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Abstract
LARC™ MPEI-1 (Langley Research Center™ modified phenylethynyl imide-1) phenylethynyl containing aromatic polyimide, is based on the reaction of biphenyl dianhydride (BPDA), 3,4′-oxydianiline (3,4′-ODA), 1,3-bis(3-aminophenoxy)benzene (APB), 2,4,6-triaminopyrimidine (TAP) and 4-phenylethynyl phthalic anhydride (PEPA), presumably resulting in a mixture of linear, branched and star shaped phenylethynyl containing imides which was evaluated as a matrix for high-performance composites. The poly(amid acid) solution of MPEI-1 in N-methypyrrolidinone was synthesized at 35% and 42% solids. Unidirectional prepreg was fabricated from these solutions and Hercules IM7 carbon fibre utilizing NASA-Langley’s multipurpose prepreg machine. The temperature-dependent volatile depletion rates, thermal crystallization behaviour and resin rheology were characterized. Based on this information, a composite moulding cycle was developed which yielded well consolidated, voidfree laminates. Composite mechanical properties such as short beam shear strength, longitudinal and transverse flexural strength and flexural modulus, longitudinal tensile strength and notched and unnotched compression strengths were measured at room temperature (RT) and elevated temperatures. These mechanical properties are compared with those of IM7/LARC™ PETI-5 composites.
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Affiliation(s)
| | | | - B J Jensen
- NASA Langley Research Center, Hampton, VA 23681-0001, USA
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2
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Santiago-Rodriguez TM, Patrício AR, Rivera JI, Coradin M, Gonzalez A, Tirado G, Cano RJ, Toranzos GA. luxS in bacteria isolated from 25- to 40-million-year-old amber. FEMS Microbiol Lett 2013; 350:117-24. [PMID: 24102660 DOI: 10.1111/1574-6968.12275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 12/31/2022] Open
Abstract
Interspecies bacterial communication is mediated by autoinducer-2, whose synthesis depends on luxS. Due to the apparent universality of luxS (present in more than 40 bacterial species), it may have an ancient origin; however, no direct evidence is currently available. We amplified luxS in bacteria isolated from 25- to 40-million-year-old amber. The phylogenies and molecular clocks of luxS and the 16S rRNA gene from ancient and extant bacteria were determined as well. Luminescence assays using Vibrio harveyi BB170 aimed to determine the activity of luxS. While the phylogeny of luxS was very similar to that of extant Bacillus spp., amber isolates exhibited unique 16S rRNA gene phylogenies. This suggests that luxS may have been acquired by horizontal transfer millions of years ago. Molecular clocks of luxS suggest slow evolutionary rates, similar to those of the 16S rRNA gene and consistent with a conserved gene. Dendograms of the 16S rRNA gene and luxS show two separate clusters for the extant and ancient bacteria, confirming the uniqueness of the latter group.
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Affiliation(s)
- Tasha M Santiago-Rodriguez
- Environmental Microbiology Laboratory, Department of Biology, University of Puerto Rico, Rico, San Juan, Puerto Rico; Department of Pathology, University of California, San Diego, CA, USA
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3
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Greenblatt CL, Baum J, Klein BY, Nachshon S, Koltunov V, Cano RJ. Micrococcus luteus -- survival in amber. Microb Ecol 2004; 48:120-127. [PMID: 15164240 DOI: 10.1007/s00248-003-2016-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2003] [Accepted: 08/27/2003] [Indexed: 05/24/2023]
Abstract
A growing body of evidence now supports the isolation of microorganisms from ancient materials. However, questions about the stringency of extraction methods and the genetic relatedness of isolated organisms to their closest living relatives continue to challenge the authenticity of these ancient life forms. Previous studies have successfully isolated a number of spore-forming bacteria from organic and inorganic deposits of considerable age whose survival is explained by their ability to enter suspended animation for extended periods of time. However, despite a number of putative reports, the isolation of non-spore-forming bacteria and an explanation for their survival have remained enigmatic. Here we describe the isolation of non-spore-forming cocci from a 120-million-year-old block of amber, which by genetic, morphological, and biochemical analyses are identified as belonging to the bacterial species Micrococcus luteus. Although comparison of 16S rRNA sequences from the ancient isolates with their modern counterparts is unable to confirm the precise age of these bacteria, we demonstrate, using complementary molecular and cell biological techniques, evidence supporting the view that these (and related modern members of the genus) have numerous adaptations for survival in extreme, nutrient-poor environments, traits that will assist in this bacteria's persistence and dispersal in the environment. The bacteria's ability to utilize succinic acid and process terpine-related compounds, both major components of natural amber, support its survival in this oligotrophic environment.
