Publications

Featured Publications

Beisel N, Callaham J, Sng N, Taylor DJ, Paul A-L, Ferl RJ (2018) Utilization of Single-Image Normalized Differential Vegetation Index (SI-NDVI) for Early Plant Stress Detection. Applications in Plant Sciences 6: e01186

Paul A-L, Sng NJ, Zupanska AK, Krishnamurthy A, Schultz ER, Ferl RJ (2017) Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight? PLoS One 12: e0180186

Zupanska AK, Schultz ER, Yao J, Sng NJ, Zhou M, Callaham JB, Ferl RJ, Paul A-L (2017) ARG1 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight. Astrobiology 17: 1077-1111

Zhou M, Callaham JB, Reyes M, Stasiak M, Riva A, Zupanska AK, Dixon MA, Paul A-L, Ferl RJ (2017) Dissecting Low Atmospheric Pressure Stress: Transcriptome Responses to the Components of Hypobaria in Arabidopsis. Frontiers in Plant Science 8: 528

Paul A-L, Zupanska AK, Schultz ER, Ferl RJ (2013) Organ-specific remodeling of the Arabidopsis transcriptome in response to spaceflight. BMC Plant Biology. 13:112 

Zupanska AK, Ferl RJ, Denison FC, Paul A‐L. (2013) Spaceflight engages heat shock protein and other molecular chaperone genes in Arabidopsis tissue culture cells American Journal of Botany. 100(1):235-248.

Paul A‐L, Amalfitano CE, Ferl RJ. (2012) Plant growth strategies are remodeled by spaceflight. BMC Plant Biology. 12:232

Paul A-L, Manak MS, Mayfield JD, Reyes MF, Gurley WB, and Ferl RJ. (2011) Parabolic flight induces changes in gene expression patterns in Arabidopsis thaliana. Astrobiology  2011 Oct;11(8):743-58

Paul, A-L, M.P Popp, W. B. Gurley, C. Guy, K.L. Norwood and R. J. Ferl (2005) Arabidopsis gene expression patterns are altered during spaceflight.  Advances in Space Research 36:1175–1181.

Paul, A-L., Daugherty, C., Bihn, E., Chapman, D., Norwood, K., and R.J. Ferl (2001)  Transgene Expression Patterns Indicate that Spaceflight Affects Stress Signal Perception and Transduction in Arabidopsis. Plant Physiology 126:613-621.

 

Full Listing of Publications

Krishnamurthy A, Ferl RJ, Paul A-L, (2018) Comparing RNA-Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight. Applications in Plant Sciences (in Press)

Beisel N, Callaham J, Sng N, Taylor DJ, Paul A-L, Ferl RJ (2018) Utilization of Single-Image Normalized Differential Vegetation Index (SI-NDVI) for Early Plant Stress Detection. Applications in Plant Sciences 6: e01186

Sng, N., A.-L. Paul, and R. J. Ferl. 2018. Phenotypic characterization of an Arabidopsis T-DNA insertion line SALK_063500. Data in Brief 18: 913-919.

Paul A-L, Sng NJ, Zupanska AK, Krishnamurthy A, Schultz ER, Ferl RJ (2017) Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight? PLoS One 12: e0180186

Zupanska AK, Schultz ER, Yao J, Sng NJ, Zhou M, Callaham JB, Ferl RJ, Paul A-L (2017) ARG1 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight. Astrobiology 17: 1077-1111

Paul A-L, Zhou M, Callaham JB, Reyes M, Stasiak M, Riva A, Zupanska AK, Dixon MA, Ferl RJ (2017) Patterns of Arabidopsis gene expression in the face of hypobaric stress. Annals of Botany Plants 9: plx030

Zhou M, Callaham JB, Reyes M, Stasiak M, Riva A, Zupanska AK, Dixon MA, Paul A-L, Ferl RJ (2017) Dissecting Low Atmospheric Pressure Stress: Transcriptome Responses to the Components of Hypobaria in Arabidopsis. Frontiers in Plant Science 8: 528

