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2014 List of papers we read
    1. Mao K, Wang K, Liu X, Klionsky DJ. (2013) The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Dev Cell., 26(1), 9-18.
    2. Blamowska M, Neupert W, Hell K. (2012) Biogenesis of the mitochondrial Hsp70 chaperone. J Cell Biol., 199(1), 123-35.
    3. Weidner J, Wang C, Prescianotto-Baschong C, Estrada AF, Spang A. (2014) The polysome-associated proteins Scp160 and Bfr1 prevent P body formation under normal growth conditions. J Cell Sci., 127(Pt 9), 1992-2004.
    4. Lackner LL, Ping H, Graef M, Murley A, Nunnari J. (2013) Endoplasmic reticulum-associated mitochondria-cortex tether functions in the distribution and inheritance of mitochondria. Proc Natl Acad Sci U S A., 110(6), E458-67.
    5. Lang MJ, Martinez-Marquez JY, Prosser DC, Ganser LR, Buelto D, Wendland B, Duncan MC. (2014) Glucose Starvation Inhibits Autophagy via Vacuolar Hydrolysis and Induces Plasma Membrane Internalization by Down-regulating Recycling. J Biol Chem., 289(24), 16736-16747.
    6. Jin C, Strich R, Cooper KF. (2014) Slt2p phosphorylation induces cyclin C nuclear-to-cytoplasmic translocation in response to oxidative stress. Mol Biol Cell., 25(8), 1396-407.
    7. Dulle JE, Stein KC, True HL. (2014) Regulation of the Hsp104 middle domain activity is critical for yeast prion propagation. PLoS One., 9(1), e87521.
    8. van Zutphen T, Todde V, de Boer R, Kreim M, Hofbauer HF, Wolinski H, Veenhuis M, van der Klei IJ, Kohlwein SD. (2014) Lipid droplet autophagy in the yeast Saccharomyces cerevisiae. Mol Biol Cell., 25(2), 290-301.
    9. Pircher A, Bakowska-Zywicka K, Schneider L, Zywicki M, Polacek N. (2014) An mRNA-derived noncoding RNA targets and regulates the ribosome. Mol Cell., 54(1), 147-55.
    10. Simpson CE, Lui J, Kershaw CJ, Sims PF, Ashe MP. (2014) mRNA localization to P-bodies in yeast is bi-phasic with many mRNAs captured in a late Bfr1p-dependent wave. J Cell Sci., 127(Pt 6), 1254-62.
    11. Cooper KF, Khakhina S, Kim SK, Strich R. (2014) Stress-induced nuclear-to-cytoplasmic translocation of cyclin C promotes mitochondrial fission in yeast. Dev Cell., 28(2), 161-73.
    12. Shah KH, Zhang B, Ramachandran V, Herman PK. (2013) Processing body and stress granule assembly occur by independent and differentially regulated pathways in Saccharomyces cerevisiae. Genetics., 193(1), 109-23.
    13. Zhao H, Li J, Han B, Li X, Chen J. (2014) Improvement of oxidative stress tolerance in Saccharomyces cerevisiae through global transcription machinery engineering. J Ind Microbiol Biotechnol., 41(5), 869-78.
    14. Takuya Inaba, Daisuke Watanabe, Yoko Yoshiyama, Koichi Tanaka, Jun Ogawa, Hiroshi Takagi, Hitomi Shimoi and Jun shima. (2013) An organic acid-tolerant HAA1-overexpression mutant of an industrial bioethanol strain of Saccharomyces cerevisiae and its application to the production of bioethanol from sugarcane molasses AMB Express., 3(1), 74.

2013 List of papers we read
    1. Yazawa H, Iwahashi H, Kamisaka Y, Kimura K, Uemura H. (2010) Improvement of polyunsaturated fatty acids synthesis by the coexpression of CYB5 with desaturase genes in Saccharomyces cerevisiae. Appl Microbiol Biotechnol., 87(6), 2185-93.
    2. Sousa MJ, Rodrigues F, Corte-Real M, Leao C. (1998) Mechanisms underlying the transport and intracellular metabolism of acetic acid in the presence of glucose in the yeast Zygosaccharomyces bailii. Microbiology., 144(Pt3), 665-70.
    3. Hector RE, Bowman MJ, Skory CD, Cotta MA. (2009) The Saccharomyces cerevisiae YMR315W gene encodes an NADP(H)-specific oxidoreductase regulated by the transcription factor Stb5p in response to NADPH limitation. N Biotechnol. , 26(3-4), 171-80.
    4. Doris KS, Rumsby EL, Morgan BA. (2012) Oxidative stress responses involve oxidation of a conserved ubiquitin pathway enzyme. Mol Cell Biol. , 32(21), 4472-81.
