Fluorescent tools for the standardized work in Gram-negative bacteria.

Standardized and thoroughly characterized genetic tools are a prerequisite for studying cellular processes to ensure the reusability and consistency of experimental results. The discovery of fluorescent proteins (FPs) represents a milestone in the development of genetic reporters for monitoring transcription or protein localization in vivo. FPs have revolutionized our understanding of cellular dynamics by enabling the real-time visualization and tracking of biological processes. Despite these advancements, challenges remain in the appropriate use of FPs, specifically regarding their proper application, protein turnover dynamics, and the undesired disruption of cellular functions. Here, we systematically compared a comprehensive set of 15 FPs and assessed their performance in vivo by focusing on key parameters, such as signal over background ratios and protein stability rates, using the Gram-negative model organism Salmonella enterica as a representative host. We evaluated four protein degradation tags in both plasmid- and genome-based systems and our findings highlight the necessity of introducing degradation tags to analyze time-sensitive cellular processes. We demonstrate that the gain of dynamics mediated by the addition of degradation tags impacts the cell-to-cell heterogeneity of plasmid-based but not genome-based reporters. Finally, we probe the applicability of FPs for protein localization studies in living cells using standard and super-resolution fluorescence microscopy. In summary, our study underscores the importance of careful FP selection and paves the way for the development of improved genetic reporters to enhance the reproducibility and reliability of fluorescence-based research in Gram-negative bacteria and beyond.

Spatial predictions of tree density and tree height across Mexico forests using ensemble learning and forest inventory data.

The National Forestry Commission of Mexico continuously monitors forest structure within the country's continental territory by the implementation of the National Forest and Soils Inventory (INFyS). Due to the challenges involved in collecting data exclusively from field surveys, there are spatial information gaps for important forest attributes. This can produce bias or increase uncertainty when generating estimates required to support forest management decisions. Our objective is to predict the spatial distribution of tree height and tree density in all Mexican forests. We performed wall-to-wall spatial predictions of both attributes in 1-km grids, using ensemble machine learning across each forest type in Mexico. Predictor variables include remote sensing imagery and other geospatial data (e.g., mean precipitation, surface temperature, canopy cover). Training data is from the 2009 to 2014 cycle (n > 26,000 sampling plots). Spatial cross validation suggested that the model had a better performance when predicting tree height r 2 = .35 [.12, .51] (mean [min, max]) than for tree density r 2 = .23 [.05, .42]. The best predictive performance when mapping tree height was for broadleaf and coniferous-broadleaf forests (model explained ~50% of variance). The best predictive performance when mapping tree density was for tropical forest (model explained ~40% of variance). Although most forests had relatively low uncertainty for tree height predictions, e.g., values <60%, arid and semiarid ecosystems had high uncertainty, e.g., values >80%. Uncertainty values for tree density predictions were >80% in most forests. The applied open science approach we present is easily replicable and scalable, thus it is helpful to assist in the decision-making and future of the National Forest and Soils Inventory. This work highlights the need for analytical tools that help us exploit the full potential of the Mexican forest inventory datasets.

Identification of an allergenic calmodulin from Amaranthus palmeri pollen.

INTRODUCTION: Pollens are an important source of allergens that trigger rhinitis or asthma. The allergenic extracts of pollens used to diagnose and treat allergies contain different allergenic antigens. Isolated allergenic proteins are employed in in vitro assays, skin tests and allergenic-specific immunotherapy. Calcium-binding allergens are clinically relevant antigens, and their allergenicity can be affected by Ca2+ binding. In this work, a calmodulin was identified as an allergen from Amaranthus palmeri pollen, an important source of pollinosis in Europe, Asia and North America. MATERIALS AND METHODS: Allergenic calmodulin from A. palmeri pollen was isolated by size-exclusion chromatography and reverse-phase chromatography and identified by mass spectrometry. Sensitization to isolated calmodulin was evaluated by skin prick tests in patients with allergy to A. palmeri pollen. RESULTS: Size-exclusion chromatography yielded two fractions that were recognized by the IgE of patients allergic to A. palmeri pollen. Mass spectrometry analysis of the fractions from reverse-phase chromatography showed peptide sequences that identified a calmodulin. Skin prick tests showed that the isolated calmodulin was recognized by 56% of patients allergic to A. palmeri pollen. CONCLUSION: A. palmeri pollen calmodulin could be a clinically relevant allergen in patients sensitized to this source.

