University of Hawai‘i at Manoa
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Last updated on Friday, September 11, 2015     Make updates ->

Gernot  Presting

Name :

Gernot Presting

Title :

Prof

Unit :

Department of Molecular Biosciences & BioEngineering

Address :

1955 East-West Rd. #218
                    Honolulu, HI 96822

Room :

St. John 515D

Phone :

(808)956-8861

Fax :

(808)956-3542

E-mail :

gernot@hawaii.edu

Website :

http://www.genomics.hawaii.edu


Professional Prep/Appointments :


PhD:  University of Wisconsin-Madison
BSc:  University of Delaware

Courses Taught:


Primary Instructor for:

MBBE/BIOL406
MBBE483
MBBE610
MBBE683

iGEM Undergraduate Research Experience
Primary faculty advisor of the first Hawaii iGEM (international Genetic Engineered Machines) team – hosted and mentored the 3 undergraduate students in our genomics/bioinformatics laboratory, advising them (with help from faculty members Dr. Sean Callahan (Microbiology) and Dr. Loren Gautz (Bioengineering)) on project design, research methods and laboratory techniques. The team won a bronze medal and “Best Rookie Team “ honors for their research presentation at MIT in November 2008.  The team also presented this work at the March 19-21, 2009 Institute of Biological Engineering Conference in Santa Clara, CA.


Guest lecturer for:

BE120 - Introduction to Quantitative Biology
BE625 - Biosensor Principles and Applications
BIOL171 - General Biology
BIOL406 - Cell Biology
BIOL406L - Cellular Biology Laboratory 
BIOL407 - Molecular Biology
Biotechnology Workshops
for Community College Instructors

Bot 600 - Grant Writing and Your Career in Science
BOT669 - Molecular Phylogenetics and Evolution

CMB621 - Cellular and Molecular Biology
INBRE - Idea Networks of Biomedical Research Excellence) Workshop

MBBE651 - Signal Transduction and Regulation of Gene Transcription
OCN403 - Marine Functional Genomics and Biotechnology
PEPS646 - Plant-Bacterial Interactions
TPSS300 - Tropical Production Systems



Research Interests :


  • Bioinformatics – computational analysis of sequence data
  • Plant Genome Evolution – evolutionary forces on genome expansion
  • Biodiversity – analysis of conserved sequences and lateral gene transfer
  • Centromeres - composition and evolution of plant centromeres


Selected Recent Publications :


Peer-Reviewed:

Sherwood AR, Carlile AL, Neumann JM, Kociolek JP, Johansen J, Lowe RL, Conklin KY, Presting G. 2014. The Hawaiian Freshwater Algae Biodiversity Survey (2009-2014): systematic and biogeographic trends with an emphasis on the macroalgae. BMC Ecology, 14:28. Doi: 10.1186/s12898-014-0028-2

Sharma A and Presting G. 2014. Evolution of Centromeric Retrotransposons in Grasses. Genome Biology and Evolution. doi: 10.1093/gbe/evu096.

Campbell MA, Presting G, Bennett MS, Sherwood, AR. 2014. Highly conserved organellar genomes in the Gracilariales as inferred using new data from the Hawaiian invasive alga Gracilaria salicornia (Rhodophyta). Phycologia, 53:109-116.

Sharma A, Wolfgruber TK, Presting G. 2013. Tandem repeats derived from centromeric retrotransposons. BMC Genomics, 14:142.

Birchler JA and Presting G. 2012. Retrotransposon insertion targeting: a mechanism for homogenization of centromere sequences on nonhomologous chromosomes. Genes and Development 26:638-640.

Sherwood AR, Wang N, Carlile AL, Neumann JM, Wolfgruber TK, Presting G. 2012. The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource. BMC Ecology, 12:22, DOI:10.1186/1472-6785-12-22.

