Simultaneous multi-site editing of individual genomes using retron arrays.

During recent years, the use of libraries-scale genomic manipulations scaffolded on CRISPR guide RNAs have been transformative. However, these existing approaches are typically multiplexed across genomes. Unfortunately, building cells with multiple, nonadjacent precise mutations remains a laborious cycle of editing, isolating an edited cell and editing again. The use of bacterial retrons can overcome this limitation. Retrons are genetic systems composed of a reverse transcriptase and a noncoding RNA that contains an multicopy single-stranded DNA, which is reverse transcribed to produce multiple copies of single-stranded DNA. Here we describe a technology-termed a multitron-for precisely modifying multiple sites on a single genome simultaneously using retron arrays, in which multiple donor-encoding DNAs are produced from a single transcript. The multitron architecture is compatible with both recombineering in prokaryotic cells and CRISPR editing in eukaryotic cells. We demonstrate applications for this approach in molecular recording, genetic element minimization and metabolic engineering.

Hexyltrimethylammonium ion enhances potential copper-chelating properties of ammonium thiomolybdate in an in vivo zebrafish model.

Ammonium and hexyltrimethylammonium thiomolybdates (ATM and ATM-C6) and thiotungstates (ATT and ATT-C6) were synthesized. Their toxicity was evaluated using both in vitro and in vivo approaches via the zebrafish embryo acute toxicity assay (ZFET), while the copper-thiometallate interaction was studied using cyclic voltammetry, as well as in an in vivo assay. Cyclic voltammetry suggests that all thiometallates form complexes with copper in a 2:1 Cu:thiometallate ratio. Both in vitro and in vivo assays demonstrated low toxicity in BALB/3T3 cells and in zebrafish embryos, with high IC50 and LC50 values. Furthermore, the hexyltrimethylammonium ion played a crucial role in enhancing viability and reducing toxicity during prolonged treatments for ATM and ATT. In particular, the ZEFT assay uncovered the accumulation of ATM in zebrafish yolk, averted by the incorporation of the hexyltrimethylammonium ion. Notably, the copper-thiometallate interaction assay highlighted the improved viability of embryos when cultured in CuCl2 and ATM-C6, even at high CuCl2 concentrations. The hatching assay further confirmed that copper-ATM-C6 interaction mitigates inhibitory effects induced by thiomolybdates and CuCl2 when administered individually. These results suggest that the incorporation of the hexyltrimethylammonium ion in ATM increase its ability to interact with copper and its potential application as a copper chelator.

Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets.

Effective population size (N e) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.

An experimental census of retrons for DNA production and genome editing.

Retrons are bacterial immune systems that use reverse transcribed DNA as a detector of phage infection. They are also increasingly deployed as a component of biotechnology. For genome editing, for instance, retrons are modified so that the reverse transcribed DNA (RT-DNA) encodes an editing donor. Retrons are commonly found in bacterial genomes; thousands of unique retrons have now been predicted bioinformatically. However, only a small number have been characterized experimentally. Here, we add substantially to the corpus of experimentally studied retrons. We synthesized >100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production, and test the relative efficacy of editing using retron-derived donors to edit bacterial genomes, phage genomes, and human genomes. We add 62 new empirically determined, natural RT-DNAs, which are not predictable from the retron sequence alone. We report a large diversity in RT-DNA production and editing rates across retrons, finding that top performing editors outperform those used in previous studies, and are drawn from a subset of the retron phylogeny.

Series en disnea. Parte 2. Análisis de sus mecanismos según pasan los años / Series on dyspnea. Part 2. Analysis of its mechanisms as the years go by

RESUMEN Este artículo está dedicado al análisis detallado de los mecanismos de disnea. Se tra tarán el control químico de la respiración, los reflejos neurales, la mecánica respiratoria, el costo de oxígeno para respirar y la inadecuación entre tensión y longitud de la fibra muscular. En general, las diferentes explicaciones estuvieron asociadas al desarrollo de aparatos y metodologías de estudio de los laboratorios pulmonares. Todas las teorías tuvieron defensores y detractores e, interesantemente, con el desarrollo de sofisticadas técnicas neurofisiológicas y de imágenes funcionales ha sido posible jerarquizar cada uno de los mecanismos. Todas han sobrevivido al paso del tiempo y ninguna puede explicar de manera unicista la disnea en todas las situaciones clínicas, lo cual habla de la naturaleza compleja y multifactorial del fenómeno.

