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Reverdy A, Hathaway D, Jha J, Michaels G, Sullivan J, McAdoo DD, Riquelme C, Chai Y, Godoy-Carter V. Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert. Front Microbiol 2024; 15:1335989. [PMID: 38516016 PMCID: PMC10955380 DOI: 10.3389/fmicb.2024.1335989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/16/2024] [Indexed: 03/23/2024] Open
Abstract
The Atacama Desert, the driest, with the highest radiation, and one of the most ancient deserts in the world, is a hostile environment for life. We have a collection of 74 unique bacterial isolates after cultivation and confirmation by 16S rRNA gene sequencing. Pigmentation, biofilm formation, antimicrobial production against Escherichia coli MG1655 and Staphylococcus aureus HG003, and antibiotic resistance were assessed on these isolates. We found that approximately a third of the colonies produced pigments, 80% of isolates formed biofilms, many isolates produce growth inhibiting activities against E. coli and/or S. aureus, and many were resistant to antibiotics. The functional characterization of these isolates gives us insight into the adaptive bacterial strategies in harsh environments and enables us to learn about their possible use in agriculture, healthcare, or biotechnology.
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Affiliation(s)
| | | | - Jessica Jha
- Northeastern University, Boston, MA, United States
| | | | | | - Daniela Diaz McAdoo
- Facultad de Ciencias Básicas, Universidad de Antofagasta, Antofagasta, Chile
| | - Carlos Riquelme
- Facultad de Ciencias Básicas, Universidad de Antofagasta, Antofagasta, Chile
| | - Yunrong Chai
- Northeastern University, Boston, MA, United States
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Michaels G, Garian R. Computational methods for protein sequence analysis. ACTA ACUST UNITED AC 2008; Chapter 2:Unit2.1. [PMID: 18429149 DOI: 10.1002/0471140864.ps0201s00] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This unit is presented as a guide to addressing the issue of what to do with a protein sequence once it is obtained. A theoretical background for protein sequence analysis is provided first, followed by a discussion of matrix methods for sequence comparison (Matrix Methods for Sequence Comparison: Dot Plots). Sequence similarity searching is then presented, including the BLAST and FASTA databases. Other aspects of protein sequence analysis covered here are alignment methods, scoring matrices, multiple alignments, cluster methods and trees, and identification of functional sites.
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Affiliation(s)
- G Michaels
- George Mason University, Fairfax, Virginia, USA
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3
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Knight M, Miller AN, Patterson CN, Rowe CG, Michaels G, Carr D, Richards CS, Lewis FA. The identification of markers segregating with resistance to Schistosoma mansoni infection in the snail Biomphalaria glabrata. Proc Natl Acad Sci U S A 1999; 96:1510-5. [PMID: 9990054 PMCID: PMC15498 DOI: 10.1073/pnas.96.4.1510] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both snail and parasite genes determine the susceptibility of the snail Biomphalaria glabrata to infection with the trematode Schistosoma mansoni. To identify molecular markers associated with resistance to the parasite in the snail host, we performed genetic crosses between parasite-resistant and -susceptible isogenic snails. Because resistance to infection in adult snails is controlled by a single locus, DNA samples from individual F2 and F1 backcross progeny, segregating for either the resistant or susceptible phenotypes, were pooled (bulked segregant). Genotypes for both parents were determined with 205 arbitrary decamer primers by random amplified polymorphic DNA-PCR. Of the 205 primers, 144 were informative, and the relative allele frequencies between the pools for these primers were determined. Two primers, OPM-04 and OPZ-11, produced fragments in the resistant parent of one cross that were inherited in a dominant fashion in the resistant F2 and backcross-bulked segregant progeny. Subsequent typing of DNA samples of individual progeny snails showed that the 1.2-kb marker amplified by primer OPM-04 and the 1.0-kb marker produced by primer OPZ-11 segregated in the same dominant fashion with the resistant phenotype. Sequence analysis of the 1.2-kb marker showed that it corresponds to a repetitive sequence in the snail genome with no homology to existing DNA sequences in the public databases. Analysis of the 1. 0-kb marker showed that it also corresponds to a repetitive sequence in the B. glabrata genome that contains an imperfect ORF, with homology to retrovirus-related group-specific antigens (gag) polyprotein.
