User:Fermenter User/Notebook/MACG F3

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<!-- sibboleth --><div id="lncal1" style="border:0px;"><div style="display:none;" id="id">lncal1</div><div style="display:none;" id="dtext">03/02/2009</div><div style="display:none;" id="page">User:Fermenter User/Notebook/MACG F3</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month"></div><div style="display:none;" id="year"></div><div style="display:none;" id="readonly">Y</div></div>

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Background color codes:
Pastel Green: Major change of setup this time
yellow: Sung-Hye's correction or question to user

Letter color codes:
Black: Basic comment
Red: Emergency Information (Power shutdown, building access, Manager's absence etc)
Blue: Fermentation Setup information
Green: Discussion
Orange: Fermentation hrs
Purple: Induction hrs


MACG F3


Day -1 (Mar 2 Mon)

  <Bioreactor headplate configuation>
   pH sensor: monitor or control pH
   dO2 sensor: monitor or control dO2
   Condenser: Gas outlet
   OD probe: monitor cell growth ==> Not used! Replate it with septum
   Triple: Addition of media, Acid or Base if necessary
   MeOH sensor: Monitor EtOH (byproduct)
   
   <Sung-Hye's Note>
    MeOH sensors also detects ethanol! :See reference #1 on the bottom of the page
   


   <Ann>                 3/2/2009 (09:30)  Prepare small culture for inoculum (5mL)
 
   <Sung-Hye>            3/2/2009 (10:30)  Pour media
                         3/2/2009 (10:30)  pH calibration
                                           No Antifoam added
                         3/2/2009 (11:11)  Autoclave bioreactor
                                            3 empty bottles/fermenter
                                            Base, Carbon source+Inoculation, Feeding

3/2/2009 (13:00) Wrap bioreactors with foil 3/2/2009 (13:34) Start Temp Control 3/2/2009 (14:00) Add carbon source using pumps at 30°C 3/2/2009 (14:05) Connect Base (400 ml) Prime the pumps 3/2/2009 (14:09) Start F1 software 3/2/2009 (14:13) Start F2 software 3/2/2009 (14:16) Start F3 software 3/2/2009 (16:00) Connect MeOH sensor


   <Ann>                 3/2/2009 (14:05)  Prepare small culture for inoculum (10mL)
   <Ann>                 3/2/2009 (18:40)  Prepare small culture for inoculum (175mL)

Day 0 (Mar 3 Tue)

   
    Sung-Hye: CHBE Class Auditing 9:30 - 11:00
   
   <Sung-Hye>           3/3/2009 (07:20)  Calibrate dO2
                        3/3/2009 (07:20)  Set dO2

<Sung-Hye and Ann> 3/3/2009 (09:00) Fermentation 00:00 Inoculation 50 ml each using pump. 3/3/2009 (09:00) Start pH control <Ann> 3/3/2009 (10:00) Fermentation 01:00 F1: OD (0.29) Contamination? (N) F2: OD (0.32) Contamination? (N) F3: OD (0.29) Contamination? (N) <Ann> 3/3/2009 (11:00) Fermentation 02:00 F1: OD (0.54) Contamination? (N) F2: OD (0.58) Contamination? (N) F3: OD (0.56) Contamination? (N) <Ann> 3/3/2009 (11:00) Fermentation 02:00 F1: Induced with Galactose (55 mL) F1: Induction 00:00 <Ann> 3/3/2009 (12:00) Fermentation 03:00 F1: OD (0.32) Contamination? (N) F1: Induction 01:00 <Ann> 3/3/2009 (13:00) Fermentation 04:00 F1: OD (0.49) Contamination? (N) F1: Induction 02:00 F2: OD (0.62) Contamination? (N) F3: OD (0.58) Contamination? (N) <Ann> 3/3/2009 (15:00) Fermentation 06:00 F1: OD (0.62) Contamination? (N) F1: Induction 04:00 F2: OD (0.97) Contamination? (N) F3: OD (0.78) Contamination? (N) <Ann> 3/3/2009 (17:00) Fermentation 08:00 F1: OD (1.20) Contamination? (N) F1: Induction 06:00 F2: OD (1.34) Contamination? (N) F3: OD (1.11) Contamination? (N) <Ann> 3/3/2009 (19:00) Fermentation 10:00 F1: OD (1.90) Contamination? (N) F1: Induction 08:00 <Ann> 3/3/2009 (21:00) Fermentation 12:00 F1: OD (2.74) Contamination? (N) F1: Induction 10:00 F2: OD (3.02) Contamination? (N) F3: OD (2.82) Contamination? (N)