ABSTRACT This article is devoted to a detailed analysis of the mechanisms of dyspnea. Chemical control of respiration, neural reflexes, respiratory mechanics, the cost of oxygen to breathe, and the mismatch between tension and muscle fiber length will be discussed. In general, the different explanations were associated with the development of apparatus and study methodologies in pulmonary laboratories. All the theories had defenders and detractors and, interestingly, with the development of sophisticated neurophysiological techniques and functional imaging it has been possible to prioritize each of the mecha nisms. All have survived the passage of time and none can explain dyspnea in all clinical situations, which speaks of the complex and multifactorial nature of the phenomenon.

Low but significant evolutionary potential for growth, phenology and reproduction traits in European beech.

Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1087 adult trees, seeds, 1-year-old seedlings and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.

Between but Not Within-Species Variation in the Distribution of Fitness Effects.

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.

Simultaneous multi-site editing of individual genomes using retron arrays.

Our understanding of genomics is limited by the scale of our genomic technologies. While libraries of genomic manipulations scaffolded on CRISPR gRNAs have been transformative, these existing approaches are typically multiplexed across genomes. Yet much of the complexity of real genomes is encoded within a genome across sites. Unfortunately, building cells with multiple, non-adjacent precise mutations remains a laborious cycle of editing, isolating an edited cell, and editing again. Here, we describe a technology for precisely modifying multiple sites on a single genome simultaneously. This technology - termed a multitron - is built from a heavily modified retron, in which multiple donor-encoding msds are produced from a single transcript. The multitron architecture is compatible with both recombineering in prokaryotic cells and CRISPR editing in eukaryotic cells. We demonstrate applications for this approach in molecular recording, genetic element minimization, and metabolic engineering.

Sexual education for university students and the community in a european project: study protocol.

BACKGROUND: The World Health Organisation (WHO) calls on stakeholders to give Higher Education a key educational importance for the future of Europe. Within the content of the training programmes at university, sexuality emerges as a relevant topic in the nursing degree, to promote integral health from a holistic perspective. However, research on the presence of sexuality at the curricular level in Higher Education suggests that it is incomplete and underdeveloped. METHODS: This is a protocol for a long-term, multi-centre, exploratory, descriptive, and cross-sectional study with a quantitative and qualitative approach lasting two years. The research will be carried out in the educational community, including, on the one hand, students, and professors and health professionals of nursing programmes from five universities in different parts of the world (Portugal, Spain, Italy, and the United States), and on the other hand, women, young people, and immigrants from these communities. The study will have several target populations. Firstly, the target is nursing students, with whom the aim is to define their perspective on the sexuality content taught at the university, and their level of knowledge. Secondly university professors and health professionals, with whom we will check their perspective on sexuality in the classroom, as well as their level of knowledge in this field. And finally, we will work with the community (women, young people, and immigrants) to whom we will try to bring sexuality from a useful and enjoyable perspective. In order to measure these variables in the protocol, instruments such as questionnaires and semi-structured interviews will be used. During data collection, ethical principles will be guaranteed and informed consent will be requested from the participants. DISCUSSION: The results of the research will have a high curricular impact on the educational community, and will last over time, since the tools generated in the project will be included as part of nursing training programmes. In addition, participation in the project will improve health education for health professionals and at the community level on sexuality in both urban and rural populations.

Reduced within-population quantitative genetic variation is associated with climate harshness in maritime pine.

How evolutionary forces interact to maintain genetic variation within populations has been a matter of extensive theoretical debates. While mutation and exogenous gene flow increase genetic variation, stabilizing selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e., experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from heterogeneous environments. Using growth, phenological and functional trait data from three clonal common gardens and 33 populations (522 clones) of maritime pine (Pinus pinaster Aiton), we estimated the association between the population-specific total genetic variances (i.e., among-clone variances) for these traits and ten population-specific indices related to admixture levels (estimated based on 5165 SNPs), environmental temporal and spatial heterogeneity and climate harshness. Populations experiencing colder winters showed consistently lower genetic variation for early height growth (a fitness-related trait in forest trees) in the three common gardens. Within-population quantitative genetic variation was not associated with environmental heterogeneity or population admixture for any trait. Our results provide empirical support for the potential role of natural selection in reducing genetic variation for early height growth within populations, which indirectly gives insight into the adaptive potential of populations to changing environments.

