Team:Hannover/Notebook

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Revision as of 16:33, 2 October 2014


Notebook

date coworkers lab activity short summary
22.09.2014 Lisa, Kathi IPG insertion of rcf21 colony-PCR –> only negative controls –> consultation of TR → modification of the protocol
19.09.2014 Fabian IPG preparation of large scale E. coli cultures For mass spectometric analyses, large amounts of bacteria with T4MBP are needed. Therefore 2 l of Origami 2 with pASK_T4MBP and 0,25 mM cadmium were prepared. The chassis Origami 2 with and without cadmium are used as controls (2 l each). Induction of proteinexpression with anhydrotetracycline. Growing at 25 °C for 3 d to reach a high OD
19.09.2014 Fabian IPG transformation of pASK (no insert) into Origami 2 Analyses showed that a comparable expression system for pASK_T4MBP is needed. Therefore chemical competent cells were made. Transformation via heat shock, incubation over weekend at 16 °C
19.09.2014 Kathi IPG insertion of rcf21 plasmid isolation from ONC; digestion of pORE-E3 (without XhoI and BglII-site) with MluI and BamHI; Annealing two primers (3 and 4) to build the rcf; phosphorylation of primer construct; dephosphorylation of digested vector. ligation of vector and insert; transformation of XL1-Blue Competent Cells. incubation over night (25 °C)
19.09.2014 Steffen IPG plasmidpreparation and sequencing -plasmidprep of ONC (red/white colony pSB1C3) and colony T4MBP

-sequencing with primer 16, T4MBP sequenced with primer 16/17
18.09.2014 Fabian IPG physiological test of T4MBP activity Origami 2 with pASK_T4MBP at different cadmium concentrations (1-0 mM) were analyzed. At 0.2 mM high grow rates were observed. In comparison to Origami 2 without T4MBP no significant effect of TMBP was seen. Problem: induction of proteinexpression reduces growth rates. Another inducible protein in Origami 2 is needed for comparison.
18.09.2014 Kathi IPG insertion of rcf21 digestion of pORE-E3 (without XhoI- and BglII-site). There was no DNA → inoculation of an ONC
18.09.2014 Steffen IPG colony-PCR -colony-PCR using E. coli colonies (16.09.2014). Using Primer 16 and 17. Detection of 1 positive clone TMBP

-red and white colonies growed (pSB1C3) colony-PCR
17.09.2014 Fabian, Steffen IPG immunostain Immunostaining blotted PVDF-membranes. Using Strep-Tag antibody and His-Tag antibody. Anti-Strep shows specific signal at 37 kD. Anti-His show signal at 37 kD as well. His was used as positive controll. Anti-Strep obviously works. Wanted protein is found in inclusion bodies and supernatant.
17.09.2014 Kathi, Björn IPG insertion of rcf21 colony-PCR with primer 1261 and 488 → all 60 colonies were negative → digestion went probably wrong. isolation of plasmid form another overnight culture via handprep
16.09.2014 Fabian, Steffen IPG SDS-PAGE, Western Blot Testing new Strep-Tag antibody. Using pASK_T4MBP in Origami2 to produce protein. Harvesting protein via ultrasound sonification. Testing protein pellet and supernatant. Runs discontinuous SDS-PAGE. Blotting porteins on PVDF. Checking transfer via Ponceau-stain. Blocking membrane over night with Roti-Block
16.09.2014 Kathi, Björn IPG insertion of rcf21 plasmid isolation from ONC; digestion of pORE-E3 (without XhoI and BglII-site) with MluI and BamHI; Annealing two primers (3 and 4) to build the rcf; phosphorylation of primer construct; dephosphorylation of digested vector. ligation of vektor and insert; transformation of XL1-Blue Competent Cells.
16.09.2014 Steffen IPG saving linearized pSB1C3 into E. coli and transformation of E. coli -1.) ligation reactions with/without ligase 2.) ligation for 1h at room temperature 5.) Transformation of XL1-Blue Competent Cells via heat-shock using 10 µl ligation reaction 6.) selection on chloramphenicol

