tag:blogger.com,1999:blog-134948112011-12-27T09:11:21.412-05:00<p>Bioinformatic analyses for the scientific research community, with emphasis upon genome informatics, gene expression analysis, molecular evolution, and phylogenetics. Based in Hamilton, Ontario, Canada.</p> <p><i><a href="http://www.epernicus.com/agm4">Epernicus</a> | <a href="http://ca.linkedin.com/pub/andrew-mcarthur/2b/355/66b">LinkedIn</a> | <a href="http://www.twitter.com/agmcarthur">Twitter</a> | <a href="mailto:amcarthur@mac.com">amcarthur@mac.com</a></i></p>Andrew G. McArthurnoreply@blogger.comBlogger851100tag:blogger.com,1999:blog-13494811.post-14215901104461302012011-12-27T09:05:00.002-05:002011-12-27T09:11:21.422-05:00

Authors: Shakya T, Stogios PJ, Waglechner N, Evdokimova E, Ejim L, Blanchard JE, McArthur AG, Savchenko A, Wright GDChemistry & Biology 2011 Dec 23;18(12):1591-601Kinase-mediated resistance to antibiotics is a significant clinical challenge. These enzymes share a common protein fold characteristic of Ser/Thr/Tyr protein kinases. We screened 14 antibiotic resistance kinases against 80 chemically

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-60088587702119128422011-12-20T09:41:00.002-05:002011-12-20T09:46:40.201-05:00

Authors: Timme-Laragy AR, Karchner SI, Franks DG, Jenny MJ, Harbeitner RC, Goldstone JV, McArthur AG, Hahn MEJournal of Biological Chemistry (in press).NF-E2-related factor 2 (NRF2, also called NFE2L2) and related NRF family members regulate antioxidant defenses by activating gene expression via antioxidant response elements (AREs), but their roles in embryonic development are not well understood

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-54297599161472699112011-10-07T11:15:00.024-04:002011-10-07T12:03:44.133-04:00

Dr. Gerry Wright - construction of a Comprehensive Antibiotic Resistance Database, http://arpcard.mcmaster.ca. Michael G. Institute for Infectious Disease Research, McMaster University, CanadaDr. John Brennan - construction of a Database of Biointerface Interactions. Biointerfaces Institute, McMaster University, CanadaDr. Joanna Wilson - phylogenetics of P450 proteins, microarray analysis,

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-17186867438563707922011-10-03T13:07:00.003-04:002011-10-03T13:12:57.586-04:00

A.G. McArthur, N. Waglechner, F. Nizam, M.A. Azad, K. Bhullar, M.J. Canova, G. De Pascale, L. Ejim, L. Kalan, A.M. King, K. Koteva, M. Morar, J.S. O’Brien, A.C. Pawlowski, P. Spanogiannopoulos, A.D. Sutherland, I. Tang, P.L. Taylor, M. Thaker, W. Wang, M. Yan, T. Yu, & G.D. Wright. 2011. Towards a Comprehensive Antibiotic Resistance Database (CARD). Oral presentation at the Generic Model Organism

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-36643006081400930092011-05-04T11:26:00.002-04:002011-05-04T11:30:14.231-04:00

Smith, E.M., A.G. McArthur, M. Galus, S. Higgins, N. Kirischian, J. Jeyaranjaan, & J.Y. Wilson. 2011. Transcriptional responses of zebrafish to chronic, low-dose pharmaceutical exposure. Oral presentation at the 16th International Symposium on Pollutant Response in Marine Organisms, Long Beach, California.Human pharmaceuticals have been well documented in receiving waters yet their impacts on

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-57369678806463058892011-02-07T13:00:00.002-05:002011-02-07T13:04:45.249-05:00

Authors: Kirischian N, McArthur AG, Jesuthasan C, Krattenmacher B, Wilson JY.J Mol Evol. 2011 Jan;72(1):56-71.Cytochrome P450 (CYP) proteins compose a highly diverse superfamily found in all domains of life. These proteins are enzymes involved in metabolism of endogenous and exogenous compounds. In vertebrates, the CYP2 family is one of the largest, most diverse and plays an important role in

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-77860623573367234332011-01-10T11:03:00.005-05:002011-02-07T13:05:33.166-05:00

Authors: Goldstone, J.V., A.G. McArthur, A. Kubota, J. Zanette, T. Parente, M. Jönsson, D.R. Nelson, & J.J. StegemanBMC Genomics 2010, 11: 643.Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-54490056256148904092011-01-05T10:25:00.003-05:002011-01-05T10:29:43.567-05:00

Authors: Davids, B.J., M.A. Gilbert, Q. Liu, D.S. Reiner, A.J. Smith, T. Lauwaet, C. Lee, A.G. McArthur, & F.D. GillinMolecular and Biochemical Parasitology 2011, 175(2):169-180.Proteolytic activity is important in the lifecycles of parasites and their interactions with hosts. Cysteine proteases have been best studied in Giardia, but other protease classes have been implicated in growth and/or

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-13507804952829320152011-01-01T13:53:00.001-05:002011-10-27T12:41:45.285-04:00

