Recent Papers related to Yeast Community Organization
Reviews:
1. Honigberg, S. M., (2016) Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation.
Microb. Cell, 3(8): p.302-28.
http://microbialcell.com/wordpress/wp-content/uploads/2016/07/2016A-Honigberg-Microbial-Cell.pdf .
2. Vachova, L., Cap, M., Palkova, Z., (2012) Yeast colonies: a model for studies of aging, environmental adaptation, and longevity. Oxid Med Cell Longev., Article ID:601836: p. 1-8.
https://www.ncbi.nlm.nih.gov/pubmed/22928081.
3. Honigberg, S. M., (2011) Cell Signals, Cell Contacts, and the Organization of Yeast Communities. Eukaryotic Cell, Apr;10(4):466-73.
http://www.ncbi.nlm.nih.gov/pubmed/21296916.
4. Palkova, Z. and Vachova, L., (2003) Ammonia Signaling in Yeast Colony Formation. Int Rev Cytol, 225: p. 229-272.
5. Palkova, Z. and Vachova, L., (2006) Life within a Community: Benefit to Yeast Long-Term Survival. FEMS Microbiol Rev, 30(5): p. 806-824.
Community Patterns:
1. Piccirillo, S., Morales, R., White, M. G., Smith, K., Kapros, T., Honigberg, S. M. (2015) Cell Differentiation and Spatial Organization in Yeast Colonies: Role of Cell-Wall Integrity Pathway Genetics, 201(4): p. 1436-48.
http://www.genetics.org/content/genetics/201/4/1427.full.pdf.
2. Vachova, L., Hadaka, L., Cap, M., Pokorna, M., Palkova, Z. (2013) Rapidly developing yeast microcolonies differentiate in a similar way to aging giant colonies Oxid Med Cell Longev 2013(102485): p. 1-9.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736409/.
3. Cap, M. Stepanek, L., Harant, K. Vachova, L. and Palkova, Z. (2012) Cell differentiation within a yeast colony: metabolic and regulatory parallels with a tumor-affected organism Molecular Cell, 46: p. 1427-38.
https://www.ncbi.nlm.nih.gov/pubmed/22560924.
4. Piccirillo, S. and Honigberg, S. M., (2010) Sporulation Patterning and Invasive Growth in Wild and Domesticated Yeast Colonies. Res Microbiol, 161(5): p. 390-398
5. Piccirillo, Sarah, White, Melissa G., Murphy, Jeffrey C., Law, Douglas J., and Honigberg, Saul M., (2010) The Rim101p/Pacc Pathway and Alkaline Ph Regulate Pattern Formation in Yeast Colonies. Genetics, 184(3): p. 707-716.
6. White, M. G., Piccirillo, S., Dusevich, V., Law, D. J., Kapros, T., and Honigberg, S. M., (2011) Flo11p Adhesin Required for Meiotic Differentiation in S. Cerevisiae Minicolonies Grown on Plastic Surfaces. FEMS Yeast Res,2011 Mar;11(2):223-32. doi: 10.1111/j.1567-1364.2010.00712.x.
7. Vachova, L., et al., (2009) Architecture of Developing Multicellular Yeast Colony: Spatio-Temporal Expression of Ato1p Ammonium Exporter. Environ Microbiol, 11(7): p. 1866-1877.
Extracellular Matrix:
1. Karunanithi, S., Vadaie, N., Chavel, C. A., Birkaya, B., Joshi, J., Grell, L., and Cullen, P. J., (2010) Shedding of the Mucin-Like Flocculin Flo11p Reveals a New Aspect of Fungal Adhesion Regulation. Curr Biol, 20(15): p. 1389-1395.
2. St'ovicek, V., Vachova, L., Kuthan, M., and Palkova, Z., (2010) General Factors Important for the Formation of Structured Biofilm-Like Yeast Colonies. Fungal Genet Biol, 47(12): p. 1012-1022.
3. Furukawa, K., Sidoux-Walter, F., Hohmann, S. (2009) Expression of the yeast aquaporin Aqy2 affects cell surface properties under the control of osmoregulatory and morphogenic signalling pathways. Mol. Microbiol, 74(5): p. 1272-1286
https://www.ncbi.nlm.nih.gov/pubmed/19889095
4. Zara, G., Zara, S., Pinna, C., Marceddu, S., and Budroni, M., (2009) Flo11 Gene Length and Transcriptional Level Affect Biofilm-Forming Ability of Wild Flor Strains of Saccharomyces Cerevisiae. Microbiology, 155(Pt 12): p. 3838-3846.
5. Beauvais, A., Loussert, C., Prevost, M. C., Verstrepen, K., and Latge, J. P., (2009) Characterization of a Biofilm-Like Extracellular Matrix in Flo1-Expressing Saccharomyces Cerevisiae Cells. FEMS Yeast Res, 9(3): p. 411-419.
Cell contacts & adhesion in the context of communities:
1. Ratcliff, W. C., Fankhauser, J. D., Rogers, D. W., Greig, D., Travisano, M., (2015) Origins of multicellular evolvability in snowflake yeast. Nat. Commun. 6(12): p. 6102.
https://www.ncbi.nlm.nih.gov/pubmed/25600558.
2. St'ovicek, V., Vachova, L., Kuthan, M., and Palkova, Z., (2010) General Factors Important for the Formation of Structured Biofilm-Like Yeast Colonies. Fungal Genet Biol, 47(12): p. 1012-1022.
