snhs-BMS.jpg (49229 bytes)

BMS 537 (02)      HUMAN GENETICS

    Feedback  Glossary  Links,Assign'm    MainPage    Contents  SlideShow   GenomeProject GeneGateway  MessageBoard

   

 

 Gene Gateway  NCBI: PubMed Medline Citation Search Google MEDLINEplus Health Information

Genetics Journal Online Mendelian Inheritance in Man: OMIM Vitrual Fly Lab Online

Human Molecular Genetics 2. 2nd ed. Strachan, Tom and Read, Andrew P. Oxford, UK: BIOS Scientific Publishers Ltd; 1999.

 Human Genome Project       Essential Genetics BlackBoard    dna1.gif (13700 bytes) BlackboardDOE's next step in genomics  CDC: Geonomic & Disease Prevention

DNA Interactive   Genetics Home Reference: your guide to understanding genetic conditions

 

 

Human Genetics Course Syllabus

(Three Credit-Hours)

Fall 2002

Section (02) 6:00 PM- 9:00 PM    Thursday   SNHS Bldg. Rm 106

Dr. Yu-Wai Peter Lin MT(ASCP), PhD

Office/Lab: SNHS Bldg. Room 330,   Ph: (305) 899-3226

E-mail: plin@mail.barry.edu  emailed.gif (14893 bytes)

Office Hours:

Posted on office door or by appointment

M  W & F   9:00 - 11:00 AM; 

Evening hour-   Th  5:00 - 6:00 PM or By appointment

 

Human Genetics Class Distribution List (Bucmail): BMS-537-02-0204@mail.barry.edu

 

 

 

DNA-horizontal.gif (17251 bytes)

 

Table of Contents

bulletCourse (Human Genetics) Outline
bulletInstructional Method
bulletClass Schedule
bulletWeek 1-4 (Aug.29 - Sept.19)
bulletWeek 5-9 (Sept.26 - Oct 24)
bulletWeek 10-14  (Oct.31 - Nov.28)
bulletMessage Center
bulletGlossary (NHGRI-NIH)
bulletLinks and Assignments
bulletGenetics in the News
bulletBookmarks
bulletCopyright Acknowledgement

 

 

bullet

Course Outline:

Presentation of reports, discussions, lectures, and papers on selected topics in Human Genetics. An examination of Principles of Heredity, from Genes and Pedigrees to current Molecular and Recombinant DNA techniques for the Identification of Human Diseases.

bullet

Goals and Objectives:

Goals -- The major goal is acquiring an understanding of current theories of mechanisms of inheritance and their implications for both basic knowledge and its application in modern medicine and technology. A secondary aim is to familiarize students with current scientific literature and the use of the vast genetics and biomedical resources on the World Wide Web, for research.

Objectives -- Upon completion of this course the student will be able to:

1. explain the fundamental aspects of chromosome structure and organization as well as eukaryotic gene expression and gene regulation.

2. apply the knowledge of normal gene expression in order to explain what happens under abnormal conditions.

3. discuss the human genome and the study of human genetic diseases on a current, molecular level.

4. increase analytical skills by reading, interpreting and discussing current scientific literature in the field of human genetics.

 

bullet

Text:

bullet

Human Molecular Genetics 2 nd Edition (Required text book)

        http://www.bios.co.uk

Tom Strachan and Andrew P. Read

BIOS Scientific Publishers Limited, A Wiley-Liss & Sons, Inc.

New York, 1999.

ISBN # 0-471-33061-2

 

bullet

The Biology Place (Required subscription)

The Biology Place, a web learning environment that includes learning activities, study and testing aids, and a wide range of content to help you succeed in your course.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               

http://www.biology.com

The Biology Place      Customer Center   Peregrine Publishers

Student Subscription Options: You can purchase a subscription to Biology Place online and pay by credit card to gain immediate access.  If you are ordering by check through the mail, a mail order form will be generated for you at the end of the process.  To order, please click on the link below.

http://www.biology.com/campbell/stureginfo.html

 

 

 

bullet

Clinical Genetics: A Case-Based Approach (Required text book)

D. Bonthron, D. FitzPatrick, M. Porteous & A. Trainer

WB Saunders Company Limited, London, 1998

ISBN # 0 7020 2351 5

 

bullet

Medical Genetics (Reference)

Lynn B. Jorde, John C. Carey and Raymond L. White

Mosby - Year Book, Inc.