My principal training was in Ecology and Statistics (undergraduate) and in Evolutionary and Molecular Biology at the University of Victoria (Canada), the National Museum of Natural History (Smithsonian Institution), and Marine Biological Laboratory. At the Marine Biological Laboratory between 1998-2006, I established an active research program in Global Infectious Disease with funding from NIH/

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-74365090467152297512010-11-29T12:43:00.001-05:002011-11-30T10:26:54.606-05:00

McArthur, A.G. Introduction to Phylogenetics. Invited seminar for the Graduate Student Association of the Department of Biochemistry, McMaster University, Hamilton, Canada. November 2011.McArthur A.G., N. Waglechner, F. Nizam, M.A. Azad, K. Bhullar, M.J. Canova, G. De Pascale, L. Ejim, L. Kalan, A.M. King, K. Koteva, M. Morar, J.S. O'Brien, A.C. Pawlowski, P. Spanogiannopoulos, A.D. Sutherland, I

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-4987487617846032442010-11-15T12:37:00.006-05:002010-12-01T09:44:26.998-05:00

Recently accepted for publication, full citations coming soon:Davids, B.J., M.A. Gilbert, Q. Liu, D.S. Reiner, A.J. Smith, T. Lauwaet, C. Lee, A.G. McArthur, & F.D. Gillin. 2010. An atypical proprotein convertase in Giardia lamblia differentiation. Molecular and Biochemical Parasitology, in press. [PubMed]Goldstone, J.V., A.G. McArthur, A. Kubota, J. Zanette, T. Parente, M. Jönsson, D.R. Nelson,

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-87429859944489040962010-11-02T20:15:00.003-04:002010-11-02T20:20:20.205-04:00

Smith, E.M., A.G. McArthur, S. Higgins, N. Kirischian, M. Galus, & J.Y. Wilson. 2010. Hepatic gene expression in zebrafish (Danio rerio) chronically exposed to pharmaceuticals. Presentation at the 31st Annual Meeting of the Society of Environmental Toxicology and Chemistry (North America), Portland, Oregon.Pharmaceuticals are entering the aquatic environment through wastewater effluent yet the

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-86906647775693691452010-10-02T10:12:00.002-04:002010-10-02T10:18:22.811-04:00

Kirischian, N., A.G. McArthur, C. Jesuthasan, B. Krattenmacher, & J.Y. Wilson. 2010. Phylogenetic and functional analyses of the cytochrome P450 families 2 and 4. Oral presentation at the 10th International Symposium on P450 Biodiversity and Biotechnology, Woods Hole, Massachussetts.In vertebrates, the CYP2 family is one of the largest and most diverse, with more than 20 subfamilies, and plays an

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-84036177018944026902010-08-23T15:06:00.003-04:002010-08-23T15:11:01.465-04:00

Authors: Birkeland SR, Preheim SP, Davids BJ, Cipriano MJ, Palm D, Reiner DS, Svärd SG, Gillin FD, McArthur AG.Molecular and Biochemical Parasitology 2010, 174(1): 62-65.We quantified mRNA abundance from 10 stages in the Giardia lamblia life cycle in vitro using Serial Analysis of Gene Expression (SAGE). 163 abundant transcripts were expressed constitutively. 71 transcripts were upregulated

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-11899291969925273402010-05-04T11:57:00.003-04:002010-05-04T12:01:12.520-04:00

McArthur, A.G., F. Nizam, N. Waglechner, & G.D. Wright. 2010. Towards a comprehensive antibiotic resistance database. Oral presentation at the 2nd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans and the Environment, Toronto, Ontario.Addressing the challenge of antibiotic resistance requires the combined efforts of researchers that span

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-29424435472065229782010-01-06T13:39:00.002-05:002010-01-06T13:43:32.610-05:00

Davids, B.J., D.S. Reiner, M.A. Gilbert, A.G. McArthur, & F.D. Gillin. 2009. Transcriptomics of the Giardia lamblia degradome. Presentation at the 49th Annual Meeting of the American Society for Cell Biology, San Diego, California.Proteolytic activity is important in the life cycle of parasites and in the interactions with their hosts. While the main class of proteases studied in the protozoan

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-33570592394012331812009-08-09T20:06:00.003-04:002009-08-09T20:11:10.916-04:00

Lauwaet, T., C.C.L. Wong, D. Reiner, B.J. Davids, S.G. Svard, A.G. McArthur, J.R. Yates, & FD. Gillin. 2009. Biological surprises from the Giardia lamblia basal body proteome. Presentation at the 13th International Congress of Protistology, Rio de Janeiro, Brazil.Encystation and excystation, which are crucial to the pathogenesis of Giardia lamblia, are marked by dramatic cytoskeletal remodeling.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1469578822330831772009-05-08T10:59:00.004-04:002009-05-08T14:12:14.755-04:00

Goldstone, J.V., A.G. McArthur, J. Zanette, M. Jonsson, T. Parente, & J.J. Stegeman. 2009. The total cytochrome P450 complement of zebrafish and the expression of CYP genes during development. Oral presentation at the 15th International Symposium on Pollutant Responses in Marine Organisms, Bordeaux, France.Kirischian, N., A.G. McArthur, C. Jesuthasan, B. Krattenmacher, & J.Y. Wilson. 2009.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-17420821729305995552009-03-16T13:14:00.003-04:002009-03-16T13:19:50.470-04:00

