Publications by faculty in the Department of Biological Sciences 2002-2008.    Please see an individual faculty’s web page for the most up-to-date list.

Webster, C. W., C. J. Huckins, J. M. Shields.  2008. Spatial Distribution of Riparian Zone Coarse Woody Debris in a Managed Northern Temperate Watershed.  American Midland Naturalist in press.

Auer, N.A. and E.A. Baker.  2007, Assessment of Lake Sturgeon Spawning Stocks Using Fixed-location, Split-beam Sonar Technology. Journal of Applied Ichthyology (in press).

Shields, J., Webster, C. R., and Glime, J. M.  2007.  Bryophyte community response to silvicultural opening size in a managed northern hardwood forest.  Forest Ecology and Management in press

Glime, J M.  2007.  Bryophyte Ecology.  Volume 1.  Physiological Ecology. Ebook sponsored by Michigan Technological University and the International Association of Bryologists.  <http://www.bryoecol.mtu.edu/>

Bellinger, B.J., Underwood, G.J.C., Ziegler, S.E. and Gretz, M.R. 2007. The significance of diatom-derived polymers in carbon flow dynamics within estuarine biofilms determined through isotopic enrichment. Limnology & Oceanography (in press).

Domozych, D.S., Elliott, L., Kiemle, S.N. and Gretz, M.R. 2007. Pleurotaenium trabecula, a desmid of wetland biofilms: The extracellular matrix and adhesion mechanisms. Journal of Phycology (in press).

Domozych, D.S., Serfis, A., Kiemle, S. and Gretz, M.R. 2007. The structure and biochemistry of charophycean cell walls. I. Pectins of Penium margaritaceum. Protoplasma.230:99-115

Huckins, C. J, and .E. A. Baker. 2007. Migrations and Biological Characteristics of Adfluvial Coaster Brook Trout in a South Shore Lake Superior Tributary. Transactions of the American Fisheries Society.in press.

Kiemle, S.N., Domozych, D.S. and Gretz, M.R. 2007. The extracellular polymeric substances of desmids (Conjugatophyceae, Streptophyta): Structural analysis and implications in wetland biofilms. Phycologia (in press).

Huckins, C. J, .E. A. Baker, K. D. Fausch and J. B. K. Leonard. 2007. Ecology and Life History of Ecology and Life History of Coaster Brook Trout Salvelinus fontinalis and Potential Bottlenecks in Their Rehabilitation. North American Journal of Fish Management. in press.

Snyder, T. P., J. L. Chiantello, E. Kjellmark and K.B. Baumgardner.  2007.  Key to the Pollen of the Bahamas.   Gerace Research Center, San Salvador, Bahamas.   link to key.

N Krom, J Recla and W. Ramakrishna. 2007. Analysis of genes associated with retrotransposons in the rice genome (submitted).

N Krom and W. Ramakrishna. 2007. Comparative analysis of divergent and convergent gene pairs in rice, Arabidopsis, and Populus (submitted).

Z Xu and W. Ramakrishna. 2007. Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history (submitted).

 RV Oakley, Y-S Wang, W Ramakrishna, SA Harding and C-J Tsai. 2007, Differential expansion and expression of the alpha- and beta-tubulin gene families in Populus. Plant Physiol 145 Issue 3.

E Nagy, T-C Lee, W Ramakrishna, Z Xu, P Klein, P SanMiguel, C-P Cheng, J Li, K Devos, K Schertz, L Dunkle and J Bennetzen. 2007.  Fine mapping of the Pc locus of Sorghum bicolor, a gene controlling the reaction to a fungal pathogen and its host-selective toxin. Theor Appl Genet 114: 961-970.

Gorantla M, Babu P, Reddy Lachagari V, Reddy A, Wusirika R, Bennetzen JL and Reddy AR. 2007.  Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings. J Exp Botany 58: 253-265.

Oyadomari, J.K. and N. A. Auer. 2006. Influence of Rearing Temperature and Feeding Regime on Otolith Increment Deposition in Larval Cisco. Transactions of the American Fisheries Society (in press).

Bowden, W. B., Glime, J. M., and Riis, T.  2006.  Macrophytes and bryophytes.  Chapter 18.  In:  Hauer, F. R. and Lamberti, G. A.  Methods in Stream Ecology.  Elsevier, Boston.  pp. 381-414.

Glime, J. M.  2006.  Bryophytes and herbivory.  Cryptogamie, Bryologie 27(1): 191-203.

Abdullahi, A.S., Underwood, G.J.C., and Gretz, M.R. 2006. Extracellular matrix assembly in diatoms (Bacillariophyceae). V. Effects of phosphate levels and salinity on polysaccharides of Phaeodactylum tricornutum. Journal of Phycology 42:363-378.

