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Published Works of CEPCEB Members
Selected Publications Related to Vacuolar Trafficking Chary SN, Hicks GR, Choi YG, Carter D, and Raikhel NV (2008) Trehalose-6-phosphate synthase/phosphatase regulates cell shape and plant architecture in Arabidopsis. Plant Physiol 146: 97-107. Sohn EJ, Rojas-Pierce M, Pan S, Carter C, Serrano-Mislata A, Madueno F, Rojo E, Surpin M, Raikhel NV (2007) The shoot meristem identity gene TFL1 is involved in flower development and trafficking to the protein storage vacuole. Proc Natl Acad Sci USA 104: 18801-18806. Rojas-Pierce M, Titapiwatanakun B, Sohn EJ, Fang F, Larive CK, Blakeslee J, Cheng Y, Cutler S, Peer WA, Murphy AS and Raikhel NV (2007) Arabidopsis P-Glycoprotein19 Participates in the Inhibition of Gravitropism by Gravacin. Chem & Biol 14: 1366-1376. Zou Y, Rojas-Pierce M, Raikhel NV and Pirrung M (2007). Preparation of Methyl Ester Precursors of Biologically Active Agents. Biotechniques (in press). Norambuena L, Zouhar J, Hicks GR and Raikhel NV (2007) Identification of cellular pathways affected by Sortin2, a synthetic compound that affects protein targeting to the vacuole in Saccharomyces cerevisiae BMC Chemical Biology (in press). Robert S, Zouhar J, Carter CJ and Raikhel NV (2007) Isolation of intact vacuoles from Arabidopsis rosette leaf-derived protoplasts. Nature Protocols 2: 259-262. Sanmartín M, Ordóñez A, Sohn EJ, Robert S, Sánchez-Serrano JJ, Surpin MA, Raikhel M+NV, and Rojo E (2007) Divergent functions of VTI12 and VTI11 in trafficking to storage and lytic vacuoles in Arabidopsis. PNAS 104: 3645-3650. Raikhel N and Hicks G (2007) Signaling from Plant Endosomes: Compartments with Something to Say! Genes & Dev 21:1578-1580. Pan S*, Carter CJ*, and Raikhel NV (2005) Understanding Protein Trafficking in Plant Cells through Proteomics (* equal contribution). Expert Rev Proteomics 2(5):781-792. Girke T, Cheng LC and Raikhel NV (2005)
ChemMine: A Compound Mining Database for Chemical Genomics. Plant Physiol 138:573-577. Horan K, Lauricha J, Bailey-Serres J, Raikhel NV, Girke T.
(2005) Genome Cluster Database. A Sequence Family Analysis Platform for Arabidopsis
and Rice. Plant Physiol 138: 47-54. Surpin M, Rojas-Pierce M, Carter C, Hicks GR, Vasquez, Raikhel
NV (2005) The Power of Chemical Genomics to Study the Link between Endomembrane
System Components and the Gravitropic Response. Proc Natl Acad Sci USA 102:4902-4907. Carter C, Pan S, Zouhar J, Avila EL, Girke T, and Raikhel NV
(2004) The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted
and unexpected proteins. Plant Cell 16:3285-3303. Rojo E, Martin R, Carter C, Zouhar J, Pan S, Plotnikova J,
Jin H, Paneque M, Sanchez-Serrano JJ, Baker B, Ausubel FM, Raikhel NV (2004) Warrior
and Executioner: VPEγ Exhibits a Caspase-like Activity that Contributes to
Defense Against Pathogens. Curr Biol 14: 1897-1906. Carter CJ, Bednarek SY, Raikhel NV (2004) Membrane trafficking
in plants: new discoveries and new approaches. Curr Opin Plant Biol 7:701-707. Zouhar J, Hicks G, Raikhel NV (2004) Sorting inhibitors (Sortins):
Chemical compounds to study vacuolar sorting in Arabidopsis. Proc Natl Acad Sci
USA 101:9497-9501. Hicks GR, Rojo E, Hong S, Carter D, Raikhel NV (2004) Geminating
Pollen Has Tubular Vacuoles, Displays Highly Dynamic Vacuole Biogenesis, and Requires
VACUOLESS1 for Proper Function. Plant Physiol 134: 1227-1239. Surpin M, Raikhel NV (2004) Traffic Jams Affect Plant Development
and Signal Transduction. Nature Reviews Mol Cell Biol 5: 100-109. Avila EL, Zouhar J, Agee AE, Carter DG, Chary SN, Raikhel NV
(2003) Tools to Study Plant Organelle Biogenesis. Point Mutation Lines with Disrupted
Vacuoles and High-Speed Confocal Screening of Green Fluorescent Protein-Tagged
Organelles. Plant Physiol 133: 1673-1676. Surpin M, Zheng Haiyan, Morita MT, Saito C, Avila E, Blakeslee
JJ, Bandyopadhyay A, Kovaleva V, Carter D, Murphy A, Tasaka M, Raikhel NV (2003)
The VTI Family of SNARE Proteins Is Necessary for Plant Viability and Mediates
Different Protein Transport Pathways. Plant Cell 15: 2885-2899. Rojo E, Zouhar J, Carter C, Kovaleva V, Raikhel NV (2003)
A Unique Mechanism for Protein Processing and Degradation in Arabidopsis Thaliana.
Proc. Natl. Acad. Sci. USA 100: 7389-7394. Rojo E, Zouhar J, Kovaleva V, Hong S, Raikhel NV (2003) The
AtC-VPS Protein Complex is Localized to the Tonoplast and the Prevacuolar Compartment
in Arabidopsis. Mol Biol Cell 14: 361-369. Sanderfoot AA, Raikhel NV (2002) The Secretory System of Arabidopsis,
The Arabidopsis Book, eds. Somerville CR and Meyerowitz EM, American Society of
Plant Biologists, Rockville, MD. DOI 10.1199/tab.0098. Price NJ, Rieter, W-D, Raikhel NV (2002) Glycosyltransferases
Involved in Polysaccharide Biosynthesis, The Arabidopsis Book, eds. Somerville
CR and Meyerowitz EM, American Society of Plant Biologists, Rockville, MD, DOI
10.1199/tab.0025. Zheng H, Bednarek SY, Sanderfoot AA, Alonso J, Ecker JR, Raikhel
NV (2002) NPSN11 is a Cell Plate-Associated SNARE Protein That Interacts with
the Syntaxin KNOLLE. Plant Physiol 129: 530-539. Rojo E, Sharma VK, Kovaleva V, Raikhel NV, Fletcher JC (2002)
CLV3 is Localized to the Extracellular Space, Where It Activates the Arabidopsis
CLAVATA Stem Cell Signaling Pathway. Plant Cell 14: 969-977. Sanderfoot, AA, Pilgrim M, Adam L, Raikhel NV (2001) Disruption
of individual members of Arabidopsis syntaxin gene families indicates each have
essential functions. Plant Cell 13: 659-666. Sanderfoot AA, Kovaleva V, Bassham DC, Raikhel NV (2001) Interactions
between syntaxins identify at least five SNARE complexes within the Golgi/Prevacuolar
system of the Arabidopsis cell. Mol Biol Cell 12:3733-3743. Rojo E, Gillmor CS, Kovaleva V, Somerville CR, Raikhel NV (2001)
VACUOLELESS1 is an essential gene required for vacuole formation and morphogenesis
in Arabidopsis. Dev Cell 1: 303-310. Sanderfoot AA, Assaad FF, Raikhel NV (2000) The Arabidopsis
Genome. An abundance of Soluble N-Ethylmaleimide-Sensitive factor adaptor protein
receptors. Plant Physiol 124: 1558-1569. Bassham DC, Sanderfoot AA, Kovaleva V, Zheng HY, Raikhel
NV (2000) AtVPS45 complex formation at the trans-Golgi network. Mol Biol Cell
11, 2251-2265. Bassham DC, Raikhel NV (2000) Unique features of the plant vacuolar sorting machinery. Curr Opin Cell Biol 12: 491-495. Bassham DC,
Raikhel NV (2000) Plant cells are not just green yeast. Plant Physiol 122: 999-1001. Ahmed
SU, Rojo E, Kovaleva V, Venkataraman S, Dombrowski JE, Matsuoka K, Raikhel NV
(2000) The plant vacuolar sorting receptor AtELP is involved in transport of NH2-terminal
propeptide-containing vacuolar proteins in Arabidopsis thaliana. J Cell Biol 149:
1335-1344. Zheng H, Fischer von Mollard G, Kovaleva V, Stevens TH, Raikhel
NV (1999) The plant vesicle-associated SNARE AtVTI1a likely mediates vesicle transport
from the trans-Golgi network to the prevacuolar compartment. Mol Biol Cell 10:
2251-2264 Vitale A, Raikhel NV (1999) What do proteins need to reach different vacuoles? Trends Plant Sci 4: 149-155.
Selected Publications Related to Cell Wall Metabolism Cocuron J-C, Lerouxel O, Drakakaki G, Alonso AP, Liepman AH, Keegstra K, Raikhel NV, and Wilkerson CG (2007) A gene from the cellulose synthase-like C family encodes a ß-1,4 glucan synthase. Proc Natl Acad Sci USA104:8550-8555. Girke T, Lauricha J, Tran
H, Keegstra K, Raikhel NV (2004) The Cell Wall Navigator Database: A Systems-Based
Approach to Organism-Unrestricted Mining of Protein Families Involved in Cell
Wall Metabolism. Plant Physiol 136:3003-3008. Vanzin GF, Madson M, Carpita NC, Raikhel, NV, Keegstra K, and
Reiter WD (2002) The mur2 mutant of Arabidopsis thaliana lacks fucoslyated xyloglucan
because of a lesion in fucosyltransferase AtFUT1. Proc. Natl. Acad. Sci. USA 99:3340-3345. Faik A, Price NF, Raikhel NV, Keegstra K (2002) Arabidopsis
Gene Encoding an α-xylosyltransferase Involved in Xyloglucan Biosynthesis.
Proc Natl Acad Sci USA 99: 7797-7802. Sarria R, Wagner TA, Neill MO, Faik A, Wilkerson C, Keegstra
K, and Raikhel NV(2001) Characterization of a family of Arabidopsis genes related
to xyloglucan fucosyltransferase. Plant Physiol 127: 1595-1606. Keegstra K and Raikhel NV (2001) Plant glycosyltransferases
Curr Opin Plant Biol 4: 219-224. Faik A, Bar-Peled M, DeRocher AE, Zeng WQ, Perrin RM,
Wilkerson C, Raikhel NV, Keegstra K (2000) Biochemical characterization and molecular
cloning of an -(1,2) fucosyltransferase that catalyzes the last step of cell wall
xyloglucan biosynthesis in pea. J Biol Chem 275: 15082-15089. Perrin RM, DeRocher AE, Bar-Peled M, Zeng W, Norambuena L,
Orellana A, Raikhel NV, Keegstra K (1999) Xyloglucan fucosyltransferase, an enzyme
involved in plant cell wall biosynthesis. Science 284: 1976-1979.
