Biological Sciences

Description of Program

The M.S.B.Sc. will provide both a traditional biological curricula and innovative approaches to instruction. You will take core and required courses spanning a wide range of disciplines, from molecular, through organismal, to ecosystem-level biology. This rigorous curriculum will provide a practical foundation that can be applied as an entry point or a terminal degree professional careers in biomedicine, biotechnology and environmental biology.

You will specialize in one of two broad areas: Molecular Biology or Organismal Biology

The M.S.B.Sc. is not a lock-step program and offers both thesis and capstone (non-thesis) tracks. The capstone (non-theses) track is the default option and will require 45 credit hours (24 hours of core/required courses, 15 hours of electives, and 6 hours of capstone). The theses track will require 39 credit hours for completion (24 hours of core/required courses, 9 hours of electives, and 6 hours of theses)  and also the approval of an OC faculty member to advise and support a specific research project.

One of the most innovative aspects of the curricula, is the possibility of working as an intern for course credit with one of our off- campus partners for expanded experience in various biological disciplines.  These include the following:

In the near future, the M.S.B.Sc. program plans to add greater focus on the growing field of genomics and molecular computational biological sciences.  For example the Ocean Center have recently launched a “Global Invertebrate Genomics Alliance (GIGA)” consortium – http://giga.nova.edu

Moreover, a new 4 course certificate in “computational molecular biology” has now been launched through the OC.  The certificate intends to give students a practical background in DNA sequence analysis and bioinformatics. The training can make them more competitive in industry job searches for this growing field. The certificate will involve 2 genomics related courses from the OC, and 2 computer science courses from the Graduate School of Computer and Information Sciences.

Relevant courses in computer sciences (some taught by the NSU Graduate school of Computer and Information Sciences) and state of the art  practical courses in bioinformatics will be added. These will enable students to gain basic training and practice that can likely translate to employment in the growing bioinformatics and genomics fields.

Learning Outcomes

Expected learning outcomes are:

Delivery System

On campus graduate classes typically meet one evening per week in a three hour session. Exceptions are field courses which may entail several days of intensive study. On-line courses meet periodically at the convenience of faculty and students  

Degree Tracts

There are two tracts for completing an M.S. degree.

Capstone

All entering M.S. students are accepted in the Capstone (also called Capstone track). Students take a minimum 13 regular courses in their selected degree for 39 credits.   Students must take Capstone Review Paper courses totaling a minimum of 6 credits (which involve submitting and defending a capstone review paper.  This is typically done at or near the completion of formal coursework.  The Capstone review paper is a scholarly review, based upon a comprehensive literature search, review, and synthesis of the chosen topic. Carrying out a Capstone review paper takes place with guidance from a major professor. Typically, Capstone students find a major professor by approaching faculty in the student's area of interest. Students will be assigned a Capstone advisor if they have difficulty in identifying a major professor. Prior to beginning a Capstone review paper and registering for Capstone Review Paper credits, the student must write a proposal which must be approved by the student's major professor, committee (define how committee is formed), and the Associate Dean of Academic Programs, and be submitted to the Director of Academic Support and Administration in the Program Office.

Thesis Optional Track

Some students desire the thesis track.  The thesis track requires an extra step.  A thesis is an original contribution to knowledge resulting from the systematic study of a significant problem or issue. A thesis track requires a minimum of 10 regular courses for 30 credits.  In addition, a minimum of 9 Thesis credits is required. To be allowed entry into the Thesis track the student must secure agreement from a faculty member to be the student's major professor. There must be adequate funding to carry out the proposed research.  Students are not provided with a thesis advisor. Prior to beginning thesis research and registering for thesis credits, the student must write a proposal which must be approved by the student's major professor, committee, and the the Associate Dean of Academic Programs, and be submitted to the Director of Academic Support and Administration in the Program Office. The Thesis option is typically a longer duration track and number of credit hours than the Capstone track.