Zhou M, Paul A-L, Ferl RJ (2017) Data for characterization of SALK_084889, a T-DNA insertion line of Arabidopsis thaliana. Data in Brief 13: 253-258

Schultz ER, Zupanska AK, Sng NJ, Paul A-L, Ferl RJ (2017) Skewing in Arabidopsis roots involves disparate environmental signaling pathways. BMC Plant Biology 17: 31

LeFrois CE, Zhou M, Amador DM, Sng N, Paul A-L, Ferl RJ (2016) Enabling the Spaceflight Methylome: DNA Isolated from Plant Tissues Preserved in RNAlater™ Is Suitable for Bisulfite PCR Assay of Genome Methylation. Gravitational and Space Research 4: 28-37

Schultz ER, Paul A-L, Ferl RJ (2016) Root Growth Patterns and Morphometric Change Based on the Growth Media. Microgravity Science and Technology: 1-11

Ferl RJ, Paul A-L (2016) The effect of spaceflight on the gravity-sensing auxin gradient of roots: GFP reporter gene microscopy on orbit. Npj Microgravity 2: 15023

Paul A-L, Ferl RJ (2015) Spaceflight exploration in plant gravitational biology. Methods in Molecular Biology 1309: 285-305

Ferl R.J., Koh J., Denison F., Paul A-L. (2015) Spaceflight Induces Specific Alterations in the Proteomes of Arabidopsis. Astrobiology 15: 32-56

Gokirmak T, Denison FC, Laughner BJ, Paul A-L, Ferl RJ (2015) Phosphomimetic mutation of a conserved serine residue in Arabidopsis thaliana 14-3-3omega suggests a regulatory role of phosphorylation in dimerization and target interactions. Plant physiology and biochemistry : PPB / Societe francaise de physiologie vegetale 97: 296-303

Bamsey MT, A-L Paul, T Graham, RJ Ferl.  (2014) Flexible imaging payload for real-time fluorescent biological imaging in parabolic, suborbital and space analog environments. Life Sciences in Space Research Life Sciences in Space Research  3: 32-44 DOI information: 10.1016/j.lssr.2014.09.002

Denison FC, Gökirmak T, Ferl RJ. Phosphorylation-related modification at the dimer interface of 14-3-3ω dramatically alters monomer interaction dynamics.  Arch Biochem Biophys. 2014 Jan 1;541:1-12. doi: 10.1016/j.abb.2013.10.025.

Paul A-L, Zupanska AK, Schultz ER, Ferl RJ (2013) Organ-specific remodeling of the Arabidopsis transcriptome in response to spaceflight. BMC Plant Biology. 13:112

Zupanska AK, Ferl RJ, Denison FC, Paul A‐L. (2013) Spaceflight engages heat shock protein and other molecular chaperone genes in Arabidopsis tissue culture cells American Journal of Botany. 100(1):235-248.

Paul A-L, Wheeler R, Levine H, Ferl RJ. (2013) Fundamental plant biology enabled by the space shuttle American Journal of Botany. 100(1):226-234.

Abboud T, Berinstain A, Bamsey M, Ferl RJ, Paul A-L, Graham T, Dixon MA, Leonardos D, Stasiak M, and Noumeir R. (2013) Multispectral Plant Health Imaging System for Space Biology and Hypobaric Plant Growth Studies. Insciences Journal 03:24-44.

Abboud T, Bamsey M, Paul A-L, Graham T, Braham S, Noumeir R, Berinstain A, and Ferl R. (2013) Deployment of a fully-automated green fluorescent protein imaging system in a high arctic autonomous greenhouse. Sensors. 13:3530-3548.

Schultz ER, Kelley KL, Paul A-L, and Ferl RJ. (2013) A Method for Preparing Spaceflight RNAlater-Fixed Arabidopsis thaliana (Brassicaceae) Tissue for Scanning Electron Microscopy. Applications in Plant Sciences. 1(8):130003.