–1.)Transformation of XL1-Blue Competent Cells via heat-shock using 5 µl ligation reaction 11.09.2014 2.) selection on chloramphenicol
15.09.2014 Kathi, Björn IPG insertion of rcf21 digestion of pORE-E3 (without XhoI and BglII-site). There was no DNA → inoculation of an overnight culture
15.09.2014 Fabian Botany selection of transformed A. thaliana seeds Sterilized the harvested A. thaliana seeds (09.09.2014) with ethanol. Plated the seed on Murashige & Skoog media with 2 % sucrose and 15 µg/ml phosphinothricin as selection. Stored them for 2 days at 4 °C. Put at 20 °C until germination
12.09.2014 Steffen IPG colony-PCR and sequencing results -Colony-PCR using E. coli colonies (11.09.2014). Using Primer 16 and 17. Detection of 0 positive clone Expansin/TMBP

-results of expansin and CBD are positive
11.09.2014 Anke, Lisa IPG plasmidpreparation and sequencing
11.09.2014 Steffen, Anke IPG growth curves of Origami 2 pASK, cloning T4MBP, CBD into pSB1C3 (shipping vector) and plasmidpreparation/sequencing -Growth of Origami 2 pASK in media containing five different cadmium concentration, measured the OD600 over a period of 7 hours (7 measurements)

-1.) PCR-Purification of PCR-products (10.09.2014) 2.) Restriction digest of PCR-product and pSB1C3 with FastDigest EcoRI and PstI 3.) Purification of digested products 4.) Ligation for 1 h at room temperature 5.) Transformation of XL1-Blue Competent Cells via heat-shock using 5 µl ligation reaction 6.) selection on chloramphenicol

-plasmidprep (before Glystocks prepared) overnigth culture positive colonies Expansin/CBD–>sequencing with primer 16
10.09.2014 Steffen IPG colony-PCR -Colony-PCR using E. coli colonies (09.09.2014). Using Primer 16 and 17. Detection of 1 positive clone Expansin

-overnight culture positive colonies CBD/Expansin
09.09.2014 Fabian, Anke Biophysics confocal microscopy Microscopy of transformed B. sinuspersici and N. tabacum from 04.09.2014.
09.09.2014 Steffen IPG colony-PCR -Colony-PCR usingE. coli colonies (08.09.2014). Using Primer 16 and 17. Detection of 1 positive clone CBD

-1.)Transformation of XL1-Blue Competent Cells via heat-shock using 5 µl ligation reaction 5.09.2014 2.) selection on chloramphenicol
08.09.2014 Fabian, Steffen Botany harvesting of transgenic seeds from A. thaliana Harvesting of mature seeds of transformed plants (transformation date: 31.07.2014)
08.09.2014 Steffen IPG transformation of E.coli Xl1-blue with pSB1C3 1.)Transformation of XL1-Blue Competent Cells via heat-shock using 5 µl ligation reaction 5.09.2014 2.) selection on chloramphenicol
05.09.2014 Steffen IPG cloning T4MBP, Expansin, CBD into pSB1C3 (shipping vector) FastDigest enzymes tested (expansin digested/not digested run on 2.5% gel)–>showed that digestion was positive

