Electives
BMB 6000 - Biotechnology Bench to Bedside - 3 Credit Hours)
Syllabus
This course will cover a variety of topics including documenting laboratory data, managing intellectual property, the basis of an invention, patents and patentability, licensing technology, working with industry, start-up companies, research vs. product development, and FDA requirements for testing and approval of new drugs and devices. The course will include a series of lectures to introduce topics followed by case studies that will incorporate small group self-directed, problem-based learning that will give students the opportunity to develop plans for translational research, potential business plans, and critical timelines for product development and regulatory pathways.
BMB 6110- Molecular Basis of Disease - 1 Credit Hour
The lectures will be presented by internationally recognized investigators in specific areas of various molecular basis of diseases. They will present their talks as a part of the UTMB BMB weekly lecture series. The topics include molecular mechanisms of such misfolded protein diseases as: (a) neurodegenerative diseases; (b) metabolic diseases; (c) diseases of aging, etc. The two-hour discussion sessions will involve the analysis by student of key papers selected by the lecturers and related to the lecture material.BMB 6206 Bioinformatics on the World Wide Web - 2 Credit Hours
Syllabus
This course introduces molecular biologists
to software tools on the World Wide Web for search, retrieval and analysis
of amino acid and nucleotide sequences. The software includes BLAST, FASTA
and Clustal_W. The course also covers secondary and tertiary structure
prediction of proteins, homology or comparative modeling and methods for
the analysis and validation of structures. 3-D modeling based on experimental & theoretical constraints
will be explained with special reference to software including MASIA, EXDIS,
DIAMOD & FANTOM. Two sessions will be given per week. The first session
will describe the scientific concepts behind the tools and the computational
procedures. The second session will be an “I day” where students
will learn to use these tools through hands on sessions on modern graphic
workstations. The goals are to provide a critical appreciation of bioinformatics
tools and enable the student to apply them to his/her research. This is
a 10 week course.
BMB 6216 Practical Algorithms for Bioinformatics and Systems Biology - 2 Credit Hours
BMB 6227 Inborn Errors of Metabolism- 2 Credit Hours
Syllabus
This course will cover the inherited diseases whose basic
metabolic disturbances have been described. Emphasis will be placed on mechanisms
contributing to enzymatic blocks. The primary aim is to give an understanding
of the basic defects and their effects on metabolism.
BMB 6265 Single Molecule detection and Manipulation, 2 Credit Hours
Single molecule methods are an important new set of tools that are currently used in many areas of biology. The goal of this course is to provide conceptual framework on single molecule experimental techniques. We will describe novel methods of single molecule manipulation and analysis. Some of the techniques that will be covered are Atomic Force Microscopy, Optical tweezers and single molecule fluorescence. We will discuss the use of these techniques to study polymer elasticity, protein mechanics, motor proteins, protein folding, RNA folding, receptor-ligand interactions, imaging of single molecule and cell mechanics. In each lecture (1hr; 2 x week) we will discuss two or more key papers.BMB 6326 Probabilistic and Statistical Methods in Bioinformatics, 3 Credit Hours
This course is an introduction to the ideas and tools of probability calculus, statistical methods and machine learning techniques for bioinformatics processing of large scale biological datasets. It consists of four parts: basic probability calculus, statistical models, machine learning and applications in proteomics and genomics. We will also provide the necessary introduction into linear algebra, R programming and algorithmic design techniques. The course build concepts for machine learning and statistical models from probabilistic and linear algebraic bases. Sample spaces, conditioning, Bayes' Rule, random variables, distributions, expectation, and Markov chains will be covered in the 1rst part of the course. Interesting examples such as the Matching problem, variations of Birthday Problem, Gambler's Ruin, Simpson's paradox, St. Petersburg Paradox, and Markov Chain examples are discussed in the context of probability modeling. Linear algebraic (matrix based) view of modeling for linear least squares, support vector machines and other statistical tools will be provided. The discussed topics in probability calculus, statistics and machine learning are later applied in the example of bioinformatics data processing. Specific examples of applications are in mass spectrometry based proteomics, genomic sequencing and sequence alignments. Future opportunities and current limitations will be critically addressed. In addition to the regular lecture sessions, supplementary sections may be scheduled to address issues related to R.BMB 6312 Introduction to FastKinetics - 3 Credit Hours
A course for advanced graduate students that provides an introduction to the theoretical and experimental aspects of transient chemical kinetic analysis of biochemical reaction mechanisms. Emphasis is placed on application of time-dependent and fast kinetic methods to study the dynamics of biomolecular interactions.BMB 6316 – Cell Signals for Growth, Differentiation and Death – 3 Credit Hours
An in depth course designed to give students an understanding of multiple signal pathways and to analyze the literature of cell signaling in normal and pathological cell growth, differentiation and death (apoptosis). Following a set of lectures, students will present and discuss publications that demonstrate specific aspects of signaling pathways involved in regulation of cell proliferation, cancer and apoptosis. Through the analysis of publications, students will be exposed to the experimental designs and techniques used to elucidate signal pathways, the role of multiple pathways in cellular regulation and the mechanisms by which normal regulatory mechanisms are subverted during transformation and carcinogenisis. Faculty will provide written evaluations of the presentations. Grades for the course will be based upon presentations and class participation.BMB 6332 Molecular Biophysics I - 3 Credit Hours
In this course, students learn thermodynamics and kinetics for biological molecules. Both theoretical and experimental aspects are covered. Students also learn the Mathematica software so that they can use it as a tool for their own research. This course will introduce the student to the use of Mathematica as a tool for problem solving, simulation, and programming. This tool will be used throughout the entire curriculum.BMB 6334 Molecular Biophysics II - 3 Credit Hours
Introduction to principles, methods, and approaches employed in the study of the structure and function of biological macromolecules. Topics include NMR, X-ray diffraction, and electron microscopy methods. This course will use Mathematica as a tool for problem solving, simulation, and programming.BMB 6336 Physical Basis of Macromolecular Structure - 3 Credit Hours
Physical Basis of Macromolecular Structure: Introduction to proteins and nucleic acids, with emphasis on physical underpinnings. Topics include primary, secondary, and tertiary structure, sequence analysis, energetics and predictive methods.BMB 6338 Computer Modeling of Macromolecular Structure and Function - 3 Credit Hours
Introduction to computational modeling methods for protein and nucleic acid structure and function. Topics include molecular dynamics, homology modeling, and sequence and genomic analysis methods.BMB 6360 Thermodynamics of Macromolecular Assembly - 3 Credit Hours
What is Systems Biology? It is a quantitative recapitulation of biological functions in cell. The course will address the following questions:1.What is the information needed for Systems Biology?
2.How does one acquire and use that information?
The course is designed to provide students with basic physical principles of ligand-protein, protein-protein and protein-nucleic acid interactions. The concept of thermodynamic linkages will be introduced and initially applied to a system of simple, small ligand binding to protein and subsequently, to multi-macromolecular systems. The specific techniques will include single molecule approaches, mass spectrometry and surface plasmon resonance in addition to other biophysical techniques. Students will be responsible for presenting the basics of these techniques with assigned readings on a few applications. Speakers with these expertises will be invited to interact with students/faculty and present seminars. Each student will propose the usage of these approaches to tackle an important issue within their own field of research. Students will be graded by their presentations, the depth of their knowledge and the successful application of principles to a new biological system. The final written examination is in the format of a grant application.
