Publications
2011
Stefanie Mangold, Jorge Valdés, David S. Holmes and Mark Dopson. Sulfur metabolism in the extreme acidophile Acidithiobacillus caldus (Front. Microbio. 2 :17, 2011).
Liljeqvist M, Valdes J, Holmes DS, Dopson M. Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3. J Bacteriol. 193:4304-5 (2011). .
Bonnefoy, V. and D. S. Holmes. Genomic insights into microbial iron oxidation and iron homeostasis in extremely acidic environments (in press, Environ. Microbiol. Reports, 2011).
Lefimil, C., Jedlicki, E. and D. S. Holmes. An artifact in studies of gene regulation using b-galactosidase reporter gene assays. (In press, Anal. Biochem, 2011).
Raúl R Araya-Secchi, José A Garate, David S Holmes and Tomás Perez-Acle. Molecular Dynamics Study of the Archaeal Aquaporin AqpM (in press, BMC Genomics, 2011).
Jorge Valdes, Francisco Ossandon, Raquel Quatrini, Mark Dopson and David S. Holmes. Draft genome sequence of the extreme acidipohillic biomining proteobacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus (in press, J. Bacteriol. 2011) .
2010
Mario Esparza, Juan Pablo Cárdenas, Botho Bowien, Eugenia Jedlicki and David S. Holmes. Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans. BMC Microbiology 10 :229 (2010).
J. Valdés, J. P. Cárdenas, R. Quatrini, M. Esparza, H. Osorio, F. Duarte, C. Lefimil, R. Sepulveda, E. Jedlicki and D. S. Holmes. Comparative genomics begins to unravel the ecophysiology of bioleaching. Hydrometallurgy 104 : 471-476 (2010).
Cárdenas, J. P., Valdés, J., Quatrini, R., Duarte, F. and D. S. Holmes. Lessons from the Genomes of Extremely Acidophilic Bacteria and Archaea with Special Emphasis on Bioleaching Microorganisms. Appl. Micobiol.Biotech. 88 : 605-620, (2010).
2009
Holmes, D. S., Cárdenas, J. P., Valdés, J., Quatrini, R., Esparza, M., Osorio, H., Duarte, F., Lefimil, C. and E. Jedlicki. Comparative Genomics Begins to Unravel the Ecophysiology of Bioleaching . Adv. Mat. Res. 71-73 , 144-150, 2009.
Valdes, J. H and D. S. Holmes. Genomic Lessons from Biomining Organisms: Case Study of the Acidithiobacillus Genus . Adv. Mat. Res. 71-73 , 215-218, 2009.
Duarte, F, Araya-Secchi, R., González, W., Perez-Acle, T., González-Nilo, D. and D. S. Holmes. Protein
Function in Extremely Acidic Conditions: Molecular Simulation Studies
of a Predicted Aquaporin and a Voltage Gated Potassium Channel in Acidithiobacillus ferrooxidans . Adv. Mat. Res. 71-73 , 211-214, 2009.
Shmaryahu, A. Lefimil, C., Jedlicki, E. and D. S. Holmes. Small Regulatory RNA Genes in Acidithiobacillus ferrooxidans: case studies of 6S RNA and frr . Adv . Mat. Res. 71-73 , 191-194, 2009.
Castro, M., Ruiz, L., Díaz M., Mamani, S., Jerez, C. A., Holmes D., Guiliani N. C-Di-GMP Pathway in Biomining Bacteria . Adv. Mat. Res. 71-73 , 223-226, 2009.
Ossandón F. J., Lazo F., Rivera G., and D. S. Holmes. Predicting the Function of Hypothetical Genes in Genomes of Bioleaching Microorganisms .Adv. Mat. Res. 71-73 , 203-206, 2009.
Esparza, M., Bowien, B., Holmes, D. S. and E. Jedlicki . Gene Organization and CO2-Responsive Expression of Four Cbb Operons in Acidithiobacillus ferrooxidans . Adv. Mat. Res. 71-73 , 207-210, 2009.
Lefimil C., Osorio H., Quatrini R., Holmes D. and Jedlicki E. Making Crucial Regulatory Decisions in Acidithiobacillus ferrooxidans : Iron Oxidation versus Iron Uptake . Adv. Mat. Res. 71-73 , 199-202, 2009.