For further details, students are referred to section 3.8 of this catalog and to the online guidelines for the capstone or thesis track found on the Oceanographic Center Student Information page

M.S. Credit Hour Requirements

The default Capstone track requires a minimum of 45 credits. This includes five 3-credit core classes, eight 3-credit specialty courses and a minimum of two 3-credit Capstone Review Paper courses (consisting of an extended literature review of an approved subject). Once a student starts registering for capstone course credits, they cannot stop registering for credits until the capstone is completed and defended. It is expected the Capstone review paper can be completed within two terms or less.  The completed Capstone review paper is presented in an open defense that includes the student's advisory committee.
The Thesis option track requires a minimum of 39 credits. This includes five 3-credit core classes, five 3-credit specialty courses, and at least nine credits of master's thesis research. The number of thesis research credits above the minimum is dependent upon the length of time needed to complete the thesis research, which may be more than the typical minimum three terms. The final thesis is formally defended in an open defense that includes the student's advisory committee.

Elective Courses

Students in a single degree are allowed to take up to two elective courses outside their degree orientation and have them count towards their final credit count.

For both the Capstone Review Paper and the Thesis degree tracks, once the proposal has been accepted, enrollment in the chosen track must continue until completion of the degree.

Joint M.S. Degrees

Also offered are Joint M.S. Degrees

The joint specialization M.S. degrees require a minimum of 57 course credits (19 courses) or 51 course credits (17 courses) (for Capstone review or Thesis respectively) including nine credits minimum thesis research or the six credits minimum for the capstone review paper. For the joint programs, students take approximately equal numbers of courses within each of the two specialties. The final thesis is formally defended in an open defense that includes the student's committee.

Core Courses

Course Numbers: BCOR-5560

Description

Globally, biodiversity is being dramatically altered by human activities. Because many species remain undiscovered and ecological roles of existing species are poorly understood, the magnitude of these changes is difficult to evaluate. This course will discuss multiple aspects of biodiversity including: definition and importance of biodiversity to conservation issues; threats to biodiversity including introductions of non-indigenous species; impediments to conservation; scientific constraints; developing tools and forums for conserving biodiversity, and evaluating existing biodiversity initiatives currently in place and planned. Management approaches such as parks, protected areas, no-take or completely protected reserves, and special management areas will be discussed and evaluated.

Learning Outcomes

The student will be able to:

  1. Understand the complex nature of the process that affect and control biodiversity,
  2. Learn the history of biodiversity, both in a traditional sense and the current post-modern synthesis, 
  3.  Become familiar with the major paradigms used to explain biogeographic pattern, and how emerging studies are calling into question long-held traditions and beliefs of what biodiversity is and how it is managed,
  4. Understand the power of hypothetico-deductive methods, and how they are employed in pattern process models of biodiversity 
  5.  Identify threats to biodiversity and what mechanisms are emerging to address its loss, 
  6.  Gain understanding of the impact and rapid spread of non-indigenous species, methods of introduction and spread, and current control measures, 
  7.  Gain knowledge of how species-specific management programs relate to biodiversity loss and conservation,  
  8.  Have a detailed understanding of the global, basin, regional, and local threats to marine environments and be able to conceptualize research and management actions to prevent loss of diversity,
  9. Understand major legislative and legal actions of governments and institutions that have been enacted to deal with threats to biodiversity, and  
  10.  Measure the success/failure of current action strategies, such as Protected Areas, by applying lessons learned and incorporation of emerging methods and data sources.

Course Numbers: BCOR-5570 and OCOR-5603

Description

This is a basic course on the practical applications of descriptive and inferential statistics. Emphasis will be on the presentation of statistical theory, and the methodology of summarizing and analyzing biological data. It is designed for students who have never had a statistics course in college. (Students who have previously had statistics in college should plan on taking OCOR-5606: Biostatistics-II.) The use of software to facilitate computations will be presented. Specifically, statistical analysis utilizing Microsoft Excel® and PHStat2.5 for Excel® will be used in class. Measures of central tendency, dispersion, and variability testing will be discussed along with basic concepts of probability, continuous distributions, confidence intervals, one-sample and two-sample hypothesis testing.