Goldstone, J., M. Jonsson, T. Parente, J. Zanette, A.G. McArthur, B.R. Woodin, D.R. Nelson, & J.J. Stegeman. 2009. Cytochrome P450 genes in zebrafish development. Presentation at the Society of Toxicology 48th Annual Meeting, Baltimore, Maryland.This presentation summarizes observations on the full complement of CYP genes in zebrafish, a non-mammalian model for pharmacological, toxicological and

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-88259949969607175922009-03-10T10:50:00.003-04:002009-04-16T11:17:00.502-04:00

Parasitology 2009, 136(5): 469-485.Authors: Taft AS, Vermeire JJ, Bernier J, Birkeland SR, Cipriano MJ, Papa AR, McArthur AG, Yoshino TP.Infection of the snail, Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke, Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-54180608788875848482009-03-10T10:43:00.003-04:002009-05-08T10:59:09.909-04:00

Infection, Genetics, & Evolution 2009, 9(3): 337-343.Authors: Githui EK, De Villiers EP, McArthur AG.Plasmodium belongs to the phylum Apicomplexa. Within the Apicomplexa, Plasmodium, Toxoplasma and Cryptosporidium are parasites of considerable medical importance while Theileria and Eimeria are animal pathogens. P. falciparum is particularly important as it causes malaria, resulting in more than 1

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-82378851245664441522008-11-18T09:21:00.000-05:002008-11-18T09:28:39.283-05:00

Transactions of the American Fisheries Society 2008, 137(5): 1378-1388.Authors: Bernier JC, Birkeland SR, Cipriano MJ, McArthur AG, Banks MA.Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-37855359717029095392008-10-22T14:34:00.000-04:002008-10-22T14:35:03.947-04:00

Goldstone, J.V., M. Jonsson, D.R. Nelson, A.G. McArthur, B.R. Woodin, & J.J. Stegeman. 2008. Cytochrome P450 in zebrafish: genomic complement and developmental expression. Poster presentation at the New England Membrane Biochemistry Meeting.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-61999804677617821632008-09-26T14:53:00.001-04:002008-09-26T14:57:06.988-04:00

Davids, B.J., M.A. Gilbert, J. Liu, D.S. Reiner, C. Lee, A.G. McArthur, & F.D. Gillin. 2008. Novel glutamyl endopeptidase activity needed for Giardia encystation. Presentation at the 19th Annual Molecular Parasitology Meeting, Woods Hole, Massachusetts.Lauwaet, T., M. Baitaluk, D.S. Reiner, E.P. Romijn, C.C.L. Wong, H. Skarin, B.J. Davids, S.R. Birkeland, M.J. Cipriano, D. Palm, S.P. Preheim, A.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-74036414672331290772008-05-16T21:10:00.001-04:002009-05-08T07:37:17.047-04:00

Lauwaet, T., M. Baitaluk, D.S. Reiner, E.P. Romijn, C.C.L. Wong, H. Skarin, B.J. Davids, S.R. Birkeland, M.J. Cipriano, D. Palm, S.P. Preheim, A. Gupta, S.G. Svard, A.G. McArthur, J.R. Yates, A. Ray, & F.D. Gillin. 2008. Proteome, transcriptome and interactome analyses reveal key roles of basal bodies in Giardia differentiation. Presentation at the 4th International Conference on Anaerobic

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-17344642186394393302008-03-27T17:05:00.000-04:002009-05-02T17:07:13.661-04:00

When extracting from fresh or frozen invertebrate specimens, we usually use the CTAB protocol (see my previous post). In the past, we also used this protocol for working with specimens that had been stored in formalin for some period before being transfered to ethanol but the results were hit and miss. The Etter/Rex group at UMass Boston developed a much superior protocol (Chase et al. 1998). It

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-22332109788843352142008-03-26T17:03:00.000-04:002009-05-02T17:05:33.796-04:00

Going with my theory that information is better cataloged on the internet than sitting collecting virtual dust on my hard drive, I'm posting some protocols in response to shortysquab's request for mollusc DNA extraction tips. That's right, I was once a malacologist and once even did laboratory work. Here is a CTAB protocol based on Doyle & Doyle (1987; Phytochemical Bulletin 19: 11-15) and a

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-87463430459803317022008-01-28T12:35:00.000-05:002008-01-28T12:43:37.294-05:00

Karchner, S.I., A.G. McArthur, D.G. Franks, B.R. Woodin, M.J. Jenny, J.V. Goldstone, J.J. Stegeman, M.J. Cipriano, & M.E. Hahn. 2008. The zebrafish embryo as a model for investigating mechanisms of developmental toxicity involving oxidative stress. 2008. Presentation at the The Fourth Aquatic Animal Models of Human Disease Conference, Durham, North Carolina.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-37764891089067124592007-12-11T12:29:00.000-05:002007-12-11T12:32:11.905-05:00

