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Thursday, 18 September 2014

Maqsudul Alam

Maqsudul Alam

Maqsudul Alam is a Bangladeshi American Scientist and Professor. Dr. Maqsudul Alam achieved Four milestones in genomics - sequencing the genomes of Papaya, Rubber, Jute and Fungus. Dr. Maqsudul Alam is a professor of the University of Hawaii at Manoa and a member of advisory board at Shahjalal University of Science and Technology.


Personal life

Dr. Maqsudul Alam was born in Bangladesh.

    M.S. Microbiology in 1979 from Moscow State University, Moscow, Russia.
    Ph.D. Microbiology in 1982 from Moscow State University, Moscow, Russia.
    Ph.D. Biochemistry in 1987 from Max-Planck-Institute of Biochemistry, Germany

Professional positions

    10/03-present Director, Advanced Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii at Manoa, Honolulu, Hawai’i

    07/01-present Professor, Department of Microbiology, University of Hawai’i at Manoa, Honolulu, Hawai’i

    08/97-06/01 Associate Professor, Department of Microbiology, University of Hawai’i at Manoa, Honolulu, Hawai’i

    08/92-07/97 Assistant Professor, Department of Microbiology, University of Hawai’i at Manoa, Honolulu, Hawai’i

    03/90-07/92 Visiting Scientist, Department of Biochemistry and Biophysics, Washington State University, Pullman, WA

    03/88-02/90 Senior Research Scientist, Institute of Bioorganic Chemistry, Academy of Sciences, Moscow, Russia

    1988-1989 Visiting Scientist, German Research Foundation, Institute of Bioorganic Chemistry, Academy of Sciences, Moscow, Russia

    1987-1988 Assistant Scientist, Max-Planck Institute of Biochemistry, Munich, Germany

    1986-1987 Alexander von-Humboldts Fellow, Max-Planck Institute of Biochemistry, Munich, Germany

    12/84-03/86 Research Associate, Biochemistry/Biophysics Program, Washington State University, Pullman, WA


• University of Hawai’i, Board of Regents' Excellence of Research Award, 2001

• NIH Shannon Award, 1997

• Humboldt Research Fellow, German Science Foundation, 1987


• Saito, J.A., Wan, X., Lee, K.S., Hou, S., Alam, M. 2008. Globin-coupled sensors and protoglobins share a common signaling mechanism. FEBS Lett. In press.

• Stott, M.B., Crowe, M.A., Mountain, B.W., Smirnova, A.V., Hou, S., Alam, M., Dunfield, P.F. 2008. Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol. In press.

• Tang, H., Bowers, J.E., Wang, X., Ming, R., Alam, M., & Paterson, A.H. 2008. Synteny and collinearity in plant genomes. Science. 320(5875):486-488.

• Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J.H., Senin, P., Wang, W., Ly, B.V., Lewis, K.L.T., Salzberg, S.L., Feng, L., Jones, M.R., Skelton, R.L., Murray, J.E., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M., Tong, E., Tang, H., Lyons, E., Paull, R.E., Michael, T.P., Wall, K., Rice, D., Albert, H., Wang, M.L., Zhu, Y.J., Schatz, M., Nagarajan, N., Acob, R.A., Guan, P., Blas, A., Wai, C.M., Ackerman, C.M., Ren, Y., Liu, C., Wang, J., Wang, J., Na, J.K., Shakirov, E.V., Haas, B., Thimmapuram, J., Nelson, D., Wang, X., Bowers, J.E., Gschwend, A.R., Delcher, A.L., Singh, R., Suzuki, J.Y., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Navajas-Pérez, R., Torres, M.J., Feltus, F.A., Porter, B., Li, Y., Burroughs, A.M., Luo, M.C., Liu, L., Christopher, D.A., Mount, S.M., Moore, P.H., Sugimura, T., Jiang, J., Schuler, M.A., Friedman, V., Mitchell-Olds, T., Shippen, D.E., dePamphilis, C.W., Palmer, J.D., Freeling, M., Paterson, A.H., Gonsalves, D., Wang, L., & Alam, M. 2008. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 452(7190):991-996.

• Eustice, M., Yu, Q., Lai, C.W., Hou, S., Thimmapuram, J., Liu, L., Alam, M., Moore, P.H., Presting, G.G., & Ming, M. 2008. Development and application of microsatellite markers for genomic analysis of papaya. Tree Genetics and Genomes. 4:333-341.

