Team:UGA-Georgia/Notebook

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Instructor: ZHE LYU
Instructor: ZHE LYU
-
'''Tasks completed before 2013/02/20'''  
+
 
 +
'''February 2013'''
-Training on anaerobic skills, i.e. use of anaerobic glassware, gassing chamber,  
-Training on anaerobic skills, i.e. use of anaerobic glassware, gassing chamber,  
anaerobic chamber, etc.  
anaerobic chamber, etc.  
-
-Transferred and grew Methanococcus transformants with the geraniol synthase
 
-
gene encoded in the plasmid that was stored via glycerol stock from Summer
 
-
2012. Transformants containing only the pAW42 vector (control) were also
 
-
transferred and grown.
 
-
-Cell samples from the cultures listed above were harvested, resuspended in
+
'''March 2013'''
-
buffer and stored at -20C for running SDS in near future.
+
-
+
-
-Cell samples from cultures listed two above were harvested, flash-frozen and
+
-
stored at -80C formRNA extraction in the near future.
+
-
-Both liquid and solid anaerobic medium was prepared for future use. Refer to
+
-Purification of GS, AT and GS+AT via revival of frozen stocks and plating of sub-cultures.
-
Appendix of protocols, I Preparation of Complex Medium for Methanococci
+
-
(McC).  
+
-
'''2013/2/20'''
 
-
-Further preparation of media tubes via inoculation of Puromycin and
+
'''April 2013'''
-
pressurization to 40 psi using H2/CO2 gas. Stored at -20C.
+
-
-Preparation of samples for SDS gel.
+
-Further continuation of purification of GS, AT and GS+AT via picking colonies, creating sub-cultures and plating.
-
+
-
-Vector (control) samples made at 1x dilution and 5x dilution
+
-
-Geranyl Synthase (GS) plasmid samples made at 1x and 5x dilution
+
-Test of Puromycin strength.
-
-An SDS gel was run using both dilutions of vector and GS samples, along with a
+
-Creation of frozen stocks of purified GS, AT and GS+AT transformants.
-
protein marker.
+
-
'''2013/2/26'''
 
-
-Four media tubes were treated with 0.1 mL Na2S solution each. Two of the tubes
+
'''June 2013'''
-
were used for inoculation of GS transformant, and the other two were used for
+
-
inoculation of GS + AT (geraniol acetyltransferase) transformant.
+
-
+
-
-200x dilution of Puromycin solution was created and properly dispensed.
+
-
-SDS gel from 2013/2/20 was imaged. Gel image quality was lacking, so it was
+
-Extraction of Geraniol from extra-cellular and intra-cellular content of samples and preparation for GC/MS evaluation
-
decided to perform a second gel.
+
-
'''2013/2/27'''
+
-Sequencing of pAW50-mCherry vector
-
-Reflecting upon first SDS gel, new sample dilutions were created in aim of  
+
-Analysis of pAW50-mCherry sequence
-
creating an easier to read gel. 2x dilution sample of GS was created and leftover
+
-
5x GS sample from first gel was also used.  4x, 6x and 8x dilutions of vector
+
-
samples were created, and leftover 5x dilution vector samples from first gel were
+
-
also used. Lastly, a protein marker ladder was used for size reference.
+
-
-Gel was run, stained, de-stained and imaged (see below). No evident expression
+
-Transformation of pAW50-mCherry vector into Methanococcus
-
of GS protein. Next verification of this will be to run an mRNA extract for
+
-
conclusive evidence of GS gene being transcribed 
+
 +
-Testing Fluorescence of pAW50-mCherry
 +
-Purification of pAW50-mCherry cultures via plating of transformants, and creating sub-cultures of colonies picked
 +
-Creation of frozen stocks of pAW50-mCherry in Methanococcus
 +
'''July 2013'''
-
[[[[[[[[[[[[[[[[[[[[Fig 1. ]]]]]]]]]]]]]]]]]]]
+
-Creation and analysis of the "killing & inhibiting" experiment where we test the maximum amount of product a 5ml culture of Methanococcus can tolerate in cultures with high OD (killing of grown cells) and low OD (inhibiting of growth).
 +
-Innovation of an adapter to allow the use of syringe needles on micropipettes.
 +
-Expanded upon the original extraction protocol for higher efficiency of extraction of geraniol from Methanococcus cultures.
 +
- GC/MS Evaluation and analysis (see results tab)
 +
'''August 2013'''
-
'''2013/03/05'''
+
-Revival and PCR of all GS and AT frozen stocks to confirm insert.
-
-6 tubes of McC media created, added Na2S (0.1mL 2.5%) and Puromycin (0.5mL of  
+
--Extraction of Geraniol from extra-cellular and intra-cellular content of all GS frozen stocks and preparation for GC/MS evaluation
-
10x)
+
-
-Inoculated vector strain Methanococcus into two tubes and GS + AT into other two
 
-
tubes. 
 
 +
'''September 2013'''
-
'''2013/03/06'''
+
-Transformation of V4 into Methanococcus
-
-Solid McC media was autoclaved so gel would melt, so we could add Na2S and
+
-Testing Fluorescence of V4
-
Puromycin to all solid media bottles for plating. Puromycin was added to all but two
+
-
bottles. These two bottles will be used as control for Puromycin.
+
-
-GS and AT cell cultures were measured for their optical density (OD). A cultures OD
+
-Purification of V4 cultures via plating of transformants, and creating sub-cultures of colonies picked
-
can tell us how well its growth and reproduction is. There is a direct correlation between
+
-
OD and cells/mL, so we will use this to determine how much we must dilute to achieve
+
-
around 150 cells/ml for optimal plating.  Appropriate dilutions were measured and
+
-
created.  These samples were added to solid media bottles is various quantities (0.3mL,  
+
-
0.6mL and 0.9mL), allowed to rest on the agar media for half an hour, then placed
+
-
vertically into a 37C incubation room.
+
-
'''2013/03/19'''
+
-Creation of frozen stocks of V4 in Methanococcus
-
-4 media tubes were prepared with 0.1 mL of 2.5% Na2S solution. These tubes
+
-GC/MS Evaluation and analysis (see results tab)
-
were then pressurized to 40 psi using H2/CO2 gas.
+
-
-Puromycin solution was prepared: 7.5mg of 200x Puromycin was added to 30
+
== '''E. coli Lab''' ==
-
mL of de-ionized water and sparged in nitrogen gas. The 30 mL was then
+
-
transferred to 6 tubes, each with 5 mL of 100x Puromycin.  
+
-
-6 solid media plates were prepared for future AT Methanococcus. The 6 bottles
+
Instructor: Rachit Jain
-
were autoclaved, and treated with 0.1 mL 100x Puromycin and 0.2 mL 2.5%
+
-
Na2S solution each. 
+
-
-1 GS (CK or control) colony, and 1 GS colony was slected and inoculated to
 