Learning Outcomes

Students will:

  • develop an understanding of the foundations of statistical thinking and analysis
  • master basic statistical methods necessary to analyze sample data and make inferences about the population of interest
  • learn to use appropriate statistical software packages to conduct basic statistical analyses
  • learn to interpret results of basic statistical analyses

Course Numbers: BCOR-5575 and OCOR-5606

Description

This course enhances student knowledge about principles and practice of biostatistics through applied statistical methods in observational and experimental study designs used in biological research.

Learning Outcomes

The student will be able to:

  • formulate the research question(s) and the corresponding statistical hypotheses
  • choose the appropriate biostatistical methods and conduct biostatistical analyses such as: descriptive statistics for the required variables choose and calculate the appropriate test statistics calculate confidence intervals for means and proportions calculate correlations and construct regressions calculate ANOVA tables in basic experimental design.
  • use computing statistical packages such as NCSS, and EpiInfo, be able to apply the biostatistical methods producing results and interpreting the computer output in an appropriate manner (e.g. test values, degrees of freedoms, p-values, confidence intervals, trend statistics, ANOVA analyzes, regression diagnostics, and regression modeling).
  • create statistical analyses that provide results comparables to other published results.

Course Numbers: BCOR-5585 and OCMB-8020

Description

The primary goal of this course is to place the growing fields of molecular biology, genomics and biotechnology into a marine context, through classroom and computer laboratory exercises. We will study the milestone discoveries which lead to the rise of genomics, characteristics of the wide spectrum of different genomes (prokaryotic, eukaryotic and organellar), innovative molecular techniques and computational tools used to study these genomes, and the impact of genomics on current marine issues and problems.

Learning Outcomes

The student will be able to:

  • demonstrate proficient library and computer skills in data gathering and analysis 
  • analyze macromolecular sequences in the context of specific biological questions 
  • navigate and apply diverse, modern genetic databases and software 
  • apply current bioinformatics and genomics methods to current marine organismal systems and problems 
  • prepare oral and written reports in an acceptable standard scientific format 
  • understand some of the larger questions and issues within genomics and large scale  data collection and analysis 
  • learn to work and cooperate as part of an interdisciplinary team

Course Numbers: BCOR-5565, CZMT-0800, MEVS-5300, and OCMB-8500

Description

This course is designed to provide tools, resources, and approaches to improve a graduate student's ability to:

  • write in a scientifically precise and accurate manner
  • interrelate complex conceptual issues in a coherent manner
  • develop skills in various approaches for oral communication of complex scientific topics
  • gain experience in presentation, critiquing, and interacting with various types of audiences in differing venues

Learning Outcomes

Participants in this course will gain understanding in:

  1. identifying and assembling information and resources on scientific subject matter research topics
  2. developing and assembling relevant information and data into an outline
  3. incorporating varying oral communication styles for various audiences
  4. improving both oral and written presentations of research projects, proposals, and scientific presentations
  5. critically evaluating and critiquing oral presentation styles of themselves and others

Course Numbers: BCOR-5580, CZMT-0715, MEVS-5480, and OCMB-8550

Description

This course provides a broad historical overview of biological sciences since Aristotle through Darwin with emphasis on both the experimental design of seminal studies as well as the evolving philosophical approaches to the acquisition of knowledge from methodological naturalism to critical rationalism, Karl Popper and the hypothetico-deductive model for scientific method.

Learning Outcomes

The student will be

  • familiar with the history of biological sciences including selected scientists and their famed experiments
  • familiar with the history of the philosophical underpinnings of the current definitions of science and the scientific method
  • able to use the hypothetico-deductive method in their own research
  • able to understand both the strengths and shortcomings of this method

* Either Biostatistics I or II will fulfill the Biostatistics core requirement.

Biological Science Courses

Course Numbers: BMME-6700 and OCMB-8030

Description

This course aims to provide practical laboratory experience with basic and advanced molecular genetics methods currently in use for molecular ecology and phylogenetics applications. Instruction on basic methods from DNA/RNA extraction of various marine organisms to gel electrophoresis will be the foundation. Secondly, students will run through other routine molecular protocols such as PCR (polymerase chain reaction), restriction digestion and polymorphism analyses, Quantitative real time (or qPCR), molecular cloning, plasmid isolation, and DNA sequence analyses in the context of marine organismal biology and molecular ecology.