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Affiliation(s)
- C L Greenblatt
- Kuvin Centre for the Study of Infectious and Tropical Disease, The Hebrew University-Hadassah School of Medicine, P.O. Box 12272, 91120 Jerusalem, Israel.
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4
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Qureshi A, Mauger JB, Cano RJ, Galazzo JL, Lee MD. MF-EA-705alpha & MF-EA-705beta, new metabolites from microbial fermentation of a Streptomyces sp. J Antibiot (Tokyo) 2001; 54:1100-3. [PMID: 11858667 DOI: 10.7164/antibiotics.54.1100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- A Qureshi
- Molecular Diversity and Screening, Microcide Pharmaceuticals, Inc., Mountain View, CA 94043, USA.
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5
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Cano RJ, Tiefenbrunner F, Ubaldi M, Del Cueto C, Luciani S, Cox T, Orkand P, Künzel KH, Rollo F. Sequence analysis of bacterial DNA in the colon and stomach of the Tyrolean Iceman. Am J Phys Anthropol 2000; 112:297-309. [PMID: 10861348 DOI: 10.1002/1096-8644(200007)112:3<297::aid-ajpa2>3.0.co;2-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The male human body found in an Alpine glacier on September 19, 1991 ("Tyrolean Iceman") has, for the first time in history, given scientists a chance to perform detailed anatomical, histological, and molecular investigations on the organs of a person from the Neolithic Age (5350-5100 B.P.). In the present study, tissue samples aseptically taken from the stomach and the colon of the mummy were utilized for DNA extraction, and the DNA was PCR-amplified, using primer pairs designed to bind to fragments of the 16s ribosomal RNA gene (16s rDNA) of a broad range of bacteria. The PCR products were cloned in plasmid vectors, and the recombinant clones (amplicons) were sequenced. The sequence data were finally used for scanning data libraries containing the corresponding sequences of present-day bacteria, to infer the putative ecophysiology of the ancient ones. The same procedure was repeated on some fragments of grass from the clothing found near the corpse. These fragments were taken as a control of the microbiological situation of the glacier. The results show that the flora of the Iceman's stomach is entirely composed of Burkholderia pickettii, an organism commonly found in aquatic habitats. The colon, on the other hand, contains several members of the fecal flora of humans, such as Clostridium perfringens, C. ghonii, C. sordellii, Eubacterium tenue, and Bacteroides sp. The Iceman's colon, however, was found to contain, rather unexpectedly, also some members of the genus Vibrio. The results are discussed in light of what is known about the preservation of microbial DNA at the Iceman's site and of previous parasitological studies performed on the Iceman himself and on human coprolites.