-
media containing 0.1 mL 2.5% Na2S. Note that these 2 colonies were not well
 
-
separated.  The 2 cultures were added to a 37C incubator.
 
-
'''2013/03/20'''  
+
'''February 2013'''
-
-200 mL liquid media was created, dispensed into 40 tubes, stoppered and capped,
+
-Training on PCR and heat shock transformation
-
pressurized to 15 psi using nitrogen and carbon dioxide, autoclaved and placed in the
+
-
anaerobic chamber.
+
-
-Frozen transformants of AT and GS+AT were placed into two properly treated media
 
-
tubes and placed into 37C incubator.
 
-
-Various appropriate dilutions of GS and AT cultures were created relative to OD
+
'''March 2013'''
-
readings as described in the process from 2013/03/06.
+
-
-These dilutions were inoculated into 8 solid media bottles for plating, and stored at 37C
+
-PCR of GS gene
-
incubation room.
+
-
'''2013/03/26'''
+
-Cloning of GS gene into pAW-50.
-
+
-
-8 media tubes were treated with 0.1 mL of 2.5% Na2S solution, 0.05 mL of 100x
+
-
Puromycin solution and pressurized to 40 psi with H2 and CO2. Two of these tubes were
+
-
inoculated with 0.2 mL of AT transformant , while 2 other tubes were inoculated with 0.2
+
-
mL of AT+GS transformant.  The remaining 4 tubes were inoculated with colonies that
+
-
formed from the GS transformant after Puromycin purification.  
+
-
-6 solid media bottles were autoclaved, treated with 0.2 mL Na2S and treated with 0.1
+
-Transformation of pAW-50 GS into species XL1-Blue. Transformed species spread onto ampicillin plates
-
mL of Puromycin for future plating.
+
-
+
-
'''2013/03/27'''
+
-
+
-
-Re-pressurize H2/CO2 culture tubes to 40 psi
+
-
+
-
-Place 1 mL of 60% glycerol/40% media solution into 20 three-mL serum bottles. These
+
-
20 bottles were stoppered and capped for future frozen culture stocks.  
+
-
-Check OD of cultures, and decided they were not sufficient enough for proper plating.
+
-Verification of GS transformants via digestion and gel verification
-
'''2013/03/28'''
 
-
-Re-pressurize H2/CO2 cultures tubes to 40 psi.
+
'''April 2013'''
-
-Measure OD of cultures tubes hoping much better growth since 2013/03/27. The OD
+
-Colonies for GS, AT, and GS+AT were selected from Methanococcus and corresponding genes were extracted. PCR and gel verification of GS, AT, and GS+AT genes. Results concluded successful in locating vectors from Methanococcus.
-
measurements provided results satisfactory for plating.  
+
-
-Various appropriate dilutions of AT and GS+AT cultures were created relative to OD
+
-PCR and gel verification of mCherry gene
-
readings as described in the process from 2013/03/06.
+
-
-These diluted samples were inoculated into 6 solid media bottles for plating and plates
+
-Cloning of mCherry gene into pAW-50 vector
-
were placed into 37C incubation room.
+
-
-3 autoclaved glycerol stock bottles made 2013/03/27 were used to create frozen culture
+
-Verification of cloning via digestion and gel verification. After positive verification, ligation of digested products and heat shock transformation into XL1-Blue. XL1-Blue transformants spread onto ampicillin plates.
-
stocks of biological replicates of GS. Namely, GS-1, GS-2 and GS-3 which were derived
+
-
from 3 different GS culture tubes. These 3 GS-inoculated glycerol stock bottles were
+
-
placed in -80C freezer.  
+
-
'''2013/04/02'''
+
-XL1-Blue colonies picked and screened. Purification of pAW-50 mCherry from colonies, and stored in -20°C freezer.
-
+
-
-400 mL of liquid media was created.  
+
-
'''2013/04/03'''
 
-
-Liquid media created 2013/04/02 was dispensed into 40 tubes, stoppered and capped. All
+
'''June 2013'''
-
tubes were pressurized to 15 psi using nitrogen and carbon dioxide then autoclaved.
+
-
-Agar was weighed out for 20 solid media bottles. Liquid media was then dispensed to
+
-Transformation of pAW-50 mCherry into XL1-Blue and creation of stock
-
these solid media bottles in addition to the agar. These bottles were stoppered, capped,
+
-
pressurized and autoclaved like the previously mentioned 40 tubes.
+
-
-All tubes and bottles were moved to anaerobic chamber.  
+
-PCR of two mCherry sequences: one without RBS sequence (V2) and one containing RBS sequence (V4). Gel Verification of tools 1 and 2.
-
-Colonies were picked from an AT and AT+GS plate. Four colonies were taken from
+
-Digestion and cloning of V2 and V4 into pAW-50 mCherry vector
-
each plate and inoculated into respective media tubes.
+
-
-Samples from the GS-1 and GS-2 frozen stock cultures were added to respective media
 
-
tubes to test if the previously created frozen stock cultures are actually viable.
 