Invited Contributions and Book Chapters Norambuena, L., Hicks, G. and Raikhel N.V. (2007) The use of chemical genomics to investigate pathways intersecting auxin-dependent responses and endomembrane trafficking in Arabidopsis thaliana. In, Methods in Molecular Biology series. Dario Bonetta, ed. Humana Press. (in press) Price NJ, Reiter WD, Raikhel NV (2002) Glycosyltransferases Involved in Polysaccharide Biosynthesis, The Arabidopsis Book, eds. C.R. Somerville and E.M. Meyerowitz, American Society of Plant Biologists, Rockville, MD, DOI 10.1199/tab.0025. Sanderfoot AA, Raikhel NV (2002) The Secretory System of Arabidopsis, The Arabidopsis Book, eds. C.R. Somerville and E.M. Meyerowitz, American Society of Plant Biologists, Rockville, MD, DOI 10.1199/tab.0098. Cech TR, Eddy SR, Eisenberg D, Hersey K, Holtzman SH, Poste GH, Raikhel NV, Scheller RH, Singer DB, Waltham MC (2002) The National Academy of Sciences-Sponsored Report: "Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences." ed. Grossblatt N, The National Academies Press, Washington DC. Publications and Press Releases on Rice Submergence Xu K, Xu K, Fukao T, Canalas P, Maghirang-Rodriguez R, Heuer S, Ismail A, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene responsive-factor-like gene that confers submergence tolerance to rice. Nature 442: 705-708. Fukao T, Xu K, Ronald PC and Bailey-Serres J (2006) A variable cluster of ethylene responsive-like factors (ERFs) regulates developmental and metabolic acclimation responses to submergence. Plant Cell 18(8):2021-2034. Publications Related to Translation and Polysomal mRNA Analyses Branco-Price C, Kawaguchi R, Ferriera R and Bailey-Serres J (2005) Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Annals of Botany 96:647-660. Kawaguchi R and Bailey-Serres J (2005) mRNA sequence features responsible for translational regulation in Arabidopsis. Nucleic Acids Research 33(3):955-965. Zanetti ME, Chang I-F, Galbraith DW, Bailey-Serres J (2005) Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol 138:624-635. Kawaguchi R, Girke T, Bray EA, and Bailey-Serres J (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant Journal 38: 823-839. Williams AJ, Werner-Fraczek J, Chang I-F and Bailey-Serres, J (2003) Regulated Phosphorylation of 40S Ribosomal Protein S6 in Root Tips of Maize. Plant Physiol. 132: 2086-2097. Kawaguchi R, Williams AJ, Bray EA and Bailey-Serres J (2003) Water-deficit-induced translational control in Nicotiana tabacum. Plant Cell and Env 26: 221-229. Kawaguchi R and Bailey-Serres J (2002) Regulation of translational initiation in plants. Curr Opin Plant Bio 5: 460-465. Baxter-Burrell AY, Yang Z, Springer PS, and Bailey-Serres J (2002) RopGAP4-Dependent Rop GTPase Rheostat Control of Arabidopsis Oxygen Deprivation Tolerance. Science 296: 2026-2028. Manjunath S, Williams AJ, and Bailey-Serres J (1999) Oxygen deprivation stimulates Ca2+-mediated phosphorylation of mRNA cap-binding protein eIF4E in maize roots. Plant J 19(1):21-30. Bailey-Serres J (1999) Selective translation of cytoplasmic mRNAs in plants. Trends in Plant Science 4:142-148. Fennoy SL, Nong T, and Bailey-Serres J (1998) Transcriptional and post-transcriptional processes regulate gene expression in oxygen-deprived roots of maize. Plant J 15:727-735. Bailey-Serres J, and Dawe RK (1996) Both 5' and 3' sequences of maize adh1 mRNA are required to enhance translation under low oxygen. Plant Physiol 112:685-695. Fennoy SL, and Bailey-Serres J (1995) Posttranscriptional regulation of gene expression in oxygen-deprived roots of maize. Plant J 7:287-295. Fennoy SL, and Bailey-Serres J (1993) Synonymous codon usage by maize nuclear genes is constrained by GC-biased mutation pressure and protein function. Nucl Acids Res 21:5294-5300. Bailey-Serres J, and Freeling M (1990) Hypoxic stress-induced changes in ribosomes of maize seedling roots. Plant Physiol 94(3):1237-1243.
Publications Related to Proteins
of Unknown Function Gollery M, Harper J, Cushman J, Mittler T, Girke T, Zhu J-K, Bailey-Serres J and Mitter R (2006). What Makes Species Unique? The Contribution of Proteins with Obscure Features. Genome Biology 7(7)R:57. Horan K, Lauricha J, Bailey-Serres J, Raikhel NV
and Girke T (2005) Genome Cluster Database: A sequence family analysis platform
for Arabidopsis and Oryza sativa. Plant Physiol 138: 47-54. Publications Related to the Oxygen Stress Response in Arabidopsis Branco-Price C, Kawaguchi R, Ferriera R and Bailey-Serres J (2005) Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot 96:647-660. Bailey-Serres J and Chang R (2005) Sensing and signalling in response to oxygen deprivation in plants and other organisms. Ann Bot 96:507-518. Fukao T and Bailey-Serres J (2004) Plant responses to hypoxia - is survival a balancing act? Trends in Plant Sciences. 9(9):449-456. Baxter-Burrell A, Chang R, Springer P, and Bailey-Serres J (2003) Gene and Enhancer Trap Transposable Elements Reveal Oxygen Deprivation-regulated Genes and their Complex Patterns of Expression in Arabidopsis. Annals of Botany 91:129-141. Baxter-Burrell AY, Yang Z, Springer PS, and Bailey-Serres J (2002) RopGAP4-Dependent Rop GTPase Rheostat Control of Arabidopsis Oxygen Deprivation Tolerance. Science 296: 2026-2028
Publications Related to Plant Ribosomes Chang I-F, Szick-Miranda K, Pan S and Bailey-Serres
J (2005) Proteomic characterization of evolutionarily conserved and variable proteins
of Arabidopsis cytosolic ribosomes. Plant Physiol 137(3): 848-862. Szick-Miranda K, and Bailey-Serres J (2001) Regulated heterogeneity
in 12-kDa P-protein phosphorylation and composition of ribosomes in maize (Zea
mays L.). J Biol Chem 276(14):10921-10928. Barakat A, Szick-Miranda K, Chang I-F, Guyot R, Blanc G, Cooke
R, Delseny R, and Bailey-Serres J (2001) The organization of cytoplasmic ribosomal
protein genes in the Arabidopsis genome. Plant Physiol 127: 398-416. Bailey-Serres J (1998) Cytoplasmic ribosomes of higher plants. In: A Look beyond Transcription: Mechanisms Determining mRNA Stability and Translation in Plants. (J. Bailey-Serres and D.R. Gallie, eds). American Association of Plant Physiologists, Rockwell, MD. pp. 125-144. Fennoy SL, Jayachandran S, and
Bailey-Serres J (1997) RNase activities are reduced concomitantly with conservation
of total cellular RNA and ribosomes in oxygen-deprived seedling roots of maize.
Plant Physiol 115(3):1109-1117. Bailey-Serres J, Vangala S, Szick K, and Lee C-HK (1997) Acidic
phosphoprotein complex of the 60S ribosomal subunit of maize seedling roots: components,
and changes in response to flooding. Plant Physiol 114:1293-1305 Bailey-Serres J, and Freeling M (1990) Hypoxic stress-induced changes in ribosomes of maize seedling roots. Plant Physiol 94(3):1237-1243.
Selected Publications Related to Heterotrimeric G Proteins in Filamentous Fungi Li L and Borkovich KA (2006) GPR-4 is a G protein-coupled receptor required for carbon source dependent asexual growth and development in Neurospora crassa, Eukaryot Cell 5: 1287-1300. Kim H and Borkovich KA (2006) Pheromones are essential for male fertility and sufficient to direct chemotropic polarized growth of trichogynes during mating in Neurospora crassa. Eukaryot Cell 5: 544-554. Krystofova S and Borkovich KA (2005) The heterotrimeric G protein subunits GNG-1 and GNB-1 form a Gβγ dimer required for normal female fertility, asexual development and Gα protein levels in Neurospora crassa. Eukaryot Cell 4: 365-378. Kays AM and Borkovich KA (2004) G proteins and MAP kinase cascades in the pheromone response of fungi. In: Cell Signaling in prokaryotes and lower metazoa, ed. I. Fairweather, Kluwer Academic Publishers, Dordrecht, The Netherlands, pp. 1-26. Kays AM and Borkovich KA (2004) Signal transduction pathways and heterotrimeric G proteins. In: The Mycota: Biochemistry and Molecular Biology (Second Edition), vol. III, eds. R. Brambl and G. Marzluf, Springer-Verlag, New York, NY, pp. 175-207. Kim H and Borkovich KA (2004) A pheromone receptor gene, pre-1, is essential for mating type-specific directional growth and fusion of trichogynes and female fertility in Neurospora crassa. Mol Microbiol 52: 1781-1798. Kays AM and Borkovich KA (2004) Severe impairment of growth and differentiation in a Neurospora crassa mutant lacking all heterotrimeric Gα proteins. Genetics 166: 1229-1240. Selected Publications Related to Genome-Wide Analysis of Neurospora Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, Weiss RL, Borkovich KA and Dunlap JC (2006) A high-throughput gene knockout procedure for Neurospora reveals functions for multiple novel transcription factors. Proc Natl Acad Sci USA 103: 10352-10357. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma, LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jeff G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CPC, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B. (2003) The genome sequence of the filamentous fungus Neorospora crassa. Nature: 422: 859-868. Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JL, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, and Pratt R (2004) Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism. Microbiol. Mol. Biol. Rev. 68: 1-108.
Selected Publications Surpin
M, Zheng Haiyan, Morita MT, Saito C, Avila E, Blakeslee JJ, Bandyopadhyay A, Kovaleva
V, Carter D, Murphy A, Tasaka M, Raikhel NV (2003) The VTI Family of SNARE Proteins
Is Necessary for Plant Viability and Mediates Different Protein Transport Pathways.
Plant Cell 15: 2885-2899. Avila EL, Zouhar J, Agee AE, Carter DG, Chary SN, Raikhel
NV (2003) Tools to Study Plant Organelle Biogenesis. Point Mutation Lines with
Disrupted Vacuoles and High-Speed Confocal Screening of Green Fluorescent Protein-Tagged
Organelles. Plant Physiol 133: 1673-1676. Girke T, Ozkan M, Carter D, Raikhel NV (2003) Towards a Modeling
Infrastructure for Studying Plant Cells. Plant Physiol 132: 410-414. Carter D (1996) Practical Considerations for Collecting Confocal Images. Methods in Molecular Biology, vol. 122: Confocal Microscopy Methods and Protocols. S. Paddock (Ed). P35-57. Goldhawk DE, Carter D and Hobkirk R (1996) Microscopic and Biochemical Analysis of the Viability and Permeability of Guinea Pig Amnion and Chorion Laevae in vitro. The Journal of Experimental Zoology 275:383-397. Matsumoto B, Carter D and Hale IL (1995) A Single Histological Preparation for Assessing the Effects of Anti-Microtubule Drugs on Microtubule and Membrane Organization with Fluorescence Confocal Microscopy. Cell Vision 2(3):244-246. Kilic F, Carter D & Trevithick JR (1994) Is Calcium Uptake an Early Indication of Lens Deterioration and Cataract Formation? Abstract & Poster. The Association for Research in Vision and Opthalmology, Annual Meeting, Fort Lauderdale, Florida May 14-19, 1995. Proceeding: Investigative Opthalmology and Visual Science (36/4) S266 1215-163. Carter D (1994) What do you get when you cross a Confocal Microscope with a Microtome? Instant 3D reconstruction of really thick or opaque specimens. Microscopical Society of Canada Bulletin 22(4):9-12. Carter, D and Locke M (1993) Why Caterpillars do not Grow Short and Fat. Int. J. Insect Morphol. & Embryol. 22 (2 - 4) :81- 102. (Featured in Discover magazine April 1993. The Mysterious Longness of Caterpillars p17.) Carter, D (1993) The Transmission Confocal Laser Scanning Microscope. Bulletin of the Canadian Microscopical Society 21(1):11-16.