St. Louis, Missouri, revised for 1997

ISBN # 0 8016 6414 4

bullet

A Dictionary of Genetics (Reference)

Robert C. King and William D. Stansfield

Oxford University Press

New York, 1997 (Fifth edition)

ISBN # 0 19 509441 7

 

Back to Table of Contents

 

bullet

Instructional Methods:

The lecture portion of the course will consist of oral presentations given by the instructor and supplemented with overhead transparencies and AV slides. Peer review, cooperative learning, and active discussions with the students are encouraged. Critical reading and discussion of recent scientific journal articles will be part of the regular student activities.

Computer assignments (HyperCELL), internet connection to biology web site on the World Wide Web (The Biology Place), online journals (BioMedNet- http://biomednet.com), CD-ROM (Current Content), Medline Search (Internet Grateful Med- http://igm.nlm.nih.gov), web connection to the National Library of Medicine, National Center for Biotechnology Information (PubMed- www.ncbi.nlm.nih.gov/pubmed) and simulations (PCGene) will be used during the course.

We will also utilize a number of On-line Scientific Journals through the Internet (Current Opinion in Genetics- http://biomednet.com, The Journal of the American Medical Association- http://www.ama-assn.org, Medline- http://igm.nlm.nih.gov, NIH AIDS information resources, www.biology.com etc.)

 

 

bullet

BIOLOGY GRADING SCALE

    A = 90-100%

    B = 80-89%

    C = 70-79%

    D = 60-69%

    F = 0-59%

 

Your Final Grade for this course will be determined as follows:

Mid-Term Exam = 300 points

Final Exam = 300 points

Homework/Library assignments = 150 points (50 pt@ x 3)

Surprise Quizzes = 150 points (50 pt@ x 3)

Subjective: Class participation, attendance, etc. = 100 points

Grade = Total points earned / 1000 x 100%

 

Note: All exams, quizzes and written assignments are the property of the School of Natural and Health Sciences.

 

Back to Table of Content

 

bullet

Quizzes, Homework/Library Assignments:

There will be three (3) surprise quizzes, and three (3) homework/library assignments (worth 50 points each) during the semester. These assignments are important to your grade in the course and are intended to help guide your studying and to familiarize you with the recent and cutting edge scientific literature and research.  Graded assignments will be returned for review within two weeks.

Reading assignments from the text are listed on the course syllabus to correspond with the material to be covered in class on a given week.  The intent of the reading assignments is to reinforce the lecture material and to provide additional information and perspective.  It is essential that you read the material for each section as it is not possible to cover all the appropriate material in class.

To gain the MOST benefit from the reading assignments, you should read the material before class.  You will be responsible for the subject matter presented in class as well as the reading and Internet assignments for the exams.  In studying for exams, use the lecture material as a guide as to the specific areas in the text to focus on.

 

bullet

Mid-Term Exam and Final Exam:

Each exam will consist of multiple choice, problem solving, matching, fill-in-the-blank, and short-essay questions. Material from the lectures AND the assigned readings will be included. The mid-term exam is scheduled for October 11, 2001. The Final Exam is scheduled for Thursday, December 13, 2001, 6:00 - 7:50 PM.

All make-up exams will be oral unless special arrangements are made by the student before hand.

 

bullet

Academic Dishonesty Policy:

Students should be aware that cheating will not be tolerated. Any student caught giving or receiving assistance during an exam, or using cheat sheet, etc. will receive a grade of ZERO for that exam. This zero grade may not be dropped or made up; and WILL be used when determining the student's final grade. Any student caught cheating a second time will receive a grade of "F" for the course and will be referred to his/her Dean for disciplinary action. The same is true with respect for quizzes. A plagiarized written assignment will receive a grade of ZERO.

(For further information concerning the dishonesty policy, please refer to your Barry University 2001-2002 Graduate Catalog.)

 

bullet

Class Attendance:

Attendance is Mandatory.

You are expected to attend and actively participate in all classes. The student who is consistently late or absent will not have the same opportunities to ask questions as punctual students who attend each lecture and seminar. Therefore, consistent tardiness and/or consistent absence will result in a significantly lower evaluation on class participation. Daily sign-in sheets will be provided for the student's protection. A record of students who arrive late for lecture will be kept. You are responsible for all material covered in classes. If you miss classes, you cannot expect to do well in this course.