-
 
-
-The 10 tubes including the AT colonies, AT+GS colonies, and frozen stock samples
 
-
were added to an incubator for growth.
 
-
'''2013/04/09'''  
+
'''July 2013'''
-
-1 mL of two different GS cultures (labeled GSF-1 and GSF-2) were inoculated in a 1 mL
+
-Purification of digested vector, ligation, and transformation of vector into XL1-Blue. Transformants plated onto ampicillin plates.
-
media/glycerol solution and stored at -80C for future use as a frozen stock culture.  
+
-
-6 agar bottles were autoclaved, treated with 0.1 mL of 100x Puromycin and 0.2 mL
+
-V2 and V4 colonies extracted and screened. Permanent stocks of V2B and V4B stored in -80°C freezer.
-
2.5% Na2S. These bottles will be used for future plating.
+
-
 
+
-
-A test of Puromycin strength was started. 2 media tubes were used, one with 0.05 mL of
+
-
Puromycin and 0.1 mL Na2S, while the other was not treated with anything (to serve as a
+
-
control). From there, 0.2 mL of Methanococcus was added to each tube, and the tubes
+
-
will be compared for Archaeal growth in the future.
+
-
 
+
-
'''2013/04/10'''
+
-
 
+
-
-Measure OD for AT and AT+GS cultures
+
-
+
-
-Various appropriate dilutions of AT and GS+AT cultures were created relative to OD
+
-
readings as described in the process from 2013/03/06.
+
-
 
+
-
-Make three plates for AT and three plates for AT+GS
+
-
 
+
-
-2 technical replicates at 10^-6 dilution at 0.6mL and 0.9mL per plate (using the
+
-
tube with the higher OD measurement).
+
-
 
+
-
-1 biological replicate at 10^-5 dilution at 0.6mL (lower of the tubes OD
+
-
measurements).
+
-
 
+
-
-Create 9 glycerol stock serum bottles as described in 2013/03/27 for future frozen
+
-
stocks. 1 mLof glycerol was added, the bottles were then stoppered, capped, autoclaved
+
-
and moved into the anaerobic chamber.
+
-
 
+
-
'''2013/04/16'''
+
-
 
+
-
-The two media tubes containing Methanococcus from 2013/04/09 were measured for
+
-
OD values. The Na2S + Puromycin containing media had on OD of 0.049A and the
+
-
control has an OD of 0.795. This data suggests that Puromycin is indeed still an effective
+
-
antibiotic.
+
-
 
+
-
-200 mL of liquid media was prepared.
+
-
 
+
-
'''2013/04/17'''
+
-
 
+
-
-Liquid media created 2013/04/16 was dispensed, stoppered, capped, pressurized to 15
+
-
psi using nitrogen and carbon dioxide, autoclaved and placed back into the anaerobic
+
-
chamber.
+
-
 
+
-
-1 plate of AT+GS and 1 plate of AT samples created 2013/04/10 were used for creating
+
-
cultures.
+
-
 
+
-
-Four colonies from each plate were inoculated into respective media tubes for plating,
+
-
and these plates were added to the incubator for growth. 
+
-
 
+
-
2013/04/19
+
-
-Colonies were picked from the plates created 2013/04/17 and inoculated into media
+
-
tubes. These tubes were added to a 37C incubator for growth. The success of these
+
-
colonies ends the purification process for all of our vectors.
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
[[[[[SUMMER SEMESTER]]]]]]]]]]]]]
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
'''2013/06/07'''
+
-
 
+
-
'''Creation of Transformation Buffer (TB), Cysteine-HCL/DTT solution, and Mc media'''
+
-
 
+
-
Smith, Peyton. Rodriguez, Nicholas. Burroway, Brandon.
+
-
 
+
-
-Creation of 100ml of transformation buffer in preparation of mcherry plasmid
+
-
transformation.
+
-
 
+
-
-Creation of 20ml of Cysteine-HCL/DTT solution in preparation of mcherry plasmid
+
-
transformation
+
-
 
+
-
-Creation of 400ml of formate liquid media - to be dispensed in 40 tubes @ 5ml each and
+
-
20 agar bottles @ 10ml each
+
-
+
-
-All three of these were sparged for an appropriate time and placed inside the anaerobic
+
-
chamber.
+
-
   
+
-
'''2013/06/10-2013/06/14'''
+
-
+
-
'''Sequencing, Laundry and Transformation Preparation'''
+
-
 
+
-
Smith, Peyton. Rodriguez, Nicholas. Burroway, Brandon. Fetchko, Travis.
+
-
 
+
-
-mcherry plasmids were received from E. coli lab, and immediately sent to the sequencing
+
-
center on campus.
+
-
 
+
-
-All necessary buffers and solutions for methanococcus transformation were prepared.
+
-
 
+
-
-Washing of all lab glassware.
+
-
 
+
-
'''2013/06/17'''
+
-
 
+
-
'''Review of GC/MS Protocol, Extraction, GC/MS Preparations, Transformation Prep'''
+
-
+
-
Smith, Peyton. Fetchko, Travis. Hampton, Michael.
+
-
 
+
-
-Extraction of AT and wild type cultures for future GC/MS analysis of geraniol
+
-
production
+
-
 
+
-
-Creation of six S0001 culture tubes to be used as the recipient methanococci for mcherry
+
-
transformation
+
-
+
-
-Preparation of geranyl acetate inoculant solution. 
+
-
 
+
-
'''2013/06/18'''
+
-
 
+
-
'''Creation of Future GC/MS-Evaluated Cultures, Extraction, GC/MS Prep'''
+
-
+
-
Smith, Peyton. Fetchko, Travis. Brandon, Burroway. Hampton, Michael.
+
-
 
+
-
-Inoculation of GS, AT, and AT+GS into 10 media tubes (2, 4, and 4, respectively)
+
-
 
+
-
-Geranyl acetate, originally created 2013/06/17, was added to two AT and two AT+GS
+
-
tubes previously mentioned
+
-
 