    5. Fu J, Hou J, Liu L, Chen L, Wang M, Shen Y, Zhang Z, Bao X. (2013) Interplay between BDF1 and BDF2 and their roles in regulating the yeast salt stress response. FEBS J., 280(9), 1991-2001.
    6. Krumpe K, Frumkin I, Herzig Y, Rimon N, Ozbalci C, Brugger B, Rapaport D, Schuldiner M. (2012) Ergosterol content specifies targeting of tail-anchored proteins to mitochondrial outer membranes. Mol Biol Cell., 23(20), 3927-35.
    7. van Roermund CW, Ijlst L, Majczak W, Waterham HR, Folkerts H, Wanders RJ, Hellingwerf KJ. (2012) Peroxisomal fatty acid uptake mechanism in Saccharomyces cerevisiae. J Biol Chem., 287(24), 20144-53.
    8. Ohdate T, Inoue Y. (2012) Involvement of glutathione peroxidase 1 in growth and peroxisome formation in Saccharomyces cerevisiae in oleic acid medium. Biochim Biophys Acta., 1821(9), 1295-305.
    9. Regot S, de Nadal E, Rodriguez-Navarro S, Gonzalez-Novo A, Perez-Fernandez J, Gadal O, Seisenbacher G, Ammerer G, Posas F. (2013) The Hog1 SAPK targets nucleoporins to control mRNA export upon stress. J Biol Chem., (in press.)
    10. Wu K, Dawe JH, Aris JP. (2000) Expression and subcellular localization of a membrane protein related to Hsp30p in Saccharomyces cerevisiae. Biochim Biophys Acta., 1463(2), 477-82.
    11. Lee YJ, Shi R, Witt SN. (2013) The Small Molecule Triclabendazole Decreases the Intracellular Level of Cyclic AMP and Increases Resistance to Stress in Saccharomyces cerevisiae. PLoS One., 8(5), e64337.
    12. Guan Q, Haroon S, Bravo DG, Will JL, Gasch AP. (2012) Cellular memory of acquired stress resistance in Saccharomyces cerevisiae. Genetics., 192(2), 495-505.
    13. Robert J, Marchesini S, Delessert S, Poirier Y. (2005) Analysis of the beta-oxidation of trans-unsaturated fatty acid in recombinant Saccharomyces cerevisiae expressing a peroxisomal PHA synthase reveals the involvement of a reductase-dependent pathway. Biochim Biophys Acta., 1734(2), 169-77.
    14. Kakoi S, Yorimitsu T, Sato K. (2013) COPII machinery cooperates with ER-localized Hsp40 to sequester misfolded membrane proteins into ER-associated compartments. Mol Biol Cell., 24(5), 633-42.
    15. Motley AM, Nuttall JM, Hettema EH. (2012) Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae. EMBO J., 31(13), 2852-68.
    16. Kim D, Hahn JS. (2013) Roles of Yap1 transcription factor and antioxidants in yeast tolerance to furfural and 5-hydroxymetylfurfural that function as thiol-reactive electrophiles generating oxidative stress. Appl EnvironMicobiol., (in press).
    17. Buchan JR, Kolaitis RM, Taylor JP, Parker R. (2013) Eukaryotic Stress Granules Are Cleared by Autophagy and Cdc48/VCP Function. Cell., 153(7), 1461-74.
    18. Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King D, Shen PS, Weibezahn J, Dunn JG, Rouskin S, Inada T, Frost A, Weissman JS. (2012) A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell, 151(5), 1042-54.
    19. Pan Y, Schroeder EA, Ocampo A, Barrientos A, Shadel GS. (2011) Regulation of yeast chronological life span by TORC1 via adaptive mitochondrial ROS signaling. Cell Metab., 13(6), 668-78.
    20. Aung-Htut MT, Lam YT, Lim YL, Rinnerthaler M, Gelling CL, Yang H, Breitenbach M, Dawes IW. (2013) Maintenance of Mitochondrial Morphology by Autophagy and Its Role in High Glucose Effects on Chronological Lifespan of Saccharomyces cerevisiae. Oxid Med Cell Longev., (in press).
    21. Grousl T, Ivanov P, Malcova I, Pompach P, Frydlova I, Slaba R, Senohrabkova L, Novakova L, Hasek J. (2013) Heat shock-induced accumulation of translation elongation and termination factors precedes assembly of stress granules in S. cerevisiae. PLoS One., e57083. doi: 10.1371.
    22. Lefevre SD, van Roermund CW, Wanders RJ, Veenhuis M, van der Klei IJ. (2013) The significance of peroxisome function in chronological aging of Saccharomyces cerevisiae. Aging Cell., 12(4), 784-93.
