parents can be tested for being genetic carriers, or their children might be tested for actually being affected by a disease. [1] DNA samples for prenatal testing can be obtained by amniocentesis, chorionic villus sampling, or even by the analysis of rare fetal cells circulating in the mother's bloodstream. PCR analysis is also essential to preimplantation genetic diagnosis, where individual cells of a developing embryo are tested for mutations.

  • PCR can also be used as part of a sensitive test for tissue typing, vital to organ transplantation. As of 2008, [update] there is even a proposal to replace the traditional antibody-based tests for blood type with PCR-based tests. [31]
  • Many forms of cancer involve alterations to oncogenes. By using PCR-based tests to study these mutations, therapy regimens can sometimes be individually customized to a patient. PCR permits early diagnosis of malignant diseases such as leukemia and lymphomas, which is currently the highest-developed in cancer research and is already being used routinely. PCR assays can be performed directly on genomic DNA samples to detect translocation-specific malignant cells at a sensitivity that is at least 10,000 fold higher than that of other methods. [32] PCR is very useful in the medical field since it allows for the isolation and amplification of tumor suppressors. Quantitative PCR for example, can be used to quantify and analyze single cells, as well as recognize DNA, mRNA and protein confirmations and combinations. [24]

Infectious disease applications Edit

PCR allows for rapid and highly specific diagnosis of infectious diseases, including those caused by bacteria or viruses. [33] PCR also permits identification of non-cultivatable or slow-growing microorganisms such as mycobacteria, anaerobic bacteria, or viruses from tissue culture assays and animal models. The basis for PCR diagnostic applications in microbiology is the detection of infectious agents and the discrimination of non-pathogenic from pathogenic strains by virtue of specific genes. [33] [34]

Characterization and detection of infectious disease organisms have been revolutionized by PCR in the following ways:

  • The human immunodeficiency virus (or HIV), is a difficult target to find and eradicate. The earliest tests for infection relied on the presence of antibodies to the virus circulating in the bloodstream. However, antibodies don't appear until many weeks after infection, maternal antibodies mask the infection of a newborn, and therapeutic agents to fight the infection don't affect the antibodies. PCR tests have been developed that can detect as little as one viral genome among the DNA of over 50,000 host cells. [35] Infections can be detected earlier, donated blood can be screened directly for the virus, newborns can be immediately tested for infection, and the effects of antiviral treatments can be quantified.
  • Some disease organisms, such as that for tuberculosis, are difficult to sample from patients and slow to be grown in the laboratory. PCR-based tests have allowed detection of small numbers of disease organisms (both live or dead), in convenient samples. Detailed genetic analysis can also be used to detect antibiotic resistance, allowing immediate and effective therapy. The effects of therapy can also be immediately evaluated.
  • The spread of a disease organism through populations of domestic or wild animals can be monitored by PCR testing. In many cases, the appearance of new virulent sub-types can be detected and monitored. The sub-types of an organism that were responsible for earlier epidemics can also be determined by PCR analysis.
  • Viral DNA can be detected by PCR. The primers used must be specific to the targeted sequences in the DNA of a virus, and PCR can be used for diagnostic analyses or DNA sequencing of the viral genome. The high sensitivity of PCR permits virus detection soon after infection and even before the onset of disease. [33] Such early detection may give physicians a significant lead time in treatment. The amount of virus ("viral load") in a patient can also be quantified by PCR-based DNA quantitation techniques (see below). A variant of PCR (RT-PCR) is used for detecting viral RNA rather than DNA: in this test the enzyme reverse transcriptase is used to generate a DNA sequence which matches the viral RNA this DNA is then amplified as per the usual PCR method. RT-PCR is widely used to detect the SARS-CoV-2 viral genome. [36]
  • Diseases such as pertussis (or whooping cough) are caused by the bacteria Bordetella pertussis. This bacteria is marked by a serious acute respiratory infection that affects various animals and humans and has led to the deaths of many young children. The pertussis toxin is a protein exotoxin that binds to cell receptors by two dimers and reacts with different cell types such as T lymphocytes which play a role in cell immunity. [37] PCR is an important testing tool that can detect sequences within the gene for the pertussis toxin. Because PCR has a high sensitivity for the toxin and a rapid turnaround time, it is very efficient for diagnosing pertussis when compared to culture. [38]

Forensic applications Edit

The development of PCR-based genetic (or DNA) fingerprinting protocols has seen widespread application in forensics:

  • In its most discriminating form, genetic fingerprinting can uniquely discriminate any one person from the entire population of the world. Minute samples of DNA can be isolated from a crime scene, and compared to that from suspects, or from a DNA database of earlier evidence or convicts. Simpler versions of these tests are often used to rapidly rule out suspects during a criminal investigation. Evidence from decades-old crimes can be tested, confirming or exonerating the people originally convicted.
  • Forensic DNA typing has been an effective way of identifying or exonerating criminal suspects due to analysis of evidence discovered at a crime scene. The human genome has many repetitive regions that can be found within gene sequences or in non-coding regions of the genome. Specifically, up to 40% of human DNA is repetitive. [4] There are two distinct categories for these repetitive, non-coding regions in the genome. The first category is called variable number tandem repeats (VNTR), which are 10–100 base pairs long and the second category is called short tandem repeats (STR) and these consist of repeated 2–10 base pair sections. PCR is used to amplify several well-known VNTRs and STRs using primers that flank each of the repetitive regions. The sizes of the fragments obtained from any individual for each of the STRs will indicate which alleles are present. By analyzing several STRs for an individual, a set of alleles for each person will be found that statistically is likely to be unique. [4] Researchers have identified the complete sequence of the human genome. This sequence can be easily accessed through the NCBI website and is used in many real-life applications. For example, the FBI has compiled a set of DNA marker sites used for identification, and these are called the Combined DNA Index System (CODIS) DNA database. [4] Using this database enables statistical analysis to be used to determine the probability that a DNA sample will match. PCR is a very powerful and significant analytical tool to use for forensic DNA typing because researchers only need a very small amount of the target DNA to be used for analysis. For example, a single human hair with attached hair follicle has enough DNA to conduct the analysis. Similarly, a few sperm, skin samples from under the fingernails, or a small amount of blood can provide enough DNA for conclusive analysis. [4]
  • Less discriminating forms of DNA fingerprinting can help in DNA paternity testing, where an individual is matched with their close relatives. DNA from unidentified human remains can be tested, and compared with that from possible parents, siblings, or children. Similar testing can be used to confirm the biological parents of an adopted (or kidnapped) child. The actual biological father of a newborn can also be confirmed (or ruled out).
  • The PCR AMGX/AMGY design has been shown to not only [clarification needed] facilitate in amplifying DNA sequences from a very minuscule amount of genome. However it can also be used for real-time sex determination from forensic bone samples. This provides a powerful and effective way to determine gender in forensic cases and ancient specimens. [39]

Research applications Edit

PCR has been applied to many areas of research in molecular genetics:

  • PCR allows rapid production of short pieces of DNA, even when not more than the sequence of the two primers is known. This ability of PCR augments many methods, such as generating hybridizationprobes for Southern or northern blot hybridization. PCR supplies these techniques with large amounts of pure DNA, sometimes as a single strand, enabling analysis even from very small amounts of starting material.
  • The task of DNA sequencing can also be assisted by PCR. Known segments of DNA can easily be produced from a patient with a genetic disease mutation. Modifications to the amplification technique can extract segments from a completely unknown genome, or can generate just a single strand of an area of interest.
  • PCR has numerous applications to the more traditional process of DNA cloning. It can extract segments for insertion into a vector from a larger genome, which may be only available in small quantities. Using a single set of 'vector primers', it can also analyze or extract fragments that have already been inserted into vectors. Some alterations to the PCR protocol can generate mutations (general or site-directed) of an inserted fragment.
  • Sequence-tagged sites is a process where PCR is used as an indicator that a particular segment of a genome is present in a particular clone. The Human Genome Project found this application vital to mapping the cosmid clones they were sequencing, and to coordinating the results from different laboratories.
  • An application of PCR is the phylogenic analysis of DNA from ancient sources, such as that found in the recovered bones of Neanderthals, from frozen tissues of mammoths, or from the brain of Egyptian mummies. [15] In some cases the highly degraded DNA from these sources might be reassembled during the early stages of amplification.
  • A common application of PCR is the study of patterns of gene expression. Tissues (or even individual cells) can be analyzed at different stages to see which genes have become active, or which have been switched off. This application can also use quantitative PCR to quantitate the actual levels of expression
  • The ability of PCR to simultaneously amplify several loci from individual sperm [40] has greatly enhanced the more traditional task of genetic mapping by studying chromosomal crossovers after meiosis. Rare crossover events between very close loci have been directly observed by analyzing thousands of individual sperms. Similarly, unusual deletions, insertions, translocations, or inversions can be analyzed, all without having to wait (or pay) for the long and laborious processes of fertilization, embryogenesis, etc. : PCR can be used to create mutant genes with mutations chosen by scientists at will. These mutations can be chosen in order to understand how proteins accomplish their functions, and to change or improve protein function.

