Team:Berlin/Project

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1

What is it all about?

  iGEM Berlin 2014: A remote control for E. coli
As the first iGEM team from Berlin to take part in the competition, we decided to construct a simple BioBrick that enables synthetic biologists to remotely control the movement of the laboratory workhorse Escherichia coli. A seemingly simple and non-invasive mechanism for this remote control is the use of magnetic fields, which enable a vast variety of applications. In nature, these are already used by several mammals, as well as bacteria for orientation. Remote-controlled E. coli cells could be used as “bacteria-based nanorobots” in order to maneuver them live in the intestine - targeting diseased tissue or even tumors. Combined with BioBricks from other iGEM teams a local, site-directed treatment of intestine cancer is envisioned[1]. Therefore, we work with the probiotic E. coli strain Nissle 1917, which already has an 80 year history as a treatment for chronically inflamed intestine tissue and is sold commonly as “Mutaflor”[2]. Our experiments should enable us to construct simple BioBricks capable to produce a diverse set of nanoparticles, including quantum dots, magnetic nanoparticles, semiconductor nanoparticles, noble metal nanoparticles and many more[3]. For example, cheap and efficient production of magnetic nanoparticles could be used in hyperthermal cancer therapy. Subsequently, we would like to investigate if our method can also be adapted to the synthesis of rare earth metals, which despite their abundance are not mineable. This would offer an alternative to the environmental hazardous mining operations that are common today. A remote control for E. coli will enable a whole variety of application relevant for bioprocess engineering. Therefore one can imagine neglecting centrifugation for cell separation - simply use a magnet. Also, it should be possible to use high frequent oscillating magnetic fields for cell lysis or even use rotating magnetic fields for self-stirring cultures in bioreactors solving scale up limiting issues like tip speed. Nature is the world’s most skilled engineer and has naturally occurring magnetotactic bacteria such as Magnetospirrilium magneticum. Under certain conditions, these organisms form magnetosomes, which are chains of magnetite nanoparticles. These function as an intracellular compass for the cell and even allow them to orientate along earth’s weak magnetic field. As previous iGEM teams have shown, synthesizing fully functional magnetosomes in E. coli is highly difficult as more than 60 highly regulated genes are involved[4]. The Berlin iGEM team came up with an alternative strategy that does not rely on the formation of magnetosomes. By knocking out the iron efflux transporter gene FieF and the iron uptake suppressor Fur, we want to increase the total iron level of the cytosol. By sequestering iron in a ferritin protein, iron crystals are formed and the cell is detoxified. In order to create ferromagnetic crystals, we will use intensive high-throughput growth medium optimization to discover the best conditions for the formation of magnetic nanoparticles in E. coli. We will work with other metal binding proteins such as metallothioneins and phytochelatin synthases in order to achieve nanoparticle synthesis. Once we have discovered the best way to magnetize E. coli bacteria, we will build and characterize suitable BioBricks that can be used by any research lab or iGEM team in the world in order to remote control the cellular movement.

Involving the Community
Although there are several scientific institutions located in Berlin which are conducting research in synthetic biology, there has never been an iGEM team from Berlin before. This is even more surprising as Berlin with its vibrant bio-arts and diy-biology community seems to be the perfect location for successful iGEM projects. As an interconnected workforce, our team incorporates members from various scientific, cultural and creative backgrounds, which makes our team able to address complex issues from various persepctives. So far, iGEM Berlin consists of students from biotechnology, history, design, medicine, theoretical physics, informatics, and more. So far our diverse team has been able to make valuable connections into the bio-arts scene of Berlin, working together with think tanks such as the Hybrid Plattform, as well as EU advisor Markus Schmidt and his Biofaction AG. Supported by the Hybrid Plattform, we organized a science and design workshop event on the 8/9.08.2014. During this event we conducted a series of short presentations about synthetic biology, as well as about prototyping and speculative design. Participants from different backgrounds designed and constructed interactions, which deal with the idea of a biological modularity. The resulting interactions addressed currently debating issues about the future of syntheic biology applications. Surpisingly the participants focused on topics like performance enhancement, transhumanism, alternative materials and housing as well as standardiziation. By explaining the basic principles of synthetic biology and approaching synthetic biology with a limited complexity synthetic biological speculation became easily accessible and reached wide variety of people. In the beginning of September, we collaborated with the artists and scientists from the c-lab collectiv (UK) as well as the Artlaboratory - a berlin bio-arts space. In the Synthetic Biology Workshop artists and other people were introduced to synthetic biology and performed their own cloning experiment. The whole event came to an end in Berlins first Science Café event for synthetic biology organized by the iGEM Berlin Team. During this event, we had speakers from different backgrounds and we discussed chosen aspects of synthetic biology with participants openly over drinks and food. The artist Ping Lui from Cologne presented his speculative design of an oracle based on magnetotactic bacteria. Rüdiger Trojok, a infamous German biohacker presented his current project, Howard Boland shared his bioart projects and former iGEM involvement with us and Johann from our team gave a short presentation about iGEM and our project. These events were designed to have a high impact on the German understanding of synthetic biology and were a major success in Berlin. One of the current major issues in synthetic biology is the laws and regulations concerning patents. iGEM generally refuses patents and promotes the idea of open source biology. However, as the success and applicability of synthetic biology depend on industry investments, there has to be a compromise in policy regulations. To discuss this topic in detail we teamed up with patent lawyers from the Adares Patentanwältekanzlei as well as Biocommons (Creative Commons license model for Synbio) activist Rüdiger Trojok to discuss patenting and fundamental principles of intellectual property.
In summary, we used art events and practical workshops to confront the German public with issues of synthetic biology. Furthermore, our project of creating a remote control for E. coli bears various practical applications as well as expands the possibilities of future functional biological systems.

References
[1] https://2012.igem.org/Team:Penn/ProjectResults (11.07.2014)
[2] http://www.mutaflor.de/cms/ (11.07.2014)
[3] Park, T. J., Lee, S. Y., Heo, N. S. and Seo, T. S. (2010), In Vivo Synthesis of Diverse Metal Nanoparticles by Recombinant Escherichia coli. Angew. Chem. Int. Ed., 49: 7019–7024.
[4] https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit (11.07.14)

2

Animation

  The following animaton visualizes the concept of using ferritin iron storage proteins as a magnetism mediating module.



This animation was developed by Florian Renner who is an science interested and very talented grafic designer based in munich. We thank Florian for his amazing job he did voluntarily for iGEM Berlin helping us to overcome the limitations of our budget.

3

Project Outline

  3.1 Basics
Advantages and basic principles of using magnetic fields
In order to control E. coli remotely, we decided to use magnetic fields because of a few key reasons. First, magnetic fields allow to control the cells by an external force field which means that cells do not have to be directly treated or media conditions have to be changed as it is the case in many chemotaxis assays. Second, magnets are widely spread and electro magnets easily built as you can see in this video: https://www.youtube.com/watch?v=wzXRFp0DDrU The accessibility and safety of magnetic fields opens up the field for new innovation and ideas using remote controlled bacteria. Third, magnetic fields do have a high energy density and are way more viable to transfer energy than other energy fields like electrical fields. However, the magnetic moment of an atom is the product of of the atoms orbital angular momentum and its electron spins. Atomic magnetism is based on unfilled electron orbits. Nobel gases and alkyl halogenide are non-magnetic or “diamagnetic”. Other elements like metals may have an increased magnetic moment as long as their electron orbit are unfilled, meaning they are unbound. Mn2+, Fe3+ have a magnetic moment of about 5 µB, Cr2+, Mn3+, Fe2+ and Co3+ have a magnetic moment of 3 µB. [http://www.diss.fu-berlin.de/diss/servlets/MCRFileNodeServlet/FUDISS_derivate_000000000626/2_f-Kapitel1.pdf?hosts=]
Because of the variety of atomar magnetic properties, magnetism can be divided into different forms by looking at apparent forces and effects. There is diamagnetism, antiferromagnetism, paramagnetism, ferrimagnetism, superparamagnetism and Ferromagnetism. Ferromagnetic forced are about 1000 times stronger than super paramagnetic forces. However, it turns out that creating ferromagnetic particels or residues is very difficult (see magnetite formation in magnetospirrilium bacteria). Also note that in a lot of biological papers, people tend to mix e.g. super paramagnetism with ferromagnetism [Various magnetic Nanoparticles Paper].
Magnetic properties are depended on the crystal structure of a metall particle. The magnetic moment is proportional to the aligment of the electron spins within an component. If electron spins are alignt magnetism can be observed. However on a nanoscale real ferromagnetism can only be noted after a critical particle size of 128 nm.[An-Hui Lu, An-Hui; E. L. Salabas; Ferdi Schüth (2007). "Magnetic Nanoparticles: Synthesis, Protection, Functionalization, and Application". Angew. Chem. Int. Ed. 46 (8): 1222–1244] This is due to thermal fluctations that prevent the alignment of electron spins and therefore prevent the development of sufficient magnetic moments. Because of this phenomena all meassurements for magnetism are usually conducted at very low temperatures.
All magnetic effects that are observed for particles between 1 nm to 100 nm are considered superparamagnetic. Superparamagnetic nanoparticles only show magnetic effects when an external magentic field is applied. This field aligns the electron spins in the particle resulting in an magnetic moment mediated by an external magnetic field. [Picture Atomarer Magnetismus]

3.2 Iron Homeostasis, E. coli Nissle and Knockouts
As an essential element for almost all life iron is often necessary for the activity of certain proteins but can also be problematic because of its toxicity and poor solubility. Organisms have evolved to regulate their iron effectively and as iron in an organism is usually supplied in a limited condition pathogens evolved iron aquisation systems to outcompete other microorganism. A very efficient iron aquisition system, which bacteria inlcuding E. coli use are siderophore mediated transport pathways. [Simon C. Andrews, Andrea K. Robinson, Francisco Rodriguez-Quinones; School of Animal and Microbial Sciences, University of Reading, Reading RG6 6AJ, UK; 2003] Iron E.coli Link

3.3 Ferritin Strategy
Ferritins as scaffolds for magnetic nanoparticle synthesis
In order to protect themselves against radical stress as well as the lack of co-factors, organisms evolved a high regulated and stable iron acquisition system, also known as iron homeostasis. [Iron Homeostasis of E. coli] To put it in a nutshell iron is taken up by iron transporters or siderophore mediated mechanism and is transporters through the outer membrane into the periplasm, in the periplasm it “changes” transporters and is transported through the inner membrane into the cytoplasm. It always gets released as Fe2+ into the cytoplasm. In order to protect themselves against superoxide formation by the Fenton-Reaction a lot of organisms evolved iron storage proteins. One of the superfamily of these proteins is called ferritin. These ferritins are highly symmertrical protein nanocages synthesizing iron concentrates required for cells to make cofactors of iron proteins. Through their ability to cage in biominerals they were the first and most obvious scaffolds for the synthesis of magnetic nanoparticles. These natural metal storage homomers form solid particles inside of their protein shell. Ferritins are ubiquitous in nature and protect the cell from redox stress through iron overload and from iron deficiency. They consist of 24 protein subunits which can consists of a heavy (catalytical active) and light chain (catalytical inactive but stabilizing). Caged ferritin minerals can have diameters as larg as 8-12 nm with thousands of iron and oxygen atoms. Between species ferritins have different affinity for phosphate. Phosphate is low in animal ferritin iron minerals (Fe:P = 8:1) whereas in bacterial and plant ferritins iron minerals are usually occurring in higher relations (Fe:P = 1:1).[1] Mössbauer studies on the superparamagnetic character of bacterioferritins (bfr) revealed that the phosphate concentration in a ferritin iron mineral reduces superparamegntic effects heavily due to replacement of the iron bridges between the iron atoms with phosphate. As these bridges have a lower exchange constant the order temperature is reduced further. [2] The hollow ferritin nanocages are used in the chemical industry as scaffolds for synthesis of magnetite particles as well as for delivery of magnetic resonance imaging (MRI) contrast agents, drug delivery and catalysis.
[1]
Ferritins for Chemistry and for Life.
Elizabeth C Theil, Rabindra K Behera, Takehiko Tosha Children's Hospital Oakland Research Institute, University of California, Berkeley ; Department of Nutritional Science and Toxicology, University of California, Berkeley. Coordination Chemistry Reviews (Impact Factor: 11.02). 01/2013; 257(2):579-586. DOI: 10.1016/j.ccr.2012.05.013
[2] Mössbauer studies of superparamagnetism in E. coli; Hawkins, C.; Williams, J. M. Journal of Magnetism and Magnetic Materials, Volume 104, p. 1549-1550

iGEM Berlin Ferritin Library
During our summer we collected a variety of ferritin-coding sequences from bacterial and mammalian sources. As ferritins are common among all organisms we categorized our ferritins in three major groups. (Table)

3.4 Inclusion body Strategy
By talking to the Fussenegger group from the ETH Zurich, who published the superparamagnetism paper about ferritins we got the tip to look for another strategy as they experienced the limitations of ferritins. [1] For this reason, we came up with a different strategy. Park et al came up with a different strategy for the synthesis of biogenic nanoparticles in E. coli. [2] A strategy where they produced impressive results showing one strategy to synthesize a whole array of diverse nanoparticles with E. coli. (See Figure 1) Two heavy metal binging proteins were combined and co-expressed on one plasmid. Peptides called phytochelatins are produced in fungus and plants to detoxify the cell from harmful heavy metals. Structurally phytochelatins are (gamma-Glu-Cys)n-Gly (n=2-7) peptides and function as metal ion accumulators through formation of peptide-metal conjugates. In this study the phytochelatin synthase from Arabidopsis thaliana (Columbia leave) was used (ATPCS). The other peptid that was used in combination with ATPCS was a metallothionein from Pseudomonas Putida KT2240 strain (PPMT). Metallothioneins are low-molecular proteins with a high content of cysteine and bind well cadmium, zinc, nickel and copper. For expression of ATPCS a trc promotor was used while PPMT was expressed using a T5 promotor. After co expressing both proteins in an standard E. coli strain(DH5alpha) for 4 h the culture broth was centrifuged and fresh metal rich LB media added. (1 – 5 mM of corresponding final metal concentration (see table 1.). After further incubation at 37°C for about 6 - 12 hours the cultures and the biogenic synthesized nanoparticles can be harvested. Park et al reported further that by incubating these ATPCS and PPMT co-expressing in 1.0 mM FeSO4 and MnCl2 magnetic nanoparticles where obtained and cell moved by high magnetic fields (see figure 2).