Downscaling satellite soil moisture using geomorphometry and machine learning.

Annual soil moisture estimates are useful to characterize trends in the climate system, in the capacity of soils to retain water and for predicting land and atmosphere interactions. The main source of soil moisture spatial information across large areas (e.g., continents) is satellite-based microwave remote sensing. However, satellite soil moisture datasets have coarse spatial resolution (e.g., 25-50 km grids); and large areas from regional-to-global scales have spatial information gaps. We provide an alternative approach to predict soil moisture spatial patterns (and associated uncertainty) with higher spatial resolution across areas where no information is otherwise available. This approach relies on geomorphometry derived terrain parameters and machine learning models to improve the statistical accuracy and the spatial resolution (from 27km to 1km grids) of satellite soil moisture information across the conterminous United States on an annual basis (1991-2016). We derived 15 primary and secondary terrain parameters from a digital elevation model. We trained a machine learning algorithm (i.e., kernel weighted nearest neighbors) for each year. Terrain parameters were used as predictors and annual satellite soil moisture estimates were used to train the models. The explained variance for all models-years was >70% (10-fold cross-validation). The 1km soil moisture grids (compared to the original satellite soil moisture estimates) had higher correlations (improving from r2 = 0.1 to r2 = 0.46) and lower bias (improving from 0.062 to 0.057 m3/m3) with field soil moisture observations from the North American Soil Moisture Database (n = 668 locations with available data between 1991-2013; 0-5cm depth). We conclude that the fusion of geomorphometry methods and satellite soil moisture estimates is useful to increase the spatial resolution and accuracy of satellite-derived soil moisture. This approach can be applied to other satellite-derived soil moisture estimates and regions across the world.

SoilGrids250m: Global gridded soil information based on machine learning.

This paper describes the technical development and accuracy assessment of the most recent and improved version of the SoilGrids system at 250m resolution (June 2016 update). SoilGrids provides global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm), in addition to predictions of depth to bedrock and distribution of soil classes based on the World Reference Base (WRB) and USDA classification systems (ca. 280 raster layers in total). Predictions were based on ca. 150,000 soil profiles used for training and a stack of 158 remote sensing-based soil covariates (primarily derived from MODIS land products, SRTM DEM derivatives, climatic images and global landform and lithology maps), which were used to fit an ensemble of machine learning methods-random forest and gradient boosting and/or multinomial logistic regression-as implemented in the R packages ranger, xgboost, nnet and caret. The results of 10-fold cross-validation show that the ensemble models explain between 56% (coarse fragments) and 83% (pH) of variation with an overall average of 61%. Improvements in the relative accuracy considering the amount of variation explained, in comparison to the previous version of SoilGrids at 1 km spatial resolution, range from 60 to 230%. Improvements can be attributed to: (1) the use of machine learning instead of linear regression, (2) to considerable investments in preparing finer resolution covariate layers and (3) to insertion of additional soil profiles. Further development of SoilGrids could include refinement of methods to incorporate input uncertainties and derivation of posterior probability distributions (per pixel), and further automation of spatial modeling so that soil maps can be generated for potentially hundreds of soil variables. Another area of future research is the development of methods for multiscale merging of SoilGrids predictions with local and/or national gridded soil products (e.g. up to 50 m spatial resolution) so that increasingly more accurate, complete and consistent global soil information can be produced. SoilGrids are available under the Open Data Base License.

[Ocular findings most frequently found in patients with allergic rhinoconjunctivitis]. / Hallazgos oculares más frecuentes en pacientes con diagnóstico de rinoconjuntivitis alérgica.