PCR has a number of advantages. It is fairly simple to understand and to use, and produces results rapidly. The technique is highly sensitive with the potential to produce millions to billions of copies of a specific product for sequencing, cloning, and analysis. qRT-PCR shares the same advantages as the PCR, with an added advantage of quantification of the synthesized product. Therefore, it has its uses to analyze alterations of gene expression levels in tumors, microbes, or other disease states. [24]

PCR is a very powerful and practical research tool. The sequencing of unknown etiologies of many diseases are being figured out by the PCR. The technique can help identify the sequence of previously unknown viruses related to those already known and thus give us a better understanding of the disease itself. If the procedure can be further simplified and sensitive non radiometric detection systems can be developed, the PCR will assume a prominent place in the clinical laboratory for years to come. [15]

One major limitation of PCR is that prior information about the target sequence is necessary in order to generate the primers that will allow its selective amplification. [24] This means that, typically, PCR users must know the precise sequence(s) upstream of the target region on each of the two single-stranded templates in order to ensure that the DNA polymerase properly binds to the primer-template hybrids and subsequently generates the entire target region during DNA synthesis.

Like all enzymes, DNA polymerases are also prone to error, which in turn causes mutations in the PCR fragments that are generated. [41]

Another limitation of PCR is that even the smallest amount of contaminating DNA can be amplified, resulting in misleading or ambiguous results. To minimize the chance of contamination, investigators should reserve separate rooms for reagent preparation, the PCR, and analysis of product. Reagents should be dispensed into single-use aliquots. Pipettors with disposable plungers and extra-long pipette tips should be routinely used. [15] It is moreover recommended to ensure that the lab set-up follows a unidirectional workflow. No materials or reagents used in the PCR and analysis rooms should ever be taken into the PCR preparation room without thorough decontamination. [42]

Environmental samples that contain humic acids may inhibit PCR amplification and lead to inaccurate results.