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Affiliation(s)
- R J Cano
- Environmental Biotechnology Institute, California Polytechnic State University, San Luis Obispo, California 93407, USA
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6
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Abstract
> Abstract Claims that organisms can be cultured from amber, if substantiated, would be significant contributions to our understanding of the evolution, tenacity, and potential spread of life. Three reports on the isolation of organisms from amber have been published. Cano and Borucki recently reported the isolation of Bacillus sphaericus and Lambert et al. have described a new species designated Staphylococcus succinus from 25-40 million year old Dominican amber. These characterized organisms were phylogenetically distant from extant relatives and the Staphylococcus sp. sufficiently far removed from other extant staphylococci to be considered a new species. Here we report the culture of bacteria from Dominican and previously untested 120 million year old Israeli (Lebanese lode) amber. Twenty-seven isolates from the amber matrix have been characterized by fatty-acid profiles (FAME) and/or 16S rRNA sequencing. We also performed a terminal restriction fragment pattern (TRF) analysis of the original amber before prolonged culture by consensus primer amplification of the 16S rRNA followed by restriction enzyme digestion of the amplicons. Sample TRFs were consistent with a sparse bacterial assemblage and included at least five of the isolated organisms. Finally, we microscopically mapped the internal topography of an amber slice.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p58.html
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Affiliation(s)
- CL Greenblatt
- Kuvin Centre and Department of Parasitology, Hebrew University, Jerusalem, Israel
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7
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Abstract
We have isolated DNA from 14 tissue samples from the internal organs of an Andean human mummy (10th-11th century A.D.) and have checked the persistence of the original human and bacterial templates using the following main approaches: 1) amino acid racemization test; 2) quantification of mitochondrial DNA copy number; 3) survey of bacterial DNA in the different organs; 4) sequence analysis of bacterial amplicons of different lengths. The results demonstrate that both the original human DNA and the DNA of the bacteria of the mummy gut are preserved. In particular, sequence analysis of two (respectively 100 and 196 bp in length) libraries of bacterial 16s ribosomal RNA gene amplicons from the mummy colon shows that while the shortest amplicons give only modest and biased indications about the bacterial taxa, the longer amplicons allow the identification several species of the genus Clostridium which are typical of the human colon. This work represents a first example of a methodological approach which is applicable, in principle, to many other natural and artificial mummies and might open the way to the study of the structure of the human microbial ecosystem from prehistory to present.
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Affiliation(s)
- M Ubaldi
- Dipartimento di Biologia Molecolare, Cellulare e Animale, Università di Camerino, Italy
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8
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Cox T, Frazier C, Tuttle J, Flood S, Yagi L, Yamashiro CT, Behari R, Paszko C, Cano RJ. Rapid detection of Listeria monocytogenes in dairy samples utilizing a PCR-based fluorogenic 5? nuclease assay. J Ind Microbiol Biotechnol 1998. [DOI: 10.1038/sj.jim.2900578] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Lambert LH, Cox T, Mitchell K, Rosselló-Mora RA, Del Cueto C, Dodge DE, Orkand P, Cano RJ. Staphylococcus succinus sp. nov., isolated from Dominican amber. Int J Syst Bacteriol 1998; 48 Pt 2:511-8. [PMID: 9731292 DOI: 10.1099/00207713-48-2-511] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two bacterial isolates, designated AMG-D1T and AMG-D2, were recovered from 25-35-million-year-old Dominican amber. AMG-D1T and AMG-D2 biochemically most closely resemble Staphylococcus xylosus; they differ physiologically from other staphylococci. Fatty acid analysis and comparisons with extensive databases were unable to show relatedness to any specific taxon. Moreover, AMG-D1T and AMG-D2 contain tuberculostearic acid and meso-diaminopimelic acid, characteristic of the G + C-rich coryneform bacteria, as opposed to L-lysine characteristic of staphylococci. AMG-D1T and AMG-D2 have a G + C ratio of 35 mol%. Phylogenetic analysis with the 16S rRNA gene indicated that AMG-D1T and AMG-D2 were most closely related to Staphylococcus equorum, S. xylosus, Staphylococcus saprophyticus and other novobiocin-resistant staphylococci. Stringent DNA-DNA hybridization studies with AMG-D1T revealed similarities of 38% with S. equorum, 23% with S. xylosus and 6% with S. saprophyticus. The results indicate that AMG-D1T and AMG-D2 represent a novel species, which was named Staphylococcus succinus sp. nov. The type strain of the new species is AMG-D1 (ATCC 700337).
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10
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Abstract
Much of what we know about extinct organisms comes from traits that are not preserved in the fossil record. Until recently, morphological analysis was the only tool available for scientists to determine relationships for extinct fossil organisms. We now know that "ancient' DNA can be preserved in the remains of extinct organisms. By targeting specific gene sequences, it may be possible to deduce biochemical characteristics and through sequence comparisons, to estimate the extent of evolutionary divergence. By comparing the amount and type of these changes, one could estimate how quickly some DNA 'evolves' relative to other segments, or which genes have the most flexibility or are more conserved over time. The compilation of these data would yield greater understanding of the physiology of extinct organisms and provide a much clearer picture of genetic change over time, and the mechanics behind 'evolution'.