Selected Publications Mlotshwa S, Yang, Kim Y, and Chen X (2006) Floral patterning defects induced by Arabidopsis APETALA2 and microRNA172 expression in Nicotiana benthamiana. Plant Molecular Biology 61: 781-793. Yu B, Chapman EJ, Yang, Carrington JC, and Chen X (2006) Transgenically expressed viral RNA silencing suppressors interfere with microRNA methylation in Arabidopsis. FEBS Letters 580: 3117-3120. Yang Z, Ebright YW, Yu B, and Chen X (2006) HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2’ OH of the 3’ terminal nucleotide. Nuclei Acids Res 34: 667-675. Chen X (2005) microRNA biogenesis and function in plants. FEBS Letters 579: 5923-5931. --- Found to be one of the top 25 downloaded papers of FEBS Letters in 2005. Li J, Yang Z, Yu B, Liu J, and Chen X (2005) Methylation protects miRNAs and siRNAs from a 3’ end uridylation activity in Arabidopsis. Current Biology 15: 1501-1507. --- Featured in “ Editors' Choice: Highlights of the recent literature”. Science 309: 1651. Chen X (2005) Post-transcriptional processes and floral patterning. Flowering newsletter 39: 19-22. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, and Chen X (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307: 932-935. Liu J, He Y, Amasino R, and Chen X (2004) SiRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes & Development 18: 2873-2878. Wang W and Chen X (2004) HUA ENHANCER3 reveals a role for a cyclin-dependent protein kinase in the specification of floral organ identity in Arabidopsis. Development 131: 3147-3156. Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025. Cheng Y and Chen X (2004) Post-transcriptional control in plant development. Current Opinion in Plant Biology 7: 20-25. Li J and Chen X (2003) PAUSED, a putative exportin-t, acts in multiple developmental processes but is dispensable for viability in Arabidopsis. Plant Physiology 132: 1913-1924. Boutet S, Vazquez F, Liu J, Béclin C, Fagard M, Gratias A, Morel J-B, Crété P, Chen X, and Vaucheret H (2003) ArabidopsisHEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling post-transcriptional gene silencing and virus resistance. Current Biology 13: 843-848. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy D, Griffiths-Jones S, Matzke M, Ruvkun G, and Tuschl T (2003) A uniform system for microRNA annotation. RNA 9: 277-279. Cheng Y, Kato N, Wang W, Li J, and Chen X (2003) Two RNA-binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre-mRNA in Arabidopsisthaliana. Developmental Cell 4: 53-66. Park W, Li J, Song R, Messing J, and Chen X (2002) CARPEL FACTORY, the Dicer homologue, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology 12: 1484-1495. Western T, Cheng Y, Liu J, and Chen X (2002) HUA ENANCER2, a putative DExH-box RNA helicase, maintains homeotic B and C gene expression in Arabidopsis. Development 129: 1569-1581. Chen X, Liu J, Cheng Y, and Jia D (2002) HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development 129: 1085-1094. Li J, and Jia D, and Chen X (2001) HUA1, a regulator of stamen and carpel identities in Arabidopsis, codes for a nuclear zinc finger protein. Plant Cell 13: 2269-2281. Chen X, Riechmann JL, Jia D and Meyerowitz EM (2000). The minimal regulatory region of the floral homeotic gene PISTILLATA does not contain a CArG box. Sexual Plant Reproduction 13: 85-94. Chen X, and Meyerowitz EM (1999). HUA1 and HUA2 are two members of the floral homeotic AGAMOUS pathway. Molecular Cell 3: 349-360.
Selected Publications Wang X-H, Aliyari R, Li W-X, Li H-W, Kim K, Carthew R, Atkinson P, Ding S-W (2006) RNA Interference Directs Innate Immunity Against Viruses in Adult Drosophila. Science 312:452-454. Lu R, Maduro M, Li F, Li HW, Broitman-Maduro G, Li WX and Ding SW (18 August 2005) Animal virus replication and RNAi-mediated antiviral silencing in Caenorhabditis elegans. Nature 436: 1040-1043. Lu R, Folimonov A, Shintaku M, Li WX, Falk BW, Dawson WO, and Ding SW (2004) Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome. Proc Natl Acad Sci USA 101: 15742-15747. Chen J, Li WX, Xie DX, Peng JR & Ding SW (2004) Viral
virulence protein suppresses RNAi mediated defense but upregulates the role of
miRNA in host gene expression. Plant Cell. 16:1302-1313. Li WX, Li HW, Lu R, Li F, Dus M, Atkinson P, Johnson KL,
Garcia-Sastre A, Brydon E, Ball LA, Palese P & Ding SW. (2004) Interferon
antagonist proteins of influenza and vaccinia viruses are suppressors of RNA silencing.
Proc Acad Natl Sci USA. 101:1350-1355 (featured in Nat Rev Immunol. 4:163). Ding SW, Li HW, Lu R, Li F and Li WX (2004) RNA silencing:
A conserved antiviral immunity of plants and animals. Virus Res. 102, 109-115. Lu R, Li HW, WX Li & Ding SW (2004) RNA-based immunity
in insects. In: Microbe-Vector Interactions in Vector-borne Diseases Ed: Gillespie
SH, Smith GL & Osbourn A. Cambridge University Press. p63-74. Xin HW & Ding SW (2003) Identification and molecular characterization
of a naturally occurring RNA virus mutant defective in the initiation of host
recovery. Virology 317: 253-262. Mlotshwa S, Voinnet V, Mette F, Matzke M, Vaucheret V, Ding
SW, Pruss G, Vance VB (2002) RNA Sillencing and the Mobile Silencing Signal. Plant
Cell: S289-S301. Li HW, Li WX and Ding SW (2002) Induction and Suppression of RNA
Silencing by an Animal Virus. Science 296: 1319-1321. Guo HS & Ding SW (2002) A viral protein inhibits the long-range
signaling activity of the gene silencing signal. EMBO J 21 (3): 398-407. Li WX and Ding SW (2001) Viral suppressors of RNA silencing.
Curr Opin Biotechnol 12: 150-154. Ji LH & Ding SW (2001) The Suppressor of Transgene RNA
Silencing Encoded by Cucumber mosaic virus Interferes with Salicylic Acid-mediated
Virus Resistance. Mol Plant-Microbe Interact 14: 715-724. Lucy AP, Guo HS, Li WX, & Ding SW (2000) Suppression of
post-transcriptional gene silencing by a plant viral protein localised in the
nucleus. EMBO J 19: 1672-1680. Ding SW. (2000) RNA silencing. Curr Opin Biotechnol 11: 152-156. Li
HW, Lucy AP, Guo HS, Li WX, Ji LH, Wong SM, & Ding SW (1999) Strong host resistance
targeted against a viral suppressor of the plant gene silencing defence mechanism.
EMBO J 18: 2683-2691. Xin HW, Ji LH, Scott SW, Symons RH & Ding SW (1998) Ilarviruses encode a cucumovirus-like 2b gene that is absent in other genera within the Bromoviridae. J Virol 72: 6956-6959. Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW &
Baulcombe DC (1998) Viral pathogenicity determinants are suppressors of transgene
silencing in Nicotiana benthamiana. EMBO J 17: 6739-6746. Ding SW, Shi BJ, Li WX & Symons RH (1996) An interspecies hybrid RNA virus is significantly more virulent that either parental virus. Proc Natl Acad Sci USA 93: 7470-7474. Ding SW, Li WX & Symons RH (1995) A novel naturally occurring hybrid gene encoded by a plant RNA virus facilitates long-distance virus movement. EMBO J 14: 5762-5772.
Eulgem T & Somssich IE (in press) Networks of WRKY transcription factors in defense signaling. Current Opinion in Plant Biology. Eulgem T, Tsuchiya T, Wang X-J, Beasley B, Cuzick A, Tör M, Zhu T, McDowell JM, Holub E & Dangl JL (2007) EDM2 is a novel component of RPP7-dependent disease resistance in Arabidopsis that affects RPP7 transcript levels. The Plant Journal 49 (5): 829–839. Knoth C, Ringler J, Dangl, JL, Eulgem T (2007) Arabidopsis WRKY70 is required for full RPP4-mediated disease resistance and basal defense against Hyaloperonospora parasitica. Molecular Plant Microbe Interactions. 20 (2): 120-128. Eulgem, T. (2005) Regulation of the Arabidopsis Defence
Transcriptome. Trends Plant Sci. 10 (2): 71-78. Teige M, Scheikl E,
Eulgem T, Dóczi R, Ichimura K, Shinozaki, K, Dangl JL, Hirt, H. (2004).
The MKK2 Pathway Mediates Cold- and Salt Stress Signaling in Arabidopsis. Molecular
Cell 15(1):141-52. Eulgem T, Weigman VJ, Chang HS, McDowell JM, Holub EB, Glazebrook
J, Zhu T, Dangl JL (2004) Gene expression signatures from three genetically separable
resistance gene signaling pathways for downy mildew resistance. Plant Physiol
135(2):1129-44. Nimchuk Z, Eulgem T, Holt BF III , and Dangl JL (2003)
Recognition and response in the plant immune system. Annual Reviews in Genetics
37: 579-609. Cormack RS, Eulgem T, Rushton PJ, Koechner P, Hahlbrock K and
Somssich IE (2002) Leucine zipper containing WRKY proteins widen the spectrum
of immediate early elicitor-induced WRKY transcription factors in parsley. Biochimica
et Biophysica Acta 1576(1-2): 92-100. Tör M, Gordon P, Cuzick A, Eulgem T, Sinapidou E,
Mert-Tuerk F, Can C, Dangl JL and Holub EB (2002) SGT1b is Required for Defense
Signalling Conferred by Several Downy Mildew Resistance Genes. Plant Cell 14(5):
993-1003. Chen W, Provart N, Glazebrook J, Katagiri F, Chang H-S, Eulgem
T, Mauch F, Luan S, Zou G, Whitham S, Budworth P, Tao Y, Xie Z, Chen X, Lam S,
Kreps J, Harper J, Si-Ammour A, Mauch-Mani B, Heinlein M, Kobayashi K, Hohn T,
Dangl J, Wang X and Zhu T (2002) Expression Profile Matrix of Arabidopsis Transcription
Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses.
Plant Cell 14: 559-574. Maleck K, Levine A, Eulgem T, Morgan A, Schmid J, Lawton KA,
Dangl JL, Dietrich RA (2000) The transcriptome of Arabidopsis thaliana
during systemic acquired resistance. Nature Genetics 26(4): 403-10. Eulgem T, Rushton PJ, Robatzek S, Somssich IE (2000) The WRKY
superfamily of plant transcription factors. Trends Plant Sci 5(5): 199-206.
