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Oklahoma State University

Microarray Core Facility & BioinfOSU

Publications

The following articles reporting research in which OMCF and/or BioinfOSU participated in some way were listed in PubMed in 2003-2009 or were published in non Pub-Med journals in 2003-2009 (reverse chronological order):

Baker, C. M., Bender, C. L., Melcher, U. K., and Fletcher, J. A., 2008, Evaluation of multiple-locus variable number tandem repeat analysis for typing of Pseudomonas syringae, Phytopathology 98(6):S17-S17.

Bentley, F. K., Luo, H., Dilbeck, P., Burnap, R. L., and Eaton-Rye, J. J., 2008, Effects of Inactivating psbM and psbT on Photodamage and Assembly of Photosystem II in Synechocystis sp PCC 6803, Biochemistry 47(44):11637-11646.

Aljamali, M. N,. Hern, L., Kupfer, D., Downard, S., So, S., Roe, B. A., Sauer, J. R. and R. C. Essenberg, 2009. Transcriptome analysis of the salivary glands of the female tick Amblyomma americanum. Insect Molecular Biology (In Press)

Hwang, H. J., Nagarajan, A., McLain, A., and Burnap, R. L., 2008, Assembly and disassembly of the photosystem II manganese cluster reversibly alters the coupling of the reaction center with the light-harvesting phycobilisome, Biochemistry 47(37):9747-9755.

Malmstrom, C. M., and Melcher, U., 2008, The emerging field of plant virus ecology, Phytopathology 98(6):S189-S189.
 
Mann, D. G. J., McKnight, T. E., McPherson, J. T., Hoyt, P. R., Melechko, A. V., Simpson, M. L., and Sayler, G. S., 2008, Inducible RNA interference-mediated gene silencing using nanostructured gene delivery arrays, Acs Nano 2(1):69-76.

Melcher, U., Muthukumar, V., Wiley, G. B., Min, B. E., Palmer, M. W., Verchot-Lubicz, J., Ali, A., Nelson, R. S., Roe, B. A., Thapa, V., and Pierce, M. L., 2008, Evidence for novel viruses by analysis of nucleic acids in virus-like particle fractions from Ambrosia psilostachya, Journal of Virological Methods 152(1-2):49-55.

Mello, A. F. S., Yokomi, R. K., Melcher, U., Chen, J. C., Wayadande, A. C., and Fletcher, J.,  2008  New perspectives on the epidemiology of citrus stubborn disease in California orchards PHYTOPATHOLOGY 98 (6) 100th Annual Meeting of the American-Phytopathological-Society JUL 26-30, Minneapolis, MN.

Mello, A. F. S., Yokomi, R. K., Melcher, U., Chen, J. C., Wayadande, A. C., and Fletcher, J., 2008, Genetic diversity of Spiroplasma citri strains from different regions, hosts, and isolation dates, Phytopathology 98(9):960-968.

Puckette, M., Peal, L., Steele, J., Tang, Y., and Mahalingam, R., 2009, Ozone responsive genes in Medicago truncatula:  Analysis by suppression subtraction hybridization Journal of Plant Physiology. In Press.

Puckette, M. C., Tang, Y., and Mahalingam, R., 2008, Transcriptomic changes induced by acute ozone in resistant and sensitive Medicago truncatula accessions, BMC Plant Biol 8:46

Strickler, M. A., Hwang, H. J., Burnap, R. L., Yano, J., Walker, L. M., Service, R. J., Britt, R. D., Hillier, W., and Debus, R. J., 2008, Glutamate-354 of the CP43 polypeptide interacts with the oxygen-evolving Mn4Ca cluster of photosystem II: a preliminary characterization of the Glu354Gln mutant, Philosophical Transactions of the Royal Society B-Biological Sciences 363(1494):1179-1187.

Thompson, D. F., Farmer, K. C., Beall, D. G., Evans, D. J., Melchert, R. B., Ross, L. A., and Schmoll, B. J., 2008, Identifying perceptions of professionalism in pharmacy using a four-frame leadership model, Am J Pharm Educ 72(4):90.

Anuradha P.,  2008, Biochemical and molecular analysis of an Arabidopsis nudix hydrolase. MS Thesis, Oklahoma State University.