+
-
-These 10 tubes will be used for GC/MS analysis of geraniol production.
+
-
+
-
-Creation of geraniol and geranyl acetate solution to be used when creating GC/MS
+
-
standards.
+
-
 
+
-
-Extraction of supernatant from GS and GS+AT cultures for future GC/MS analysis of
+
-
geraniol production.
+
-
 
+
-
-Cell pellets from GS and GS+AT cultures were frozen in -20C for 1h and thawed before
+
-
being resuspended
+
-
+
-
-Extraction of lysed cell pellets from GS and GS+AT cultures for future GC/MS analysis
+
-
of geraniol production 
+
-
 
+
-
'''2013/06/19'''
+
-
 
+
-
'''Sequence analysis & Transformation Prep'''
+
-
 
+
-
Smith, Peyton. Hampton, Michael.
+
-
 
+
-
-Analysis of mcherry plasmid sequence
+
-
 
+
-
-Final preparations for transformation
+
-
 
+
-
'''2013/06/20'''
+
-
 
+
-
'''MCherry Plasmid Transformation into Methanococcus'''
+
-
+
-
Smith. Peyton. Hampton, Michael. Rhode, Benji. Fetchko, Travis. Rodriguez, Nicholas.
+
-
Burroway, Brandon.
+
-
 
+
-
-Transformation of mcherry plasmid into methanococcus was completed in two balch
+
-
tubes according to protocol. These tubes were respectively labeled A and B.
+
-
+
-
-Transformation was also completed in parallel in a modified version of the protocol. The
+
-
majority of the transformation was completed inside the chamber in 1.5ml
+
-
microcentrifuge tubes that could be centrifuged inside the chamber. The volumes of
+
-
media and DNA were proportionally decreased according to the protocol. Four
+
-
microcentrifuge tubes were made and proceeded through the protocol until the first
+
-
addition of TB. Here, we combined the four microcentrifuge tubes into two to increase
+
-
the number of recipient cells as OD values are expected to decrease during the
+
-
transformation process. For TB and TB+PEG, one microcentrifuge tube received the
+
-
amount according to the protocol, whereas the other microcentrifuge tubes received 60%
+
-
the amount of TB and TB+PEG as the protocol indicates. These tubes were labeled A and
+
-
B, respectively. Due to microcentrifuge tube B’s inability to form a proper cell pellet, A
+
-
and B were combined into one balch tube, labeled AB, before being taken out of the
+
-
chamber where we added 1ml of media, pressurized, and added to the incubator
+
-
overnight. 
+
-
 
+
-
'''2013/06/21'''
+
-
 
+
-
'''Plating of Transformants and Creation of Puromycin Enriched Transformant Cultures'''
+
-
+
-
Smith, Peyton.
+
-
 
+
-
-Serial dilutions of the transformants were created in dilutions of 10^-1, 10^-2 and 10^-3.
+
-
 
+
-
-For each of the three transformants, namely A, B and AB, plates were created using 1ml
+
-
of inoculant for 10^-1 and 10^-2 and 2ml for 10^-3. A tenth plate was inoculated with
+
-
s0001 as a positive control.
+
-
 
+
-
-Puromycin was then added to all serial dilutions tubes so we may analyze fluorescence in
+
-
enriched cultures in parallel to growing colonies.  A puromycin enriched tube was also
+
-
created for a tube containing the pAW50 vector to serve as a negative control. 
+
-
 
+
-
-All serial dilution tubes and negative control were added to the incubator, and all plates
+
-
including positive control were added to the warm room.
+
-
 
+
-
'''2013/06/24'''
+
-
 
+
-
'''Transformation Results, GC/MS Sample Creation, GS, AT and GS+AT Inoculation/Revival'''
+
-
 
+
-
Smith, Peyton. Fetchko, Travis.
+
-
 
+
-
-OD of puromycin enriched cultures originally created 2013/06/21 were read. 10^-1 and
+
-
10^-2 dilutions were between 0.6-0.9, but 10^-3 dilution was 0.2-0.4, so they were put
+
-
back into the incubator to continue growing. 
+
-
 
+
-
-Plates of transformants of 10^-1 dilution are beginning to show small colonies.
+
-
+
-
-Hexane-extracted samples for GC/MS have finished drying, so final samples 100ul-200ul
+
-
were added to tubes and added to the iGEM box of GC/MS samples. These samples will
+
-
be analyzed for geraniol production in the GC/MS lab as soon as the lab becomes
+
-
available.
+
-
 
+
-
-GS, AT, and GS+AT cultures originally created 2013/06/18 for GC/MS analysis still
+
-
show no signs of growth, so we decided to make new ones.
+
-
+
-
-The room temperature cultures used to create the cultures that were unsuccessful were
+
-
inoculated into 6 balch tubes, 3 with puromycin, 3 without.
+
-
 
+
-
-Glycerol stock samples were revived for each inoculant into 6 balch tubes, 2 tubes per
+
-
inoculant respectively. All 6 tubes were without puromycin These can ideally be
+
-
transferred into tubes with puromycin in the future.
+
-
 
+
-
-Note: glycerol stock GS-1 may be compromised due to prolonged thawing.
+
-
+
-
'''2013/06/25'''
+
-
+
-
'''Fluorescence Testing of MCherry, Creation of Media'''
+
-
+
-
Smith, Peyton. Fetchko, Travis. Rodriguez, Nicholas
+
-
 
+
-
-In E. coli lab: verification of successful expression of mcherry in methanococcus through
+
-
use of fluorometer. See Rachit for raw data.
+
-
 
+
-
-Prepared 400ml of formate media
+
-
 
+
-
'''2013/06/26'''
+
-
+
-
'''Picking MCherry Colonies & Dispensing Media'''
+
-
 
+
-
Smith, Peyton. Fetchko, Travis. Rodriguez, Nicholas.
+
-
 
+
-
-Dispensed media originally created 2013/06/25 into 80 tubes which were stoppered,
+
-
sealed, pressurized to 15 psi using N2/CO2, and autoclaved.
+
-
 
