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Halobacteria Group:
PUBLICATIONS
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Recent Halo Group Publications:
Young Ah Goo, Eugene C. Yi, Baliga, N., Weiguo A. Tao, Pan, M., Ruedi Aebersold, David R. Goodlett,
Leroy Hood, and Ng. W.V. 2003. Proteomic analysis of an extreme halophilic
archaeon,Halobacterium sp. NRC-1. Molecular and Cellular Proteomics.
M300044-MCP200.
Baliga,
Nitin:
Baliga, N.S.,
DasSarma S. 1999. Saturation mutagenesis of the TATA box and
upstream activator sequence in the haloarchaeal bop gene promoter.
J Bacteriol.181(8):2513-8.
Baliga,
N., Goo, Y.A., Ng. W.V., Hood, L.,
Daniels, C.J., and DasSarma, S.. 2000. Is gene expression in Halobacterium NRC-1
regulated by multiple TBP and TFB transcription factors? Mol.
Microbiol. 36:1184-5
Baliga, N.S.,
Kennedy, S.P., Ng. W.V., Hood, L.,
DasSarma, S. 2001. Genomic and
genetic dissection of an archaeal regulon. Proc Natl Acad Sci U S
A 98:2521-5.
Baliga, N.,Pan, M., Goo, Y.A., Yi, E.C., Goodlett, D.R.,
Dimitrov, K., Shannon, P., Aebersold, R., Ng. W.V., Hood, L. 2002. Coordinate regulation of energy
transduction modules in Halobacterium sp. analyzed by a global systems
approach. Proc Natl Acad Sci U S A 99:14913-8
DasSarma, S., Kennedy, S.P., Berquist,
B., Ng. W.V., Baliga, N.S., Spudich, J.L., Krebs, M.P.,
Eisen, J.A., Johnson, C.H., Hood, L. 2001. Genomic perspective on the photobiology of
Halobacterium species NRC-1, a phototrophic, phototactic, and
UV-tolerant haloarchaeon. Photosyn. Res. 70:3-17.
Ng.
W.V., Kennedy SP, Mahairas GG, Berquist B, Pan,
M., Shukla HD, Lasky SR, Baliga, N.,
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 97(22):12176-81.
Young Ah Goo, Eugene C. Yi, Baliga, N., Weiguo A. Tao, Pan, M., Ruedi Aebersold, David R. Goodlett,
Leroy Hood, and Ng. W.V. 2003. Proteomic analysis of an extreme halophilic
archaeon,Halobacterium sp. NRC-1. Molecular and Cellular Proteomics. M300044-MCP200.
Top
Recent Baliga, Nitin Bonneau, Rich Facciotti, Marc Ng, Victor Pan, Min |
Bonneau, Rich:
Bonneau, R.,
Dylan Chivian, Charlie EM Strauss, Carol Rohl, David Baker. (2002) De Novo
Prediction of Three Dimensional Structures for Major Protein Families.
JMB, 322(1):65-78.
Bonneau, R.,
Ingo Ruczinski, Jerry Tsai, David Baker. (2002) Contact
Order and ab initio Structure Prediction. Protein Science,
11(8):1937-44.
Bonneau, R.,
Jerry Tsai, Ingo Ruczinski, Dylan Chivian, Carol Rohl, Charlie EM
Strauss, David Baker. (2001) Rosetta in CASP4: Progress in ab
initio protein structure prediction. Proteins.
45(S5)119-126.
Bonneau, R.,
Jerry Tsai, Ingo Ruczinski, David Baker. (2001) Functional
inferences from blind ab initio protein structure predictions. J.
Struct. Biol. 134(2-3),186-90.
Bonneau, R.,
Strauss, C. & Baker, D. (2001). Improving
the performance of Rosetta using multiple sequence alignment
information and global measures of hydrophobic core formation.
Proteins 43(1), 1-11.
Bonneau, R.
& Baker, D. (2001). Ab Initio
Protein Structure Prediction: Progress and Prospects. Annu. Rev.
Biophys. Biomol. Struct. 30, 173-89. Review.