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Affiliation(s)
- M Knight
- Biomedical Research Institute, 12111 Parklawn Drive, Rockville, MD 20852, USA
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Uzawa H, Schlierf G, Chirman S, Michaels G, Wood P, Kinsell LW. HYPERGLYCERIDEMIA RESULTING FROM INTAKE OF MEDIUM CHAIN TRIGLYCERIDES. Am J Clin Nutr 1996; 15:365-9. [PMID: 14240485 DOI: 10.1093/ajcn/15.6.365] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
A new electron paramagnetic resonance (EPR)-based method was developed to obtain selective information on pO2 in a specific intracellular compartment (phagosomes). This method did not require the use of a broadening agent thereby eliminating one of the potential sources of experimental error with EPR oximetry. An oxygen-sensitive probe (4-(Trimethylammonium) 2,2,6,6-tetramethylpiperidine-d17-1-oxyl iodide (d-Cat1)) which has a net positive charge, was incorporated selectively into the phagosomes of macrophages stimulated with zymosan. Extracellular oxygen was measured by addition of a neutral nitroxide (4-oxo-2,2,6,6-tetramethylpiperidine-d16-1-oxyl (15N PDT)) to this same sample. Measurements based on EPR linewidths showed the average intraphagosomal oxygen concentration to be 11.2 +/- 3.4 microM lower than that measured from the extracellular compartment when the sample was perfused with air, and this was increased on stimulation of mitochondrial consumption or by increasing the oxygen concentration in the extracellular compartment. These experiments provide what we believe to be the first reported measurements of the oxygen concentration in a specific intracellular location (intraphagosomal) and its comparison with the oxygen concentration in the extracellular space. The observed gradient cannot be explained in terms of known coefficients of diffusion, and these results are consistent with previous reports that a gradient in oxygen concentration can occur between the average intracellular and extracellular concentration of oxygen.
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Affiliation(s)
- P E James
- Department of Radiology, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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Affiliation(s)
- P J van Galen
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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Graessmann M, Michaels G, Berg B, Graessmann A. Inhibition of SV40 gene expression by microinjected small antisense RNA and DNA molecules. Nucleic Acids Res 1991; 19:53-8. [PMID: 1849259 PMCID: PMC333533 DOI: 10.1093/nar/19.1.53] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We tested the impact of antisense RNA and DNA molecules on SV40 gene expression by microinjection into TC7 cells. Short antisense stretches, complementary to either hairpin or loop structures on the T antigen mRNA, inhibited T antigen synthesis. In contrast, full-length antisense RNA and DNA molecules did not effect T antigen synthesis.
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Affiliation(s)
- M Graessmann
- Institut für Molekularbiologie und Biochemie der Freien Universität Berlin, FRG
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Jacobs G, Michaels G. Zinc finger gene database. New Biol 1990; 2:583. [PMID: 2088507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Abstract
The pyrB-pyrI region of the Salmonella typhimurium LT2 chromosome has been cloned and sequenced. The two genes were found to constitute an operon, with pyrI being the distal gene and separated from pyrB by a 15-bp intercistronic region. Sequence analysis revealed the presence of two potential promoters; transcription initiated from the promoter proximal to pyrB would produce a transcript which could direct the synthesis of a 33-amino-acid leader peptide. The leader sequence possesses the requisite features of a rho-independent transcriptional terminator (attenuator) which is positioned 22 bp upstream from the pyrB structural gene. A regulatory mutation imparting a 30-fold elevated expression of pyrBI was identified as a two-base-pair deletion in the track of A X T base pairs located on the 3' side of the region of dyad symmetry of the attenuator. The leader sequence also has an additional region of dyad symmetry (putative transcriptional pause site) located 33 nucleotides upstream from the start of the proposed attenuator. The intervening sequence between the putative pause site and the indicated attenuator is characterized by encoding a high content of uracil residues in the transcript. Construction and analysis of transcriptional and translational fusions provided evidence that the leader region has the necessary features to mediate polypeptide synthesis in vivo, the removal of the region corresponding to the pause site and attenuator results in constitutive expression and the more distant potential promoter does not appear to facilitate significant transcriptional activity. Strong homology exists with the pyrBI operon from Escherichia coli K-12 but notable differences are observed.
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Gamze M, Michaels G. 20 years cogeneration at a hospital. Heat Piping Air Cond 1986; 58:91-6. [PMID: 10278520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Virtually all of the recoverable heat energy from the engine generator sets--jacket cooling, flue gas, and oil cooler--can be used to meet space cooling, space heating, and process loads at a 300 bed hospital.
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Michaels G, Kelln RA. Construction and use of pyr::lac fusion strains to study regulation of pyrimidine biosynthesis in Salmonella typhimurium. Mol Gen Genet 1983; 189:463-70. [PMID: 6223200 DOI: 10.1007/bf00325910] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The technique developed by Rosenfeld and Brenchley [J Bacteriol 144, 848-851 (1980)] has been used to introduce Mu d1 (Apr lac) into Salmonella typhimurium for purposes of constructing pyr::lac fusion strains. A stable pyrB::lac fusion mutant was subsequently derived and used for the genetic characterization of the pyrB gene. The direction of transcription of pyrB was determined to be counterclockwise on the S. typhimurium linkage map and argI was shown to be located clockwise of pyrB. Mutants altered in the regulation of expression of pyrB were isolated and two of the isolates chosen for further study were tentatively categorized as promoter or operator mutants.