ABSENCE FROM CLASS IS NO EXCUSE FOR

MISUNDERSTANDINGS ABOUT ASSIGNMENTS OR QUIZZES

 

bullet

Disability Statement:

Students with documented special learning needs may want to inform the instructor so that accommodations may be made, or contact the Barry University Office of Services for Students with Disabilities 305 899 3489

 

bullet

Student Behavior Statement:

All Barry University students are expected to behave according to accepted norms that ensure a climate wherein all can exercise their right to learn. Disruptive behavior is not acceptable in the classroom. Students engaging in such behavior may be asked to leave or may be removed from the class by security personnel. Actions such as violence, shouting, use of cell phones and/or beepers, using profanity, interrupting, and any other behavior that the instructor believes creates an unpleasant environment in the classroom will be grounds for withdrawal from the course, judicial proceedings, or failure of the course.

 

 

Back to Table of Contents

 

sky.gif (37164 bytes)

SKY (Spectral Karyotype)

http://www.genome.gov/glossary.cfm?key=spectral%20karyotype%20(SKY)

NCBI  GENES AND DISEASE  http://www.ncbi.nlm.nih.gov/disease/

 

 

 

BMS 537 (02)      HUMAN GENETICS      Fall 2002

    Tentative Class Schedule:

 

bullet

Week 1-2    Fundamentals of Genes and Chromosomes    pp.1-70

 

bullet

Aug.29    Composition of DNA, Chromosome, RNA,  Proteins

Transcription of eukaryotic genes

RNA splicing

Mutation and DNA repair, DNA Packaging

Chromosome Banding, Centromeres, Telomeres, ORIs

Chromosome Abnormalities

Construction of mammailia artificial chromosomes: prospects for defining an optimal centromere. BioEssays, 21, 76-83; Schindelhauer D (1999). (pdf format)

DOE HGP Genomic Primers

Primer on Molecular Genetics- http://www.ornl.gov/hgmis/publicat/primer/primer.pdf

This primer was prepared by Denise Casey (Human Genome Management Information System - Oak Ridge National Laboratory) for the 1991-92 DOE Human Genome Program Report and modified for Web access by Dan Jacobson

 

Medline Search: PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi)

National Library of Medicine-http://www.nlm.nih.gov

 

Genetics Basis for Bioinformatics: Using Human Genome as an Example. By Ming-yi Chung NYMU,  Dec 24 , 2001;  Genetic basis for bioinformatics [PDF]

 

 

 

bullet

Sep. 5     Genes and Pedigrees

Mendelian Inheritance, Mitochondrial Inheritance

Genetic Imprinting, Mosaicism and Chimerism

 

Internet Tutorial

http://www.biology.com

The Biology Place- Investigative and Learning Activities

 

Ist Assignment (Due Sept 12):

Investigating a Neurological Condition

Keith A. Johnson (keith@bwh.harvard.edu), J. Alex Becker (jabecker@mit.edu)

 

Investigating a Neurological Disorder

http://www.biology.com/learning/neurological/introduction.html

by John Postlethwait, University of Oregon
© 1996, Peregrine Publishers, Inc., All Rights Reserved

 

bullet

Week 3-4    Fundamentals of Gene Cloning and

Molecular Hybridization     pp.71-138

 

Restriction Enzyme Digestion of DNA: An Interactive Study Guide

By Peter Russell, Reed College

http://www.biology.com/learning/red/introduction.html

A Hypothetical (Tutorial) DNA Mapping Example

http://www.biology.com/learning/red/mapping.html

Restriction Enzyme Cleavage of DNA

http://www.people.virginia.edu/~rjh9u/restdna1.html

Edvotek Biotechnology: DNA Mapping / Sequencing / Bioinformatics

206 - Restriction Enzyme Mapping

 

Map construction with probe fingerprints

Map assembly

 

Multiple Complete Digest Mapping

http://www.genome.washington.edu/UWGC/protocols/MapStrategy.cfm

 

 

bullet

Sep. 12     1st assignment due

Principles of DNA Cloning

Vector system, Expression Cloning

Molecular hybridization

 

bullet

Sep. 19     Polymerase Chain Reaction (PCR)

PCR-based DNA Cloning and DNA Analyses

Cloning- http://www.roslin.ac.uk/public/cloning.html

Application of PCR techniuqe:

Cloning and sequencing of Fundulus heteroclitus gonadotropins. 

Lin, Y.-W. P., B. A. Rupnow, D. A. Price, R. M. Greenberg, and R. A. Wallace (1992). Fundulus heteroclitus gonadotropins 3. Molecular cloning and sequencing of beta subunits of two distinct gonadotropins (GTH I and GTH II) from pituitary cDNA library using the Polymerase Chain Reaction. Mol. Cell. Endocrinol. 85: 127-139.                                                                                Medline Accession No.  PMID: 1526312;   UI: 92405806.   /Abstract                                               

 

_________________________________________________

 

2nd Assignment (Due Oct 3):

Copyright 1998, Peregrine Publishers, Inc. All Rights Reserved.