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Affiliation(s)
- R J Cano
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo
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11
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Cano RJ, Norton DM, Inzunza AE, Sánchez JG, Oste C. Polymerase Chain Reaction Assay Coupled with Fluorescence Detection on Microwell Plates for Listeria monocytogenes in Foods. J Food Prot 1995; 58:614-620. [PMID: 31137438 DOI: 10.4315/0362-028x-58.6.614] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This study evaluates a polymerase chain-reaction assay coupled with fluorescence detection (PCR-FD) in microwell plates for Listeria monocytogenes in dairy and food samples. Guanidinium thiocyanate/silica-extracted cultures and milk and dairy-food samples were used as templates for a PCR assay in microwell plates, with a primer pair that amplifies a 221 bp segment of the internal transcribed spacer (ITS), in the presence of 0.5 μg/ml of ethidium bromide. Fluorescence of the PCR products was measured with a CytoFluor 2300 fluorescence measurement system (Millipore Corporation, Bedford, MA). The lowest level of detection of the assay was 10 to 100 CFU. A total of 326 food samples were tested, both by culture and by PCR-FD. The overall sensitivity of the PCR-FD assay was 95.2% and the specificity was 89.9%. Positive and negative predictive values were 74.8% and 99.4%, respectively. Based on the results obtained in this study it appears that the PCR-FD assay described here can be useful for screening a large number of milk and dairy-food samples for contamination by Listeria monocytogenes .
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Affiliation(s)
- Raúl J Cano
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407 USA
| | - Dawn M Norton
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407 USA
| | - Alma E Inzunza
- Departamento de Microbiología y Medicina Familiar, Universidad Nacional Autónoma de México, Mexico, D. F
| | | | - Christian Oste
- Beckman Instruments, 2500 Harbor Boulevard, Fullerton, CA 92634 USA
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12
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Abstract
A bacterial spore was revived, cultured, and identified from the abdominal contents of extinct bees preserved for 25 to 40 million years in buried Dominican amber. Rigorous surface decontamination of the amber and aseptic procedures were used during the recovery of the bacterium. Several lines of evidence indicated that the isolated bacterium was of ancient origin and not an extant contaminant. The characteristic enzymatic, biochemical, and 16S ribosomal DNA profiles indicated that the ancient bacterium is most closely related to extant Bacillus sphaericus.
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Affiliation(s)
- R J Cano
- Biological Sciences, California Polytechnic State University, San Luis Obispo 93407, USA
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13
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Abstract
We report here the isolation of DNA from abdominal tissue of four extinct stingless bees (Proplebeia dominicana) in Dominican amber, PCR amplification of a 546-bp fragment of the 16S rRNA gene from Bacillus spp., and their corresponding nucleotide sequences. These sequences were used in basic local alignment search tool searches of nonredundant nucleic acid data bases, and the highest scores were obtained with 16S rRNA sequences from Bacillus spp. Phylogenetic inference analysis by the maximum-likelihood method revealed close phylogenetic relationships of the four presumed ancient Bacillus sequences with Bacillus pumilus, B. firmus, B. subtilis, and B. circulans. These four extant Bacillus spp. are commonly isolated from abdominal tissue of stingless bees. The close phylogenetic association of the extracted DNA sequences with these bee colonizers suggests that a similar bee-Bacillus association existed in the extinct species P. dominicana.
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Affiliation(s)
- R J Cano
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo 93407
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14
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Rasmussen SR, Rasmussen HB, Larsen MR, Hoff-Jørgensen R, Cano RJ. Combined polymerase chain reaction-hybridization microplate assay used to detect bovine leukemia virus and Salmonella. Clin Chem 1994; 40:200-5. [PMID: 8313594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Here we describe the use of an assay that integrates the polymerase chain reaction (PCR) with hybridization of the amplified product for detection in the same microwell. Traditional PCR requires transportation of the amplified product to another system for characterization of samples. Transportation means time-consuming manipulation and risk of contaminating the laboratory with amplified product. Integration of amplification and specific product detection greatly reduces sample manipulations and the risk of contamination. We used the assay for detection of bovine leukemia virus and Salmonella. The results were identical with those produced by two traditional PCR methods. This assay could easily be adapted for other organisms, simply by using other primers and probes.
