Phyllis Strauss
Northeastern University

Oxidative DNA damage-is it all bad?

Friday May 18, 2012 12:00 PM in the Candle House 104/105

Garbuz, D.G., Yushenova, I.A., Zatsepina, O.G., Przhiboro, A.A., Bettencourt, B.R., Evgen'ev, M.B. (2011) Organization and evolution of hsp70 clusters strikingly differ in two species of Stratiomyidae (Diptera) inhabiting thermally contrasting environments. BMC Evol Biol. 11:74.

Gladyshev, E.A., Arkhipova I.R. (2011). A widespread class of reverse transcriptase-related cellular genes. Proc. Natl. Acad. Sci. USA 51: 20311-20316.

Chandsawangbhuwana, C., Shi, L.Z., Zhu, Q., Alliegro, M.C., and Berns, M.W. 2012. High-throughput automated optofluidic system for the laser microsurgery of non-adherent oocytes. J. Biomed. Optics. (in press)

Alliegro, M.C., Hartson, S., and Alliegro, M.A. (2012). Composition and dynamics of the nucleolinus, a physiological link between the nucleolus and cell division apparatus. J. Biol. Chem. (in press)

Sun, Y., Cai, Y., Huse, S.M., Knight, R., Farmerie, W.G., Wang, X., and Mai, V. (2012) A Large-scale Benchmark Study of Existing Algorithms for Taxonomy Independent Analysis. Briefings in Bioinformatics.

Valm, A. M., Welch, J. L. M., and Borisy, G. G. (submitted manuscript on September 29, 2011). "CLASI-FISH: Principles of Combinatorial Labeling and Spectral Imaging." Systematic and Applied Microbiology.

Welch, J. L. M., Valm, A. M., Xun, L., Tierney, B., Dewhirst, F. E., and Borisy, G. G. (submitted manuscript on October 14, 2011). "Design of Probes and Probe Sets for CLASI-FISH." Systematic and Applied Microbiology

Eren, A. M., Zozaya, M., Taylor, C. M., Dowd, S. E., Martin, D. H., and Ferris, M. J. (2011). "Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation." PLoS ONE, 6(10), e26732.

Agogué, H., Lamy, D., Neal, P.R., Sogin, M.L., Herndl, G.J. Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing (2011). Mol Ecol. 20(2):258-74.

Mark Welch, D.B., and Huse, S.M. (2011) Microbial diversity in the deep sea and the underexplored “rare biosphere". In Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. de Bruijn, F.J. (ed): Wiley and Sons. p. 245-252

Huse, S.M., and Mark Welch, D.B. (2011) Accuracy and quality of massively parallel DNA pyrosequencing. In Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. de Bruijn, F.J. (ed): Wiley and Sons. p.149-156

Gobet, A., Boer, S.I., Huse, S. M., van Beusekomm, J.E.E., Quince, C., Sogin, M.L., Boetius, A., and Ramette, R. (2012). Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME Journal

Smith, J., Morgan, J. R., Zottoli, S. J., Smith, P. J., Buxbaum, J. D., and Bloom, O. E. (2011). "Regeneration in the era of functional genomics and gene network analysis." The Biological bulletin, 221(1), 18-34.

Yelton, A.P., B.C. Thomas, P. Wilmes, S.L. Simmons, B.J. Baker, G.J. Dick, A. Zemla, M.P. Thelen, J.F. Banfield (2011). A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated Bacterial and Archaeal genes. PLoS Computational Biology 7(10), e1002230

Xia, Li Charlie, J.A. Steele, J. Cram, Z.G. Cardon, S.L. Simmons, J.J. Vallino , J.A. Fuhrman, F. Sun (2011). Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Systems Biology 5(Suppl 2), S15.

Perry, D.A., Morrison, H.G., and Adam, R.D. (2011). "Optical map of the genotype A1 WB C6 Ciardia lamblia genome isolate." Molecular and Biochemical Paratisology.

Gast, R.J., Moran, D.M., Dennett, M.R., Wurtsbaugh, W.A. and Amaral-Zettler, L.A. (2011). "Amoebae and Legionella pneumophila in saline environments." Journal of Water and Health, 9(1), 37-352.

Amaral-Zettler, L. A., Zettler, E.R., Theroux, S.M., Palacios, C., Aguilera, A. and Amils, R. (2011) "Microbial community struction across the tree of life in the extreme Rio Tinto." The ISME journal, 5 (1), 42-50

Alliegro, M.C. (2011). The centrosome and spindle as a ribonucleoprotein complex. Chrom. Res. 19:367-376.

Alliegro, M.C. (2011). The nucleolinus: A disappearing, forgotten, and (maybe) misnamed organelle. Comm. Integr. Biol. 4:147-149.

Bogaert, D., Keijser, B., Huse, S., Rossen, J., Veenhoven, R., van Gils, E. et al. (2011) Variability and Diversity of Nasopharyngeal Microbiota in Children: A Metagenomic Analysis. PLoS ONE 6: e17035.

Crielaard, W., Zaura, E., Schuller, A., Huse, S.,, Montijn, R., and Keijser, B. (2011) Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Medical Genomics 4: 22.