1.) PCR-Purification of PCR-product (4.09.2014) 2.) Restriction digest of PCR-product and pSB1C3 with FastDigest EcoRI and PstI 3.) Purification of digested products 4.) Ligation for 1 h at room temperature
04.09.2014 Fabian Botany transient plant transformation A. tumefaciens mediated transformation of B. sinuspersici and N. tabacum. Used constructs: pORE_Expa~GFP~CBD, pEarley103_GFP, pEarley103_Plmamembranemarker. Using leaf infiltration for tobacco and vacuum ilfiltration for Bienertia.
03.09.2014 Steffen IPG colony-PCR Colony-PCR using E. coli colonies (02.09.2014). Using Primer 16 and 17. Detection of 0 positive clones
02.09.2014 Steffen IPG cloning T4MBP, Expansin, CBD into pSB1C3 (shipping vector) 1.) PCR-Purification of PCR-product (1.09.2014) 2.) Restriction digest of PCR-product and pSB1C3 with NEB EcoRI and PstI 3.) Purification of digested products 4.) Ligation for 1 h at room temperature 5.) Transformation of XL1-Blue Competent Cells via heat-shock and selection on chloramphenicol
01.09.2014 Fabian, Steffen, Anke, Andi Biophysics confocal microscopy Microscopy of transformed B. sinuspersici and N. tabacum from 29.08.2014.
29.08.2014 Fabian Botany transient plant transformation A. tumefaciens mediated transformation of B. sinuspersici and N. tabacum. Used constructs: pORE_Expa~GFP~CBD, pEarley103_GFP, pEarley103_Plmamembranemarker. Using leaf infiltration for tobacco and vacuum infiltration for Bienertia.
27.08.2014 Melanie, Lisa IPG plasmidpreparation and sequencing.v1 plasmidprep with 12 colonies, double digest (XhoI and NcoI), all probes on gel, 7 might be without BglII AND XhoI → sequencing with primer ??? (IPG) positive → pORE_E3 2x35S (without T4MPB) and without BglII- and XhoI-site
26.08.2014 Melanie IPG ONC of 13 colonies (12+1 pos. control) several colonies on each plate (including pos. control), pick of 3 to 4 per plate, ONC
25.08.2014 Melanie, Lisa IPG ligation, transformation of E. coli with pORE_E3 2x35S (without T4MBP and without BglII-site) ?without? XhoI-site ligation, transformation of XL1-Blue Competent Cells via heat-shock, 3 x plating on Can
22.08.2014 Melanie IPG digest of pORE_E3 2x35S (without T4MBP and without BglII-site) with XhoI, proofreading PCR digest of pORE_E3 2x35S (without T4MPB and without BglII-site) with XhoI for 1h 37 °C showed complete digestion; proofreading-PCR to avoid A-Tailing (Phusion)
22.08.2014 Fabian Botany colony-PCR Colony-PCR using E. coli colonies (20.08.2014). Using Primer 11 (AG Offermann) and 1261. Detection of 15 positive clones. Using 3 colonies for ONC
21.08.2014 Fabian Botany cloning Expa~GFP~CBD into pORE 1.) PCR-Purification of PCR-product (19.08.2014) 2.) Restriction digest of PCR-product and pORE E3 2x35S with BamHI and MluI 3.) Gelelectrophoresis 4.) Gelextraction of digested vector and PCR-product 5.) Ligation for 1h 6.) Transformation of XL1-Blue Competent Cells via heat-shock and selection on kanamycin
20.08.2014 Melanie IPG sequencing.v3 (new primer) sequencing with primer 1356 was positive → BglII-site destroyed
20.08.2014 Kathi, Björn IPG insertion of T4MBP in pASK sequencing confirms the insertion of T4-MBP in pASK
19.08.2014 Fabian Botany Phusion PCR Phusion PCR using Expa~GFP~CBD-sequence from EMP as template
19.08.2014 Melanie IPG sequencing.v2 (same primer) sequencing with primer 1261 (IPG) again stopped 10 bp before BglII-site, no definite result → again
18.08.2014 Kathi, Björn IPG insertion of T4MBP in pASK sequencing of pASK with T4MBP not long enough
15.08.2014 Lisa IPG plasmidpreparation and sequencing.v1 plasmidprep with 10 colonies, digest with BglI (twice), poor results, only 2 probes on gel, 1 might be without BglII → sequencing with primer 1261 (IPG) of this probe stopped 10 bp before BglII-site, no definite result → again