Osorio, H., Cárdenas, J.P. Valdés, J. and Holmes, D. S Prediction and Experimental Validation of Genes and Metabolic Pathways involved in Anaerobic Growth of Acidithiobacillus ferrooxidans . Adv. Mat. Res. 71-73 , 195-198, 2009.
Cárdenas, J-P., V, Martínez, P. Covarrubias, D. S. Holmes, and R. Quatrini, Predicting CO/CO2 Fixation in Ferroplasma spp. Through a Novel Chimaeric Pathway . Adv. Mat. Res. 71-73 , 219-222, 2009.
Levicán, G., Katz, A., Valdés, J., Quatrini, R., Holmes, D. S. and O. Orellana. A 300 Kb Genome Segment, including a Complete Set of tRNA Genes, is Dispensable for Acidithiobacillus ferrooxidans. Adv. Mat. Res. 71-73 , 187-190, 2009.
Nieto, P. A., Covarrubias, P. C., Jedlicki, E., Holmes, D. S. and R. Quatrini. Selection
and evaluation of reference genes for improved interrogation of
microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans . BMC Mol Biol. 2009 Jun 25;10(1):63
Raquel Quatrini, Corinne Appia-Ayme, Jorge Valdés, Yann Denis, Eugenia Jedlicki David S. Holmes and Violaine Bonnefoy. Extending the Models for Iron and Sulfur Oxidation in the extreme acidophile Acidithiobacillus ferrooxidans . In press .
Jorge Valdes, Raquel Quatrini, Kevin Hallberg, Stefanie Mangold, Mark Dopson, Pablo D.T. Valenzuela and David S. Holmes. Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the Acidithiobacillus genus . J. Bacteriol. Jul 17 . [Epub ahead of print], 2009.
Quatrini, R., Valdes, J., Jedlicki, E. and D. Holmes. The
Use of Bioinformatics and Genome Biology to Advance Our Understanding
of Bioleaching Microorganisms , pp 221-239 in “Microbial Processing of Metal Sulfides” eds. E. Donati and W. Sand. Springer (2007). [Abstract] Bruscella, P., Appia-Ayme, C., Levicán, G., Ratouchniak, J., Jedlicki, E., Holmes, D. S., and V.Bonnefoy. Differential expression of two bc1 complexes in the acidophilic chemolithoautotrophic bacterium Acidthiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation . Microbiology, 153: 102-110, 2007.
[Abstract] Mariella Rivas, Michael Seeger, Eugenia Jedlicki, David S. Holmes. A second acyl homoserine lactone (AHL) producing system in the extreme acidophile, Acidithiobacillus ferrooxidans . Appl. Environ. Microbiol. (PMID:17351095 [PubMed, 2007).
[Abstract] Quatrini, R., Lefimil, C., Veloso, F., Pedroso, I., D. S. Holmes and Jedlicki, E. Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans . Nuc. Acid Research (MID: 17355989 [PubMed, 2007).
[Abstract] [Full text]
Quatrini., R., Appia-Ayme, C., Denis, Y., Ratouchniak, J.,
Veloso, F., Valdes, J., Lefimil, C., Silver, S., Roberto, F., Orellana,
O., Denizot, F., Jedlicki, E., Holmes D. S., Bonnefoy, V. Insights
into the Iron and Sulfur Energetic Metabolism of Acidthiobacillus
ferrooxidans by Microarray Transcriptome Profiling, Hydrometallurgy ,83: 263-272, (2006). [Abstract] Appia-Ayme C, Quatrini R, Denis Y, Denizot F, Silver S, Roberto
F, Veloso F, Valdes J, Cárdenas JP, Esparza M, Orellana O, Jedlicki
E, Bonnefoy V, Holmes DS. Microarray and Bioinformatic Analyses
Suggest Models for Carbon Metabolism in the Autotroph Acidithiobacillus
ferrooxidans , Hydrometallurgy,83: 273-280, (2006). [Abstract] Silva, E., Valdés, J., Holmes, D., Shmaryahu, A. and Pablo
D. T. Valenzuela. Generation and analysis of expressed sequence
tags from Botrytis cinerea . Biol Res 39: 367-376,
2006. [Abstract] [Full text] Holmes, D and V. Bonnefoy. Genetic and Bioinformatic
Insights into Iron and Sulfur Oxidation Mechanisms of Bioleaching
Organisms, pp 281-307 in: “Biomining” eds. D. Rawlings and B. Johnson. Springer-Verlag, Berlin (2006).
