Maerkl:Back Door

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Instruments

Lab Server

Qarray2

Arrayworx

Nikon Ti-E

Thermocyclers

Microplate Incubator

Group Meeting

Fridays, 11am in AI 2142

Agenda

Jan. 16th topics: journal club, lab duties, new lab in general (to do list, items we need, ...)

Jan. 30th: cold storage, equipment update, DNA oligos,

Journal Club

  • Nature (weekly) (Marcel)
  • Science (weekly) (Nicolas)
  • Cell (bi-weekly) (Alina)
  • PNAS (weekly) (Arun)
  • PLOS (bio + compbio)(monthly) (Alina)
  • Nature Methods (monthly) (Sylvie)
  • Nature Biotech (monthly) (Meltem)
  • Mol Sys Bio (monthly) (Sylvie)
  • Nucleic Acid Res (bi-weekly)
  • JACS (weekly) (Luis)
  • Lab on a Chip (monthly) (Meltem, Luis)
  • Analytical Chemistry (Luis)
  • PRL (Lina)
  • Nature Photonics (Lina)

Lab Duties

Webpages (Sebastian)

  • update content (Sebastian)
  • handle useraccounts (Sebastian)

Cold Storage (Nicolas)

  • organize storage -> Nicolas
  • defrost when necessary -> Nicolas

Common supply / Lab consumables

  • PDMS -> Nicolas
  • Chemicals & solvents -> Arun
  • pipette tips, gloves, cell culture PW, 15ml/50ml falcons, filters, syringes, eppendorf tubes, PCR -> Sylvie, Marcel

Equipment care (rotate, revisit)

  • Qarray2 / QPix2 / QFill -> Nicolas
  • ArrayWorx -> Marcel
  • Autoclave --> Sylvie
  • Millipore System, PDMS Spinner --> Arun

Chemical Inventory (Arun)

  • cont. update (Arun)
  • handle MSDS (Arun)

Lab Server (Nicolas)

  • manage backups
  • keep it running
  • manage user accounts
  • etc.

Mail and packaging material (garbage) (Rotation schedule: Arun, Sylvie, Nicolas, Marcel)

IT

FTP server

Lab folder: stisrv.epfl.ch/ibi2/lbnc

E-buying

How to subscribe to our mailing list

Journals

Search Engines

Editing Wikis:

Calendar

All Calendars

To Do List

  • Equipment to order:
    • Microplate Reader (SM)
      • Spectramax M2e or similar
    • Second Jenkons Incubator (SM)
    • High-content plate incubator (Nicolas and Sylvie)
    • Speed-Vac (SM)
  • Misc items to order:
    • Coffee machine (bean based machine, quote + expected cost, place)

Reading List

Sylvie:

  1. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, and Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006 Mar 30;440(7084):637-43. DOI:10.1038/nature04670 | PubMed ID:16554755 | HubMed [Krogan-2006]
  2. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, and Weissman JS. Global analysis of protein expression in yeast. Nature. 2003 Oct 16;425(6959):737-41. DOI:10.1038/nature02046 | PubMed ID:14562106 | HubMed [Ghae-2003]
  3. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, and Sakaki Y. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):1143-7. PubMed ID:10655498 | HubMed [Ito-2001]
  4. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, and Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74. DOI:10.1073/pnas.061034498 | PubMed ID:11283351 | HubMed [ito-2000]
  5. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, and Rothberg JM. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000 Feb 10;403(6770):623-7. DOI:10.1038/35001009 | PubMed ID:10688190 | HubMed [Uetz-2000]
  6. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sørensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, and Tyers M. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002 Jan 10;415(6868):180-3. DOI:10.1038/415180a | PubMed ID:11805837 | HubMed [Ho-2002]
  7. Jones RB, Gordus A, Krall JA, and MacBeath G. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature. 2006 Jan 12;439(7073):168-74. DOI:10.1038/nature04177 | PubMed ID:16273093 | HubMed [Jones-2006]
  8. Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau AY, Walter JC, and LaBaer J. Self-assembling protein microarrays. Science. 2004 Jul 2;305(5680):86-90. DOI:10.1126/science.1097639 | PubMed ID:15232106 | HubMed [Ramachandran-2004]
  9. Gavin AC, Bösche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, and Superti-Furga G. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002 Jan 10;415(6868):141-7. DOI:10.1038/415141a | PubMed ID:11805826 | HubMed [Gavin-2002]
  10. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, and Snyder M. Global analysis of protein activities using proteome chips. Science. 2001 Sep 14;293(5537):2101-5. DOI:10.1126/science.1062191 | PubMed ID:11474067 | HubMed [Zhu-2001]
  11. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, and Snyder M. Global analysis of protein phosphorylation in yeast. Nature. 2005 Dec 1;438(7068):679-84. DOI:10.1038/nature04187 | PubMed ID:16319894 | HubMed [Ptacek-2005]
  12. Sachs K, Perez O, Pe'er D, Lauffenburger DA, and Nolan GP. Causal protein-signaling networks derived from multiparameter single-cell data. Science. 2005 Apr 22;308(5721):523-9. DOI:10.1126/science.1105809 | PubMed ID:15845847 | HubMed [Sachs-2005]
  13. Tarassov K, Messier V, Landry CR, Radinovic S, Serna Molina MM, Shames I, Malitskaya Y, Vogel J, Bussey H, and Michnick SW. An in vivo map of the yeast protein interactome. Science. 2008 Jun 13;320(5882):1465-70. DOI:10.1126/science.1153878 | PubMed ID:18467557 | HubMed [Tarassov-2008]
All Medline abstracts: PubMed | HubMed