[1] Kim T, Moore D, Fussenegger M. Genetically programmed superparamagnetic behavior of mammalian cells. J Biotechnol. 2012 Dec 31;162(2-3):237-45. doi: 10.1016/j.jbiotec.2012.09.019. Epub 2012 Oct 2. PubMed PMID: 23036923.
[2] Park, T. J., Lee, S. Y., Heo, N. S. and Seo, T. S. (2010), In Vivo Synthesis of Diverse Metal Nanoparticles by Recombinant Escherichia coli. Angew. Chem. Int. Ed., 49: 7019–7024. doi: 10.1002/anie.201001524
[3] Wu CM, Lin LY. Immobilization of metallothionein as a sensitive biosensor chip for the detection of metal ions by surface plasmon resonance. Biosens Bioelectron. 2004 Nov 1;20(4):864-71. PubMed PMID: 15522603.

3.5 Magnetic modelleing (Andres)

4

Flow Chart

 

5

The Results

  Results, jo!

6

Lab Summary

 

Week 1: 02.04.2014 – 06.04.2014

Cultivation of E. coli Nissle 1917
Genomic DNA extraction of E.coli Nissle strain
Production of BfR, FTNA1 and FTNA2
Restriction digest
PCR Purification
Ligation Assay
Transformation into DH5α-Cells

Week 2: 07.04.2014 – 13.04.2014

Colony PCR to check the results
Bfr, FTNA 1, FTNA 2 primar designed for amplification
Transformation of pQE_80L into DH5α
Cultivation of BfR, FTNA 1, FTNA 2 in LB

Week 3: 14.04.2014 – 20.04.2014

Miniprep of the cells from Week 2
DNA concentration determination and sequencing
Expression of BfR, FTNA 1, FTNA 2 and induction with IPTG
Production of a Mutaflor-Supression culture and streaking

Week 4: 21.04.2014 – 27. 04.2014

Minirep

Week 5: 28.04.2014 – 04.05.2014

PCR Plasmid/Primar and Parameter check with Q5 Polymerase and Phusion Polymerase
Miniprep of [pKD46+ DH5α] and [pKD4 + DH5 α]
Genomic DNA extraction from Pseudomonas putida
Enzyme digestion of different plasmids

Week 6: 05.05.2014 – 11.05.2014

Preculture of strains from Budisa strain databse in LB medium and Midiprep
Canamycin cassette PCR of pKD4
Restriction digest of Plasmid pKD4 and pKD46v

Week 7: 12.05.2014 – 18.05.2014

Biotransformation of Ferritin and pKD46 in Nissle and DH5 α strains

Week 8: 19.05.2014 – 25.05.2014

Gel extraction of FieF PCR
Gene Knockout of FieF in [RV + pKD46] and [WM10+pKD46]
Transformation of pKD46 in Nissle and MG 1655
PCR of ATPCS and PPMT
Digestion of pQE_80L for cloning

Week 9: 26.05.2014 – 01.06.2014

Production of LB plates
AMB-1 and Microfluidic Chip were picked up from Max-Plank Institute

Week 10: 02.06.2014 – 08.06.2014

Colony PCR and analytical gel electrophoresis for identifying the right clones
PCR of ATPCS and PPMT to identify the correct amplification parameter.
Colony PCR for Knockout.
PCR of ATPCS and PPMT with Q5 High Fidelity Mastermix.

Week 11: 09.06.2014 – 15.06.2014

Refine the PCR of PPMT and ATPCS with DMSO

Week 12: 16.06.2014 – 22.06.2014

PCR amplification of ATPCS from cDNA
Colony PCR to seperate cells with FieF Knockout
Restrcition digest of pQE_80L and ATPCS-PCR Fragment
Test expression of Ferritin in RV308 (pSB1C3_Ferritin) and Nissle (pSB1C3_Ferritin)

Week 13: 23.06.2014 – 29.06.2014

Amplification of ATPCS from cDNA and PCR Purification
Preparation of Nissle, Nissle + Ferritin, RV 308, Rv 308 + Ferritin pre-cultures
Transformation of human Ferritin on PC514 to Nissle and RV 308
Induction of Ferritin expression with IPTG

Week 14: 30.06.2014 – 06.07.2014

Colony PCR and Ligation of ATPCS
Knockout of FieF and FUR in RV308 and Nissle
Transformation of RFP device and Ferritin in RV308, Nissle and WM110 strains.
PCR amplification of knockout cassette FUR/FieF
Expression of RV308 (RFP) and RV308 (RFP + Ferritin) after Induction with IPTG

Week 15: 07.07.2014 – 13.07.2014

Preparation of cryostocks and pre-cultures of ATPCS clone 1-10, WM 110, RV 308, Nissle
PCR of PPMT with goTaq Polymerase
Miniprep of ATPCS clone number 3

Week 16: 14.07.2014-20.07.2014

Midiprep of pQE_80L , PMA-T_PPMT, pKD46
Digestion of pQE_80L with Hind III and SacI

Week 17: 21.07.2014-27.07.2014

Miniprep and Restriction of pBADex-mYFP Venus (Amp); pEx-HisII (Amp); pJS418_Phagemid (dummy) (Cm)
Ligation of PPMT Fragment from pMAC_PPMT into pEX_HisII

Week 18: 28.07.2014-3.08.2014

Degradation test of prepped TB-Expression Plasmids
Transformation of pEX_His_PPMT in MG1655, DH5α, DH10B strains
Colony PCR of the PPMT clones
Miniprep and Sequencing of pEX_His_PPMT in DH5 α
Ligation of ATPCS PCR Fragment into pQE_80 L
Colony PCR of pQE_80L_ATPCS

Week 19: 04.08.2014 -10.08.2014

Preculture of ATPCS clones for Sequencing
PCR of BamHI_PPMT_GS, GS_ATPCS_HindIII, BamHi_HuFerritin_HindIII
Transformation of BFR M52H in DH10B.

Week 20: 11.08.2014 - 17.08.2014

Prepare chemically competent cells
Generation of Heme-free BFR by Site-directed Mutagenesis
Digestion of various PCR fragements for cloning into pQE_80L
Colony PCR of pQE_80L
Clone Sequencing

Week 21: 18.08.2014 – 24.08.2014

SDS-PAGE with Coomasie staining for identification of protein expression

Week 22: 25.08.2014 – 31.08.2014

Calibration curve for iron concentration measurement

Week 23: 15.09.2014 – 21.09.2014

Preparing cultures for fluorescence microscopy
Constructing pQE_80L_T5_ATPCS_lac_PPMT
Digest and Dephosphorylation of vector pQE_80L_ATPCS
PCR of Biobrick parts (BB0-BB3)
Digest of pSB1C3-Ferritin

Week 24: 22.09.2014 – 28.09.2014

Preparation of pre-cultures
Checking insertion of gene in ATPCS_PPMT clones by colony PCR
Digestion of miniprepped pSB1C3_Ferritin (Calgary) for extraction of vector for Biobrick preparation
Mutagenesis of ATPCS in different plasmid_ATPCS construct
Berlin Vector – pQE-80L-JBFS- huFerritin Assembly PCR
Isolation of plasmid DNA of pQE80L_ATPCSMut_GS_PPMT and pQE80L_ATPCS_PPMT
Repeat PCR of Biobricks

Week 25: 29.09.2014 – 05.10.2014

Digestion of Biobrick parts
Ligation of Biobrick parts with pSB1C3 backbone
Plasmid Digestion and checked with PCR

Week 25 06.10.2014 – 12.10.2014

Colony PCR
Miniprep of cultures and preparation of sequencing samples
Preculture of knockouts
PCR of pSB1C3 backbone
Extraction of PCR Product (pSB1C3 linearised)
Iron concentration measurement in knockout strains
7

Notebook

 

04/02 Wednesday - Cultivating E. coli Nissle 1917

LB plates were produced without antibiotic. Therefore 10 ml MQ-H2O were sterile filtered in 15 ml falcon tube. 1 capsule Mutaflor 331800 was solved in the sterile water. The E. coli Nissle solution was incubated at 37°C and 200 rpm for 1 h and crossed out at 4 plates to get different dilution of cells.

dilution E. coli Nissle solution H2O dilution factor
I 2 µl 1998 µl 1:103
II 100 µl from dilution I 900 µl 1:104
III 10 µl from dilution II 990 µl 1:105
           
            

04/03 Thursday - Genomic DNA extraction of ECN - first step

For extraction of the genomic DNA of E. coli Nissle, 2 E. coli colonies were oicked from LB plate (dilution 1:103) and used for inocculation of 6 ml LB precultures. These were grown over night at 37°C and 200 rpm.

04/04 Friday - Genomic DNA extraction of ECN - second step

For preperation of the genomic DNA 1 ml of each preculture was taken and a genomic extraction performed using the Wizard Genomic DNA purification Kit. See instructions of the purification Kit by Promega. Genomic DNA was stored at 12°C in fridge. As E. coli Nissle is a natural organism without resistence genes both precultures were streaked out on LB, LB+KAN and LB+AMP. All plates were incuvated over the weekend at 37°C. DNA concentration was meassured by 260 nm using Goldi. DNA was diluted 1:40 in a UV cuvette and DNA absorption meassured at 260/28 nm in goldi.
'''For genomic DNA:'''
1: 1390 ng/µl
2: 988 ng/µl

04/05 Saturday - Genomic DNA extraction of ECN - results

Bacteria growth only on LB plate indicates that there was no contamination with AMP or KAN restinatant E. coli. This doesn´t mean that there is no contamination at all. See for sure on PCR.

LB LB+KAN LB+AMP
+ - -
              
            

04/06 Sunday

           Production of BfR, FTNA1 and FTNA2
           Restriction digest
           After 2 purifications of plasmids:


p1 84ng/µl 10µl
p2 72,2ng/µl 10µl
p3 54,8ng/µl 23µl
           Restriction program
1x 4x
plasmid P2 3µl 12µl
BamHI (FD) 1µl 4µl
HindIII (FD) 1µl 4µl
Buffer (FD) 2µl 8µl
H2O 13µl 52µl
           --> 37°C for 1h (restriction)
           --> 80°C for 10min (deactivation)
PCR 6,38µl 4,56µl 2,71µl
BamHI (FD) 1µl 1µl 1µl
HindIII (FD) 1µl 1µl 1µl
Buffer (FD) 2µl 2µl 2µl
H2O 19,62µl 21,44µl 23,29µl
           --> 37°C for 1h (restriction)
           --> 80°C for 10min (deactivation)
Plasmid 1 2 3
P 10µl 10µl 18µl
BamHI (FD) 1µl 1µl 1µl
HindIII (FD) 1µl 1µl 1µl
Buffer (FD) 2µl 2µl 3µl
nuc.free H2O 6µl 6µl 7µl
           --> 37°C for 1h (restriction)
           --> 80°C for 10min (deactivation)
           PCR Purification (without isopropanol)
           Elution buffer 20µl; 1min incubated
plasmid P1-3 45,3ng/µl
BfR 12,9ng/µl
FTNA1 34,4 ng/µl
FTNA2 29,9ng/µl
           Ligation Assay
- Control BFR BFR BFR FTNA1 FTNA1 FTNA1 FTNA2 FTNA2 FTNA2 BFR_E BFR_E BFR_E
Dilution - 1x 3x 5x1x 3x 5x1x 3x 5x 1x 3x 5x
Vector DNA 1,1 1,1 1,1 1,1 1,1 1,1 1,1 1,1 1,1 1,1 1,1 1,1 1,1
Insert DNA 0 0,4 1,6 2,0 0,10 0,47 0,79 0,18 0,52 0,90 0,40 1,16 2,0
Buffer 1 1 1 1 1 1 1 1 1 1 1 1 1
T4 DNA-Ligase 0,25 0,25 0,25 0,25 0,25 0,25 0,25 0,25 0,25 0,25 0,25 0,25 0,25
H2O 7,65 7,25 6,5 5,65 7,5 7,20 6,85 7,50 7,20 6,85 7,25 6,50 5,65
           Transformation
           --> Transformation of 5µl Sample into DH5α-Cells
           --> Incubation o/n at 37°C after streating out on LB+amp plates using sterile beads
BFR FTNA1 FTNA2
5,2ng 5,51ng 5,43ng
15,6ng 16,5ng 16,27ng
26,0ng 27,4ng 27,13ng