14.08.2014 Kathi IPG insertion of T4MBP in pASK plasmid isolation → shipping to Seqlab
13.08.2014 Kathi IPG insertion of T4MBP in pASK colony PCR with primers 729 and 734 → one positive colony → ONC
13.08.2014 Melanie, Lisa IPG ONC of 10 colonies (9+1 pos. control) several colonies on each plate (including pos. control), pick of 3 per plate, ONC
12.08.2014 Melanie IPG transformation of E. coli with pORE_E3 2x35S (without T4MBP) ?without? BglII via heat-shock, 3 x plating on Can
12.08.2014 Kathi, Björn IPG insertion of T4MBP in pASK Preparations of XL1-Blue Competent Cells; transformation of XL1-Blue Competent Cells with ligation mixture
11.08.2014 Kathi IPG insertion T4MBP in pASK amplification of T4MBP with primers 8 and 9. Addition of EcoRI und NcoI sites via Primers; puriciation of PCR reaction mixture via kit; digestion of pASK and amplificat with EcoRI and NcoI; ligation over night (16 h, 16°C)
11.08.2014 Melanie, Lisa IPG digest of pORE_E3 2x35S (without T4MBP) with BglII, proofreading PCR, ligation digest of pORE_E3 2x35S (without T4MPB) with BglII for 1h 37 °C showed complete digestion; proofreading-PCR to avoid A-Tailing (Phusion), ligation
11.08.2014 Kathi, Björn IPG insertion of T4MBP in pASK amplification of T4MBP by adding EcoRI and NcoI sites with the primers 8 and 9; digestion of amplificat and pASK vector with EcoRI and NcoI; simulatnous dephosphorlyation of pASK, ligation of pASK and T4-MBP (16 h, 16 °C)
10.08.2014 Andi IPG immunostain.v2 see 07.08; still no difference between control and samples; 9 min are enough for the final incubation of substrate buffer
09.08.2014 Andi IPG colony-PCR, SDS-PAGE.v2 with oligonucleotides 729, 734 (BCH) & Ta = 48 °C (1:30 Min)
08.08.2014 Andi IPG plasmid-isolation, pASK-traformation.v2 Isolation of pORE-E3 for future cloning and EMP_in_pMA_Colony1 for sequencing. Transformation of Kathis and Björns ligation-product in freshly prepared heatshock competent BL21 (DE3) pLyss cells.
08.08.2014 Kathi, Björn IPG insertion of T4MBP in pASK isolation of pASK from overnight culture
07.08.2014 Andi IPG immunostain, colony-PCR, ONC polyclonal anti-Flag-antibody were used as primary, and anti-rabbit alkaline phosphatase as secondary antibody (both 1:2000 diluted). after incubating the substrate buffer for 13 min, the same signals (all over the lanes; very unspecific) were observed in the samples and control, respectively. We were not sure, if problems in the sample handling are the cause for that, and suggest a repetition. Although colony-PCR (F1+R1) confirmed the insertion of GFP, another primer set (BCH: 1101+625) targeting the backbone of pMA did not bind in the colony, but showed a not expected amplificate length of ~1200 bp in the negative control (expected for pMA: ~1600 bp) ONC of pORE-E3,
07.08.2014 Kathi, Björn IPG insertion of T4MBP in pASK only colonies on positive control → again inoculation of overnight culture
06.08.2014 Anke, Andi IPG SDS-PAGE, Coomassie-stain & Blotting The volume of cellulose-bound protein samples were reduced by direct application of „Polyethylenglykol 6000“ on top of the tube. All samples were loaded into a 12 % SDS-PAGE.
06.08.2014 Kathi, Björn IPG insertion of T4MBP in pASK Amplification of CDS (without HIS-TAG) with primers 8 and 9 (Botany) via Phusion. Purification of the product with „Wizard-PCR and Gel Kit) Double digest of PCR product and pASK vector with EcoRI and NcoI for 30 min. Purification of both samples. Poor results. Ligation of insert and pASK for 2 h (22 °C); transformation over night (37 °C)