+
-
-5 colonies from mcherry plates originally created 2013/06/21 were picked and inoculated
+
-
into 5 media tubes with 2.5% Na2S and puromycin. 1 colony was picked from sample B
+
-
10^-2, 1 colony was picked from sample C 10^-2, and 3 colonies were picked from
+
-
sample C 10^-1 and placed into respectively labeled tubes. These tubes were placed the
+
-
incubator.
+
-
 
+
-
'''2013/7/02-05'''
+
-
 
+
-
-Some of the AT, AT+GS and GS cultures inoculated on 6/24/13 came up and had O.D. taken by
+
-
LZ. Those cultures were further subcultured. 
+
-
 
+
-
'''2013/07/10'''
+
-
 
+
-
'''Creation of Sub-Cultures for Feeding Experiments'''
+
-
 
+
-
Smith, Peyton. Rodriguez, Nicholas.
+
-
 
+
-
-AT, GS, and AT+GS samples that were revived from frozen glycerol stocks were
+
-
observed with high OD values.
+
-
+
-
-Sub cultures were created of these samples so that we may use them for future feeding
+
-
experiments when measuring geraniol production.
+
-
 
+
-
-These sub cultures were placed in the incubator overnight.
+
-
+
-
-List of sub-cultures:
+
-
+
-
o GS without any feed x2 (one was inoculated from room-temp culture, and the
+
-
other was direct inoculation from frozen stock)
+
-
+
-
o AT without any feed x2 (derived from room temp cultures)
+
-
+
-
o AT fed with geranyl acetate (GA) x2 (GA diluted in hexanes)
+
-
+
-
o AT fed with GA x2 (GA diluted in ethanol)
+
-
 
+
-
o AT+GS without any feed x2 (derived from room temp cultures)
+
-
+
-
o AT+GS fed with geranyl acetate (GA) x2 (GA diluted in hexanes)
+
-
 
+
-
o AT+GS fed with GA x2 (GA diluted in ethanol)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
'''2013/07/12'''
+
-
 
+
-
'''Extraction of AT and AT+GS and Creation of Killing/Inhibiting Experiment'''
+
-
 
+
-
Smith, Peyton. Rodriguez, Nicholas.
+
-
 
+
-
-Extraction protocol was completed for AT and AT+GS subcultures without any added
+
-
feed that were originally created 2013/07/10. This extraction was completed for the sub-
+
-
cultures’ supernatant.
+
-
+
-
-The fed cultures’ inability to grow in the same amount of time from biological replicates
+
-
as those that did grow without any feed lead us to create another experiment, where we
+
-
shall test Methanococcus’ reaction to the exposure of all possibilities that could have
+
-
caused it to not grow.
+
-
 
+
-
-In this experiment we will test geranyl acetate (GA), geraniol, hexane, and ethanol’s
+
-
affect on the growth/sustainability of Methanococcus. 
+
-
+
-
-Six grown cultures with high OD values were used to create sub cultures for the
+
-
inhibiting experiment. After inoculation of sub-cultures, the six original cultures were
+
-
used for the killing experiment.
+
-
 
+
-
-List of samples and treatments: Inhibiting
+
-
 
+
-
o AT with hexane with respective negative control
+
-
 
+
-
o AT with ethanol with respective negative control
+
-
+
-
o AT x2 with GA with respective negative controls
+
-
+
-
o AT+GS x2 with geraniol with respective negative controls
+
-
 
+
-
-List of samples and treatments: killing
+
-
 
+
-
o AT with hexane
+
-
 
+
-
o AT with ethanol
+
-
 
+
-
o AT with GA x2
+
-
 
+
-
o AT+GS with geraniol x2
+
-
 
+
-
'''2013/07/15'''
+
-
 
+
-
'''Analysis of Killing/Inhibiting Experiment and Creation of Maximum Boundary
+
-
Experiment'''
+
-
 
+
-
Smith, Peyton. Rodriguez, Nicholas.
+
-
 
+
-
-The following were observed from the killing/inhibiting experiment:
+
-
 
+
-
o Ethanol at the dilution used to introduce GA to a culture is enough to be both
+
-
inhibiting to the growth of a culture and also enough to be lethal to a grown
+
-
culture.
+
-
+
-
o Hexane at the dilution used to introduce GA to a culture has no effect on the
+
-
growth or lethality of a culture.
+
-
 
+
-
o Geranyl Acetate (GA) introduced to a culture at a concentration of 10ng/5ml has
+
-
no effect on the growth or lethality of a culture
+
-
 
+
-
o Geraniol inoculated cultures showed significantly higher OD readings in the
+
-
growth cultures compared to their respective negative controls, but geraniol
+
-
inoculated cultures with initially high OD values, had no change. Geraniol may be
+
-
beneficial to the growth of methanococcus, but this observation is inconclusive.
+
-
Future experiments will be conducted to further test this hypothesis.
+
-
 
+
-
-Since cultures grew well in 10ng/5ml conentration of GA and geraniol, we decided to
+
-
begin a new experiment to test the upper boundary of how much GA and geraniol a 5ml
+
-
methanococcus culture could handle, also as a test to determine methanococcus’ highest
+
-
possible production yield, at least in its current condition.
+
-
 
+
-
-Sub-cultures of AT and AT+GS were created and inoculated with GA. For these 2
+
-
samples, 2 treatments were created, namely 10ng/5ml and 1000ng/5ml, and 1 replicate
+
-
was created for al. These samples were placed into the incubator for growth
+
-
 
+
-
-Note: for inoculation, we ran out of GA solution, so one of the tubes which was labeled
+
-
to have 1000ng of GA added to it actually received <500ng GA, but we did not mark
+
-
which one it was.
+
-
 
+
-
-Innovation of an adapter to allow the use of syringe needles on micropipettes. 
+
-
 