Paul A‐L, Amalfitano CE, Ferl RJ. (2012) Plant growth strategies are remodeled by spaceflight. BMC Plant Biology. 12:232

Paul A-L, Denison FC, Schultz ER, Zupanska AK, Ferl RJ (2012) 14-3-3 phosphoprotein interaction networks – does isoform diversity present functional interaction specification? Frontiers in Plant Science 3: 190

Schultz E, Zupanska A, Manning-Roach S, Camacho J, Levine H, Paul A-L and Ferl RJ (2012) Testing the Bio-compatibility of Aluminum PDFU BRIC Hardware. Gravitational and Space Biology 26(2): 48-63.

Paul A-L, Zupanska A, Ostrow DT, Zhang Y, Sun Y, Li J-L, Shanker S, Farmerie WG, Amalfitano CE, Ferl RJ. Spaceflight transcriptomes: unique responses to a novel environment (2012) Astrobiology 12(1): 40-56

Mayfield JD, Paul A-L, Ferl RJ (2012) The 14-3-3 proteins The 14-3-3 proteins of Arabidopsis regulate root growth and chloroplast development as components of the photosensory system.  J. Experimental Botany (doi: 10.1093/jxb/ers022)

Denison F., A-L. Paul, A.K. Zupanska, R.J. Ferl, (2011) 14-3-3 Proteins in Plant Physiology Seminars in Cell and Developmental Biology 22(7): 720-727

Paul A-L and Ferl RJ (2011) Using green fluorescent protein (GFP) reporter genes in RNAlater™ fixed tissue  Gravitational and Space Biology 25(1): 40-43

Paul A-L, Manak MS, Mayfield JD, Reyes MF, Gurley WB, and Ferl RJ. (2011) Parabolic flight induces changes in gene expression patterns in Arabidopsis thaliana. Astrobiology  2011 Oct;11(8):743-58

Ferl RJ,  Zupanska A, Spinale  A, Reed  D,  Manning-Roach S, Guerra  G, Cox D, Paul A-L (2011) Performance of KSC Fixation Tubes with RNALater for orbital experiments: a case study in ISS operations for molecular biology. Advances in Space Research 48: 199-206

Gokirmak T, Paul A-L, Ferl RJ (2010) Plant phosphopeptide-binding proteins as signaling mediators. Curr Opin Plant Biol 13: 527-532

Visscher AM, A-L Paul, M Kirst, CL. Guy, AC. Schuerger, and RJ. Ferl (2010) Responses of wildtype arabidopsis and ion transporter mutants to high levels of magnesium sulfate; consequences for (extra)terrestrial plant growth. PLoS One 5(8): e12348

Ferl RJ, Paul A-L (2010) Lunar Plant Biology – A Review the Apollo Era. Astrobiology 10: 261-74.

Bamsey M, Berinstain A, Graham T, Neron P, S. B, Giroux R, Ferl RJ, Paul A-L, Dixon MA (2009) Developing strategies for automated remote plant production systems: Environmental control and monitoring of the Arthur Clarke Mars Greenhouse in the Canadian High Arctic.  Advances in Space Research  44: 1367-1381

Visscher, A.M., A-L. Paul, M. Kirst, A. K. Alling, S. Silverstone, G. Nechitailo, M. Nelson, W.F. Dempster, M. Van Thillo, J. P. Allen, R. J. Ferl. (2009) Effects of a Spaceflight Environment on Heritable Changes in Wheat Gene Expression.  Astrobiology   9: 359-67

Paul, A-L.,  L. Liu, S. McClung, B. Laughner, S. Chen and R. J. Ferl (2009) Comparative Interactomics: Analysis of Arabidopsis in vivo 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants.  J Proteome Res  8:1913-1924.

Paul, A-L., Bamsey, M., Berinstain, A., Braham. S., Neron, P., Murdoch T., Graham, T.  and R. J. Ferl (2008). Deployment of a Prototype Plant GFP Imager at the Arthur Clarke Mars Greenhouse of the Haughton Mars Project. Sensors, 8: 2762-2773.

