Cell Biology Lab

Nanodrop DNA Necklace RestrictionEnzyme MicroArray Sequencing Feedback Contents Links,Assig'm MainPage GenomeProject Dictionary FundulusGTH NobelPrize BioLab On-Line MessageBoard TheCellPlace DropBox

BIO330L CELL BIOLOGY LAB

Complementary & Sequence Translation (SEMO)

To find Complementary Sequence and Translation using “DNA Tools” by Dr. Allen Gathman (Southeast Missouri State University, SEMO)

[Step-by-Step Example]

DNA Tools

http://biology.semo.edu/cgi-bin/dnatools.pl

Copyright 1996 by Allen Gathman.

Biology Department | vhowell@semo.edu| (573) 651-2170| 11/11/2009| disclaimer
© Southeast Missouri State University | One University Plaza | Cape Girardeau, MO 63701 | (573) 651-2000

Enter the sequence in FASTA format. Unknown nucleotides may be represented as N -- characters other than a,t,c,g, and n in the sequence will be disregarded. The program is case-insensitive.

Choose the function desired.
Format DNA Sequence
Format DNA Sequence (no numbers)
Format Protein Sequence
Format Protein Sequence (no numbers)
Complementary Sequence
Translate
Find Restriction Sites
Get GC content and Base Count
Get Tm of oligos

This page generated by DNATools.
Copyright 1996 by Allen Gathman.

DNA Sequencing

DNA from the beginning

DNA and Proteins are key molecules of the cell nucleus

The DNA molecule is shaped like a twisted ladder

DNA words are three letters long

A gene is a discrete sequence of DNA nucleotides (DNA Sequencing)

Essential Biochemistry - DNA Sequencing

http://www.wiley.com/college/pratt/0471393878/student/animations/dna_sequencing/index.html

DNA sequencing - Wikipedia, the free encyclopedia

The term DNA sequencing encompasses biochemical methods for determining the order of the nucleotide bases, adenine, guanine, cytosine, and thymine, in a DNA ...
en.wikipedia.org/wiki/DNA_sequencing - 120k - Cached - Similar pages - Note this

http://en.wikipedia.org/wiki/DNA_sequencing A typical sequencing result

The University of Michigan DNA Sequencing Core

How do we Sequence DNA?

http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/sequencing.html

DNA Sequencing is at the center of the Human Genome Project, which promises to revolutionize
the Biomedical Sciences and the treatment of human diseases. This page is designed to help you
understand how DNA is sequenced.

If you are looking for information on our DNA sequencing service facility, our home page is here:
The University of Michigan DNA Sequencing Core

Biology Animation Library
The Dolan DNA Learning Center has been developing multimedia animation programs since 1990. Many of these programs remain the most downloaded items from our Internet site.
Biology Animation Library http://www.dnalc.org/ddnalc/resources/animations.html

Animations can be viewed within your web browser (the Macromedia Flash plugin is required) or downloaded for play from your computer.

DOWNLOAD FOR:

PLAY

PC

MAC

DNA Restriction {a}

Gel Electrophoresis {a}

DNA Transformation 1 {a}

DNA Transformation 2 {a}

Polymerase Chain Reaction {a}

Sanger Sequencing {a}

Cycle Sequencing {a}

DNA Arrays {a}

GeneChip (R) {a}

Model Organisms {a}

MICROARRAYS: CHIPPING AWAY AT THE MYSTERIES OF SCIENCE AND MEDICINE

http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html

Gene expression values from microarray experiments can be represented as heat maps to visualize the result of data analysis

Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail.

http://en.wikipedia.org/wiki/DNA_microarray

A microarray is a tool for analyzing gene expression that consists of a small membrane or glass slide containing samples of many genes arranged in a regular pattern.

The Colors of a Microarray

An image depicting the color expression of a microarray.