[Abstract] Lieph, R., Veloso, F. and D. S. Holmes. Thermophiles
like Hot T. Trends Microbiol. 14: 423-426 (2006). [Abstract] Holmes, D. S and G. Mora. Taking the Pulse of Latin American Microbiology . (Int. J. Micriobiol., 9: 306-308, 2006). [Full text]
2005
Felipe Veloso, Gonzalo Riadi, Daniela Aliaga, Ryan Lieph and
David S. Holmes. Large Scale, Multi-Genome Analysis of Alternate
Open Reading Frames in Bacteria and Archaea . OMICS 9, 91-105
(2005). [Abstract] Quatrini, R., Lefimil, C., Holmes, D. S. and E. Jedlicki.
The Ferric Iron Uptake Regulator (Fur) from the Extreme
Acidophile, Acidithiobacillus ferrooxidans . Microbiology,
151: 2005-2015 (2005). [Abstract] [Full text] . Raquel Quatrini, Eugenia Jedlicki and David S. Holmes. Genomic
Insights into the Iron Uptake Mechanisms of the Biomining Microorganism
Acidithiobacillus ferrooxidans . J. Industrial
Microbiology and Biotechnology, 32: 606-614 (2005). [Abstract] [Full text] . Marlen Barreto, Eugenia Jedlicki and David S Holmes. A
Gene Cluster for the Formation of Extracellular Polysaccharide (EPS)
Precursors in the Chemolithoautotroph Acidithiobacilus
ferrooxidans . Appl. Environ. Microbiol. 71: 2907-2909
(2005). [Abstract] [Full text] . Kathleen L. McGuire and David S. Holmes. The role
of complementary proteins in autoimmunity: an old idea reemerges
with new twists. Trends in Immunology, 26, 367-372 (2005). [Abstract] . Marlen Barreto, Tilman Gehrke, Kerstin Harneit, Wolfgang Sand,
Eugenia Jedlicki and David Holmes. Unexpected Insights into
Biofilm Formation by Acidithiobacillus ferrooxidans Revealed
by Genome Analysis and Experimental Approaches, pp 817-825
in: Proc. 16th International Biohydrometallurgy Symposium, Cape
Town, South Africa, 2005, eds S. Harrison, D Rawlings and J. Peterson,
Compress www.compress.co.za. Quatrini R, Appia-Ayme C, Denis Y, Ratouchniak J, Veloso F,
Valdés J, Lefimil C, Silver S, Roberto F, Orellana O, Denizot F,
Jedlicki E, Holmes DS & Bonnefoy V. Global analysis of the
ferrous iron and sulfur energetic metabolism of Acidithiobacillus
ferrooxidans by microarray transcriptome profiling ,
pp 761-771 in: Proc. 16th International Biohydrometallurgy Symposium,
Cape Town, South Africa, Eds S. Harrison, D Rawlings and J. Peterson,
2005. Appia-Ayme C, Quatrini R, Denis Y, Denizot F, Silver S, Roberto
F, Veloso F, Valdés J, Cárdenas JP, Esparza M, Orellana O, Jedlicki
E, Bonnefoy V & Holmes DS. Insights Into The Central Carbon
Metabolism Of Acidithiobacillus ferrooxidans Revealed By
Bioinformatic And Microarray Analysis , pp 753-760 in: Proc.
16th International Biohydrometallurgy Symposium, Cape Town, South
Africa, Eds S. Harrison, D Rawlings and J. Peterson, 2005. Rivas, M., Seeger, M., Holmes, D. S. and E. Jedlicki. A
Lux-like quorum sensing system in the extreme acidophile Acidithiobacillus
ferrooxidans . Biological Res. 38: 283-297 (2005)
[Abstract] [Full text] .
2004
Valdés, J., Jedlicki, E. and Holmes, D. Bioinformatic Analysis
of Sulfur Assimilation in Acidithiobacillus ferrooxidans ,
pp 1187-1194 in: BioHydrometallurgy: A Sustainable Technology in
Evolution. Eds: M. Tsezos, A. Hatzikioseyian and E. Remoudaki. National
Technical University of Athens, ISBN numbers 960-88415-0-X, 2004.
Quatrini, R., Veloso F., Jedlicki E. and D.S. Holmes. Bioinformatic
Analysis of Iron Uptake in Acidithiobacillus ferrooxidans ,
pp 989-996 in: BioHydrometallurgy: A Sustainable Technology in Evolution.