Yakabe LE, Maccree MM, Sudarshana P, McClean AE, Parker SR, Wechter WP, Presting G, Marutani-Hert M and Kluepfel DA. 2012. Novel PCR primers for detection of genetically diverse virulent Agrobacterium tumefaciens biovar 1 strains. Journal of General Plant Pathology, DOI: 10.1007/s10327-012-0364-z.

Birchler JA, Gao Z, Sharma A, Presting G and Han F. 2011. Epigenetic aspects of centromere function in plants. Current Opinion in Plant Biology, 14:217-222.

Schneider K, Marrero G, Alvarez A and Presting G. 2011. Rapid identification of plant pathogenic bacteria below the species level using a computationally derived DNA marker. PLoS ONE 6(4): e18496. doi:10.1371/journal.pone.0018496.

Gent JI, Schneider KL, Topp CN, Rodriguez C, Presting GG and Dawe RK. 2011. Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning. Epigenetics & Chromatin, 4:3 doi:10.1186/1756-8935-4-3.

Sherwood AR, Sauvage T, Kurihara A, Conklin KY and Presting G. 2010. A comparative analysis of COI, LSU and UPA marker data for the Hawaiian florideophyte Rhodophyta: implications for DNA barcoding of red algae. Cryptogamie-Algologie, 31(4):451-465.

Sherwood AR, Kurihara A, Conklin KY, Sauvage T and Presting G. 2010. The Hawaiian Rhodophyta Biodiversity Survey (2006-2010): a summary of principal findings. BMC Plant Biology, 10:258. doi:10.1186/1471-2229-10-258.

Shi J, Wolf SE, Burke JM, Presting GG, Ross-Ibarra J, Dawe RK. 2010. Widespread Gene Conversion in Centromere Cores. PLoS Biol 8(3): e1000327. doi:10.1371/journal.pbio.1000327.

Wolfgruber TK, Presting G. 2010. JunctionViewer: customizable annotation software for repeat-rich genomic regions. BMC Bioinformatics, 11:23. doi:10.1186/1471-2105-11-23.

Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo D-H, Shi J, Lee H, Gao Z, Han F, Xu R, Allison J, Birchler JA, Jiang J, Dawe RK, Presting G. 2009. Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic loci shaped primarily by retrotransposons. PLoS Genet 5(11): e1000743. doi:10.1371/journal.pgen.1000743.

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney W, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W,
Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy M, McMahan L, Buren PV, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia J, Deragon J, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton DS, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. 2009. The B73 maize genome: complexity, diversity and dynamics. Science, 326:1112-1115.

Wang N, Sherwood AR, Kurihara A, Conklin KY, Sauvage T, Presting G. 2009. The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data. BMC Plant Biology, 9:117.

Sharma A, Schneider KL and Presting G. 2008. Sustained retrotransposition is mediated by nucleotide deletions and inter-element recombinations. Proc Natl Acad Sci USA, 105:15470-15474.

Paull RE, Irikura B, Wu P, Turano H, Chen NJ, Blas A, Fellman JK, Gschwend AR, Wai CM, Yu Q, Presting G, Alam M, Ming R. 2008. Fruit development, ripening and quality related genes in the papaya genome. Tropical Plant Biol. 1:246–277.

Sharma A, Presting G. 2008. Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity. Mol Gen Genomics, 279:133–147.

Sherwood A, Chan YL and Presting G. 2008. Application of universally amplifying plastid primers to environmental sampling of a stream periphyton community. Mol Ecol Resour, 8 (5), 1011-1014.

Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice D, Albert H, Wang M, Zhu YJ, Schatz M, Nagarajan N, Agbayani R, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na J, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Pérez RN, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo M, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen D, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M. 2008. Genome of the transgenic tropical fruit tree papaya (Carica papaya L.). Nature, 452:991-996.

Sherwood AR, Vis ML, Entwisle TJ, Necchi O and Presting G. 2008. Contrasting intra- versus inter-specific sequence variation for representatives of the Batrachospermales (Rhodophyta): a comparison of two markers. Phycological Research, 56:269-279.