Apoya, M.D., Yin, L., Underwood, G.J.C. and Gretz, M.R. 2006. Movement modalities and responses to environmental changes of the mudflat diatom Cylindrotheca closterium. Journal of Phycology 42:379-390.

Hanlon, A.R.M., Bellinger, B.J., Xiao, G., Haynes, K, Ball, A.S., Osborn, M., Gretz, M.R., and Underwood, G.J.C. 2006. Dynamics of EPS production and loss in an estuarine, diatom-dominated microalgal biofilm over a tidal emersion-immersion period. Limnology & Oceanography.51:79-93.

Ballor, N.R., Nesbitt, C.C. and Lueking, D.R. 2006. Recovery of Scrap Iron Metal Value using Biogenerated Ferric Iron. Biotechnol. Bioeng. , Vol. 93, No. 6, pp. 1089-1094.

Yayintas, O. T. and Glime, J. M.  2005.  Second record of Grimmia unicolor for Turkey.  Lindbergia 30: 113-115.

Bellinger, B.J., Abdullahi, A.S., Gretz, M.R. and Underwood, G.J.C. 2005. Biofilm Polymers: Relationship between carbohydrate biopolymers from estuarine mudflats and unialgal cultures of benthic diatoms. Aquatic Microbial Ecology.38:169-180

Subhash, G., Yao, S., Bellinger, B. & Gretz, M.R. 2005. Investigation of mechanical properties of diatom frustules using nanoindentation. Journal of Nanoscience and Nanotechnology 5:44-50.

VanDusen, P. J., C. J Huckins, D. J. Flaspohler. 2005. Associations among selection logging history, brook trout, macroinvertebrates and habitat in Northern Michigan headwater streams. Transactions of the American Fisheries Society. 134:762-774.

Li, H., Lueking, D.R., Mihelcic, J.R. and Peterson, K. 2005. Biogeochemical Analysis of Hydrogen Sulfide Removal by a Lava Rock Packed Biofilter. Water Environ. Res. 77, 179-186.

Munirathinam Sundaramoorthy, Heather L. Youngs, Michael H. Gold and Thomas L.Poulos.  2005. High Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes. Biochemistry 44:6463-6470.

Youngs, H. L., Hamann, T., Osborne, E., Somerville, C.  2005. The cellulose synthase superfamily. Cellulose book chapter (in press).

Auer, N.A. and J.E. Kahn. 2004. Abundance and distribution of benthic invertebrates, with emphasis on Diporeia, along the Keweenaw Peninsula, Lake Superior. Journal of Great Lakes Research. Vol 30. Supplement 1,340-359.

Holtgren, J.M. and N.A. Auer. 2004. Movement and habitat of juvenile lake sturgeon in the Sturgeon River/Portage Lake Michigan.  Journal of Freshwater Ecology.  19(3): 419-432

Oyadomari, J.K. and N.A. Auer. 2004. Inshore-Offshore distribution of larval fishes in Lake Superior off the western coast of the Keweenaw Peninsula, Michigan. Journal of Great Lakes Research. Vol. 30. Supplement 1, 369-384.

Liu, Y., Li, Z.-Y., Cao, T., and Glime, J. M.  2004.  The influences of high temperature stress on cell damage and shoot survival rates of Plagiomnium acutum.  Journal of Bryology 26: 265-271.

Bub, B.R., D. J. Flaspohler, and C. J. F. Huckins. 2004. Riparian and upland breeding-bird assemblages along headwater streams in Michigan's Upper Peninsula. J. of Wildlife Management 68:383-392.

Osenberg, C. W., C. J F. Huckins, A. Kaltenberg, and A. Martinez. 2004. Resolving within and between population variation in feeding ecology with a biomechanical model of crushing force. Oecologia. 141:57-65.

Link, J. S., J. H. Slegeby, and R. E. Keen. 2004. Changes in the Lake Superior Crustacean Zooplankton Community. Journal of Great Lakes Research 30(Supplement 1):327-33

Barnhisel, D.R. and W. C. Kerfoot. 2004. Fitting into food webs: Behavioral and functional response of young lake trout (Salvelinus namaycush) to an introduced prey, the spiny cladoceran (Bythotrephes cederstroemi). J. Great Lakes Research 30 (Supplements 1) 300-314. PDF File

Churchill, J. H., W. C. Kerfoot, and M. T. Auer. 2004 Exchange of water between the Keweenaw Waterway and Lake Superior: Characterstics and forcing mechanisms. J. Great Lakes Research 30 (Supplement 1): 55-63. PDF File

Compton, J. A. and W. C. Kerfoot. 2004. Colonizing inland lakes: Consequences of YOY fish ingesting the spiny cladoceran (Bythotrephes cederstroemi). J. Great Lakes Research. 30 (Supplement 1): 315-326.