Lauwaet, T., D. Reiner, E.P. Romijn, M. Baitaluk, D. Palm, B. Davids, S.Svard, A.G. McArthur, A. Ray, A. Gupta, J. Yates, & F.D. Gillin. 2007. Transcriptome and interaction analyses of the Giardia lamblia basal body proteome. Presentation at the Annual Meeting of the American Society for Cell Biology, Washington, D.C.Encystation and excystation are crucial to the pathogenesis of Giardia lamblia.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-34002793832735887852007-10-30T22:33:00.000-04:002007-10-30T22:36:24.317-04:00

Experimental Parasitology 2007 Nov;117(3):246-58. Epub 2007 May 13.Authors: Williams DL, Sayed AA, Bernier J, Birkeland SR, Cipriano MJ, Papa AR, McArthur AG, Taft A, Vermeire JJ, Yoshino TP.Despite the widespread use of chemotherapy and other control strategies over the past 50 years, transmission rates for schistosomiasis have changed little. Regardless of the approach used, future control

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-74592082597176455542007-09-29T13:02:00.002-04:002008-10-20T10:14:50.243-04:00

Science. 2007 Sep 28;317(5846):1921-6.Authors: Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, Olsen GJ, Best AA, Cande WZ, Chen F, Cipriano MJ, Davids BJ, Dawson SC, Elmendorf HG, Hehl AB, Holder ME, Huse SM, Kim UU, Lasek-Nesselquist E, Manning G, Nigam A, Nixon JE, Palm D, Passamaneck NE, Prabhu A, Reich CI, Reiner DS, Samuelson J, Svard SG, Sogin MLThe genome of the eukaryotic protist

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-74460070739348238522007-08-28T22:43:00.001-04:002007-08-29T22:13:20.999-04:00

Mol Phylogenet Evol. 2007 Sep;44(3):1284-94Authors: Smith SS, Pfluger SL, Hjort E, McArthur AG, Hager KMCoatomer coated (COPI) vesicles play a pivotal role for multiplemembrane trafficking steps throughout the eukaryotic cell. Our focusis on betaCOP, one of the most well known components of the COPImulti-protein complex. Amino acid differences in betaCOP may dictatefunctional divergence across

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1352873010073885272007-07-20T11:12:00.000-04:002007-07-20T11:20:12.588-04:00

LongSAGE transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi (GEO GSE8376) - release of published Replete, Low Nitrogen, and Low Phosphate culture SAGE data.In vitro generation of human high-density-lipoprotein-resistant Trypanosoma brucei brucei (GEO GSE8369) - release of published bloodstream form 427-221 and 427-800 culture SAGE data.Nitric oxide-dependent

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-84202476208269335232007-06-05T10:05:00.001-04:002007-06-05T10:06:18.357-04:00

Mol Microbiol. 2007 Jun;64(5):1154-63Authors: Brown MT, Goldstone HM, Bastida-Corcuera F, Delgadillo-Correa MG, McArthur AG, Johnson PJMatrix proteins of mitochondria, hydrogenosomes and mitosomes aretypically targeted and translocated into their respective organellesusing N-terminal presequences that are subsequently cleaved by apeptidase. Here we characterize a approximately 47

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-37023464613953636582007-03-26T10:29:00.000-04:002007-03-26T10:37:26.974-04:00

Sogin, M.L., D.J. Patterson, & A.G. McArthur. 2007. The origin and diversification of eukaryotes. In, W.T. Sullivan & J. Barros (eds), “Planets & Life: The Emerging Science of Astrobiology”. Cambridge University Press, Cambridge, U.K.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-39238741396628130302007-03-26T10:26:00.000-04:002007-07-26T13:46:45.424-04:00

Hahn, M.E., S.I. Karchner, D.G. Franks, B.R. Woodin, K.L. Barott, M.J. Cipriano, & A.G. McArthur. 2007. The transcriptional response to oxidative stress in fish embryos and cells exposed to tert-butly hydroguinone (tBHQ) or 2,3,7,8-tetrachlorodibenzo-p-diozin (TCDD). Presentation at the 14th International Syposium on Pollutant Response in Marine Organisms, Florianopolis, Brazil.Isokpehi, R.D.,

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-15309265736423328182007-02-26T09:57:00.000-05:002007-02-26T10:00:14.818-05:00

Lauwaet, T., B.J. Davids, A. Torres-Escobar, S.P. Preheim, S.R. Birkeland, M.J. Cipriano, D. Palm, S.G. Svard, A.G. McArthur & F.D. Gillin. 2007. Protein phosphatase 2A plays a crucial role in Giardia lamblia differentiation. Molecular and Biochemical Parasitology, 152, 80-89.The ability of Giardia lamblia to undergo two distinct differentiations in response to physiologic stimuli is central to

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1166802260418607752006-12-22T10:41:00.000-05:002006-12-22T10:44:20.770-05:00

Davids, B.J., D.S. Reiner, S.R. Birkeland, S.P. Preheim, M.J. Cipriano, A.G. McArthur, & F.D. Gillin. 2006. A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein. PLoS ONE, 1, e44.Since the Giardia lamblia cyst wall is necessary for survival in the environment and host infection, we tested the hypothesis that it contains proteins other than the three known cyst

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1166063706503556882006-12-13T21:30:00.000-05:002006-12-13T21:35:06.916-05:00