Temporally resolved transcriptional recording in E. coli DNA using a Retro-Cascorder.

Biological signals occur over time in living cells. Yet most current approaches to interrogate biology, particularly gene expression, use destructive techniques that quantify signals only at a single point in time. A recent technological advance, termed the Retro-Cascorder, overcomes this limitation by molecularly logging a record of gene expression events in a temporally organized genomic ledger. The Retro-Cascorder works by converting a transcriptional event into a DNA barcode using a retron reverse transcriptase and then storing that event in a unidirectionally expanding clustered regularly interspaced short palindromic repeats (CRISPR) array via acquisition by CRISPR-Cas integrases. This CRISPR array-based ledger of gene expression can be retrieved at a later point in time by sequencing. Here we describe an implementation of the Retro-Cascorder in which the relative timing of transcriptional events from multiple promoters of interest is recorded chronologically in Escherichia coli populations over multiple days. We detail the molecular components required for this technology, provide a step-by-step guide to generate the recording and retrieve the data by Illumina sequencing, and give instructions for how to use custom software to infer the relative transcriptional timing from the sequencing data. The example recording is generated in 2 d, preparation of sequencing libraries and sequencing can be accomplished in 2-3 d, and analysis of data takes up to several hours. This protocol can be implemented by someone familiar with basic bacterial culture, molecular biology and bioinformatics. Analysis can be minimally run on a personal computer.

Analyzing respiratory muscle weakness and thoracopulmonary restriction in subjects with duchenne muscular dystrophy / Análisis de la debilidad de los músculos respiratorios y de la restricción toracopulmonar en sujetos con distrofia muscular de Duchenne

Abstract Objective: To analyze the underlying components of reduced maximal static inspiratory (MIP) and expiratory (MEP) pressures in subjects with Duchenne muscular dystrophy. Methods: Forty-three subjects were assessed based on routine pulmonary function tests. MIP and MEP were measured the subjects performed maximal expirations and inspirations using a snorkel mouthpiece. Lung volumes were measured us ing the helium dilution technique. Results: The mean age was 13 years (range, 7-20 years). Median total lung capacity (TLC) and residual volume (RV) were 78.0 (49.0-94.0) and 27.0 (19.7-30.1) of the predicted values re spectively. The RV/TLC relationship was 35.3% (28.1-47.7). Thirty-five subjects had a TLC below the lower limit of normal, while 31 had an RV/TLC ratio above the upper limit of normal. The median (IQR) MIP and MEP values were -53.0 (-65.5 to -41.8) and 58.0 (41.5-74.8) cmH2O respectively. MIP and MEP in percent of the predicted values (predicted TLC and RV) were 42.6 (33.3-50.8) and 33.7 (23.9-44.5). MIP in percent of the RV reached for Group A (7-11 years old) was higher (p 0.025) while MEP in percent of the TLC reached for Group B (12-16 years) and C (17-20 years) were higher too (0.031). Conclusions: In subjects with Duchenne muscular dystrophy, the intrinsic weakness of respiratory muscles and mechanical disadvantage lead to inadequate maximal static pressure generation. Maximal static pressures should be interpreted cautiously as they overestimate respiratory muscle weakness when compared to predicted values obtained at TLC and RV. Our results provide additional data supporting absolute values use rather than predicted values.