Eds: M. Tsezos, A. Hatzikioseyian and E. Remoudaki. National Technical
University of Athens, ISBN numbers 960-88415-0-X, 2004. Marlen Barreto, Mariella Rivas, Eugenia Jedlicki and David
Holmes. Bioinformatic Analysis of Biofilm Formation in Acidithiobacillus
ferrooxidans , pp 1271-1278 in BioHydrometallurgy:
A Sustainable Technology in Evolution. Eds: M. Tsezos, A. Hatzikioseyian
and E. Remoudaki. National Technical University of Athens, 2004.
ISBN numbers 960-88415-0-X Brasseur G, Levican G, Bonnefoy V, Holmes D, Jedlicki E, Lemesle-Meunier
D. Apparent redundancy of electron transfer pathways via
bc(1) complexes and terminal oxidases in the extremophilic chemolithoautotrophic
Acidithiobacillus ferrooxidans . Biochem. Biophys.
Acta. 1656:114-126 (2004) [Abstract]
2003
Barreto M, Quatrini R, Bueno S, Arraigada C, Valdés J, Silver
S, Jedlicki E, Holmes DS. Aspects of the predicted physiology
of Acidithiobacillus ferrooxidans deduced from an analysis
of its partial genome sequence. Hydrometallurgy 71: 97–105.
2003. [Abstract] José Luis Ramírez and David Holmes. The need for Genomics
Networking in Latin America. Science Development,
21 Aug. 2003, [Abstract] . Valdes, J., Jedlicki E. and David Holmes. Metabolic
Reconstruction of Sulfur Assimilation in the Extremophile Acidithiobacillus
ferrooxidans Based on Genome Analysis BMC Genomics
4, 2003, online: [Abstract] [Full text] .
2002
Levican, G., P. Bruscella, M. Guacucano, C. Inostroza, V.
Bonnefoy, D. S Holmes and E. Jedlicki. Characterization
of the petC and resB Operons in Acidithiobacillus ferrooxidans .
J. Bacteriol. 184: 1498-1501 (2002). [Abstract] [Full text] . Ramírez, J. L., Alicia González, José María Cantú, Pamela Chavez-Crooker,
Juan Carlos Leiva, Jenny Blamey, Hernan Cortes and David Holmes.
Latin-American Genome Initiative, the Creation of a Network and
Web-Based Resource to Aid and Nurture Genome Biology in Developing
Countries. Electronic Journal of Biotechnology 5, Dec 15,
2002 accessible at
2001
Holmes, D. S., Zhao, H-L, Levican, G., Ratouchniak, J., Bonneyfoy,
V., Varela, P., and Jedlicki E. ISAfe1, an ISL3 Family Insertion
Sequence in Acidihiobacillus ferrooxidans . J.
Bacteriol. 183: 4323-4329 (2001) [Abstract] [Full text] . Holmes, D. S., Barreto, M., Valdes, J., Dominguez, C., Arriagada,
C., Silver, S. Bueno, S. and E. Jedlicki. Whole Genome Sequence
of Acidithiobacillus ferrooxidans : Metabolic Reconstruction,
Heavy Metal Resistance and Other Characteristics . pp 237-251,
in Biohydrometallurgy: Fundamentals, Technology and Sustainable
Development. eds Ciminelli, V. and O Garcia, Elsevier Press, 2001.
2000
Selkov, E., R. Overbeek, Y. Kogan, L. Chu, V. Vonstein, D.
Holmes, S. Silver and M. Fonstein. Functional Analysis of
Gapped Microbial Genomes: Principles with Examples from Thiobacillus
ferrooxidans . Proc. Natl. Acad. Sci. U S A. 97: 3509-
3514 (2000) [Abstract] [Full text] . Guacucano, M., Levican, G., Holmes D. S. and E. Jedlicki. An
RT-PCR Artifact in the Characterization of Bacterial Operons.
Electronic Journal of Biotechnology [online]. 15 December vol. 3,
No. 3. (2000) [Abstract] [Full text] .
Cabrejos, M-E., H-L Zhao, M. Guacucano, S. Bueno, G. Levican,
E. Garcia, E. Jedlicki and D. S. Holmes. IST1 Insertional
Inactivation of the resB Gene: Implications for Phenotypic Switching
in Thiobacillus ferrooxidans . FEMS Microbiol.
