Audrey L. Atkin:Publications

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==Selected Publications==
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Johnson, B., R. Steadman, K. D. Patefield, J. J. Bunker, A. L. Atkin and P. Dussault.  N--phosphonoacetyl-L-ornithine (PALO): A convenient synthesis and investigation of its effect on regulation of amino acid biosynthetic genes in Saccharomyces cerevisiae.  Bioorg. Med. Chem. Letters. In press. <br> <br>
+
Nickerson, K. W., A. L. Atkin, J. C. Hargarten, R. Pathirana, and S. Hasim. Thoughts on quorum sensing and fungal dimorphism.  Invited review for Biocommunication in Fungi, Ed. G. Witzany, Springer Verlag, in press. <br><br>
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Atkin, A. L. Yeast bioinformatics and strain engineering resources.  Methods in Molecular Biology,  Strain Engineering: Methods and Protocols Ed. J. A. Williams, Humana Press Inc., Totowa, NJ. In press. <br> <br>
+
Kebaara, B. W., K. E. Baker, K. D. Patefield and A. L. Atkin, 2012.  Analysis of Nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Current Protocols in Cell Biology Chapter 27:Unit27.3. [http://www.ncbi.nlm.nih.gov/pubmed/22422476] <br><br>
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Langford, M. L., S. Hasim, K. W. Nickerson, and A. L. Atkin, 2010.  Activity and toxicity of farnesol towards Candida albicans is dependent on growth conditions.  Antimicrobial Agents and Chemotherapy, 54(2):940-942. <br> <br>
+
Deliz-Aguirre, R., A. L. Atkin and B. W. Kebaara, 2011.  Copper tolerance of Saccharomyces cerevisiae nonsense-mediated mRNA decay mutants.  Current Genetics 57(6):421-430. [http://www.ncbi.nlm.nih.gov/pubmed/21918884] <br><br>
-
Langford, M. L., A. L. Atkin, and K. W. Nickerson, 2009.  Cellular interactions of farnesol, a quorum-sensing molecule produced by Candida albicans.  Future Microbiology 4(10):1353-62. <br> <br>
+
Atkin, A. L., 2011. Yeast bioinformatics and strain engineering resources.  Methods in Molecular Biology, vol. 765, Strain Engineering: Methods and Protocols, Ed. J. A. Williams, Humana Press Inc., Totowa, NJ. pp 173-187. [http://www.ncbi.nlm.nih.gov/pubmed/21815093] <br><br>
 +
Johnson, B., R. Steadman, K. D. Patefield, J. J. Bunker, A. L. Atkin, and P. Dussault, 2011.  N-(5)-phosphonoacetyl-L-ornithine (PALO): A convenient synthesis and investigation of its effect on regulation of amino acid biosynthetic genes in Saccharomyces cerevisiae.  Bioorg. Med. Chem. Letters 21(8):2351-2353. [http://www.ncbi.nlm.nih.gov/pubmed/21421312]<br> <br>
 +
Atkin, A. L., 2011 Yeast bioinformatics and strain engineering resources.  Methods in Molecular Biology, Vol. 765,  Strain Engineering: Methods and Protocols, Ed. J. A. Williams, Humana Press Inc., Totowa, NJ. pp 173-187. 
 +
[http://www.ncbi.nlm.nih.gov/pubmed/21815093]<br> <br>
 +
Langford, M. L., S. Hasim, K. W. Nickerson, and A. L. Atkin, 2010.  Activity and toxicity of farnesol towards Candida albicans is dependent on growth conditions.  Antimicrobial Agents and Chemotherapy, 54(2):940-942. [http://www.ncbi.nlm.nih.gov/pubmed/19933803] <br> <br>
 +
Langford, M. L., A. L. Atkin, and K. W. Nickerson, 2009.  Cellular interactions of farnesol, a quorum-sensing molecule produced by Candida albicans.  Future Microbiology 4(10):1353-62. [http://www.ncbi.nlm.nih.gov/pubmed/19995193] <br> <br>
Kebaara, B.K. and A. L. Atkin, 2009.  Long 3’-UTRs target wild type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae.  Nucleic Acids Research, 37(9):2771-2778.
Kebaara, B.K. and A. L. Atkin, 2009.  Long 3’-UTRs target wild type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae.  Nucleic Acids Research, 37(9):2771-2778.
 +
[http://www.ncbi.nlm.nih.gov/pubmed/19270062] <br> <br>
