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Alves LPS, Almeida AT, Cruz LM, Pedrosa FO, de Souza EM, Chubatsu LS, Müller-Santos M, Valdameri G. A simple and efficient method for poly-3-hydroxybutyrate quantification in diazotrophic bacteria within 5 minutes using flow cytometry. ACTA ACUST UNITED AC 2017; 50:e5492. [PMID: 28099582 PMCID: PMC5264536 DOI: 10.1590/1414-431x20165492] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/26/2016] [Indexed: 11/24/2022]
Abstract
The conventional method for quantification of polyhydroxyalkanoates based on
whole-cell methanolysis and gas chromatography (GC) is laborious and time-consuming.
In this work, a method based on flow cytometry of Nile red stained bacterial cells
was established to quantify poly-3-hydroxybutyrate (PHB) production by the
diazotrophic and plant-associated bacteria, Herbaspirillum
seropedicae and Azospirillum brasilense. The method
consists of three steps: i) cell permeabilization, ii) Nile red staining, and iii)
analysis by flow cytometry. The method was optimized step-by-step and can be carried
out in less than 5 min. The final results indicated a high correlation coefficient
(R2=0.99) compared to a standard method based on methanolysis and GC.
This method was successfully applied to the quantification of PHB in epiphytic
bacteria isolated from rice roots.
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Affiliation(s)
- L P S Alves
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - A T Almeida
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L M Cruz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - F O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - E M de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L S Chubatsu
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - M Müller-Santos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - G Valdameri
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil.,Departamento de Análises Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Stets MI, Etto RM, Galvão CW, Ayub RA, Cruz LM, Steffens MBR, Barana AC. Microbial community and performance of slaughterhouse wastewater treatment filters. Genet Mol Res 2014; 13:4444-55. [PMID: 25036349 DOI: 10.4238/2014.june.16.3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The performance of anaerobic filter bioreactors (AFs) is influenced by the composition of the substrate, support medium, and the microbial species present in the sludge. In this study, the efficiency of a slaughterhouse effluent treatment using three AFs containing different support media was tested, and the microbial diversity was investigated by amplified ribosomal DNA restriction analysis and 16S rRNA gene sequencing. The physicochemical analysis of the AF systems tested suggested their feasibility, with rates of chemical oxygen demand removal of 72±8% in hydraulic retention times of 1 day. Analysis of pH, alkalinity, volatile acidity, total solids, total volatile solids, total Kjeldahl nitrogen, and the microbial community structures indicated high similarity among the three AFs. The composition of prokaryotic communities showed a prevalence of Proteobacteria (27.3%) and Bacteroidetes (18.4%) of the Bacteria domain and Methanomicrobiales (36.4%) and Methanosarcinales (35.3%) of the Archaea domain. Despite the high similarity of the microbial communities among the AFs, the reactor containing pieces of clay brick as a support medium presented the highest richness and diversity of bacterial and archaeal operational taxonomic units.
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Affiliation(s)
- M I Stets
- Departamento de Engenharia de Alimentos, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brasil
| | - R M Etto
- Laboratório de Biologia Molecular Microbiana, Departamento de Química, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brasil
| | - C W Galvão
- Laboratório de Biologia Molecular Microbiana, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brasil
| | - R A Ayub
- Laboratório de Biotecnologia Vegetal, Departamento de Fitotecnia e Fitossanidade, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brasil
| | - L M Cruz
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - M B R Steffens
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - A C Barana
- Departamento de Engenharia de Alimentos, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brasil
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Dallagassa CB, Huergo LF, Stets MI, Pedrosa FO, Souza EM, Cruz LM, Assis FEA, Wolf S, Volanski W, Picheth G, Pigatto-Denardi CP, Farah SMSS, Fadel-Picheth CMT. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis of Escherichia coli categories. Genet Mol Res 2014; 13:716-22. [PMID: 24615036 DOI: 10.4238/2014.january.29.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The mass profiles of cell-free extracts of 180 commensal and pathogenic strains of Escherichia coli were determined by MALDI-TOF mass spectrometry (MS). While some peaks were highly conserved in all E. coli, several peaks occurred only in some strains, showing heterogeneity among them. We did not detect strain-specific peaks for any of the E. coli categories tested. However, review of the fully conserved and the variable peaks suggested that MALDI-TOF MS has the potential to distinguish commensal and uropathogenic E. coli strains. Additionally, eight Shigella sonnei isolates were tested and found to be indistinguishable from E. coli by MALDI-TOF MS under the test conditions.