Al Jorf, F., 2008.  Effect of water stress in the expression of proteins in hard red spring wheat Triticum aestivum cv. Butte 86. Ph.D. Dissertation, Oklahoma State University.

Puckette, M, H. Weng and Mahalingam, R.  2007.  Physiological and biochemical responses to acute ozone-induced oxidative stress in Medicago truncatula.  Plant Physiology and Biochemistry. 40:70-79.

Mahalingam, R., Jambunathan, N., and Penaganti, A.  2007.  Pyridine nucleotide homeostasis in plant development and stress. International Journal of Plant Developmental Biology 1: 194-201.

Carver B. F., Hunger R. M., Edwards, J. T., Porter, D. R., Peeper, T. F., Seabourn, B. W., Rayas-Duarte, P., Klatt A. R., and Martin, B. C.  2007.  Registration of 'OKfield' wheat. Journal of Plant Registrations 1(2):102-103.

 Soares, R.M.D., de Francisco, A., Rayas-Duarte, P., and Soldi, V.  2007.  Brazilian hull-less and malting barley genotypes: I. Chemical composition and partial characterization.  J. Food Quality 30:357-371.

 Soares, R.M.D., de Francisco, A., Rayas-Duarte, P., and Soldi, V.  2007.  Brazilian hull-less and malting barley genotypes: II. Thermal and rheological properties of starch.  J. Food Quality 30:372-385.

Joray, M. L, Rayas-Duarte, P., Mohamed, A., van Santen, E.  2007.  Coated whole bean lupin snack.  J. Food Quality 30(2):267-279.
 
Al-Jorf, F. and Kalyanaraman, P., and Rayas-Duarte, P. 2007.  Assessment of gluten proteins from Triticum aestivum grown under optimum and water stressed conditions. Food and Agricultural Products Center /Institute of Food Technologists – Oklahoma Section Research Symposium, February 21-22, 2007 Stillwater OK.  P24, Abstract book.

Pottosin, II,  Schonknecht, G, Vacuolar calcium channels. Journal Of Experimental Botany, 58(7):1559-1569.  2007
 
Trebacz, K., Schonknecht, G., Dziubinska, H., Hanaka, A.  Characteristics of anion channels in the tonoplast of the liverwort  Conocephalum conicum .  PLANT AND CELL PHYSIOLOGY, 48(12): 1747-1757. 2007

Anyomi, F. M., A. D. Bior, R. C. Essenberg, and J. R. Sauer. 2006. Gene expression in male tick salivary glands is affected by feeding in the presence of females. Archives of Insect Biochemistry and Physiology 63:159-168.

Schenk A, Berger M, Keith LM et al. The algT gene of Pseudomonas syringae pv. glycinea and new insights into the transcriptional organization of the algT-muc gene cluster. Journal of Bacteriology 2006; 188 (23):8013-21.

Sreedharan A, Penaloza-Vazquez A, Kunkel BN et al. CorR regulates multiple components of virulence in Pseudomonas syringae pv. tomato DC3000. Molecular Plant-Microbe Interactions 2006; 19 (7):768-79.

Fletcher J, Bender C, Budowle B et al. Plant pathogen forensics: Capabilities, needs, and recommendations. Microbiology and Molecular Biology Reviews 2006; 70 (2):450

Elizabeth, S. V., and C. L. Bender. 2007. The phytotoxin coronatine from Pseudomonas syringae pv. tomato DC3000 functions as a virulence factor and influences defense pathways in edible Brassicas. Mol. Plant Pathol. 8: 83-92.

Scheets K, Redinbaugh MG. Infectious cDNA transcripts of Maize necrotic streak virus: Infectivity and translational characteristics. Virology 2006; 350 (1):171-83

Bernardo A, Bai G, Guo P, Xiao K, Guenzi AC, and Ayoubi, P.  2007.  Fusarium graminearum-induced differential gene expression between Fusarium head blight-resistant and susceptible wheat cultivars.  Funct Integr Genomics.  7:69-77.

de la Fuente J, Ayoubi P, Blouin EF, Almazan C, Naranjo V, Kocan KM.  2006.  Anaplasmosis: focusing on host-vector-pathogen interactions for vaccine development. Ann N Y Acad Sci. 1078:416-23.