04/07 Monday - Cloning Results

Sample CFU
Control 13
tBFR 1 121
tBFR 3 38
tBFR 5 664
BFR 1 87
BFR 3 151
BFR 5 150
FTNA1 1 65
FTNA1 3 131
FTNA1 6 191
FTNA2 1 84
FTNA2 3 114
FTNA2 5 151
           --> picked 5 colos per construct for coloPCR (50µl TE-buffer; 96°C; 10min)
           --> rescue plate
           colPCR Programm
- 1x Mastermix 23x
nuc.free H2O 13,7µl 315,1µl
10x Dream Taq Buffer 2µl 46µl
25mM MgCl2 1,2µl 27,6µl
10mM dNTPs 0,5µl 11,5µl
Primer T5 prom (PB16) 0,5µl 11,5µl
Primer T5 term (PB17) 0,5µl 11,5µl
boiled colos 1µl + 18,4ml Mastermix
Taq Polymerase 0,5µl
Temperature Time
95°C 3'
30 cycles
95°C 30
55°C 30
72°C 1'
72°C 10'
12°C hold

04/08 Tuesday - Amplification of ferritin genes

Primer designed for amplification:

           primer Bfr:
           FW: 5'   GC   G| G A T C C AAAGGTGATACTAAAGTTATAAATTATCTC(GC 23,33% Tm = 57,5)  3'  OK
           RW: 5'   GC   A| A G C T T TCAACCTTCTTCGCG(GC 50% Tm = 58,5)  3'                    OK
           primer FtnA1:
           FW: 5'   GC   G| G A T C C GCAACCGCTGGAATG(GC 60%  Tm = 60,5) 3'                    OK
           RW: 5'   GC   A| A G C T T TCAATGCAGCTGATGC(GC 50,0% Tm = 58,5)  3'                 OK
           primer FtnA2:
           FW: 5'   GC   G| G A T C C CTGAAACCAGAAATGATTG(GC 36,8%  Tm = 65,1)  3'             OK
           RW: 5'   GC   A| A G C T T TTAGTTTTGTGTGTCGAGG(GC 42,1%  Tm = 56,8)  3'             OK


           Using the Thermoscientific  PCR mastermix phusion polymerase, 2x 50 µl reactions per amplification:
Nuc-free H2O 39,5 µl
2x mastermix 50,0 µl
FW primer 5,0 µl
RW primer 5,0 µl
template DNA 0,5 µl


           PCR programs:
98°C 10s 1x
98°C 5s 30x
primer Bfr/ FtnA1/ FtnA2 60,5°C/ 58,9°C/ 56,1°C 30x
72°C 10s 30x
72°C 60s Beispiel 1x


           Transformation of pQE_80L into DH5alpha
           Plasmid from plasmid database of TU workgroup by Prof. Budisa was taken: 
plasmid ID: 4; concentration = 308 ng/µl
           Unthaw 50 µl aliquot of DH5alpha or BL21 DE3 gold on ice for 10 min.Than Use 308 ng and 616 ng of plasmids to bind on Ca2+-surface of the cell membranes. Heat shock was performed for 30-90 s. The cells were incubated on ice for 2 min and than there was added 950 µl LB media. The cells were incubated at 37°C for 60 min. After this 70 µl of transformed E. coli suspension was streacked out onto a plate with the appropriate selection marker. The plate was incubated over night at 37°C. To prepare preculture 2 colonies were picked and added into 5 ml LB media + 5 µl AMP. The precultures were incubated over night at 37°C and 200 rpm.
 
            

04/10 Thursday - Expression of Ferritin in LB

→Innoculate 20ml LB + amp with 1ml of a preculture
Title No. Wavelength Absobance Volume
BfR 1 600nm 0,529A 1,51ml
FTNA1 2 600nm 0,307A 3,25ml
FTNA2 3 600nm 0,605A 1,32ml
           →Incubation for 2h until OD600=0,6-08
Title No. Wavelength Absobance
BfR 1 600nm 0,825A
FTNA1 2 600nm 0,883A
FTNA2 3 600nm 0,859A
           → Take SDS Sample non-induced
→Induce with 20µl IPTG
→Add Fe2+
→Expression: 4h at 22°C
Cultivation was aborted because of heat development
.

04/14 Monday - Miniprep

Miniprep of the cell-seperation streak out of the cloning procedure from december 2013
Miniprep-Kit of ThermoScientific
- Title Concentration in ng/µl
A4 BfR 66
B3 FTNA1 138
C5 FTNA2 88
D2 BfR_Electro 144
           DNA Concentration Determination
Dilution Factor 20
Integration Time 1s
Factor 50
Units µg/ml
- Title No. 260nm 280nm 320nm Ratio Conc.
A4 BfR 1 0,056 -0,022 -0,010 2,05 66
B3 FTNA1 2 0,135 0,067 -0,003 1,96 138
C5 FTNA2 3 0,078 0,035 -0,008 2,00 86
D2 BfR-Electro 4 0,150 0,078 0,006 2,02 144

04/16 Wednesday - Sequencing

Preparation of the sequencing for the Samples from 16.01.2013

T5 prom. Primer 3µl
Plasmid 12µl
A4 6µl
B3 6µl
C5 6µl
D2 6µl
           
            

04/17 Thursday - Expression of BfR and FTNA1/2

4x sterile 250ml Erlenmeyer
+50ml LB
+50µl amp
+2,5ml preculture
Incubation: 1h at 30°C
No. Title Wavelength Absorbance
1 BfR 600nm 0,909A
2 FTNA1 600nm 0,980A
3 FTNA2 600nm 0,930A
4 BfR+20?? 600nm 0,970A

→Take SDS-Sample
→Induction with 50µl IPTG
→Addition of 0,0525g Fe-citrate (20mM dissolved in 1ml sterile Water)
→Incubation for 3h at 30°C
→continue incubation o/n
→Centrifuge with 6800g for 5min

04/18 Friday - Production of LB-Plates

Production of a Mutaflor-Supression-culture →10ml sterile LB
→Add the content of a Mutaflor capsula (white pouder)
Incubation: 37°C at 220rpm
Production of Dilutions of the Supression-culture and out streaking →1µl of the supression-culture to 999µl LB (1:1000)
→100µl of that dilution to 900µl LB (1:104)
→10µl of that dilution to 990µl LB (1:105)
→Streak out 50µl of each culture on LB with sterile beads
Incubation: 37°C

04/24 Thursday - Mini-Prep

1 PSB D40 9fP CR/LB
2 PSB D20 9fP CR/LB
3 PSB D40 fs LB/CR
4 PSB D40 LB/CR
5 PSB AB Turyu CR/LB
6 PSB D48 9fP CB/CR
           
            

04/28 Monday -PCR Plasmid/ Primer and Parameter Check

(Salah and Christina)
Check of:
-Plasmids/Primer
-Annealing temperature
-Phusion and Q5 Polymerase Plasmids
           iGEM Plasmid pkD4 (Stock 200ng/µl) =>1:200 diluted = 1ng/µl
           WH (Willi Hauke) Plasmid pkD4 (0,72ng/µl)
           Primer
           P1 FieF (iGEM)                                   fwd tnaA KO (WH)
           P2 FieF (iGEM)                                   rev  tnaA KO (WH)


           Combinations
           (4 combinations with Phusion; 4 combinations with Q5 )


Plasmid Primer Primer
1. iGEM Plasmid P1 (iGEM) P2 (iGEM)
2. WH Plasmid fwd tnaA KO rev tnaA KO POSITIVCONTROL
3. iGEM Plasmid fwd tnaA KO rev tnaA KO
4. WH Plasmid P1 (iGEM) P2 (iGEM)
           Each of the four combinations was prepared 3 times => for Gradient PCR


           Phusion Polymerase PCR Assay
           20µl Reaction
Plasmid Primer Primer
1. iGEM Plasmid P1 (iGEM) P2 (iGEM)
2. WH Plasmid fwd tnaA KO rev tnaA KO POSITIVCONTROL
3. iGEM Plasmid fwd tnaA KO rev tnaA KO
4. WH Plasmid P1 (iGEM) P2 (iGEM)


           Q5 Polymerase PCR Assay
           20µl Reaction
5xQ5 Reaction Puffer (G2 runder Behälter) 4µl 1x
10mM dNTPs 0,4µl200µM
10µM forward Primer1µl0,5µM
10µM reverse Primer1µl0,5µM
Template DNA1µl1pg-1ng sein
Q5 High Fidelity DNA Polymerase0,2µl0,02U/µl
GC enhancer4 µl
Nuclease-Free Water to 20µl
8,4µl
           FUR PCR Assay


           (Along with the above mentioned PCR Assays another Gradient PCR with FUR-Primer is performed)
           Aliquot of the FUR Primer (100µM) 1:10 diluted =>10µM
           20µl Reaction with Phusion-Polymerase (see above)
           with WH Plasmid and P1 FUR & P2 FUR Primer


           Gradient PCR Program
           Thermocycling Conditions for the Gradient PCR 
           Programm-NAME: Q5 grad trp KO
Step TEMP TIME
Initial Denaturation98°C30 sec
5 Cycles98°C8 sec
64±5°C25 sec GRADIENT
72°CTrp ko: 1528bpà45s
25 Cycles98°C8 sec
72°C70 sec
Final Extension72°C2 min
Hold8°C


           Gel-Electrophoresis
           1% Agarose Gel
           5µl Sample +1µl loading dye (1:6)
           8µl diluted GeneRuler Mix ladder
           MODE: 90V 25min


           Sample label:


           P = with Phusion Polymerase
           Q = with Q5 Polymerase
           1 = 1. Kombination
           2 = 2. Kombination
           3 = 3. Kombination
           4 = 4. Kombination


           Gradient
           1 = 59°C
           4 = 63°C
           8 = 69°C
Gel 1 Phusion ' ' ' ' ' ' ' ' ' ' ' ' '
P FURP1P1P1P2P2P2MarkerP3P3P3P4P4P4
8148148148148
Gel 2 Q5
Q1Q1Q1Q2Q2Q2MarkerQ3Q3Q3Q4Q4Q4
148148148148



           Results


Gel 1 Phusion Result: For FUR-Primer no Amplifikation
For iGEM-Plasmid no Amplifikation
Combination 2 (WH Plasmid & Primer)= only non-specific amplification
Combination 4 (WH Plasmid & iGEM Primer)=Bands for 59°C and 63°C + non-specific amplification
Gel 2 Q5 Result:For iGEM-Plasmid no Amplifikation
Combination 2 (WH Plasmid & Primer) = bands for all three annealing temperature observed+non-specific amplification
Combination 4 (WH Plasmid & iGEM Primer)= Bands at all three annealing temperature+non-specific amplification



iGEM Plasmid not to be used anymore. FUR need to be checked again.

04/29 Tuesday - Mini-Prep

(Aritra)
[pKD46 + DH5α]→ 155ng/µl
[pKD4 + DH5α]→ 302ng/µl

05/02 Friday - Genomic DNA extraction from Psedomonas putida

(Johann)
-->see Protocol Wizard ® Genomic DNA Purification Kit - Strain from VLB Martin Senz PHO Psedomonas putida KT2242 B_0712 from 29.04.2014 culture
- 2 days in 30°C Shaking Incubator.
- Mikro 22R Centrifuge Hettich (16000g)
Final DNA Concentration measured after purification = 95ng/µl

02.05.2014 - DNA Digestion to test Plasmids

Samples Conc. DNA (ng/µl) Enzymes used Expected band length Evaluation
pKD4302Xbal1874,1393Possible plasmid, failed
pKD4640EcoRI4820,1509Failed
pKD4639EcoRI4820,1509Failed
pKD460Xbal1874,1393Possible(passed); whole plasmid
pSBAC388SpeI/EcoRI2047,22Possible (passed); smallpattern
pSBAC3-D20-GFP115SpeI/EcoRI2047,957whole plasmid; failed
pSBAC3-D40-Bfr86SpeI/EcoRI2047, 774Whole plasmid; failed
pSBAC3-D40-GFP80SpeI/EcoRI2047,1014Whole plasmid; failed
pSBAC3-AB-Tyrosin110SpeI/EcoRI2047,3319Failed
pSBAC3-D40164SpeI/EcoRI2047,267Failed
pSBAC3-D40-GFP-ssr106SpeI/EcoRI2047,1032Passed; whole plasmid
           Gel Electrophoresis
           Key:
-band1: Ladder
-band5:Ladder
-residual bands, see table above

Results pKD4 with 60(ng/µl) best candidate for PCR.

05/05 Monday - Preculture of strains from Budisa strain database in LB Medium

1. BU31 (pKD4) in 50 ml LB+Kanamycin+Ampicillin 37°C 220 rpm
2. BU32 (pKD46) in 50 ml LB+Ampicillin 30°C 240rpm
3. BU31 (pKD46) in LB plate+Ampicillin 30°C
Midiprep Midiprep of BU31 (pKD4) and BU32 (pKD46) from strain Database.
Concentration pKD4 = 104 ng/µl
Concentartion pKD46 = 161 ng/µl

05/06 Tuesday - Gel-Electrophoresis

Kanamycin Cassette PCR (pKD4 from MidiPrep 05.05.2014 104ng/µl Christina)
Key:
- 1st: Ladder
           - 2nd and 3rd: Fief
           - 4th: Negative control
- 7th and 8th: FUR

Results FieF worked well; FUR no bands Restriction digest of Plasmid pKD4 and pKD46
' ' '
pKD4pKD46
Plamid 19.2µl12.5µl
Digestion EnzymXbal 1µlXmal 1µl
nuclease free H2O24.8µl31.5µl
10xFO green Buffer5µl5µl
Total50µl50µl
              - Both the reaction mix incubated at 37°C for 1 hr.
              - After that another 1 hr at RT.