Folta K.M., Paul A-L, Mayfield J.D., Ferl R.J. (2008) 14-3-3 isoforms participate in red light signaling and photoperiodic flowering. Plant Signaling and Behavior 3(5): 304 – 306

Paul A-L, Folta K.M., Ferl R.J. (2008) 14-3-3 Proteins, red light, and photoperiodic flowering: A point of connection? Plant Signaling and Behavior 3(8) ISSN: 1559-2324

Mayfield J.D., Folta K.M., Paul A-L, Ferl R.J. (2007) The 14-3-3 proteins μ (mu) and υ (upsilon) influence transition to flowering and early phytochrome response. Plant Physiology 145(4): 1692–1702

Sabina RL, Paul AL, Ferl RJ, Laber B, Lindell SD (2007) Adenine Nucleotide Pool Perturbation Is a Metabolic Trigger for AMP Deaminase Inhibitor-Based Herbicide Toxicity. Plant Physiology. 143:1752

Paul A-L and Ferl R.J, Meisel, M.W. (2006) High magnetic field induced changes of gene expression in arabidopsis. Biomagnetic Research and Technology Dec 22;4(1):7

Richards, J.T., K.A. Corey, A-L. Paul, R.J. Ferl, R.M. Wheeler, A.C. Schuerger (2006) Implications for Low-Pressure Bioregenerative Life Support Systems for Human Exploration Missions and Terraforming on Mars.  Astrobiology 6:851-66

Davis, J.Ch., A-L. Paul  R.J. Ferl, M.W. Meisel (2006) Topographical imaging technique for qualitative analysis of microarray data. BioTechniques  41: 554-558

Stutte, G.W.,  O. Monje,  R.D. Hatfield  A-L. Paul  R.J. Ferl  C.G. Simone (2006) Microgravity Effects on leaf morphology, cell structure, carbon metabolism and mRNA expression of dwarf wheat Planta 224:1038-1049

Ferl, R.J., A.C. Schuerger, A-L. Paul, M.A. Dixon, P. Fulford and C. McKay (2006) Mars plant biology: A workshop report and recommendations for plant biology in the exploration era. Habitation 11:1-4

Paul A-L and Ferl R.J. (2006) The Biology Of Low Atmospheric Pressure- Implications For Exploration Mission Design And Advanced Life Support.  Gravitational and Space Biology 19:3-17

Paul, A-L, P. Sehnke, R.J. Ferl (2005) Isoform specific subcellular localization among 14-3-3 proteins in Arabidopsis appears to be driven by client interactions. Molecular Biology of the Cell 16: 1735-43

Paul, A-L, M.P Popp, W. B. Gurley, C. Guy, K.L. Norwood and R. J. Ferl (2005) Arabidopsis gene expression patterns are altered during spaceflight.  Advances in Space Research 36:1175–1181.

Paul A-L, Levine HG, McLamb W, Norwood, KL, Reed D, Stutte GW,  Wells HW, Ferl, R J (2005) Plant molecular biology in the space station era: Utilization of KSC Fixation Tubes with RNAlater. Acta Astronautica 56:623-8.

Paul, A-L., A. C. Schuerger, M. Popp, J. T. Richards, M. Manak, R. J. Ferl (2004) Arabidopsis Gene Expression at Low Atmospheric Pressure. Plant Physiology 134:215-223

Paul A-L, Murdoch T, Ferl E, Levine HG, Ferl R J (2003). The TAGES Imaging System: Optimizing a Green Fluorescent Protein Imaging System for Plants. SAE Technical Paper 2003-01-2477 ICES Warrendale, PA: SAE International

Paul, A-L. and R. J. Ferl (2003). Gene expression in space biology experiments. Plant Biotechnology 2002 and Beyond. I. Vasil. Kluwer Academic Press: 343-346

Paul, A-L., and R.J. Ferl. (2002).  Molecular aspects of stress gene regulation during spaceflight.  J. Plant Growth Regulation 21:166-176

Ferl, R.J., R.Wheeler, H. G. Levine, A-L. Paul. (2002) Plants in Space. Curr Opin Plant Biol 5:258-263

Ferl, R.J., A. Schuerger, A-L. Paul, W.B. Gurley, K. Corey, R. Buckland (2002) Plant Adaptation to low atmospheric pressures. Life Support Biosph Sci 8:93-101.