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Affiliation(s)
- C B Dallagassa
- Departamento de Patologia Médica, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L F Huergo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - M I Stets
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - F O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - E M Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L M Cruz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - F E A Assis
- Departamento de Patologia Médica, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - S Wolf
- Departamento de Patologia Médica, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - W Volanski
- Departamento de Patologia Médica, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - G Picheth
- Departamento de Patologia Médica, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - C P Pigatto-Denardi
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, Matão, SP, Brasil
| | - S M S S Farah
- Laboratório Central do Estado do Paraná, Curitiba, PR, Brasil
| | - C M T Fadel-Picheth
- Departamento de Patologia Médica, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Magnani GS, Cruz LM, Weber H, Bespalhok JC, Daros E, Baura V, Yates MG, Monteiro RA, Faoro H, Pedrosa FO, Souza EM. Culture-independent analysis of endophytic bacterial communities associated with Brazilian sugarcane. Genet Mol Res 2013; 12:4549-58. [PMID: 24222230 DOI: 10.4238/2013.october.15.3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sugarcane is an economically important culture in Brazil. Endophytic bacteria live inside plants, and can provide many benefits to the plant host. We analyzed the bacterial diversity of sugarcane cultivar RB-72454 by cultivation-independent techniques. Total DNA from sugarcane stems from a commercial plantation located in Paraná State was extracted. Partial 16S rRNA genes were amplified and sequenced for library construction. Of 152 sequences obtained, 52% were similar to 16S rRNA from Pseudomonas sp, and 35.5% to Enterobacter sp. The genera Pantoea, Serratia, Citrobacter, and Klebsiella were also represented. The endophytic communities in these sugarcane samples were dominated by the families Enterobacteriaceae and Pseudomonadaceae (class Gammaproteobacteria).
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Affiliation(s)
- G S Magnani
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A. Qualimap: evaluating next-generation sequencing alignment data. ACTA ACUST UNITED AC 2012; 28:2678-9. [PMID: 22914218 DOI: 10.1093/bioinformatics/bts503] [Citation(s) in RCA: 589] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MOTIVATION The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments for next-generation sequencing data. SAM/BAM files usually contain information from tens to hundreds of millions of reads. Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. The systematic detection of such biases is a non-trivial task that is crucial to drive appropriate downstream analyses. RESULTS We have developed Qualimap, a Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides graphical and statistical analyses for the evaluation of data. Such quality-control data are vital for highlighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses. AVAILABILITY Qualimap is freely available from http://www.qualimap.org.
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Affiliation(s)
- Fernando García-Alcalde
- Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
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Etto RM, Cruz LM, Jesus EC, Galvão CW, Galvão F, Souza EM, Pedrosa FO, Steffens MBR. Prokaryotic communities of acidic peatlands from the southern Brazilian Atlantic Forest. Braz J Microbiol 2012; 43:661-74. [PMID: 24031878 PMCID: PMC3768831 DOI: 10.1590/s1517-83822012000200031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 06/07/2012] [Indexed: 11/22/2022] Open
Abstract
The acidic peatlands of southern Brazil are ecosystems essential for the maintenance of the Atlantic Forest, one of the 25 hot-spots of biodiversity in the world. In this work, we investigated the composition of prokaryotic communities in four histosols of three acidic peatland regions by constructing small-subunit (SSU) rRNA gene libraries and sequencing. SSU rRNA gene sequence analysis showed the prevalence of Acidobacteria (38.8%) and Proteobacteria (27.4%) of the Bacteria domain and Miscellaneous (58%) and Terrestrial (24%) groups of Crenarchaeota of the Archaea domain. As observed in other ecosystems, archaeal communities showed lower richness than bacterial communities. We also found a limited number of Euryarchaeota and of known methanotrophic bacteria in the clone libraries.