Eulgem T, Rushton PJ, Schmelzer E, Hahlbrock K, Somssich
IE (1999) Early nuclear events in plant defence signalling: rapid gene activation
by WRKY transcription factors. EMBO J 18(17): 4689-99. Cheng S, Gallie DR (2007) eIF4G, eIFiso4G, and eIF4B bind the poly(A)-binding protein through overlapping sites within the RNA recognition motif domains. J. Biol. Chem. 282: 25247-25258. Siddiqui N, Osborne MJ, Gallie DR, and Gehring K (2007) Solution structure of the PABC domain from wheat poly (A)-binding protein: an insight into RNA metabolic and translational control in plants. Biochemistry 46: 4221-4231. Cheng S, and Gallie D.R. (2006) Wheat eukaryotic initiation factor 4B organizes assembly of RNA and eIFiso4G, eIF4A, and poly(A)-binding protein. J. Biol. Chem. 281: 24351-24364. Chen Z, and Gallie DR (2006) Dehydroascorbate reductase affects leaf growth, development, and function. Plant Physiol. 142: 775-787. Ray S, Yumak H, Domashevskiy A, Khan MA, Gallie DR, and Goss DJ (2006) Tobacco etch Krab IM, Gallie DR, and Bol JF (2005) Coat protein enhances translational efficiency of Alfalfa mosaic virus RNAs and interacts with the eIF4G component of initiation factor eIF4F. J. Gen. Virol. 86: 1841-1849. Chen Z, and Gallie DR (2005) Increasing tolerance to ozone by elevating foliar ascorbic acid confers greater protection against ozone than does increasing avoidance. Plant Physiol. 138: 1673-1689. Zeenko V and Gallie DR (2005) Cap-independent translation of tobacco etch virus is conferred by an RNA pseudoknot in the 5' leader. J. Biol. Chem. 280: 26813-26824. Geisler-Lee J, and Gallie DR (2005) Aleurone cell identity is suppressed following connation in maize kernels. Plant Physiol. 139: 204-212 Young TE, and Gallie DR (2004) The ethylene biosynthetic and perception machinery is differentially expressed during maize endosperm and embryo development. Mol. Gen. Genomics 271: 267-281. Chen Z, and Gallie DR (2004) The ascorbic acid redox state controls guard cell signaling and stomatal movement. Plant Cell 16: 1143-1162. Young TE, Giesler-Lee J, and Gallie DR (2004) Senescence induced expression of cytokinin reverses pistil abortion during maize flower development. Plant J. 38: 910-922. Chen Z, Ling J, and Gallie DR (2004) RNase activity requires formation of disulfide bonds and is regulated by the redox state. Plant Mol. Biol. 55: 83-96. Young TE, Meeley RB, and Gallie DR (2004) ACC synthase expression regulates leaf performance and drought tolerance in maize. Plant J. 40: 813-825. Gallie DR (2004) The role of the initiation surveillance complex in promoting efficient protein synthesis. Biochem Soc Trans. 32: 585-588. Agarwal M, Sahi C, Katiyar-Agarwal S, Agarwal S, Young T, Gallie DR, Sharma, V.M., Ganesan, K., Grover, A. (2003) Molecular characterization of rice hsp101: complementation of yeast hsp104 mutation by disaggregation of protein granules and differential expression in indica and japonica rice types. Plant Mol Biol. 51: 543-553. Chen Z, Young TE, Ling, J., Chang SC, Gallie DR (2003) Increasing vitamin C content of plants through enhanced ascorbate recycling. Proc. Natl. Acad. Sci. U.S.A. 100: 3525-3530. Gallie DR, Chang S-C, Young T.E (2002) Induction of RNase and nuclease activity in cultured maize endosperm cells following sucrose starvation. Plant Cell, Tissue, Organ Culture 68: 163‑170. Dhaubhadel S, Browning KS, Gallie DR, Krishna P (2002) Brassinosteroid functions to protect the translational machinery and heat‑shock protein synthesis following thermal stress. Plant J. 29: 681‑691. Gallie DR. (2002) The 5'‑leader of tobacco mosaic virus promotes translation through enhanced recruitment of eIF4F. Nucl. Acids Res. 30: 3401‑311. Gallie DR, Fortner, D, Peng J, and Puthoff D (2002) ATP‑dependent hexameric assembly of the heat shock protein, Hsp101, involves multiple interaction domains and a functional C‑proximal nucleotide‑binding domain. J. Biol. Chem. 277: 39617‑39626. Ling J, Morley SJ, Pain VM, Marzluff WF, and Gallie DR (2002) The histone 3'-terminal stem loop binding protein enhances translation through a functional and physical interaction with eIF4G and eIF3. Mol. Cell. Biol. 22: 7853‑7867. Le H and Gallie DR (2000) Sequence diversity and conservation of the poly(A)-binding protein in plants. Plant Sci. 152: 101-114. Young TE and Gallie DR (2000) Regulation of programmed cell death in maize endosperm by abscisic acid. Plant Mol. Biol. 42: 397-414. Le H, Browning KS, and Gallie DR (2000) The phosphorylation state of poly(A)‑binding protein specifies its binding to poly(A) RNA and its interaction with eukaryotic initiation factor (eIF) 4F, eIFiso4F, and eIF4B. J. Biol. Chem. 275: 17452‑17462. Ling J, Wells DR, Tanguay RL, Dickey LF, Thompson WF, and Gallie DR (2000) Heat shock protein HSP101 binds to the Fed‑1 internal light regulatory element and mediates its high translational activity. Plant Cell 12: 1213‑1228. Gallie DR, Ling J, Niepel M, Morley SJ, and Pain VM (2000) The role of 5'‑leader length, secondary structure and PABP concentration on cap and poly(A) tail function during translation in Xenopus oocytes. Nucl. Acids Res. 28: 2943‑2953. Young TE, and Gallie DR (1999) Analysis of programmed cell death in wheat endosperm reveals differences in endosperm development between cereals. Plant Mol. Biol. 39: 915-926. Niepel M, and Gallie DR (1999) Identification and characterization of the functional elements within the tobacco etch viral 5'-leader required for cap-independent translation. J. Virol. 73: 9080-9088. Niepel M, Ling J and Gallie DR (1999) The effect of secondary structure on the functional interaction between the 5'-cap and the poly(A) tail during translation. FEBS Lett. 462: 79-84. Gallie DR, Le H, Caldwell C, and Browning KS (1998) Analysis of translation elongation factors from wheat during development and following heat shock. Biochem. Biophys. Res. Comm. 245: 295-300. Gallie DR, Le H, Tanguay RL, and Browning KS (1998) Translation initiation factors are differentially regulated in cereals during development and following heat shock. Plant J. 14: 715-722. Le H, Browning KS, and Gallie DR (1998) The phosphorylation state of the wheat translation initiation factors eIF4B, eIF4A, and eIF2 is differentially regulated during seed development and germination. J. Biol Chem. 273: 20084-20089. Wells DR, Tanguay RL, Le H, and Gallie DR (1998) HSP101 functions as a specific translational regulatory protein whose activity is regulated by nutrient status. Genes & Devel. 12: 3236-3251. Gallie DR, Le H, Caldwell C, Tanguay RL, Hoang NX, and Browning KS (1997) The phosphorylation state of translation initiation factors is regulated developmentally and following heat shock in wheat. J. Biol. Chem. 272: 1046-1053. Le H, Chan, S-C, Tanguay RL, and Gallie DR (1997) The wheat poly(A)-binding protein functionally complements Pab1p in yeast. Eur. J. Biochem. 243: 350-357. Chang S.-C., and Gallie DR (1997) RNase activity decreases following a heat shock in wheat leaves and correlates with its posttranscriptional modification. Plant Physiol. 113: 1253-1263. Le H, Tanguay RL, Balasta ML, Wei C-C, Browning KS, Metz AM, Goss DJ, and Gallie DR (1997) Translation initiation factors eIF-iso4G and eIF-4B interact with the poly(A)-binding protein and increase its RNA binding activity. J. Biol Chem. 272: 16247-16255. Smith BL, Gallie DR, Le H, and Hansma, P.K. (1997) Visualization of poly(A)-binding protein complex formation with poly(A) RNA using atomic force microscopy. J. Struc. Biol. 119: 109-117. Young TE, Gallie DR and DeMason DA (1997) Ethylene mediated programmed cell death during maize endosperm development of Su and sh2 genotypes. Plant Physiol. 115: 737-751. Gallie DR and Chang S-C (1997) Signal transduction in the carnivorous plant Sarracenia purpurea: regulation of secretory hydrolase expression during development and in response to resources. Plant Physiol. 115: 1461-1471.
Selected Publications Sunkar R, Girke T, Jain PK and Zhu JK (2005) Cloning and Characterization of MicroRNAs from Rice. Plant Cell 17: 1397-1411. Girke T, Cheng LC and Raikhel NV (2005) ChemMine: A Compound Mining Database for Chemical Genomics. Plant Physiol 138:573-577. Horan K, Lauricha J, Bailey-Serres J, Raikhel NV, Girke T. (2005) Genome Cluster Database. A Sequence Family Analysis Platform for Arabidopsis and Rice. Plant Physiol 138: 47-54. Carter C, Pan S, Zouhar J, Avila EL, Girke T, and Raikhel NV (2004)
The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and
unexpected proteins. Plant Cell 16: 3285-3303. PubMed Girke T, Lauricha J, Tran H, Keegstra K, Raikhel NV (2004)
The Cell Wall Navigator Database: A Systems-Based Approach to Organism-Unrestricted
Mining of Protein Families Involved in Cell Wall Metabolism. Plant Physiol 136:
3003-3008. PubMed Heilmann I, Pidkowich M, Girke T & Shanklin J (2004) Switching desaturase enzyme specificity by alternate subcellular targeting. Proc Natl Acad Sci U S A 101: 10266-10271. PubMed Kawaguchi R, Girke T, Bray E & Bailey-Serres J (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J 38: 823-839. PubMed Gibbons R, Dugaiczyk L, Girke T, Duistermars B, Zielinski R & Dugaiczyk A (2004) Distinguishing Humans from Great Apes with AluYb8 Repeats. J Mol Biol 339: 721-729. PubMed Girke
T, Carter D, Ozkan M & Raikhel N (2003) Towards a Modeling Infrastructure
for Studying Plant Cells. Plant Physiol 132: 1-5. PubMed
Ruuska S, Girke T, Benning C & Ohlrogge J (2002) Contrapuntal networks of gene expression during Arabidopsis seed filling. Plant Cell 14: 1191-1206. PubMed Sperling
P, Lee M, Girke T, Zähringer Z, Stymne S & Heinz E (2000) A bifunctional
D6-fatty acyl acetylenase/desaturase from the moss Ceratodon purpureus: A new
member of the cytochrome b5 superfamily. Eur J Biochem 267: 3801-3811. PubMed Ohlrogge J, Pollard M, Bao X, Focke M, Girke T, Ruuska S, Mekhedov S & Benning C (2000) Fatty acid synthesis: from CO2 to functional genomics. Biochem Soc Trans 28: 567-573. PubMed White
J, Girke T, Todd J, Newman T, Focks N, Martínez de Ilárduya O, Jaworski
J, Ohlrogge J & Benning C (2000) A New Set of Arabidopsis Expressed Sequence
Tags from Developing Seeds: The Metabolic Pathway from Carbohydrates to Seed Oil.