05.08.2014 Andi IPG cellulose-bound-protein GFP_in_pMA_EMP2 Dialyzing four times to remove Urea from the cellulose samples (1x overnight, 2x during the day, 1x overnight). Repetion of EMP-PCR(2) reaction mix no. 2 (protocol of Anke). After an agarosegel confirmed the correct fragment length, the reaction mix was purfied using the „Wizard-Kit“ (BCH), phosphorylated and ligated overnight according to Ankes protocol.
05.08.2014 Kathi, Björn IPG insertion of T4MBP in pASK Isolation of Plasmid (pORE_E3_2x35S_Expa_T4MBP_CBD) from E. coli overnight culture via Plasmidprep. MiniKit (Firma?). Amplification of CDS (without HIS-TAG) with Primers 8 and 9 (Botany) via Phusion. → did not work → again
04.08.2014 Anke, Andi IPG isolation of transient expressed protein from N. tabacum Isolation of cellulose-bound and unbound protein from N. tabaccum. The material was cooled by liquid nitrogen, automatically macerated by „Precellys“ and resuspended in 1 x SDS-sample buffer. Per plant one sample was taken. The debris-pellet from centrifugation was washed with ddH20 two times and incubated in 1 ml 8 M Urea overnight.
31.07.2014 Steffen, Fabian Botany floral dip transformation of A. thaliana Transformation of A. thaliana via Floral Dip by using A. tumefaciens as vector. Construct: pORE_E3_2x35S_Expa_T4MBP_CBD
31.07.2014 Anke, Björn IPG transient transformation of N. tabacum with pORE_E3_2x35S_Expa_TMBP_CBD transient Transformation of 5 N. tabacum plants with pORE_E3_2x35S_TMBP in GV1301 and 4 plants without GV1301. Using 1ml / leave and two leaves / plant.
25.07.2014 Anke IPG colony-PCR of EMP2-transformation Colony-PCR with primers 1011 and 625 (IPG) and 10 new colonies. Poor result…
23.07.2014 Anke IPG colony-PCR of EMP2-transformation Colony-PCR with primers 1011 and 625 (IPG). Poor result….
22.07.2014 Anke IPG transformation of E. coli with EMP2 Transformation of XL1-Blue Competent Cells
21.07.2014 Anke,
Andi
IPG EMP 2 GfP Screening the functional amount of megaprimer with and without F1: 20 ng Megaprimer + F1 + R2
21.07.2014 Fabian Botany colony-PCR of Agor-Trafo Colony-PCR with primer 11 (AG Offermann and 1484). Poor result, proabably of too high annealing temperature. New colony-PCR with 11 and 1261. Prepare 2 days cultures for Arabidopsis transformation
18.07.2014 Anke IPG EMP 1 GfP EMP1 with F1, R2 and GFP-vector to genererate Megaprimer. Result is fine.
18.07.2014 Fabian Botany transformation of Agrobacterium with pORE_E3_2x35S_Expa_TMBP_CBD Using electrocompetent GV3101 cells.
17.07.2014 Steffen, Fabian Botany plasmidpreparation and sequencing Using ONC of E. coli with pORE and insert. Plasmidprep via Thermo Kit. Sequencing from both directions with primer 11 (AG Offermann) and 1261. Poor results for reverse direction. Resequencing of reverse sequence with 1484
15.07.2014 Steffen, Fabian Botany colony-PCR of pORE with Insert Taq-PCR of 27 colonies using primer 11 of AG Offermann (binds to 35S) and 1012. Poor result, wrong reverse primer used. Doing new colony PCR with other reverse primer 1261 (binds to NOS-terminator. Result is fine. ONC
14.07.2014 Steffen, Fabian Botany cloning of CDS (Expa_T4MBP_CBD) into pORE2x35S 1. PCR-Purification of Phusion-PCR (11.7) to get rid of disturbing enzymes. 2.) double digest of purified PCR-product and vector with MluI and BamHI for 1 h. 3.) Preparative Gelelctrophoresis. Cutting out specific bands. 4.) Gelextraction. 5.) Ligation of digested insert and vector for 1 h. 6.) Transformation of chemical competent E. coli DH5alpha with ligated DNA via heatshock
11.07.2014 Fabian Botany amplification of CDS from polyprotein Phusion-PCR. Using Geneart-Shipping vector with insert as template. Primers 106 and 859
03.07.2014 Kathi IPG negative colony-PCR (continued by Fabian and Steffen)
02.07.2014 Kathi IPG repetition of day 27.06.2014: Transformation of XL1blue with T4MBP in pORE-E3 with 35S-Promotor