Day 1 (Mar 4 Wed)

   <Ann>                3/4/2009 (01:00)  Fermentation 16:00
                             F1: OD (6.30) Contamination? (N) F1: Induction 14:00
                             F2: OD (5.02) Contamination? (N)
                             F3: OD (4.42) Contamination? (N)
   <Ann>                3/4/2009 (7:00)  Fermentation 22:00
                             F1: OD (8.40) Contamination? (N) F1: Induction 20:00
                             F2: OD (6.86) Contamination? (N)
                             F3: OD (6.99) Contamination? (N)
   <Sung-Hye>           3/4/2009 (07:00)  Fermentation 00:00
                             F1: Base consumption 400 ml - 300 ml = 100 ml total 
                             F2: Base consumption 400 ml - 320 ml =  80 ml total
                             F3: Base consumption 400 ml - 340 ml =  60 ml total
   <Ann>                3/4/2009 (09:00)   Fermentation 24:00
                             F1: OD (9.35) Contamination? (N) F1: Induction 22:00
                             F2: OD (6.49) Contamination? (N)
                             F3: OD (6.26) Contamination? (N)
   <Ann>                3/4/2009 (09:00)  Fermentation 24:00 
                             F2: Induced with Galactose (55 mL)  F2: Induction 00:00      
                             F3: Induced with Galactose (55 mL)  F3: Induction 00:00 
                             Start feeding: (10 rpm) <-- Supposed to be 1 rpm
   File:Watsonpump.tif
   <Ann>                3/4/2009 (11:00)  Fermentation 26:00
                             F1: OD (11.54) Contamination (N)
                                 Harvest F2: Induction 24:00 
                             F2: OD (7.14) Contamination? (N)F2: Induction 02:00 
                             F3: OD (7.68) Contamination? (N)F3: Induction 02:00 
   <Ann>                3/4/2009 (13:00)  Fermentation 28:00 
                             F2: OD (9.75) Contamination? (N)F2: Induction 04:00 
                             F3: OD (10.55) Contamination? (N)F3: Induction 04:00 
   <Ann>                3/4/2009 (15:00)  Fermentation 30:00 
                             F2: OD (10.90) Contamination? (N)F2: Induction 06:00 
                             F3: OD (11.70) Contamination? (N)F3: Induction 06:00 
  <Ann>                3/4/2009 (17:00)  Fermentation 32:00 
                             F2: OD (11.70) Contamination? (N)F2: Induction 08:00 
                             F3: OD (12.55) Contamination? (N)F3: Induction 08:00 
  <Ann>                3/4/2009 (19:00)  Fermentation 34:00 
                             F2: OD (11.60) Contamination? (N)F2: Induction 10:00 
                             F3: OD (13.50) Contamination? (N)F3: Induction 10:00 
  <Ann>                3/4/2009 (21:00)  Fermentation 36:00 
                             F2: OD (12.40) Contamination? (N)F2: Induction 12:00 
                             F3: OD (12.50) Contamination? (N)F3: Induction 12:00 
  <Ann>                3/4/2009 (23:00)  Fermentation 38:00 
                             F2: OD (12.00) Contamination? (N)F2: Induction 14:00 
                             F3: OD (13.60) Contamination? (N)F3: Induction 14:00 

Day 2 (Mar 5 Thu)