Resumen Objetivo: Analizar los componentes subyacentes de las presiones inspiratorias (MIP) y espiratorias (MEP) es táticas máximas reducidas en sujetos con distrofia de Duchenne (DMD). Métodos: Se evaluaron 43 pacientes mediante pruebas de función pulmonar rutinarias. MIP y MEP fueron medidas a inspiración y espiración máximas. Los volúmenes pulmonares se midieron mediante dilución de helio. Resultados: Edad media 13 años (rango 7-20 años). La capacidad pulmonar total (TLC) y el volumen residual (RV) fueron 78.0% (49.0-94.0) y 27.0% (19.7- 30.1) de los valores predichos. El RV/TLC fue de 35.3% (28.1-47.7). Treinta y cinco sujetos tenían una TLC por debajo del límite inferior de normalidad, 31 tenían una RV/TLC por encima del límite superior de la normalidad. MIP y MEP fueron -53.0 (-65.5 a -41.8) y 58.0 (41.5-74.8) cmH2O, mientras que en % de los predichos (TLC y RV predichos) fueron 42.6 (33.3-50.8) y 33.7 (23.9-44.5). MIP en % del RV alcanzado (Grupo A 7-11 años) fue mayor (p 0.025), y MEP en % de la TLC alcanzada Grupo B (12-16 años) y C (17-20 años), también fue mayor (0.031). Conclusiones: En sujetos con DMD, debilidad intrínseca de los músculos respiratorios y desventaja mecánica conducen a generación de presión estática máxima inadecuada. Las mismas deben interpretarse con cautela, ya que sobrestiman la debilidad de los músculos respiratorios si se las compara con las tablas de valores predichos obtenidos a TLC y RV. Nuestros resultados proporcionan datos adicionales que respaldan la utilización de valores absolutos en lugar de los predichos.

Analyzing respiratory muscle weakness and thoracopulmonary restriction in subjects with Duchenne muscular dystrophy.

OBJECTIVE: To analyze the underlying components of reduced maximal static inspiratory (MIP) and expiratory (MEP) pressures in subjects with Duchenne muscular dystrophy. METHODS: Forty-three subjects were assessed based on routine pulmonary function tests. MIP and MEP were measured the subjects performed maximal expirations and inspirations using a snorkel mouthpiece. Lung volumes were measured using the helium dilution technique. RESULTS: The mean age was 13 years (range, 7-20 years). Median total lung capacity (TLC) and residual volume (RV) were 78.0 (49.0-94.0) and 27.0 (19.7-30.1) of the predicted values respectively. The RV/TLC relationship was 35.3% (28.1-47.7). Thirty-five subjects had a TLC below the lower limit of normal, while 31 had an RV/TLC ratio above the upper limit of normal. The median (IQR) MIP and MEP values were -53.0 (-65.5 to -41.8) and 58.0 (41.5-74.8) cmH2O respectively. MIP and MEP in percent of the predicted values (predicted TLC and RV) were 42.6 (33.3-50.8) and 33.7 (23.9-44.5). MIP in percent of the RV reached for Group A (7-11 years old) was higher (p 0.025) while MEP in percent of the TLC reached for Group B (12-16 years) and C (17-20 years) were higher too (0.031). CONCLUSIONS: In subjects with Duchenne muscular dystrophy, the intrinsic weakness of respiratory muscles and mechanical disadvantage lead to inadequate maximal static pressure generation. Maximal static pressures should be interpreted cautiously as they overestimate respiratory muscle weakness when compared to predicted values obtained at TLC and RV. Our results provide additional data supporting absolute values use rather than predicted values.

OBJETIVO: Analizar los componentes subyacentes de las presiones inspiratorias (MIP) y espiratorias (MEP) estáticas máximas reducidas en sujetos con distrofia de Duchenne (DMD). Métodos: Se evaluaron 43 pacientes mediante pruebas de función pulmonar rutinarias. MIP y MEP fueron medidas a inspiración y espiración máximas. Los volúmenes pulmonares se midieron mediante dilución de helio. RESULTADOS: Edad media 13 años (rango 7-20 años). La capacidad pulmonar total (TLC) y el volumen residual (RV) fueron 78.0% (49.0-94.0) y 27.0% (19.7- 30.1) de los valores predichos. El RV/TLC fue de 35.3% (28.1-47.7). Treinta y cinco sujetos tenían una TLC por debajo del límite inferior de normalidad, 31 tenían una RV/TLC por encima del límite superior de la normalidad. MIP y MEP fueron -53.0 (-65.5 a -41.8) y 58.0 (41.5-74.8) cmH2O, mientras que en % de los predichos (TLC y RV predichos) fueron 42.6 (33.3-50.8) y 33.7 (23.9-44.5). MIP en % del RV alcanzado (Grupo A 7-11 años) fue mayor (p 0.025), y MEP en % de la TLC alcanzada Grupo B (12-16 años) y C (17-20 años), también fue mayor (0.031). CONCLUSIONES: En sujetos con DMD, debilidad intrínseca de los músculos respiratorios y desventaja mecánica conducen a generación de presión estática máxima inadecuada. Las mismas deben interpretarse con cautela, ya que sobrestiman la debilidad de los músculos respiratorios si se las compara con las tablas de valores predichos obtenidos a TLC y RV. Nuestros resultados proporcionan datos adicionales que respaldan la utilización de valores absolutos en lugar de los predichos.