Learning Outcomes

Students will:

  • practice basic aseptic and safe laboratory methods
  • demonstrate knowledge of common biochemical and molecular reagents (enzymes, chemicals etc), how and why they are applied, and calculate correct quantities of each in specific experiments
  • demonstrate practical ability in proper use of molecular laboratory equipment, such as micropipettors, spectrophotometry, electrophoresis, PCR amplification,qPCR, centrifuges, as well as biological samples and microbiological cultures
  • interpret results of molecular experimental data using comparative databases and computational biology tools (computers, software)
  • apply molecular genetics tools and methods to marine ecological and biological problems; develop testable hypotheses and molecular methods to test them

Course Numbers: BMME-6770 and OCMB-6010

Description

Microbial populations evolve and adapt to their surroundings in rapid and facile ways. This course is designed to familiarize the evolution/ecology/microbiology student with an understanding of the evolutionary genetic mechanisms that govern diversity of the microbial world with a particular emphasis on bacterial species and strains.  Numerous genetic mechanisms will be discussed that can rapidly diversify or homogenize bacterial populations including hypermutation, recombination, and the selective deletion of DNA.  Many of these adaptive changes lead to the acquisition of dangerous traits among bacteria including enhanced virulence attributes, multi-drug resistance, and unusual tolerance to environmental insults. In addition, methods and assays capable of detecting and measuring these kinds of evolutionary changes among bacterial species and strains will be reviewed.  Finally, a survey of analytical approaches currently deployed for ascertaining population and evolutionary diversity within a bacterial population will be undertaken.

Learning outcomes

Upon completion of this course, the upper-level student of ecology, evolution, and/or microbiology will be able to:

  • recognize and understand the role of bacterial mutators and the hypermutable phenotype in the persistence and survival of bacterial populations
  • comprehend the importance and impact of horizontal gene transfer and genetic recombination on the evolutionary structure of the bacterial strain and bacterial population
  • explain the emergence of dangerous phenotypes within bacterial populations including antibiotic resistance, virulence factors, and stress responses.
  • detect and quantify the presence and extent of adaptive evolutionary mechanisms including recombination among bacterial species and strains
  • understand the importance and roles of next-generation strategies deployed for effectively measuring populational diversity within a bacterial species

Course Numbers: BMME-8040, MEVS-5755, and OCMB-6460

Description:

This course presents the microscopic anatomy of scleractinian corals and gorgonians (Phylum Cnidaria, Class Anthozoa) to support studies on their ecology, physiology, reproduction, biochemistry, systematics, molecular biology/genetics, immunology, embryology, and pathology. Topics covered include histology; coral diseases; sample collection, preservation, processing, and histoslide preparation (lecture and discussion only, no laboratory); and slide reading of healthy and diseased specimens using light microscopy and virtual microscopy. The course begins with online readings and research, and then students will meet at NSUOC for one week of full-time lecture and laboratory sessions. Participants may bring histoslides from their own research to share with the group and discuss with Dr. Peters.

Learning Outcomes

At the conclusion of this course the student will be able to:

  • demonstrate a basic understanding of the microscopic structure of cnidarian cells and tissues
  • relate their structure and composition to metabolic function and organismal processes
  • compare the microscopic anatomy of different anthozoan species
  • understand pathobiology concepts and investigations
  • describe the histological techniques used to prepare tissue sections for microscopic examination
  • distinguish diseased tissue from tissue that is within normal limits
  • identify diverse symbionts and their roles in the holobiont (viruses, bacteria, protozoa, algae, fungi, metazoans)
  • appreciate the value of histology to inform various fields of scientific investigation

Course Numbers: BMME-7090, MEVS-5550, and OCMB-6560

Description

The deep sea is the largest living space on the planet, with some of the most diverse, complex and extreme environments on the planet.  This course will cover major topics in deep-sea biology, including depth zonation, energetics, adaptations, extreme environments, sensory biology, bentho-pelagic coupling and anthropogenic threats.  This course will provide you with a basic understanding of what we know (and don¿t know) about deep-sea ecosystems, the methods used to study this environment and inhabitants, and it will create an opportunity to discuss major current questions and exciting new discoveries.