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15
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Rasmussen SR, Rasmussen HB, Larsen MR, Hoff-Jørgensen R, Cano RJ. Combined polymerase chain reaction-hybridization microplate assay used to detect bovine leukemia virus and Salmonella. Clin Chem 1994. [DOI: 10.1093/clinchem/40.2.200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Here we describe the use of an assay that integrates the polymerase chain reaction (PCR) with hybridization of the amplified product for detection in the same microwell. Traditional PCR requires transportation of the amplified product to another system for characterization of samples. Transportation means time-consuming manipulation and risk of contaminating the laboratory with amplified product. Integration of amplification and specific product detection greatly reduces sample manipulations and the risk of contamination. We used the assay for detection of bovine leukemia virus and Salmonella. The results were identical with those produced by two traditional PCR methods. This assay could easily be adapted for other organisms, simply by using other primers and probes.
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16
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Palomares Folía JC, Cano RJ. ["Antisense": microbiological therapy and diagnosis]. Enferm Infecc Microbiol Clin 1993; 11:502-6. [PMID: 8305560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- J C Palomares Folía
- Departamento de Microbiología, Hospital Universitario Virgen Macarena, Facultad de Medicina, Universidad de Sevilla
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17
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Cano RJ, Rasmussen SR, Sánchez Fraga G, Palomares JC. Fluorescent detection-polymerase chain reaction (FD-PCR) assay on microwell plates as a screening test for salmonellas in foods. J Appl Bacteriol 1993; 75:247-53. [PMID: 8244903 DOI: 10.1111/j.1365-2672.1993.tb02773.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
This study evaluates a polymerase chain reaction assay coupled with a fluorescent detection in microwell plates for salmonellas in food samples. Chelex 100-extracted cultures and bulk and processed food samples were used as templates for a PCR assay in microwell plates, with a primer pair that amplifies a 206 bp segment of IS200. The PCR products were then denatured by heat and transferred to CovaLink NH plates (Nunc) to which capture oligonucleotides were covalently bound. Hybridization was performed for 1 h at 55 degrees C, the microwells were washed and an alkaline phosphatase-labelled probe, complementary of an internal sequence of the PCR product, was added. After stringent washes, 100 microliters of 1 mmol 1(-1) AttoPhos (JBL Scientific) was then added to the wells and the fluorescence measurement system (Millipore). The level of detection of the assay was as low as 1-10 cfu. A total of 172 food samples were tested, both by culture and FD-PCR. Of these 53 were culture positive and 119 culture negative. The sensitivity of the FD-PCR assay was 100% and the specificity was 90.1%. Positive and negative predictive values were 82.8 and 100%, respectively. Based on the results obtained in this study it appears that the FD-PCR assay described here can be useful to screen a large number of food samples for contamination by salmonellas.
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Affiliation(s)
- R J Cano
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo 93407
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18
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Cano RJ, Poinar HN. Rapid isolation of DNA from fossil and museum specimens suitable for PCR. Biotechniques 1993; 15:432-4, 436. [PMID: 8217155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We describe a simple process for extraction of DNA from amber-entombed fossils and museum specimens that is suitable for enzymatic amplification by PCR. Five to ten milligrams of the macerated specimen were mixed in 300 microliters of silica matrix and shaken at 55 degrees C for 1 h in a sterile, screw-capped microcentrifuge tube. After incubation, the silica matrix was transferred to the upper chamber of a SpinFilter, centrifuged at maximum speed for 1 min and then washed twice with 500 microliters of wash solution and the DNA eluted with 50 microliters of TE buffer. The eluate was used as template for PCR, and the results were evaluated by electrophoresis and nucleotide sequence analysis. All samples tested yielded positive results, which were subsequently verified by sequence analysis. It appears, at least in our hands, that the procedure described here is a rapid and efficient way of obtaining small amounts of DNA for PCR in museum and fossilized specimens.
