Browsing by Subject "DNA sequencing"

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    Comprehensive analysis of different adhesives in aerobiological sampling using optical microscopy and high-throughput DNA sequencing
    (Elsevier, 2019-04-05) Rojo, Jesús; Núñez, Andrés; Lara, Beatriz; Sánchez-Parra, Beatriz; Moreno, Diego A.; Pérez-Badía, Rosa; Genética y Microbiología
    The standardization and unification of the procedures to analyze and quantify the airborne pollen concentrations are very important topics. In this work, the effectiveness of the two most used adhesives in aerobiological sampling, silicone prepared with cyclohexane solvent (Silicone) and petroleum jelly (Vaseline), was compared under outdoor conditions. This comparison was carried out using the traditional method based on the identification and quantification by optical microscopy (OM) of the airborne pollen and the novel methodology by high-throughput sequencing analysis (HTS). Globally, the results from both methods of analysis (OM and HTS) showed a good agreement between the two adhesives tested regarding the abundance of the main pollen types present in the samples: Cupressaceae, Olea, Poaceae, Platanus, Quercus. We concluded that the results from both adhesives are comparable data. Furthermore, the comparisons between methodologies, OM vs. HTS, showed that both techniques can accurately identify the most abundant pollen types in the atmosphere for the studied periods, with a good agreement of their relative abundances especially when the airborne pollen diversity is low but showing some divergences as the number of pollen types increases.
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    Distribution of airborne pollen, fungi and bacteria at four altitudes using high-throughput DNA sequencing
    (Elsevier, 2020-10-11) Sánchez-Parra, Beatriz; Núñez, Andrés; García, Ana M.; Campoy, Pascual; Moreno, Diego A.; Genética y Microbiología
    The diversity and composition of bioaerosols in the atmosphere have been studied in the recent years in multiple places and under very different meteorological conditions. Pollen grains, fungal propagules and bacteria are the most studied airborne biological particles, usually individually, and correlated to environmental factors such as temperature, wind speed, rain, air pollution, etc. to understand their influence. However, the effect of the height on the distribution and composition of these bioaerosols has not been properly described so far. In this research, we analyzed concurrently these three biological particles at four different heights (1.5 m, 130 m, 500 m and 1000 m) by high-throughput DNA sequencing. We observed that the atmosphere contains a homogeneous distribution and composition of biological particles regardless of the altitude tested. Only a minority of the taxa is differently distributed. Therefore, we here deduce that the altitude does not drastically influence the airborne bioparticles distribution and composition under similar meteorological conditions. We also studied the co-occurrence between different bioaerosols, finding new potential relationships.
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    Effect of the passive natural ventilation on the bioaerosol in a small room
    (Elsevier, 2021-10-13) Núñez, Andrés; García, Ana M.; Genética y Microbiología
    Natural passive ventilation (windows opening) is frequently used in many houses and old buildings to renovate the air, remove unpleasant odors and dust, and reduce the physicochemical pollutants indoor. However, little is known about the effect on biological particles such as pollen grains and fungal spores (both allergenic) or bacteria (potentially infectious and pathogenic). In the present research, the bioaerosols composition in a small room naturally ventilated was analyzed by high-throughput DNA sequencing. Pollen grains were the most abundant particles outdoors while microbial phyla Actinobacteria, Firmicutes, Proteobacteria and Ascomycota were predominant indoors. The main divergences in bioaerosols between indoor and outdoor environments were caused by the different abundance of the biological particles rather than the different taxa composition. Keeping the window open for 2 h did not change significantly the microbial community present indoors, although there was a tendency to mix the components of both environments. The abundance of human-related and potentially harmful microorganisms was higher indoors and was not remarkably affected by natural ventilation. In our study, natural ventilation through window opening had a poor effect on removing these microorganisms from the atmosphere indoor, suggesting that additional mechanisms such as air filtering systems would be required in order to improve the air quality of these environments from a microbiological point of view.
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    Interferon regulatory factor 8 expression and features in blastic plasmacytoid dendritic cell neoplasm and extranodal NK/T-cell lymphoma, nasal type
    (2025) Xiaoqin Dai; Li Sun; Ge Tang; Yu Dong; Fenfen Zhang; Anjia Han; Yuejiao Lang; Biología Celular e Histología
    Aims. To investigate the diagnostic value of Interferon regulatory factor 8 (IRF8) in blastic plasmacytoid dendritic cell neoplasm (BPDCN) and extranodal NK/T-cell lymphoma, nasal type (ENKTL). Methods. Immunohistochemistry staining was used to detect IRF8 expression in 19 cases of BPDCN and 59 cases of ENKTL. In addition, 21 cases of myeloid sarcoma, 30 of B-lymphoblastic leukemia/lymphoma (B-ALL/LBL), 30 of T-lymphoblastic leukemia/lymphoma (T-ALL/LBL), 10 of histiocytic sarcoma, 10 of Langerhans cell histiocytosis, and 9 of follicular dendritic cell sarcoma were also included. DNA sequencing detected IRF8 genetic variation in 6 cases of BPDCN and 20 cases of ENKTL. Results. IRF8 expression was detected in 100.00% (19/19) of BPDCN, exhibiting a strong and uniform staining pattern, and in 91.53% (54/59) of ENKTL, with varying degrees of staining intensity. Weak and focal staining was detected in 33.33% (7/21) of myeloid sarcoma, 13.33% (4/30) of B-ALL/LBL, and 11.11% (1/9) of follicular dendritic cell sarcoma. No expression was found in T-ALL/LBL, histiocytic sarcoma, or Langerhans cell histiocytosis. The proportion of IRF8 positive expression was higher in BPDCN and ENKTL than in other hematolymphoid neoplasms. In ENKTL, the average IRF8 expression was higher in nasal cases than in extranasal cases and in cases with mitosis figures of more than 4/10 high-power field (HPF). Predominant-ly large transformed cell morphology and extranasal involvement site might serve as independent prognostic factors of two-year survival in ENKTL. IRF8 genetic point mutations were found in 33.33% (2/6) of BPDCN and 10.00% (2/20) of ENKTL. Conclusion. The study demonstrated the promising value of IRF8 in the diagnosis of BPDCN and ENKTL.
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    The aerobiome in a hospital environment: characterization, seasonal tendencies and the effect of window opening ventilation
    (Elsevier, 2023-01-16) Núñez, Andrés; García, Ana M.; Genética y Microbiología
    The urban atmosphere carries biological particles (bioaerosols) that may cause several diseases and allergies. These bioaerosols infiltrate and mix with those present inside the buildings, including hospitals. However, little is known about the behavior of these particles around health facilities. Here, we described the bioaerosols composition of an urban hospital indoor and outdoor at two different periods (winter and summer) using DNA sequencing. We observed that the seasonality and composition of the bioaerosols outdoor was also displayed indoor, and, in some cases, the taxa showed different trends depending on the season. Pathogenic species of bacteria and fungi were found indoors at low levels but also outdoors, being mostly environmental species, which would reject the idea that hospitals may be acting as a source of emission via aerosols. Skin-related bacteria were the most prevalent group related to human microbiome, being more abundant indoors. Air temperature was the principal factor affecting the bioaerosols composition in the samples but, in general, meteorological parameters outdoors were poor descriptors of the bioaerosols indoors. Similarly, the concentrations of the main indoor air pollutants did not correlate with microbial abundances. Globally, natural ventilation through a window opening did not significantly alter the composition of the bioaerosols indoor.