Naranjo V, Ayoubi P, Vicente J, Ruiz-Fons F, Gortazar C, Kocan KM, de la Fuente J.  2006.  Characterization of selected genes upregulated in non-tuberculous European wild boar as possible correlates of resistance to Mycobacterium bovis infection.  Vet Microbiol. 116:224-31.

Park SJ, Huang Y, Ayoubi P.  2006.  Identification of expression profiles of sorghum genes in response to greenbug phloem-feeding using cDNA subtraction and microarray analysis.  Planta. 223:932-47.

Zhang Q, Melcher U, Zhou L et al. Genomic comparison of plant pathogenic and nonpathogenic Serratia marcescens strains by suppressive subtractive hybridization. Applied and Environmental Microbiology 2005; 71 (12):7716-23.

Joshi BD, Berg M, Rogers J et al. Sequence comparisons of plasmids pBJS-O of Spiroplasma citri and pSKU146 of Spiroplasma kunkelii: Implications for plasmid evolution. BMC Genomics 2005; 6.

Huang, Y. Phloem feeding regulates the plant defense pathways responding to both aphid infestation and pathogen infection. Proceeding of the 11th International Association for Plant Tissue Culture & Biotechnology. (in press)

Wren JD, Roossinck MJ, Nelson RS et al. Plant virus biodiversity and ecology. Plos Biology 2006; 4 (3):314-5.

Comer, J., J. Fletcher, R.E. Davis and U. Melcher. 2006. Characterization of the Spiroplasma P58 multigene family. Bioch. Genet. 44:9-10.

Mahalingam R, Jambunathan N, Gunjan SK et al. Analysis of oxidative signalling induced by ozone in Arabidopsis thaliana. Plant Cell and Environment 2006; 29 (7):1357-71.

Spicer LJ, Aad PY, Allen D et al. Growth differentiation factor-9 has divergent effects on proliferation and steroidogenesis of bovine granulosa cells. Journal of Endocrinology 2006; 189 (2):329-39.

Lents CA, Wettemann RP, White FJ et al. Influence of nutrient intake and body fat on concentrations of insulin-like growth factor-I, insulin, thyroxine, and leptin in plasma of gestating beef cows. Journal of Animal Science 2005; 83 (3):586-96.

Aad PY, Voge JL, Santiago CA et al. Real-time RT-PCR quantification of pregnancy-associated plasma protein-A mRNA abundance in bovine granulosa and theca cells: Effects of hormones in vitro. Domestic Animal Endocrinology 2006; 31 (4):357-72.

Aad PY, Echternkamp SE, Spicer LJ. IGF type II receptor gene expression in granulosa and theca cells of cattle selected for twin ovulations and births. Biology of Reproduction 2006:173 (abstract, no pdf available).

Prado-Cooper MJ, Rubio I, Davis MP et al. Effect of body condition on plasma concentrations of IGF-I in postpartum beef cows treated with somatotropin. Journal of Animal Science 2006; 84:31(abstract, no pdf available).

Caloni F, Ranzenigo G, Spicer LJ. Fusariotoxins and pig granulosa cells: In vitro effects on cellular proliferation. Veterinary Research Communications 2006; 30:281-3.

Ranzenigo G, Caloni F, Cremonesi F et al. Fusarium mycotoxins affect progesterone and estradiol production of pig granulosa cells in vitro. Reproduction in Domestic Animals 2006; 41 (4):365 (abstract, no pdf available).

Zhang, Y, A. C. Guenzi, M. P. Anderson, C. M. Taliaferro and R. A. Gonzales. 2006 Enrichment of bermudagrass genes associated with tolerance to the spring dead spot fungus Ophiosphaerella herpotricha. Physiological and Molecular Plant Pathology (In Press)

Chenault, K. D. , M. Gallo, J. C. Seib and V. James. 2007. Non-destructive Seed Sampling Method for PCR-based Analyses in Marker Assisted Selection and Transgene Screening. Peanut Science, in press.