           Gel-Electrophoresis
           - 20µl of both the samples together with whole plasmids loaded on 1% Agarose Gel
Results Key:
-1st: pKD4 (XbaI digested)
-2nd: pKD4 (undigested)
- 3rd: Ladder
- 4th: pKD46 (undigested)
-5th: pKD46 (XmaI digested)


           Gel Extraction
           -Used GeneJet GelExtraction Kit by Thermo Scientific
           Results
           DNA Concentration: 16ng/µl

05/16 Friday - Biotransformation of Ferritin and pKD46 in Nissle and DH5-α strain

concentration Ferritin 120ng/µl
concentration pKD 46 95 ng/µl

           Protocol
           *electro competent cells of DH5α and Nissle were thawed on ice
           *0.4µl of Ferritin and 0.53 µl of pKD46 was added to the cells
           *cells with DNA were transferred to cuvettes for electroporation, then 950ml (LB-medium) was added to the cells immediately
           *incubation at 37°C for ferritin, 30°C for pKd46 for 1 h with shaking
           *the cells were plated on Amp plates for pKD46 and CM for Ferritin
           *Transformation did not work.
           
            

05/21 Wednesday - PCR Gel-Extraction of FieF

1% Agarosegel + 0,5µl EtBr
45µl Sample+9µl Loading Dye
8µl Ladder
--> Gel-Extraction Kit used with 50µl nuclease-free water for elution
Gene Knockout of FieF (Salah) Preparation of the preculture Used Precultures:
- RV +pKD46
- WM10 +pKD46
The precultures was diluted to OD600=0,1 and then incubated for 2h at 30°C until they reach OD600=0,6
Title Wavelength Absorbance
Reference 600nm 0,000A
RV+pKD46 600nm 0,066A
WM10+pKD46 600nm 0,050A
           (The culture was diluted 1/10 for the OD measurement)
→The precultures are ready for the Rekombinase induction with Arabinose Induction with Arabinose The cultures have been induced with 500µl arabinose (1M) →After the induction, the cultures have to be incubated for further 30min at 30°C
Title Wavelength Absorbance
Reference 600nm 0,000A
RV+pKD46 600nm 0,084A
WM10+pKD46 600nm 0,067A
           →From now on the cultures need to be cooled on ice
           Preparation for the Electroporation
           Electroporation
           Electroporation-Program: Ec1
-Amount of DNA sample: 75-150ng
Sample Conc Used Volume Strain Electroporation Time
FieF1 42ng/µl 2µl (84ng) RV 4,4ms
FieF2 9ng/µl 10µl (90ng) RV 4,1ms
FieF1 42ng/µl 2µl (84ng) WM10 4,3ms
FieF2 9ng/µl 10µl (90ng) WM10 4,8ms
           After the transformation, the cultures was immediately prepared with 950µl SOC and incubated for 60min at 30°C without antibiotics --> recovery
           Selection-cultures
           The selection of positive clones is done by using LB plates with kan+amp
Incubation: 30°C o/n

05/22 Thursday - Transformation of pKD46

Preparation of the preculture Used Precultures:
- MG1655
- Nissle
The precultures was diluted to OD600=0,1 and then incubated for 2h at 30°C until they reach OD600=0,6
Title Wavelength Absorbance
Reference 600nm 0,000A
MG1655 600nm 0,062A
NIssle 600nm 0,054A
           (The culture was diluted 1/10 for the OD measurement)
           →From now on the cultures need to be cooled on ice
           Preparation for the Electroporation
           Electroporation
           Electroporation-Program: Ec1
-Amount of DNA sample: 75-150ng
Sample Conc Used Volume Strain Electroporation Time
MG1655 1 42ng/µl 2µl (84ng) RV 5,4ms
MG1655 2 9ng/µl 10µl (90ng) RV 5,8ms
Nissle 1 42ng/µl 2µl (84ng) WM10 0,7ms (thrown away)
Nissle 2 9ng/µl 10µl (90ng) WM10 5,8ms
           After the transformation, the cultures was immediately prepared with 950µl SOC and incubated for 60min at 30°C without antibiotics --> recovery
           Selection-cultures
           The selection of positive clones is done by using LB plates with amp
Incubation: 30°C o/n
            PCR of ATPCS and PPMT 
Mastermix ATPCS PPMT
nuc.free water 18.9 17.5
2x Fusion Mastermix 25 25
Fw Primar 2.5 2.5
Rw Primar 2.5 2.5
template DNA 1.1 2.5
ATPCS Programm
98°C 10
98°C 5 30 cycles
62°C 5 30 cycles
72°C 5 30 cycles
72°C 60 secs
8°C store
PPMT Programm
98°C 10
98°C 5 30 cycles
63,1°C 5 30 cycles
72°C 21 30 cycles
72°C 60 secs
8°C store
           ATPCS 1469 bp; PPMT 234 bp
           --> wrong Programm
           
            

05/23 Friday - Digestion of Vector for Cloning

Plasmid: pQE80L
Old Plasmid of Johann:
-P1≈1000ng
-P3≈400ng
P3 P1
SacI 1µl SacI 1µl
HindIII 1µl BamHI 1µl
Buffer 2µl Buffer 2µl
Plasmid 1 4µl Plasmid 3 16µl
nuc.water 12µl nuc. water 0µl
           --> Incubation: 1,5h at 37°C
--> Deactivation: 20min at 80°C

05/27 Tuesday - Production of LB Plates

LB Agar Plates prepared:
4x with Ampicillin (25µl in 25ml)
4x with Ampicillin+ Kanamycin (25µl+25µl in 25ml)
4x Cm (25µl in 25ml)

05/28 Wednesday

Picked up from MPI: AMB-1 and Microfluidic Chip. (From the two AMB-1 cultures, one is in the freeze and the other one in the RT-Incubator)
Digestion of pQE80L:
Marker: 2 log DNA ladder 5µl
Sample 1: P1 Sacl-BamHI 10µl
Sample 2: P3 Sacl-HindIII 10µl

06/02 Monday - Colony PCR and analytical gel electrophoresis for identifying the right clones

Primer: C1 C2
                      C2   C5
Components 20 µL Reaktion
Nuc. Free water13.7
10x Dream Taq Polymerase Puffer2
25mM MgCl21.2
10mM dNTPs0.5
10mM FW Primer0.5
10mM RW Primer0.5
Colony1
Taq DNA Pol0.6
Denaturation 95°C 10min '
Denaturation95°C30sec
Annealing55°C30 sec
Extension72°CX min30x
Extension72°C10 min
End12hold

Backup plates done. Cells given direct to PCR. 11 colonies selected.
Colony PCR with some of the clones performed. (All negative)

06/03 Tuesday - Strategy 2: PCR of ATPCS 2PPMT

             PCR Assay
- Sample1(PPMT) Sample2(ATPCS)
nuc. free water 17,5µl 18,9µl
FW Primer 2,5µl 2,5µl
RW Primer 2,5µl 2,5µl
2x Phusion Mastermix 25µl 25µl
Template DNA 2,5µl (250ng) 1,1µl (250ng)
             PCR Program
PPMT (234bp) ATPCS (1469bp)
98°C 10' 98°C 10'
30cycles start
98°C 5" 98°C 5"
62°C 5" 63°C 5"
72°C 10" 72°C 45"
30cycles stop
72°C 1' 72°C 1'
8°C hold 8°C hold
             Gel-Electrophoresis
             Key: 
2nd band= Ladder
3rd band= PPMT
5th band= ATPCS

06/04 Wednesday - PCR amplification of ATPCS and PPMT

(see under protocol "Amplification BamHI_PPMT_Sacl and Sacl_ATPCS_HindIII" After Gel: 1 Band visible for ATPCS around 1500bp (expected); no band for PPMT Purification of the ATPCS-PCR product from gel. conc. of ATPCS-fragment 6ng/microL freezed at -20°C on 1st floor

04.06.2014 - Colony PCR for Knockout

6 clones were picked from 2 Agar plates; Agar plates labelled with numbers with RED

             3 PCR:  a) Primers C1, C3
                     b) Primers C2, C4
                     c) Primers C1, C5
BandNr: Clone Nr: PCR type Primers
16CC1,C5
21AC1,C3
32AC1, C3
43AC1, C3
54AC1, C3
65AC1, C3
76AC1, C3
81BC2,C4
92BC2,C4
10Marker
113BC2,C4
124BC2,C4
135BC2,C4
146BC2,C4
151CC1,C5
162CC2,C4
173CC2,C4
184CC2,C4
195CC2,C4

Results: all samples with same primers are identical PCR A: one band an dimer (900-800bp) PCR B: one band (1200bp) PCR C: two bands (800 and 400 bp) - 2 of the colonies are quite luckily mix colonies that contains our knockout, bands are shown for wildtype and 2 show amplification for kanR cassette - they should be transfered to a new plate for single colony test

06/05 Thursday - New PCR protocol for ATPCS and PPMT with Q5 High Fidelity MasterMix

             PPMT PCR Reaction:


Component 25µl Final Conc.
2x Q5 MM12. Mai1x
10µM FW Primer02. Mai0,5µM
10µM RW Primer2,50,5µM
95ng/µL Putida genomic DNA2.63 (250ng)9.99 ng/µL
Nuc. Free waterApr 87
             ATPCS PCR Reaktion
             result
Component 25µl Final Conc.
2x Q5 MM1.,51x
10µM FW PrimerJan 250,5µM
10µM RW PrimerJan 250,5µM
230ng/µL Arabidopsis cDNA1.1 (250ng)10 ng/µL
Nuc. Free water08. Sep
             PCR Program
             PPMT 234 bp   
             result
denaturing 98°C 180sec
Denaturing98°C10 sec
Annealing 30x
64°C30 sec
Elongation72°C20 sec
Final Elongation72°C2min
Store8°C
             ATPCS 1469bp 
             result
denaturing 98°C 30 sec
Denaturing98°C10 sec
Annealing 30x
62°C30 sec
Elongation72°C60 sec
Final Elongation72°C2min
Store8°C
             
              

05.06.2014

Cryostocks: RV 308 ferritin (Cm)
Nissle ferritin (Cm)
500 µl 7%DMSO+ 500 µl Cell Culture medium => -80°C

06/06 Friday - PCR for ATPCS and PPMT with Q5 High Fidelity MasterMix

PPMT PCR Reaction:
Component 25µl 25µl Final Conc.
2x Q5 MM12. Mai12,51x
10µM FW Primer02. MaiJan 250,5µM
10µM RW Primer2,5Jan 250,5µM
95ng/µL Putida genomic DNA5,26 (500ng)5,26 (500 ng)
Nuc. Free waterApr 874,74
             ATPCS PCR Reaction
Component 25µl Final Conc.
2x Q5 MM12. Mai1x
10µM FW PrimerJan 250,5µM
10µM RW PrimerJan 250,5µM
230ng/µL Arabidopsis cDNA2.2 (500ng)
Nuc. Free water08. Sep
             PCR programm
             PPMT 234 bp
denaturing 98°C 120sec
Denaturing98°C10 sec
Annealing 30x
64°C30 sec
Elongation72°C20 sec
Final Elongation72°C2min
Store8°C
             ATPCS 1469bp
denaturing 98°C 30 sec
Denaturing98°C10 sec
Annealing 30x
62°C30 sec
Elongation72°C60 sec
Final Elongation72°C2min
Store8°C

10µl of PCR reaction + 2µl 6XDNA loading dye was loaded onto a 1 % agarose gel
ATPCS (one clear thick epxacted band at Test of purity and quality of genomic DNA by running it through a 1% agarose gel1400 bp)
PPMT1 (no band)
PPMT2 (no band)

>

             Test of genomic DNA of P.Putida for purity and quality by running it on a 1% agarose gel


             - looks fine on a gel. One clear band over 10 000 bp


             !!! Improve PPMT !!!:
             Try using DMSO (NEB PCR grad) and set Annealingtemperature down to 55°C
             Try different DMSO conc. : 0; 1; 5; 8  %
             

              

06/11 Wednesday - Continuation of work from 06.06.2014: PCR for (ATPCS and) PPMT with Q5