   <Ann>                3/5/2009 (01:00)  Fermentation 40:00
                             F2: OD (12.40) Contamination? (N)F2: Induction 16:00 
                             F3: OD (13.90) Contamination? (N)F3: Induction 16:00 
   <Ann>                3/5/2009 (03:00)  Fermentation 42:00
                             F2: OD (13.10) Contamination? (N)F2: Induction 18:00 
                             F3: OD (14.90) Contamination? (N)F3: Induction 18:00 
   <Ann>                3/5/2009 (05:00)  Fermentation 44:00
                             F2: OD (12.00) Contamination? (N)F2: Induction 20:00 
                             F3: OD (13.80) Contamination? (N)F3: Induction 20:00 
   <Ann>                3/5/2009 (07:00)  Fermentation 46:00
                             F2: OD (12.80) Contamination? (N)F2: Induction 22:00 
                             F3: OD (14.80) Contamination? (N)F3: Induction 22:00 
   <Sung-Hye>           3/5/2009 (07:00)  Fermentation 00:00
                             F1: Base consumption 400 ml - 270 ml = 130 ml
                             F2: Base consumption 400 ml - 220 ml = 180 ml
                             F3: Base consumption 400 ml - 280 ml = 120 ml
   <Ann>                3/5/2009 (09:00)  Fermentation 48:00 
                             F2: OD (12.90) Contamination? (N)F2: Induction 24:00 
                             F3: OD (14.80) Contamination? (N)F3: Induction 24:00 
   <Ann>                3/5/2009 (11:00)  Fermentation 50:00
                             F2: OD (12.20) Contamination? (Y/N)F2: Induction 26:00 
                             F3: OD (15.20) Contamination? (Y/N)F3: Induction 26:00 
   <Ann>                3/5/2009 (11:00)  Fermentation 50:00
                             F2: Harvest F2: Induction 26:00 
                             F3: Harvest F3: Induction 26:00

References

  1. www.ravenbiotech.com/product.html [Paper1]


  1. High Cell Density Fermentation of Saccharomyces cerevisiae JUL3 in Fed-batch Culture for the Production of β-Glucan (2007) 13, 1, 153-158 [Paper2]
  File:IE13-1-0153.pdf
  Fermentation condition: 30°C, 200 rpm, no pH control, 1 vvm
  
  1. Optimization of enterokinase fermentation using a recombinant Saccharomyces cerevisiae. (2005) 40, 717-722 [Paper3]
  File:PB-40-717.pdf
  Fermentation condition: 30°C, 500 rpm, no pH control, 2 vvm
  1. Alakomi HL, Paananen A, Suihko ML, Helander IM, and Saarela M. Weakening effect of cell permeabilizers on gram-negative bacteria causing biodeterioration. Appl Environ Microbiol. 2006 Jul;72(7):4695-703. DOI:10.1128/AEM.00142-06 | PubMed ID:16820461 | HubMed [Paper4]
  1. Peamiability test: Aliquots (100 µl) of this cell suspension were pipetted into fluoroplate wells, 
     which contained NPN (10 µM) and, as test substances, either EDTA (1.0 and 0.1 mM), PEI (10 µg ml–1), 
     DMSA (1 mM), AOT (1 mM), or HEPES buffer (control) to make up a total volume of 200 µl. If desired, 
     MgCl2 was added to the cell suspension before addition of NPN. Fluorescence was monitored within 
     3 min from four parallel wells per sample (excitation, 355 nm; half bandwidth, 38 ± 3 nm; emission, 
     402 nm; half bandwidth, 50 ± 5 nm). Each assay was performed at least three times. 
  1. Hounsa CG, Brandt EV, Thevelein J, Hohmann S, and Prior BA. Role of trehalose in survival of Saccharomyces cerevisiae under osmotic stress. Microbiology. 1998 Mar;144 ( Pt 3):671-80. DOI:10.1099/00221287-144-3-671 | PubMed ID:9534237 | HubMed [Paper5]
  1. OD600 unit is equivalent to 0.64 +/- 0.02 g cells (dry weight)/L
  1. Hao Q, Hong SH, and Maret W. Lipid raft-dependent endocytosis of metallothionein in HepG2 cells. J Cell Physiol. 2007 Feb;210(2):428-35. DOI:10.1002/jcp.20874 | PubMed ID:17111383 | HubMed [Paper6]
  1. To demonstrate the localization of the proteins relative to the cells, cell contours were visualized 
     with Alexa 647-concanavalin A.
  1. Drew D, Newstead S, Sonoda Y, Kim H, von Heijne G, and Iwata S. GFP-based optimization scheme for the overexpression and purification of eukaryotic membrane proteins in Saccharomyces cerevisiae. Nat Protoc. 2008;3(5):784-98. DOI:10.1038/nprot.2008.44 | PubMed ID:18451787 | HubMed [Paper7]
  1. Newstead S, Kim H, von Heijne G, Iwata S, and Drew D. High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):13936-41. DOI:10.1073/pnas.0704546104 | PubMed ID:17709746 | HubMed [Paper8]
  1. Kostov Y, Albano CR, and Rao G. All solid-state GFP sensor. Biotechnol Bioeng. 2000 Nov 20;70(4):473-7. PubMed ID:11005931 | HubMed [Paper8]
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