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Affiliation(s)
- R J Cano
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo 93407
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19
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Abstract
DNA has been successfully isolated from both fossilized plant and animal tissues. The oldest material, dated as 25-40 million years old (Tertiary), was obtained from amber-entombed bees and termites. Tissues from both these insects yielded DNA of good quality, which could be amplified by the polymerase chain reaction (PCR) and subsequently sequenced, including the genes encoding 18S ribosomal RNA and 16S rRNA. We report here the extraction of DNA from a 120-135-million-year-old weevil (Nemonychidae, Coleoptera) found in Lebanese amber, PCR amplification of segments of the 18S rRNA gene and the internal transcribed spacer, and the corresponding nucleotide sequences of their 315- and 226-base-pair fragments, respectively. These sequences were used for preliminary phylogenetic analysis of the nemonychid's sequence with three extant coleopterans: Lecontellus pinicola (Nemonychidae), Hypera brunneipennis (Curculionidae) and the mealworm Tenebrio molitor (Tenebrionidae), and two extant dipterans: the fruitfly Drosophila melanogaster (Drosophilidae) and mosquito Aedes albopictus (Culicidae) for the purpose of ascertaining the origin of the extracted and amplified DNA. The results revealed that the PCR-amplified material is that of the extinct nemonychid weevil. This represents the oldest fossil DNA ever extracted and sequenced, extending by 80 million years the age of any previously reported DNA.
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Affiliation(s)
- R J Cano
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo 93407
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20
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Palomares JC, Rodríguez Iglesias MJ, Cano RJ, Torres MJ. [Polymerase chain reaction. Should it be used in clinical microbiologic laboratories?]. Med Clin (Barc) 1992; 99:261-4. [PMID: 1405808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- J C Palomares
- Departamento de Microbiología, Universidad de Sevilla
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21
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Cano RJ, Palomares JC, Torres MJ, Klem RE. Evaluation of a fluorescent DNA hybridization assay for the detection of Neisseria gonorrhoeae. Eur J Clin Microbiol Infect Dis 1992; 11:602-9. [PMID: 1396767 DOI: 10.1007/bf01961666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [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: 12/26/2022]
Abstract
This study evaluates a four-hour fluorescent DNA hybridization assay using both known bacterial isolates and clinical specimens. A biotinylated oligonucleotide probe from a sequence of the plasmid-encoded gene cppB was used. Hybrids were detected by addition of a streptavidin-alkaline phosphatase conjugate, followed by incubation for 30 min in a fluorescent substrate for alkaline phosphatase. The level of detection of the fluorescent assay was 0.1 pg of cryptic plasmid DNA or 200 cfu of the plasmid-containing strain NG 34/85 of Neisseria gonorrhoeae. A total of 119 reference strains of Neisseria gonorrhoeae and other related bacteria were tested for reactivity with the probe. All Neisseria gonorrhoeae strains, including eight plasmid-free strains, hybridized with the probe. Fluorescence ratios were 2.67 for plasmid-free strains and 3.85 for plasmid-containing strains. Of the heterologous microorganisms tested, only one of six strains of Neisseria cinerea gave a fluorescence ratio above the 2.0 cut-off value for positivity with the probe at a cell density of 1 x 10(4) cfu. The probe was also evaluated using clinical specimens from 100 patients attending a clinic for sexually transmitted diseases. The sensitivity of the assay was 100% while the specificity was 97.5%. Positive and negative predictive values were 91.2% and 100%, respectively. The fluorescent DNA hybridization assay for the detection of Neisseria gonorrhoeae described here thus appears to be a highly specific and sensitive assay.
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Affiliation(s)
- R J Cano
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo 93407
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22
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Cano RJ, Torres MJ, Klem RE, Palomares JC, Casadesus J. Detection of salmonellas by DNA hybridization with a fluorescent alkaline phosphatase substrate. J Appl Bacteriol 1992; 72:393-9. [PMID: 1618717 DOI: 10.1111/j.1365-2672.1992.tb01852.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This study evaluates a DNA hybridization assay for salmonella with AttoPhos (JBL Scientific, San Luis Obispo, CA), a fluorescent substrate for alkaline phosphatase. The probe used (50 ng/ml) was a biotinylated 600 bp fragment consisting of a tandem repeat of an insertion sequence (IS200) found in most Salmonella spp. evaluated. The hybridization was carried out at 65 degrees C for 2 h without prior prehybridization and hybrids were detected by the addition of a streptavidin-alkaline phosphatase conjugate. Circles (5 mm) were cut from the membrane and placed in a cuvette containing 1 ml of 1 mmol/l AttoPhos. The reaction was evaluated after 30 min at 37 degrees C with a fluorometer with an excitation wavelength of 440 nm and an emission wavelength of 550 nm. The sensitivity of the probe was estimated to be 10,000 copies of target DNA or 5 x 10(-20) mol of DNA. All 74 salmonella strains tested reacted with the probe but none of the 98 heterologous species tested gave positive results. The results of this study indicate that our assay method, which employs a biotinylated tandem repeat of IS200 and AttoPhos, is a specific and highly sensitive quantitative method for the detection of salmonellas.