Plant Physiol 124: 1582-1594. PubMed Girke T, Todd J, Ruuska S, White J, Benning C & Ohlrogge
J (2000) Microarray Analysis of Developing Arabidopsis seeds. Plant Physiol 124:
1570-1581. PubMed Girke T, Schmidt H, Zähringer U, Reski R & Heinz E (1998) Identification of a novel D6-acyl-group desaturase by targeted gene disruption in Physcomitrella patens. Plant J 15: 39-48.PubMed Publications Related to Cell/Molecular/Developmental Biology of Oils and Proteins in Seeds Kim HU, Li Y, Huang AHC (2005) Ubiquitous and endoplasmic reticulum-located lysophosphatidyl acyltransferase, LPAT2, is essential for female but not male gametophyte development in Arabidopsis. Plant Cell 17: 1073-1089. Kim KU, Huang AHC (2004) Plastid lysophosphatidyl acyltransferase is essential for embryo development in Arabidopsis. Plant Physiol 134: 1206-1216. Hsieh K, Huang AHC (2004) Endoplasmic reticulum, oleosins, and oils in seeds and tapetum cells. Plant Physiol 136: 3427-3434. (a review) Ting JTL, Balsamo
RA, Ratnayake C, Huang AHC (1997) Oleosin of plant seed oil bodies is correctly
targeted to the lipid bodies in transformed yeast. J Biol Chem 272: 3699-3706. Publications Related to Cell/Molecular/Developmental Biology of Flowers, with emphases on the tapetum cells in the anthers Hsieh K, Huang AHC (2005) Lipid-rich tapetosomes in Brassica tapetum are composed of oleosin-coated oil droplets and vesicles, both assembled in and then detached from the endoplasmic reticulum. Plant J 43: 889-899. Suen DF, Wu SSH, Chang HC, KS Dhugga, Huang AHC (2003) Cell wall reactive proteins in the coat and wall of maize pollen. Potential role in pollen tube growth on the stigma and through the style. J Biol Chem 278: 43672-43681. Wu SSH, Suen DF, Chang HC, Huang AHC (2002) Maize tapetum xylanase is synthesized as a precursor, processed and activated by a serine protease, and deposited on the pollen. J Biol Chem 277: 49055-49064. Kim HU, Hsieh K, Ratnayake C, Huang AHC (2002) Expression of Arabidopsis oleosin genes and characterization of their encoded oleosins. J Biol Chem 277:22677-22684. Kim HU, Wu SSH, Ratnayake C, Huang AHC (2001) Brassica rapa has three genes that encode proteins associated with different neutral lipids in plastids of specific tissues. Plant Physiol 126:330-341. Bih FY, Wu SSH, Ratnayake C, Walling LL, Nothnagel EA, Huang AHC (1999) The predominant protein on the surface of maize pollen is an endo-xylanase synthesized by a tapetum mRNA with a long 5' leader. J Biol Chem 274: 22884-22894. Ting JTL, Wu SSH, Ratnayake C, Huang AHC (1998) Constituents of the tapetosomes and elaioplasts in Brassica campestris and their degradation and retention during microsporogenesis. Plant J 16: 541-551. Wu SSH, Platt KA, Ratnayake C, Wang TW, Ting JTL, Huang AHC (1997) Isolation and characterization of novel neutral-lipid-containing organelles and globuli-filled plastids from Brassica napus tapetum. Proc. Natl. Acad. Sci USA 94:12711-12716. Wang TW,
Balsamo RA, Ratnayake C, Platt KA, Ting JTL, Huang AHC (1997) Identification,
subcellular localization, and developmental studies of oleosins in the anther
of Brassica napus. Plant J. 11:475-487. Selected Publications Figueroa A, Borneman J, and Jiang T (2003) Clustering binary fingerprint vectors with missing values for DNA array data analysis. Journal of Computational Biology (accepted). Jia L, Clegg M, and Jiang T (2003) Excess nonsynonymous substitutions suggest that positive selection episodes operated in the DNA-binding domain evolution of Arabidopsis R2R3-MYB genes. Plant Molecular Biology 52: 627-642. Vogl C, Badger J, Kearney P, Li M, Clegg M, and Jiang T (2003) Probabilistic analysis indicates discordant gene trees in chloroplast evolution. Journal of Molecular Evolution 56(3): 330-340. Li J and Jiang T (2003) Efficient inference of haplotypes from genotypes on a pedigree. Journal of Molecular Evolution 56(3): 330-340 [also presented at Research in Computational Molecular Biology (RECOMB) International Conference (RECOMB 2003)]. Lin Y-L, Huang X, Jiang T and Chao KM (2003) MAVG: Locating CpG islands in a genomic sequence. Bioinformatics 19-1: 151-152. Jiang T, Lin G, Ma B, and Zhang K (2002) A general edit distance between RNA structures. Journal of Computational Biology 9(2): 371-388. Jiang T, Xu Y, and Zhang M (eds.). (Feb. 2002) Current Topics in Computational Biology. The MIT Press Series on Computational Molecular Biology. MIT Press. Ellrott K, Yang C, Sladek FM and Jiang T (2002) Identifying transcription factor binding sites through Markov chain optimization. Bioinformatics 18: Suppl. 2. Xu Y, Xu D, Kim D, Olman V, Razumovskaya J, and Jiang T (Feb. 2002) Automated assignment of backbone NMR peaks using constrained bipartite matching. IEEE Computing in Science and Engineering (feature article) 50-62. Borneman J, Chrobak M, Della Vedova G, Figueroa A, and Jiang T (2001) Probe selection algorithms with applications in the analysis of microbial communities. Bioinformatics 17: S39-S48. Adebiyi EF, Kaufmann M and Jiang T (2001) An efficient algorithm for finding short approximate non-tandem repeats. Bioinformatics 17. Jiang T, Kearney P and Li M (2001) A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM Journal on Computing 30(6): 1942-1961. Wang L, Jiang T and Gusfield D (2000) A more efficient approximation scheme for tree alignment. SIAM Journal on Computing 30-1: 283-299. Fasulo D, Jiang T, Karp R, Settergren R, and Thayer E (1999) An algorithmic approach to multiple complete digest mapping, Journal of Computational Biology 6(2).
Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas Jr A, Zhu J-K, Staskawicz B and Jin H (2006) A pathogen-inducible endogenous siRNAs in plant immunity. PNAS (in press). Jin H (corresponding author),Li S and Villegas Jr A (2006)Down Regulation of 26S Proteasome Subunit RPN9 Inhibits Viral Systemic Transport and Alters Plant Vascular Development. Plant Physiol 142: 651-661. Rojo E, M.R., Carter C, Zouhar J, Pan S, Plotnikova J,Jin H, Paneque M, Sanchez-Serrano JJ, Baker B, Ausubel FM, Raikhel NV (2004) VPEgamma Exhibits a Caspase-like Activity that Contributes to Defense against Pathogens.Current Biol, 14: 1897-906. Brigneti G, Martín-Hernández AM, Jin H, Chen J, Baulcombe DC, Baker B and Jones JDG (2004) Virus-Induced Gene Silencing in Solanum Species. The Plant Journal. 39: 264-272. Jin H, Liu Y, Yang KY, Kim CY, Baker B and Zhang S (2003) Function of a mitogen-activated protein kinase pathway in N gene-mediated resistance in tobacco. The Plant Journal. 33: 719-731. Liu Y, Jin H, Yang KY, Kim CY, Baker B, Zhang S (2003) Interaction between two mitogen-activated protein kinase during tobacco defense signaling. The Plant Journal. 34: 149-160. Ronning CM, Stegalkina S, Ascenzi R, Bougri O, Hart A, Utterbach T, Vanaken S, Riedmuller S, White J, Cho J, Pertea G, Lee Y, Karamycheva S, Sultana R, Tsai J, Quackenbush J, Myers K, Restrepo S, Smart C, Fry W, van der Hoeven R, Tanksley S, Zhang P, Jin H, Yamamoto M, Baker B, and Buell CR (2003) Comparative Analyses of Potato Expressed Sequence Tag Libraries. Plant Physiol. 131(2): 419-429. Jin H, Axtell MJ, Dahlbeck D, Ekwenna O, Zhang S, Staskawicz B and Baker B (2002) NPK1, an MEKK1-like mitogen-activated protein kinase kinase kinase, regulates innate immunity and development in plants. Developmental Cell 3(2): 291-297. Martin C, Bhatt K, Baumann K, Jin H, Zachgo S, Roberts K, Schwarz-Sommer Z, Glover B and Perez-Rodrigues M (2002) The mechanics of cell fate determination in petals. The Royal Society 357: 809-813. Jin H, Cominelli E, Bailey P, Parr A, Mehrtens F, Tonelli C, Weisshaar B and Martin C (2000) Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis. EMBO Journal. 19: 6150-6161. Meissner R*, Jin H* (*: Joint First Authors), Cominelli E, Denekamp M, et.al (1999) Function search in a large transcription factor gene family in Arabidopsis: assessing the potential of reverse genetics to identify insertion mutants in R2R3 MYB genes. Plant Cell. 11(10): 1827-40. Jin H, Martin C (1999) Multifunctionality and diversity within the plant MYB-gene family. Plant Mol Biol. 41(5): 577-85. Kranz HD, Denekamp M, Greco R, Jin H, Leyva A, Meissner R, Petroni K, Urzainqui A, Bevan M, Martin C, Smeekens S, Tonelli C, Paz-Ares J, Weisshaar B (1998) Towards functional characterisation of the members of the R2R3- MYB gene family from Arabidopsis thaliana. The Plant Journal. 16(2): 263-276.