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Affiliation(s)
- R M Etto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná , Curitiba, PR , Brasil
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Pisa G, Magnani GS, Weber H, Souza EM, Faoro H, Monteiro RA, Daros E, Baura V, Bespalhok JP, Pedrosa FO, Cruz LM. Diversity of 16S rRNA genes from bacteria of sugarcane rhizosphere soil. Braz J Med Biol Res 2011; 44:1215-21. [PMID: 22042267 DOI: 10.1590/s0100-879x2011007500148] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 10/13/2011] [Indexed: 11/22/2022] Open
Abstract
Sugarcane is an important agricultural product of Brazil, with a total production of more than 500 million tons. Knowledge of the bacterial community associated with agricultural crops and the soil status is a decisive step towards understanding how microorganisms influence crop productivity. However, most studies aim to isolate endophytic or rhizosphere bacteria associated with the plant by culture-dependent approaches. Culture-independent approaches allow a more comprehensive view of entire bacterial communities in the environment. In the present study, we have used this approach to assess the bacterial community in the rhizosphere soil of sugarcane at different times and under different nitrogen fertilization conditions. At the high taxonomic level, few differences between samples were observed, with the phylum Proteobacteria (29.6%) predominating, followed by Acidobacteria (23.4%), Bacteroidetes (12.1%), Firmicutes (10.2%), and Actinobacteria (5.6%). The exception was the Verrucomicrobia phylum whose prevalence in N-fertilized soils was approximately 0.7% and increased to 5.2% in the non-fertilized soil, suggesting that this group may be an indicator of nitrogen availability in soils. However, at low taxonomic levels a higher diversity was found associated with plants receiving nitrogen fertilizer. Bacillus was the most predominant genus, accounting for 19.7% of all genera observed. Classically reported nitrogen-fixing and/or plant growth-promoting bacterial genera, such as Azospirillum, Rhizobium, Mesorhizobium, Bradyrhizobium, and Burkholderia were also found although at a lower prevalence.
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Affiliation(s)
- G Pisa
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Vicente VA, Attili-Angelis D, Pie MR, Queiroz-Telles F, Cruz LM, Najafzadeh MJ, de Hoog GS, Zhao J, Pizzirani-Kleiner A. Environmental isolation of black yeast-like fungi involved in human infection. Stud Mycol 2011; 61:137-44. [PMID: 19287536 PMCID: PMC2610314 DOI: 10.3114/sim.2008.61.14] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The present study focuses on potential agents of chromoblastomycosis and other endemic diseases in the state of Paraná, Southern Brazil. Using a highly selective protocol for chaetothyrialean black yeasts and relatives, environmental samples from the living area of symptomatic patients were analysed. Additional strains were isolated from creosote-treated wood and hydrocarbon-polluted environments, as such polluted sites have been supposed to enhance black yeast prevalence. Isolates showed morphologies compatible with the traditional etiological agents of chromoblastomycosis, e.g. Fonsecaea pedrosoi and Phialophora verrucosa, and of agents of subcutaneous or systemic infections like Cladophialophora bantiana and Exophiala jeanselmei. Some agents of mild disease were indeed encountered. However, molecular analysis proved that most environmental strains differed from known etiologic agents of pronounced disease syndromes: they belonged to the same order, but mostly were undescribed species. Agents of chromoblastomycosis and systemic disease thus far are prevalent on the human host. The hydrocarbon-polluted environments yielded yet another spectrum of chaetothyrialean fungi. These observations are of great relevance because they allow us to distinguish between categories of opportunists, indicating possible differences in pathogenicity and virulence.