    23. Gaspar ML, Hofbauer HF, Kohlwein SD, Henry SA. (2011) Coordination of storage lipid synthesis and membrane biogenesis: evidence for cross-talk between triacylglycerol metabolism and phosphatidylinositol synthesis. J Biol Chem., 286(3), 1696-708
    24. Postnikoff SD, Malo ME, Wong B, Harkness TA. (2012) The yeast forkhead transcription factors fkh1 and fkh2 regulate lifespan and stress response together with the anaphase-promoting complex. PLoS Genet., 8(3), e1002583
    25. Huang HT, Maruyama J, Kitamoto K. (2013) Aspergillus oryzae AoSO is a novel component of stress granules upon heat stress in filamentous fungi. PLoS One., 8(8), e72209.
    26. Silva A, Sampaio-Marques B, Fernandes A, Carreto L, Rodrigues F, Holcik M, Santos MA, Ludovico P. (2013) Involvement of yeast HSP90 isoforms in response to stress and cell death induced by acetic acid. PLoS One., 8(8), e71294.
    27. Qiu Y, Fakas S, Han GS, Barbosa AD, Siniossoglou S, Carman GM. (2013) Transcription factor Reb1p regulates DGK1-encoded diacylglycerol kinase and lipid metabolism in Saccharomyces cerevisiae. J Biol Chem., 288(40), 29124-33.
    28. Hurto RL, Hopper AK. (2011) P-body components, Dhh1 and Pat1, are involved in tRNA nuclear-cytoplasmic dynamics. RNA., 17(5), 912-24.
    29. De Smet CH, Vittone E, Scherer M, Houweling M, Liebisch G, Brouwers JF, de Kroon AI. (2012) The yeast acyltransferase Sct1p regulates fatty acid desaturation by competing with the desaturase Ole1p. Mol Biol Cell., 23(7), 1146-56.

2012 List of papers we read
    1. Arribere JA, Doudna JA, Gilbert WV. (2011) Reconsidering movement of eukaryotic mRNAs between polysomes and P bodies. Mol Cell., 44(5), 745-58.
    2. Schuck S, Prinz WA, Thorn KS, Voss C, Walter P. (2009) Membrane expansion alleviates endoplasmic reticulum stress independently of the unfolded protein response. J Cell Biol., 187(4), 525-36.
    3. Roach C, Feller SE, Ward JA, Shaikh SR, Zerouga M, Stillwell W. (2004) Comparison of cis and trans fatty acid containing phosphatidylcholines on membrane properties. Biochemistry., 43(20), 6344-51.
    4. Rajyaguru P, She M, Parker R. (2012) Scd6 targets eIF4G to repress translation: RGG motif proteins as a class of eIF4G-binding proteins. Mol Cell., 45(2), 244-54.
    5. Li BZ, Yuan YJ. (2010) Transcriptome shifts in response to furfural and acetic acid in Saccharomyces cerevisiae. Appl Microbiol Biotechnol., 86(6), 1915-24.
    6. Ferreira TC, de Moraes LM, Campos EG. (2011) Cell density-dependent linoleic acid toxicity to Saccharomyces cerevisiae. FEMS Yeast Res., 11(5), 1567-1364.
    7. Kurischko C, Kim HK, Kuravi VK, Pratzka J, Luca FC. (2011) The yeast Cbk1 kinase regulates mRNA localization via the mRNA-binding protein Ssd1. J Cell Biol., 192(4), 583-98.
    8. Berchtold D, Piccolis M, Chiaruttini N, Riezman I, Riezman H, Roux A, Walther TC, Loewith R. (2012) Plasma membrane stress induces relocalization of Slm proteins and activation of TORC2 to promote sphingolipid synthesis. Nat Cell Biol., 14(5), 542-7.
    9. Jacquier N, Choudhary V, Mari M, Toulmay A, Reggiori F, Schneiter R. (2011) Lipid droplets are functionally connected to the endoplasmic reticulum in Saccharomyces cerevisiae. J Cell Sci., 124(14), 2424-37.
    10. Beopoulos A, Nicaud JM, Gaillardin C. (2011) An overview of lipid metabolism in yeasts and its impact on biotechnological processes. Appl Microbiol Biotechnol., 90(4), 1193-206.
    11. De Smet CH, Vittone E, Scherer M, Houweling M, Liebisch G, Brouwers JF, de Kroon AI. (2012) The yeast acyltransferase Sct1p regulates fatty acid desaturation by competing with the desaturase Ole1p. Mol Biol Cell., 23(7), 1146-56.