Selected Publications Related to Spore Biology Kim K, and Judelson HS (2003) Sporangia-specific gene expression in the oomycete phytopathogen Phytophthora infestans. Eukaryotic Cell (in press). Ah Fong A, and Judelson HS (2003) Cell cycle regulator Cdc14 is expressed during sporulation but not hyphal growth in the fungus-like oomycete Phytophthora infestans. Molecular Microbiology 50: 487-494. Fabritius
A.-L and Judelson HS (2003) A mating-induced protein of Phytophthora infestans
is a member of a family of elicitors with divergent structures and stage-specific
patterns of expression. Molecular Plant-Microbe Interactions 16: 926-935. Cvitanich C and Judelson HS (2003) A gene expressed during sexual and
asexual sporulation in Phytophthora infestans is a member of the Puf family
of translational regulators. Eukaryotic Cell 2: 465-473. Judelson HS
and Roberts S (2002) Novel protein kinase induced during sporangial cleavage in
the oomycete Phytophthora infestans. Eukaryotic Cell 1: 687-695. Fabritius
A.-L. and Judelson HS (2002) Stage-specific gene expression during mating in Phytophthora
infestans. Molecular Microbiology 45: 1057-1066. Judelson HS (1997) Expression and inheritance of sexual preference and selfing propensity in Phytophthora infestans. Fungal Genetics and Biology 21: 188-197. Fabritius A.-L.,
and Judelson, HS (1997) Mating type loci segregate aberrantly in Phytophthora
infestans but normally in Phytophthora parasitica: implications for
models of mating type determination. Current Genetics 32: 60-65. Publications Related to Phytophthora Genetics and Genomics Cvitanich C and Judelson HS (2003) Transformation of the oomycete, Phytophthora infestans, using microprojectile bombardment. Current Genetics 42: 228-235. Judelson HS (2002) Sequence variation and genomic amplification of a family of Gypsy-like sequences in the oomycete genus Phytophthora. Molecular Biology and Evolution 19, 1313-1322. Randall TA, Ah Fong A., and Judelson HS (2002) Chromosomal heteromorphism and an apparent translocation detected using a BAC contig spanning the mating type locus of Phytophthora infestans. Fungal Genetics and Biology 38: 75-84. Judelson HS, and Fabritius A-L (2000) A linear RNA replicon from the oomycete, Phytophthora infestans. Molecular and General Genetics 263: 395-403. Randall TA. and Judelson HS (1999) Construction
of a bacterial artificial chromosome library of Phytophthora infestans
and transformation of clones into P. infestans. Fungal Genetics and Biology
28: 160-170. Judelson HS and Roberts S (1999) Multiple loci determining
insensitivity to phenylamide fungicides in Phytophthora infestans. Phytopathology
89: 754-760. Judelson HS and Yang G (1998) Recombination pathways in
Phytophthora infestans: polyploidy resulting from aberrant sexual development
and zoospore-mediated heterokaryosis. Mycological Research 102: 1245-1253. Fabritius A.-L., Shattock RC, and Judelson HS (1997) Genetic
analysis of metalaxyl insensitivity loci in Phytophthora infestans using
linked DNA markers. Phytopathology 87: 1034-1040. Judelson HS (1996) Chromosomal heteromorphism associated with the mating type locus of the oomycete, Phytophthora infestans. Molecular and General Genetics 252: 155-161. Judelson
HS (1996) Physical and genetic variability at the mating type locus of the oomycete,
Phytophthora infestans. Genetics 144: 1005-1013. Judelson HS and Whittaker SL (1995) Inactivation of transgenes in Phytophthora
infestans is not associated with their deletion, methylation, or mutation.
Current Genetics 28: 571-579. Judelson HS (1993) Intermolecular ligation mediates efficient cotransformation in Phytophthora infestans. Mol Gen Genet 239: 241-250.
Recent Selected Publications Kurtz S, Lonardi S (2004) Computational Biology, Handbook on Data Structures and Applications, eds. Dinesh Mehta and Sartaj Sahni, CRC Press, Boca Raton, FL (in press) Apostolico A, Gong F, Lonardi S (2003) Verbumculus and the Discovery
of Unusual Words. J Comp Science Tech (special issue in Bioinformatics) (in press). Apostolico A, Bock ME, Lonardi S (2003) Monotony of surprise and
large-scale quest for unusual words. J. Comp Biol 10:2/3 283-311. Apostolico A, Bock ME, Lonardi S, Xu S (2002) Efficient Detection
of Unusual Words. J Comp Biol 7: 71-94. Apostolico A, Lonardi S (2000) Off-line Compression by Greedy
Textual Substitution, Proc IEEE 88: 1733-1744. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ,
Kravitz SA, Mobarry DM, Reinert KHJ, Remington KA, Anson EL, Bolanos RA, Chou
H-H, Jordan DM, Halpern AL, Lonardi S, Beasley EM, Brandon RC, Chen L, Dunn PJ,
Lai Z, Liang Y, Nusskern DR, Zhan M, Zhang Q, Zheng X, Rubin GM, Adams MD, Venter
JC (2000) A Whole-Genome Assembly of Drosophila. Science 287: 2196-2204.
Selected Publications in Cell and Developmental
Biology Chae K, Zhang K, Zhang L, Morikis D, Kim ST, Mollet J-C, de la Rosa N, Tan K, and Lord EM (2007) Two SCA (Stigma/style Cysteine-rich Adhesion) Isoforms Show Structural Differences that Correlate with Their Levels of in vitro Pollen Tube Adhesion. Journal of Biol Chem (in press) Kim ST, Zhang K, Dong J, and Lord EM (2006) Exogenous Free Ubiquitin Enhances Lily Pollen Tube Adhesion to an in Vitro Stylar Matrix and May Facilitate Endocytosis of SCA. Plant Physiol 142:1397-1411. Gu Y, Li S, Lord EM and Yang Z (2006) Members of a Novel Class of Arabidopsis Rho Guanine Nucleotide Exchange Factors Control Rho GTPase-Dependent Polar Growth. The Plant Cell 18:366-381. Dong J, Kim ST and Lord EM (2005) Plantacyanin Plays a Role in Reproduction in Arabidopsis. Plant Physiol 138:778-789. Ravindran S, Kim S, Martin R, Lord EM and Ozkan CS (2005)
Quantum dots as bio-labels for the localization of a small plan adhesion protein.
Nanotechnology 16: 1-4. Kim S, Dong J and Lord EM (2004) Pollen Tube Guidance: The
Role of Adhesion and Chemotropic Molecules. Curr Top Dev Biol 61:61-79. Zhao
J, Yang H-Y, Lord EM (2004) Calcium levels increase in the lily stylar transmitting
tract after pollination. Sex Plant Reprod 16:259-263. Lord EM (2003) Adhesion and Guidance in Compatible Pollination. Journal of Experimental Botany, Vol. 54/No. 380:47-54. Kim S, Mollet J-C, Dong J, Zhang K, Park S-Y and Lord EM (2003)
Chemocyanin, a Small, Basic Protein from the Lily Stigma, Induces Pollen Tube
Chemotropism. Proc. Natl. Acad. Sci. USA 100:16125-16130. Li S, Blanchoin L, Yang Z and Lord EM (2003) The Putative Arbidopsis
Arp2/3 Complex Controls Leaf Cell Morphogenesis. Plant Physiol 132: 2034-2044. Park S-Y, and Lord EM (2003) Expression Studies of SCA in Lily
and Confirmation of Its Role in Pollen Tube Adhesion. Plant Molecular Biology
51:183-189. Mollet J-C, Park S-Y, and Lord EM (2003) Interaction of a stylar
pectic polysaccharide and a basic protein (SCA) mediates lily pollen tube adhesion,
pp 1-14. In Voragen F., H. Schols and R. Visser (eds.), Advances in Pectin and
Pectinase Research. Kluwer Academic Publishers, Dordrecht. Georgiady
M, Whitkus R and Lord EM (2002) Genetic analysis of traits distinguishing outcrossing
and self-pollinating forms of currant tomato (Lycopersicon pimpinelliforium).
Genetics 161:333-344. Lord EM and Russell (2002) Mechanisms of pollination and fertilization
in plants. Annu Rev Cell Devel Biol 18:81-105. Lord EM and Georgiady MS (2002) Evolution of the inbred flower
form in the currant tomato, Lycopersicon Pimpinellifolium. Int J Plant
Sci 163(4): 531-541. Lord EM, Mollet J-C, and Park S-Y (2001) In vivo pollen tube growth: tube cell adhesion and movement in lily. In, Cell Biology of Plant and Fungal Tip Growth, A. Geitmann, M. Cresti and I.B. Heath (eds). IOS Press, Washington, DC. Lord EM (2001) Adhesion molecules in lily pollination. Sex
Plant Reprod 14:57-62. Park S-Y., Jauh GY, Mollet J-C, Eckard KJ, Nothnagel EA, Walling
LL, and Lord EM (2000) A lipid transfer-like protein is necessary for lily pollen
tube adhesion to an in vitro stylar matrix. Plant Cell 12:151-163. Mollet J-C, Park S-Y, Nothnagel EA, and Lord EM (2000) A stylar
pectin is necessary for pollen tube adhesion in an in vitro stylar matrix. Plant
Cell 12: 1737-1749. Lord EM, Holdaway-Clarke T, Roy SJ, Jauh GY and Hepler PK (2000) Arabinogalactan-proteins in pollen tube growth. In, Cell and Developmental Biology of Arabinogalactan-Proteins. E. Nothnagel, A. Bacic and A.E. Clarke (eds). Kluwer Academic/Plenum Publishers, New York. pp. 153-167. Lord EM (2000)
Adhesion and cell movement during pollination: cherchez la femme. Trends Plant
Sci 5: 368-373. Lennon K A and Lord EM (2000) The in vivo pollen tube cell
of Arabidopsis thaliana. I. Tube cell cytoplasm and wall. Protoplasma 214:
45-56. Roy S, Holdaway-Clarke T, Hackett GR, Kunkel J, Lord EM, and
Hepler PK (1999) Uncoupling secretion and tip growth in lily pollen tubes: evidence
for the role of calcium in exocytosis. Plant J 19:379-386. Lennon K, Roy S, Hepler PK, and Lord EM (1998) The structure
of the transmitting tissue of Arabidopsis thaliana (L.) and the path of pollen
tube growth. Sex Plant Reprod 11:49-59. Jauh GY, Eckard KJ, Nothnagel EA, and Lord EM (1997) Adhesion
of lily pollen tubes on an artificial matrix. Sex Plant Reprod 10:178-180. Selected Publications Coroian C, Broitman-Maduro G, and Maduro M (2006) Med-type GATA factors and the evolution of mesendoderm specification in nematodes. Dev Biol 289 : 444-455. Lu R, Maduro M, Li F, Li HW, Broitman-Maduro G, Li WX, and Ding SW (2005) Animal virus replication and RNAi-mediated antiviral silencing in Caenorhabditis elegans. Nature 436: 1040-1043. Broitman-Maduro G, Maduro MF, Rothman JH (2005) The Noncanonical Binding Site of the MED-1 GATA Factor Defines Differentially Regulated Target Genes in the C. elegans Mesendoderm. Dev Cell 8: 427-433. Maduro MF, Rothman JH (2002) Making worm guts: the gene regulatory network of the Caenorhabditis elegans endoderm. Dev Biol 246: 68-85. Maduro MF, Meneghini MD, Bowerman B, Broitman-Maduro G, Rothman JH (2001) Restriction of mesendoderm to a single blastomere by the combined action of SKN-1 and a GSK-3 beta homolog is mediated by MED-1 and -2 in C. elegans. (Cover article) Mol Cell 7: 475-485.