White, J., Gilbert, J., Hill, G., Hill, E., Huse, S.M., Weightman, A.J., and Mahenthiralingam, E. (2011) Culture-Independent Analysis of Bacterial Fuel Contamination Provides Insight into the Level of Concordance with the Standard Industry Practice of Aerobic Cultivation. Appl. Environ. Microbiol. 77: 4527-4538.

Gribble, K. E., T.W. Snell, D. B. Mark Welch. 2011. Gene and protein structure of the mate recognition protein gene family in Brachionus manjavacas (Rotifera). Hydrobiologia 662(1): 35-42.

Valm AM, Mark Welch, JL, Rieken CW, Hasegawa Y, Sogin ML, Oldenbourg R, Dewhirst FE, Borisy GG. Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4152-7. Epub 2011 Feb 16

Wolf B, SchwarzerA, Cote AL, Hampton TH, Schwaab T, Huarte E, Tomlinson CR, Gui J, Fisher J, Fadul CE, Hamilton JW, Ernstoff MS. Gene expression profiles in peripheral blood lymphocytes from metastatic renal cell cancer patients treated with IL-2, interferon-a and autologous dendritic cell vaccine. Cancer Res, in press, 2011.

Gladyshev E.A., and Arkhipova I.R. (2011) A widespread class of reverse transcriptase-related cellular genes. Proc. Natl. Acad. Sci. USA Aug 29 [Epub ahead of print], PMID: 21876125, doi/10.1073/pnas.1100266108.

Arkhipova I.R., (2011). Telomerase, retrotransposons, and evolution. In: Telomerases: Chemistry, Biology and Clinical Applications, N. Lue and C. Autexier, eds. John Wiley and Sons, Inc., Hoboken, NJ (in press).

Garbuz D.G., Astakhova L.N., Zatsepina O.G., Arkhipova I.R., Nudler E., and Evgen’ev M.B. (2011). Functional organization of the Hsp70 cluster in camel (Camelus dromedarius) and other mammals. PLoS One 6(11), e27205.

Pollastri MP and Campbell RK. Target repurposing for neglected diseases. Future Medicinal Chemistry. 2011 (10):1307-15.

Woo Jun Sul, James R. Cole, Ederson da C. Jesus, Qiong Wang, Ryan J. Farris, Jordan A. Fish, and James M. Tiedje Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering PNAS 2011 108: 14637-14642.

Resing, J. A., Rubin, K. H., Embley, R. W., Lupton, J. E., Baker, E. T., Dziak, R. P., Baumberger, T., Lilley, M. D., Huber, J. A., Shank, T. M., Butterfield, D. A., Clague, D. A., Keller, N. S., Merle, S. G., Buck, N. J., Michael, P. J., Soule, A., Caress, D. W., Walker, S. L., Davis, R., Cowen, J. P., Reysenbach, A.-L., and Thomas, H. (2011). Active submarine eruption of boninite in the northeastern Lau Basin. Nature Geoscience 4: 1-8. .

Bland ND, Cuihua Wang C, Tallman C, Gustafson AE, Wang Z, Ashton TD, Ochiana SO, McAllister G, Cotter K, Fang AP, Gechijian L, Garceau N, Gangurde R, Ortenberg R, Ondrechen MJ, Campbell, RK & Pollastri MP. (2011) Pharmacological Validation of Trypanosoma brucei Phosphodiesterases B1 and B2 as Druggable Targets for African Sleeping Sickness. Journal of Medicinal Chemistry. 54(23), 8188-94

McLuskey K, Paterson NG, Bland ND, Isaacs NW, Mottram JC. Crystal structure of Leishmania major oligopeptidase B gives insight into the enzymatic properties of a trypanosomatid virulence factor. J Biol Chem. 2010 Dec 10;285(50):39249-59

N.H. Akerman, R. E. Price, T. Pichler, and J. P. Amend (2011). Energy sources for chemolithotrophs in an arsenic- and iron-rich shallow-sea hydrothermal system. Geobiology 9: 436–445.

Valm AM, Mark Welch, JL, Rieken CW, Hasegawa Y, Sogin ML, Oldenbourg R, Dewhirst FE, Borisy GG. Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4152-7. Epub 2011 Feb 16

Post, A.F., Penno, S., Zandbank, K., Paytan, A., Huse, S., and Mark Welch, D.B. (2011) Long term seasonal dynamics of Synechococcus population structure in the Gulf of Aqaba, Northern Red Sea . Frontiers in Aquatic Microbiology.

Finkel O.M., Burch A.Y., Lindow S.E., Post A.F. and Belkin S. (2011). Phyllosphere microbial communities of a salt-excreting desert tree: geographic loaction determines population structure. Appl. Environ. Microbiol., 77(21), 7647-55.

Atamna-Ismaeel, N., Finkel, O.M., Glaser, F., Sharon, I., Sharon, A.J., Schneider, R., Post, A.F., Béjà, O. & Belkin, S. (2012) Microbial rhodopsins on leaf surfaces of terrestrial plants. Environ. Microbiol.14(1), 140-146

Sukenik A., Kaplan-Levy R.N., Mark Welch J. and Post A.F. (2011). Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria). ISME J., 2011 Oct 6. doi: 10.1038/ismej.2011.128. [Epub ahead of print]

Post A.F., Rihtman B. and Wang Q. (2011). Decoupling of ammonium regulation and ntcA transcription in the diazotrophic marine cyanobacterium Trichodesmium sp. ISME J., in press.