Umylny B, Presting G and Ward WS. 2007. Evidence of Alu expression in dbEST. Archives of Andrology, 53:207-18.

Eustice M, Yu Q, Lai CWJ, Moore PH, Presting G and Ming R. 2007. Development and use of microsatellite markers for genetic analysis in papaya. Tree Genetics and Genomes, 4:333-341, DOI 10.1007/s11295-007-0112-2.

Umylny B, Presting G, Efird J and Ward WS. 2007. Near full-length Alu and B1 repeat sequences within protein coding regions and other expressed transcripts. Journal of Cellular Biochemistry, 102:110-121, DOI: 10.1002/jcb.21278.

Sherwood AR, Presting G. 2007. Universal primers amplify a potential DNA barcode region for eukaryotic algae. Journal of Phycology, 43:605-608.

Presting G. 2006. Identification of conserved regions in the plastid genome – implications for DNA barcoding and biological function. Canadian Journal of Botany, 84:1434-1443.

Luce A, Sharma A, Mollere O, Wolfgruber TK, Nagaki K, Jiang J, Presting G, Dawe RK. 2006. Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-PCR. Genetics 174:1057-61.

Jenkins DM, Chami B, Kreuzer M, Presting G, Alvarez A, Liaw BY. 2006. Hybridization probe for femtomolar quantification of selected nucleic acid sequences on a disposable electrode. Anal Chem. 78:2314-8.

Lai CW, Yu Q, Hou S, Skelton RL, Jones MR, Kanako LTJ, Murray J, Eustice M, Agbayani R, Guan P, Moore P, Ming R, Presting G. 2006. Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol. Gen. Genomics 276:1-12.

Gabriel DW, Allen C, Schell M, Denny T, Greenberg J, Duan YP, Flores-Cruz Z, Huang Q, Clifford JM, Presting G, Gonzalez ET, Reddy J, Elphinstone J, Swanson J, Yao J, Mulholand V, Liu L, Farmerie W, Patnaikuni M, Balogh B, Norman D, Alvarvez A, Castillo JA, Jones J, Saddler G, Walunas T, Zhukov A and Mikhailova N. 2006. Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2. Mol. Plant Microbe Interactions. 19:69-79.

Book Chapters:

Xie Z, Presting G. 2015. Chromatin immunoprecipitation to study the plant epigenome, In: Plant Cytogenetics, coming soon.

Presting G. 2013. Maize centromeres, In: Plant Centromere Biology, Jiang J, Birchler J A, eds. John Wiley & Sons, pp. 25-38.

Lange BM, Presting G. 2004. Genomic survey of metabolic pathways in rice, In: Recent Advances in Phytochemistry, Romeo, John T., ed., Elsevier Science, Amsterdam, pp. 111-137.

Wing RA, Yu Y, Presting G, Frisch D, Wood T, Woo S-S, Budiman MA, Mao L, Kim HR, Rambo T, Fang E, Blackmon B, Goicoechea JL, Higingbottom S, Sasinowski M, Tomkins J, Dean RA, Soderlund C, McCombie WR, Martienson R, de al Bastide M, Wilson R, Johnson D. 2002.Sequence-tagged connector / DNA fingerprint framework for rice genome sequencing. In: Rice Genetics IV. pp. 215 to 225. The International Rice Research Institute. Science
Publishers Inc. New Delhi, India.

Presting G, Budiman MA, Wood T, Yu Y, Kim HR, Goicoechea JL, Fang E, Blackman B, Jiang J, Woo SS, Dean RA, Frisch D, Wing RA. 2001. A framework for sequencing the rice genome. In: Rice Biotechnology: Improving yield, stress tolerance and grain quality, Jamie A. Goode and Derek Chadwick, eds., John Wiley & Sons, New York, pp. 236:13-27.