Books Morikis, D. and Lambris, J. D., Eds. (2005) Structural Biology of the Complement System , 370 pages, CRC Press/Taylor & Francis Group, Boca Raton, FL, USA. ISBN: 0-8247-2540-9. Book reviews at: Clinical Immunology 116, 303. Book Chapters Morikis D, Floudas CA, and Lambris JD (2005) Structure-based integrative computational and experimental approach for the optimization of drug design, in ICCS 2005, Lecture Notes in Computer Science: Computational Science, p.p. 680-688, V. S. Sunderam, G. D. van Albada, P. M. A. Sloot, and J. J. Dongarrai (Eds.), Springer-Verlag, Berlin-Heidelberg. Morikis D and Lambris JD (2005) The building blocks of the complement system, in Structural Biology of the Complement System, p.p. 1-18, D. Morikis and J. D. Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL, USA. Morikis D, Holland MCH, and Lambris JD (2005) Structure of anaphylatoxins C3a and C5a, in Structural Biology of the Complement System, p.p. 161-177, D. Morikis and J. D. Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL, USA. Morikis D and Lambris JD (2005) Structure, dynamics, activity, and function of compstatin and design, of more potent analogs in Structural Biology of the Complement System, p.p. 317-340, D. Morikis and J. D. Lambris (Eds.), CRC Press/Taylor & Francis Group, Boca Raton, FL, USA. Sahu A, Morikis D, and Lambris JD (2000) Complement inhibitors targeting C3, C4, and C5, in Contemporary Immunology: Therapeutic Interventions in the Complement System, p.p. 75-112, J. D. Lambris and V. M. Holers (Eds.), Humana Press Inc., Totowa, New Jersey. Morikis D, Newlon MG, and Jennings PA (2000) Structure calculations of symmetric dimers using molecular dynamics/simulated annealing and NMR restraints: The case of the RIIa subunit of protein kinase A, in Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches, p.p. 141-156, C. A. Floudas and P. M. Pardalos (Eds.), Nonconvex Optimization and its Applications v. 40, Kluwer Academic Publishers, Dordrecht, the Netherlands. Morikis D, Sahu A, Moore WT, and Lambris JD (1999) Design, structure, function and application of compstatin, in Bioactive Peptides in Drug Discovery and Design: Medical Aspects, p.p. 235-246, J. Matsoukas and T. Mavromoustakos (Eds.), Biomedical and Health Series, Ios Press, Amsterdam, the Netherlands. Review Articles Morikis D and Lambris JD (2004) Physical methods for structure, dynamics and binding in immunological research Trends in Immunology 25, 700-707. Holland MCH, Morikis D, and Lambris JD (2004) Synthetic small-molecule complement inhibitors Current Opinion in Investigational Drugs 5, 1164-1173. Mastellos D, Morikis D, Strey C, Holland MC, and Lambris JD (2004) From atoms to systems: a cross-disciplinary approach to complement-mediated functions Molecular Immunology 41, 153-164. Morikis D, Soulika AM, Mallik B, Klepeis JL, Floudas CA, and Lambris JD (2004) Improvement of the anti-C3 activity of compstatin using rational and combinatorial approaches Biochemical Society Transactions 32, 28-32. Mastellos D, Morikis D, Isaacs S N, Holland MC, Strey CW, and Lambris JD (2003) Complement: structure, functions, evolution, and viral molecular mimicry, Immunologic Research 27, 367-386. Morikis D, and Lambris JD (2002) Structural aspects and design of low-molecular-mass complement inhibitors, Biochemical Society Transact ions 30, 1026-1036. Research Articles Mallik B and Morikis D (2005) Development of a quasi-dynamic pharmacophore model for anti-complement peptide analogues Journal of the American Chemical Society 127, 10967-10976. Sfyroera G, Katragadda M, Morikis D, Isaacs SN, and Lambris JD (2005) Electrostatic modeling predicts the activities of orthopoxvirus complement control proteins Journal of Immunology 174, 2143-2151. Mallik B, Katragadda M, Spruce LA, Carafides C, Tsokos CG, Morikis D, and Lambris JD (2005) Design and NMR characterization of active analogs of compstatin containing non-natural amino acids Journal of Medicinal Chemistry 48, 274-286. Katragadda M, Morikis D, and Lambris JD (2004) Thermodynamics studies on the interaction of the third complement component and its inhibitor, compstatin Journal of Biological Chemistry 279, 54987-54995. Kim JH, Morikis D, and Ozkan M (2004) Adaptation of inroganic quantum dots for stable molecular beacons Sensors and Actuators B: Chemical 102, 315-319. Kim JH, Stephens JP, Morikis D, and Ozkan M (2004) Hybrid inorganic-organic molecular beacons Sensor Letters 2, 85-90. Morikis D and Lambris JD (2004) The electrostatic nature of C3d-complement receptor 2 association Journal of Immunology 172, 7537-7547. Klepeis JL, Floudas CA, Morikis D, Tsokos CG, and Lambris JD (2004) Design of peptide analogues with improved activity using a novel de novo protein design approach Industrial & Engineering Chemistry Research 43, 3817-3826. Mallik B Lambris JD, and Morikis D (2003) Conformational inter-conversion of compstatin probed with molecular dynamics simulations, Proteins: Structure, Function, and Genetics 53, 130-141. Morikis D, Elcock AH, Jennings PA, and McCammon JA (2003 ) The pH dependence of stability of the activation helix and the catalytic site of GART, Biophysical Chemistry 105, 279-291. Soulika AM, Morikis D, Sarrias M-R, Roy M, Spruce LA, Sahu A, and Lambris JD (2003) Studies of Structure-Activity Relations of Complement Inhibitor Compstatin, Journal of Immunology 170, 1881-1890. Banky P, Roy M, Newlon MG, Morikis D, Haste NM, Taylor SS, and Jennings PA (2003) Related protein-protein interaction modules present drastically different surface topographies despite a conserved helical platform, Journal of Molecular Biology 330, 1117-1129. Klepeis JL, Floudas CA, Morikis D, Tsokos CG, Argyropoulos E, Spruce L, and Lambris JD (2003) Integrated computational and experimental approach for lead optimization and design of compstatin variants with improved activity, Journal of the American Chemical Society 125, 8422-8423. Sahu A, Morikis D, and Lambris JD (2003) Compstatin, a peptide inhibitor of complement, exhibits species-specific binding to complement component C3, Molecular Immunology 39, 557-566. Morikis D, Roy M, Newlon M, Scott JD, and Jennings PA (2002) Electrostatic properties of the structure of the docking and dimerization domain of protein kinase A IIa, European Journal of Biochemistry 269, 2040-2051. Morikis D, Roy M, Sahu A, Troganis A, Jennings PA, Tsokos GC, and Lambris JD (2002) The structural basis of compstatin activity examined by structure-function-based design of peptide analogs and NMR, Journal of Biological Chemistry 277, 14942-14953. Morikis D, Elcock AH, Jennings PA, and McCammon JA (2001) Native state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations, Protein Science 10, 2363-2378. Morikis D, Elcock AH, Jennings PA, and McCammon JA (2001) Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations, Protein Science 10, 2379-2392. Newlon MG, Roy M, Morikis D, Carr D, Westphal R, Scott JD, and Jennings PA (2001) A novel mechanism of PKA anchoring revealed by solution structures of anchoring complexes, EMBO Journal 20, 1651-1662. Sahu A, Soulika A., Morikis D, Spruce L, Moore WT, and Lambris JD (2000) Binding kinetics, structure-activity relationship, and biotransformation of the complement inhibitor Compstatin, Journal of Immunology 165, 2491-2499. Klepeis JL, Floudas CA, Morikis D, and Lambris JD (1999) Predicting peptide structures using NMR data and deterministic global optimization, Journal of Computational Chemistry 20, 1354-1370. Newlon MG, Roy M, Morikis D, Hausken ZE, Coghlan V, Scott JD, and Jennings PA (1999) The molecular basis for protein kinase A anchoring revealed by solution NMR, Nature, Structural Biology 6, 222-227. Morikis D, Assa-Munt N, Sahu A, and Lambris JD (1998) Solution structure of compstatin, a potent complement inhibitor, Protein Science 7, 619-627. Morikis D and Wright PE (1996) Hydrogen exchange in the carbon monoxide complex of soybean leghemoglobin, European Journal of Biochemistry 237, 212-220. Brüschweiler R, Morikis D, and Wright PE (1995) Hydration of the partially folded peptide RN-24 studied by multidimensional NMR, Journal of Biomolecular NMR 5, 353-356. Morikis D, Lepre CA, and Wright PE (1994) 1H resonance assignments and secondary Structure of the carbon monoxide complex of soybean leghemoglobin determined by homonuclear two-dimensional and three-dimensional NMR spectroscopy, European Journal of Biochemistry 219, 611-626. Merutka G, Morikis D, Brüschweiler R, and Wright PE (1993) NMR evidence for multiple conformations in a highly helical model peptide, Biochemistry 32, 13089-13097. Morikis D, Brüschweiler R, and Wright PE (1993) Determination of local ligand conformations in slowly tumbling proteins by homonuclear 2D and 3D NMR: Application to heme propionates in leghemoglobin, Journal of the American Chemical Society 115, 6238-6246. Sage JT, Morikis D, Li P, and Champion PM (1992) Low pH myoglobin photoproducts, Biophysical Journal 61, 1041-1044. Zhu L, Sage JT, Rigos AA, Morikis D, and Champion PM (1992) Conformational interconversion in protein crystals, Journal of Molecular Biology 224, 207-215. Wells AV, Sage JT, Morikis D, Champion PM, Chiu ML, and Sligar SG (1991) The iron-histidine mode of myoglobin revisited: Resonance Raman studies of isotopically labeled Escherichia coli expressed myoglobin, Journal of the American Chemical Society 113, 9655-9660. Morikis D, Li P, Bangcharoenpaurpong O, Sage JT, and Champion PM (1991) Resonance Raman scattering as a probe of electron-nuclear coupling: Applications to heme proteins, Journal of Physical Chemistry 5, 3391-3398. Sage JT, Morikis D, and Champion PM (1991) Spectroscopic studies of myoglobin at low pH: Heme structure and ligation, Biochemistry 30, 1227-1237. Egeberg KD, Springer BA, Martinis SA, Sligar SG, Morikis D, and Champion PM (1990) Alteration of sperm whale myoglobin heme axial ligation by site directed mutagenesis, Biochemistry 29, 9783-9791. Morikis D, Champion PM, Springer BA, Egeberg KD, and Sligar SG (1990) Resonance Raman studies of iron spin and axial coordination in distal pocket mutants of ferric myoglobin, Journal of Biological Chemistry 265, 12143-12145. Morikis D, Champion PM, Springer B.A, and Sligar SG (1989) Resonance Raman investigations of site-directed mutants of myoglobin: Effects of distal histidine replacement, Biochemistry 28, 4791-4800. Sage JT, Morikis D, and Champion PM (1989) Resonance Raman studies of oriented chromophores: Metmyoglobin single crystals, Journal of Chemical Physics 90, 3015-3032. Morikis D, Sage JT, Rizos AK, and Champion PM (1988) Resonance Raman studies of myoglobin single crystals, Journal of the American Chemical Society 110, 6341-6342. Sligar SG, Egeberg KD, Sage JT, Morikis D, and Champion PM (1987) Alteration of heme axial ligands by site-directed mutagenesis: A cytochrome becomes a catalytic demethylase, Journal of the American Chemical Society 109, 7896-7897. Articles in Conference Proceedings Floudas CL, Klepeis JL, Lambris JD, and Morikis D (2004) De novo protein design: an interplay of global optimization, mixed-integer optimization and experiments in Sixth International Conference on Foundations of Computer-Aided Process Design, Discovery through Product and Process Design (FOCAPD 2004) , pp 133-146, C. L. Floudas and R. Agrawal (Eds.), CACHE Corporation, Austin TX. Proceedings of the Conference held at Princeton University, Princeton, NJ, July 11-16, 2004. Champion PM, Morikis D, Li P, and Sage, J. T. (1990) Resonance Raman investigations of native and mutant myoglobins, in Proceedings of the XII International Conference on Raman Spectroscopy (ICORS) , pp. 664-665, J. R. Durig and J. F. Sullivan (Eds.), John Wiley and Sons Inc. Proceedings of the Conference held at Columbia, SC, August 13-17, 1990. Champion PM, Morikis D, Springer B, and Sligar SG (1988) Resonance Raman studies of site directed mutants and single crystals of myoglobin, in Proceedings of the XI International Conference on Raman Spectroscopy (ICORS) , pp. 687-688, R. J. H. Clark and D. A. Long (Eds.), John Wiley and Sons Inc. Proceedings of the Conference held at London, UK, September 5 9, 1988.