Mukherjee, M., M.T. Brown, A.G. McArthur & P.J. Johnson. 2006. Proteins of the glycine decarboxylase complex in the hydrogenosome of Trichomonas vaginalis. Eukaryotic Cell, 5, 2062-2071.Trichomonas vaginalis is a unicellular eukaryote that lacks mitochondria and contains a specialized organelle, the hydrogenosome, involved in carbohydrate metabolism and iron-sulfur cluster assembly. We report the

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1165278094038401852006-12-04T19:20:00.000-05:002006-12-04T19:23:21.300-05:00

Messerli, S.M., W. Morgan, S.R. Birkeland, J. Bernier, M.J. Cipriano, A.G. McArthur & R.M. Greenberg. 2006. Nitric oxide-dependent changes in Schistosoma mansoni gene expression. Molecular and Biochemical Parasitology, 150, 367-370.Williams, D.L., A.A. Sayed, D. Ray, & A.G. McArthur. 2006. Schistosoma mansoni albumin, a major defense against oxidative damage, was acquired by lateral gene transfer

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1163434460809715372006-11-13T11:14:00.000-05:002006-11-13T11:14:40.506-05:00

Goldstone, H.M.H., S.K. Kummerfeld, S.A. Teichmann, & A.G. McArthur. 2006. The Giardia lamblia regulome: origins of eukaryotic transcriptional regulation? Poster presentation at the 2006 Molecular Evolution Gordon Conference, Ventura, California AND the 17th Molecular Parasitology Meeting, Woods Hole, MALauweat, T., D. Reiner, E. Romijn, S.R. Birkeland, M.J. Cipriano, D. Palm, B. Davids, S.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1163434188524604462006-10-03T11:07:00.000-04:002006-11-17T20:28:41.673-05:00

Hahn, M.E., S.I. Karchner, D.G. Franks, B.R. Woodin, K.L. Barott, M.J. Cipriano, & A.G. McArthur. 2007. Transcriptional response to oxidative stress in embryos exposed to tBHQ or TCDD. Presentation at the Meeting of the Society of Toxicology, Charlotte, North Carolina.Oxidative stress resulting from environmental exposures has been implicated in a variety of human diseases ranging from chemical

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1163433895577516332006-10-03T11:00:00.000-04:002006-11-13T11:20:23.946-05:00

Dyhrman, S.T., S.T. Haley, S.R. Birkeland, L. Wurch, M.J. Cipriano, & A.G. McArthur. 2007. Genomic approaches for studying nutrient acquisition strategies in the coccolithophore Emiliania huxleyi. Presentation at the Meeting of the American Society of Limnology and Oceonography, Santa Fe, New Mexico.The coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1163441250348400172006-08-01T13:07:00.000-04:002006-11-13T13:09:37.803-05:00

Faulkner, S.D., M.W. Oli, R. Kieft, L. Cotlin, J. Widener, A. Shiflett, M.J. Cipriano, S.E. Pacocha, S.R. Birkeland, S.L. Hajduk & A.G. McArthur. 2006. In vitro generation of human HDL resistant Trypanosoma brucei brucei. Eukaryotic Cell, 5, 1276-1286.The host range of African trypanosomes is influenced by innate protective molecules in the blood of primates. A subfraction of human high density

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1148572620779789802006-05-25T11:57:00.000-04:002006-05-25T12:29:46.510-04:00

Messerli, S.M., S.R. Birkeland, W. Morgan, J. Bernier, M.J. Cipriano, A.G. McArthur & R.M. Greenberg. 2006. NO-induced upregulation of superoxide dismutase in Schistosoma mansoni. Presentation by S.M. Messerli at the Meeting of the Society for Neuroscience, Atlanta, Georgia.Schistosomiasis, a leading worldwide parasitic infection which affects approximately 200 million people globally, killing

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1146055979668816282006-04-26T08:52:00.000-04:002006-11-17T20:28:12.506-05:00

We have been collaborating with Kristen Hager's group at Notre Dame on the bioinformatic analysis of a protein involved in Toxoplasma protein transport, with some of the results being presented at the next CAMP meeting:Hjort, E.E., S.S. Smith, K. Hager, A.G. McArthur, & X. Gu. 2006. Molecular evolution of beta-COP, a vesicle coat component. Poster presentation at the meeting of the Chicago Area

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1145916251679082822006-04-24T18:04:00.000-04:002006-04-24T18:13:18.720-04:00

After eight years in Woods Hole, Andrew and his family have made the difficult decision to return to Canada in late May 2006. Andrew's wife will be taking up a Assistant Professor position at McMaster University in Hamilton, Ontario, Canada. Andrew's plans for the short term are to raise children and write manuscripts. Thanks to all of our friends and colleagues in Woods Hole for eight wonderful

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1138807473782550322006-02-01T10:24:00.000-05:002006-11-13T12:14:38.840-05:00

Update - Shanda has joined the laboratory of Robert Sabatini, which has just moved to the University of Georgia.Shanda Birkeland has been accepted to the Molecular Biology, Cell Biology, and Biochemistry graduate program at Brown University. Shanda has been a research assistant in the McArthur laboratory for the last 2+ years and in that time produced a remarkable amount of SAGE data for Giardia

