27 August 2015 Kominist presented his master thesis: “Developing Molecular Tools to Genetically Engineer the Microlaga Nannochloropsis” Well done Master Kominist!
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NanoTechnology & NanoImaging
Imaging and manipulating structures at the nanometer scale are crucial skills for developing novel materials. Macromolecular assemblies that have a large range of functionalities are natively produced by bacteria and can be altered to adapt to new functionalities. NanoStructures We use use bacteria to generate native and synthetic nanostructures that may be used for electron transport (nanowires/pili) and probes (ferritin).…
Chlorophyllide reductase
Genes in Chlorophyllide reductase SYNPCC7002_A0210 por light-dependent protochlorophyllide reductase SYNPCC7002_A1652 ChlB light-independent protochlorophyllide reductase, B subunit SYNPCC7002_A2345 ChlN light-independent protochlorophyllide reductase, N subunit SYNPCC7002_A2347 ChlL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein to delete: SYNPCC7002_A1652, SYNPCC7002_A2345, SYNPCC7002_A2347 He Q, Brune D, Nieman R, Vermaas W (1998) Chlorophyll alpha synthesis upon interruption and deletion of por coding for the light-dependent NADPH: protochlorophyllide…
photosystems & chlorophyll
PsbA SYNPCC7002_A0157 photosystem q(b) protein X SYNPCC7002_A1418 photosystem q(b) protein X SYNPCC7002_A2164 photosystem q(b) protein X PsbB SYNPCC7002_A2199 photosystem q(a) protein X SYNPCC7002_A1560 photosystem q(a) protein SYNPCC7002_A1559 psbC Replace PsaA/B with CT2020/19 and check if there is phototrophic growth? PsaA SYNPCC7002_A1961 PsaB SYNPCC7002_A1962 CT2020 photosystem P840 reaction center, large subunit CT2019 photosystem photosystem P840 reaction center iron-sulfur protein from: Learning…
tRNA
Pipeline: tRNA identification and characterization Workflow _1_ acquire/access data _2_ detect tRNAs in data _3_ assign Operational Taxonomy Units (OTG for each tRNA) _4_ determine MFE (free energy for each tRNA) _5_ create output file (for each tRNA) DETAILS _1_ acquire/access data _Sources __genome __Biosample __Bioproject __GSS _Question __How to access data source (local versus NCBI server) _2_ detect…
Synecho7002 tools
Neutral sites– strains with neutral sites Inducable promotor: – XylS/Pm – Ara Selection cassettes – positive selection (antibiotics) – negative selection (counterselection) : see http://2012.igem.org/Team:Edinburgh/Project/Non-antibiotic-Markers/Plac-RFP-SacB Antibiotic resistance background strains – strains with antibiotic casettes Reporter genes – GFP / YFP – Spinach Strains – Phycobilin-deficient strain – Photosystem I / II-deficient strain
Phycobilins7002
17 genes identified containing phyco* in cyanobase for Syn7002 SYNPCC7002 SYNPCC7002_A0348 definition phycobiliprotein lyase related protein, HEAT-like repeat SYNPCC7002 SYNPCC7002_A0639 definition phycocyanin-associated phycobilisome rod-core linker polypeptide SYNPCC7002 SYNPCC7002_A0811 definition Phycobilisome rod-core linker polypeptide cpcG (L-RC 28.5) SYNPCC7002 SYNPCC7002_A1631 definition allophycocyanin beta-18 subunit SYNPCC7002 SYNPCC7002_A1821 definition putative phycobilisome degradation protein SYNPCC7002 SYNPCC7002_A1928 definition allophycocyanin-associated phycobilisome 7.8-kDa core-linker polypeptide SYNPCC7002 SYNPCC7002_A1929 definition…
Neutral sites Syn7002
-> between: SYNPCC7002_A0935 and SYNPCC7002_A0936 Davies FK, Work VH, Beliaev AS, Posewitz MC (2014) Engineering Limonene and Bisabolene Production in Wild Type and a Glycogen-Deficient Mutant of Synechococcus sp. PCC 7002. Front Bioeng Biotechnol 2:21 http://www.ncbi.nlm.nih.gov/pubmed/25152894 -> glpK (SYNPCC7002_A2842) Begemann MB, Zess EK, Walters EM, Schmitt EF, Markley AL, Pfleger BF (2013) An organic acid based counter selection system for…
Carotenoids
for absorption spectra, MS spectra, masses and references: http://epic.awi.de/view/creators/Jeffrey=3AS=2E_W=2E=3A=3A.html Phytoplankton Pigments in Oceanography: Guidelines to Modern Methods