BACKGROUND: Allergic etiology is suspected whenever a patient with conjunctivitis presents the typical clinical features; however, in ophthalmic practice, confirmation of the immune disease is uncommon. Ocular involvement is common in allergic rhinitis, and the current name of this entity is allergic rhinoconjunctivitis (ARC). Conjunctivitis diagnosis in ARC is inferred by the symptoms, but the most common ocular findings in patients with a confirmed allergic disease are unknown. The most common findings in allergic patients with ocular involvement were identified. METHODS: Anterior segment of patients with an ARC diagnosis offered by an immunologist were evaluated, and the rates of the most common (whether considered related to allergy or not) were determined; 95% confidence intervals (CI) for rates were calculated. RESULTS: One hundred and nineteen patients were evaluated, and the most common finding was conjunctival fornix edema (89.7%, 95% CI 83.5-94.7), followed by tarsal papillae (70.6%, 95% CI 62.4-78.8); the most common non-allergy-related finding was tear film deficiency (52.9%, 95% CI 43.9-61.9). CONCLUSIONS: Conjunctival fornix edema was consistently more frequent than most of the signs used to diagnose allergic conjunctivitis in medical journals. It is suggested to intentionally look for this as recommended, in order to make a more easy diagnosis.

[Th1 and Th2 lymphocytes in perennial allergic rhinitis]. / Linfocitos Th1 y Th2 en rinitis alérgica perenne.

BACKGROUND: The study of perennial allergic rhinitis is a good model to evidence the unbalance between Th1 and Th2 lymphocytes. This functional unbalance is manifested by the exaggerated production of pro-inflammatory cytokines and a reduction of the antiinflammatory ones. OBJECTIVE: To corroborate these alterations in patients with perennial allergic rhinitis. PATIENTS AMD METHOD: In nine patients with perennial allergic rhinitis who had no immunotherapy treatment we measured the IFNgamma, IL-4, IL-10 and IL-13 levels through a flow citometry. RESULTS: We found high levels of IL-10 (42%) and reduced IFNgamma values. We did not find IL-4 or IL-13 expressions in the studied patients. CONCLUSIONS: These results make us to consider a Th1/Th2 unbalance towards a Th2 hyperfunction.

[Lymphocytes B and NK in respiratory allergy]. / Linfocitos B y NK en alergia respiratoria.

BACKGROUND: High affinity immunoglobulin E (IgE) receptors may activate the mast cell degradation; on the other hand, the ones of low affinity may activate B lymphocytes so they act as antigen-presenting cells and as producers of the same immunoglobulin. As allergic patients produce a great quantity of IgE they are prone to get an infection. OBJECTIVE: To quantify the IgE increase in 28 patients with allergic rhinitis or asthma, or both without having received a previous treatment. PATIENTS AND METHODS: 38 patients with allergic rhinitis, bronchial asthma, allergic conjunctivitis or atopic dermatitis diagnosis were included. B lymphocytes and NK cells immunophenotypification was made. Flow cytometry was used for cells lecture. Data were analyzed with descriptive statistics applying central tendency measurements. RESULTS: No variations were found in the values of any cell lineage. CONCLUSIONS: Proliferation and activation of B lymphocytes should be considered in allergic diseases as its quantification in serum may be a measurement parameter of allergic activity.

[Th1 lymphocytes in patients with extrinsic asthma]. / Linfocitos T cooperadores-1 en pacientes con asma extrínseca.

BACKGROUND: Bronchial asthma is a multifactorial disease affecting the functionality of the bronchial tree and immunological changes. OBJECTIVE: To determine if lymphocytes Th-1 have a role in extrinsic asthma of Mexican patients. MATERIAL AND METHODS: We included in the study 39 patients with extrinsic asthma, living in Mexico City, and 27 healthy subjects, without allergy antecedents, with nutritional and immunological characteristics similar. It was determined the following data: production of IL-2 (in 5 patients and 5 controls), its receptor (in all participants), IFN-g (in 8 patients and 5 controls), and TNF-a (in 8 patients and 5 controls). RESULTS: Values of IL-2, its receptor and IFN-gamma were higher in patients than in controls, with significant differences. There were not important differences about TNF-alpha. CONCLUSIONS: Even causes of action change between lymphocytes Th-1 and Th-2 are not known, it is confirmed the moving from Th-2 to Th-1 as an active phenomenon in asthma.