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1132936154414016302006-01-30T11:29:00.000-05:002006-04-26T09:05:20.410-04:00

The Molecular Evolution Gordon Research Conference is held every two years, and brings together leading junior and senior scientists from around the globe in a small and informal conference setting to discuss current research as well as emerging opportunities and challenges in molecular evolution. This years meeting includes recent work on on ancestral protein reconstruction, computational

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1138807416979476522006-01-01T10:23:00.000-05:002006-02-21T17:11:10.546-05:00

Seungho Kang will be spending part of 2006 working in the McArthur lab. Seungho is a new graduate student in the laboratory of David Williams at Illinois State University and will be working Schistosoma SAGE library construction while at MBL. Welcome Seungho!Seungho will be joined part-time by Polina Bulygina, a student at Falmouth High School. Polina will be assisting with DNA sequencing of

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1134588444990280512005-12-14T14:27:00.000-05:002006-04-26T09:10:27.160-04:00

We have been collaborating with Sonya Dyhrman's group at the Woods Hole Oceanographic Institution on the marine protist Emiliania huxleyi. This work is being published in Applied and Environmental Microbiology as well as being presented at the 2006 ASLO Meeting:Dyhrman, S.T., S.T. Haley, S.R. Birkeland, L.L. Wurch, M.J. Cipriano, & A.G. McArthur. 2006. Long-SAGE (serial analysis of gene

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1138982977671793292005-12-08T11:09:00.000-05:002006-02-03T11:17:30.480-05:00

The goal of this meeting is to create a forum for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research. For more information, please see the meeting web site. Some of our work on Trichomonas is being presented:Hayes R.D., J.M. Carlton, M.J. Cipriano, A.G. McArthur, & P.J.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1133280533096959972005-11-29T11:08:00.000-05:002006-04-26T09:10:57.406-04:00

ICOPA is convened every four years by the World Federation of Parasitologists (WFP) and in 2006 the British Society for Parasitology has the honour of hosting this meeting at the Scottish Exhibition and Conference Centre. We are presenting some of our Schistosoma results:Williams, D.L., A.A. Sayed, J. Bernier, S.R. Birkeland, M.J. Cipriano, A. Papa, & A.G. McArthur. 2006. Transcriptional

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1132936143528324512005-11-25T11:29:00.000-05:002005-11-25T18:00:48.730-05:00

This First International Conference on Phylogenomics aims to reunite experts focusing on two distinct aspects of phylogenomics: the use of genome data inferring species phylogeny and the use of phylogenetic approaches to gain insights into gene functions. The methods developed for phylogenetic inference (especially the models of sequence evolution) are quite advanced and could benefit to function

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1131397411518402652005-11-07T16:03:00.000-05:002006-02-03T11:20:50.763-05:00

The 2006 Host-parasite Interactions GRC Conference will focus on the latest findings on molecular aspects of protozoan organisms and how these relate to human and animal diseases such as (but not limited to) malaria, toxoplasmosis, African and American trypanosomiasis, leishmaniasis, trichomoniasis, giardiasis and entamoebiasis. The aim of the meeting is to define current state of this dynamic

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1128542912092497512005-10-04T16:08:00.000-04:002005-10-05T16:20:41.196-04:00

The McArthur lab is again teaching at the MBL-TIGR Genomes Course. This is a comprehensive, four-week course in Genome Science that integrates Bioinformatics with the latest laboratory techniques for genome sequencing, genome analysis, and high throughput gene expression (DNA microarrays). A distinguished faculty from major universities, bioinformatic centers, The Institute for Genomic Research

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1128543346006440262005-10-03T16:15:00.000-04:002006-02-21T16:58:51.146-05:00

Jeremiah Bernier has finished his visit to the McArthur laboratory. Jeremiah was here for the last six months to learn Serial Analysis of Gene Expression by working with us on construction and sequencing of Schistosoma mansoni SAGE libraries. He also produced his own SAGE data for his master's project on chinook salmon behavioral ecology. Before entirely leaving us, Jeremiah will be attending

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1128543225138736232005-09-29T16:13:00.000-04:002006-02-21T16:59:31.646-05:00

Michael Cipriano has moved on west (San Francisco) to pursue the next stage of his career. Michael has been the lead computational biologist in the McArthur laboratory, responsible for developing genome assembly, sequence annotation, and gene expression analytical and visualization tools in the context of the Generic Model Organism Database (GMOD; gmod.mbl.edu) paradigm. Michael was also a very

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1125329817183849102005-08-29T11:36:00.000-04:002005-08-30T12:20:35.130-04:00

Michael Cipriano and Andrew McArthur, along with Sibel Karchner from the Woods Hole Oceanographic Institution, are spending August 29-30 at Agilent Technologies in Cambridge, MA. While there they will be evaluating the BioAnalyzer technology for assessing RNA quantity and quality, plus performing a preliminary experiment using TCDD and tBHQ exposed zebrafish embryos and the Agilent zebrafish

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1125077412017408182005-08-26T13:30:00.000-04:002005-08-26T13:32:19.490-04:00

The next Generic Model Organism Database (GMOD) developers meeting has been scheduled for October 27-28 (see http://www.gmod.org/ register.shtml). This is immediately followed by the Cold Spring Harbor Laboratory Genome Informatics Meeting (October 28 - November 1).