Learning outcomes

At the conclusion of this course the student will be able to:demonstrate an understanding of ecological, geological, chemical and biological concepts as they relate to deep-sea ecosystems

  • describe the co-varying effects of temperature, pressure, oxygen and light levels on the adaptations of deep-sea organisms
  • demonstrate an understanding of the ecology of deep-sea organisms
  • evaluate the potential impacts of anthropogenic activities on deep-sea animals
  • read and understand a scientific paper, evaluate its findings and discuss the implications of those findings
  • synthesize a body of literature on a topic and present a clear summation of the topic, with a comprehensive background and description of relevant controversies
  • demonstrate effective communication skills and a full understanding of the scientific method

Course Numbers: BMME-6600

Description

This course is designed to give the qualified graduate student hands-on, practical experience at a non-NSU biological laboratory. Methods to be learned and implemented will vary according to the sponsoring external laboratory but will generally involve modern biological, biochemical, environmental molecular and biotechnological methods. The student will work closely on a predetermined project, with a designated supervisor at the external lab. Development of hypotheses, experimental goals and interpretation of results will be expected.

Prerequisite: Lab safety course, at least two undergraduate laboratory courses.

Learning Outcomes

The student will:

  • conduct specific experimental procedures from start to finish according to supervisor's directions
  • interpret scientific results either independently or with supervisor's guidance
  • demonstrate an understanding of the overall experimental hypotheses and goals
  • demonstrate adequate recording of experimental details, observations and results in a standard laboratory notebook
  • conduct research within a professional, team or multidisciplinary setting

Course Numbers: BMME-6750

Description

This course is designed to extend training provided in biotechnology internship I. The student will continue to show application of existing or novel biotechnology methods, and also provide evidence of performing an independent research project at the external laboratory. The course is designed to provide the graduate student hands-on, practical experience at a non-NSU biological laboratory. Methods to be learned and implemented will vary according to the sponsoring external laboratory but will generally involve modern biological, biochemical, environmental molecular and biotechnological methods. Development of hypotheses, experimental goals and interpretation of results will be expected.

Prerequisite: External biology/biotechnology internship I.

Learning Outcomes

The student will:

  • conduct specific experimental procedures from start to finish according to supervisor's directions
  • interpret scientific results either independently or with supervisor's guidance
  • demonstrate an understanding of the overall experimental hypotheses and goals
  • demonstrate adequate recording of experimental details, observations and results in a standard laboratory notebook
  • conduct research within a professional, team or multidisciplinary setting
  • plan to to derive, summarize and present scientific conclusions via standard routes: formal grey paper reports, publications or oral presentations

Course Numbers: BMME-6000, OCMB-6100, CZMT-0639, and MEVS-5023

Description

This course provides hands on training with the latest techniques in Geographic Information Systems and Remote Sensing. Course work includes lecture and hands on computer training. Areas covered (utilizing both ERDAS Imagine 8.3 and ESRI Arcview 3.0) include: GIS/Remote Sensing Theory, Image Georeferencing and Mosiacking, Image Enhancement and Classification Procedures, Accuracy Assessment Procedures, Importing GPS Polygons, Establishing Database and Mutimedia Hot links, Importing Tables, Joining, Building Queries, Charting and Map Creation. Instruction of class will be centered on application of these techniques to actual environmental case studies.

Learning Outcomes

The students will be:

  • taught the fundamentals of GIS, its potential as well as its limitations. Remote sensing is presented as an integral part of the GIS hierarchy and introduced using both marine and terrestrial examples
  • installed with a broad and comprehensive understanding of remote Earth observation, and will become familiar with the suite of sensors currently used for routine environmental monitoring
  • directed towards recent literature in a variety of current topics so as to ensure that by the end of the course, all students will be aware of the current status of remote sensing and GIS technology
  • not only familiar with the many types of remote sensing imagery used for Earth observation, they will also have a grounding in the physics behind the imagery, so as to allow a critical evaluation of the technology as a real-world tool

Course Numbers: BMME-6760, MEVS-5520, and OCMB-6510

Description

This is an introductory course on the procedures and techniques of tissue preparation for histology. Lectures and laboratory exercises will be utilized to teach tissue processing, embedding, sectioning, and staining. Through light microscopy, students will examine and evaluate coral samples for normal and impaired tissue structure. Although the course will be taught in the context of coral anatomy and tissue structure, histology techniques are generally applicable to other marine organisms.