Cell to Cell and Person to Person:
Investigating AIDS and HIV
Part I: The Discovery and Epidemiology of AIDS
Part II: Investigating HIV so as to Devise AIDS Therapies

http://www.biology.com/learning/hiv2/introduction.html

by John Postlethwait, University of Oregon
© 1997, Peregrine Publishers, Inc., All Rights Reserved

 

Back to Table of Contents

 

 

bullet

Week 5-6   The Human Genome   pp.139-208

 

bullet

Sept. 26     The Nuclear Genome

Organization of Human Genes

The Immunoglobulin Gene Family

 

bullet

Oct. 03    2nd assignment due

Multi-Gene Families

Human Gene Expression

The Human Gene Map- www.ncbi.nlm.nih.gov/SCIENCE96

Complete Genomes- www.ncbi.nlm.nih.gov/Complete_Genomes

 

 

bullet

Week 7-9   DNA Mutation        pp. 209-240

bullet

Oct. 10     Mid-Term EXAM

bullet

Oct. 17    Mutation, Polymorphism and DNA Repair

Classification of Mutations

 

_________________________________________

3rd Assignment (Due Nov 7):

Copyright 1998, Peregrine Publishers, Inc. All Rights Reserved.

Recent Research on Co-receptor CKR5

http://www.biology.com/learning/hiv2/entry5.html

 

bullet

Oct. 24     Pathogenic Mutations

Pathogenic Potential of Repeated Sequences

 

Cancer Resource- http://cancer.med.upenn.edu

Online Mendelian Inheritance in Man- OMIM online database for genetic diseases- www.ncbi.nlm.nih.gov/Omim

 

 

Back to Table of Contents

 

 

 

bullet

Week 10-11   Mapping the Human Genomes    pp. 241-282

 

bullet

Oct.31      Physical Mapping

Low Resolution Physical Mapping

High Resolution Mapping

 

bullet

Nov. 07    3rd assignment due    

Genetic Mapping of Medelian Characters

        Recombinants and Nonrecombinants

        Restriction Fragment Length Polymorphisms (RFLPs)

 

 

bullet

Week 12-14       Human Genome Project     pp.295-314

 

bullet

Nov. 14     Construction of DNA Maps

The Human Genome Project

Gene Identification

 

logoDOE and NIH logos

About the Human Genome Project   Human Genome Project Information

http://www.ornl.gov/TechResources/Human_Genome/home.html

 

To Know Ourselves

http://www.ornl.gov/hgmis/publicat/tko/index.html

 

Exploring the Genomic Landscape

Genomic Geography

http://www.ornl.gov/hgmis/publicat/tko/04a_img.html

 

An emerging gene map

http://www.ornl.gov/hgmis/publicat/tko/04c_img.html

 

The Institute for Genomic Research

U.S. Department of Energy- Human Genome Program-

http://www.er.doe.gov/production/ober/hug_top.html

 

Back to Table of Content

 

bullet

Nov. 21     Strategies for Gene Therapy        pp.515-543

Ethics of Human Gene Therapy

 

Cancer Genome Anatomy Project-

www.ncbi.nlm.nih.gov/ncicgap

ExPASy-- Molecular Biology Server-

http://expasy.hcuge.ch

 

bullet

Nov. 28     No class,    Thanksgiving Holiday

 

 

bullet

Week 15      Dec. 5      Review

 

bullet

Week 16     Dec. 12    Final EXAM

 

Back to Table of Contents

 

 

MESSAGE  CENTER

bullet

Send message to Dr Lin's Mail Box  emailed.gif (14893 bytes)

bullet

Discussion Forum, OPEN  (Public)  MESSAGE BOARD

bullet

Comment ;    Feedback

Back to Table of Content

 

 

 

 

 

bulletLinks and Assignments

 

bulletDr. Lin's Biology Links (framed version)
bulletDr. Lin's Biology Links (unframed version)
bulletDNA Tools
bulletGenetics Links
bulletMolecular Biology Concepts
bulletGenetics Assignments
bulletHuman Genome Project Links
bulletGenetics in the News