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1124820512743009482005-08-23T14:08:00.000-04:002006-02-21T17:01:32.836-05:00

Alex Papa has finished her summer research in the McArthur laboratory and has returned to UMass Amherst. Alex spent the summer sequencing Schistosoma mansoni SAGE libraries, with emphasis upon identification of genes involved in sexual differentiation while the worms were in the mammalian host. Thanks for your help this summer, Alex!

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1124460692214785402005-08-19T10:11:00.000-04:002006-04-26T09:06:44.490-04:00

The McArthur lab is helping to develop the Trichomonas vaginalis Genome Project Database by sharing code from our Generic Model Organism Database projects. Preliminary results are being presented at the International Conference on Anaerobic Protists:Hayes R.D., J.M. Carlton, M.J. Cipriano, A.G. McArthur, & P.J. Johnson. 2005. TrichoDB: a web-based resource for the Trichomonas vaginalis genome.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1120061528009960262005-07-27T12:12:00.000-04:002006-04-26T09:07:10.556-04:00

Presentation of some of our preliminary Schistosoma gene expression results at ASTMH 2005:Messerli, S.M., S.R. Birkeland, J. Bernier, M.J. Cipriano, A.G. McArthur, & R.M. Greenberg. 2005. NO-dependent changes in Schistosoma mansoni gene expression identified by SAGE. Presentation by S.M. Messerli at the American Society of Tropical Medicine and Hygiene 54th Annual Meeting.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1122490543682173982005-07-15T14:55:00.000-04:002005-07-27T14:58:10.200-04:00

The genomes of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major have been published!

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1119290559884187772005-06-20T14:02:00.000-04:002005-06-20T15:19:29.006-04:00

As part of the growing Brown-MBL Joint Graduate Program, Andrew McArthur has joined the faculty of Brown's Department of Molecular Biology, Cell Biology, and Biochemistry at Brown University. This enables Andrew to teach in the MCB Graduate Program and for Brown graduate students to join or spend time in Andrew's laboratory at MBL. Andrew will be giving a seminar at this year's MCB Graduate

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118318362263642582005-06-19T07:59:00.000-04:002006-04-26T09:07:34.056-04:00

Heather Handley-Goldstone has won Best Presentation at the 13th Annual Symposium on Pollutant Responses in Marine Organisms (Alessandria, Italy, June 19-22, 2005) for research she performed while a post-doc in John Stegeman's laboratory at the Woods Hole Oceanographic Institution:Handley-Goldstone, H.M. and J.J. Stegeman (2005) Minimum unlikelihood: gene duplication and gene conversion in the

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118749963373843722005-06-14T07:52:00.000-04:002006-04-26T09:17:16.396-04:00

This essential meeting in Parasitology covers all aspects of parasite molecular biology, cell biology, biochemistry, genetics and genomics, focusing on protozoan parasites. Abstracts will be available online soon - here is what the McArthur lab has submitted:Cipriano, M.J., T. Ochsenreiter, A.G. McArthur, and S.L. Hajduk. 2005. Development of a bioinformatic tool for guide RNA analysis. Computer

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118505636076208452005-06-11T12:00:00.000-04:002005-06-11T12:02:43.940-04:00

The deadline for the MBL-TIGR Advances in Genome Technology and Bioinformatics Course is rapidly approaching. The McArthur lab will again be teaching aspects of bioinformatics and SAGE.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118250044459327102005-06-08T13:00:00.000-04:002006-02-21T17:02:57.266-05:00

As part of her continuing work on Giardia lamblia, Shanda Birkeland will be attending the NIH Meeting on the Evolution of Infectious Diseases. Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist, often hypothesized to be the most basal eukaryote. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118256702689007392005-06-08T12:51:00.000-04:002005-06-08T14:55:36.816-04:00

The Cold Spring Harbor Laboratory Genome Informatics meeting is this fall,October 28 to November 1, 2005. The Abstract deadline is August 3, 2005. For more information see the CSHL website at http://meetings.cshl.edu/meetings/info05.shtml

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118245550286842102005-06-08T11:45:00.000-04:002006-02-21T17:03:24.793-05:00

As part of her post-doctoral research, Heather Handley-Goldstone will be attending a Systems Biology Course at the New England Complex Systems Institute which focusses in part of the evolution of transcriptional networks.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118244874803186852005-06-06T11:34:00.000-04:002006-02-21T17:04:03.256-05:00

Michael Cipriano spent a few days in June teaching with Dr. Raphael Isokpeki (a former GID program scholar) at Jackson State University on various aspects of bioinformatics, plus continued a collaboration on the annotation of the Giardia lamblia genome.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118196587514781892005-06-01T22:09:00.000-04:002005-06-20T07:53:50.930-04:00

This symposium is organized under the COST-B22 Action by the Department of Biomedical Sciences, Center for Biotechnology Development and Biodiversity Research of the University of Sassari. The congress is scheduled to be held in Alghero, in Sardinia (Italy), from 17th to 20th September 2005. The ICAP Conference will provide the leading international scientists working on the diverse aspects of

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118319978995610542005-05-24T08:26:00.000-04:002006-04-26T09:12:39.930-04:00

Ochsenreiter, T., M.J. Cipriano, and S.L. Hajduk. 2005. RNA editing creates novel open reading frames in Trypanosoma brucei. Poster presentation at the Tenth Annual Meeting of the RNA Society, Banff, Canada.