  • Allele-specific PCR: a diagnostic or cloning technique based on single-nucleotide variations (SNVs not to be confused with SNPs) (single-base differences in a patient). It requires prior knowledge of a DNA sequence, including differences between alleles, and uses primers whose 3' ends encompass the SNV (base pair buffer around SNV usually incorporated). PCR amplification under stringent conditions is much less efficient in the presence of a mismatch between template and primer, so successful amplification with an SNP-specific primer signals presence of the specific SNP in a sequence. [43] See SNP genotyping for more information.
  • Assembly PCR or Polymerase Cycling Assembly (PCA): artificial synthesis of long DNA sequences by performing PCR on a pool of long oligonucleotides with short overlapping segments. The oligonucleotides alternate between sense and antisense directions, and the overlapping segments determine the order of the PCR fragments, thereby selectively producing the final long DNA product. [44]
  • Asymmetric PCR: preferentially amplifies one DNA strand in a double-stranded DNA template. It is used in sequencing and hybridization probing where amplification of only one of the two complementary strands is required. PCR is carried out as usual, but with a great excess of the primer for the strand targeted for amplification. Because of the slow (arithmetic) amplification later in the reaction after the limiting primer has been used up, extra cycles of PCR are required. [45] A recent modification on this process, known as Linear-After-The-Exponential-PCR (LATE-PCR), uses a limiting primer with a higher melting temperature (Tm) than the excess primer to maintain reaction efficiency as the limiting primer concentration decreases mid-reaction. [46]
  • Convective PCR: a pseudo-isothermal way of performing PCR. Instead of repeatedly heating and cooling the PCR mixture, the solution is subjected to a thermal gradient. The resulting thermal instability driven convective flow automatically shuffles the PCR reagents from the hot and cold regions repeatedly enabling PCR. [47] Parameters such as thermal boundary conditions and geometry of the PCR enclosure can be optimized to yield robust and rapid PCR by harnessing the emergence of chaotic flow fields. [48] Such convective flow PCR setup significantly reduces device power requirement and operation time.
  • Dial-out PCR: a highly parallel method for retrieving accurate DNA molecules for gene synthesis. A complex library of DNA molecules is modified with unique flanking tags before massively parallel sequencing. Tag-directed primers then enable the retrieval of molecules with desired sequences by PCR. [49]
  • Digital PCR (dPCR): used to measure the quantity of a target DNA sequence in a DNA sample. The DNA sample is highly diluted so that after running many PCRs in parallel, some of them do not receive a single molecule of the target DNA. The target DNA concentration is calculated using the proportion of negative outcomes. Hence the name 'digital PCR'.
  • Helicase-dependent amplification: similar to traditional PCR, but uses a constant temperature rather than cycling through denaturation and annealing/extension cycles. DNA helicase, an enzyme that unwinds DNA, is used in place of thermal denaturation. [50]
  • Hot start PCR: a technique that reduces non-specific amplification during the initial set up stages of the PCR. It may be performed manually by heating the reaction components to the denaturation temperature (e.g., 95 °C) before adding the polymerase. [51] Specialized enzyme systems have been developed that inhibit the polymerase's activity at ambient temperature, either by the binding of an antibody[12][52] or by the presence of covalently bound inhibitors that dissociate only after a high-temperature activation step. Hot-start/cold-finish PCR is achieved with new hybrid polymerases that are inactive at ambient temperature and are instantly activated at elongation temperature.
  • In silico PCR (digital PCR, virtual PCR, electronic PCR, e-PCR) refers to computational tools used to calculate theoretical polymerase chain reaction results using a given set of primers (probes) to amplify DNA sequences from a sequenced genome or transcriptome. In silico PCR was proposed as an educational tool for molecular biology. [53]
  • Intersequence-specific PCR (ISSR): a PCR method for DNA fingerprinting that amplifies regions between simple sequence repeats to produce a unique fingerprint of amplified fragment lengths. [54]
  • Inverse PCR: is commonly used to identify the flanking sequences around genomic inserts. It involves a series of DNA digestions and self ligation, resulting in known sequences at either end of the unknown sequence. [55]
  • Ligation-mediated PCR: uses small DNA linkers ligated to the DNA of interest and multiple primers annealing to the DNA linkers it has been used for DNA sequencing, genome walking, and DNA footprinting. [56]
  • Methylation-specific PCR (MSP): developed by Stephen Baylin and James G. Herman at the Johns Hopkins School of Medicine, [57] and is used to detect methylation of CpG islands in genomic DNA. DNA is first treated with sodium bisulfite, which converts unmethylated cytosine bases to uracil, which is recognized by PCR primers as thymine. Two PCRs are then carried out on the modified DNA, using primer sets identical except at any CpG islands within the primer sequences. At these points, one primer set recognizes DNA with cytosines to amplify methylated DNA, and one set recognizes DNA with uracil or thymine to amplify unmethylated DNA. MSP using qPCR can also be performed to obtain quantitative rather than qualitative information about methylation.
  • Miniprimer PCR: uses a thermostable polymerase (S-Tbr) that can extend from short primers ("smalligos") as short as 9 or 10 nucleotides. This method permits PCR targeting to smaller primer binding regions, and is used to amplify conserved DNA sequences, such as the 16S (or eukaryotic 18S) rRNA gene. [58]
  • Multiplex ligation-dependent probe amplification (MLPA): permits amplifying multiple targets with a single primer pair, thus avoiding the resolution limitations of multiplex PCR (see below).
  • Multiplex-PCR: consists of multiple primer sets within a single PCR mixture to produce amplicons of varying sizes that are specific to different DNA sequences. By targeting multiple genes at once, additional information may be gained from a single test-run that otherwise would require several times the reagents and more time to perform. Annealing temperatures for each of the primer sets must be optimized to work correctly within a single reaction, and amplicon sizes. That is, their base pair length should be different enough to form distinct bands when visualized by gel electrophoresis.