Manak, M.S., A-L Paul, P.C. Senhke, R.J. Ferl (2002) Remote sensing in planta: transgenic plants as monitors of exogenous stress perception in real-time. Life Support Biosph Sci 8:83-91.

Paul, A-L., Daugherty, C., Bihn, E., Chapman, D., Norwood, K., and R.J. Ferl. (2001) Transgenic plant biomonitors: Stress gene biocompatibility evaluation of the Plant Growth Facility for PGIM-01. SAE Technical Paper 2001-01-2181 ICES Warrendale, PA: SAE International.

Paul, A-L., Daugherty, C., Bihn, E., Chapman, D., Norwood, K., and R.J. Ferl (2001)  Transgene Expression Patterns Indicate that Spaceflight Affects Stress Signal Perception and Transduction in Arabidopsis. Plant Physiology 126:613-621.

Paul A-L., C. Semer, T. Kucharek,  R.J. Ferl (2001)  The fungicidal and phytotoxic properties of benomyl and PPM™ in supplemented agar media supporting transgenic arabidopsis plants for a Space Shuttle flight experiment. Journal of Applied Microbiology and Biotechnology   55:480-480

Paul A-L, R.J. Ferl (1999)  Higher-order chromatin structure: looping long molecules. Plant Molecular Biology 41:713-720.

Paul A-L, R.J. Ferl (1998)  Direct measurement of chromatin domain loops in maize and arabidopsis plants. The Plant Cell  10:1349-1359

Paul A-L, R.J. Ferl (1998)  Permeabilized arabidopsis protoplasts provide new insight into the chromatin structure of three plant alcohol dehydrogenase genes. Developmental Genetics,  22:7-16

Paul A-L, R.J. Ferl  (1997) In vivo footprinting in Arabidopsis.  Methods in Molecular Biology, 82:417-429.

Bihn, E.A., A-L. Paul, S.W. Wang, G.W. Erdos and R.J. Ferl (1997) Localization of 14-3-3 proteins in the nuclei of Arabidopsis and Maize. Plant Journal, 12:1439-1445.

Paul, A-L. and R.J. Ferl (1997) The anoxic response of three Adh genes: in vivo and in vitro footprinting of DNA/protein interactions describe multiple signaling connections. Annals of Botany, 79:33-37

Vega-Palas, M.A., A-L. Paul and R.J. Ferl. (1996) Chromatin. In: Methods in Plant Molecular Biology.  49: 391-399. J.A. Bryant ed. Academic Press.

Lu, G., A-L. Paul, D.J. McCarty and R.J. Ferl (1996) Transcription factor veracity: is GBF3 responsible for ABA-regulated expression of Arabidopsis Adh? The Plant Cell,  8:847-857.

Paul, A-L. and R.J. Ferl (1995) In vivo Footprinting. In: Methods In Cell Biology, Vol. 49: 391-400.  D.W. Galbraith, D.P. Bourque and H.J. Bohnert, eds. Academic Press.

Paul, A-L. and R.J. Ferl (1994) Analyses of Plant Chromatin and In vivo Protein-DNA Interactions.  In: Plant Molecular Biology Manual, I3: 1-20. ed. S.B. Gelvin, R.A. Schilperoort and D.P.S. Verma, Kluwer Academic Publications (2nd edition).