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118251917074180402005-05-17T13:31:00.000-04:002005-06-09T17:33:45.586-04:00

The latest version of MrBayes has been released! In version 3.1, all known bugs have been addressed. Several major additions have been made. Perhaps most important of these, MrBayes can now run several independent analyses simultaneously and uses the samples from these to calculate convergence diagnostics on the fly. This makes it possible, for instance, to stop a run automatically when

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118281701479222902005-05-16T21:48:00.000-04:002006-02-21T17:05:39.013-05:00

In support of their efforts in expanding the JBPC Generic Model Organism Database Server, Michael Cipriano and Susan Huse attended the Spring 2005 GMOD Meeting in Menlo Park, California.The Generic Model Organism Database Project (GMOD) is a largely open source project to develop a complete set of software for creating and administering a model organism database. Components of this project

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118252673112517512005-05-01T13:44:00.000-04:002006-02-21T17:04:49.253-05:00

Alex Papa (undergraduate student, UMass Amherst) and Jeremiah Bernier (master's student, Oregon State University) have joined us for the summer to work on a number of Serial Analysis of Gene Expression (SAGE) projects. Jeremiah is here to learn the technique by working with us on construction and sequencing of Schistosoma mansoni SAGE libraries, plus he will be producing his own SAGE data for his

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118242881966213032005-04-12T11:01:00.000-04:002006-04-26T09:09:04.946-04:00

The purpose of the KMCBM is to provide a forum for anyone working on or interested in the Molecular Cell Biology of Trypanosomes and Leishmania and related model organisms, without restrictions on attendance. Participants whose primary focus is on pathogenesis and drug development will also be welcome. Presentations (talks and posters) of research-in-progress by young investigators are strongly

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118317125584759182005-04-06T07:38:00.000-04:002005-06-09T07:45:54.326-04:00

Dear all,As many of you know, we have bioinformatics servers for hosting internal and public genome, EST, and SAGE projects, plus for analysis of publicly available genome sequences. Currently we are hosting genome, EST, and SAGE data on projects involving Antonospora, Aureococcus, Blochmannia, Emiliania, Giardia, Marinobacter, Philodina, Schistosoma, Trypanosoma cruzi, and Trypanosoma brucei (

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118254546436890072005-03-31T14:15:00.000-05:002006-04-26T09:11:51.300-04:00

Giardia lamblia is a protozoan parasite infecting the upper mammalian small intestine. Infection relies upon the ability of the parasite to attach to the intestine via a unique cytoskeletal organelle, the ventral disk. We determined the composition and structure of the disk throughout the life cycle of the parasite and identified a new disk protein, SALP-1. SALP-1 is an immunodominant

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118255908010106562005-03-01T14:38:00.000-05:002006-04-26T09:13:32.570-04:00

A collaboration between David Williams (PI, Illinois State University) and the McArthur laboratory:Schistosomiasis is an important tropical parasitic disease. In spite of the widespread use ofherapy and other control strategies over the past 50 years, transmission rates for schistosomiasis havechanged little. Currently, a single drug is in widespread use and there is concern that drug resistant

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1122490856552527902005-02-24T15:00:00.000-05:002006-04-26T09:14:12.656-04:00

The complete genome of Entamoeba histolytica has been published!

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118254584150899772005-02-09T14:16:00.000-05:002006-04-26T09:14:51.746-04:00

Through a genome survey and phylogenetic analysis, we have identified and sequenced 14 new coding regions for alpha-giardins in Giardia lamblia. These proteins are related to annexins and comprise a multi- gene family with 21 members. Many alpha giardins are highly expressed proteins that are very immunogenic during acute giardiasis in humans. However, little is known about the function of

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118228044228187882005-01-15T06:54:00.000-05:002005-06-08T13:51:31.000-04:00

Advances in Genome Technology and Bioinformatics CourseMarine Biological Laboratory & The Institute for Genome ResearchOctober 4 - October 30, 2005Course Web PageA comprehensive, four-week course in Genome Science that will integrate Bioinformatics with the latest laboratory techniques for genome sequencing, genome analysis, and high throughput gene expression (DNA microarrays). A distinguished

Andrew G. McArthurnoreply@blogger.comtag:blogger.com,1999:blog-13494811.post-1118254632583704652005-01-01T14:17:00.000-05:002006-04-26T09:15:14.743-04:00

Aromatase (cytochrome P450 19, CYP19, P450arom) is the enzyme responsible for the production of estrogens, hormones critical for development and reproduction. Aromatase was sequenced from a white- sided dolphin (Lagenorhynchus acutus) ovary, transiently transfected into HEK 293 cells, and the expressed protein was characterized for aromatase activity in the presence of androstenedione and

Andrew G. McArthurnoreply@blogger.com