Genetics  Links

bullet

Primer on Molecular Genetics- http://ww.gdb.org/Dan/DOE/intro.html

bullet

Medline Search: Internet Grateful Med-http://igm.nlm.nih.gov

bullet

National Library of Medicine-http://www.nlm.nih.gov

bulletOnline Mendelian Inheritance in Man- OMIM online database for genetic diseases- www.ncbi.nlm.nih.gov/Omim
bulletCloning- http://www.roslin.ac.uk/public/cloning.html
bullet

Cloning News: http://www.nap.edu/issues/14.3/cookdg.htm

National Academies on Cloning, NIH search on Cloning

Hello Dolly: A WebQuest   http://powayusd.sdcoe.k12.ca.us/dolly/main.htm

 

 

                                                                             

Back to Table of Content

                              

globe_6-26.jpg (17130 bytes)    

Copyright (C) 2000 MacNeil-Lehrer Productions. All Rights Reserved.   

GENOME UNRAVELED  

genomebhead.jpg (13411 bytes)
June 26, 2000
http://www.pbs.org/newshour/bb/health/jan-june00/genome_6-26.html

 

 

Copyright © 2000 MacNeil-Lehrer Productions. All Rights Reserved.

http://www.pbs.org/newshour/bb/health/july-dec99/gene_therapy_splash.htm

http://www.pbs.org/newshour/health/genetics/

Cloning

PBS- Cloning

http://www.pbs.org/newshour/health/cloning.html

 

Back to Table of Content

 

 

     The Rough Draft of the Blueprint

The Human Genome is now available! Find out what a "rough" draft means, and what needs to be done to interpret the information encoded in our genes.

 © 2000 Cold Spring Harbor Laboratory

http://vector.cshl.org/resources/abouthumangenome.html

 

 

Back to Table of Content

 

 

 

[Briefing Room header]

June 25, 2000

PRESIDENT CLINTON ANNOUNCES THE COMPLETION OF THE FIRST SURVEY OF THE ENTIRE HUMAN GENOME 

Hails Public and Private Efforts Leading to This Historic Achievement

THE WHITE HOUSE    Office of the Press Secretary

http://www.ornl.gov/hgmis/project/clinton1.html

 

Back to Table of Content


           

Science News Online

The Meaning of Life
Computers are unscrambling genomes to reveal the secrets in
DNA codes


By T. Hesman

mice     

Geneticists predict that computer programs that compare human DNA with mouse DNA will uncover secrets in the human genome. (Human Genome Proj./Oak Ridge Nat. Lab.)

http://www.sciencenews.org/20000429/bob2.asp

 

Back to Table of Content

 

GENETICS:
Zebrafish Earns Its Stripes in Genetic Screens

Gretchen Vogel

Researchers are using the zebrafish to search for a variety of genes involved in everything from obesity to bone diseases

http://www.sciencemag.org/cgi/content/full/288/5469/1160

Science Volume 288, Number 5469 Issue of 19 May 2000, pp. 1160 - 1161
©2000 by The American Association for the Advancement of Science.

 

Back to Table of Content

 

 

      home    

WEBSCAN Genes on the Web 

by Pamela M. Gannon

http://news.bmn.com/hmsbeagle/83/reviews/insitu  

Harvard University's recent conference Internet & Society 2000: Changing Our Lives (IS2K), held May 31 - June 2, 2000, included an exciting breakout session called "Genes on the Web." A panel of experts discussed how the Internet accelerates discoveries related to the human genome and spreads the information to researchers. In the introduction, Josh Lerner of the Harvard Business School called the current state of genomics research the "marriage of information technology with biotechnology and bioinformatics.

BioMedNet

© Elsevier Science Limited 2000

 

Back to Table of Content

 

 

November-December 2000 Issue of
American Scientist

New Technology Unravels the Mystery of Gene Function

Gene Chips and Functional Genomics

A new technology will allow environmental health scientists to track the expressions of thousands of genes in a single, fast and easy test

http://www.amsci.org/amsci/articles/00articles/Hamadeh.html

 

Back to Table of Content

 

 

Genomes to Life is the proposed next step at the Department of Energy to use data and resources from the Human Genome Project to accelerate understanding of dynamic living systems.