Kerfoot, W. C., G. G. Mittelbach, N. G. Hairston, Jr. and J. J. Elser. 2004. Planktonic biodiversity: Scaling up and down. Limnology and Oceanography 49: 1225-1228.

Jarnagin, S. T., W. C Kerfoot and B. K. Swan 2004. Zooplankton life cycles: Direct documentation of pelagic births and deaths relative to diapausing egg production. Limnology and Oceanography 49: 1317-1332. PDF File

Kerfoot, W. C. J. W. Budd, B. J. Eadie, H. A. Vanderploeg, and M. Agy. 2004. Winter storms: Sequential sediment traps record Daphnia ephippial production, resuspension and sediment interactions. Limnology and Oceanography 49: 1365-1381. PDF File

Kerfoot,W. C., S. L. Harting, J. Jeong, J. A. Robbins and R. Rossmann. 2004. Local, Regional, and Global Implications of Elemental Mercury in Metal (Copper, Silver, Gold, and Zinc) Ores: Insights from Lake Superior Sediments. J. Great Lakes Research 30 (Supplement 1): 162-184. PDF File

Kerfoot, W. C., G. G. Mittelbach, N. G. Hairston, Jr. and J. J. Elser. 2004. Planktonic biodiversity: Scaling up and down. Limnology and Oceanography 49: 1225-1228.

Kerfoot, W.C. and L. J. Wieder. 2004. Experimental paleoecology (resurrection ecology): Chasing Van Valen’s red queen hypothesis. Limnology and Oceanography 49: 1300-1316. PDF File

Kerfoot, W. C., X. Ma, C. S. Lorence. 2004. Toward resurrection ecology: Daphnia mendotae and D. retrocurva in the coastal region of Lake Superior, among the first successful outside invaders? J. Great Lakes Research 30 (Supplement 1): 285-299. PDF File

Kerfoot, W.C. and L. J. Wieder. 2004. Experimental paleoecology (resurrection ecology): Chasing Van Valen’s red queen hypothesis. Limnology and Oceanography 49: 1300-1316. PDF File

Lueking, D. R. and Nesbitt, C.C. 2004. Ferric Iron Biogeneration: An Extreme Approach. Soc. Indus. Microbiol., Vol 54, No. 1, pp. 4-9.

Bennetzen, J.L., C Coleman, R Liu, J Ma and W Ramakrishna. 2004. Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biology 7: 732-736.

Lai, J., J Ma, Z Swigonová, W Ramakrishna, E Linton, V Llaca, B Tanyolac, Y-J Park, O-Y Jeong, J L Bennetzen, and J Messing. 2004. Gene loss and movement in the maize genome. Genome Res 14: 1924-1931.

Swigonová, Z. J Lai, J Ma, W Ramakrishna. 2004. Close split of sorghum and maize genome progenitors. V Llaca, JL Bennetzen and J Messing. Genome Res 14: 1916–1923.

Yan, L., A Loukoianov, A Blechl, G Tranquilli, W Ramakrishna, P SanMiguel, JL Bennetzen, V Echenique and J Dubcovsky. 2004. The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303: 1640-1644.

Assaad, F. F., Qui, J. L., Youngs, H., Ehrhardt, D., Zimmerli, L., Kalde, M., Peck, S., Wanner, G., Ramonell, K., Somerville, C., Somerville, S., Thordal-Christensen, H. 2004. The PEN1 syntaxin defines a novel compartment upon fungal attack and is required for the timely assembly of papilla. Molecular Biology of the Cell 15: 5118-5129.

Hamann, T., Osborne, E., Youngs, H. L., Mission, J., Zimmerli, L., Somerville, C. 2004. Global expression of CESA and CSL genes in Arabidopsis. Cellulose 11:279-286.

Somerville, C., S. Bauer, G. Brininstool, M. Facette, T. Hamann, J. Milne, E. Osborne, A. Paredez, S. Persson, T. Raab, S. Vorwerk and H. L.  Youngs. 2004. Toward a systems approach to understanding plant cell walls. Science 306: 2206-2211.

Liu, Y., Cao, T., and Glime, J. M. 2003. The changes of membrane permeability of mosses under high temperature stress. Bryologist 106: 55-62..

