User:Jarle Pahr/Microbiology: Difference between revisions
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=Concepts/Glossary= | =Concepts/Glossary= | ||
*Passage number | *Passage number | ||
*SPANC balance: Balance between self-protection and nutritional capability. | |||
Four heresies (see http://webspace.pugetsound.edu/facultypages/momartin/Micro/2008%20Micro%20lectures/Micro09.pdf) | |||
*Phenotypic variation in wild-type vs lab strains. ''Continual cultivation is essentially a selective agent'' | |||
*Biofilms as the natural state of microbes. | |||
*Bacteria communicate and respond to population size and structure | |||
*The great plating anomaly | |||
=Labs/research groups= | |||
Richard Lenski: http://myxo.css.msu.edu/ | |||
=Strain collections= | =Strain collections= | ||
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Microbiology-themed blogs: http://www.microbe.net/microbiology-blogs/ | Microbiology-themed blogs: http://www.microbe.net/microbiology-blogs/ | ||
World Federation for Culture Collections: http://www.wfcc.info/ | |||
=Growth data= | =Growth data= | ||
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http://kunde.datakvalitet.no/SIHF/Mikrobiologi/ | http://kunde.datakvalitet.no/SIHF/Mikrobiologi/ | ||
=Morphology= | |||
http://schaechter.asmblog.org/schaechter/2013/04/e-coli-cells-face-facs-and-get-back-into-shape.html | |||
=Blogs= | =Blogs= | ||
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http://www.microbe.net/microbenet-blog/ | http://www.microbe.net/microbenet-blog/ | ||
=Resources= | |||
http://www.microbelibrary.org/ | |||
Encyclopedia of Life: http://eol.org/ | |||
=Links= | =Links= | ||
http://www.earthmicrobiome.org/ | http://www.earthmicrobiome.org/ | ||
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http://schaechter.asmblog.org/schaechter/2013/02/bacterial-antidepressants-avoiding-stationary-phase-stress.html | http://schaechter.asmblog.org/schaechter/2013/02/bacterial-antidepressants-avoiding-stationary-phase-stress.html | ||
http://schaechter.asmblog.org/schaechter/2013/04/e-coli-cells-face-facs-and-get-back-into-shape.html | |||
Protocol outline for sequencing of environmental isolates: http://www.microbe.net/2013/08/12/summary-of-undergraduate-genome-sequencing-project/ | |||
=Culturing= | |||
http://schaechter.asmblog.org/schaechter/2010/07/the-uncultured-bacteria.html | http://schaechter.asmblog.org/schaechter/2010/07/the-uncultured-bacteria.html | ||
The water agar test: a new test to measure the bacteriological quality of cream.: http://www.ncbi.nlm.nih.gov/pubmed/1097493 | |||
=Bibliography= | =Bibliography= | ||
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12352.html | |||
The last generation of bacterial growth in limiting nutrient | |||
A Bren, Y Hart, E Dekel, D Koster, U Alon - BMC systems biology, 2013 | |||
DNA signature-based approaches for bacterial detection and identification: http://www.sciencedirect.com/science/article/pii/S0048969708010838 | |||
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http://link.springer.com/article/10.1007/s00284-013-0401-y | http://link.springer.com/article/10.1007/s00284-013-0401-y | ||
http://www.microbialcellfactories.com/content/7/1/31 | |||
=Equipment= | |||
http://microbiologybuyersguide.com/ | |||
=Software= | |||
http://weizhong-lab.ucsd.edu/cd-hit/ | |||
=Journals= | |||
Microbiology: http://mic.sgmjournals.org/ | |||
BMC Microbiology | |||
Molecular Microbiology | |||
Journal of Bacteriology | |||
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLY | |||
Journal of Experimental Microbiology and Immunology (JEMI): http://www.microbiology.ubc.ca/undergraduate/jemi | |||
=Mycoplasmas= | |||
http://mmbr.asm.org/content/62/4/1094.full | |||
=Books= | |||
Bergey's Manual of Systematic Bacteriology: | |||
*Volume 1: | |||
*Volume 2: | |||
*Volume 3: | |||
*Volume 4: | |||
The Desk Encyclopedia of Microorganisms: http://www.amazon.com/Desk-Encyclopedia-Microbiology-Second-Edition/dp/0123749808 | |||
Brock's Microbiology | |||
Microbiology: An evolving science. | |||
=Software= | |||
OpenCFU: | |||
http://sourceforge.net/projects/opencfu/?source=directory | |||
=Supplies= | |||
http://www.amazonsupply.com/microbiology-supplies/s/393446011/ref=gw_c_ls_ms |
Latest revision as of 05:58, 22 August 2013
Notes on microbiology:
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0059310
Rapid microbiological methods: http://www.rapidmicrobiology.com/test-methods/Rapid-Method-Pharma.php
When Is a Microbial Culture “Pure”? Persistent Cryptic Contaminant Escapes Detection Even with Deep Genome Sequencing: http://mbio.asm.org/content/4/2/e00591-12.abstract
http://cellculture.bitesizebio.com/articles/cell-culture-passage-number-explained/
Concepts/Glossary
- Passage number
- SPANC balance: Balance between self-protection and nutritional capability.