Lett., 175: 223-229 (1999). Holmes, D. S. Biotechnology: Miners in miniature.
Chemistry and Industry, 1: 20-24 (1999). Holmes, D. S. , Jedlicki E., Cabrejos M. E., Vasquez O., Guacacano
M., Levican, G., Varela P. and Garcia E. The use of insertion
sequences to analyze gene function in Thiobacillus ferrrooxidans :
a case study involving cytochrome c-type biogenesis proteins in
iron oxidation, pp 139-147, in Biohydrometallurgy and the
Environment: Toward the Mining of the 21st. Century. Eds. R . Amils
and A. Ballester. Elsevier, Amsterdam (1999). D.S. Holmes. "Biorecovery of Metals from Mining Wastes" ,
pp 517-545 in Bioconversion of Waste Materials to Industrial Products,
ed. A.M. Martin. Chapman Hall, London (1998). Bengrine, N. Guiliani, C. Appia-Ayme, E. Jedlicki and D. S.
Holmes, M. Chippaux and V. Bonneyfoy. Sequence and Expression
of the Rusticyanin Structural Gene from Thiobacillus ferrooxidans
ATCC33023 strain . Biochem. Biophys. Acta. 1443: 99-112
(1998). S. K. Dubey and D. S. Holmes. Biological cyanide destruction
mediated by microorganisms. World Journal of Microbiology
and Biotechnology 11: 257-265 (1996).
Holmes, D. S. (1995). "Genetic and Phenotypic Switching
Instability in Thiobacillus ferrooxidans and Why
These Phenomena Are Important to Understand." pp 85-93
in Minerals Processing II eds. D.S. Holmes and R. W. Smith; TMS
Publ.Warrendale, PA, USA. Holmes, D. S. and R. W. Smith. (1995). "Advances in
Mineral Processing." pp ix-xiii in Minerals Processing
II, eds D.S. Holmes and R. W. Smith; TMS Publ.Warrendale, PA, USA. Holmes, D.S. and S. Gangolli. (1995). "A Biosensor
that Reports the Bioavailability of Copper Ions and its Use in the
Design of New Reagents for Metal Binding." pp159-166 in
Biohydrometallurgical Processing, eds C. A. Jerez, T. Vargas, H.
Toledo and J. V. Wiertz; University of Chile, Santiago. Cadiz, R., L. Gaete, E. Jedlicki, J. Yates, D. S. Holmes and
O. Orellana. "Transposition of IST2 in Thiobacillus
ferrooxidan s." Mol. Microbiol. 12: 165-170 (1994). Holmes, D. S., S. K. Dubey and S. S. Gangolli. "Development
of Biosensors for the Detection of Mercury and Copper Ions" .
Environ. Geochem. & Health. 16: 229- 233 (1994). Lau, P. C. K., M. Drolet, P. Zanga and D. S. Holmes (1993).
"Plasmid Technology for Biomining Applications."
pp 635-644 in Biohydrometallurgical Technologies Vol II eds A.E.
Torma, M. L. Apel and C. L. Brierley, TMS, Warrendale, PA, USA (1993). Zhao, H. and D. S. Holmes. "Insertion Sequence ISTI
and Associated Phenotypic Switching in Thiobacillus ferrooxidans ."
pp 667-671 in Biohydrometallurgical Technologies Vol II eds A.E.
Torma, M. L. Apel and C. L. Brierley, TMS, Warrendale, PA, USA (1993). Holmes, D. S. Bioluminescent Biosensors ,
report for the Office of Naval Research, USA (1993). Holmes, D. S. "The Story Behind the Development of
the Rapid Boil Preparation of Bacterial Plasmids" . Scientific
Citation Classics 36: 7-8 (1993).
Holmes, D. S., S. K. Dubey and S. Gangolli. "Development of Biosensors
to Measure Metal Ion Bioavailability in Mining and Metal Wastes" ,
pp 659-666 in Biohydrometallurgical Technologies Vol II eds A.E.
Torma, M. L. Apel and C. L. Brierley, TMS, Warrendale, PA, USA (1993).