Selected Publications in Plant Cell Biology Yadav MP, Igartuburu JM, Yan Y, and Nothnagel EA (2006) Chemical investigation of the structural basis of the emulsifying activity of gum arabic. Food Hydrocol (in press). Yadav MP, Johnston DB, Hicks KB, and Nothnagel EA (2006) The role of lipid and protein components in the emulsification properties of gum arabic and corn fiber gum. Foods Food Ingredients J Jpn 211:243-254. Wong LS, Green HM, Feugate JE, Yadav M, Nothnagel EA, and Martins-Green M (2004) Effects of "second-hand" smoke on structure and function of fibroblasts, cells that are critical for tissue repair and remodeling. BMC Cell Biology 5:13 (electronic resource, 39 manuscript pages). Guan Y and Nothnagel EA (2004) Binding of arabinogalactan proteins by Yariv phenylglycoside triggers wound-like responses in Arabidopsis cell cultures. Plant Physiol 135:1346-1366. Nothnagel EA, Bacic A, and Clarke AE (eds.) (2000) Cell and Developmental Biology of Arabinogalactan-Proteins. Kluwer Academic/Plenum Publishers, New York, NY, 322 pp. Nothnagel EA, Münster A, and Majewska-Sawka A (2000) Arabinogalactan proteins in differentiation of gametes and somatic cells. In, Biotechnological Approaches for Utilization of Gametic Cells (Bohanec, B., ed.), European Commission, Brussels, Belgium, pp. 237-246. Majewska-Sawka A and Nothnagel EA (2000) The multiple roles of arabinogalactan proteins in plant development. Plant Physiol 122:3-9. Eyvazzadeh JA and Nothnagel EA (2000) Cell cycle arrest by perturbation of arabinogalactan-proteins with Yariv phenylglycoside. In, Cell and Developmental Biology of Arabinogalactan-Proteins (Nothnagel, E. A., Bacic, A., and Clarke, A. E., eds.), Kluwer Academic/Plenum Publishers, New York, NY, pp. 71-81. Svetek J, Yadav MP and Nothnagel EA (1999) Presence of a glycosylphosphatidylinositol lipid anchor on rose arabinogalactan proteins. J Biol Chem 274:14724-14733. Serpe MD and Nothnagel EA (1999) Arabinogalactan-proteins in the multiple domains of the plant cell surface. Adv Bot Res 30:207-289. Nothnagel EA (1997) Proteoglycans and related components in plant cells. Int. Rev Cytol 174:195-291. Langan KJ and Nothnagel EA (1997) Cell surface arabinogalactan-proteins and their relation to cell proliferation and viability. Protoplasma 196:87-98. Serpe MD and Nothnagel EA (1996) Lipid lateral mobility in the plasma membrane of whole plant cells. Pflugers Arch.-Eur J Physiol 431(S2):R253-R254. Serpe M D and Nothnagel EA (1996) Heterogeneity of arabinogalactan-proteins on the plasma membrane of rose cells. Plant Physiol 112:1261-1271. Svetek J, Furtula V, Nemec M, Nothnagel EA and Schara M (1995) Transport and dynamics of molecules dissolved in maize root cortex membranes. J Membrane Biol 143:19-28. Serpe MD and Nothnagel EA (1995) Fractionation and structural characterization of arabinogalactan-proteins from the cell wall of rose cells. Plant Physiol 109:1007-1016. Serpe MD and Nothnagel, EA (1994) Effects of Yariv phenylglycosides on Rosa cell suspensions: Evidence for the involvement of arabinogalactan-proteins in cell proliferation. Planta 193:542-550. Koster KL, Tengbe MA, Furtula V and Nothnagel EA (1994) Effects of low temperature on lateral diffusion in plasma membranes on maize (Zea mays L.) root cortex protoplasts: Relevance to chilling sensitivity. Plant Cell Environ 17:1285-1294. Sun S, Furtula V and Nothnagel EA (1992) Mechanical release and lectin labeling of maize root protoplasts. Protoplasma 169:49-56. Komalavilas P, Zhu J-K and Nothnagel EA (1991) Arabinogalactan-proteins from the suspension culture medium and plasma membrane of rose cells. J Biol Chem 266:15956-15965. Furtula V, Khan IA, and Nothnagel EA (1990) Selective osmotic effect on diffusion of plasma membrane lipids in maize protoplasts. Proc Natl Acad Sci USA 87:6532-6536.
Selected Publications Related to Telomeres Chandra A, Hughes TR, Nugent CI, and Lundblad V (2001) Cdc13 both positively and negatively regulates telomere replication. Genes Dev. 15: 404-414. Nugent CI, Bosco G, Ross L, Evans SK, Salinger AP, Moore JK, Haber JE, and Lundblad V (1998) Telomere maintenance is dependent on activities required for end repair of double strand breaks. Curr. Biol. 8: 657-660. Evans SK, Sistrunk ML, Nugent CI and Lundblad V (1998) Telomerase, Ku, and telomeric silencing in Saccharomyces cerevisiae. Chromosoma 107:352-358. Nugent CI and Lundblad V (1998) The telomerase reverse transcriptase: components and regulation. Genes Dev. 12: 1073-1085. Nugent
CI, Hughes TR, Lue NF and Lundblad V (1996) Cdc13p: a single-strand telomeric
DNA-binding protein with a dual role in yeast telomere maintenance. Science 274:
249-252.
Selected Publications Yang M, Zhang X and Ozkan CS. (Submitted to Journal of Biomedical Microdevices in September 2002) The design of piezoresistive microcantilevers for bio-sensing applications. (invited contribution). Khaled A, Vafai K, Yang M, Zhang X and Ozkan CS. Analysis and control of microcantilever deflections in bio-sensing systems. Accepted for publication in Journal of Sensors and Actuators, B. Tunaboylu, Ozkan CS, Ring K and Esener S (2002) Phase transformation and paired-plate precipitate formation in Pb0.91La0.09Zr0.65Ti0.35 O3 films grown on sapphire substrates. Accepted for publication in Journal of Materials Science in Semiconductor Processing. (Anticipated Date of Publication: early 2003). Ozkan M, Wang M, Ozkan CS, Flynn R and Esener S (2002) Optical and electrophoretic manipulation of objects in microfluidic devices. Accepted for publication in Journal of Biomedical Microdevices (invited contribution). (Anticipated Date of Publication: early 2003). Ozkan M, Ozkan CS, Kibar
O, Wang M, Bhatia S, Esener S (2001) Heterogeneous integration through electrokinetic
migration. Engineering in Medicine and Biology, 20:6:144. Tunaboylu
B, Ring K, Esener S, Ozkan CS and Ata A (2001) Precipitate splitting in piezoelectric
thin films. Journal of Materials Research, 16:10:2763. Gao H, Ozkan CS, Nix WD, Zimmerman J and Freund LB (1999) Atomistic models of dislocation formation at crystal surface ledges in Si-Ge heteroepitaxial thin films. Philosophical Magazine A, 79:2:349-370. Ozkan CS, Nix WD and
Gao H. (1999) Stress induced surface evolution: anisotropy of the 2-D roughening
mode. Journal of Materials Research. 14:8: 3247. Mullner P, Gao H and Ozkan CS. (1997) A twinned wedge in a Si-Ge heteroepitaxial film: two fold sigma-9 twinning. Philosophical Magazine A. 75:925-938. Ozkan CS, Nix WD and Gao H (1997) Strain relaxation and defect formation in heteroepitaxial Si1-xGex films via surface roughening induced by controlled annealing experiments. Applied Physics Letters. 70:2247-2249.
Selected Publications Flynn RA, Ozkan M, Esener S (2002) Two-Beam Optical Trap System for Detection of Optical Property and Size of Colloids and Live Cells. Optical Communication (in review) Ozkan M, Hartmann D, Ozkan CS, Tu E, Esener S, Heller M, Bhatia S (2002) Patterning of Biological Species and Inorganic Objects by Electrokinetic Movement. IEEE, Transactions on Information Technology in Biomedicine (in review) Ozkan M, Pisanic T, Sheel J, Barro C, Esener Sand Bhatia S (2002) An Integrated Electro-Optical System for the Rapid Arraying and Manipulation of Live Cells. Special issue on the Biomolecular Interface, Langmuir (in review) Ozkan M, Bhatia S, Esener S (2002) Optical Addressing of Polymer Beads in Microdevices. Sensors and Materials (in press) Birkbeck AL, Flynn RA, Gross M, Ozkan M, Shao B, Wang MM and Esener SC (2002) Parallel transport of biological cells using individually addressable VSCEL arrays as optical tweezers. Sensors and Actuators B Ozkan M, Ozkan C, Kibar O, Wang M, Bhatia Sand Esener S (2001) Heteregenous Integration Through Electrokinetic Migration. IEEE EMB Ozkan M, Ozkan C, Kibar O and Esener S (2000) Massively parallel low cost pick and place of optoelectronic devices via electrochemical fluidic processing. Optical Letters
Selected Publications Sohn E, Rojas-Pierce M, Pan S, Carter C, Serrano A, Madueño F, Rojo E, Surpin M, Raikhel NV (2007). The shoot meristem identity gene TFL1 demonstrates role for the protein storage vacuole in plant development. PNAS 104(47):18801-18806. Batelli G, Verslues PE, Agius F, Qiu Q, Fujii H, Pan S, Schumaker K, Grillo S, and Zhu J (2007). SOS2 promotes salt tolerance in part by interacting with the vacuolar H+-ATPase and upregulating its transport activity. Molecular Cellular Biology 27(22):7781-7790. Faiola F, Wu Y, Pan S, Zhang K, Farina A, Martinez E (2007). Max is acetylated by p300 at several nuclear localization residues. Biochemical Journal 403(3):397-407. Faiola F, Liu X, Lo S, Pan S, Zhang K, Lymar E, Farina A, and Martinez E (2005). Dual regulation of c-Myc by p300 via acetylation-dependent control of Myc protein turnover and coactivation of Myc-induced transcription. Molecular Cellular Biology 25(23):10220-10234. Pan S*, Carter CJ*, and Raikhel NV (2005) Understanding Protein Trafficking in Plant Cells through Proteomics (*equal contribution). Expert Rev Proteomics 2(5):781-792. Chang IF, Szick-Miranda K, Pan S, and Bailey-Serres J (2005). Proteomic characterization of evolutionarily conserved and variable proteins of Arabidopsis thaliana cytosolic ribosomes. Plant Physiology 137(3):848-862. Carter C*, Pan S*, Zouhar J*, Avila
EL, Girke T, and Raikhel NV (2004) The vegetative vacuole proteome of Arabidopsis
thaliana reveals predicted and unexpected proteins. (*equal contribution). Plant
Cell 16:3285-3303. |