 +
Ghosh, S., D. H. M. L. P. Navarathna, D. D. Roberts, J. T. Cooper, A. L. Atkin,T. M. Petro, and K. W. Nickerson, 2009.  Arginine induced germ tube formation in Candida albicans is essential for escape from murine macrophage cell line RAW264.7.  Infection and Immunity, 77(4):1596-1605. [http://www.ncbi.nlm.nih.gov/pubmed/19188358]
<br> <br>
<br> <br>
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Ghosh, S., D. H. M. L. P. Navarathna, D. D. Roberts, J. T. Cooper, A. L. Atkin,T. M. Petro, and K. W. Nickerson, 2009.  Arginine induced germ tube formation in Candida albicans is essential for escape from murine macrophage cell line RAW264.7.  Infection and Immunity, 77(4):1596-1605.
+
Ghosh, S., B. Kebaara, A. L. Atkin, and K. W. Nickerson, 2008.  Regulation of aromatic alcohol production in Candida albicans.  Applied and Environmental Microbiology, 74:7211-7218. [http://www.ncbi.nlm.nih.gov/pubmed/18836025]
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<br> <br>
+
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Ghosh, S., B. Kebaara, A. L. Atkin, and K. W. Nickerson, 2008.  Regulation of aromatic alcohol production in Candida albicans.  Applied and Environmental Microbiology, 74:7211-7218.
+
<br> <br>
<br> <br>
Kebaara, B. W., M. L. Langford, D. H. M. L. P. Navaranthna, R. Dumitru, K. W. Nickerson, and A. L. Atkin, 2008.  Candida albicans Tup1 is involved in farnesol-mediated inhibition of filamentous growth induction.  Eukaryotic Cell, 7: 980-987.  
Kebaara, B. W., M. L. Langford, D. H. M. L. P. Navaranthna, R. Dumitru, K. W. Nickerson, and A. L. Atkin, 2008.  Candida albicans Tup1 is involved in farnesol-mediated inhibition of filamentous growth induction.  Eukaryotic Cell, 7: 980-987.  
 +
[http://www.ncbi.nlm.nih.gov/pubmed/18424510] <br> <br>
 +
Dumitru, R., D. H. M. L. P. Navarathna, C. P. Semighini, C. G. Elowsky, R. V. Dumitru, D Dignard, M. Whiteway, A. L. Atkin, K. W. Nickerson, 2007.  In vivo and in vitro anaerobic mating in Candida albicans.  Eukaryotic Cell, 6:465-472. [http://www.ncbi.nlm.nih.gov/pubmed/17259544] <br>  Rated as an exceptional paper by Faculty 1000 <br> <br>
 +
Kebaara, B. W., L. E. Nielson, K. W. Nickerson, and A. L. Atkin, 2006.  Determination of mRNA half-lives in Candida albicans using thiolutin as a transcription inhibitor.  Genome, 49:894-899. [http://www.ncbi.nlm.nih.gov/pubmed/17036064]
<br> <br>
<br> <br>
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Dumitru, R., D. H. M. L. P. Navarathna, C. P. Semighini, C. G. Elowsky, R. V. Dumitru, D Dignard, M. Whiteway, A. L. Atkin, K. W. Nickerson, 2007.  In vivo and in vitro anaerobic mating in Candida albicans.  Eukaryotic Cell, 6:465-472. <br>  Rated as an exceptional paper by Faculty 1000 <br> <br>
+
Nickerson, K. W., A. L. Atkin, and J. M. Hornby, 2006. Quorum sensing in dimorphic fungi:  Farnesol and beyond, Appl. Environ. Microbiol., 72:3805-3813. [http://www.ncbi.nlm.nih.gov/pubmed/16751484]<br> <br>
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Kebaara, B. W., L. E. Nielson, K. W. Nickerson, and A. L. Atkin, 2006.  Determination of mRNA half-lives in Candida albicans using thiolutin as a transcription inhibitor.  Genome, 49:894-899.
+
Jensen, E. C., J. M. Hornby, N. E. Pagliaccetti, C. M. Wolter, K. W. Nickerson, and A. L. Atkin, 2006.  Farnesol restores wild-type colony morphology to 96% of Candida albicans colony morphology variants recovered following treatment with mutagens. Genome, 49:346-353. [http://www.ncbi.nlm.nih.gov/pubmed/16699554] <br> <br>
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<br> <br>
+