DOE's next step in genomics        logo     Genomes to Life

DOE's proposed Genomes to Life program would make important contributions in the quest to venture beyond characterizing such individual life components as genes and other DNA sequences toward a more comprehensive, integrated view of biology at a whole-systems level. The DOE offices of Biological and Environmental Research and Advanced Scientific Computing Research have formed a strategic alliance to meet this grand challenge

http://doegenomestolife.org/

 

Back to Table of Content

 

 

Cloning (Sun-Sentinel Aug 08 2001)

Researchers debate human cloning  

 Cloning  Problems associated with cloning (145K; KRT)  

Problems associated with cloning (145K; KRT) (View Video)

How cloning would be performed on humans (600K; KRT) (QuickTime)

PPL Therapeutics Research Director Alan Colman, at the conference, on human cloning
Aug 7, 2001

National Academies on Cloning, NIH search on Cloning

The Roslin Institute

 © copyright 2000 Roslin Institute: all rights reserved | designed by edNET

Roslin Institute, Edinburgh, England: http://www.roslin.ac.uk/index.html

Which Type of Cloning?: http://www.roslin.ac.uk/public/cloning.html

Sheep cloned by nuclear transfer from a cultured cell line.Campbell, K.H.S., McWhir, J., Ritchie, W.A., & Wilmut, I.* (1996) Nature 380: 64-66.  Abstract

Hello Dolly: A WebQuest  http://powayusd.sdcoe.k12.ca.us/projects/dolly/

 

Cloning and Nuclear Transfer Links

 

 

 

Back to Table of Contents

 

 

 

bulletNational Center for Biotechnology Information www.ncbi.nlm.nih.gov

NCBI GenBank

Understanding nature’s mute but elegant language of living cells is the quest of modern molecular biology. From an alphabet of only four letters representing the chemical subunits of DNA, emerges a syntax of life processes whose most complex expression is man. The unraveling and use of this "alphabet" to form new "words and phrases" is a central focus of the field of molecular biology. The staggering volume of molecular data and its cryptic and subtle patterns have led to an absolute requirement for computerized databases and analysis tools. The challenge is in finding new approaches to deal with the volume and complexity of data, and in providing researchers with better access to analysis and computing tools in order to advance understanding of our genetic legacy and its role in health and disease.

The late Senator Claude Pepper recognized the importance of computerized information processing methods for the conduct of biomedical research and sponsored legislation that established in November, 1988, the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM). The NLM was chosen for its experience creating and maintaining biomedical databases, and because as part of the National Institutes of Health (NIH), it could establish an intramural research program in computational molecular biology. NCBI’s mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. Its mandate includes four major tasks:

bulletCreate automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics;
bulletPerform research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules;
bulletFacilitate the use of databases and software by biotechnology researchers and medical personnel; and
bulletCoordinate efforts to gather biotechnology information worldwide.

National Center for Biotechnology Information (NCBI)  http://www.ncbi.nlm.nih.gov/

 

Back to Table of Contents

 

OMIM™
Online Mendelian Inheritance in Man

http://www.ncbi.nlm.nih.gov/Omim/

Welcome to OMIM(TM), Online Mendelian Inheritance in Man. This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE articles and sequence information.

 

 

bullet

Glossary of Genetic Terms  NIH

             http://www.nhgri.nih.gov/DIR/VIP/Glossary/

NHGRI

 

 

bullet

Genomic and Genetic Resources on the World Wide Web

  http://www.nhgri.nih.gov/Data/

Genomic and Genetic Resources on the World Wide Web

 

Back to Table of Contents

 

bullet

Medline Search: Internet Grateful Med-http://igm.nlm.nih.gov

National Library of Medicine presents Internet Grateful Med

Internet Grateful Med (IGM) is a World Wide Web application running on a gateway system at the U.S. National Library of Medicine (NLM). Internet Grateful Med is most often used to search in MEDLINE -- more than nine million citations to the biomedical literature of the world, from 1966 to the present. IGM provides assisted searching in MEDLINE (including PREMEDLINE) and 14 other databases: AIDSLINE, AIDSDRUGS, AIDSTRIALS, DIRLINE, HealthSTAR, HSRPROJ, HISTLINE, OLDMEDLINE, SDILINE, SPACELINE, BIOETHICSLINE, POPLINE, TOXLINE and ChemID. A brief description of each database is available from the IGM introductory screen. Internet Grateful Med User's Guide http://igm-01.nlm.nih.gov/splash/IGM.survival.guide.html#intro

 

bulletPubMed NLM's search service to access the 9 million citations in MEDLINE and Pre-MEDLINE (with links to participating on-line journals), and other related databases.

   http://www.ncbi.nlm.nih.gov/PubMed/

 

bullet

National Library of Medicine-http://www.nlm.nih.gov

U.S. National Library of Medicine (NLM)  MEDLINEplus Homepage

 

Back to Table of Contents

 

 

Genes and disease header bar

THE QUEST for an understanding of how genetic factors contribute to human disease is gathering speed. Forty years ago, the structure of DNA had just been solved and the precise number of human chromosomes was still under debate. The association between Trisomy 21 and Down's syndrome was on the eve of discovery and a state-of-the-art computer weighed in at 30 tons, covering about 1000 square feet of floor space.
   We now know that there are 46 human chromosomes, which between them house 3000 million base pairs of DNA and encode about 60,000 to 80,000 proteins. These coding regions make up only about 2% of the genome (the function of the remaining 98% is unknown) and some chromosomes have a higher density of genes than others.