Effect of Altitude on Respiratory Functional Status in COVID-19 Survivors: Results from a Latin American Cohort-FIRCOV.

Laura Gochicoa-Rangel, Santiago C. Arce, Carlos Aguirre-Franco, Wilmer Madrid-Mejía, Mónica Gutiérrez-Clavería, Lorena Noriega-Aguirre, Patricia Schonffeldt-Guerrero, Agustín Acuña-Izcaray, Arturo Cortés-Telles, Luisa Martínez-Valdeavellano, Federico Isaac Hernández-Rocha, Omar Ceballos-Zúñiga, Rodrigo Del Rio Hidalgo, Sonia Sánchez, Erika Meneses-Tamayo, and Iván Chérrez-Ojeda; and on Behalf of the Respiratory Physiology Project in COVID-19 (FIRCOV). Effect of altitude on respiratory functional status in COVID-19 survivors: results from a Latin American Cohort-FIRCOV. High Alt Med Biol 24:37-48, 2023. Persistent symptoms and lung function abnormalities are common in COVID-19 survivors. Objectives: To determine the effect of altitude and other independent variables on respiratory function in COVID-19 survivors. Methods: Analytical, observational, cross-sectional cohort study done at 13 medical centers in Latin America located at different altitudes above sea level. COVID-19 survivors were invited to perform pulmonary function tests at least 3 weeks after diagnosis. Results: 1,368 participants (59% male) had mild (20%), moderate (59%), and severe (21%) disease. Restriction by spirometry was noted in 32%; diffusing capacity of the lung for carbon monoxide (DLCO) was low in 43.7%; and 22.2% walked less meters during the 6-minute walk test (6-MWT). In multiple linear regression models, higher altitude was associated with better spirometry, DLCO and 6-MWT, but lower oxygen saturation at rest and during exercise. Men were 3 times more likely to have restriction and 5.7 times more likely to have a low DLCO. Those who had required mechanical ventilation had lower DLCO and walked less during the 6-MWT. Conclusions: Men were more likely to have lower lung function than women, even after correcting for disease severity and other factors. Patients living at a higher altitude were more likely to have better spirometric patterns and walked farther but had lower DLCO and oxygen saturation.

Common microgeographical selection patterns revealed in four European conifers.

Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.

Combining Climatic and Genomic Data Improves Range-Wide Tree Height Growth Prediction in a Forest Tree.

AbstractPopulation response functions based on climatic and phenotypic data from common gardens have long been the gold standard for predicting quantitative trait variation in new environments. However, prediction accuracy might be enhanced by incorporating genomic information that captures the neutral and adaptive processes behind intrapopulation genetic variation. We used five clonal common gardens containing 34 provenances (523 genotypes) of maritime pine (Pinus pinaster Aiton) to determine whether models combining climatic and genomic data capture the underlying drivers of height growth variation and thus improve predictions at large geographical scales. The plastic component explained most of the height growth variation, probably resulting from population responses to multiple environmental factors. The genetic component stemmed mainly from climate adaptation and the distinct demographic and selective histories of the different maritime pine gene pools. Models combining climate of origin and gene pool of the provenances as well as height-associated positive-effect alleles (PEAs) captured most of the genetic component of height growth and better predicted new provenances compared with the climate-based population response functions. Regionally selected PEAs were better predictors than globally selected PEAs, showing high predictive ability in some environments even when included alone in the models. These results are therefore promising for the future use of genome-based prediction of quantitative traits.

Recording gene expression order in DNA by CRISPR addition of retron barcodes.

Biological processes depend on the differential expression of genes over time, but methods to make physical recordings of these processes are limited. Here we report a molecular system for making time-ordered recordings of transcriptional events into living genomes. We do this through engineered RNA barcodes, based on prokaryotic retrons1, that are reverse transcribed into DNA and integrated into the genome using the CRISPR-Cas system2. The unidirectional integration of barcodes by CRISPR integrases enables reconstruction of transcriptional event timing based on a physical record through simple, logical rules rather than relying on pretrained classifiers or post hoc inferential methods. For disambiguation in the field, we will refer to this system as a Retro-Cascorder.

Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon.

Beneficial microorganisms are used to stimulate the germination of seeds; however, their growth-promoting mechanisms remain largely unexplored. Bacillus subtilis is commonly found in association with different plant organs, providing protection against pathogens or stimulating plant growth. We report that application of B. subtilis to melon seeds results in genetic and physiological responses in seeds that alter the metabolic and developmental status in 5-d and 1-month-old plants upon germination. We analysed mutants in different components of the extracellular matrix of B. subtilis biofilms in interaction with seeds and found cooperation in bacterial colonization of seed storage tissues and growth promotion. Combining confocal microscopy with fluorogenic probes, we found that two specific components of the extracellular matrix, amyloid protein TasA and fengycin, differentially increased the concentrations of reactive oxygen species inside seeds. Further, using electron and fluorescence microscopy and metabolomics, we showed that both TasA and fengycin targeted the oil bodies in the seed endosperm, resulting in specific changes in lipid metabolism and accumulation of glutathione-related molecules. In turn, this results in two different plant growth developmental programmes: TasA and fengycin stimulate the development of radicles, and fengycin alone stimulate the growth of adult plants and resistance in the phylloplane to the fungus Botrytis cinerea. Understanding mechanisms of bacterial growth promotion will enable the design of bespoke growth promotion strains.

Superposición Asma-EPOC: los hallazgos en el estudio EPOC AR / Asthma-COPD Overlap: Findings of the EPOC AR Study

Introducción: Asma y EPOC son enfermedades heterogéneas, algunos pacientes comparten características clínicas de ambas. Existen incertidumbres en los criterios para definir superposición asma-EPOC (ACO) y la prevalencia es entre el 15% y el 25% de la población adulta con obstrucción crónica del flujo aéreo. Motiva este estudio determinar la prevalencia de ACO en Argentina, que es desconocida. Objetivos: Primario: Determinar prevalencia de ACO en el estudio EPOC-AR. Se cundarios: Evaluar y analizar las características clínicas de los pacientes con ACO, la gravedad de los síntomas, la frecuencia y gravedad de exacerbaciones. Describir y comparar el tratamiento entre ACO vs. EPOC puros. Base de datos del estudio EPOC.AR: Espirometrías, asma, atopía o rinitis, síntomas respiratorios: CAT (prueba de evaluación de EPOC) y mMRC (Medical Research Council modificado), frecuencia de exacerbaciones/año previo, comorbilidades y tratamientos. Guías GOLD 2017 para determinar grados de obstrucción espirométrica y Grupos A, B, C y D. Criterios diagnósticos de ACO (comité expertos USA, Europa del Este y Asia-Denver 2015): CRITERIOS MAYORES: 1. Obstrucción persistente (FEV1/FVC pos-BD <70% o LIN) en ≥ 40 años. 2. TBQ ≥ 10 paquetes/año, contaminación ambiental o biomasa. 3. Historia documentada de asma antes de los 40 años o respuesta pos-BD ≥ 400 mL en FEV1. CRITERIOS MENORES: 1. Historia documentada de atopía o rinitis alérgica. 2. Res puesta pos-BD en FEV1 > 200 mL. 3. Recuento de eosinófilos en sangre periférica ≥ 300 células-Ul-1 (no realizado en EPOC.AR). Prueba de Chi-cuadrado, Chi-cuadrado de Pearson, razón de verosimilitud, asociación lineal por lineal. Resultados: EPOC (n498), n95 con criterios de ACO, masculino (53,4%) y edad pro medio 63,6 años. El 1%, sin asma y respuesta BD ≥ 400 mL; el 32,7%, asmáticos (3,6% respuesta BD ≥ 400 mL y el 14,5%, entre 200-400 mL); n23 respuesta BD ≥ 400 mL (4,6%). Prevalen cia ACO: 19,08% (IC 15,6-22,5) y del 2,6% del total de la población de EPOC.AR. En población ACO vs. EPOC, se detectó: menor promedio de edad y de FEV1 pre BD (p < 0,01), mayor respuesta BD (p < 0,05), mayor frecuencia de sibilancias (p < 0,01; IC 2,75-7,64), mayor frecuencia de diagnóstico previo de asma (p < 0,01; IC 3,79-10,05) y el 26,08% tenían antecedentes familiares de asma. Mayor uso de ATB (p < 0,05) e ICS/LABA (p < 0,05; IC 1,1-5,3). Mayor frecuencia de exacerbaciones (12,47%; IC 9,56-15,39) que motivaron indicación de medicación en un 90,48% y 2,49 veces más de alteraciones en actividades diarias y ausentismo laboral. No se registraron diferencias significativas entre pacientes con ACO frente a EPOC puros en frecuencia de grupos A, B, C y D. Conclusiones: La prevalencia de ACO fue del 19,08% en pacientes EPOC del es tudio EPOC.AR; tenían significativamente menor edad, mayor grado de obstrucción, frecuencia de sibilancias, uso de antibióticos/año previo y CI (LABA/CI). Destacamos la importancia de identificar este fenotipo para un tratamiento adecuado por sus impli cancias clínicas, y deterioro en calidad de vida.