• Saito, J.A., Freitas, T.A.K., & Alam, M. 2008. Cloning, expression, and purification of the N-terminal heme-binding domain of globin-coupled sensors. Methods Enzymol. 437: 163-172.

• Nardini, M., Pesce, A., Thijs, L., Saito, J.A., Dewilde, S., Alam, M., Ascenzi, P., Coletta, M., Ciaccio, C., Moens, L., & Bolognesi, M. 2008. Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity. EMBO Rep. 9(2):157-163.

• Yu, Q., Hou, S., Feltus, F.A., Jones, M.R., Murray, J.E., Veatch, O., Lemke, C., Saw, J.H., Moore, R.C., Thimmapuram, J., Liu, L., • Freitas, T.A.K., Saito, J.A., Wan, X., Hou, S., & Alam, M. 2007. Protoglobin and globin-coupled sensors. In Ghosh, A. (Ed.) The smallest biomolecules: diatomics and their interactions with heme proteins. pp. 175–202.

• Dunfield, P.F., Yuryev, A., Senin, P., Smirnova, A.V., Stott, M.B., Hou, S., Ly, B., Saw, J.H., Zhou, Z., Ren, Y., Wang, J., Mountain, B.W., Crowe, M.A., Weatherby, T.M., Bodelier, P.L., Liesack, W., Feng, L., Wang, L. & Alam, M. 2007. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature. 450(7171):879-882.

• Chen, C., Yu, Q., Hou, S., Li, Y., Eustice, M., Skelton, R.L., Veatch, O., Herdes, R., Diebold, L., Saw, J., Feng, Y., Qian, W., Bynum, L., Wang, L., Moore, P.H., Paull, R.E., Alam, M. & Ming, R. 2007. Construction of a Sequence-Tagged High Density Genetic Map of Papaya for Comparative Structural and Evolutionary Genomics in Brassicales. Genetics. 177(4):2481-2491.

• Thijs, L., Vinck, E., Bolli, A., Trandafir, F., Wan, X., Hoogewijs, D., Coletta, M., Fago, A., Weber, R.E., Van Doorslaer, S., Ascenzi, P., Alam, M., Moens, L. & Dewilde, S. 2007. Characterization of a globin coupled sensor with a gene regulating function. J Biol Chem. 282(52):37325-37340.

• Yu, Q., Hou, S., Hobza, R., Feltus, F.A., Wang, X., Jin, W., Skelton, R.L., Blas, A., Lemke, C., Saw, J.H., Moore, P.H., Alam, M., Jiang, J., Paterson, A.H., Vyskot, B. & Ming, R. 2007. Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. Mol Genet Genomics. 278(2):177-185.

• Donachie, S.P., Bowman, J.P. & Alam, M. 2006. Nesiotobacter exalbescens gen. nov., sp. nov., a moderately thermophilic alphaproteobacterium from an Hawaiian hypersaline lake. Int J Syst Evol Microbiol. 56(Pt 3):563-567.

• Shibata, S., Alam, M., & Aizawa, S-I. 2005. Flagellar Filaments of the Deep-sea Bacteria Idiomarina loihiensis Belong to a Family Different from those of Salmonella typhimurium. J Mol Biol. 352:510-516.

• Donachie, S. P., Bowman, J. P., On, S. L. W., & Alam, M. 2005. Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter. Int J Syst Evol Microbiol. 55(Pt 3):1271-1277.

• Freitas, T.A., Saito, J.A., Hou, S., & Alam, M. 2005. Globin-coupled sensors, protoglobins, and the last universal common ancestor. J Inorg Biochem. 99(1):23-33.

• Hou, S., Saw, J.H., Lee, K.S., Freitas, T.A., Belisle, C., Kawarabayasi, Y., Donachie, S.P., Galperin, M.Y., Koonin, E.V., Makarova, K.S., Omelchenko, M.V., Sorokin, A., Wolf, Y.I., Li, Q., Keum, Y.S., Campbell, S., Denery, J., Aizawa, S.-I., Shibata, S., Malahoff, A., & Alam, M. 2004. Genome Sequence of the deep-sea ?-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Pro Natl Acad Sci USA. 101(52):18036-18041.