Ruczinski, I., Kooperberg, C., Bonneau, R., Baker, D. (2001) Distributions of beta sheets in proteins
with application to structure prediction. Proteins 48(1), 85-97.
Simons, K. T., Bonneau,
R., Ruczinski, I. & Baker, D. (1999). Ab initio protein structure prediction of
CASP III targets using ROSETTA. Proteins 37(S3), 171-176.
Tsai J, Bonneau R,
Morozov A, Kuhlman B, Rohl C, Baker D. Enhancement
of Rosetta de novo structure prediction through explicit side chain
modeling. (2002) Protein Science. [In Press]
Chivian, D., Bonneau,
R., Baker, D. et al. (2003) Chapter
27: Ab initio structure prediction. (In)Bourne, P.E. editor (2003)
Structural Bioinformatics. New York: John Wiley & Sons; ISBN:
0471201995. [In Press]
Top Recent
Baliga, Nitin Bonneau, Rich Facciotti,
Marc Ng, Victor Pan, Min
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Facciotti,
Marc:
Facciotti,
M.T. and Yuan, L. 1998. Molecular
dissection of the plant acyl-acyl carrier protein thioesterases.
FETT Lipid. 100:4-5. 167-172.
Facciotti,
M.T., Bertain, P.B., and Yuan, L. 1999. Improved stearate phenotype in transgenic
canola expressing a modified acyl-acyl carrier protein thioesterase.
Nature Biotechnology. 17. 593-597.
Facciotti,
M.T., Cheung, V., Nguyen, D., Rouhani, S., and Glaeser, R.M. 2003. Crystal structure of the bromide-bound
D85S mutant of bacteriorhodopsin: principles of ion pumping.
Biophysical Journal. 85. 451-458.
Facciotti,
M.T., Cheung, V., Lunde, C.S., Rouhani, S., Baliga, N., and
Glaeser, R.M. Comparative study of substrate specificity in
bacteriorhodpsin and the D85S mutants. (in preparation)
Facciotti,
M.T., Rouhani, S., Burkard, F.T., Betancourt, F.M., Downing, K.H.,
Rose, R.B., McDermott, G., and Glaeser, R.M. 2001. Structure of and early intermediate in the
M-state phase of the bacteriorhodopsin photocycle.
Biophysical Journal. 81. 3442-3455.
Glaeser, R., Facciotti, M.T., Walian, P.,
Rouhani, S., Holton, J., MacDowell, A., Celestre, R., Cambie, D., and
Padmore, H. 2000. Characterization
of conditions required for X-ray diffraction experiments with protein
microcrystals. Biophysical Journal. 78. 3178-3185.
Kennis, J.T.M., Larsen, D.S., Ohta, K., Facciotti, M.T., Glaeser, R.M.,
and Fleming, G.R. 2002. Ultrafast
protein dynamics of bacteriorhodopsin probed by photon echo and
transient absorption spectroscopy. Journal of Physical
Chemistry B. 106(23). 6067-6080.
Rouhani, S., Cartailler, J-P., Facciotti, M.T., Walian, P.,
Needleman, R., Lanyi, J.K., Glaeser, R.M., and Luecke, H. 2001. Crystal structure of the D85S mutant of
bacteriorhodopsin: Model of an O-like photocycle intermediate.
Journal of Molecular Biology. 313. 615-628.
Rouhani, S., Facciotti, M.T., Woodcock, G.,
Cheung, V., Cunningham., Nguyen, D., Rad, B., Lin, C., Lunde, C.S., and
Glaeser, R.M. 2002. Crystallization
of membrane proteins from media composed of connected-bilayer gels.
Biopolymers. 66. 300-316.
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Top Recent
Baliga, Nitin Bonneau, Rich Facciotti,
Marc Ng, Victor Pan, Min
Ng, Victor:
Ng. W.V.,
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
97(22):12176-81
Ng. W.V., Arora, P., and
DasSarma, S. 1994. Large deletion in
class III gas vesicle-deficient mutants of Halobacterium halobium.
System. Appl. Microbiol. 16: 560-568.