Dubey, S. K., S. S. Gangolli and D. S. Holmes. "Development
of Biosensors to Measure Metal Ion Bioavailability in Environmental
Samples" . Northeastern Geol. And Environmental Sci. 15:
188-194 (1993). H. Bungay, L. Clesceri, Y-H Lin and D. S. Holmes."Metabolism
of Toxic Wastes in Auxostat Mode of Continous Culture ",
Report for The Hazadous Waste Center, Buffalo, New York, USA. (1992). L. Geiselhart, M. Osgood and D.S. Holmes. "Construction
and Evaluation of a Self-Luminescent Biosensor" . N.Y. Academy
Sci. 646: 53-60 (1992).
D.S. Holmes and K.H Debus "Opportunities for Biological
Metal Recovery" . pp 57-78 in Minerals Bioprocessing. eds.
Ross W. Smith and Manoranjan Misra, Reno, NV ( 1991). D.S. Holmes. "The Use of DNA Probes for the Identification
and Enumeration of Biomining Microorganisms: An Overview for the
Non-Specialist" , pp. 1-12, in Bioleaching: From Molecular
Biology to Industrial Applications, eds R. Badilla-Ohlbaum, T. Vargas,
L. Herrera.Editorial Universitaria, Santiago, Chile, (1991). D.S. Holmes and K.H. Debus. "Biological Opportunities
for Metal Recovery" , pp. 341-358, in Biotechnology for
Energy, Eds. K.A. Malik, S.H.M. Naqui and M.I.H. Aleem. NIAB Press,
Faisalabad, Pakistan, (1991).
D.S. Holmes and R. Haq. "Adaptation of Thiobacillus
ferrooxidans for Industrial Applications" , pp. 115-127
in Biohydrometallurgy ed., J. Salley, R.G.L. McCready and P.L. Wichlacz.
Canmet, Ottawa, Canada (1990). D.S. Holmes. "Genetic Engineering of Microorganisms
for Pollution Control" , pp. 29-39 in "Hazardous Waste Treatment:
Biosystems for Pollution Control". Air & Waste Management Assoc.,
Pittsburgh, PA (1989). D.S. Holmes. "Biotechnology in the Mining and Metal-Processing
Industries. Challenges and Opportunities" , Minerals Metallurgical
Processing. 5: 49-56 (1988). J.R. Yates, R.R. Cunningham and D.S. Holmes. "IST2:
A New Insertion Sequence in Thiobacillus ferrooxidans " ,
Proc. Natl. Acad. Sci. USA. 85: 7284-7287 (1988). J. Schrader and D.S. Holmes. "Phenotypic Switching
of Thiobacillus ferrooxidans" , J. Bacteriol. 170: 3915-3923
(1988). D.S. Holmes, J.R. Yates, J. Schrader and R. Ul Haq. "The
Use of Thiobacillus ferrooxidans for Metal-Recovery: Problems
and Prospects" , Applications of Genetic Engineering, Lahore
Press, Pakistan, pp. 19-26 (1988). D.S. Holmes, J.R. Yates and J. Schrader. "Mobile Repeated
DNA Sequences in Thiobacillus ferrooxidans and
their Significance for Biomining" , In: Biohydrometallurgy,
P.R. Norris and D.P. Kelley eds., pp. 153-160 (1988). Science and
Tech. Letters. D.S. Holmes. "Molecular Enzyme Engineering" ,
In: Advanced Biochemical Engineering. H.R. Bungay and G. Belford,
eds., Wiley, New York, Sciences, Inc., pp. 129-165 (1987). C.L. Spiro, D.S. Holmes, J.H., Lobos and D.H. Maylotte.
"X-Ray Computed Tomographic Assay in in situ Microbial Desulfurization
of Lump Coal" , p 27-28, In: Industrial and Engineering
Chemistry, 1st Int. Symp. on Separation Sciences, 191st Am. Chem.
Soc. Meet., April 1986 (1987). T.K. Leib amd D.S. Holmes. "Designed Metal-Binding
Proteins" , Biotech. 87: 208-215 (1987). J.R. Yates and D.S. Holmes. "Two Families of Repeated
DNA Sequences in Thiobacillus ferrooxidans " , J.