Learning outcomes

Students will have:

  • in depth knowledge of coral anatomy and tissue structure
  • effective communication through lab reports and presentation of case studies
  • full understanding of scientific methods of histological processing

Course Number: BMME-8000, MEVS-5560, and OCMB-5670

Description

The course will provide an overview of the science behind plant biotechnology with a focus on plant improvement and industrial applications. It will include an introduction plant tissue culture and transformation techniques, plant molecular biology techniques and plant genomics. Specific case studies on the risks and benefits of plant genetic modification will be discussed.

Learning outcomes

Upon completion of the course the student will be able to:

  • demonstrate an understanding of the basic theoretical background in plant biology and in molecular and biochemical pathways unique to plants
  • describe basic methods in plant molecular biology, plant molecular diagnosis and plant genomics
  • perform basic techniques in plant tissue culture, including sterile techniques, media preparation and micropropagation
  • describe secondary metabolite production and give examples of plant biotechnology application in biofuels, pharmaceuticals/nutraceuticals, agriculture, and production of new materials 
  • describe methods of plant genetic engineering including their specific advantages, disadvantages and applications

Course Number: BMME 6001, MEVS 6001, and OCMB 6001

Description

The use of q-PCR has been implemented in microbiology studies to quantify abundance and expression of taxonomic and functional gene markers that pose contamination threats to drinking, recreational, marine, and fresh waters. Its use allows viable results for the indication of microbial presence associated with human pollution that supersedes the abilities of culture based fecal coliform and enterococci studies. The use of PCR chemistries is a more advanced, precise and sensitive method for estimating microbial species in environments. Within PCR chemistries, q-PCR allows for expedient results coupled with greater accuracy to determine if human pollution is contaminating a water source and in what amounts quantitatively.

Learning outcomes

Students will:

  • understand the significance of indicator microorganism to fecal water pollution studies
  • become familiar with classical culture procedures for determination of fecal coliform and enterococci and the interpretation of their significance
  • become familiar with q-PCR procedures to determine the same indicator species as done with culture methods
  • run actual water samples using culture methods and q-PCR methods
  • establish advantages and disadvantages of both techniques and relative specificity to human waste

Course Numbers: BMME-5750, MEVS-5470, and OCMB-6230

Description

The course centers on the systematics, ecology, behavior, and resource management of marine fishes with emphasis on the inshore fishes of the tropical Atlantic. A self-paced laboratory and some field work are integral to the course.

Learning Outcomes

Students will:

  1. be knowledgeable on systematics, ecology, behavior, of marine fishes
  2. knowledgeable on systematics, ecology, behavior, of inshore fishes
  3. have a working knowledge of fisheries resource management.

Course Numbers: BMME-8020, MEVS-5280, and OCMB-6095

Course Description

This course examines various aspects of the functional biology of marine animals, including physiology, feeding, locomotion, morphology and sensory biology.  Basic functional biology and physiological concepts will be taught, and then expanded upon to identify how animals have adapted to deal with major biological challenges found in the marine environment, such as pressure and temperature extremes, large salinity fluctuations, extremely low light levels, etc.

Learning outcomes

At the conclusion of this course, the student will be able to:

  • demonstrate an understanding of the basic physiology and morphology of marine animals
  • understand physiological/morphological adaptations to environment
  • understand adaptations to extreme environments ( e.g. Antarctic, hydrothermal vents)
  • evaluate the abilities of different marine groups to deal with anthropogenic  changes in their environments
  • read and critically evaluate primary literature in the field
  • synthesize a body of literature on a topic and present an effective powerpoint summary of the topic

Course Numbers: BMME-8030, MEVS-5080, and OCMB 6450

Description

Speciation is fundamental to evolutionary biology and is the process by which new biological species arise.  We have only recently begun to understand the process of speciation in marine organisms. Few extrinsic barriers to gene flow exist in the sea; therefore, marine speciation challenges the idea of allopatric speciation (new species only arise when populations are geographically isolated).