Guo, P., Bai, G., Carver, B., Li, R., Bernardo, A. and Baum, M.  Transcriptional analysis between two wheat near-isogenic lines contrasting in aluminum tolerance under aluminum stress. 2007. Mol. Genet. Genomics 277:1-12.

Nakare, H., Palyada, K., Panciera, R., Marlow, D. and Stintzi, A.  Major role for feoB in Campylobacter  jejuni ferrous iron acquisition, gut colonization, and intracellular survival. 2006. Infection Immunity 74:5433-5444.

Patil, M. A., M. L. Pierce, A. L. Phillips, B. J. Venters, and M. Essenberg. 2005. Identification of genes up-regulated in bacterial-blight-resistant upland cotton in response to inoculation with Xanthomonas campestris pv. malvacearum. Physiological and Molecular Plant Pathology 67:319-335.

Chenault, K. D., and Damicone, J. 2007. Screening of F1/F2 seed for the presence of a molecular marker for Sclerotinia minor. Partners in Progress Peanuts pp.34-38

Taliercio, E., R. D. Allen, M. Essenberg, N. Klueva, H. Nguyen, M. A. Patil, P. Payton, A. C. M. Millena, A. L. Phillips, M. L. Pierce, B. Scheffler, R. Turley, J. Wang, D. S. Zhang, and J. Scheffler. 2006. Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs. Genome 49:306-319.

Udall, J. A., J. M. Swanson, K. Haller, R. A. Rapp, M. E. Sparks, J. Hatfield, Y. S. Yu, Y. R. Wu, C. Dowd, A. B. Arpat, B. A. Sickler, T. A. Wilkins, J. Y. Guo, X. Y. Chen, J. Scheffler, E. Taliercio, R. Turley, H. McFadden, P. Payton, N. Klueva, R. Allen, D. S. Zhang, C. Haigler, C. Wilkerson, J. F. Suo, S. R. Schulze, M. L. Pierce, M. Essenberg, H. Kim, D. J. Llewellyn, E. S. Dennis, D. Kudrna, R. Wing, A. H. Paterson, C. Soderlund, and J. F. Wendel. 2006. A global assembly of cotton ESTs. Genome Research 16:441-450.

Fernando, S. C., Najar, F. Z., Guo, X., Zhou, L., Fu, Y., Geisert, R. D., Roe, B. A., and  DeSilva, U*. 2007 Isolation and Characterization of the Porcine Kallikrein Gene Family: Genomic Structure, Radiation-Hybrid Mapping and Differential Expression Analysis. Genomics 89: 429-438

Bommineni, Y.R., Dai, H., Gong, Y. X., Soulages, J. L., Fernando, C. S., DeSilva, U., Prakash, O., and Zhang, G. 2007 Fowlicidin-3 is an alpha-helical cationic host defense peptide with potent antibacterial and lipopolysaccharide-neutralizing activities. FEBS Journal 274 (2): 418-428

Ashworth, M.D., Ross, J.W., Hu, J., White, F.J., Stein, D.R., DeSilva, U., Johnson, G.A., Spencer, T.E., and Geisert, R.D. 2006. Expression of porcine endometrial prostaglandin synthase during the estrous cycle and early pregnancy, and following endocrine disruption of pregnancy. Biol.Reprod. 74:1007-1015

Fernando, S. C., Ashworth, M.S., Ross, J. W., Geisert, R. D., and DeSilva, U*. 2006 Porcine endometrial and conceptus tissue kallikrein 1,4,11 and 14 gene expression.  Reproduction 132,1-10

Purvis II, H., Fernando, S., Rutz, K., Najar, F., Roe, B., and DeSilva, U. 2006 Evaluation of Rumen Microbial Fluctuations in Response to Sub Acute Rumen Acidosis Using 16S rDNA Profiles. Journal of Animal Science 84:86 (abstract, no reprint available)

Ayalew, S., Blackwood, E.R. and Confer, A.W. (2005). Sequence diversity of the immunogenic outer membrane lipoprotein PlpE from Mannheimia haemolytica serotypes 1, 2, and 6. Vet Microbiol

de la Fuente, J., Ayoubi, P., Blouin, E.F., Almazan, C., Naranjo, V. and Kocan, K.M. (2005). Gene expression profiling of human promyelocytic cells in response to infection with Anaplasma phagocytophilum. Cell Microbiol 7: 549-59.