  • Nanoparticle-Assisted PCR (nanoPCR): some nanoparticles (NPs) can enhance the efficiency of PCR (thus being called nanoPCR), and some can even outperform the original PCR enhancers. It was reported that quantum dots (QDs) can improve PCR specificity and efficiency. Single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) are efficient in enhancing the amplification of long PCR. Carbon nanopowder (CNP) can improve the efficiency of repeated PCR and long PCR, while zinc oxide, titanium dioxide and Ag NPs were found to increase the PCR yield. Previous data indicated that non-metallic NPs retained acceptable amplification fidelity. Given that many NPs are capable of enhancing PCR efficiency, it is clear that there is likely to be great potential for nanoPCR technology improvements and product development. [59][60]
  • Nested PCR: increases the specificity of DNA amplification, by reducing background due to non-specific amplification of DNA. Two sets of primers are used in two successive PCRs. In the first reaction, one pair of primers is used to generate DNA products, which besides the intended target, may still consist of non-specifically amplified DNA fragments. The product(s) are then used in a second PCR with a set of primers whose binding sites are completely or partially different from and located 3' of each of the primers used in the first reaction. Nested PCR is often more successful in specifically amplifying long DNA fragments than conventional PCR, but it requires more detailed knowledge of the target sequences.
  • Overlap-extension PCR or Splicing by overlap extension (SOEing) : a genetic engineering technique that is used to splice together two or more DNA fragments that contain complementary sequences. It is used to join DNA pieces containing genes, regulatory sequences, or mutations the technique enables creation of specific and long DNA constructs. It can also introduce deletions, insertions or point mutations into a DNA sequence. [61][62]
  • PAN-AC: uses isothermal conditions for amplification, and may be used in living cells. [63][64]
  • quantitative PCR (qPCR): used to measure the quantity of a target sequence (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA. quantitative PCR is commonly used to determine whether a DNA sequence is present in a sample and the number of its copies in the sample. Quantitative PCR has a very high degree of precision. Quantitative PCR methods use fluorescent dyes, such as Sybr Green, EvaGreen or fluorophore-containing DNA probes, such as TaqMan, to measure the amount of amplified product in real time. It is also sometimes abbreviated to RT-PCR (real-time PCR) but this abbreviation should be used only for reverse transcription PCR. qPCR is the appropriate contractions for quantitative PCR (real-time PCR).
  • Reverse Complement PCR (RC-PCR): Allows the addition of functional domains or sequences of choice to be appended independently to either end of the generated amplicon in a single closed tube reaction. This method generates target specific primers within the reaction by the interaction of universal primers (which contain the desired sequences or domains to be appended) and RC probes.
  • Reverse Transcription PCR (RT-PCR): for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR. RT-PCR is widely used in expression profiling, to determine the expression of a gene or to identify the sequence of an RNA transcript, including transcription start and termination sites. If the genomic DNA sequence of a gene is known, RT-PCR can be used to map the location of exons and introns in the gene. The 5' end of a gene (corresponding to the transcription start site) is typically identified by RACE-PCR (Rapid Amplification of cDNA Ends).
  • RNase H-dependent PCR (rhPCR): a modification of PCR that utilizes primers with a 3’ extension block that can be removed by a thermostable RNase HII enzyme. This system reduces primer-dimers and allows for multiplexed reactions to be performed with higher numbers of primers. [65]
  • Single Specific Primer-PCR (SSP-PCR): allows the amplification of double-stranded DNA even when the sequence information is available at one end only. This method permits amplification of genes for which only a partial sequence information is available, and allows unidirectional genome walking from known into unknown regions of the chromosome. [66]
  • Solid Phase PCR: encompasses multiple meanings, including Polony Amplification (where PCR colonies are derived in a gel matrix, for example), Bridge PCR [67] (primers are covalently linked to a solid-support surface), conventional Solid Phase PCR (where Asymmetric PCR is applied in the presence of solid support bearing primer with sequence matching one of the aqueous primers) and Enhanced Solid Phase PCR [68] (where conventional Solid Phase PCR can be improved by employing high Tm and nested solid support primer with optional application of a thermal 'step' to favour solid support priming).
  • Suicide PCR: typically used in paleogenetics or other studies where avoiding false positives and ensuring the specificity of the amplified fragment is the highest priority. It was originally described in a study to verify the presence of the microbe Yersinia pestis in dental samples obtained from 14th Century graves of people supposedly killed by the plague during the medieval Black Death epidemic. [69] The method prescribes the use of any primer combination only once in a PCR (hence the term "suicide"), which should never have been used in any positive control PCR reaction, and the primers should always target a genomic region never amplified before in the lab using this or any other set of primers. This ensures that no contaminating DNA from previous PCR reactions is present in the lab, which could otherwise generate false positives.
  • Thermal asymmetric interlaced PCR (TAIL-PCR): for isolation of an unknown sequence flanking a known sequence. Within the known sequence, TAIL-PCR uses a nested pair of primers with differing annealing temperatures a degenerate primer is used to amplify in the other direction from the unknown sequence. [70]
  • Touchdown PCR (Step-down PCR): a variant of PCR that aims to reduce nonspecific background by gradually lowering the annealing temperature as PCR cycling progresses. The annealing temperature at the initial cycles is usually a few degrees (3–5 °C) above the Tm of the primers used, while at the later cycles, it is a few degrees (3–5 °C) below the primer Tm. The higher temperatures give greater specificity for primer binding, and the lower temperatures permit more efficient amplification from the specific products formed during the initial cycles. [71]
  • Universal Fast Walking: for genome walking and genetic fingerprinting using a more specific 'two-sided' PCR than conventional 'one-sided' approaches (using only one gene-specific primer and one general primer—which can lead to artefactual 'noise') [72] by virtue of a mechanism involving lariat structure formation. Streamlined derivatives of UFW are LaNe RAGE (lariat-dependent nested PCR for rapid amplification of genomic DNA ends), [73] 5'RACE LaNe [74] and 3'RACE LaNe. [75]