Ng.
W.V. and DasSarma, S. 1993. Minimal
replication origin of the 200 kilobase Halobacterium plasmid pNRC100. J. Bacteriol. 175:
4584-4596.
Ng.
W.V. and DasSarma ,S. 1991. Physical
and genetic mapping of the unstable gas vesicle plasmid in
Halobacterium halobium NRC-1. In F. Rodriguez-Valera (ed.),
“General and applied aspects of halophilic microorganisms”, Plenum
Press, New York, p.305-311.
Ng.
W.V., C.-F. Yang, J.T., Halladay, P. Arora, and S. DasSarma. 1995. Isolation of genomic and plasmid DNA from
Halobacterium halobium. In S. DasSarma and E.M. Fleishmann
(ed.), “Archaea: A laboratory manual - Halophiles”, Cold spring Hrbor
Laboratory press, p155-160.
Ng.
W.V., Halladay, J.T., and DasSarma, S. 1991. Isolation of large Halobacterium halobium
plasmids, p. 3.5.1-3.5.3. In E.M. Fleischmann, A.R. Place, F.T.
Robb, and H.J. Schreier (ed.), Protocols for archaebacterial research.
University of Maryland, Baltimore.
Ng. W.V.,
Kothakota, S., and DasSarma, S. 1991. Structure
of the gas vesicle plasmid in Halobacterium halobium: inversion
isomers, inverted repeats, and insertion sequences. J. Bacteriol.
173:1958 1964.
Ng.
W.V., Schummer, M., Cirisano, F.D., Baldwin, R.E., Karlan, B.Y.,
and Hood, L. 1996. High-throughput
plasmid mini preparation facilitated by micro-mixing. Nucleic
Acids Res. 24:5045-5047.
Ng.
W.V. et al. 2000. Genome sequence
of Halobacterium sp. NRC-1. Proc Natl Acad Sci 97:12176-81.
Ng.
W.V. et al. 1998. Snapshot of a
large dynamic replicon in a halophilic archaeon: megaplasmid or
minichromosome? Genome Res. 8:1131-41.
Baliga,
N., Goo, Y.A., Ng. W.V.,
Hood, L., Daniels, C.J., and DasSarma, S.. 2000. Is gene expression in Halobacterium NRC-1
regulated by multiple TBP and TFB transcription factors? Mol.
Microbiol. 36:1184-5
Baliga,
N., Pan, M., Goo, Y.A., Yi, E.C.,
Goodlett, D.R., Dimitrov, K., Shannon, P., Aebersold, R., Ng. W.V.., Hood, L. 2002. Coordinate regulation of energy
transduction modules in Halobacterium sp. analyzed by a global systems
approach. Proc Natl Acad Sci U S A 99:14913-8
Baliga,
N.S., Kennedy, S.P., Ng.
W.V., Hood, L., DasSarma, S. 2001. Genomic and genetic dissection of an
archaeal regulon. Proc Natl Acad Sci U S A 98:2521-5.
Bobovnikova, Y., Ng. W.V., DasSarma, S., and
Hackett, N.R. 1994. Restriction
mapping the genome of Halobacterium halobium strain NRC-1. System.
Appl. Microbiol. 16: 597-604.
DasSarma, S., Kennedy, S.P., Berquist, B., Ng. W.V.,Baliga, N.S., Spudich, J.L.,
Krebs, M.P., Eisen, J.A., Johnson, C.H., Hood, L. 2001. Genomic perspective on the photobiology of
Halobacterium species NRC-1, a phototrophic, phototactic, and
UV-tolerant haloarchaeon. Photosyn. Res. 70:3-17.
Halladay, J.T, Ng. W.V., and DasSarma, S.
1992. Genetic transformation of a
halophilic archaebacterium with a gas vesicle gene cluster restores its
ability to float. Gene 119: 131-136.
Huang, G.M., Ng. W.V., Farkas, J., He, L.,
Liang, H.A., Gordon, D., Yu, J., and Hood, L. 1999. Prostate cancer expression profiling by
cDNA sequencing analysis. Genomics 59:178-86.