Taylor, R., B.  W. Kebaara, T. Nazarenus, A. Jones, R. Yamanaka, R. Uhrenholdt, J. P. Wendler, and A. L. Atkin, 2005.  Gene set co-regulated by the Saccharomyces cerevisiae nonsense-mediated mRNA decay pathway.  Eukaryotic Cell, 4(12):2066-2077. [http://www.ncbi.nlm.nih.gov/pubmed/16339724] <br> <br>
-
Nickerson, K. W., A. L. Atkin, and J. M. Hornby, 2006. Quorum sensing in dimorphic fungi:  Farnesol and beyond, Appl. Environ. Microbiol., 72:3805-3813.<br> <br>
+
Mosel, D.D., R. Dumitru, J. M. Hornby, A. L. Atkin, and K. W. Nickerson, 2005.  Farnesol concentrations required to block germ tube formation in Candida albicans in the presence and absence of serum.  Appl. Environ. Microbiol., 71:4938-4940. [http://www.ncbi.nlm.nih.gov/pubmed/16085901]
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Jensen, E. C., J. M. Hornby, N. E. Pagliaccetti, C. M. Wolter, K. W. Nickerson, and A. L. Atkin, 2006.  Farnesol restores wild-type colony morphology to 96% of Candida albicans colony morphology variants recovered following treatment with mutagens. Genome, 49:346-353. <br> <br>
+
-
Taylor, R., B.  W. Kebaara, T. Nazarenus, A. Jones, R. Yamanaka, R. Uhrenholdt, J. P. Wendler, and A. L. Atkin, 2005.  Gene set co-regulated by the Saccharomyces cerevisiae nonsense-mediated mRNA decay pathway.  Eukaryotic Cell, 4(12):2066-2077. <br> <br>
+
-
Mosel, D.D., R. Dumitru, J. M. Hornby, A. L. Atkin, and K. W. Nickerson, 2005.  Farnesol concentrations required to block germ tube formation in Candida albicans in the presence and absence of serum.  Appl. Environ. Microbiol., 71:4938-4940.
+
<br> <br>
<br> <br>
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Nazarenus, T., R. Cedarberg, R. Bell, J. Cheatle, A. Forch, A. Haifley, A. Hou, B. Kebaara, C. Shields, K. Stoysich, R. Taylor, and A. L. Atkin, 2005. Upf1p, a highly conserved protein required for nonsense-mediated mRNA decay, interacts with two nuclear pore proteins, Nup100p and Nup116p. Gene 345:199-212.
+
Nazarenus, T., R. Cedarberg, R. Bell, J. Cheatle, A. Forch, A. Haifley, A. Hou, B. Kebaara, C. Shields, K. Stoysich, R. Taylor, and A. L. Atkin, 2005. Upf1p, a highly conserved protein required for nonsense-mediated mRNA decay, interacts with two nuclear pore proteins, Nup100p and Nup116p. Gene 345:199-212. [http://www.ncbi.nlm.nih.gov/pubmed/15716093]
<br> <br>
<br> <br>
-
Shields, C. M., R. Taylor, T. Nazarenus, J. Cheatle, A. Hou, A. Tapprich, A. Haifley, and A. L. Atkin, 2003. Saccharomyces cerevisiae Ats1p interacts with Nap1p, a cytoplasmic protein that controls bud morphogenesis. Curr. Genet., 44:184-194.
+
Shields, C. M., R. Taylor, T. Nazarenus, J. Cheatle, A. Hou, A. Tapprich, A. Haifley, and A. L. Atkin, 2003. Saccharomyces cerevisiae Ats1p interacts with Nap1p, a cytoplasmic protein that controls bud morphogenesis. Curr. Genet., 44:184-194. [http://www.ncbi.nlm.nih.gov/pubmed/13680156]
<br> <br>
<br> <br>
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Kebaara, B., T. Nazarenus, R. Taylor, A. Forch, and A. L. Atkin, 2003.  The Upf-dependent decay of wild-type PPR1 mRNA depends on its 5’-UTR and first 92 ORF nucleotides.  Nucleic Acids Res. 31:3157-3165.
+
Kebaara, B., T. Nazarenus, R. Taylor, A. Forch, and A. L. Atkin, 2003.  The Upf-dependent decay of wild-type PPR1 mRNA depends on its 5’-UTR and first 92 ORF nucleotides.  Nucleic Acids Res. 31:3157-3165. [http://www.ncbi.nlm.nih.gov/pubmed/12799443]
<br> <br>
<br> <br>
-
Kebaara, B., T. Nazarenus, R. Taylor, and A.L. Atkin, 2003.  Genetic background affects relative nonsense mRNA accumulation in wild-type and upf mutant yeast strains.  Curr. Genet, 43:171-177.
+
Kebaara, B., T. Nazarenus, R. Taylor, and A.L. Atkin, 2003.  Genetic background affects relative nonsense mRNA accumulation in wild-type and upf mutant yeast strains.  Curr. Genet, 43:171-177. [http://www.ncbi.nlm.nih.gov/pubmed/12695845]