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Affiliation(s)
- R J Cano
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo 93407
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Torres MJ, Cano RJ, Rodríguez A, Palomares JC. [Chlamydia trachomatis detection by DNA-RNA hybridization]. Enferm Infecc Microbiol Clin 1992; 10:152-4. [PMID: 1576189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND A one-chain DNA probe, that complements ribosomal RNA of Chlamydia trachomatis was used as a detection method for this microorganism on clinical samples. We compare the method with the cell culture one. METHODS A total of 175 samples (cervix swabs) from women seen at the STD center of the Facultad de Medicina de Sevilla were examined by both diagnostic techniques. When the results were different, a third method (ELISA) was also used. RESULTS Using serial dilutions of a C. trachomatis cell culture as reference pattern, we determine the minimum number of inclusion forming units needed in order to be detected by the probe was 1000. Of all 175 samples, in 24 (14%) cell culture was positive for C. trachomatis, and 26 were positive using the DNA probe test. Sensitivity and specificity for this test were 93% and 95%, respectively. CONCLUSIONS We believe that the DNA probe test was similar to the cell culture test as screening test in Chlamydia trachomatis infections diagnosis, specially among high risk populations.
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Affiliation(s)
- M J Torres
- Departamento de Microbiología, Universidad de Sevilla
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Cano RJ, Torres MJ, Klem RE, Palomares JC. DNA hybridization assay using ATTOPHOS, a fluorescent substrate for alkaline phosphatase. Biotechniques 1992; 12:264-9. [PMID: 1616721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A fluorometric procedure for the detection of DNA-DNA hybrids is described. The procedure involved the detection of probe-bound alkaline phosphatase with the fluorescent substrate ATTOPHOS. This substrate is converted to ATTOFLUOR by alkaline phosphatase and fluoresces strongly at 550 nm when excited with a wavelength of 440 nm. DNA hybridization assays were performed both with dilutions of purified target plasmid DNA (pSE9 or PBR322) and whole bacterial cells. Streptavidin-alkaline phosphatase conjugates were added to react with bound probe. Fluorometric assays, as well as colorimetric assays, using 5-bromo-4-chloro-3-indolylphosphate + nitroblue tetrazolium for alkaline phosphatase activity were performed. The fluorescence of the substrate was measured at time intervals, and the slope of the regression line calculated. A slope four times greater than that of background was considered positive. One hundred femtograms or 2.2 x 10(4) molecules of homologous DNA were detected with the fluorescent assay as compared with 10,000 femtograms or 2.2 x 10(6) molecules of homologous DNA with the colorimetric assay. Similar results were obtained with whole cells. Approximately 1 x 10(3) homologous cells were detected fluorometrically and 1 x 10(5) cells were detected colorimetrically. Based on these results, we conclude that, in our hands, the DNA hybridization assay described here using ATTOPHOS as the substrate for alkaline phosphatase is a very sensitive assay for the detection of DNA-DNA hybrids.