PPMT PCR without success last weak. Therefore the temperature of the annealing step should reduce from 64°C up to 55°C in the pcr programm.
1) corrected pcr programm for PPMT
' T [°C] t [s]
Denaturating98120
Denaturating9810
Annealing5530
Elongation7260
Final Elongation72120
Store8
             2) PPMT pcr reaction
             Different samples with concentrations on DMSO 0%, 1%, 5%, 8% were prepared. Use 99,97% DMSO the samples were prepared with the following pattern:
             The final volume is 25μl.
' #1 [μl] #2 [μl]
Q5 MM12,512,5
10 μl FW Primer2,51,25
10 μl RW Primer2,51,25
Putida genomic DNA 95 ng/μl 5,26 5,26
dazu 1.: DMSO,00
nuclease free H2O2,244,74
dazu 2.: DMSO,0,250,25
nuclease free H2O1,994,49
dazu 3.: DMSO,1,251,25
nuclease free H2O0,993,49
dazu 4.: DMSO,22
nuclease free H2O0,242,74
             the 7 samples were labeled by the following schema:
             PPMT.1.1, PPMT.1.2, PPMT.1.3, PPMT.1.4 (Primer je 2,5μl, DMSO Konz. 0,1,5,8 %)
             PPMT.2.2, PPMT.2.3., PPMT.2.4 (Primer je 1,25μl, DMSO Konz. 1,5,8 %) 
               
              

06/12 Thursday - PCR of PPMT

Amplification of PPMT with DMSO
''(Continuation of work from 06.06.2014: PCR for PPMT with Q5'' For Protocol please see Labjournal from 11.06.2014
             following labeling for 8 samples was used:
             PPMT.1.1, PPMT.1.2, PPMT.1.3, PPMT.1.4 (Primer je 2,5μl, DMSO Konz. 0,1,5,8 %)
             PPMT 2.1, PPMT.2.2, PPMT.2.3., PPMT.2.4 (Primer je 1,25μl, DMSO Konz. 0,1,5,8 %)


             Gel Electrophoresis
             1µl loading buffer+5 µl sample  loaded on 1% agarose gel; 90V
             (rest of sample in iGEM freezer)



             Results
             contamination from water (band 3000bp for every sample)
             with higher DMSO conc. (5% and 8%) bands from visible
 
              

06/17 Tuesday - PCR Amplification of ATPCS from cDNA

PCR-pipetting scheme
Volume [µl] Chemicals
12,5 2x Q5 Mastermix
1,25 10µM fwd Primer
1,25 10µM rev Primer
2,2 Arabinopsis Thaliana cDNA
8,9 nucl.free H2O
26,1µl total volume
             PCR-program
PCR-step Temperature [°C] Time [sec]
Denaturation 98 30
"30 cycles start"
Denaturation 98 10
Annealing 62 30
Elongation 72 60
"30 cycles stop"
Final Elongation 72 120
Store 8
 

              PCR Purification of ATPCS
              - Kit Purification
- Elutionbuffer: 30µl

- Final concentration: 69 µg/ml

06/18 Wednesday - PCR of drag outs to separate cells for FieF Knockout

Pick up 7 single colonies + 20µl d. H2O each (on ice)
--> Labeling: K1, K2, K3, K4, K5, K6, K7
PCR for each colony with Primer combinations: C1-C3, C2-C4, C1-C5 --> 7x3= 21 Samples
             PCR Assay
Amount [µl] Chemical
1 Sample (Colony)
13,5 d. H2O
2 10x Dream Taq Polymerasebuffer
1,2 25mM MgCl2
0,5 10µM fwd Primer
0,5 10µM rev Primer
0,5 10mM dNTPs
0,6 Taq DNA Polymerasse
             PCR Program
             Colony-PCR: Elongation Time : 1,2 Min, Annealing Temp.: 55°C 
Gel Electrophoresis

Result RV-strain is not appropriate for Fief-Knockout. Unknown genome leads to unspecific binding of designed primers, too many bonds in gel electrophoresis picture.

06/19 Thursday

Continue working with colonies: K1, K5, K6, K7 from 18.06.2014
PCR-programme:
Amount [µl] Chemical
1 Sample (Colony)
13,5 d. H2O
2 10x Dream Taq Polymerasebuffer
1,2 25mM MgCl2
0,5 10µM fwd Primer C1
0,5 10µM rev Primer C4
0,5 10mM dNTPs
0,6 Taq DNA Polymerasse
             PCR-programme: 
Elongation time: 2Min, Annealing Temperature: 56°C


              Magnetization of E. coli by expression of human Ferritin, 1st Experiment part 1 of 4 
             Aim: 
             Test the possibility of Magnetization of E.coli cells by the expression of human Ferritin:


             Procedure:
             To evaluate the effect of Ferritin  on the Magnetization different cultures were compared:


             For Both RV308 and Nissle
Culture 1 2 3 4
Plasimd + - + +
iron + + - +
induction + + + -


             - Transform the Human Ferritin gen carried on the Plasmid PC514 provided from (iGEM Team of Calgary university, Canada) to E. coli strains
             (Nissle and  RV308) via electroporation, plate on (Amp) plates for selection.
 
              

06/20 Friday Restriction digest of pQE_80L and ATPCS-PCR fragment

1x 5x Mastermix pQE_80L
H2O nucfree23,1µl115,5µl2µl
10x green FD buffer2µl10µl2µl
DNA2,89µl14,5µl14µl
BamHI1µl0µl1µl
SacI1µl0µl1µl
             5x Mastermix = Mastermix for ATPCS 
             Enzymes were added to each single aliqout and not into the Mastermix


             Incubation: for 1,5 h at 37 °C
             Deactivation: 80°C for 5 min


             I used the wrong restriction enzymes as I got confused with the PCR fragment. Digestion with SacI and HindIII is needed not  BamHI.
             Repeat PCR for ATPCS as well as restriction digest!


             Test expression of Ferritin in RV308 (pSB1C3_Ferrtin) and Nissle (pSB1C3_Ferrtin)
             5ml overnight culture used as an inoculum.
             4 ml culture were diluted to 40 ml with LB and grown for 1 h at 37°C until an OD600 of 0.7 and 0.8 was reached.
             Non-induced SDS sample was taken and induced with 1 mM IPTG
             After expression for 3 h induced SDS sample was taken.
             SDS PAGE
             Ferritin band ecpected at 21kDa
Key:
- 1st band: Nissle (non induced)
- 2nd band: RV308 (non induced)
- 3rd band: Ladder
- 4th band: Nissle (induced)
- 5th band: RV308 (induced)

06/25 Wednesday - Amplification of ATPCS (cDNA)

PCR-pipetting scheme

Volume [µl] Chemicals
12,5 2x Q5 Mastermix
1,25 10µM fwd Primer
1,25 10µM rev Primer
1,5 Arabinopsis Thaliana cDNA
8,9 nucl.free H2O
25,4µl total volume
             PCR-program
PCR-step Temperature [°C] Time [sec]
Denaturation 98 30
"30 cycles start"
Denaturation 98 10
Annealing 62 30
Elongation 72 60
"30 cycles stop"
Final Elongation 72 120
Store 8
             PCR Purification
             -Purification Kit 
             →DNA concentration measurement showed, that the Absorbance ratio of 260nm:280nm is quite low, which means that targeted DNA got contaminated.
             Preparation of pre-culture
             Strains:
- e.coli nissle
- e.coli nissle + ferritin
- RV308
- RV308 + ferritin
             Assay
             - 5ml LB media + 1 picked clone of the pre-day
- Addition of 5µl CN37 to the strains with ferritin
             Incubation: 37°C; 170rpm; o/n
              
              

06/27 Friday

Magnetization of E. coli by expression of human Ferritin, 1st Experiment part 2 of 4 - Preculture of 1 positive clone over night ( preculture: 7 ml LB+ 7µL Amp + 1 Clone)

06/28 Saturday

Magnetization of E. coli by expression of human Ferritin, 1st Experiment part 3 of 4
             - Transfer the Precultures (OD= 0.4-0.5) to 25, 50 mL flasks (half filled with LB) and cultivate them at 37°C for 3 hours
             RV308 (+,+,+) & (-,+,+) And Nissle (+,+,+) were cultivated in 50 mL flasks


              Strain:  OD
RV308 0,78
Nissle 0,86
             - Induction with (20µl (50 ML flasks)/10µl (25 ML flasks)) IPTG (concentation 1 M).
- Add FeCl2 and MnCl2 (100µL in 50ml flasks/ 50µl in 25ml flasks) Incubation over night at 37C°


              Strain:  OD
RV308 2.56
Nissle 2.8

06/29 Sunday

Magnetization of E. coli by expression of human Ferritin, 1st Experiment part 4 of 4 -Sampling for testing the Ferritin content via SDS-Page, different ODs were taken in consideration!
-Prepare the sample for SDS-gel by centrifuation and discard the supernatant then add (60µl Dis.water + 15 SDS+ MH-EtoH), boil for 10 min at 94°C.
- Test the Magnetization using an permanent magnet under light microscope.
             Evaluation:
             SDS Page:  was not clear! 
             Magnetization :
             
             RV308                                             
Culture 1 2 3 4
Plasimd + - + +
iron + + - +
induction + + + -
Nissle In samples with Iron aggregates were observed with strong Mag.effect.

06/30 Monday - Colony PCR and Ligation ATPCS

PCR pipetting scheme
Culture 1 2 3 4
Plasimd + - + +
iron + + - +
induction + + + -
Volume [µl] Chemicals
13,7 nucl.free H2O
2 10x Dream Taq Buffer
1,2 25mM MgCl2
0,5 10mM dNTPs
0,5 10µM fwd Primer
0,5 10µM rev Primer
1 Sample (Colony)
0,6 Dream Taq DNA Polymerase
20µl Total Volume
             PCR program


PCR-step Temperature [°C] Time [sec]
Denaturating 95 180
30 cycles start
Denaturating 95 30
Annealing 55 30
Elongation 72 120
30cycles stop
Final Elongation 72 600
Store 12
             Gel Electrophoresis
             1% Agarose gel with EtBr; 8µl sample; 5µl Ladder
"Key:"
First band= Ladder
Each other band is a different picked clone (10 clones were picked)

07/01 Tuesday - ATPCS Ligation

The ligation of ATPCS was checked with 1% Agarose gel (stained with ethidiumbromid) after colony pcr.

07/02 Wednesday - Knockout of Fief and Fur in RV308 and Nissle

To pepare the knockout 5 µl CM solution (pFerritin with canamycin resistance cassette)and 500 µl culture solution were added to 5 ml LB media. For each stain two samples were determined (RV1/2 and N1/2). The samples were incubated at 37°C up to an OD600 of 0.53-0.55. After incubation 1 ml of each culture was transfered in sterile eppi and washed for 7 min at 7000 rpm and 4°C. The supernatant was descarded, the pellet was resuspended in 1 ml sterile H2O and washed for 7 min at 7000 rpm and 4°C and descarded the supernatant. The pellet of N1 was resuspended in 25 µl pRFP (c = 41 ng/µl) and 25 µl sterile H2O. The pellets of N2 and RV1/2 were resuspended in 2 µl pRFP and 50 µl sterile H2O. 50 µl of each suspension were transfered in electroporation cuvette and electroporated for a few sec (table below). Directly after this, 1 ml fresh LB media (37°C) was added, the suspension was transfered in a sterile eppi and incubated at 37°C at 600 rpm. The cultures were recovered, deleted on CM+Amp plates and incubated at 37°C ove night.
Überschrift [kV] [ms]
N1 1,8 2,3
N2 1,2 5,4
RV1 1,2 5,3
RV2 1,5 5,3


             Transformation of stains RV, Nissle, WM
             The stains RV308[ferritin], Nissle[ferritin], RV308, Nissle and WM110 were transformed with RFP. RV308[ferritin] and Nissle[ferritin] were deleted on CM+Amp plates and 5 ml culture was added with CM/Amp and incubated at 37°C. The transformed strains RV308, Nissle and WM110 were deleted on Amp plates and 5 ml culture was added with Amp and incubated at 37°C.



             Results of transformation
stain colonies on plate cells in culture
Nissle1 + RFP 3 Yes
Nissle2 + RFP 19 Yes
WM110 1 + RFP 0 Yes
WM110 2 + RFP n.d. Yes
RV308 1 + RFP 0 Yes
RV308 2 + RFP 87 Yes
Nissle[ferritin]1 + RFP 108 No
Nissle[ferritin]2 + RFP 0 No
RV308[ferritin] 1 + RFP 330 Yes
RV308[ferritin] 2 + RFP 300 Yes

The cultures of WM110 1 + RFP and WM110 2 + RFP were deleted on Amp plates and incubated at 37°C. Moreover 5 ml precultures from RV308 + RFP + Amp and RV308[ferritin] + RFP + CM+Amp were prepared.

07/03 Thursday - PCR amplification of knockout cassette FUR/FieF

The pcr preparation was performed at the pattern in the table below.

pcr preparation FUR (25µl) FieF (50µl)
Os High Fedility 2x Mastermix 12,5 µl 25 µl
forward primer 10mM 1,25 µl 2 µl
reverse primer 10mM 1,25 µl 2,5 µl
pkD4 plasmid DNA 1 ng/µl 1 µl 1 µl
nuclease-free H2O to 25 µl to 50 µl
             The amplification was performed with the programm in the table below.
step T [°C] t [sec]
initial denaturation 98 30
5 cycles 98/ 63/ 72 8/ 25/ 45
25 cycles 98/ 72 8/ 70
final elongation 72 120
             --> hold at 8°C
             The amplification results were analysed in agarose gelelectrophorese (1% agarose; 0,5µl Gel Red; 10x diluted ladder; 6x loading dye).