<br> <br>
<br> <br>
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Atkin, A. L., 1999.  Preparation of yeast cells for confocal microscopy.  Methods in Molecular Biology, vol. 122:  Confocal Microscopy Methods and Protocols Ed. S. Paddock, Humana Press Inc., Totowa, NJ. pp. 131-139. <br>
+
Atkin, A. L., 1999.  Preparation of yeast cells for confocal microscopy.  Methods in Molecular Biology, vol. 122:  Confocal Microscopy Methods and Protocols Ed. S. Paddock, Humana Press Inc., Totowa, NJ. pp. 131-139. [http://www.ncbi.nlm.nih.gov/pubmed/10231788] <br> <br>
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J. N. Dahlseid, J. Puziss, R. L. Shirley, A. L. Atkin, P. Hieter, and M. R. Culbertson, 1998.  Accumulation of mRNA coding for yeast Ctf13 kinetocore subunit depends on the same factors that promote rapid decay of nonsense mRNAs.  Genetics, 150:1019-1035. [http://www.ncbi.nlm.nih.gov/pubmed/9799255] <br> <br>
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<biblio>
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Atkin, A. L., L. R. Schenkman, M. Eastham, J. D. Dahlseid, and M. R. Culbertson, 1997.  Relationship between yeast polyribosomes and Upf proteins required for nonsense mRNA decay.  J. Biol. Chem., 272:22163-22172. [http://www.ncbi.nlm.nih.gov/pubmed/9268361] <br> <br>
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#Paper1 pmid=19933803
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Atkin, A. L., N. Altamura, P. Leeds, and M. R. Culbertson, 1995.  The majority of yeast UPF1 co-localizes with polyribosomes in the cytoplasm.  Mol. Biol. Cell., 6:611-625. [http://www.ncbi.nlm.nih.gov/pubmed/7545033] <br>
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#Paper2 pmid=19995193
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#Paper3 pmid=19270062
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#Paper4 pmid=19188358
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#Paper5 pmid=18836025
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#Paper6 pmid=18424510
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#Paper7 pmid=17259544
+
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// Rated as an exceptional paper by Faculty 1000
+
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#Paper8 pmid=17036064
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#Paper9 pmid=16751484
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#Paper10 pmid=16699554
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#Paper11 pmid=16339724
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#Paper12 pmid=16085901
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#Paper13 pmid=15716093
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#Paper14 pmid=13680156
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#Paper15 pmid=12799443
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#Paper16 pmid=12695845
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#Paper17 pmid=10231788
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#Paper18 pmid=9799255
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#Paper19 pmid=9268361
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#Paper20 pmid=7545033
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#Paper21 pmid=8244031
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#Paper22 pmid=1398091
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#Paper23 pmid=2370870
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#Paper24 pmid=1975790
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#Paper25 pmid=2109180
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</biblio>
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Revision as of 15:53, 22 June 2012