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Affiliation(s)
- V A Vicente
- Department of Basic Pathology, Federal University of Paraná, Curitiba, PR, Brazil
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Serrato RV, Sassaki GL, Cruz LM, Carlson RW, Muszyński A, Monteiro RA, Pedrosa FO, Souza EM, Iacomini M. Chemical composition of lipopolysaccharides isolated from various endophytic nitrogen-fixing bacteria of the genus Herbaspirillum. Can J Microbiol 2010; 56:342-7. [PMID: 20453901 DOI: 10.1139/w10-011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacteria from the genus Herbaspirillum are endophytes responsible for nitrogen fixation in gramineous plants of economic importance such as maize, sugarcane, sorghum, rice, and wheat. Some species are known to produce plant growth substances. In contrast, Herbaspirillum rubrisubalbicans strains are known to be mild plant pathogens. The molecular communication between the plant and the microbes might involve lipopolysaccharides present in the outer membrane of these gram-negative bacteria. Phenol-water extraction was used to obtain lipopolysaccharides from 7 strains of Herbaspirillum seropedicae (SmR1, Z67, Z78, ZA95, and M2) and H. rubrisubalbicans (M1 and M4). The electrophoretic profiles and chemical composition of the lipopolysaccharides obtained in the phenol and aqueous extracts were shown herein.
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Affiliation(s)
- R V Serrato
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil
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Abstract
Endophytic bacteria live inside plant tissues without causing disease. Studies of endophytes in sugarcane have focused on the isolation of diazotrophic bacteria. We examined the diversity of endophytic bacteria in the internal tissues of sugarcane stems and leaves, using molecular and biochemical methods. Potato-agar medium was used to cultivate the endophytes; 32 isolates were selected for analysis. DNA was extracted and the 16S rRNA gene was partially sequenced and used for molecular identification. Gram staining, catalase and oxidase tests, and the API-20E system were used to characterize the isolates. The strains were divided into five groups, based on the 16S rRNA sequences. Group I comprised 14 representatives of the Enterobacteriaceae; group II was composed of Bacilli; group III contained one representative, Curtobacterium sp; group IV contained representatives of the Pseudomonadaceae family, and group V had one isolate with an uncultured bacterium. Four isolates were able to reduce acetylene to ethylene. Most of the bacteria isolated from the sugarcane stem and leaf tissues belonged to Enterobacteriaceae and Pseudomonaceae, respectively, demonstrating niche specificity. Overall, we found the endophytic bacteria in sugarcane to be more diverse than previously reported.
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Affiliation(s)
- G S Magnani
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Coelho J, Brauer L, Amaral A, Taniguchi L, Park M, Cruz L. Crit Care 2003; 7:P26. [DOI: 10.1186/cc2222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
The total-lipid composition of 21 lichens of the ascomycetous genera Cladonia (11) and Cladina (1) of the family Cladoniacea, Cladia (1), Parmotrema (3), Ramalina (2), Leptogium (1), Cetraria (1), and the basidiomycetous genus Dictyonema (1) was determined. Analyses of those of Dictyonema glabratum were carried out with a total extract and those obtained after successive extractions with various solvents. Each extract was partitioned between n-heptane/isopropanol and 1 M sulfuric acid, giving triglycerides (TG) in the upper phase. Extracts were methanolyzed and the resulting methyl esters were analyzed by gas chromatography-mass spectrometry. Methanolyzates of TG unexpectedly contained esters of 9-oxodecanoic, 9-methyl-tetradecanoic, 6-methyl-tetradecanoic, 3-hydroxy-decanoic, nonanedioic, and decanedioic acids, as well as common fatty acids. Fatty acid methyl ester profiles from the lichens were submitted to cluster analysis, and the resulting dendogram showed a cluster consistent with Cladonia spp., suggesting an efficient aid to lichen taxonomy. The total carbohydrate content of each lipid extract was determined by a modified phenol-sulfuric acid method, which compensated for the presence of pigments.
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Affiliation(s)
- G L Sassaki
- Departamento de Bioquímica, Universidade Federal do Paraná, Curitiba-PR, Brazil
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Páez de Reyes F, De Franco V, De Dorado YH, De Rangel R, De Vanegas ML, Cruz LM, Garzón N, Cascante M, Palacio R, Quintero S, Ramírez C. [Planning for the future of nursing education]. ANEC 1967; 2:26-39. [PMID: 5185852] [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: 01/14/2023]
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