Peet, G. H., Crum, H. A., and Glime, J. M. 2003. Orthothecium diminutivum discovered at Scott's Falls in Alger County, Michigan. Michigan Botanist 42: 103-104

Ramakrishna, W.  Z Deng, C-K Ding, AK Handa and RH Ozminkowski Jr. 2003. A novel small heat shock protein gene, vis1, contributes to pectin depolymerization and juice viscosity in tomato fruit. Plant Physiol 131: 725-735.

Auer, N. A. and E.A. Baker.  2002. Duration and drift of larval lake sturgeon in the Sturgeon River, Michigan. Journal of Applied Ichthyology. 18(2002):557-564.

Glime, J. M. 2002. Bryophytes associated with hart's tongue fern (Asplenium scolopendrium var. americanum) on dolomite rocks in Mackinac County, Michigan. Accepted for Michigan Botanist 41(1): 5-11.

Glime, J. M. 2002. Bryophytes of the Pictured Rocks National Lakeshore, Michigan, USA. Michigan Botanist 41(2): 31-45.

Glime, J. M. and Hong, W. S. 2002. Bole epiphytes on three conifer species from Queen Charlotte Islands, Canada. Bryologist 105: 451-464

Flaspohler, D. J., C. J F. Huckins, B. R. Bub, and P. J. VanDusen. 2002. Temporal patterns in aquatic and avian communities following selective logging. Forest Science 48:339-350.

Martin, RW, H Li., JR Mihelcic, J. C. Crittenden, D. R. Lueking, CR Hatch, P Ball (2002). “Optimizaiton of biofiltration for odor control: Model Calibration, Validation and Applications. Water Environ. Res., 74, 17-23

Ramakrishna, W., J Dubcovsky, Y-J Park, C. Busso, J. Emberton, P. SanMiguel and J. L. Bennetzen. 2002. Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal denomes. Genetics 162: 1389-1400.

Ramakrishna, W., P. SanMiguel, J. Emberton, M. Ogden, J. Messing and J. L. Bennetzen. 2002. Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex. Plant Physiol 130: 1728-1738.

Ramakrishna, W.  et al. 2002. Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis. Comparative and Functional Genomics 3: 165-166.

Ramakrishna, W., P. SanMiguel, J. Emberton, M. Ogden, J. L. Bennetzen. 2002. Structural analysis of the maize Rp1 complex uncovers numerous sites and unexpected mechanisms of local rearrangement. Plant Cell 14: 3213-3223.

Ramakrishna W., P SanMiguel, J Emberton, M Ogden, J Messing and JL Bennetzen. 2002. Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex. Plant Physiol 130: 1728-1738.

Bennetzen, J.L., and W. Ramakrishna. 2002. Exceptional haplotype variation in maize. Proc Natl Acad Sci USA 99: 9093-9095.

Bennetzen, J. L. and W. Ramakrishna. 2002.  Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 48: 821-827.

L., V. Echenique, C. Busso, W. Ramakrishna, P. SanMiguel, J. L. Bennetzen, S. Harrington and J. Dubcovsky. 2002. Cereal genes similar to Snf2 define a new subfamily that includes human and mouse genes. Mol Genet Genomics 268: 488-499.

Reddy, A. R., W. Ramakrishna, A. Chandra Sekhar, N. Ithai, P. Ravindra Babu, M. F.  Bonaldo, M. B. Soares and J. L. Bennetzen.  2002. Novel genes are enriched in normalized cDNA libraries from drought-stressed seedlings of rice (Oryza sativa L. subsp. indica cv. Nagina 22). Genome 45: 204-211.

Stam, M., C. Belele, W. Ramakrishna, J. E. Dorweiler, J.L. Bennetzen and V. L. Chandler.  2002.   The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences.Genetics 162: 917-930.

Yan, N Rostoks, Y-J Park, W. Ramakrishna, J. Ma, A. Druka, B. A. Shiloff, P. J.  SanMiguel, Z. Jiang, R. Brueggeman, D. Sandhu, K. Gill, J. L. Bennetzen and A. Kleinhofs. 2002. Genomic sequencing reveals gene content, genomic organization and recombination relationships in barley. Functional and Integrative Genomics 2: 51-59.

SanMiguel, P., W. Ramakrishna, J. L. Bennetzen, C. S. Busso and J. Dubcovsky. 2002. Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5Am.Functional and Integrative Genomics 2: 70-80.

Glime, J. M.  2007.  Bryophyte Ecology.  Volume 5.  Uses. Ebook sponsored by Michigan Technological University and the International Association of Bryologists.  <http://www.bryoecol.mtu.edu/>.

Glime, J. M.  2007.  Economic and ethnic uses of bryophytes.  In:  Flora of North America Editorial Committee.  (eds.).  Flora of North America North of Mexico.  Vol. 27.  Bryophyta, part 1.  Oxford University Press, New York.  pp. 14-41.