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Selected Publications

Nickerson, K. W., A. L. Atkin, J. C. Hargarten, R. Pathirana, and S. Hasim. Thoughts on quorum sensing and fungal dimorphism. Invited review for Biocommunication in Fungi, Ed. G. Witzany, Springer Verlag, in press.

Kebaara, B. W., K. E. Baker, K. D. Patefield and A. L. Atkin, 2012. Analysis of Nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Current Protocols in Cell Biology Chapter 27:Unit27.3. [1]

Deliz-Aguirre, R., A. L. Atkin and B. W. Kebaara, 2011. Copper tolerance of Saccharomyces cerevisiae nonsense-mediated mRNA decay mutants. Current Genetics 57(6):421-430. [2]

Atkin, A. L., 2011. Yeast bioinformatics and strain engineering resources. Methods in Molecular Biology, vol. 765, Strain Engineering: Methods and Protocols, Ed. J. A. Williams, Humana Press Inc., Totowa, NJ. pp 173-187. [3]

Johnson, B., R. Steadman, K. D. Patefield, J. J. Bunker, A. L. Atkin, and P. Dussault, 2011. N-(5)-phosphonoacetyl-L-ornithine (PALO): A convenient synthesis and investigation of its effect on regulation of amino acid biosynthetic genes in Saccharomyces cerevisiae. Bioorg. Med. Chem. Letters 21(8):2351-2353. [4]

Atkin, A. L., 2011 Yeast bioinformatics and strain engineering resources. Methods in Molecular Biology, Vol. 765, Strain Engineering: Methods and Protocols, Ed. J. A. Williams, Humana Press Inc., Totowa, NJ. pp 173-187. [5]

Langford, M. L., S. Hasim, K. W. Nickerson, and A. L. Atkin, 2010. Activity and toxicity of farnesol towards Candida albicans is dependent on growth conditions. Antimicrobial Agents and Chemotherapy, 54(2):940-942. [6]

Langford, M. L., A. L. Atkin, and K. W. Nickerson, 2009. Cellular interactions of farnesol, a quorum-sensing molecule produced by Candida albicans. Future Microbiology 4(10):1353-62. [7]

Kebaara, B.K. and A. L. Atkin, 2009. Long 3’-UTRs target wild type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Nucleic Acids Research, 37(9):2771-2778. [8]

Ghosh, S., D. H. M. L. P. Navarathna, D. D. Roberts, J. T. Cooper, A. L. Atkin,T. M. Petro, and K. W. Nickerson, 2009. Arginine induced germ tube formation in Candida albicans is essential for escape from murine macrophage cell line RAW264.7. Infection and Immunity, 77(4):1596-1605. [9]

Ghosh, S., B. Kebaara, A. L. Atkin, and K. W. Nickerson, 2008. Regulation of aromatic alcohol production in Candida albicans. Applied and Environmental Microbiology, 74:7211-7218. [10]

Kebaara, B. W., M. L. Langford, D. H. M. L. P. Navaranthna, R. Dumitru, K. W. Nickerson, and A. L. Atkin, 2008. Candida albicans Tup1 is involved in farnesol-mediated inhibition of filamentous growth induction. Eukaryotic Cell, 7: 980-987. [11]