07/04 Friday - Expression von RV308 (RFP) und RV308 (RFP + Ferritin)

50 ml LB + 50 µl Amp inoculated with 5 ml overnight culture of RV308 (RFP)
50 ml LB + 50 µl Amp/Cm inoculated with 5 ml overnight culture of RV308 (RFP + Ferritin)
After a OD of 0.6-0.7 was reached 50 ml cultures were portioned into 4 sterile 100 ml flasks so that there was a final volume of 10 ml in each flask.
The cultures were then cultred the following:

RV308 (RFP) RV308 (RFP + Ferritin)
Induced 1 mM IPTG+-+-+-+-
Fe/Mn each 1 mM*++--++--
             *Fe/Mn were solubilized by autoclaving and 1M stock solution

Altough not planned IPTG and metal ion solutions were added simultaneously due to time constraints. It was planned to add metal ions 2h after induction

07/07 Monday - Preculture prepared of:

1. ATPCS Klon 1 - 10 (Amp) --> check if anything grew and contact Johann
2. WM110 (RFP), RV308 (RFP), Nissle (RFP), RV308 (Ferritin + RFP) --> make Cryostock for each
Overgrown WM110 (RFP) plate streaked out again, please take out and put in cool room
Rune:
PCR of PPMT and ATPCS

07/09 Wednesday - PCR for PPMT with goTaq (Promega)

25 mikrol reaction:
12,5 mikrol goTaqMastermix
1,25 mikrol fw Primer 10mikrom
1,25 mikrol b Primer 10mikrom
1,0 mikrol DNA Template PPMT
9,0 mikrol nucleasefreies Wasser
'''Mit folgenden PCR-Programm Parametern:''' Denaturation 98°C 10 min
Denaturation loop 98°C 1 min
Annealing Temp loop 56°C 1 min
Elongation Time loop 72°C 1 min
Final Elongation 72°C 5 min
Storage 8°C infinite
Miniprep Miniprep of ATPCS clone number 3 = 94ng/µl and sent for Sequencing

07/17 Thursday - Midiprep

#pQE_80L = 183 ng/µl
#pMA-T_PPMT =321ng/µl
#pKD46 = 218ng/µl
Digestion
Digestion pQE_80L with HindIII and SacI
deactivated at 80°C for 10 mins

07/24 Thursday - miniPrep + restriktion PPMT und iGEM plasmids

Plasmide: 1. pBADex-mYFP Venus (Amp)
2. pEx-HISII (Amp)
3. pJS418_phagemid(dummy) (Cm)
Restriction-enzymes: XbaI | PstI (used SpeI instead :X)
kit-miniprep
1. 220ng/µl 2. 130ng/µl 3. 430ng/µl
restriction:
500 ng DNA + 1µl XbaI + 1µl PstI + 5µl 10x Buffer + ->50µl Wasser (x3) [ppmt x4]
1. 2,3µl 2. 3,8µl 3. 1,2 µl PPMT 1,6µl
2nd try w/ right enzyme:
1,5 µg DNA + 0.5 µl enzymes + 3µl BUffer + -> 30 µl Wasser
1. 6,5µl 2. 11 µl 3. 3,5 µl PPMT 4,5 µl (x3)
Fragments: 1. 4043/700 2. 4450/55 3. 3800/861 PPMT 2400/251
Gel1 L|3| 1 |1|2|2|2|P|3|3 Gel2 L|P|P|P
Neu: Gel 1|2|3|L|P|P|P
GelEx QiagenKit -> extrakte in grüner box im freezer
Ligation 2 + P
10µl Ansatz: 1µl BUffer + 0.5 µl Ligase + 1.4 µl PPMT + 7.14 µl pEX-HisII [78ng]

07/25 Friday

1. Ordered Primer for cloning hu_Ferritin into pQE80L
2.) Ligation of PPMT Fragment from pMAC_PPMT into pEX_HisII
pMAC_PPMT and pEX_HisII were digested with HF PstI and HF XbaI (NEB)
PPMT (Insert) and cut pEX_HisII (Vector DNA) were purified via an Gel extraction
Ligation was performed using NEB T4 DNA Ligase in molar ratios of (Insert:Vector) and 40 ng Vector were used.
0:1 2:1 3:1 5:1

Ratio 02:01 03:01 05:01
Amount Insert4,04 ng6,06 ng10,1 ng

Ligase was deactivated and ligation transformed after weekend

07/28 Monday

1. Degradation test of prepped TB-Expression Plasmids by running samples on agarose gel
pBADex_MYFP_Venus (no observable degradation)
pEX_HisII (no observable degradation)
pJS418_Phagemid (Dummy) (no observable degradation)
Data:
Fabian : 28072014_1
2.Transformation of 0.2 µl pEX_His_PPMT ligation into DH5alpha, DH10b, and MG1655 via electroporation

07/29 Tuesday

1.) Transformation worked and we got colonies for pEX_HisII_PPMT
Colony PCR was performed (Sascha)
See Standard Protocol
2.) Ligation of ATPCS PCR Fragment into pQE_80L
ATPCS PCR fragment and PQE80L Vector were digested with FD HindIII and FD SacI (ThermoScientific)
ATPCS was purified via PCR purification and Vector DNA was purified via an Gel extraction
Vector DNA was dephosphorylised using Fast-AP and deactivated
Ligation was performed using NEB T4 DNA Ligase in molar ratios of (Insert:Vector) and 40 ng Vector were used.
0:1 2:1 3:1 5:1

Ratio 02:01 03:01 05:01
Amount Insert24,96 ng37,41 ng62,36 ng
             Ligase was deactivated and ligation transformed next day



             <img src="Team_berlin_0009.jpg" alt="" />
             #pMAC_PPMT*
             #pQE_80L*
             #pSB1c3
             #pKD46*

(*)Bands at 20 kbp for Promega prepped Plasmids.

07/30 Wednesday

Results Colony PCR for pEX-HisII-PPMT clones preculture 4 and 5 in incubator for Miniprep and Sequencing

              Transformation 
             Chemical competent cells XL Blue 
             * 3 µl for each Ligation Assay
             * 10 min incubation on ice
             *60 s Heat schock
             * 2 min incubation on ice
             *950µl LB added
             *1h --> 37 °C for Recovery
             *platted on Amp-plates
              Eporation 
             *0.2 µl Ligationassay in competent DH5α [iGEM]
             *1.7 kV
             * 1h; 37°C
             * platted on Amp plates
              
              

07/31 Thursday

Miniprep for sequencing of pEx_His_ppmt in DH10B? 90-100 ng/µl
Cryostock & miniprep of pjs418 in DH5a 518ng/µl
PCR of 7 clones with pQe80l_ATPCS
16 µl wasser
2 green dreamtaq buffer
0.5 dNTP
0.5 primer (each)
colony
0.6 dream taq
95° 3min
95° 30s x30
55° 30s x30
72° 2min x30
72° 10min
Colonie PCR did not work--> no positive clones concentration after MiniPrep
* pJS418 = 518 ng/µl * Klone 4 = 90 ng/µl * Klone 5= 105 ng/µl

08/06 Wednesday

PCR
' BamHI_PPMT_GS GS_ATPCS_HindIII BamHI_HuFerritin_HindIII
Q5 2x Mastermix12,512,525
10 µM Primer fw1,251,251,25
10 µM Primer rev1,251,251,25
template (1ng) 0,30 0,5 1
nucfree H2O 9,7 9,5 19
             Program:
BamHI_PPMT_GS ' ' GS_ATPCS_HindIII ' ' BamHI_HuFerritin_HindIII '
9830 9830 9830
981098109810
583056,33058,630
721272607245
722'722'722'
8end8end8end

Analytical Gel Expacted Bands clearly seen for PPMT and Ferritin. Only little ATPCS band shows Primer Dimer inhibit PCR. Anyhow we will try a Gel extraction and after a Assembly PCR Generation of Heme-free BFR by Site-directed Mutagenesis, part 1 of 5
Site-directed mutagenesis was performed by the QuickChange method
Primer design with http://www.bioinformatics.org/primerx/ methionine (on position 52) was substituted by histidine BFR M52H

08/07 Thursday

Analysing 2 colonies of pQE80L_ATPCS whether ATPCS was inserted by sequencing revealed no proper results.
Tested by colony PCR (see protocols) using 55°C Annealing temp and 2' Elongation time (expected bands should be 2000bps).
Gel showed PCR was about 500 bp big -> ATPCS NOT INSERTED.
Outcome:BamHI_PPMT_GS super
GS_ATPCS_HindIII bad
BamHI_Ferritin super

08/08 Friday - Gradienten PCR GS_ATPCS_HindIII

             PCR
' 3x GS_ATPCS_HindIII
Q5 2x Mastermix12,5
10 µM Primer fw1,25
10 µM Primer rev1,25
template (1ng) 0,5
nucfree H2O 9,5
             Program:
GS_ATPCS_HindIII ' '
98°C30
98°C10
56,3-62°C3034
72°C60
72°C2'
8°Cend
             - preparative agarose gel 1% and gel ex of GS_ATPCS_HindIII bands at ca. 1490 bp
             - accidentally also loaded BamHI_PPMT_GS onto Gel and was also  extracted (elution with 25 µl elution buffer).
             - BamHI_Ferritin_HindIII was PCR purified
             - DNA concentration meassurement for  purificated pcr fragments:
             GS_ATPCS_HindIII = 33 ng/µl
             BamHI_PPMT_GS = 48 ng/µl
             BamHI_Ferritin_HindII = 125 ng/µl
             Assembly PCR
             An Assembly PCR was used to align BamHI_PPMT_GS with GS_ATPCS_HindIII and amplify the complementary structure in order to form a fusion protein coding sequence.
             Therefore, both fragments were added a templated equal molar amounts.
             Calcultation:
             bpATPCS = 1493
             bpPPMT = 255
             mATPCS/bpATPCS = mPPMT/bpPPMT
             mATPCS = (1ng * 1493) / 255
             mATPCS= 58 ng
' BamHI_PPMT_GS_ATPCS_HindIII
Q5 2x Mastermix25
100 µM Primer fw0.25 (not added till later to second PCR run)
100 µM Primer rev0.25 (not added till later to second PCR run)
template (1ng) 1,750 µl ATPCS + 0.208 µl PPMT
nucfree H2O 18.042
             Program:
1. PCR BamHI_PPMT_GS_ATPCS_HindIII ' '
9830
9810
6830 5
7255
721'
8end
2. PCR BamHI_PPMT_GS_ATPCS_HindIII ' '
9830
9810
6830 30
7255
722'
8end



              Transformation into DH10B 
             #BFR M52H
             # BFR M52H
             *Recover in LB--> 1h at 37°C
             
              

08/11 Monday - Plan-prepare fragments for digest

Constructs aimed for *In pQE_80L (Amp) BamHI_PPMT_GS_ATPCS_Hind III (PCR Construct available) Construct Size 1724 of 4731
             *In pQE_80L (Amp)    BamHI_FTH_FTL_Hind III   (PCR Construct available)
             Construct Size 1077 of 4731
             *In pQE_80L (Amp)   Sacl_ATPCS_Hind III    (PCR Construct not available)
             Construct Size 1400 of 4731
             *In pJS418 (CM)    XbaI_PPMT_PstI       (PCR Construct available)
             Construct Size 255 of 3800
Q5 MasterMix 25μl
ATPCS SacI 2.5
ATPCS Hind III 2.5
cDNA At. 0.5
H2O 19.5
PCR Programm
98°C 30 sec
98°C 10 sec
62°C 34cycles 30 sec
72°C 60 sec
72°C 2 mins
4°C Store


             PCR Fragmente PPMT_GS_ATPCS+ATPCS+Purification (Gelex)

After Gelex:
PPMT 48ng/μl
Ferritin 125ng/μl (Pur from PCR)
ATPCS 33ng/μl

08/12 Tuesday - Preparing chemically competent cells

V=100ml, 37°C
BU36=DH10B OD at 600nm=0.461A
DH10B competent cells

             Digestion
Inserts PCR Pur JBH1 PPMT_GS_ATPCS 1 JBH2 PPMT_GS_ATPCS 2 JBH3 Ferritin JSH ATPCS
PCR Fragment 20 20 8 20
Buffer 3 3 3 3
FD BamHI /FD SacI 1 1 1 1
FD Hind III 1 1 1 1
nuclease free H2O 5 5 17 5
Vector VBH pQE_80L VSH pQE_80L SacI 2x PJS_418 2x P_Mac_PPMT
Vector 5.5 5.5 1.9 3.2
Enzyme 1 1 BamHI 1 SacI 1 FDxBa 1 FDxBa
Enzyme 2 1 HindIII 1 HindIII 1 FD PST 1 FD PST1
Buffer 3 3 2 2
Fast AP 1 1 0 0
nuclease free H2O 18.5 18.5


             * 35 ng/L  PPMT ATPCS 1
             * 15ng/L  PPMT ATPCS 2
             * 25ng/L  ATPCS
             * 13ng/L  P_Mac_PPMT
             * 31ng/L  PJS_418
              


Ligation 5:1 JBH1 in VBH JBH2 in VBH JBH3 in VBH JSH in VSH PPMT in PJS_418
10x T4 DNA ligase Buffer 1μl 1μl 1μl 1μl 1μl
Vector 1.42 1.42 1.42 1.33 1.29
Insert 3.29 7.08 1.36 7.17 1.03
Nuclease free H2O 3.79 0 5.72 0 6.18
T4 DNA ligase (NEB) 0.5 0.5 0.5 0.5 0.5