J.G. Jones, Hackett, N.R.,. Halladay, J.T,
Scothorn, D.J., Yang, C.-F., Ng.
W.V., and DasSarma, S. 1989. Analysis
of insertion mutants reveals two new genes in the pNRC100 gas vesicle
cluster of Halobacterium halobium. Nucleic Acids Res. 17:7785-7793.
Kennedy, S.P., Ng. W.V., Salzberg, SL., Hood,
L., DasSarma, S. 2001. Understanding
the adaptation of Halobacterium species NRC-1 to its extreme environment
through computational analysis of its genome sequence. Genome
Res. 11:1641-50.
Nelson, P.S., Ng. W.V.,. Schummer, M., True,
L.D., Liu, A.L., Bumgarner, R., Ferguson, C., Dimak, A. and Hood, L. An expressed-sequence-tag database of the
human prostate: Sequence analysis of 1,168 cDNA clones. Genomics
47: 12-25, 1998.
Nelson, P.S., Hawkins, V., Schummer, M.,
Bumgarner, R, Ng. W.V.,
Ideker, T., Ferguson, C., and Hood, L. 1999 Negative selection: a method for obtaining
low-abundance cDNAs using high-density cDNA clone arrays. Genet
Anal 15:209-15
Peck, R.F., Echavarri-Erasun, C., Johnson,
E.A., Ng. W.V.., Kennedy,
S.P., Hood, L., DasSarma S., Krebs, M.P. 2001. brp and blh are required for synthesis of
the retinal cofactor of bacteriorhodopsin in halobacterium salinarum.
J. Biol. Chem 276:5739-44.
Schummer, M., Ng. W.V., Bumgarner, R.E.,
Nelson, P.S., Schummer, B., Bednarski, D.W., Hassell, L., Baldwin, R.L.,
Karlan, B. Y., and Hood, L. 1999. Comparative
hybridization of an array of 21,500 ovarian cDNAs for the discovery of
genes overexpressed in ovarian carcinomas. Gene 238:375-85.
Schummer, M., Ng. W.V., Nelson, P. S.,
Bumgarner, R.E, and Hood, L. An
inexpensive and-held device for the construction of high density nucleic
acid arrays. Biotechniques 23: 1087-1092, 1997.
Wang, K, Gan, L., Jeffery, E., Gayle, M.,
Gown, A.M., Skelly, M., Nelson, P.S., Ng. W.V., Schummer, M., Hood,
L., and Mulligan, J. 1999. Monitoring
gene expression profile changes in ovarian carcinomas using cDNA
microarray. Gene 229:101-8.
Young Ah Goo, Eugene C. Yi, Baliga, N., Weiguo A. Tao, Pan, M., Ruedi Aebersold, David
R. Goodlett, Leroy Hood, and Ng.
W.V. 2003. Proteomic analysis of an extreme halophilic
archaeon,Halobacterium sp. NRC-1. Molecular and Cellular Proteomics.
M300044-MCP200.
Top Recent Baliga, Nitin Bonneau, Rich Facciotti, Marc Ng, Victor Pan, Min
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Pan, Min:
Baliga, N.,Pan, M., Goo, Y.A., Yi, E.C.,
Goodlett, D.R., Dimitrov, K., Shannon, P., Aebersold, R., Ng. W.V., Hood, L. 2002. Coordinate regulation of energy
transduction modules in Halobacterium sp. analyzed by a global systems
approach. Proc Natl Acad Sci U S A 99:14913-8
Ng.
W.V., 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
97(22):12176-81.
Young Ah Goo, Eugene C. Yi, Baliga, N., Weiguo A. Tao, Pan, M., Ruedi Aebersold, David
R. Goodlett, Leroy Hood, and Ng.
W.V. 2003. Proteomic analysis of an extreme halophilic
archaeon,Halobacterium sp. NRC-1. Molecular and Cellular Proteomics.
M300044-MCP200.
Top Recent Baliga, Nitin Bonneau, Rich Facciotti, Marc Ng, Victor Pan, Min |
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Institute for Systems Biology