• Donachie, S.P., Hou, S., Lee, K.S., Riley, C.W., Pikina, A., Belisle, C., Kempe, S., Gregory, T.S., Bossuyt, A., Boerema, J., Liu, J., Freitas, T.A., Malahoff, A., & Alam, M. 2004. The Hawaiian Archipelago: a microbial diversity hotspot. Microb Ecol. 48(4):509-520.

• Donachie, S.P., Bowman, J.P., & Alam, M. 2004. Psychroflexus tropicus sp. nov., an obligately halophilic Cytophaga-Flavobacterium-Bacteroides group bacterium from an Hawaiian hypersaline lake. Int J Syst Evol Microbiol. 54: 935-940.

• Freitas, T.A.K., Hou, S., Dioum, E.M., Saito, J.A., Newhouse, J., Gonzalez, G., Gilles-Gonzalez, M., & Alam, M. 2004. Ancestral Hemoglobins in Archaea. Proc Natl Acad Sci USA. 101(17):6675-6680.

• Donachie S.P., J.P. Bowman & M. Alam (2003) Psychroflexus tropicus, sp. nov., a novel, obligately halophilic Cytophaga-Flavobacterium-Bacteroides group bacterium from an Hawai’ian hypersaline lake. Int. J. Syst. Evol. Microbiol., in press.

• Donachie, S.P., S. Hou, T.S. Gregory, A. Malahoff & M. Alam (2003) Idiomarina loihiensis, sp. nov., a novel, halophilic g-Proteobacterium from the Loihi submarine volcano, Hawai'i. Int. J. Syst. Evol. Microbiol., in press.

• Boudko D, Yu HS, Ruiz M, Hou S, Alam M. (2003) A time-lapse capillary assay to study aerotaxis in the archaeon Halobacterium salinarum. J Microbiol Methods. 53(1):123-6.

• Donachie SP, Christenson BW, Kunkel DD, Malahoff A, Alam M. (2002) Microbial community in acidic hydrothermal waters of volcanically active White Island, New Zealand. Extremophiles. 6(5):419-25.

• Malahoff, A. Gregory, T. Bossuyt, A. Donachie, S. Alam, M. (2002) A seamless system for the collection and cultivation of extremophiles from deep-ocean hydrothermal vents. IEEE J. Ocean. Eng, 27:862-869.

• Yu HS, Saw JH, Hou S, Larsen RW, Watts KJ, Johnson MS, Zimmer MA, Ordal GW, Taylor BL, Alam M. (2002) Aerotactic responses in bacteria to photoreleased oxygen. FEMS Microbiol Lett. 217(2):237-42.

• Hou S, Belisle C, Lam S, Piatibratov M, Sivozhelezov V, Takami H, Alam M. (2001) A globin-coupled oxygen sensor from the facultatively alkaliphilic Bacillus halodurans C-125. Extremophiles. 5(5):351-4.

• Hou S, Freitas T, Larsen RW, Piatibratov M, Sivozhelezov V, Yamamoto A, Meleshkevitch EA, Zimmer M, Ordal GW, Alam M. (2001) Globin-coupled sensors: a class of heme-containing sensors in Archaea and Bacteria. Proc Natl Acad Sci U S A. 98(16):9353-8. • Piatibratov M, Hou S, Brooun A, Yang J, Chen H, Alam M. (2000) Expression and fast-flow purification of a polyhistidine-tagged myoglobin-like aerotaxis transducer. Biochim Biophys Acta. 1524(2-3):149-54.

• Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S. (2000) Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A. 24;97(22):12176-81.

• Hou S, Larsen RW, Boudko D, Riley CW, Karatan E, Zimmer M, Ordal GW, Alam M. (2000) Myoglobin-like aerotaxis transducers in Archaea and Bacteria. Nature 403(6769):540-4.

• Larsen RW, Yang J, Hou S, Helms MK, Jameson DM, Alam M. (1999) Spectroscopic characterization of two soluble transducers from the Archaeon Halobacterium salinarum. J Protein Chem. 18(3):269-75.

• Hou S, Brooun A, Yu HS, Freitas T, Alam M. (1998) Sensory rhodopsin II transducer HtrII is also responsible for serine chemotaxis in the archaeon Halobacterium salinarum. J Bacteriol. 180(6):1600-2.