Background: Asthma and COPD are heterogeneous diseases, and some patients share clinical features of both conditions. There are uncertainties about the criteria to define asthma-COPD overlap (ACO), and its prevalence is 15-25% in the adult population with chronic airflow obstruction. The purpose of this study was to determine the prevalence of ACO in Argentina, which is unknown. Objectives: Primary: to determine the prevalence of ACO in the EPOC.AR study. Secondary: to evaluate and analyze the clinical features of patients with ACO, the severity of the symptoms, and the frequency and severity of exacerbations. to describe and compare the treatment of ACO with that of pure COPD. Database of the EPOC.AR study: spirometries, asthma, atopy or rhinitis, respiratory symptoms: CAT (COPD Assesment Test) and mMRC (Modified Medical Research Council) scale, frequency of exacerbations/previous year, comorbidities and treatments. 2017 GOLD Guides (Global Initiative for Chronic Obstructive Lung Disease) to determine airflow obstruction degrees and Groups A, B, C, and D. ACO diagnostic criteria (expert committee from USA, East Europe and Asia that took place in Denver, 2015): MAJOR CRITERIA: 1. Persistent obstruction (post-BD [bronchodilator] FEV1/FVC (forced expiratory volume in the first second/forced vital capacity) < 70% or LLN [lower limit of normal] ) in ≥ 40 years. 2. SM (smoking) ≥ 10 packs/year, air pollution or biomass. 3. Documented history of asthma before 40 years or post-BD response ≥ 400 ml in FEV1. MINOR CRITERIA: 1. Documented history of atopy or allergic rhinitis. 2. Post-BD response in FEV1 > 200 ml. 3. Peripheral blood eosinophil count ≥ 300 cells-Ul-1 (not performed in EPOC.AR). Chi-Square Test, Pearson's Chi Square Test, likelihood ratio, linear-by-linear association. Results: COPD (n 498), n 95 with ACO criteria, males (53.4%), mean age 63.6 years. 1% without asthma and BD response ≥ 400 ml; 32.7% asthmatics (3.6% with BD response ≥ 400 ml and 14.5% between 200-400 ml); n 23 with BD response ≥ 400 ml (4.6%). ACO prevalence: 19.08% (CI [Confidence Interval] 15.6-22.5) and 2.6% of the total population of EPOC.AR. In the comparison between the ACO and COPD populations, we detected the following: lower mean age and pre-BD FEV1 (p < 0.01), higher frequency of BD response (p < 0.05), higher frequency of sibilance (p < 0.01; CI 2.75-7.64), higher frequency of previous asthma diagnosis (p < 0.01; CI 3.79-10.05); and 26.08% had family history of asthma. Greater use of ATBs (antibiotics) (p < 0.05) and ICS (inhaled corticosteroids)/ LABA (long-acting beta- adrenergic agonists) (p < 0.05; CI 1.1-5.3). Higher frequency of exacerbations (12.47%; CI 9.56-15.39) that motivated the indication of medication in 90.48% and 2.49 times more alterations in daily activities and absence from work. There weren't any significant differences between patients with ACO and pure COPD regarding frequency of groups A, B, C and D. Conclusions: the prevalence of ACO was 19.08% in the COPD patients of the EPOC. AR study; they were significantly younger, with higher degree of obstruction, frequency of sibilance, use of antibiotics/previous year and inhaled corticosteroids (LABA/IC). We emphasize the importance of identifying this phenotype in order to use a suitable treat ment, given its clinical implications and deterioration in quality of life.