+
-
'''2013/07/16'''
+
-
 
+
-
'''Creation of Formate Media, 100ml Cultures, and Inoculation of 100ml Cultures'''
+
-
+
-
Smith, Peyton. Rodriguez, Nicholas. Hampton, Michael.
+
-
+
-
-After some calculations taking into account the lipid biosynthesis pathway that geraniol is
+
-
created from, it is very unlikely that 5ml cultures are able to produce the 2ng/ul of
+
-
geraniol that is necessary for detection in GC/MS. We decided to create three 100ml
+
-
cultures of AT, GS, and AT+GS so that we may break the 2ng/ul detection limit.
+
-
 
+
-
-300ml x2 of media was created, pressurized, autoclaved and placed into the chamber to
+
-
later be dispensed into three large culture bottles and 60 media tubes.
+
-
 
+
-
-The three 100ml cultures were inoculated with 5ml of our highest-OD culture of AT, GS,
+
-
and AT+GS without any feed that was originally created 2013/07/10. This inoculation
+
-
process should be completed through use of a vacutainer needle. Note: repressurize the
+
-
5ml culture tubes before inoculating via vacutainer needle!
+
-
 
+
-
-These three 100ml culture bottles were placed into metal cylinders (barrels) and placed
+
-
into the large incubator.
+
-
 
+
-
'''2013/07/18'''
+
-
 
+
-
'''Further Investigation of Maximum Boundary Experiment and GC/MS Booking'''
+
-
+
-
Smith, Peyton. Rodriguez, Nicholas. Burroway, Brandon. Rahul.
+
-
 
+
-
-OD values were read of the feeding experiment created 2013/07/15. One of the tubes
+
-
from the experiment somehow was exposed to oxygen, so the culture was pink, dead and
+
-
not usable. All of the remaining tubes which had 10ng of GA grew with high OD values.
+
-
All of the tubes with 1000ng of GA did not show any growth except for one. One tube
+
-
labeled to have added 1000ng of GA did grow, could this have been the one that actually
+
-
received <500ng? The result it this is inconclusive because we did not mark which tube
+
-
received <500ng GA
+
-
 
+
-
-New feeding experiments were created to further test the upper limit of GA/geraniol
+
-
tolerance in methanococcus. 12 tubes were taken to create a similar experiment using 2
+
-
samples, 3 treatments, and 1 replicate. The samples were AT and AT+GS, the treatments
+
-
were 100ng, 500ng, and 1000ng of GA, and 1 replicate of each to ensure results. Note:
+
-
these tubes contain puromycin.
+
-
+
-
-OD values of the three 100ml cultures were taken, none of which were high enough to
+
-
begin extraction, but AT and AT+GS were moved to room temperature, and GS was
+
-
added back to the incubator.
+
-
 
+
-
-We visited Dr. Dennis Phillips to discuss GC/MS. We booked an official GC/MS
+
-
appointment to test for geraniol on Tuesday, 2013/07/23
+
-
 
+
-
'''2013/07/19'''
+
-
 
+
-
'''Modification of Extraction Protocol, Extraction via Modified Protocol, Creation of GC/MS
+
-
Standards, Extraction Efficiency Experiment.'''
+
-
 
+
-
Smith, Peyton. Burroway, Brandon.
+
-
 
+
-
-Research was done looking into the solubility of geraniol into hexane, and the
+
-
consequential efficiency of the extraction procedure. See: Coriander_oil.pdf and
+
-
http://www.nbb.cornell.edu/neurobio/ragusolab/Floral%20Scent%20primer.html
+
-
 
+
-
-We found that geraniol’s solubility in hexane is 1ug/ml, when we’ve been using 15ml of
+
-
hexane to extract ~10ng of potential geraniol. Also, we found that solubility is increased
+
-
through the use of a 9:1 solution of hexane : acetone. We decided to modify the
+
-
extraction protocol in accordance to these findings to increase extraction efficiency and
+
-
efficiency of sample drying.
+
-
+
-
-9:1 hexane/acetone solution was created and sealed for future use
+
-
 
+
-
-GC/MS geraniol standards were created. These standards include concentrations of
+
-
84ng/ul, 42 ng/ul, 8.4ng/ul and 0.84ng/ul
+
-
 
+
-
-OD values were read for the three 100ml cultures, and they were within enough range to
+
-
begin extraction.
+
-
 
+
-
-Modified version of extraction protocol (see below) was completed for the extraction of
+
-
the three 100ml culture of AT, GS and AT+GS. It is not known for sure whether or not
+
-
geraniol created by methanococcus is excreted from the cell. So, extraction protocol for
+
-
the cellular content (see below) was completed for the cells pelleted in the extraction
+
-
protocol.
+
-
 
+
-
-Extraction protocol was completed for an extraction efficiency experiment using anerobic
+
-
water and 840ng geraniol. 
+
-
 
+
-
-Drying was completed down to 10ul for the supernatent extraction from the 100ml
+
-
cultures of AT, GS and AT+GS and were added to GC/MS sample bottles.
+
-
 
+
-
-Cellular content extraction for all three samples and extraction efficiency had not finished
+
-
drying and will be completed Monday.
+
-
 
+
-
-Innovation of a creative device to increase drying efficiency of multiple samples by
+
-
100%.
+
-
   
+
-
'''2013/07/22'''
+
-
 
+
-
'''Extraction of Feeding-Experiments & Final Preparation for GC/MS
+
-
'''
+
-
Smith, Peyton. Rodriguez, Nicholas.
+
-
 
+
-
-Drying process was completed for the remaining samples that were extracted 2013/07/19
+
-
including cell extract of all three 100ml cultures and the extraction efficiency experiment.
+
-
+
-
-Extraction was completed via modified protocol for four feeding-experiment cultures
+
-
originally created 2013/07/18. These four cultures were single replicates AT and AT+GS
+
-
which had 500ng and 1000ng GA treatments.
+
-
 
+
-
-All extraction samples were prepared for GC/MS and final gathering of
+
-
materials/preparations were done.
+
-
 