Nicolas:

  1. Di Carlo D, Aghdam N, and Lee LP. Single-cell enzyme concentrations, kinetics, and inhibition analysis using high-density hydrodynamic cell isolation arrays. Anal Chem. 2006 Jul 15;78(14):4925-30. DOI:10.1021/ac060541s | PubMed ID:16841912 | HubMed [Ryley-2006]
  2. Ryley J and Pereira-Smith OM. Microfluidics device for single cell gene expression analysis in Saccharomyces cerevisiae. Yeast. 2006 Oct-Nov;23(14-15):1065-73. DOI:10.1002/yea.1412 | PubMed ID:17083143 | HubMed [Carlo-2006]
  3. Charvin G, Cross FR, and Siggia ED. A microfluidic device for temporally controlled gene expression and long-term fluorescent imaging in unperturbed dividing yeast cells. PLoS One. 2008 Jan 23;3(1):e1468. DOI:10.1371/journal.pone.0001468 | PubMed ID:18213377 | HubMed [Charvin-2008]
  4. Lamprecht MR, Sabatini DM, and Carpenter AE. CellProfiler: free, versatile software for automated biological image analysis. Biotechniques. 2007 Jan;42(1):71-5. PubMed ID:17269487 | HubMed [Carpenter-2006]
  5. Bennett MR, Pang WL, Ostroff NA, Baumgartner BL, Nayak S, Tsimring LS, and Hasty J. Metabolic gene regulation in a dynamically changing environment. Nature. 2008 Aug 28;454(7208):1119-22. DOI:10.1038/nature07211 | PubMed ID:18668041 | HubMed [Bennett-2008]
  6. Di Talia S, Skotheim JM, Bean JM, Siggia ED, and Cross FR. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature. 2007 Aug 23;448(7156):947-51. DOI:10.1038/nature06072 | PubMed ID:17713537 | HubMed [DiTalia-2007]
  7. Chin CS, Chubukov V, Jolly ER, DeRisi J, and Li H. Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. PLoS Biol. 2008 Jun 17;6(6):e146. DOI:10.1371/journal.pbio.0060146 | PubMed ID:18563967 | HubMed [Chin-2008]
  8. Skotheim JM, Di Talia S, Siggia ED, and Cross FR. Positive feedback of G1 cyclins ensures coherent cell cycle entry. Nature. 2008 Jul 17;454(7202):291-6. DOI:10.1038/nature07118 | PubMed ID:18633409 | HubMed [Skotheim-2008]
  9. Shcheprova Z, Baldi S, Frei SB, Gonnet G, and Barral Y. A mechanism for asymmetric segregation of age during yeast budding. Nature. 2008 Aug 7;454(7205):728-34. DOI:10.1038/nature07212 | PubMed ID:18660802 | HubMed [Shcheprova-2008]
  10. Orlando DA, Lin CY, Bernard A, Wang JY, Socolar JE, Iversen ES, Hartemink AJ, and Haase SB. Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature. 2008 Jun 12;453(7197):944-7. DOI:10.1038/nature06955 | PubMed ID:18463633 | HubMed [Orlando-2008]
  11. Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, Altman RB, Davis RW, Nislow C, and Giaever G. The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science. 2008 Apr 18;320(5874):362-5. DOI:10.1126/science.1150021 | PubMed ID:18420932 | HubMed [Hillenmeyer]
  12. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, and O'Shea EK. Global analysis of protein localization in budding yeast. Nature. 2003 Oct 16;425(6959):686-91. DOI:10.1038/nature02026 | PubMed ID:14562095 | HubMed [Huh-2003]
All Medline abstracts: PubMed | HubMed