The heat-resistant enzymes that are a key component in polymerase chain reaction were discovered in the 1960s as a product of a microbial life form that lived in the superheated waters of Yellowstone’s Mushroom Spring. [76]

A 1971 paper in the Journal of Molecular Biology by Kjell Kleppe and co-workers in the laboratory of H. Gobind Khorana first described a method of using an enzymatic assay to replicate a short DNA template with primers in vitro. [77] However, this early manifestation of the basic PCR principle did not receive much attention at the time and the invention of the polymerase chain reaction in 1983 is generally credited to Kary Mullis. [78]

When Mullis developed the PCR in 1983, he was working in Emeryville, California for Cetus Corporation, one of the first biotechnology companies, where he was responsible for synthesizing short chains of DNA. Mullis has written that he conceived the idea for PCR while cruising along the Pacific Coast Highway one night in his car. [79] He was playing in his mind with a new way of analyzing changes (mutations) in DNA when he realized that he had instead invented a method of amplifying any DNA region through repeated cycles of duplication driven by DNA polymerase. In Scientific American, Mullis summarized the procedure: "Beginning with a single molecule of the genetic material DNA, the PCR can generate 100 billion similar molecules in an afternoon. The reaction is easy to execute. It requires no more than a test tube, a few simple reagents, and a source of heat." [80] DNA fingerprinting was first used for paternity testing in 1988. [81]

Mullis and Professor Michael Smith, who had developed other essential ways of manipulating DNA, [82] were jointly awarded the Nobel Prize in Chemistry in 1993, seven years after Mullis and his colleagues at Cetus first put his proposal to practice. [83] Mullis's 1985 paper with R. K. Saiki and H. A. Erlich, "Enzymatic Amplification of β-globin Genomic Sequences and Restriction Site Analysis for Diagnosis of Sickle Cell Anemia"—the polymerase chain reaction invention (PCR) – was honored by a Citation for Chemical Breakthrough Award from the Division of History of Chemistry of the American Chemical Society in 2017. [84] [1]

At the core of the PCR method is the use of a suitable DNA polymerase able to withstand the high temperatures of >90 °C (194 °F) required for separation of the two DNA strands in the DNA double helix after each replication cycle. The DNA polymerases initially employed for in vitro experiments presaging PCR were unable to withstand these high temperatures. [1] So the early procedures for DNA replication were very inefficient and time-consuming, and required large amounts of DNA polymerase and continuous handling throughout the process.

The discovery in 1976 of Taq polymerase—a DNA polymerase purified from the thermophilic bacterium, Thermus aquaticus, which naturally lives in hot (50 to 80 °C (122 to 176 °F)) environments [13] such as hot springs—paved the way for dramatic improvements of the PCR method. The DNA polymerase isolated from T. aquaticus is stable at high temperatures remaining active even after DNA denaturation, [14] thus obviating the need to add new DNA polymerase after each cycle. [2] This allowed an automated thermocycler-based process for DNA amplification.

Patent disputes Edit

The PCR technique was patented by Kary Mullis and assigned to Cetus Corporation, where Mullis worked when he invented the technique in 1983. The Taq polymerase enzyme was also covered by patents. There have been several high-profile lawsuits related to the technique, including an unsuccessful lawsuit brought by DuPont. The Swiss pharmaceutical company Hoffmann-La Roche purchased the rights to the patents in 1992 and currently [ when? ] holds those that are still protected.

A related patent battle over the Taq polymerase enzyme is still ongoing in several jurisdictions around the world between Roche and Promega. The legal arguments have extended beyond the lives of the original PCR and Taq polymerase patents, which expired on March 28, 2005. [85]


4.3: Viruses Lab (Instructor Materials Preparation) - Biology

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