Efecto del calentamiento sobre el VEF-1 en niños con asma sometidos a reto por ejercicio / The effect of a heating routine in children with asthma

Antecedentes: el broncoespasmo inducido por ejercicio, también llamado asma por ejercicio, es una afección frecuente que acompaña comúnmente al paciente asmático. Su frecuencia es de alrededor del 80 al 90 por ciento para los pacientes con asma; se presenta en 40 al 50 por ciento de los niños con rinitis alérgica, en 14 por ciento de los atletas y en 12 por ciento de la población en general. Objetivo: determinar la eficacia de una rutina de calentamiento como agente preventivo del broncoespasmo inducido por ejercicio. Método: se incluyeron 30 pacientes de entre 10 y 16 años de edad, asmáticos y con broncoespasmo inducido por ejercicio diagnosticado mediante prueba de reto al ejercicio. Todos los pacientes realizaron una rutina de ejercicio con duración de 20 minutos durante los cuales se efectuaron movimientos de elasticidad, calistenia y actividad leve dirigida al ejercicio a desarrollar, tomando como parámetro objetivo el 60 por ciento de la frecuencia cardiaca submáxima. Enseguida, todos los pacientes realizaron nuevamente reto al ejercicio, en la que se utilizó una banda sinfín, con velocidades que se incrementaron progresivamente de 1 a 8 km/h y con inclinación de 0 - 10 0. Los registros espirométricos se efectuaron antes del reto y a los 2, 5, 10, 15, 20, 25, 30 y 60 minutos después del mismo. Resultados: el promedio de edad de los pacientes fue de 12.8 ñ 2 años con talla de 157 ñ 10 cm. Conclusión: el calentamiento en niños con broncoespasmo inducido por ejercicio actúa como un agente protector contra el decremento del VEF-1. Si bien el calentamiento puede ser un buen método de control en el paciente asmático, es necesario tener en cuenta que no todos los pacientes tienen un beneficio con dicha protección.Éste sólo puede utilizarse en pacientes con actividad física programada, ya que en los preescolares no es posible implantar una rutina de calentamiento por las características propias de su actividad.

Grado y duración de la broncodilatación mediante la administración de un agonista ß2 solo vs un agonista ß2 más bromuro de ipratropio en niños con asma aguda / Bronchodilation

Antecedentes: el asma es el padecimiento crónico de las vías respiratorias más frecuente de la edad pediátrica. Material y método: estudio prospectivo, longitudinal, doble ciego, al azar con 40 pacientes (divididos en dos grupos) con crisis asmática con edades de 8 a 15 años. A todos se les realizaron pruebas de funcionamiento pulmonar efectuadas de manera basal y posterior a la inhalación del medicamento. Los medicamentos se administraron en dos inhalaciones por tres ocasiones y con intervalos de 10 minutos entre cada dosis. Se consideró que el tratamiento fue efectivo si la mejoría de las pruebas de función pulmonar (VEF1) presentaban un incremento del 15 por ciento de su valor inicial. Resultados: para cada una de las pruebas realizadas en los diferentes tiempos se encontraron incrementos significativos en VEF1 (p <0.05) en ambos grupos comparados con la basal y permanecieron significativos hasta ocho horas después de la administración de ambos esquemas terapéuticos. Conclusión: el efecto broncodilatador del salbutamol solo y en combinación con bromuro de ipratropio es similar en intensidad y en tiempo de acción demostrado por el VEF1.

Medición de la flujimetría en niños alérgicos a ácaros antes y después del reto con pruebas por prick / Flujimetry subsequent to the Dermatophagoides pteronisinnus through tests cutaneous for prick in allergy children

Objetivo. Determinar la obstrucción del flujo aéreo por flujimetría posterior a la aplicación de pruebas cutáneas específicas (dermathophagoides pteronisinnus), en niños sensibles a éste. Material y método. Se estudiaron 44 pacientes de uno y otro sexo con diagnóstico de asma y antecedente de sensibilidad al ácaro Dermathophagoides pteronisinnus mediante pruebas cutáneas por prick, con una edad promedio de 6 a 16 años, captados de la consulta externa del servicio de alergia del Hospital Infantil de México Federico Gómez. Es un estudio longitudinal, prospectivo, ciego cruzado, en el que previamente se hizo una prueba de reto con antígeno estandarizado de Dermatophagoides pteronisinnus o glicerina, previa lectura de flujimetría. Resultados. De los pacientes retados con antígeno en 23 hubo descenso del flujo espiratorio máximo, con una p<0.05, pero sin significado clínico. Cuando se retaron con placebo sólo disminuyó en siete pacientes el flujo espiratorio máximo, también estadísticamente significativo, pero sin relevancia clínica. Conclusión. Las pruebas cutáneas son una herramienta útil en alergia y seguras, pues casi no producen reacciones sistémicas graves