This course will review the evolutionary concepts associated with the process of speciation, with a particular emphasis on the mechanisms of speciation.  We will then delve into the primary literature to examine and critique speciation studies in marine organisms.  Topics covered in this course include as they relate to marine organisms: biodiversity, modes of speciation, reproductive isolation, species concepts, mate recognition, natural selection, cospeciation, sexual conflict, sexual selection, and reinforcement.  At the very least, students should have a basic understanding of evolution prior to taking this course.

Learning Outcomes

Students will

  • gain an overview of the process of speciation
  • describe the species concepts, modes of speciation, marine barriers to gene flow, and mechanisms of reproductive isolation
  • understand the challenges of study speciation in the sea and the differences between terrestrial and marine mechanisms of speciation
  • obtain the background necessary to understand and critique the primary literature on speciation in the ocean
  • be expected to lead discussions on a specific topic related to speciation

Course Numbers: BMME-5500, OCMB-8036, and MEVS-5135

Description

The basis of organic evolution is the changes that take place at the genetic level, due to mutation and genomic changes. This course will delve into evolutionary principles, focusing specifically on the mechanisms and dynamics of change at the molecular level of DNA and proteins. Focus will be on the neutral theory of molecular evolution; genome wide changes; synonymous versus nonsynonymous mutations; detecting selection at the molecular level; reconstructing molecular phylogenies; phylogeography and natural history with molecules, and understanding current computational software used to analyze molecular changes.

Learning Outcomes

The student will be able to:

  • describe several lines of scientific evidence supporting molecular evolution
  • explain the theoretical basis of molecular evolution, microevolution, population genetics, Darwin's principle of natural selection, and Kimura's Neutral theory and the molecular clock
  • compile and analyze molecular evolution and phylogenetics data
  • demonstrate the ability to integrate factual and conceptual information regarding evolution in examination essay questions
  • demonstrate ability to apply current software in molecular evolutionary analyses
  • discuss and evaluate current historical and philosophical controversies concerning molecular evolution
  • organize complex data in a concise and logical manner for oral and/or written presentations

Course Numbers: BMME-6650 and OCMB-6390

Description

Objectives: The objective of this class is to introduce the student to Forensic Biology, its history, its methods and the application of DNA typing to a court of law. The class will introduce the students to basic genetics and population genetics as it applies to forensic biology. The class will also introduce the students to both human and non-human DNA typing techniques and instrumentation. It will also introduce the students to critical thinking and problem solving approaches.

Learning Outcomes

The students will become proficient in:

  • understanding the basic biology of DNA typing
  • learn and apply scientific and critical thinking skills
  • to research and report on a relevant topic related to DNA typing as it relates to human or non-human DNA

Course Numbers: BMME-5800, OCMB-6500, CZMT-0910, and MEVS-5450

Description

Stable isotope ratios provide a natural way to follow and trace elemental cycling in a number of environments. This course will focus on the use CHNOS isotope distribution and cycling in different biomes. The information provided will cover migration and invasion, food webs, mixing, plants, animals, microbes, atmospheric gases; and the focus of the course will be more closely tailored to the needs of students. Students will process a limited number of individual project samples and learn to interpret the stable isotope data. Course evaluation will be based on participation, a project report and a research paper on the use and evolution of stable isotopes in an area of environmental science.

Learning Outcomes

The students will acquire:

  • a background and working knowledge of stable isotope ratios
  • learn how to identify how isotopes tracers can help solve environmental questions
  • sample processing techniques, laboratory analysis and data interpretation for many types of biological material
  • students will be able to identify how to appropriately use stable isotope ratios to answer ecological questions

Course Numbers: BMME-5600

Description

Molecular biology has grown as a discipline since the 1970¿s, and now encompasses a wide variety of methods and theory. In order to perform growing research in genomics and bioinformatics, basic training in fundamental molecular methods are necessary. This course will train an upper level undergraduate or entry level graduate student in the basic techniques, such as DNA extractions from diverse organisms, gel electrophoresis, polymerase chain reaction, DNA sequencing reaction and analysis, restriction enzyme digests, and molecular cloning among others.