• Brooun A, Bell J, Freitas T, Larsen RW, Alam M. (1998) An archaeal aerotaxis transducer combines subunit I core structures of eukaryotic cytochrome c oxidase and eubacterial methyl-accepting chemotaxis proteins. J Bacteriol. 180(7):1642-6.

• Muthyala RS, Alam M, Liu RS. (1998) Alkylated Azulenic Retinal and Bacteriorhodopsin Analogs. Tetrahedron Letters. 39:5-8.

• Bell J.R, Muthyala RS, Larsen RW, Alam M, Liu RS. (1998) Photoactivities of the Red-Shifted Azulenic Bacteriorhodopsin Analogues. J. Phys. Chem. 102:5481-5483.

• Yu HS, Alam M. (1997) An agarose-in-plug bridge method to study chemotaxis in the Archaeon Halobacterium salinarium. FEMS Microbiology letters, 156:256-269.

• Brooun A, Zhang W, Alam M. (1997) Primary structure and functional studies of the soluble transducer HtrXI from the Archaeon Halobacterium salinarium. J. Bacteriol. 179:2963-2968.

• Zhu J, Spudich EN, Alam M, Spudich JL. (1997) Effects of substitutions D73E, D73N, D103N and V106M on signaling and pH titration of sensory rhodopsin II. Photochem Photobiol. 66(6):788-91.

• Spudich EN, Zhang W, Alam M, Spudich JL. (1997) Constitutive signaling by the phototaxis receptor sensory rhodopsin II from disruption of its protonated Schiff base-Asp-73 interhelical salt bridge. Proc. Natl. Acad. Sci. USA, 94:4960-4965

• Zhang W, Brooun A, McCandless J, Banda P, Alam M. (1996) Signal Transduction in the Archaeon Halobacterium salinarum is processed through three subfamilies of thirteen soluble and membrane-bound transducer proteins. Proc. Natl. Acad. Sci. USA, 93: 4649-4654.

• Zhang W, Brooun A, Mueller MM, Alam M. (1996) The primary structures of the Archaeon Halobacterium salinarum blue light receptor sensory rhodpsin II and its transducer, a methyl-accepting protein. Proc. Natl. Acad. Sci. USA, 93:8320-8235.

• Nordmann B, Lebert MR, Alam M, Nitz S, Kollmannsberger H, Oesterhelt D, Hazelbauer GL. (1994) Identification of volatile forms of methyl groups released by Halobacterium halobium. J. Biol. Chem. 269:16449-16454.

• Alam M, Hazelbauer GL. (1991) Structural features of methyl-accepting taxis proteins conserved between archaeabacteria and eubacteria revealed by antigenic cross-reaction. J. Bacteriol. 173:5837-5842.

• Marwan W, Alam M, Oesterhelt D. (1991) Rotation and switching of the flagellar motor assembly in Halobacterium halobium. J Bacteriol. 173(6):1971-7.

• Sundberg SA, Alam M, Lebert M, Spudich JL, Oesterhelt D, Hazelbauer GL. (1990) Characterization of Halobacterium halobium mutants defective in taxis. J Bacteriol. 172(5):2328-35.

• Alam M, Lebert M, Oesterhelt D, Hazelbauer GL. (1989) Methyl-accepting taxis proteins in Halobacterium halobium. EMBO J 8(2):631-9.

• Alam M, Oesterhelt D. (1987) Purification, reconstitution and polymorphic transition of halobacterial flagella. J Mol Biol. 194(3):495-9.

• Sundberg SA, Alam M, Spudich JL. (1986) Excitation signal processing time in Halobacterium halobium phototaxis. J. Biophys. 50:895-900.

• Alam M, Claviez M, Oesterhelt D, Kessel M. (1984) Flagellar and motility behavior of square bacteria. EMBO J. 3:2899-2903. This paper was reviewed in the News and Views section. Nature. 1985. 313:183.

• Alam M, Oesterhelt D. (1984) Morphology, function and isolation of halobacterial flagella. J. Mol. Biol. 176:459-475. This paper was reviewed in the News and Views section. Nature. 1984. 310:367.

• Alam M. (1983) Chemosensory behavior of marine luminescent bacteria. FEMS Microbiology letters. 17:291-293.

• Alam M, Glagolev AN. (1982) delta mu H+-sensing in taxis of Vibrio harveyi. FEBS letters. 143(1):144-6.

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