Sehnke, P.C., L. Pedrosa, A-L. Paul, A.E. Frankel and R.J. Ferl (1994) Expression of active, processed ricin in transgenic tobacco. J. Biol. Chem., 269: 22473-22476

Daugherty, C.J., M. Rooney, A-L. Paul, N. De Vetten, M. Vega-Palas, G. Lu, W.B. Gurley and R.J. Ferl (1994) Environmental stress and gene regulation.  In:  Arabidopsis.  ed. C.R. Summerville and E. Meyerowitz, Cold Spring Harbor

Paul, A-L. and R.J. Ferl  (1994)  Genomic sequencing in maize.  In: The Maize Genetics Hand­book.  ed. V. Walbot and M. Freeling, Springer-Verlag publishers. pp. 579-585.

Paul, A-L. and RJ Ferl (1994)  In Vivo Footprinting Identifies an Activating Element of the Maize Adh2 Promoter Specific for Root and Vascular Tissues.  The Plant Journal 5:523-33

Paul, A-L. and R.J. Ferl (1993) Osmium tetroxide footprinting of a scaffold attachment region in the maize Adh1 promoter. Plant Molecular Biology 22:1145-1151

Ferl, R.J. and A-L. Paul (1992)  Chemical detection of Z-DNA within the maize Adh1 promoter.  Plant Molecular Biology 18:1181-1184.

Paul, A-L. and R.J. Ferl (1991) In vivo footprinting reveals unique  cis-elements and different modes of hypoxic induction in maize Adh1 and Adh2. The Plant Cell 3:159-168.

Paul, A-L. and R.J. Ferl (1991) Adh1 and Adh2 regulation.  Maydica 36:129-131.

McKendree, W.L., A-L. Paul, A.J. DeLeslie and R.J. Ferl (1990) In vivo and in vitro characterization of protein interactions with the dyad G-box of the Arabidopsis Adh gene.  The Plant Cell  2:207- 214.

Paul, A-L., and R.J. Ferl (1989) Assays for studying chromatin structure.  In: Plant Molecular Biology Manual. ed. S.B. Gelvin, R.A. Schilperoort and D.P.S. Verma, Kluwer Academic Publications.

Ferl, R.J. and A-L. Paul (1989) Chromatin structure of plant genes.  In: Chromosomes: Eukaryotic, Prokaryotic and Viral. ed. K.W. Adolf, CRC Press.

Paul, A-L. and R.J. Ferl (1989) Chromatin structure and gene regulation.  In: Cell Culture and Somatic  Cell Genetics of Plants, Vol. 6 – Molecular Biology of Nuclear Genes.  eds. J. Schell and I.K. Vasil, Academic Press.

Paul, A-L., R.J. Ferl, G.S. Boudreaux and M.W. Meisel (1989) A simple optoelectric device for controlling an electrophoresis apparatus. Rev. Sci. Instruments  60:3072-3073.

Paul, A-L., M. Ashraf, S. Bollinger and R.J. Ferl. (1988) Architecture of the 5′ flanking regions of the maize Adh  genes. In: Architecture of Eukaryotic Genes. ed. K. Kahl, VCH Press

Ferl, R.J. and A-L. Paul (1988) Methods of chromatin structure analysis.  In: Methods in Plant Molecular Biology.  ed. S. Gelvin, Martinus-Nijhoff Press.

Ferl, R.J., A-L. Paul, M. Ashraf and S. Bollinger (1987) Analysis of chromatin structure and gene regulation.  In: Tailoring Genes for Crop Improvement– An Agricultural Perspective.  eds. G. Bruen­ing, T. Kosuge, J. Harada and A. Hollender, Plenum Press.

Paul, A-L., V. Vasil, I.K. Vasil and R.J. Ferl (1987)  Constitutive and anaerobically induced DNase I hypersensitive sites in the 5′ region of the maize Adh1 gene.  Proceedings of the National Academy of Sciences USA (PNAS)  84:799-803.

Herrin, D.L., A.S. Michaels and A-L. Paul (1986) Regulation of genes encoding the large subunit of ribulose-1,5-bisphospate carboxylase and the photosystem II polypeptides D-1 and D-2 during the cell cycle of Chlamydomonas reinhardtii.  J. Cell Biol. 103:1837-1845.