Donnelly, B.E., Madden, R.D., Ayoubi, P., Porter, D.R. and Dillwith, J.W. (2005). The wheat (Triticum aestivum L.) leaf proteome. Proteomics 5: 1624-33.

Joshi, B.D., Berg, M., Rogers, J., Fletcher, J. and Melcher, U. (2005). Sequence comparisons of plasmids pBJS-O of Spiroplasma citri and pSKU146 of S. kunkelii: implications for plasmid evolution. BMC Genomics 6: 175.

Park, S.J., Huang, Y. and Ayoubi, P. (2005). Identification of expression profiles of sorghum genes in response to greenbug phloem-feeding using cDNA subtraction and microarray analysis. Planta 1-16.

Poly, F., Threadgill, D. and Stintzi, A. (2005). Genomic diversity in Campylobacter jejuni: identification of C. jejuni 81-176-specific genes. J Clin Microbiol 43: 2330-8.

Ross, J.W., Smith, T.K., Krehbiel, C.R., Malayer, J.R., DeSilva, U., Morgan, J.B., White, F.J., Hersom, M.J., Horn, G.W. and Geisert, R.D. (2005). Effects of grazing program and subsequent finishing on gene expression in different adipose tissue depots in beef steers. J Anim Sci 83: 1914-23.

Stintzi, A., Marlow, D., Palyada, K., Naikare, H., Panciera, R., Whitworth, L. and Clarke, C. (2005). Use of genome-wide expression profiling and mutagenesis to study the intestinal lifestyle of Campylobacter jejuni. Infect Immun 73: 1797-810.

Te, J., Melcher, U., Howard, A. and Verchot-Lubicz, J. (2005). Soilborne wheat mosaic virus (SBWMV) 19K protein belongs to a class of cysteine rich proteins that suppress RNA silencing. Virol J 2: 18.

Uppalapati, S.R., Ayoubi, P., Weng, H., Palmer, D.A., Mitchell, R.E., Jones, W. and Bender, C.L. (2005). The phytotoxin coronatine and methyl jasmonate impact multiple phytohormone pathways in tomato. Plant J 42: 201-17.

Wang, Y., Zou, Z. and Jiang, H. (2005). An expansion of the dual clip-domain serine proteinase family in Manduca sexta: Gene organization, expression, and evolution of prophenoloxidase-activating proteinase-2, hemolymph proteinase 12, and other related proteinases. Genomics

Wren, J.D., Hildebrand, W.H., Chandrasekaran, S. and Melcher, U. (2005). Markov model recognition and classification of DNA/protein sequences within large text databases. Bioinformatics 21: 4046-53.

Zhang, Q., Melcher, U., Zhou, L., Najar, F.Z., Roe, B.A. and Fletcher, J. (2005). Genomic comparison of plant pathogenic and nonpathogenic Serratia marcescens strains by suppressive subtractive hybridization. Appl Environ Microbiol 71: 7716-23.

Zou, Z. and Jiang, H. (2005). Gene structure and expression profile of Manduca sexta prophenoloxidase-activating proteinase-3 (PAP-3), an immune protein containing two clip domains. Insect Mol Biol 14: 433-42.

Madden, R.D., Sauer, J.R. and Dillwith, J.W. (2004). A proteomics approach to characterizing tick salivary secretions. Exp Appl Acarol 32: 77-87.

Onodera, K. and Melcher, U. (2004). Selection for 3' end triplets for polymerase chain reaction primers. Mol Cell Probes 18: 369-72.

Palyada, K., Threadgill, D. and Stintzi, A. (2004). Iron acquisition and regulation in Campylobacter jejuni. J Bacteriol 186: 4714-29.

Poly, F., Threadgill, D. and Stintzi, A. (2004). Identification of Campylobacter jejuni ATCC 43431-specific genes by whole microbial genome comparisons. J Bacteriol 186: 4781-95.

Ray, A., Macwana, S., Ayoubi, P., Hall, L.T., Prade, R. and Mort, A.J. (2004). Negative subtraction hybridization: an efficient method to isolate large numbers of condition-specific cDNAs. BMC Genomics 5: 22.