Reproduced with permission from the Office of Science

The proper and harmonious expression of a large number of genes is a critical component of normal growth and development and the maintenance of proper health. Disruptions or changes in gene expression are responsible for many disease

GCAT Assessment Online

http://www.bio.davidson.edu/projects/gcat/assessment/assess.html

1) At the begining of the semester or project, take a student pre-survey that collects biographical information and a 12 question survey that should take 15 minutes or less.
Click here for pre-survey 2008 - 2009 academic year.
2) At the end of the semester or project, each student should take the post survey ( < 15 minutes).
Click here for post-survey 2008 - 2009 academic year.

DNA Microarray Methodology - Flash Animation

http://www.bio.davidson.edu/Courses/genomics/chip/chip.html

       Introduction to DNA Microarrays (GCAT)

Introduction to Methodology

Yeast Lesson

Lymphoma Lesson

Making a Project

Slide Layout and Gene List

Addressing and Gridding

Segmentation

Log Transforming Data

DeRisi et al. 1997 reprint (PDF File)

Discussion DeRisi Experiment

MicroArray Genome Imaging & Clustering Tool

Developed at Davidson College by Laurie Heyer and her undergraduate students.

Download MAGIC Tool software

MAGIC Tool: Integrated microarray data analysis (Bioinformatics, 2005)

MAGIC Tool analysis software
plus practice tiff files

Documentation

User's Guide (1.9 MB PDF file)

Herramienta MAGIC Guía del Usuario (3.3 MB PDF)

Instructor's Guide with additional math background for understanding data analysis (2.1 MB PDF file)

NEW Flash Tutorials - animations illustrating how to use MAGIC Tool (More coming soon!)

Download small sample files (1 grid and 4 grid) for practice

[4Grid_MT_genelist.txt;   Green_4grid.tif;   Red_4grid.tif;    Hypothetical_4grid.exp;   yeastgenes.info]

Gene 'roadmap' for lung cancers

The most complete survey yet of the genes which go wrong when lung cancer takes hold has been carried out by US researchers.

http://news.bbc.co.uk/2/hi/health/7682453.stm

Breaking Cancer's Gene Code
U.S. News & World Report - Oct 23, 2008
By Bernadine Healy MD Imagine cancer, 2040. A 45-year-old woman who has never smoked develops lung cancer, which today kills more people than any other kind.
Researchers Find More Genes Linked to Lung Cancer Washington Post
CORRECTED - Gene study turns up 26 lung cancer genes Reuters
Los Angeles Times - WebMD - BBC News - The Associated Press
all 229 news articles »

Nature 455, 1069-1075 (23 October 2008) | doi:10.1038/nature07423;

Somatic mutations affect key pathways in lung adenocarcinoma

Restriction Enzyme

Restriction Enzyme Digestion of DNA

http://phschool.com/science/biology_place/biocoach/red/intro.html

0.8% Agarose Gel Electrophoresis

Copyright ©2009 Pearson Education, Inc. or its affiliates. All Rights Reserved.

Click here to download a copy of the Restriction Enzyme Lab Manual

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Restriction Enzyme Digestion: HindIII, BamH1, EcoR1

Ethidium Bromide Staining of DNA

Standard Curve Construction

Copyright ©2009 Pearson Education, Inc. or its affiliates. All Rights Reserved.

Photodocumentation of DNA Gel

Restriction Map Construction

Explanations: Clues & Tricks

for a successful Map Construction (Partial Digestion) (Key4)

Double Restriction Enzyme Digest (Complete Digestion)



More Answer Keys for Restriction Map Construction

Key1; Key2; Key3; Key4

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Welcome to RestrictionMapper - on line restriction mapping the easy way.

Maps sites for restriction enzymes, a.k.a. restriction endonucleases, in DNA sequences. Also does virtual digestion.

http://www.restrictionmapper.org/

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Restriction map - Wikipedia, the free encyclopedia

A restriction map is a map of known restriction sites within a sequence of DNA. Restriction mapping requires the use of restriction enzymes. ...



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Restriction mapping

Dr. David W. Ussery, Roanoke College, Salem, Virginia

www.cbs.dtu.dk/.../roanoke/genetics980211.html

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http://web.virginia.edu/Heidi/chapter11/chp11.htm

University of Virginia

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Restriction Mapping Tutorial



http://homepages.strath.ac.uk/~dfs99109/BB206/RestMapTutorial.html

Dr. Eve Lutz (eve.lutz@strath.ac.uk) University of Strathclyde in Glasgow (http://www.strath.ac.uk).