Bacteriol., 169: 1861-1870 (1988). C.L.Spiro, D.S. Holmes, J.H. Lobos and D.H. Maylotte. "Use
of X-ray Computed Tomographic to Examine Microbial Desulfurization
of Lump Coal" , J. Energy and Fuels 1: 76-79 (1987). T.K. Leib, T-M Su and D.S. Holmes. "Metal-binding
Proteins for Strategic Metal Recovery and Metal Detoxification" ,
Energy Res. Abstr. 11: 32796-32807 (1986). D.S. Holmes. "Biotechnological Considerations for
Designed Metal-Recovery Operations" , R.M.L. McCready, ed.,
Biominet Proc. Energy, Mines and Resources Conf., Canada, Report
SP85/6, pp. 25-36 (1986). T-M Su and D.S. Holmes. "A Novel Technique for On-Line
Detection of Cupro-protein by HPLC" , Proc. Int. Sump. on
HPLC of Proteins and Peptides, Toronto, Canada. 1985 (1986). D. Maylotte, C.L. Spiro, J.H. Lobos and D.S. Holmes.
"A Study of Thiobacillus ferrooxidans Penetration Depth
into Lump Coal Using X-Ray Computed Tomography" , In: Fundamental
and Applied Biohydrometallurgy, R.W. Lawrence, R.M.R. Branion and
H.G. Ebner, eds., Elsevier Science Publ., Amsterdam, The Netherlands,
pp. 483 (1986). H. Ehrlich and D.S. Holmes. "Biotechnology for Mining,
Metal-Refining Fossil Fuel Processing Industries" , Biotechnol.
Bioeng. Symp. 16: 2-3 (1986), ISBN: 0471851027) J. R. Yates and D.S. Holmes. "Construction and Use
of Molecular Probes to Identify and Quantitate Bioleaching Microorganisms" ,
R.M.R. Branion and H.G. Ebner, eds., Fundamental and Applied Biohydrometallurgy
, Elsevier Science Publ., Amsterdam, The Netherlands, pp. 409-418
(1986). J.R. Yates and D.S. Holmes. "Molecular Probes for
the Identification and Quantification of Microorganisms found in
Mines and Mine Tailing" , Biotechnol. Bioeng. Symp. 16:
310-319 (1986). D.S. Holmes, J.R. Yates, J.H. Lobos and M.V. Doyle.
"Strategy for the Establishment of a Genetic System for the Acidophilic
Heterotroph, Acidiphilium organovorum " , Biotech.
Appl. Biochem, 8: 1-11 (1986). J.R. Yates, J. H. Lobos and D.S. Holmes. "The Use
of Genetic Probes to Detect Microorganisms in Biomining Operations" ,
J. Ind. Microbiol. and Biotechnology 1: 129-135 (1986). J.H. Lobos, T.E. Chisholm, L.H. Bopp and D.S. Holmes,
"Acidiphilium organovorum sp . nov., An Acidophilic Heterotroph
Isolated from a Thiobacillus ferrooxidans Culture" ,
Int. J. Syst. Bacteriol. 36: 139-144 (1986). T-M Su and D.S. Holmes. "A Novel Technique for the
Detection of Copper-Containing Proteins" , R.H. Sarma, ed.,
4th Conversation in Biomolecular Stereodynamics, Adenine Press,
Albany, NY, pp 317-318 (1985). D. S. Holmes, J.R. Yates, J.H. Lobos and M.V. Doyle.
"Genetic Engineering of Biomining Organisms" , Biotech.
84, 67-84 . Online Publications, New York, NY (1984). • D.S. Holmes. "Improved Rapid Heating Technique for
Screening Recombinant DNA Plasmids in E. coli " ,
Biotechniques 2: 68-69 (1984). D.S. Holmes, J.H. Lobos, L.H. Bopp and G.C. Welch.
"Cloning of a Thiobacillus ferrooxidans Plasmid in E.
coli ." , J. Bacteriol., 157: 324-326 (1984). D.S. Holmes. "The Cot Curve" , Trends in Biochemistry.
8: 437 (1984). D.S. Holmes. "Biotechnology: Applications for Microbiology" ,
Am. Soc. Microbiol. Eastern New York Branch Newsletter, Nov.-Dec.,
pp. 2-3 (1983). D.S. Holmes, J.H. Lobos, L.P. Bopp and G.C. Welch. "Setting
up a de novo Genetic System for Studying the Acidophilic Bacterium
Thiobacillus ferrooxidans " , GE Report 83CRD160
(1983). D.S. Holmes, J.H. Lobos, L.H. Bopp and G.C. Welch. "Setting
Up a Genetic System de novo for Studying the Acidophilic Thiobacillus
T. ferrooxidans " , In: Recent Progress in Biohydrometallurgy.
G. Rossi and A.E. Torma, eds., Associazione Mineroria Sarda Inglesias,
Italy, pp. 541-544 (1983). A.J. Eisenberg and D.S. Holmes. "A Note on the Use
of CsCl Centrifugation to Purify Bacterial Plasmids Prepared by
the Rapid Boiling Method" , Anal. Biochem. 127, 434 (1982). D.S. Holmes. "Rapid Purification of Bacterial Plasmids
and Colifage M13 RF Without CsCl Centrifugation" , Anal.