Tzafrir, I., Pena-Muralla, R., Dickerman, A., Berg, M., Rogers, R., Hutchens, S., Sweeney, T.C., McElver, J., Aux, G., Patton, D. and Meinke, D. (2004). Identification of genes required for embryo development in Arabidopsis. Plant Physiol 135: 1206-20.

Wang, H.L., Postier, B.L. and Burnap, R.L. (2004). Alterations in global patterns of gene expression in Synechocystis sp. PCC 6803 in response to inorganic carbon limitation and the inactivation of ndhR, a LysR family regulator. J Biol Chem 279: 5739-51.

Rascoe, J.E., Berg, M., Melcher, U., Mitchell, F.L., Bruton, B.D. , Pair, S.D. & Fletcher, J. (2003), Identification, phylogenetic analysis and biological characterization of strains of Serratia marcescens causing cucurbit yellow vine disease., Phytopathology 93(10): 1233-1239.

Zhang, Q., Weyant, R., Melcher, U., Bruton, B. D., Pair, S. D., Mitchell, F., & J. Fletcher (2003), Genotyping of Serratia marcescens strains associated with cucurbit yellow vine disease., Phytopathology 93 (10): 1240-1246.

Bruton, B. D., Mitchell, F., Fletcher, J., Pair, S.D., Wayadande, A., Melcher, U., Brady, J., Bextine, B. & Popham, T. H. (2003), Serratia marcescens, a phloem-colonizing, squash bug-transmitted bacterium: causal agent of cucurbit yellow vine disease., Plant Disease 87: 937-944.

Melcher, U (2003), Turnip vein-clearing virus, from pathogen to host expression profile. Molec. Plant Pathol. 4: 133-140.

An, H., Melcher, U., Doss, P., Payton, M., Guenzi, A. C. & Verchot-Lubicz, J. (2003). Evidence that the 37 kDa protein of Soil-borne wheat mosaic virus is a virus movement protein. J Gen Virol 84: 3153-63.

Geisert, R. D., Ashworth, M. D. & Malayer, J. R. (2003). Expression of inter-alpha-trypsin inhibitor heavy chains in endometrium of cyclic and pregnant gilts. Reproduction 126: 621-7.

Wang, H. L., Postier, B. L. & Burnap, R. L. (2003). Alterations in global patterns of gene expression in Synechocystis sp. PCC 6803 in response to inorganic carbon limitation and the inactivation of ndhR, a LysR family regulator. J Biol Chem

Sengupta, S., Onodera, K., Lai, A. & Melcher, U. (2003). Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization. J Clin Microbiol 41: 4542-50.

Gou, D., Jin, N. & Liu, L. (2003). Gene silencing in mammalian cells by PCR-based short hairpin RNA. FEBS Lett 548: 113-8.

Aljamali, M. N., Bior, A. D., Sauer, J. R. & Essenberg, R. C. (2003). RNA interference in ticks: a study using histamine binding protein dsRNA in the female tick Amblyomma americanum. Insect Mol Biol 12: 299-305.

Postier, B. L., Wang, H. L., Singh, A., Impson, L., Andrews, H. L., Klahn, J., Li, H., Risinger, G., Pesta, D., Deyholos, M., Galbraith, D. W., Sherman, L. A. & Burnap, R. L. (2003). The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy. BMC Genomics 4: 23.

Stintzi, A. (2003). Gene expression profile of Campylobacter jejuni in response to growth temperature variation. J Bacteriol 185: 2009-16.

Ross, J., Jiang, H., Kanost, M. R. & Wang, Y. (2003). Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships. Gene 304: 117-31.

Tzafrir, I., Dickerman, A., Brazhnik, O., Nguyen, Q., McElver, J., Frye, C., Patton, D. & Meinke, D. (2003). The Arabidopsis SeedGenes Project. Nucleic Acids Res 31: 90-3.

Ross, J. W., Ashworth, M. D., Hurst, A. G., Malayer, J. R. & Geisert, R. D. (2003). Analysis and characterization of differential gene expression during rapid trophoblastic elongation in the pig using suppression subtractive hybridization. Reprod Biol Endocrinol 1: 23.


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