Kamennaya N.A. and Post A.F. (2011). Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp. Appl. Environ. Microbiol., 77 (1), 291-301.

Kamennaya N.A., Schwarz A., Fertig T., Dery E., Wickham S., Hammar K.M., Mark Welch D. and Post A.F. (in revision). Members of an ancient Prochlorococcus clade in the Antarctic Circumpolar Current. Proc Natl. Acad Sci.

Mackey K.R.M., Bristow L., Parks D.R., Altabet M.A., Post A.F., and Paytan A. (2011). The influence of light on nitrogen cycling and the primary nitrite maximum in a seasonally stratified sea. Prog. Oceanogr., http://dx.doi.org/10.1016/j.pocean.2011.09.001.

Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, et al. (2011). The Genomic Standards Consortium. PLoS Biol 9(6): e1001088. doi:10.1371/journal.pbio.1001088

Zinger L, Amaral-Zettler L, Fuhrman JA, Horner-Devine MC, Huse SM, Mark Welch DB, Martiny JBH, Sogin M, Boetius A, Ramette A (2011). Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 6(9): e24570 (2011). . PLoS ONE 6(9):

McCliment, Elizabeth A., Craig E. Nelson, Craig A. Carlson, Alice L. Alldredge, Jan Witting, and Amaral-Zettler, L. A., 2011, An All-Taxon Microbial Inventory of the Moorea Coral Reef Ecosystem. The ISME Journal, advance online publication, 8 September 2011, doi:10.1038/ismej.2011.108

Yilmaz P, Gilbert J, Knight R, Amaral-Zettler L, Karsch-Mizrachi I, Chochrane G, Nakamura Y, Sansone SA, Oliver Glockner F and Field D (2011). The genomic standards consortium: bringing standards to life for microbial ecology ISME Journal 5: 1565-1567

Gilbert, J.A., Steele, J.A., Caporaso, J.G., Steinbruck, L., Reeder, J., Temperton, B., Huse, S. M., McHardy, A.C., Knight, R., Joint, I., Somerfield, P., Fuhrman, J.A., Field, D. (2011). Defining seasonal marine microbial community dynamics. ISME Journal, (epub ahead of print)

Eugene A. Gladyshev and Irina R. Arkhipova Telomerase and Retrotransposons: Reverse Transcriptases That Shaped Genomes Special Feature Sackler Colloquium: A widespread class of reverse transcriptase-related cellular genes PNAS 2011 : 1100266108v1-201100266.

Rodrigues JL, Serres, MH, Tiedje JM. Large scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at genus level. Appl Environ Microbiol. 2011 Jun 3. [Epub ahead of print] PMID: 21642407

Oleksiak, M.F., Karchner, S.I., Jenny, M.J., Franks, D.G., Mark Welch, D.B., Hahn, M.E. 2011. Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish Fundulus heteroclitus from a marine Superfund site. BMC Genomics 2011, 12 :263

Yilmaz P, Kottmann R, Field D, Knight R, Cole JA, Amaral-Zettler LA et al (2011). The "Minimum Information about a MARKer gene Sequence" (MIMARKS) specification. Nature Biotechnology 29: 415-420.

Pawlowski J, Christen R, Lecroq Ba, Bachar D, Shahbazkia HR, Amaral-Zettler L et al (2011). Eukaryotic Richness in the Abyss: Insights from PyrotagSequencing. PLoS One 6: e18169.

Nelson CE, Alldredge AL, McCliment EA, Amaral-Zettler LA, Carlson CA (2011). Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapidly flushing coral reef ecosystem. ISME J doi:10.1038/ismej.2011.12.

Nuzzio, DB., Zettler, E., Aguilera, A., Amaral-Zettler, L., A direct in situ fingerprinting method for acid rock drainage using voltammetric techniques with a single renewable gold microelectrode Science of the Total Environment 409 (2011) 1984-1989.

Jennifer L Bowen, Bess B Ward, Hilary G Morrison, John E Hobbie, Ivan Valiela, Linda A Deegan and Mitchell L Sogin Microbial community composition in sediments resists perturbation by nutrient enrichment The ISME Journal advance online publication, 17 March 2011; doi:10.1038/ismej.2011.22

Andrew Adey, Hilary G. Morrison, Asan, Xu Xun, Jacob O. Kitzman, Emily H. Turner, Bethany Stackhouse, Alexandra P. MacKenzie, Nicholas C. Caruccio, Xiuqing Zhang, Jay Shendure1 Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition Genome Biology 2011, 11:R119 doi:10.1186/gb-2010-11-12-r119

Gribble, K. E., T.W. Snell, D. B. Mark Welch. 2011. Gene and protein structure of the mate recognition protein gene family in Brachionus manjavacas (Rotifera). Hydrobiologia 662(1): 35-42.