Learning Outcomes

Students will

  • demonstrate practical ability to independently perform basic molecular biology protocols
  • demonstrate independent ability to interpret molecular biology results from PCR, restriction enzyme digests (RFLP), gel electrophoresis and DNA sequences
  • demonstrate ability to adequately record experimental protocols, results and interpretations in a standard laboratory notebook format
  • demonstrate ability to write a concise and detailed report on experiments

Course Numbers: BMME-7080, MEVS-5145, and OCMB-6530

Description

This course will examine the ultrastructure of marine organisms and range in focus from bacteria to fish. Lectures and labs will be conducted to examine scanning and transmission electron microscopy (SEM and TEM) of tissue and cells from many marine groups. Lectures will include discussion of basic theory of electron optics and include elemental analysis (EDS). The preparation of specimens for SEM and TEM including fixation, dehydration, embedding, sectioning and staining will be discussed in lectures. Additionally, examination of the application of electron microscopy to the field of biomineralization will be discussed. In the labs students will prepare their own research specimens for SEM and/or TEM following the protocols discussed in lecture. Students will conduct presentations and submit a term paper at the end of the semester.

Learning outcomes

Students will:

  • obtain a basic understanding of electron opticsd
  • obtain skills required for preparation of specimens for SEM and TEM will be acquired
  • acquire the knowledge required for operation of the SEM and TEM
  • use techniques for collection of SEM/TEM images and image processing
  • understand the relationship between ultrastructure and biomineralization
  • give a formal presentation of ultrastructure research results
Course Number: BMME-7000

Description

Research and thesis preparation. Requires prior consultation with major professor and submission of an approved thesis proposal.

Learning Outcomes

The student will

  • learn about hypothesis driven research
  • learn scientific methods
  • learn how to handle large databases (statistically)
  • learn scientific writing
  • gain experience presenting complex data in public

Course Numbers: BMME-7030

Description

Research and thesis preparation. Requires prior consultation with major professor and submission of an approved thesis proposal.

Learning Outcomes

The student will

  • learn about hypothesis driven research
  • learn scientific methods
  • learn how to handle large databases (statistically)
  • learn scientific writing
  • gain experience presenting complex data in public

Course Numbers: BMME-7060

Description

Research and thesis preparation. Requires prior consultation with major professor and submission of an approved thesis proposal.

Learning Outcomes

The student will

  • learn about hypothesis driven research
  • learn scientific methods
  • learn how to handle large databases (statistically)
  • learn scientific writing
  • gain experience presenting complex data in public

Course Numbers: BMME-7010

Description

An extended literature review of a subject approved by the student’s advisory committee. The paper should demonstrate proficiency in library research, organization, and writing. Requires prior consultation with major professor and submission of an approved capstone proposal.

Learning Outcomes

The student will:

  • learn how to research scientific topics using published information
  • master the art of compiling a scientific review of a subject
  • gain experience in scientific writing
  • learn how to present a seminar

Course Numbers: BMME-7040

Description

An extended literature review of a subject approved by the student’s advisory committee. The paper should demonstrate proficiency in library research, organization, and writing. Requires prior consultation with major professor and submission of an approved capstone proposal.

Learning Outcomes

The student will:

  • learn how to research scientific topics using published information
  • master the art of compiling a scientific review of a subject
  • gain experience in scientific writing
  • learn how to present a seminar

Course Numbers: BMME-7070

Description

An extended literature review of a subject approved by the student’s advisory committee. The paper should demonstrate proficiency in library research, organization, and writing. Requires prior consultation with major professor and submission of an approved capstone proposal.

Learning Outcomes

The student will:

  • learn how to research scientific topics using published information
  • master the art of compiling a scientific review of a subject
  • gain experience in scientific writing
  • learn how to present a seminar