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Dr. James Godde

James GoddeProfessor of Biology

Contact Information

Phone: 309-457-2350

Office: Rm. 244, CSB

Office Hours

Off campus in Merida, Mexico during Spring '17


B.S. 1987, Western Illinois University
Ph.D. 1993, University of Illinois
Post-doc, National Institutes of Health

Courses taught

Cell Biology, Genetics, Molecular Biology, Microbiology, Life on Earth, Biotechnology and Human Values, Bioinformatics, Global Perspectives: World Impact of East Asian Science, Introduction to the Liberal Arts, The Tao of Travel, Sacred Places, Wilderness: Rainforest Ecosystems, Wilderness: Galapagos Ecosystems, Wilderness: Caribbean Ecosystems, Introduction to Environmental Science, Environmental Microbiology: the Extremophiles, Plants and Society, 3D Animation, Advanced 3D Animation (College for Kids)

Research Interests

Much progress has been made in recent years in the determination of the DNA sequence of a large variety of genomes, with over 1000 complete genomes published and nearly four times this amount ongoing.  Precisely how this genetic information is expressed, however, remains poorly understood.  While it is possible to perform top-down methods to measure the transcriptome and/or the proteome of a given cell type under a given set of conditions in a particular organism of interest, this is currently not feasible for all of the combinations which exist.  A better understanding of gene expression would facilitate our being able to convert the fairly straight-forward information encoded in the sequence of nucleotide bases which make up a genome into the exceedingly more complex information that remains the ultimate goal of systems biology: monitoring the changes in the levels of every protein found in every cell throughout the lifetime of an organism.  While much of the information which controls levels of gene expression is found in the non-protein coding regions of the genome and is therefore the subject of the genome projects in question, a considerable amount of gene expression, especially in eukaryotes, is controlled by reversible epigenetic changes to the DNA and its packaging, information which is not directly encoded by the DNA sequence.  Epigenetic factors which control gene expression include DNA methylation, non-coding RNAs, chromatin remodeling, as well as changes in histone subtype and/or chemical modification. 

My laboratory is interested in investigating the epigenetic control of eukaryotic gene expression.  Our research involves the expression and purification of the components required to reconstitute long arrays of nucleosomes in vitro.  These include both a DNA fragment which specifically positions long nucleosomal arrays as well as the recombinant proteins required for chromatin reconstitution.  The proteins which we chromatographically purify include the four core histones (H2A, H2B, H3 & H4), various linker histones (including B4 and H1A), along with NAP-1, a histone chaperone whose presence is required for the correct assembly of linker histone-containing arrays of nucleosomes.  Following the purification of the required components, we work to reconstitute long linker histone-containing arrays of nucleosomes, in vitro.  This is a rather simple procedure involving salt dialysis but must be carefully monitored in order to ensure that the reconstituted chromatin mimics physiological conditions.  Once these objectives are achieved, we then measure the relative sedimentation of reconstituted arrays under varying conditions of added linker histone and MgCl2 using ultracentrifugation techniques.  This approach determines whether our reconstituted chromatin is in the extended form typically associated with transcriptionally active chromatin or in a more compact state, such as that which is typically associated with transcriptionally repressed chromatin.  A final experimental approach is required to determine which parts of the linker histones in question are critical for changes in their chromatin compaction abilities by using chimeric histones containing various tripartite regions which have been swapped with other linker histones in the above reconstitution studies. 

Recent Publications

Godde, J.S. (2016) "Histone acetylation/deacetylation" in Salem Encylopedia of Health and Medicine: Cancer, 2nd Ed., Vol. 3, 803, Grey House Publishing: Armenia, NY

Godde, J.S. (2015) "Studying Abroad" in Salem Health: Adolescent Health & Wellness, 941-943, Grey House Publishing: Armenia, NY

Godde, J.S. (2012) Breaking through a phylogenetic impasse: a pair of associated archaea may have played host in the endosymbiotic origin of eukaryotes., Cell & Bioscience, 2:29.