01.07.2014 Kathi IPG due to unsuccessful transformation repetition of day 26.06.2014: ligation of T4MBP with pORE-E3 with 35S-Promotor Digestion of pASK with T4MBP and pORE-E3 with 2x35S promotor with MluI and BamHI, overnight ligation
30.06.2014 Andi IPG sequencing Bielefelder-CBDs Sequencing (Seqlab/ Microsynth) was done with primer no. 611 (GCTGGCCTTTTGCTCAGATGTTCTTTCCTGCGTTATC) and revealed that the obtained sequencing result matched the given sequence online
30.06.2014 Kathi IPG negative colony-PCR
27.06.2014 Kathi IPG transformation of XL1-Blue with T4MBP in pORE-E3 with 35S-Promotor
26.06.2014 Kathi IPG ligation of T4MBP with pORE-E3 with 35S-Promotor Digestion of pASK with T4MBP and pORE-E3 with 2x35S promotor with Mlu1 and BamHI, overnight ligation
26.06.2014 Kathi IPG plasmidpreparation of pASK Digestion of pASK with T4MBP and pORE-E3 with 2x35S promotor with Mlu1 and BamHI, overnight ligation
25.06.2014 Kathi IPG colony-PCR of transformated XL1blue with T4MBP in pASK Primer for colony PCR: T7 and BackSeq-pGII
24.06.2014 Kathi IPG transformation to back up the synthesised T4MBP located in pASK vector Transformation of XL1-Blue Competent Cells
24.06.2014 Melanie IPG linearization of Bielefelder-CBDs
linearizing BBa_K863101 & BBa_K863111
24.06.2014 Melanie, Andi IPG isolation of Bielelfelder-CBDs Isolating BBa_K863101 & BBa_K863111 with PeqGOLD Plasmid Miniprep Kit by PeqLab GmbH and selfmade solutions
20.06.2014 Andi IPG ONC of Bielefelder-CBDs Culturing XL1 containg pSB1C3 plasmid with parts BBa_K863101 & BBa_K863111 in 10 ml LB medium and 10 µl Chloramphenicol
19.06.2014 Fabian Botany plasmidpreparation Preparation of the 3 E. coli clones which were expected to have the right insert (using Thermo Mini-Prep Kit). Plasmids of one all 3 clones were send for sequencing, using Primer 1011 (IPG). Sequencing worked fine. All 3 clones have the insert at the right position
18.06.2014 Fabian Botany new colony-PCR New Colony-PCR for detecting transformed E. coli clones. Using primers 1011 and 1012 (IPG). Detecting 3 positive clones wich were used for over-night cultures
16.06.2014 Fabian Botany plasmidpreparation Preparation of 2E. coli clones wich were expected to have the right insert (using Thermo Mini-Prep Kit). Plasmid of one clone was send for sequencing, using Primer 962 (IPG). Sequencing didn't work (second sequncing trial by seqlab failed as well). Probably Primer 962 isn't working (even without 2x35S insertion sequencing should have work)
13.06.2014 Fabian Botany colony-PCR Colony-PCR for detecting transformed E. coli clones. Using amplification primers 01 and 02 AND 1011 (IPG). Colony-PCR worked more or less, results were interpreted wrongly. False clones were used for over-night cultures
12.06.2014 Fabian Botany digest, ligation and transformation of 2x35S into pORE 1) Gelextraction of 2x35S (using Qiagen-Kit). 2) Digest of 2x35S and pORE with XhoI and BamHI (37 °C for 1 h). 3) Gelelectophoresis for separation of cutted pORE, using the large fragment (Gelextraction). 4) Ligation of 2x35S and pORE (using T7-Ligase). 5) Transformation of chemical competent E. coli DH5-Alpha and plating on LB-plates with Kanamycin
10.06.2014 Fabian Botany amplification of 2x35S Promotor Using Primer 01 and 02 to amplify 2x35S promotor from template DNA. Separation of fragments via gelelectophoresis and preparation on fragments from the gel
21.05.2014 Fabian Botany BamHI, MluI-digest Analysing if both Enzymes (BamHI and MluI) cut while double digesting pORE E3
19.05.2014 Anke IPG - Preparing Glystock
19.05.2014 Steffen, Fabian Botany - plasmid isolation pORE-E3
16.05.2014 Steffen, Andi IPG „over-weekend“- culture pORE-E3 Culturing JM109 bacteria cells containing pORE-E3 (250 µM from Glystock) in 10 ml LB media including 10 µM Kanamycin (Stock?) over weekend at 27 °C