+
-
'''2013/07/23'''
+
-
+
-
'''GC/MS Evaluation and Analysis'''
+
-
 
+
-
Smith, Peyton. Fetchko, Travis. Hampton, Michael. Westbrook, Marquise.
+
-
+
-
-GC/MS evaluation and analysis was completed for over 30 samples.
+
-
 
+
-
-See all raw data (via LZ or Peyton)
+
-
+
-
-Three culture samples gave positive results for production of geraniol. (see below)
+
-
 
+
-
-Modified extraction protocol shows ~65% efficiency, not differing much from the
+
-
original extraction protocol.
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
[[[[[[[[[[[[[Fig. 3 Geraniol Standard (sample 32, approx. 8.4ng/ul)]]]]]]]]]]]]]]]]]
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
[[[[[[[[[[[[[[Fig. 4 AT or WT Supernatant (sample 6) ]]]]]]]]]]]]]]]]]]]]]]]]]]
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
[[[[[[[[[[[[[[[Fig. 5 Geraniol matched against database of mass spec entries peak at 7.81min (sample 6)]]]]]]]]]]
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
[[[[[[[[[Fig. 6 GS or AT+GS S/C (sample 7)]]]]]]]]]]]]]
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
[[[[[[[[[[[[Fig. 7 AT(0.46) Supernatant (sample 12) ]]]]]]]]]]]]]]]
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
'''2013/07/30'''
+
-
 
+
-
'''GC/MS Analysis and Revival of Frozen Stocks for Future GC/MS Trials'''
+
-
 
+
-
Smith, Peyton. Hampton, Michael. Rodriguez, Nicholas.
+
-
+
-
-Analysis of GC/MS results
+
-
 
+
-
-Revived 4 AT, 4 GS, and 4 AT+GS samples from frozen glycerol stock, all to be
+
-
evaluated by GC/MS for geraniol production
+
-
 
+
-
-2 sub-cultures of wild type s0001 were created from 1 room temperature stock
+
-
+
-
-Subcultures of the 5 mCherry colonies picked were created to later be made into frozen
+
-
stocks. These 5 subcultures were labeled c1-5, respectively.
+
-
 
+
-
-Note: Samples GS-4, GS+AT-8, and AT-12 were inoculated with 0.2ml from frozen
+
-
glycerol stocks due to prolonged thawing.
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
[[[[[[[[[FALL SEMESTER]]]]]]]]]]]]]]
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
'''2013/08/06'''
+
-
 
+
-
'''Geraniol Extractions'''
+
-
 
+
-
Smith, Peyton
+
-
 
+
-
-Take OD values of the 19 cultures (originally created 2013/07/31)
+
-
 
+
-
-Complete extraction protocol for all cultures with OD value greater than 0.5
+
-
 
+
-
o GS: 15ml hexanes, supernatant and cell extract
+
-
 
+
-
o AT and AT+GS: 15ml hexanes, supernatant
+
-
 
+
-
o Wild Type: 15ml hexanes, supernatant and cell extract
+
-
 
+
-
o Evaporate to 200ul and 50ul for supernatant and cell extract, respectively
+
-
 
+
-
-Re-inoculate not yet grown cultures
+
-
 
+
-
o pAW50-mCherry: use original parent strains
+
-
 
+
-
o AT and AT+GS: use grown replicate strains.
+
-
 
+
-
-Wash GC/MS bottles with ethanol
+
-
+
-
'''2013/08/09'''
+
-
 
+
-
'''Geraniol Extractions and mCherry Frozen Stock'''
+
-
 
+
-
Smith, Peyton
+
-
 
+
-
-Take OD values for cultures that were re-inoculated on 2013/08/06
+
-
 
+
-
-Complete extraction protocol for all remaining cultures
+
-
 
+
-
-Create pAW-50 mCherry-C2 frozen stock.
+
-
+
-
'''2013/08/12'''
+
-
 
+
-
'''GC/MS Final Preparations and mCherry Frozen Stocks'''
+
-
 
+
-
Smith, Peyton
+
-
 
+
-
-Finish all extractions and place all samples into GC/MS sample bottles
+
-
 
+
-
-Create frozen stocks of pAW-50 mCherry C1 and C5
+
-
 
+
-
-Assemble and autoclave anaerobic glass syringes
+
-
 
+
-
'''2013/08/14'''
+
-
 
+
-
'''GC/MS Evaluation and Analysis'''
+
-
 
+
-
-10 samples were run using the method described in the first GC/MS evaluation
+
-
 
+
-
-No positive results came from these 10 samples.
+
-
 
+
-
-The positive samples from the first GC/MS evaluation were run, and still showed presence of geraniol.
+
-
 
+
-
-See raw data (via LZ)
+
-
 
+
-
-Our hypothesis is that we did not receive any positive results from the second round of GC/MS because we restricted ourselves to extracting from only 1 GS frozen stock which was derived from 1 colony during the purification process. In comparison, the first GC/MS trials used at least 2 GS frozen stocks/colonies. We have decided to begin a final geraniol production centred experiment. We will revive all frozen stocks/colonies of GS and AT, verify for insert via PCR and complete extraction. We hope by including all of the possible colony derivatives, we can reach conclusive results and determine which frozen stock produced geraniol in the first GC/MS trials.
+
-
 
+
-
'''2013/08/21'''
+
-
 
+
-
'''Inoculation of Samples for Future GC/MS Evaluations'''
+
-
 
+
-
Smith, Peyton
+
-
 
+
-
-GS-1, GS-3, and GSF samples were all revived with respective biological replicates.
+
-
 
+
-
-AT-1, AT-3, and AT-4 samples were all revived.
+
-
 
+
-
-Room-temp wild type samples were inoculated to create 3 samples for future extraction
+
-
 