3. Zara, G., Zara, S., Pinna, C., Marceddu, S., and Budroni, M., (2009) Flo11 Gene Length and Transcriptional Level Affect Biofilm-Forming Ability of Wild Flor Strains of Saccharomyces Cerevisiae. Microbiology, 155(Pt 12): p. 3838-3846.
4. Bumgarner, S. L., Dowell, R. D., Grisafi, P., Gifford, D. K., and Fink, G. R., (2009) Toggle Involving Cis-Interfering Noncoding Rnas Controls Variegated Gene Expression in Yeast. Proc Natl Acad Sci U S A, 106(43): p. 18321-18326.
5. Wolf, J. J., Dowell, R. D., Mahony, S., Rabani, M., Gifford, D. K., and Fink, G. R., (2010) Feed-Forward Regulation of a Cell Fate Determinant by an Rna-Binding Protein Generates Asymmetry in Yeast. Genetics,'a0 185(2): p. 513-522.
Cell-cell signals:
1. Piccirillo, S., Kapros, T., Honigberg, S. M., (2016) Phenotypic plasticity within yeast colonies: differential partitioning of cell fates. Curr Genet, 62(2): p. 467-473.
https://www.ncbi.nlm.nih.gov/pubmed/26743103.
2. Wang, L., Tian, X., Gyawali, R., Lin, X., (2013) Fungal adhesion protein guides community behaviors and autoinduction in a paracrine manner. Proc Natl Acad Sci U S A, 110(28): p. 11571-6.
https://www.ncbi.nlm.nih.gov/pubmed/23798436.
3. Cap, M., Vachova, L., and Palkova, Z., (2009) Yeast Colony Survival Depends on Metabolic Adaptation and Cell Differentiation Rather Than on Stress Defense. J Biol Chem, 284(47): p. 32572-32581.
4. Cap, M., Vachova, L., and Palkova, Z., (2010) How to Survive within a Yeast Colony?: Change Metabolism or Cope with Stress? Commun Integr Biol, 3(2): p. 198-200.
5. Piccirillo, Sarah, White, Melissa G., Murphy, Jeffrey C., Law, Douglas J., and Honigberg, Saul M., (2010) The Rim101p/Pacc Pathway and Alkaline Ph Regulate Pattern Formation in Yeast Colonies. Genetics, 184(3): p. 707-716.
6. Vachova, L., et al., (2009) Architecture of Developing Multicellular Yeast Colony: Spatio-Temporal Expression of Ato1p Ammonium Exporter. Environ Microbiol, 11(7): p. 1866-1877
7. Vopalenska, I., St'ovicek, V., Janderova, B., Vachova, L., and Palkova, Z., (2010) Role of Distinct Dimorphic Transitions in Territory Colonizing and Formation of Yeast Colony Architecture. Environ Microbiol, 12(1): p. 264-277.
Methods Papers:
1. Cullen, P. (2015) Biofilm/Mat assays for budding yeast Cold Spring Harb Protoc, 'a0 2015(2): p. 172-5.
https://www.ncbi.nlm.nih.gov/pubmed/25646504.
2. Ruusuvuori, P., Lin, J., Scott, A. C., Tan, Z., Sorsa, S., Kallio, A., Nykter, M., Yli-Harja, O., Shmulevich, I., Dudley, A. M. (2014) Quantitative analysis of colony morphology in yeast Biotechniques, 56(1): p. 18-27
https://www.ncbi.nlm.nih.gov/pubmed/24447135.
3. Piccirillo, S. and Honigberg, S. M., (2011) Yeast Colony Embedding Method. J Vis Exp., 'a0 49(2510): p. 1-4.
https://www.ncbi.nlm.nih.gov/pubmed/21445054.
Some Favorite Classic Papers on Yeast Communities:
1. Lindegren, Carl C. and Hamilton, Elizabeth, (1944) Autolysis and Sporulation in the Yeast Colony. Botanical Gazette, 105: p. 316-321
2. Meunier, J. R. and Choder, M., (1999) Saccharomyces Cerevisiae Colony Growth and Ageing: Biphasic Growth Accompanied by Changes in Gene Expression. Yeast, 15(12): p. 1159-1169.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10487919
3. Vachova, L. and Palkova, Z., (2005) Physiological Regulation of Yeast Cell Death in Multicellular Colonies Is Triggered by Ammonia. J Cell Biol, 169(5): p. 711-717.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15939758
4. Palkova, Z., Janderova, B., Gabriel, J., Zikanova, B., Pospisek, M., and Forstova, J., (1997) Ammonia Mediates Communication between Yeast Colonies. Nature, 390(6659): p. 532-536.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9394006.
5. Engelberg, D., Mimran, A., Martinetto, H., Otto, J., Simchen, G., Karin, M., and Fink, G. R., (1998) Multicellular Stalk-Like Structures in Saccharomyces Cerevisiae. J Bacteriol, 180(15): p. 3992-3996.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9683500
6. Reynolds, T. B. and Fink, G. R., (2001) Bakers' Yeast, a Model for Fungal Biofilm Formation. Science, 291(5505): p. 878-881.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11157168.
7. Halme, A., Bumgarner, S., Styles, C., and Fink, G. R., (2004) Genetic and Epigenetic Regulation of the Flo Gene Family Generates Cell-Surface Variation in Yeast. Cell, 116(3): p. 405-415.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15016375.