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Logic of constructing a circular restriction map

All text material © 2007 by Steven M. Carr (Memorial University of Newfoundland )

http://www.mun.ca/biology/scarr/Restriction_mapping_circular.html

The logic of Restriction Mapping

All text material © 2008 by Steven M. Carr (Memorial University of Newfoundland )

http://www.mun.ca/biology/scarr/Restriction_Mapping.html

http://www.mun.ca/biology/scarr/RFLP_animation.gif

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Creating a Map by Partial Digests of End-Labeled DNA

http://www.vivo.colostate.edu/hbooks/genetics/biotech/enzymes/maps.html

R. A. Bowen DVM PhD rbowen@colostate.edu Colorado State University

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Microbial Genetics (Restriction Mapping) Problems

http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/problems/in-vitro/RE-mapping/

(Dr. Stanley Maloy, San Diego State University.)

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Partial Digest Problem

http://snhs-plin.barry.edu/cell-biology-lab/Restriction_Digest_MIT_Lippert.htm

http://www-math.mit.edu/~lippert/18.417/

Dr. Ross A. Lippert (Massachusetts Institute of Technology MIT)

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Restriction Mapping Tutorial

http://faculty.plattsburgh.edu/donald.slish/RestMap/RestMapTutorial.html

Dr. Donald F. Slish, (Plattsburgh State University, NY)

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Sequence Manipulation Suite:

Restriction Map
http://www.bioinformatics.org/sms2/rest_map.html

DNA Origami

DNA Extraction: DNA Necklace

Proceedings of National Academy of Sciences (USA)

Nanodrop

DNA Measurement: NanoDrop Spectrophotometer, Accuracy & Precision

(Supported in parts by a NSF-GCAT Instrument Grant)

NanoDrop Class Results (15 Sep 2009)

Class Results (16Sep08):

Cell Lab "Class In-Action" Photo

NanoDrop

www.nanodrop.com/

The Thermo Scientific NanoDrop^TM 1000 Spectrophotometer enables highly accurate UV/Vis analyses of 1 ul samples with remarkable reproducibility. The patented sample retention system eliminates the need for cuvettes and capillaries which decreases the measurement cycle time. In addition, the high absorbance capability eliminates the need for most dilutions. You’ll find yourself making fewer dilutions and taking more readings than ever before, essentially becoming a more quantitative laboratory.

View the "NanoDrop It Like It's Hot" Video
http://www.nanodrop.com/LikeItsHotVideo.aspx

Our Molecular Selves

Our Molecular Selves includes a dynamic, 3-D, computer-animated video takes you "inside" for a close-up look at how we're made. Watch as the mysteries of the Human Genome are literally "unraveled."
Read Transcript

Go to Multimedia Downloads to download Our Molecular Selves to your computer.

You will need the latest version of Adobe Flash Player to play this video.

Essential Biochemistry - DNA Sequencing

DNA sequencing - Wikipedia, the free encyclopedia

How do we Sequence DNA?

DNA Sequencing is at the center of the Human Genome Project, which promises to revolutionize
the Biomedical Sciences and the treatment of human diseases. This page is designed to help you
understand how DNA is sequenced.

If you are looking for information on our DNA sequencing service facility, our home page is here:
The University of Michigan DNA Sequencing Core

Gene 'roadmap' for lung cancers

Welcome to RestrictionMapper - on line restriction mapping the easy way.

Restriction map - Wikipedia, the free encyclopedia

Our Molecular Selves

Read Transcript

Enter the sequence in FASTA format. Unknown nucleotides may be represented as N -- characters other than a,t,c,g, and n in the sequence will be disregarded. The program is case-insensitive.
	Choose the function desired. Format DNA Sequence Format DNA Sequence (no numbers) Format Protein Sequence Format Protein Sequence (no numbers) Complementary Sequence Translate Find Restriction Sites Get GC content and Base Count Get Tm of oligos