A great deal of effort over the past ten years has been put into creating a physical map of the human genome - ordering genes within the genome by placing landmarks to navigate by. As well as providing an excellent framework for the complete sequencing of the human genome, the physical map has assisted directly in identifying about 100 disease-causing genes.
   ONE OF THE most difficult challenges ahead is to find genes involved in diseases that have a complex pattern of inheritance, such as those that contribute to diabetes, asthma, cancer and mental illness. In all these cases, no one gene has the yes/no power to say whether a person has a disease or not. It is likely that more than one mutation is required before the disease is manifest. A number of genes may each make a subtle contribution to a person's susceptibility to a disease; genes may also affect how a person reacts to environmental factors. Unravelling these networks of events will undoubtedly be a challenge for some time to come.
   Fifty years on, the sequence of the human genome and the fruits it will bear will undoubtedly make a significant contribution to improving the diagnosis and treatment of disease.

NCBI  GENES AND DISEASE  http://www.ncbi.nlm.nih.gov/disease/

 

Back to Table of Content

http://genomeathome.stanford.edu/

Project goal: understanding genomes

The Human Genome Project is nearing completion, and scientists are working hard to develop the understanding needed to use this wealth of genetic information in ways that will be significant to medicine and humankind. One of the most important ways to do this is to study the other genomes and individual gene sequences that are already available to us. By understanding how these genomes work, we will be able to put the huge amounts of data (over 50, 000 genes and 3 billion nucleotide base pairs) from the Human Genome Project into biological and medical context, giving it real meaning.

Proteins, the molecular products encoded by genomes, are the functional units of all cellular machinery. Our partner project, Folding@home, is striving to understand how existing proteins attain their specific, functional three-dimensional structures. The goal of Genome@home is to design new genes that can form working proteins in the cell. Genome@home uses a computer algorithm (SPA), based on the physical and biochemical rules by which genes and proteins behave, to design new proteins (and hence new genes) that have not been found in nature. By comparing these "virtual genomes" to those found in nature, we can gain a much better understanding of how natural genomes have evolved and how natural genes and proteins work. Some important applications of the Genome@home virtual genome protein design database:

bulletengineering new proteins for medical therapy
bulletdesigning new pharmaceuticals
bulletassigning functions to the dozens of new genes being sequenced every day
bulletunderstanding protein evolution

As you can probably guess by now, designing just one new gene sequence is already computationally demanding. To design hundreds of new sequences for hundreds of proteins, literally thousands of computers are needed

(See Scientific background for more details about genomes, proteins, how proteins and genes are related).

 

Back to Table of Content

 

 

 

bulletAssignments:

biologyplace.gif (1600 bytes)

The Biology Place: http://www.biology.com

User ID- STU/lin

Password- *********

 

1 st Assignment (Due: Sept 12)

bulletInteractive Learning Activities:
Investigating a Neurological Condition

 

(This pedigree has been adapted from J.F. Gusella, et al. (1983) Nature 306: 234-238.)

Back to Table of Content

 

2 nd Assignment  (Due: Oct 3)

bulletThe Genes of HIV

           http://www.biology.com/learning/hiv2/hivgenes.html

bulletCell to Cell and Person to Person:
Investigating AIDS and HIV
Part I: The Discovery and Epidemiology of AIDS
Part II: Investigating HIV so as to Devise AIDS Therapies
http://www.biology.com/learning/hiv2/introduction.html

by John Postlethwait, University of Oregon
© 1997, Peregrine Publishers, Inc., All Rights Reserved

 

Back to Table of Content

 

 

3 rd Assignment (Due: Nov 7)

 

 

Dean et.al. 1996, Science, 273:1856-1862, Fig.2

 

Genetic Restriction of HIV-1 Infection and Progression to AIDS by a Deletion Allele of the CKR5 Structural Gene
Michael Dean, Mary Carrington, Cheryl Winkler, Gavin A. Huttley, Michael W. Smith, Rando Allikmets, James J. Goedert, Susan P. Buchbinder, Eric Vittinghoff, Edward Gomperts, Sharyne Donfield, David Vlahov, Richard Kaslow, Alfred Saah, Charles Rinaldo, Roger Detels, Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study, and Stephen J. O'Brien
Science 1996 September 27; 273: 1856-1862. (in Reports) [Abstract] [Full Text] [Text Only][html version]

 

bulletRecent Research on Co-receptor CKR5

http://www.biology.com/learning/hiv2/entry5.html

Copyright 1998, Peregrine Publishers, Inc. All Rights Reserved.