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Affiliation(s)
- R J Cano
- Biological Sciences Department, California Polytechnic University, San Luis Obispo 93407
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Cano RJ, Murrieta CM, Spaulding DC, Pascual A. Evaluation of a DNA probe of plasmid origin for the detection of Chlamydia trachomatis in cultures and clinical specimens. Mol Cell Probes 1991; 5:419-27. [PMID: 1779980 DOI: 10.1016/s0890-8508(05)80013-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [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: 12/28/2022]
Abstract
This study evaluates five cryptic plasmid-derived DNA probes in a 4-h slot-blot hybridization assay for the detection of Chlamydia trachomatis in cultures and clinical specimens. The probes, consisting of either the entire cloned 7.5 kbp cryptic plasmid pSE8 or one of four Hin dIII/Eco RI fragments measuring 710, 1055, 710, and 500 bp, respectively, were labelled with Photoprobe biotin. The probe was detected using a streptavidin-alkaline phosphatase conjugate followed by addition of BCIP and NBT. The sensitivity of the assay, using 25 ng of probe DNA, ranged from 50 pg (with the entire plasmid as probe) to 5 ng (with the 500 bp fragment as probe). A total of 103 reference strains of Chlamydia trachomatis and other bacteria were tested for reactivity with the probes. All 18 reference strains of C. trachomatis hybridized with the probes. None of the DNA from the heterologous organisms tested was found to hybridize with any of the probes. A total of 174 samples taken from patients visiting the STD clinic at the University Hospital, University of Seville were used in the study. The overall sensitivity of the assay, using the 710 bp biotinylated probe was 94.5% compared to culture while the specificity was 97.5%. Positive and negative predictive values were 96.5% and 97.5%, respectively. It appears that the plasmid-derived probes used in this study could serve as useful tools for the rapid and specific detection of Chlamydia trachomatis in cell cultures and clinical specimens.
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Affiliation(s)
- R J Cano
- Biological Sciences Department, California Polytechnic University, San Luis Obispo 93407
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Abstract
An indirect fluorescence antibody (IFA) test was developed for the detection of Gardnerella vaginalis. Antisera were prepared in rabbits by using five strains of G. vaginalis. A pool of the antisera was tested for specificity with a variety of isolates known to colonize the human vagina and (or) morphologically resemble G. vaginalis. Six heterologous bacterial isolates reacted with the pooled antiserum at dilutions of 1:10, but none reacted at the working dilution of 1:200. Vaginal swab specimens were collected from symptomatic and asymptomatic patients in order to further evaluate the IFA procedure. The presence of G. vaginalis in the specimens was determined both by culture and by the IFA procedure. Absorbed antisera reacted with all isolates of G. vaginalis tested. In a clinical trial the IFA procedure detected the presence of G. vaginalis in smears from 23 (24.2%) of the patients with nonspecific vaginitis (NSV), from 22 (29.8%) of the asymptomatic individuals tested, and from 3 patients with vaginitis other than NSV. The presence of G. vaginalis in smears as detected by the IFA procedure was confirmed by cultures in all cases using Vaginalis agar supplemented with colistin and nalidixic acid (V-CNA). It is suggested that the IFA procedure may be of use in conjunction with V-CNA in epidemiological studies of the carriage and transmission of G. vaginalis in human populations. It appears that the IFA procedure, at least in our hands, is a useful test for the rapid detection of G. vaginalis even when this microorganism is not the predominant colonizer of the human vagina.
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Cano RJ, Taylor JJ. Experimental adiaspiromycosis in rabbits. Evaluation of protoplasmic proteins and Sephadex G-100 fractions as specific antigens. Can J Microbiol 1974; 20:987-91. [PMID: 4858116 DOI: 10.1139/m74-153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Laboratory rabbits experimentally infected with aerosolized conidia of Chrysosporium parvum or C. parvum var. crescens were skin-tested with partially purified protoplasmic protein (P) antigens extracted from the fungi, and with several components of P antigens separated by Sephadex G-100 fractionation. Ten micrograms of conidial or 5 μg of adiaspore P antigen produced delayed type skin responses only in those animals infected with the homologous strain. Large quantities of antigens elicited skin reactions in both homologously and heterologously infected rabbits. Skin-reactive components of P antigens were either strain-specific or non-specific, and were recovered from aleuriospores, or adiaspores, or from both. One strain-specific fraction (21) recovered from both aleuriospores and adiaspores may merit clinical and (or) epidemiological trial as a skin-test antigen.
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Cano RJ, Taylor JJ. Experimental adiaspiromycosis in rabbits: host response to Chrysosporium parvum and C. parvum var. crescens antigens. Sabouraudia 1974; 12:54-63. [PMID: 4276215] [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: 01/09/2023]
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