Godde, J.S. (2012)  “DNA Analysis” in Encyclopedia of Applied Sciences, 515-520, Salem Press: Pasadena, CA.

Godde, J. S. (2011) “Biopiracy and Bioprospecting” in Encyclopedia of Environmental Issues, Revised Ed., 162-164, Salem Press: Pasadena, CA.

Coyne, M. S. & Godde, J. S. (2010) “Environmental Biotechnology” in Encyclopedia of Global Resources, 372-375, Salem Press: Pasadena, CA.

Gossett, D. R. & Godde, J. S. (2010) “Biotechnology” in Encyclopedia of Global Resources, 124-129, Salem Press: Pasadena, CA.

Godde, J. S. (2010) “Wolf-Hirschhorn Syndrome” in Genetics and Inherited Disorders: Revised Edition, Vol. 3, 1242-1243, Salem Press: Pasadena, CA.

Godde, J. S. (2010) “Genetic Resources” in Encyclopedia of Global Resources, Vol. 2, 490-494, Salem Press: Pasadena, CA.

Godde, J. S. (2009) “Biotechnology” in Encyclopedia of Global Warming, Vol. 1, 142-145, Salem Press: Pasadena, CA.

Godde, J. S. & Ura, K. (2009) Dynamic alterations of linker histone variants during development., Int. J. Dev. Biol., 53:215-224.

Godde, J. S. (2008) “Chromosomes and cancer” in Salem Encyclopedia of Health and Medicine: Cancer, Vol. 1, 274-276, Salem Press: Pasadena, CA.

Godde, J. S. (2008) “STR (short tandem repeat) analysis” in Encyclopedia of Forensic Science, Vol. 3, 920, Salem Press: Pasadena, CA.

Godde, J. S. & Ura, K. (2008) Cracking the enigmatic linker histone code., J. Biochem. 143:287-293.

Godde, J. S. (2007) “Last human chromosome sequenced” in Magill’s Medical Encyclopedia, 4th rev. ed., Vol. 2, 1122, Salem Press: Pasadena, CA.

Godde, J. S. & Bickerton, A. J. (2006) The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes., J. Molec. Evol., 62, 718-729.

Godde, J. S. (2005) “Genomics” in Magill’s Medical Encyclopedia, 3rd rev. ed., 1066-1070, Salem Press: Pasadena, CA.

Godde, J. S. (2004) “Telomere Length in Clones” in Encyclopedia of Genetics, rev. ed., 730, Salem Press: Pasadena, CA.

Feig, J., Hussein, Y., & Godde, J. S. (2001) Combinatorial libraries of porphyrin derivatives: finding G-quadruplex interactive agents with a high specificity for human telomeric repeats., J Biomol. Struct. Dyn., 18, 967.

Goldman, K., Lembeck, M., & Godde, J. S. (1999) Probing the structure of (CGG)n triplet repeats in the human FMR1 gene via interstrand crosslinking., J Biomol. Struct. Dyn., 16, 1274-1275.

Goldman, K., Donaire, M., & Godde, J. S. (1998) Mapping mitomycin crosslink sites in the human Fragile X gene., National Minority Research Symposium Proceedings., 88.

Godde, J. S., Kas, S.U., Hirst, M. & Wolffe, A.P. (1996) Nucleosome assembly on methylated CGG triplet repeats in the Fragile X Mental Retardation Gene 1 promoter., J. Biol. Chem., 271, 24325-24329.

Godde, J. S., & Wolffe, A.P. (1996) Nucleosome assembly on CTG triplet repeats., J. Biol. Chem., 271, 15222-15229.

Godde, J. S., Nakatani, Y., & Wolffe, A.P. (1995) The amino-terminal tails of the core histones and the translational position of the TATA box determine TBP/TFIIA association with nucleosomal DNA., Nucleic Acids Research., 23, 4557-4564.

Godde, J. S., & Wolffe, A.P. (1995) Disruption of reconstituted nucleosomes: the effect of particle concentration, MgCl2 and KCl concentration, the histone tails and temperature., J. Biol. Chem., 270, 27399-27402.

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