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Michaels G, Milner Y, Moskovitz BR, Wood HG. Pyruvate, phosphate dikinase. Metal cation requirements and inactivation of the enzyme by sulfhydryl agents. J Biol Chem 1978; 253:7656-61. [PMID: 212431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Michaels G, Milner Y, Moskovitz B, Wood H. Pyruvate, phosphate dikinase. Metal cation requirements and inactivation of the enzyme by sulfhydryl agents. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)34421-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Milner Y, Michaels G, Wood HG. Pyruvate, phosphate dikinase of Bacteroides symbiosus. Catalysis of partial reactions and formation of phosphoryl and pyrophosphoryl forms of the enzyme. J Biol Chem 1978; 253:878-83. [PMID: 202599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Milner Y, Michaels G, Wood H. Pyruvate, phosphate dikinase of Bacteroides symbiosus. Catalysis of partial reactions and formation of phosphoryl and pyrophosphoryl forms of the enzyme. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)38186-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Abstract
The question of the importance of aquatic borne Klebsiella pneumoniae to public health has been argued as the organism has appeared often in both polluted effluents and oligotrophic systems. Using a selective medium, double violet agar, which also differentiates K. pneumoniae from other organisms found in aquatic systems, we sampled water from three ponds and a large man-made lake, over a 3-month period. Results indicate that K. pneumoniae can be isolated consistently and in high numbers from eutrophic waters even when environmental stress reduces total numbers, but that isolations from cleaner waters are erratic. We conclude that mere isolation of the organism as an occasional contaminant probably does not present a hazard to public health.
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Michaels G, Milner Y, Reed GH. Magnetic resonance and kinetic studies of pyruvate, phosphate dikinase. Interaction of oxalate with the phosphorylated form of the enzyme. Biochemistry 1975; 14:3213-9. [PMID: 167819 DOI: 10.1021/bi00685a028] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pyruvate, orthophosphate dikinase (EC 2.7.9.1) carries out its catalytic function in three successive partial reactions, the final step being the reaction of pyruvate with a stable phosphoenzyme intermediate to give phosphoenolpyruvate and free enzyme (Evans, H.J., and Wood, H. G. (1968), Proc. Natl. Acad. Sci. U.S.A. 61, 1448). Interactions of oxalate, a structural analog of enolpyruvate, with the phosphorylated form of the enzyme have been investigated by kinetic inhibition measurements and by magnetic resonance studies of manganous ion complexes with the enzyme. Oxalate inhibits the reaction catalyzed by pyruvate, phosphate dikinase, and the inhibition is linearly competitive with respect to pyruvate. The inhibitor constant for oxalate of 25 mu-M is fourfold lower than the Michaelis constant for pyruvate. The enhancement in the longitudinal relaxation rate of water protons (PRR) which occurs upon binding of Mn(II) to the enzyme has been used to monitor binding of oxalate to Mn(II)-enzyme complexes. PRR titrations indicate that the dissociation constant of oxalate from the Mn(II) complex of the free form of the enzyme is an order of magnitude weaker than the kinetically determined Ki. On the other hand, titrations of solutions which contain the phosphorylated form of the enzyme reveal a much stronger binding of oxalate. Moreover, the strength of oxalate binding to the phosphorylated enzyme is a function both of the species and of the concentration of monovalent cations in the solution. In the presence of Tl+, which has the most favorable activator constant for the final partial reaction, the dissociation constant for oxalate from its complex with the phosphorylated enzyme is less than 1 mu-M. Electron paramagnetic resonance (EPR) spectra for the enzyme-bound Mn(II) are sensitive to structural perturbations which occur upon binding of substrates or of oxalate to the enzyme. The EPR spectrum for the Mn(II)-phosphoenzyme-oxalate species is distinguished from spectra for other complexes of the enzyme by unusually narrow line widths and consequent resolution of fine structure from electronic quadrupole splitting. The narrow lines in the EPR spectrum are indicative of a rigid, pseudocrystalline environment for the bound Mn(II). The magnitude and frequency dependence of the PRR for the Mn(II)-phosphoenzyme-oxalate complex indicate that if any water molecules are bound to the Mn(II), their exchange with the bulk water is severely retarded. The kinetic and magnetic resonance studies support the hypothesis that oxalate mimics the reactive intermediate, enolpyruvate, in a complex with the phosphorylated enzyme which may resemble the structure of the transition state of the final partial reaction.
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Michaels G, Matles AL. The role of the ligamentum teres in congenital dislocation of the hip. Clin Orthop Relat Res 1970; 71:199-201. [PMID: 5433380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Glatzer RL, Perlman RD, Michaels G, Matles A. Fractures of both bones of the distal forearm in children. Bull Hosp Joint Dis 1967; 28:14-25. [PMID: 6040413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Gunning B, Michaels G, Neumann L, Splitter S, Kinsell L. Effects of a Diet High in Polyunsaturated Fat on the Plasma Lipids of Normal Young Females. J Nutr 1963; 79:85-92. [PMID: 13951281 DOI: 10.1093/jn/79.1.85] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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