 

Scientific American   (http://www.sciam.com)

   

© 1996, 1997, 1998, 1999, 2000 Scientific American, Inc. All rights reserved.

click here!

The Search of AIDS-Resistance Gene. 

Stephen J. O'Brien and Michael Dean.   Scientific American, September, 1997  (http://www.sciam.com/0997issue/0997obrien.html) [PDF version]

 

 

 

Back to Table of Contents

 

 

bulletReading Assignments :

Primary Source Article

Genetic Restriction of HIV-1 Infection and Progression to AIDS by a Deletion Allele of the CKR5 Structural Gene.  Michael Dean et.al.  Science 273:1858-1862 (1996) (http://www.sciencemag.org)

Scientific American   (http://www.sciam.com)

The Search of AIDS-Resistance Gene.  Stephen J. O'Brien and Michael Dean.   Scientific American, September, 1997  (http://www.sciam.com/0997issue/0997obrien.html)

SKY

Multicolor Spectral Karyotyping of Human Chromosomes.  E. Schrock, et.al. Science 273:494-497 (1996) (http://www.sciencemag.org)

Hidden chromosome abnormalities in haematological malignancies detected by multicolour spectral karyotyping. Tim Veldman, Christine Vignon, Evelin Schrock, Janet D. Rowley & Thomas Ried.  Nature Genetics 15:406-410 (1997)

Genome Sequence

Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. S. T. Cole et.al.  Nature 393:537-544     [M. tuberculosis genome sequence]

Complete genome sequence of Treponema pallidum, the syphilis spirochete. Claire M. Fraser, et. al. Science 281:375-388 (1998) (http://www.sciencemag.org)          [T. pallidium genome sequence]

BRCA1

BRCA1 required for transcription-coupled repair of oxidative DNA damage. Lori C. Gowen, Anna V. Avrutskaya, Anne M. Latour, Beverly H Koller, Steven A. Leadon.  Science 281:1009-1012 (1998) (http://www.sciencemag.org)

 

 

-The New England Journal of Medicine- © Copyright 1999 Massachusetts Medical Society.

You can get full text and search The New England Journal of Medicine online by going to: http://www.nejm.org/content/index.asp

Click on "LOG ON TO FULL TEXT" and enter:

Username: BARRYMED

Password: ***********

A Collection of Articles
from the New England Journal of Medicine on

Breast Cancer

http://www.nejm.org/content/collections/breastcancer.asp

 

Back to Table of Content

 

Bookmarks

Genome Data

Arabidopsis

KAOS: Arabidosis Genome
MIPS Arabidopsis thaliana genome project
The TIGR Arabidopsis thaliana Database

Cloning

Online NewsHour : Cloning-- March 10, 1997
Cloning

Human Genome

The Human Transcript Map
DOE Human Genome Program
Complete Genomes

DNA Tools

GenBank Database Query Form
BLAST Search
The Molecular Similarity Game
DNA Tools
DNA Sequence Collaborator's Page
PCR Reference Information
ExPASy-Molecular Biology Server
Ambion-RNA Techniques

TIGR DataBase

THE INSTITUTE FOR GENOMIC RESEARCH
Mycoplasma genitalium Genome Position Search
The Mycoplasma genitalium Genome Database (MGDB)
The Mycoplasma genitalium Genome Image Map
National Center for Genome Resources
DNA Info. & Stock Center, Japan
GenomeNet WWW server, Japan
National Ctr for Biotech Information
Primer on Molecular Genetics
OMIM- Online Mendelian Inheritance in Man
CGAP-Cancer Genome Anatomy Project
Wiley - Strachan / Human Molecular Genetics
National Human Genome Research Institute (NHGRI)
Glossary of Genetic Terms

 

bullet

Copyright Acknowledgement

Permission to use the Copyright DNA image granted by:

-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-

             Paul A. | paul@grserv.med.jhmi.edu | Johns Hopkins

        Thiessen | http://cherubino.med.jhmi.edu/~paul | University

-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-

 

Back to the Top