Biochem. 127: 428-439 (1982). Bush and D.S. Holmes. "The Use of Agar for Electrophoresis
of DNA Fragments" , Anal. Biochem. 119: 164-166 (1982). D.S. Holmes and M. Quigley. "A Rapid Method for Plasmid
DNA Preparations" , Focus 3, 2 (1981). D.S. Holmes and M. Quigley. "Rapid Plasmid Preparation" ,
Biotechnology News 1, 4 (1981). D.S. Holmes and M. Quigley. "A Rapid Method for the
Preparation of Plasmids" , Anal. Biochem. 114: 193-197 (1981). H. Grimmond and D.S. Holmes. "Specific Increase of
Perchloric Acid Extractable Chromosomal Proteins During Mammalian
Erythropoieses" , Comp. Biochem. Physiol. 698: 303-306 (1981). W. Colquhoun and D.S. Holmes. "Structure of the Chromosomal
Material in Inactive Nuclei of Chicken Red Blood Cells" ,
Chromosoma 79: 159-167 (1980). S. Bodansky, L.B. Mintz and D.S. Holmes. "The Mesokaryote
Gyrodinium cohnii Lacks Nucleosomes" , Biochem. Biophys.
Res. Commun. 88: 1329-1336 (1979). M. Pellegrini, D.S. Holmes and J. Manning. "Applications
of the Avidin biotin Methods of Gene Enrichment to the Isolation
of Long Double-Stranded DNA Containing Specific Gene Sequences" ,
Nucleic Acids Res. 9: 2961-2973 (1977). D.S. Holmes, N. Davidson, R.H. Cohn and L.H. Kedes. "Positions
of Sea Urchin Histone Genes Relative to Restriction Endonuclease
Sites on the Chimeric Plasmids pSp2 and pSp17" , Biochemistry
16: 1504-1512 (1977). M. Wu, D.S. Holmes, N. Davidson, R.H. Cohn and L.H. Kedes.
"The Relative Positions of the Coding and Spacer Regions
on Sea Urchin Histone Genes on the Chimeric Plasmids pSp2 and pSp17
as Studies by Electron Microscopy" , Cell 9: 163-169 (1976). D.S. Holmes and J. Bonner. "Interspersion of Repetitive
and Single Copy Sequences in High Molecular Weight Nuclear RNA" ,
Proc. Natl. Acad. Sci. USA 71: 1108-1112 (1974). D.S. Holmes, J.E. Mayfield and J. Bonner. "Sequence
Composition of Chromosomal RNA" , Biochemistry 13, 849-855
(1974). D.S. Holmes and J. Bonner. "Sequence Composition of
Rat Nuclear DNA and High Molecular RNA" , Biochemistry 13:
841-848 (1974). D. S. Holmes and J. Bonner. "Sequence Composition
and Organization of the Genome and Nuclear RNA of Higher Organisms:
An Approach to Understanding Gene Regulation" . In: The
Role of RNA in Development, M. Niu and S. Segal, eds., American
Elsevier Publishing Co., Inc., New York, NY, pp. 204-323 (1973). S. Holmes. Sequence Composition and Organization of
the High Molecular Weight Nuclear RNA of Rat. Ph.D thesis,
California Institute of Technology (1973) • D.S. Holmes and J. Bonner. "Preparation, Molecular
Weight, Base Composition and Secondary Structure of Giant Nuclear
RNA" , Biochemistry 12: 2322-2329 (1973). D.S. Holmes, J.E. Mayfield, G. Sander and J. Bonner.
"Composition and Secondary Structure of Giant Nuclear RNA" ,
Biochemistry 12: 2330-2338 (1973). S. Holmes, J.E. Mayfield and J. Bonner. Chromosomal
RNA: its properties. Science , 177: 72-74 (1973)
CC - [Rene S.. 2006] - [ Last update 19/10/2011 ]