Four heresies (see http://webspace.pugetsound.edu/facultypages/momartin/Micro/2008%20Micro%20lectures/Micro09.pdf)
- Phenotypic variation in wild-type vs lab strains. Continual cultivation is essentially a selective agent
- Biofilms as the natural state of microbes.
- Bacteria communicate and respond to population size and structure
- The great plating anomaly
Labs/research groups
Richard Lenski: http://myxo.css.msu.edu/
Strain collections
American Type Culture Collection (ATCC): http://www.lgcstandards-atcc.org/Products/Cells%20and%20Microorganisms/Primary%20Cells.aspx?geo_country=no
NCMA (Previously CCMP): https://ncma.bigelow.org/
Microbiology-themed blogs: http://www.microbe.net/microbiology-blogs/
World Federation for Culture Collections: http://www.wfcc.info/
Growth data
Growth data from cultures:
Strain/plasmid | Date | Volume | Medium | Container | Incubation conditions | Incubation time | OD600 | # of samples used for measuring OD600 | Comment |
---|---|---|---|---|---|---|---|---|---|
Dh5a:pJP-3 | 22.5.13 | 5 mL | LB + 50 ug/mL Kan | 13 mL tube | 37 C, 225 RPM | ~ 13 h | 1 | ||
BW27784 | 1.6.13 | 5 mL | LB | 13 mL tube | 37 C, 225 RPM | ON | 7,7 | ||
BW27786 | 1.6.13 | 5 mL | LB | 13 mL tube | 37 C, 225 RPM | ON | 2,9 | ||
BW27784 | 08.6.13 | ~3 mL | LB | 13 mL tube | ~20 C (on bench) | ON | 0,9 | 1 |
Educational
http://invisiblelife.yourwildlife.org/
http://media.hhmi.org/biointeractive/vlabs/bacterial_id/index.html
Handbooks and references
http://kunde.datakvalitet.no/SIHF/Mikrobiologi/
Morphology
http://schaechter.asmblog.org/schaechter/2013/04/e-coli-cells-face-facs-and-get-back-into-shape.html
Blogs
http://covertlab.stanford.edu/publicationpdfs/ChaosJKarr2013.pdf
microBEnet blog:
http://www.microbe.net/microbenet-blog/
Resources
http://www.microbelibrary.org/
Encyclopedia of Life: http://eol.org/
Links
http://www.earthmicrobiome.org/
http://www.microbemagazine.org/
American society for Microbiology (ASM): www.asm.org
http://schaechter.asmblog.org/schaechter/2013/04/e-coli-cells-face-facs-and-get-back-into-shape.html
Protocol outline for sequencing of environmental isolates: http://www.microbe.net/2013/08/12/summary-of-undergraduate-genome-sequencing-project/
Culturing
http://schaechter.asmblog.org/schaechter/2010/07/the-uncultured-bacteria.html
The water agar test: a new test to measure the bacteriological quality of cream.: http://www.ncbi.nlm.nih.gov/pubmed/1097493
Bibliography
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12352.html
The last generation of bacterial growth in limiting nutrient A Bren, Y Hart, E Dekel, D Koster, U Alon - BMC systems biology, 2013
DNA signature-based approaches for bacterial detection and identification: http://www.sciencedirect.com/science/article/pii/S0048969708010838
Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4 : http://genomea.asm.org/content/1/2/e00086-13.full
http://link.springer.com/article/10.1007/s00284-013-0401-y
http://www.microbialcellfactories.com/content/7/1/31
Equipment
http://microbiologybuyersguide.com/
Software
http://weizhong-lab.ucsd.edu/cd-hit/
Journals
Microbiology: http://mic.sgmjournals.org/
BMC Microbiology
Molecular Microbiology
Journal of Bacteriology
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLY
Journal of Experimental Microbiology and Immunology (JEMI): http://www.microbiology.ubc.ca/undergraduate/jemi
Mycoplasmas
http://mmbr.asm.org/content/62/4/1094.full
Books
Bergey's Manual of Systematic Bacteriology:
- Volume 1:
- Volume 2:
- Volume 3:
- Volume 4:
The Desk Encyclopedia of Microorganisms: http://www.amazon.com/Desk-Encyclopedia-Microbiology-Second-Edition/dp/0123749808
Brock's Microbiology
Microbiology: An evolving science.
Software
OpenCFU: http://sourceforge.net/projects/opencfu/?source=directory
Supplies
http://www.amazonsupply.com/microbiology-supplies/s/393446011/ref=gw_c_ls_ms