             Ampicillin  
JBH1 in VBH
JBH2 in VBH
JSH in VSH
             Chloramphenicol 
PPMT in PJS_418
             Transformation in DH10b (cc.c)
106 Kolonie for every approach

08/13 Wednesday - pQE 80L Colony PCR

Mastermix 1x 35x 10x
nuclease free H2O 14 490 140
10 dreamtaq 1 70 20
25µM MgCl2 1.2 42 12
10mM dNTPs 0.5 17.5 5
10mM Forward Primar 0.5 17.5 5
10mM Reverse Primar 0.5 17.5 5
Taq 0.3 10.5 3
PCR Programm
95°C 3 mins
95°C 30 secs
55°C 30 secs
72°C 60 secs
72°C 10 min
8°C Store


             Samples : 
# PPMT GS ATPCS size 1912 # PPMT GS ATPCS size 1912 # ATPCS in pQE80L size 1770 # Ferritin in pQE80L size 1376 # PPMT in PJS size 420


             pQE80L=300bp  
pJS = 170bp
             Sequence clones A - H + J


              Generation of Heme-free BFR by Site-directed Mutagenesis, part 2 of 5 


             QuickChange Site-Directed Mutagenesis
             20µL approach:
Überschrift component
2 µL 10x Pfu Buffer (MgSO4)
0,6 µL 10µM forward Primer
0,6 µL 10µM reverse Primer
x µL 30ng Template
0,4 µL dNTPs
0,6 µL Pfu Polymerase
to 20 µL PCR Wasser


             Template BFR: 
             0,5 µL              A4 (66ng/µL)
             0,2 µL    D2 (144ng/µL)


labeling Template Annealing Temp.
17 D2 (144ng/µL) 71°C
15 D2 (144ng/µL) 55°C
67 A4 (66ng/µL) 71°C
65 A4 (66ng/µL) 55°C


             PCR Program
Temp time
95°C 30sec
________ ______
16 Cyclen
95°C 30sec
55/71°C 1min
68°C 5min
________ ______
68°C 10sec
4°C finale
             Σ20µL -8µL fürs Gel= 12µL +1µL DpnI 


             37°C 90min
             chemical Transformation (Fabian)
             
             in DH10b

plating out on Amp plates

08/15 Friday - Clone Sequencing

Clone Name Construct present concentration after isolation
A pQE_80L_PPMT GS ATPCS yes 388ng/µL
B pQE_80L_PPMTGSATPCS yes 373ng/µL
C pQE_80L_PPMTGSATPCS yes 442ng/µL
D pQE_80L_PPMTGSATPCS no 389 ng/µL
E pQE_80L_huFerritin yes 490ng/µL
F pQE_80L_huFerritin no 402ng/µL
G pQE_80L_ATPCS yes 497ng/µL
H pQE_80L_ATPCS yes 443 ng/µL
I pJS418_PPMT yes 596 ng/µL

08/19 Tuesday

Generation of Heme-free BFR by Site-directed Mutagenesis, part 3 of 5 ÜN culture
5ml LB + 5µL Amp →shakingincubator

08/20 Wednesday

Generation of Heme-free BFR by Site-directed Mutagenesis, part 4 of 5 MiniPrep nach Protocol
Photometer
4µL Probe + 76µL dilution (Wasser)

08/21 Thursday

Generation of Heme-free BFR by Site-directed Mutagenesis, part 5 of 5 Sequencing:
Primer PB 16
Crystocks:
ÜN culture
500µL culture + 500µL DMSO
2xclon 17
2xclon 67

08/22 Friday - SDS-PAGE with Coomasie staining

Samples

             # Marker
             # Pellet ATPCS/PPMT
             #15:00 after induction ATPCS/PPMT
             #overnight ATPCS/PPMT
             #GS Pellet
             #PGSA after induction 15:00
             #GS P/A overnight
             #human Ferritin Pellet
             #human Ferritin after induction 15:00
             #human Ferritin overnight


             Analysis of Expression
Human Ferritin = 42 kDa (Potparam Expasy)
ATPCS = 56.3 kDA (Potparam Expasy)
PPMT = 7.9 kDA (Potparam Expasy)
ATPCSGSPPMT = 64.3 kDa (Potparam Expasy)

08/29 Friday - Calibration curve for Iron concentration measurement

Überschrift Überschrift
0.017A 10 µg/ml
0.105A 50 µg/ml
1.076A 100 µg/ml
2.095A 150 µg/ml
2.747A 200 µg/ml
              
              

09/03 Wednesday

Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 1 of 8 Aim: Test the possibility of Magnetization of E.coli cells by the expression of human Ferritin:


             Procedure: ...

-Precultures of Nissle and RV308 (wild types)

09/04 Thursday

Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 2 of 8 -Prepare chemical competent cells ( Nissle and RV308) . see Protocol

09/05 Friday

Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 3 of 8 -Chemical biotransforamtion (double Trafo, 200ng of each) of, red fluorescence protein carried on plasmid (kan) Human-Ferritin carried on PQE-80L (Amp) [was prepared by iGEM-Berlin using the '''Biobrick''' from Calgary, unlike does not contains polypeptide at the beginning].

09/06 Saturday

Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 4 of 8 -Positive colones for both RV308 and Nissle

09/11 Thursday

Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 5 of 8 - Precultures of the transformed colones

09/12 Friday

Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 6 of 8 - Transfer the precultures into 250ml filled until 100ml with LB and incubate them at 37°C Strain OD
RV308 0.71
Nissle 0.6
- Induction with 100µl IPTG (1M), incubation over night at '''30°C''' and 200rpm

09/13 Saturday

Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 7 of 8 -samples were taken for protein analysis SDS-Page Strain OD
RV308 6.2
Nissle 5.2
- adding 7ml of 1M Mn-citrate (wrongly) and incubated at 4°C over weekend

09/15 Monday

Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 8 of 8

             -Test the Magnetization using a permanent magnet under Fluorescent microscope. 
             Evaluation 
             -Cells grew
             -no red fluorescence observed
             -no Magnetization observed
             Possible Explanation:
             - Adding Mn ions instead of Fe could be effected the Magnetization 
             - The red Fluorescence gen contains a cadaverin chain, this could explain the non-fluorescence.
              
              

09/16 Tuesday

Preparing Cultures for flouruscence microscopy
E. coli Nissle 1917 (pQE_80L Hu_Ferritin + RFP)
E. coli RV308 (pQE_80L_HuFerritin + RFP)
Nissle OD600 = 5.08
RV 308 OD600 = 5.81
take OD=1
wash in 1000 µl PBS three times ( centrifuge at 6000g for 2min, discard supertanent and resuspend pellet in PBS) finally resuspend pellet in 500 µl Put it into a cool box and take it over to the fluorescence microscope facility. Constructing PQE_80L_T5_ATPCS_lac_PPMT
Plasmid for Co-Expression of PPMT and ATPCS on one plasmid. Source: pJS418_PPMT (amplifying insert) pQE_80L_ATPCS (as target vector) PCR of HindIII_lac_PPMT_HindIII Construction of the HindIII_lac_PPMT_HindIII in pQE80L_Hind III
3x HindIII_lac_PPMT_HindIII
Q5 2x Mastermix 12,5
10 µM Primer fw 1,25
10 µM Primer rev 1,25
template (1ng) 0,5
nucfree H2O 9,5
              Program 
Temperature Durattion in seconds Cycles
98 30 1
98 5 loop start
62-65 15 loop 32
72 10 loop end
72 2' 1
8 infinite 1
              
              

09/17 Wednesday - Digest and Dephosphorylation of vector pQE_80L_ATPCS

pQE80L_ATPCS digest 1x 3x
pQE_80L_ATPCS 2 µl 7 µl
FD HindIII 1 µl 3 µl
10x FD Buffer 2µl 7 µl
FastAP (Thermo) 1 µl 3 µl
nucfree H2O 14 µl 51 µl

Gelextraction resulted in HindIII cut pQE80L_ATPCS 20 µl with 12 ng/µl
In parallel the PCR fragment HindIII_lac_PPMT_HindIII was purified and is ready for digest.

09/18 Thursday

Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 1 of 7

             'Aim
             
             -Double Trafo of the Human-Ferritin and fluorescence marker.
             Procedure:
             Stains: RV308, Nissle and DH0B (control)
-chemical Double-biotransformation of:
-0.5 µl of Human-ferrtin on PQE-80L(490 ng/µl) with (Amp)
-3 µl green fluorescence protein Nerm ASGP-R-GFP (83 ng/µl) with (Kan)
             for control:
- 3 µl green fluorescence protein Nerm ASGP-R-GFP (83 ng/µl) with (Kan) is transformed into DH05
- Double Trafo of (pJS418_PPMT and pQE_80L_ATPCS)

09/19 Friday

PCR of BB0 - BB3 parts (Saba)
compound V/µl (50µl total)
Q5 2xMM 25.0
10µM P_fv 2.5
10µM P_rev 2.5
DNA (template 1ng) 2.0 (of diluted plasmid)
nuc.-free H2O 28.0
             Primers
Reaction fw Primer rev. Primer TmTm/°C Template bp
BB0 BBa_K1438000_fw BBa_K1438000_rev 62 pQE80L_BFR 507
BB1 BBa_K1438000_fw BBa_K1438000_rev 62 pQE80L_BFR M52H 507
BB2 BBa_K1438002_fw BBa_K1438002_rev 68 pQE80L_Hu-Fer 1000
             PCR Programms
             BB0 & BB1
T/°C t/min cycles
98 0:30 30
98 0:10 30
62 0:30 30
72 0:15 30
72 2:00 30
8 infinity 30
             BB2
T/°C t/min cycles
98 0:30 30
98 0:10 30
68 0:30 30
72 0:40 30 (probably too long since ~1000bp and not 1408bp however worked well as seen on gel)
72 2:00 30
8 infinity 30

              

Biobricks derived from pQE80L constructs
BB1 BFR 191µg/ml
BB2 BFRM 173µg/ml
BB2 HuFerritin 166 µg/ml Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 2of 7 -No positive colones were detected for double-trafo expect these for control (transformation was successful in DH05).

09/20 Saturday - Digest of PSB1C3-Ferritin

Plasmid: PSB1C3 - ferritin with Peptid 120ng/µl
component µL
NEB Xba1 2 µL
NEB Pst1 2 µL
NEB Buffer 3.1 20 µL
nucleasefree H2O 151 µL
PSB1C3 Feriitin 25 µL
total volume 200µL
             37°C for 1,5h
             (inactivate for 20min at 80°C)


             Gel electrophoresis 
             1% Agarose-Gel 
+ 3 µL EthBr
             200µL Probe + 40 µL loading dye (6x)
             5 µL GenRuler-Mix
             no Gel-extraction, because nothing was seen on the gel, except the marker (GenRuler) 
             (add Figure)
Figure not in Dropbox


              Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 3 of 7 
             -Transformation of RF (red fluorescence protein) on with (Kan) into DH05
              
              

09/21 Sunday

Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 4 of 7 -Transformation was successful

09/22 Monday - Precultures

Precultures of PSB1K3_RFP in DH10b (Kan)
pQE80L_ATPCS & pJS418_PPMT in Dh10b (Amp & Cm)
Clones with pQE80L_ATPCS'n'PPMT in DH10b (Amp)
PSB1C3_Ferritin in DH10b (Cm) Checking Insertion of gene by colony PCR
Performing PCR for clones of ATPCS-PPMT construct
1x in µl 12x in µl 10x in µl
nuclease free H2O 14 168 140
10x DreamTaq buffer 2 24 20
25mM MgCl2 1.2 14.4 12
10mM dNTPs 0.5 6 5
10mM FW Primar
HindIII-lac-prom-fw
0.5 6 5
10mM RW Primar
PB17 (T7 term_rev)
0.5 6 5
Taq Polymerase 0.3 3.6 3
Programm colony PCR Temp Time
Denaturing 95°C 7 min
Denaturing 95°C 30
Annealing 69°C 30
Elongation 72°C 1 min
Final Elongation 72°C 10 min
Store 8°C

Dissolved colonies 4 and 6 which showed band at 400 bp were grown each in a cultivation tube with LB+Amp100 at 37°C

09/23 Tuesday - Mutagenesis of ATPCS

The elimination of the XbaI restriction site of all our ATPCS containing constructs was achieved by quick change mutagenesis.

             ... Details Saba....
             After digest with DpnI the reaction was transformed into competent DH10b E. coli cells via heat shock transformation.
After streaking out all aliquots on LB-Amp Agar plates, they were incubated at 37 °C over night.
              Digest of miniprepped PSB1C3_Ferritin (Calgary) for extraction of vector for BioBrick preparation 
Components Volume in µl
NEB XbaI 2
NEB PstI 1,5
NEB Buffer 3.1 5
nucfree H2O 26,5
plasmid PSB1C3_ferritin (Calgary) 15
50 µl reaction
             
The reaction was incubated at 37 °C for 1,5 h.


