BIOL200 2013

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EXPERIMENT # 4

BIOL 200 Cell Biology II LAB, Spring 2013

Hunter College of the City University of New York

Course information

Instructors: TBD

Class Hours: Room TBD HN; TBD

Office Hours: Room 830 HN; Thursdays 2-4pm or by appointment

Contact information:

  • Dr. Weigang Qiu: weigang@genectr.hunter.cuny.edu, 1-212-772-5296


Experiment #4

The Tree of Life and Molecular Identification of Microorganisms

Objective

To classify microorganisms and determine their relatedness using molecular sequences.

LAB REPORT GRADING GUIDE

CELL BIO II Experiment #4:

  • Introduction 1 point :
 Statement of objectives or aims of the experiment in the student’s own words.
 (not to be copied from the Lab Manual)
  • MATERIALS AND METHODS 0 points :
 This should be a brief synopsis and must include any changes or deviations 
 from the procedures outlined in the Lab Manual. Specify which organisms were 
 used to create the phylogram.
  • RESULTS 4 points :
 A print out of the phylogram will suffice.
  • DISCUSSION 4 points :
 Responses to discussion questions.
  • SUMMARY |CONCLUSION 1 point :
 Two sentence summary of your findings.
  • REFERENCES 1 point :
 Credit is given for pertinent references obtained from sources other than the Lab Manual.
 This point is in addition to the 10 for the lab report..

INTRODUCTION

MATERIALS

  • Required hardware: Computer

Table 1

Volume 1A (Gram-negative bacteria)

Escherichia coli

ACCESSION #174375

Helicobacter pylori

ACCESSION #402670

Salmonella typhi

ACCESSION #2826789

Serratia marcescens

ACCESSION #4582213

Treponema pallidum

ACCESSION #176249

Additional species: Agrobacterium tumefaciens, Boredetella pertussis, Thermus aquaticus, Yersinia pestis, Borrelia burgdorferi. (Note: To search for unlisted 16S sequences, type key words such as “yersinia AND 16S [gene]” in the NCBI GenBank search box.)

Volume 1B (Rikettsias and endosymbionts)

Baronella bacilliformis

ACCESSION #173825

Chlamydia trachomatis

ACCESSION #2576240

Rickettsia rickettsii

ACCESSION #538436

Additional species: Coxiella burnetii, Thermoplasma acidophilum

Volume 2A (Gram-positive bacteria)

Bacillus subtilis

ACCESSION #8980302

Dinococcus radiodurans

ACCESSION #145033

Staphylococcus aureus

ACCESSION #576603

Additional species: Bacillus anthracis, Clostridium botulinum, Lactobacillus acidophilus, Streptococcus pyogenes

Volume 2B (Mycobacteria and nocardia)

Mycobacterium haemophilum

ACCESSION #406086

Mycobacterium tuberculosis

ACCESSION #3929878

Additional species: Mycobacterium bovis, Nocardia orientalis

Volume 3A (Phototrophs, chemolithotrophs, sheathed bacteria, gliding bacteria)

Anabaena sp.

ACCESSION #39010

Cytophaga latercula

ACCESSION #37222646

Nitrobacter wiogradskyi

ACCESSION #402722

Additional species: Heliothrix oregonensis, Myxococcus fulvus, Thiobacillus ferrooxidans

Volume 3B (Archeobaceria)

''Methanococcus jannaschii

ACCESSION #175446

Thermotoga subterranean

ACCESSION #915213

Additional species: Desulfurococcus mucosus, Halobacterium salinarium, Pyrococcus woesei

Volume 4 (Actinomycetes)

Actinomyces bowdenii

ACCESSION #6456800

Actinomyces neuii

ACCESSION #433527

Actinomyces turicensis

ACCESSION #642970

Eukaryotic representative (used as outgroup for rooting the phylogenetic tree)

Saccharomyces cerevisiae

ACCESSION #172403

ANALYSIS

  1. Copy the Lyme disease bacterium lp17 plasmid file "/data/yoda/b/student.accounts/bio425_2011/data/lp17.fas" into your home directory.
  2. Run long-orf, extract, build-icm, and glimmer3.
  3. Show your commands and "cat" the final output.
  4. Describe key elements of a prokaryotic gene in addition to the open reading frame.
  5. Textbook Questions (pg152-153): 6.6, 6.9, 6.15

February 26

March 5

March 12

March 19

  • REVIEW Session for MID-TERM EXAMS

March 26

  • MID-TERM

April 2

April 9

April 16

  • Topic: Relational Database and SQL
  • Tutorial: the Borrelia Genome Database
  • Homework: SQL-embedded PERL

April 23

NO CLASSES (Spring recess)

April 30

May 7

  • Chapter 6 (Gene Expression) & Chapter 8 (Proteomics)
  • Tutorial: Array Data Visualization and Analysis ( Micro-Array Analysis Slides)
  • Homework:Data Analysis using R

May 14

  • Chapter 7. Protein Structure Prediction

May 21

  • Final Project Due (TBA)

Useful Links

Unix Tutorials

Perl Help

  • Professor Stewart Weiss has taught CSCI132, a UNIX and Perl class. His slides go into much greater detail and are an invaluable resource. They can be found on his course page here.
  • Perl documentation at perldoc.perl.org. Besides that, running the perldoc command before either a function (with the -f option ie, perldoc -f substr) or a perl module (ie, perldoc Bio::Seq) can get you similar results without having to leave the terminal.

Bioperl

SQL

R Project

  • Install location and instructions for Windows
  • Install location and instructions for Mac OS X
  • For users of Ubuntu/Debian:
sudo apt-get install r-base-core
  • For users of Fedora/Red Hat:
su -
yum install R

Utilities

Other Resources


© Weigang Qiu, Hunter College, Last Update Jan 2013