    12. Marr N, Foglia J, Terebiznik M, Athenstaedt K, Zaremberg V. (2012) Controlling lipid fluxes at glycerol-3-phosphate acyltransferase step in yeast: unique contribution of Gat1p to oleic acid-induced lipid particle formation. J Biol Chem., 287(13), 10251-64.
    13. Sweet T, Kovalak C, Coller J. (2012) The DEAD-Box Protein Dhh1 Promotes Decapping by Slowing Ribosome Movement. PLoS Biol., 10(6), e1001342.
    14. Wang CW, Lee SC. (2012) The ubiquitin-like (UBX)-domain-containing protein Ubx2/ Ubxd8 regulates lipid droplet homeostasis. J Cell Sci., (in press.)
    15. Takahara T, Maeda T. (2012) Transient Sequestration of TORC1 into Stress Granules during Heat Stress. Mol Cell., (in press.)
    16. Tanigawa M, Kihara A, Terashima M, Takahara T, Maeda T. (2012) Sphingolipids regulate the yeast high-osmolarity glycerol response pathway. Mol Cell Biol., 32(14), 2861-70.
    17. Liu ZL. (2011) Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysates. Appl Microbiol Biotechnol., 90(3), 809-25.
    18. Bhattacharya S, Shcherbik N, Vasilescu J, Smith JC, Figeys D, Haines DS. (2009) Identification of lysines within membrane-anchored Mga2p120 that are targets of Rsp5p ubiquitination and mediate mobilization of tethered Mga2p90. J Mol Biol., 385(3), 718-25.
    19. Masek T, Valasek L, Pospisek M. (2011) Polysome analysis and RNA purification from sucrose gradients. Methods Mol Biol., 703, 293-309.
    20. Moreira KE, Schuck S, Schrul B, Frohlich F, Moseley JB, Walther TC, Walter P. (2012) Seg1 controls eisosome assembly and shape. J Cell Biol., 193(3), 405-20.
    21. Garcia-Gomez JJ, Babiano R, Lebaron S, Froment C, Monsarrat B, Henry Y, de la Cruz J. (2011) Nop6, a component of 90S pre-ribosomal particles, is required for 40S ribosomal subunit biogenesis in Saccharomyces cerevisiae. RNA Biol., 8(1), 112-24.
    22. Duennwald ML, Echeverria A, Shorter J. (2012) Small heat shock proteins potentiate amyloid dissolution by protein disaggregases from yeast and humans. PLoS Biol., 10(6).
    23. Gomar-Alba M, Jimenez-Marti E, Del Olmo M. (2012) The Saccharomyces cerevisiae Hot1p regulated gene YHR087W (HGI1) has a role in translation upon high glucose concentration stress. BMC Mol Biol., 13(19)
    24. Tudisca V, Simpson C, Castelli L, Lui J, Hoyle N, Moreno S, Ashe M, Portela P. (2012) PKA isoforms coordinate mRNA fate during nutrient starvation. J Cell Sci., (in press.)
    25. Rowe LA, Degtyareva N, Doetsch PW. (2012) Yap1: a DNA damage responder in Saccharomyces cerevisiae. Mech Ageing Dev., 133(4), 147-56.
    26. Ta MT, Kapterian TS, Fei W, Du X, Brown AJ, Dawes IW, Yang H. (2012) Accumulation of squalene is associated with the clustering of lipid droplets. FEBS J., 279(22), 4231-44.
    27. Rice C, Cooke M, Treloar N, Vollbrecht P, Stukey J, McDonough V. (2010) A role for MGA2, but not SPT23, in activation of transcription of ERG1 in Saccharomyces cerevisiae. Biochem Biophys Res Commun., 403(3-4).
    28. Shah KH, Zhang B, Ramachandran V, Herman PK. (2012) Processing Body and Stress Granule Assembly Occur by Independent and Differentially Regulated Pathways in Saccharomyces cerevisiae. Genetics., (in press.)
    29. Babour A, Bicknell AA, Tourtellotte J, Niwa M. (2010) A surveillance pathway monitors the fitness of the endoplasmic reticulum to control its inheritance. Cell, 142(2), 256-69.
    30. Mitchell SF, Jain S, She M, Parker R. (2013) Global analysis of yeast mRNPs. Nat Struct Mol Biol., 20(1), 127-33.
    31. Rojas M, Farr GW, Fernandez CF, Lauden L, McCormack JC, Wolin SL. (2012) Yeast Gis2 and Its Human Ortholog CNBP Are NovelComponents of Stress-Induced RNP Granules. PLoS One., 7(12).
    32. Gulshan K, Lee SS, Moye-Rowley WS. (2011) Differential oxidant tolerance determined by the key transcription factor Yap1 is controlled by levels of the Yap1-binding protein, Ybp1. J Biol Chem., 286(39), 34071-81.
      33.

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