+
-
'''2013/08/23'''
+
-
 
+
-
'''PCR of GS and AT Cultures to Confirm Insert'''
+
-
 
+
-
Smith, Peyton. Westbrook, Marquise. Hampton, Michael.
+
-
 
+
-
-OD values of the cultures inoculated on 2013/08/21 were taken.
+
-
 
+
-
-PCR was completed for all the aforementioned GS and AT samples. The following is the gel from the PCR confirming that some of the GS cultures indeed contain the GS gene and some of the AT samples contain the AT gene.
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
[[[[[[[[[[[[[[[Fig. PCR gel of GS and AT cultures from LZ]]]]]]]]]]]]]]]]
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
'''2013/08/26'''
+
-
 
+
-
'''Extraction of Geraniol from PCR-verified GS Cultures and Wild Type Cultures'''
+
-
 
+
-
Smith, Peyton
+
-
 
+
-
-The original extraction protocol was completed for all GS cultures and the three wild type cultures originally created 2013/08/21
+
-
 
+
-
-The 15ml organic solvent from extraction of geraniol was split into two 7.5ml containers to dry. One 7.5ml sample was allowed to dry naturally under the fume hood, and the other 7.5ml sample was dried under a stream of N2 gas.
+
-
 
+
-
'''2013/09/02'''
+
-
 
+
-
'''GC/MS Sample Preparation, and Preparation of V4 Transformation'''
+
-
 
+
-
Smith, Peyton
+
-
 
+
-
-All samples for GC/MS evaluation are prepared, and we have booked a time to work in the GC/MS lab.
+
-
 
+
-
-All necessarily materials were prepared for the transformation of V4 into methanococcus.
+
-
 
+
-
'''2013/09/03'''
+
-
 
+
-
'''Transformation of V4 into Methanococcus'''
+
-
 
+
-
.
+
-
 
+
-
'''2013/09/04'''
+
-
 
+
-
'''Plating of V4 Transformants, Creation of Puromycin-Enriched Transformant Cultures'''
+
-
 
+
-
.
+
-
 
+
-
'''2013/09/05'''
+
-
 
+
-
'''Testing of Fluorescence of Puromycin-Enriched V4 Transformants'''
+
-
 
+
-
.
+
-
 
+
-
'''2013/09/06'''
+
-
 
+
-
'''GC/MS Evaluation and Analysis'''
+
-
 
+
-
.
+
-
 
+
-
== '''E. coli Lab''' ==
+
-
 
+
-
Instructor: Rachit Jain
+

Latest revision as of 23:26, 22 September 2013

Notebook

Methanococcus Lab

Instructor: ZHE LYU


February 2013

-Training on anaerobic skills, i.e. use of anaerobic glassware, gassing chamber, anaerobic chamber, etc.


March 2013

-Purification of GS, AT and GS+AT via revival of frozen stocks and plating of sub-cultures.


April 2013

-Further continuation of purification of GS, AT and GS+AT via picking colonies, creating sub-cultures and plating.

-Test of Puromycin strength.

-Creation of frozen stocks of purified GS, AT and GS+AT transformants.


June 2013

-Extraction of Geraniol from extra-cellular and intra-cellular content of samples and preparation for GC/MS evaluation

-Sequencing of pAW50-mCherry vector

-Analysis of pAW50-mCherry sequence

-Transformation of pAW50-mCherry vector into Methanococcus

-Testing Fluorescence of pAW50-mCherry

-Purification of pAW50-mCherry cultures via plating of transformants, and creating sub-cultures of colonies picked

-Creation of frozen stocks of pAW50-mCherry in Methanococcus


July 2013

-Creation and analysis of the "killing & inhibiting" experiment where we test the maximum amount of product a 5ml culture of Methanococcus can tolerate in cultures with high OD (killing of grown cells) and low OD (inhibiting of growth).

-Innovation of an adapter to allow the use of syringe needles on micropipettes.

-Expanded upon the original extraction protocol for higher efficiency of extraction of geraniol from Methanococcus cultures.

- GC/MS Evaluation and analysis (see results tab)


August 2013

-Revival and PCR of all GS and AT frozen stocks to confirm insert.

--Extraction of Geraniol from extra-cellular and intra-cellular content of all GS frozen stocks and preparation for GC/MS evaluation


September 2013

-Transformation of V4 into Methanococcus

-Testing Fluorescence of V4

-Purification of V4 cultures via plating of transformants, and creating sub-cultures of colonies picked

-Creation of frozen stocks of V4 in Methanococcus

-GC/MS Evaluation and analysis (see results tab)

E. coli Lab

Instructor: Rachit Jain


February 2013

-Training on PCR and heat shock transformation


March 2013

-PCR of GS gene

-Cloning of GS gene into pAW-50.

-Transformation of pAW-50 GS into species XL1-Blue. Transformed species spread onto ampicillin plates

-Verification of GS transformants via digestion and gel verification


April 2013

-Colonies for GS, AT, and GS+AT were selected from Methanococcus and corresponding genes were extracted. PCR and gel verification of GS, AT, and GS+AT genes. Results concluded successful in locating vectors from Methanococcus.

-PCR and gel verification of mCherry gene

-Cloning of mCherry gene into pAW-50 vector

-Verification of cloning via digestion and gel verification. After positive verification, ligation of digested products and heat shock transformation into XL1-Blue. XL1-Blue transformants spread onto ampicillin plates.

-XL1-Blue colonies picked and screened. Purification of pAW-50 mCherry from colonies, and stored in -20°C freezer.


June 2013

-Transformation of pAW-50 mCherry into XL1-Blue and creation of stock

-PCR of two mCherry sequences: one without RBS sequence (V2) and one containing RBS sequence (V4). Gel Verification of tools 1 and 2.

-Digestion and cloning of V2 and V4 into pAW-50 mCherry vector


July 2013

-Purification of digested vector, ligation, and transformation of vector into XL1-Blue. Transformants plated onto ampicillin plates.

-V2 and V4 colonies extracted and screened. Permanent stocks of V2B and V4B stored in -80°C freezer.

Retrieved from "http://2013.igem.org/Team:UGA-Georgia/Notebook"