             The digested vector was purified using a 1% agarose gel and the Roth GelNebulizer purifiction kit. The vector band was expected at 2000 bp and the insert band at about 1000 bp.
             both colonies from Saba were grown --> Mini-prep (Johann) to harvest plasmid DNA
             Mutagenesis of ATPCS
             in 
                pQE80L_ATPCS-GS-PPMT
pQE80L_ATPCS_PPMT
pQE80L_ATPCS
3x PCR-Reactions
Q5 MM 12.0µl
PB_for SN_ATPCS_xbaI_Mut_for 1.25µl
PB_rev SN_ATPCS_xbaI_Mut_rev 1.25µl
nuc.-free H2O 10.5µl
template (1ng) ~ 1.0µl (dilations of original plasmids)
Total 26µl
             PCR Programm
T/°C t/min
98 0:30
98 0:10
69 0:30
72  :
72 2:00
             Trafo of 5µl PCR-Product in DH10b cells --> incubation at 37 °C
              Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 5 of 7 
             - Preculture of DH05 with RF plasimd

09/24 Wednesday

Berlin Vector - pQE-80L-JBFS-huFerritin Assembly PCR Running Gel Electrophoresis

             * 1% Agarose, Ethidium bromide 
             * 50µL Assembly PCR product + 10µL 6*DNA dye
             * 10µL GeneRuler DNA Ladder Mix (ThermoScientific)
             * Gel Electrophoresis conditions 100V, 30min
              


Gel Extraction Gel Extraction using GeneJET Gel Extraction Kit (ThermoScientific) * Determination of Concentration by Ultraviolet Spectrophotometry
             ?
             Double Digest 
             * Digestion of 1μg of purified Insert DNA using FastDigest BamHI / HindIII
             * 1h at 37°C
             ?
             * Heat inactivation of FastDigest BamHI / HindIII, 15min at 80°C
             PCR purification 
             * PCR purification of BamHI / HindIII digested insert using GeneJET PCR Purification Kit (ThermoScientific)
             * Determination of Concentration by Ultraviolet Spectrophotometry
             ?
             Ligation 
             * Using the Molar Ligation Ratio 1:5 (1 times vector and 5 times insert)


             * 20min at RT
             Chemical Transformation 
             * 100µL Aliquots of Chemically Competent Cells - DH10B E.coli + 10µL Ligation approach chilled on ice for 30 min
             * Heat shock for 1min at 42°C
             * Add 900µL preheated (37°C) LB
             * Incubate the cells for 1h at 37°C with shaking approx. 200rpm
             * Plate 200µL and spin down the rest and plate on LB Ampicillin, incubate overnight at 37°C
             Saba
             o/n culture of clones from successful pQE80L_ATPCS-mut_GS_PPMT and pQE80L_ATPCS-mut_PPMT transformation
             --> 37°C, 200pm, o/n 5-6 nl LB+AB (Amp)
              Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 6 of 7 


             - Miniprep of the Preculture, DNA concentration 71 ng/µl
             Chemical Biotransformation of:
              -3 µl of RFP 71 ng/µl
              -2 µl Ferritin jbfs_m (different ferrtin)(120 ng/µl) with  (Amp)'


             in RV308 and Nissle (2 plates each)
              
              

09/25 Thursday - PCR of Biobrick Parts

Isolation of plasmid-DNA with Mini-Prep Kit of pQE80L_ATPCSMut_GS_PPMT and pQE80L_ATPCS_PPMT PCR of Biobrick-Parts 03,04,06 & 10-15
BB PB_fw PB_rew Tm/°C template bp part
03 BBa-K1438003_fw BBa-K1438003_rew 67 pQE80L_PPMT_GS_ATPCS 1715 PPMT GS ATPCS
04 BBa-K1438004_fw BBa-K1438003_rew 65 pQE80L_PPMT_ATPCS 1408 ATPCS
10 XbaI_T7_prom for Lambda_Term_suffix_rew 66 -->67 pQE80L_BFR 690 (+377bp-->cp) BFR_cp
11 " " 66 -->67 pQE80L_BFRM52H 690 (+377bp) BFRM52H_cp
12 " " 66 -->65 pQE80L_FTH_FLH(HuFer) 1337(+377bp) FTH_FLH_cp
13 " " 66 -->67 pQE80L_PPMT_GS_ATPCS 1968(+377bp) PPMT_GSATPCS_cp
14 " " 66 -->67 pQE80L_PPMT_ATPCS 2091(+377bp) ATPCS_cp
06 " " 66 pQE80L_fbfs_mil_Ferritin 1403(+377bp) fbfs_mil_Ferritin_cp
             PCR-Ansätze V/µl
                Q5 2xMM       25.0
                10µM PB_fw    2.5
                10µM PB_rew   2.5
                template      2.0 (~1ng)
                nuc.-free H2O 18.0
             PCR-Programm
T/°C t/min cycles
98 30" 30
98 10" "
66/67 30" "
72 40"/12"/1' "
72 2' "
8 infinity "
             PCR purification of 1,2, 3 (Jbfs_mil_Ferritin_cp),BF-cp and BFM-cp biobrick parts
Concentration µg/ml
fbfs_mit_Ferritin1 42
fbfs_mit_Ferritin2 35
fbfs_mit_Ferritin3 42
ATPCS and PPMT -12 too low
Bacterioferritin CP 56
BFM52H CP 57

Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 7 of 7
- Double-trafo was successful in all RV308 plates but not in Nissle

09/30 Tuesday

Ligation of Biobrick parts with PSBIC3 backbone (digested on 23.09.2014 by Johann Transformation into DH10b c.c.cells by chemical transformation
5µl of each ligation was transformed to 100µl aligusted cells each
--> after recovery at 37°C, 30min cells were plated on Cm/LB-Agar plates after centrifuging-->pelleting and resuspending in 100µl LB to plate all cells. --> incubation at 37°C, o/n Mini Prep von pSB 1U 3-RFP concentration 112 ng/µl
Preculture
pQE-80L-jbfs-Ferritin 5ml LB+5µl Amp at 37°C overnight

10/01 Wednesday - Plasmid Digestion & PCR Probe

Plasmid Digestion

Plasmid Digestion
NEB Buffer 3.1 5µl
NEB XbaI 0.5µl
NEB PstI 0.5µl
P_MA_T_PPMT 312ng/µl 3.2µl
null. free water 40.5µl

PCR Probe Ligation plates evaluated:
All plates had clones except for BFR_cp from each plate transformation one clone was cultivated with LB/Cm (~5ml) o/n at 37°C

10/02 Thursday - Cultures were Mini-preped

--> elution with 40µl EB --> DNA contration measurement

10/06 Monday- Colony PCR

Biobrick Sequenzierung Sequenz (?) (???)
BB0 BFR 100Y BFR M52H -A ws ATGf (??)
BB1 BFR M52H 100% BFR -A wr
BB2 HFTN_LFFN (?) 96Y HuFerritin (Rw Sep nötig) ??
AnP ATPCS f 70% ok, aber Fragment f PCR nochmal ... Gelex (?)
BFM1cp BFR1cp  ?
BFM2cp BFR2cp  ?
HuFecp HuFerritin cp  ?
             Colony-PCR of other clones
             PCR-Programm
T/°C t/min cycles
95 7' 30
95 30" 30
52 30" 30
72 1' 30
72 10" 30
8 infinity 30
             --> gel (1% Agarose)
             Clones 3, 5, 6, 7 and 13 were grown o/n in LB/Cm for Mini-prep on the following day. therefore 5µl of the disolved clones were used for each inoculation
             --> 37°C, 200rpm


             2x M9 Media Production
             (Christina)
             2X M9 mineral medium
             For 500 ml M9 minearal medium add to XXX ml sterile water:
100ml M9 salt solution (10X) Na2HPO4
             KH2PO4
NaCl
NH4Cl || 67.4mM
44.0mM
17.10mM
18.70mM

10/07 Tuesday

Mini-Prep of cultures (Ben) and preparation of sequencing samples (Saba): 9µl nuc.-free H2O + 3µl DNA + 3µl PB794


Preculture of Knockouts * λΔ FieF +PCP 20 : 5ml LB+tet/amp (1:1000) * λΔ FUR : 5ml LB+tet/kan (1:1000) * MG1655 ΔFieF: 5ml LB + amp/kan (1:1000)
incubation at 30°C

10/08 Wednesday - PCR of PSB1C3 Backbone

Q5 Mastermix 2x
Component Volume in µl
Q5 Mastermix 2x 25
Primer fw (PSB1C3 Suffix fw) 2,5
Primer rev (PS1C3 Prefix rev 2,5
template (PSB1C3_BBa_K1189018) 2
nuc free H2O 18
Temperature in °C Time Nr. of cyles
98 30
98 5 loop start
70 15 30
72 1' loop end
72 2'
8 infinit
              Extraction of PCR Product (PSB1C3 linearised) 
             After extracting the expected band at 2000 bp it was purified using the EMDMillipore Montage Gel Extraction Device.
Resulting in about 120 µl DNA extract in TAE buffer with an concentration of 9ng/µl


Digestion of PCR Product
NEB Buffer 3.1 15µl
NEB PstI 1.5µl
NEB XbaI 1.5µl
nuc. free water 83µl
PCR Product 100µl
             * 1.5 hours at 37°C
             * PCR Purification
             * DNA concentraion measurement = 35ng/µl
              Ligation 
             Calculation
             *BFM52H = 3.22µl
             *BF_cp= 6.7µl
             *jbfs_m = 8.06 µl
             *BB_AnP = 10.64 µl
             * HuFer = 9.45 µl
              Iron Concentration measurement 
             278 mg FeSO4.7H2O dissolved in 10 ml d.H2O 
λ FieF PCP2 Amp 1:100 ---> 3.0 OD
iGEM BV125 tet 1:100 --> 3.0 OD
λ FieF PCP1 Amp 1:20 -->3.26 OD iGEM BV125 tet 1:20---> 2.44
too high OD!
             Both samples diluted 1:2
             Samples
             #  FieF + 5µl 0.1 M Fe-stock solution
             # FieF + 15 µl 0.1 M Fe-Stock solution
             # BV + 5 µl 0.1M Fe-stock solution
             # BV + 15 µl 0.1 M Fe-stock solution
             Overnight incubation at 30°C on a shaker 
             
              

              

10/09 Thursday

Mini Prep (using: AccuPrep Plasmid Mini Extraction Kit Ver. 2.0, Company: BIONEER), using 100µl Elution Buffer
and dsDNA Measurement: 4 µl Sample + 76µl MilliQ, blanked with MilliQ
Samplenumber Samplename dsDNA conc [ng/µl] Sample [µl] used for Sequencing nucl.free Water [µl] used for Sequencing
#1 cp HuF 111 9 3
#2 AGSP 107 9,4 2,6
#3 AGSP 59 12 0
#4 AGSP 64 12 0
#5 jbfs_Fer 54 12 0
#6 A'n'P 67 12 0
             For Sequencing:
             *total volume: 15µl
             *Primer used: PB795 3µl each Sequencing approach
             *Sample [µl] see table
             *nucl.free Water [µl] see table
             evaluation of Trafos ---> no growth --->Repeat Trafo in other cells
             
              



              

10/10 Friday - STRATEGY 1 - Knockout of FieF and FUR Genes

Detection PCR kan-deletion-cassette for FieF and FUR Genes was transformed into 2 different strains (MG1655 and λ MAGE). Additionally pCP20 was already transformed into one of the λ MAGE Clones (has to be re-validated).
The positive clones have to be validated.
Detection-PCR of one clone of Plates 1-3:
Plate 1: MG1655 ΔFieF
Plate 2: λ ΔFieF + pCP20
Plate 3: λ ΔFUR
Primer-Combinations FieF
- Combination WT length Clone length Annealing Temperature range
A C1+C2 2060bp 2654bp 58,4-60,1°C
B C1+C3 0 1046bp 59,5-60,1°C
C C4+C2 0 1181bp 57,5-58,4°C
D C1+C5 1134bp 0 60,1-60,5°C
             --> Annealing Temperature: 57°C
             FUR
- Combination WT length Clone length Annealing Temperature range
A C1+C2 1130bp 2219bp 59,5°C
B C1+C3 0 823bp 59,5°C
C C4+C2 0 969bp 57,5-59,5°C
D C1+C5 500bp 0 59,5°C
             --> Annealing Temperature: 57°C
              PCR-Assay 
- 1x Mastermix 15x
nuc.free H2O 14,4µl 216µl
10x Dream Taq Buffer 2µl 30µl
50mM MgCl2 0,6µl 9µl
10mM dNTPs 0,5µl 7,5µl
10mM Primer Combination 1µl
10µl nuc.free H2O+ picked colony 1µl + 18,4ml Mastermix
Taq Polymerase 0,5µl
              PCR-Program 
Temperature Time
95°C 7'
30 cycles
95°C 30"
57°C 30"
72°C 2'40"
72°C 5'
12°C hold
             
               Gel-Electrophoresis 
1% Agarose-Gel + 1µl GelRed; 90V; 30min

10/14 Tuesday - Iron-Assay

1. Day: inoculation of 5ml LB Media (+ Antibiotics)
* 37°C or 30°C/ON

2.Day:inoculation of 10ml LB (1:10)
* 30°C or 37°C
* grow until OD600 0,6
* take 1ml
* centrifuge 2min at max. speed
* discard the supernatant
* wash with 1X M9 Media

* 1XM9:
:500µL 2X M9+
:500µL sterile water
* wash 2x and recover 1mL 1XM9 Media
* diluted 1:1000 with 1X M9
* plate 20µL per well 24well plate without Antibiotics
*A:MG1655 wt *B:Nissel 1917 wt *C:RV308 wt *D:DH10b
concentration of Fe-citrat
0 0,5 1 2 5 10mM