Dumitru, R., D. H. M. L. P. Navarathna, C. P. Semighini, C. G. Elowsky, R. V. Dumitru, D Dignard, M. Whiteway, A. L. Atkin, K. W. Nickerson, 2007. In vivo and in vitro anaerobic mating in Candida albicans. Eukaryotic Cell, 6:465-472. [12]
Rated as an exceptional paper by Faculty 1000

Kebaara, B. W., L. E. Nielson, K. W. Nickerson, and A. L. Atkin, 2006. Determination of mRNA half-lives in Candida albicans using thiolutin as a transcription inhibitor. Genome, 49:894-899. [13]

Nickerson, K. W., A. L. Atkin, and J. M. Hornby, 2006. Quorum sensing in dimorphic fungi: Farnesol and beyond, Appl. Environ. Microbiol., 72:3805-3813. [14]

Jensen, E. C., J. M. Hornby, N. E. Pagliaccetti, C. M. Wolter, K. W. Nickerson, and A. L. Atkin, 2006. Farnesol restores wild-type colony morphology to 96% of Candida albicans colony morphology variants recovered following treatment with mutagens. Genome, 49:346-353. [15]

Taylor, R., B. W. Kebaara, T. Nazarenus, A. Jones, R. Yamanaka, R. Uhrenholdt, J. P. Wendler, and A. L. Atkin, 2005. Gene set co-regulated by the Saccharomyces cerevisiae nonsense-mediated mRNA decay pathway. Eukaryotic Cell, 4(12):2066-2077. [16]

Mosel, D.D., R. Dumitru, J. M. Hornby, A. L. Atkin, and K. W. Nickerson, 2005. Farnesol concentrations required to block germ tube formation in Candida albicans in the presence and absence of serum. Appl. Environ. Microbiol., 71:4938-4940. [17]

Nazarenus, T., R. Cedarberg, R. Bell, J. Cheatle, A. Forch, A. Haifley, A. Hou, B. Kebaara, C. Shields, K. Stoysich, R. Taylor, and A. L. Atkin, 2005. Upf1p, a highly conserved protein required for nonsense-mediated mRNA decay, interacts with two nuclear pore proteins, Nup100p and Nup116p. Gene 345:199-212. [18]

Shields, C. M., R. Taylor, T. Nazarenus, J. Cheatle, A. Hou, A. Tapprich, A. Haifley, and A. L. Atkin, 2003. Saccharomyces cerevisiae Ats1p interacts with Nap1p, a cytoplasmic protein that controls bud morphogenesis. Curr. Genet., 44:184-194. [19]

Kebaara, B., T. Nazarenus, R. Taylor, A. Forch, and A. L. Atkin, 2003. The Upf-dependent decay of wild-type PPR1 mRNA depends on its 5’-UTR and first 92 ORF nucleotides. Nucleic Acids Res. 31:3157-3165. [20]

Kebaara, B., T. Nazarenus, R. Taylor, and A.L. Atkin, 2003. Genetic background affects relative nonsense mRNA accumulation in wild-type and upf mutant yeast strains. Curr. Genet, 43:171-177. [21]

Atkin, A. L., 1999. Preparation of yeast cells for confocal microscopy. Methods in Molecular Biology, vol. 122: Confocal Microscopy Methods and Protocols Ed. S. Paddock, Humana Press Inc., Totowa, NJ. pp. 131-139. [22]

J. N. Dahlseid, J. Puziss, R. L. Shirley, A. L. Atkin, P. Hieter, and M. R. Culbertson, 1998. Accumulation of mRNA coding for yeast Ctf13 kinetocore subunit depends on the same factors that promote rapid decay of nonsense mRNAs. Genetics, 150:1019-1035. [23]

Atkin, A. L., L. R. Schenkman, M. Eastham, J. D. Dahlseid, and M. R. Culbertson, 1997. Relationship between yeast polyribosomes and Upf proteins required for nonsense mRNA decay. J. Biol. Chem., 272:22163-22172. [24]

Atkin, A. L., N. Altamura, P. Leeds, and M. R. Culbertson, 1995. The majority of yeast UPF1 co-localizes with polyribosomes in the cytoplasm. Mol. Biol. Cell., 6:611-625. [25]

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