Natural variation in response to combined water and nitrogen deficiencies in Arabidopsis.

Understanding plant responses to individual stresses does not mean that we understand real world situations, where stresses usually combine and interact. These interactions arise at different levels, from stress exposure to the molecular networks of the stress response. Here, we built an in-depth multi-omics description of plant responses to mild water (W) and nitrogen (N) limitations, either individually or combined, among five genetically different Arabidopsis (Arabidopsis thaliana) accessions. We highlight the different dynamics in stress response through integrative traits such as rosette growth and the physiological status of the plants. We also used transcriptomics and metabolomics profiling during a stage when the plant response was stabilized to determine the wide diversity in stress-induced changes among accessions, highlighting the limited reality of a 'universal' stress response. The main effect of the WxN interaction was an attenuation of the N-deficiency syndrome when combined with mild drought, but to a variable extent depending on the accession. Other traits subject to WxN interactions are often accession-specific. Multi-omics analyses identified a subset of transcript-metabolite clusters that are critical to stress responses but essentially variable according to the genotype factor. Including intra-specific diversity in our descriptions of plant stress response places our findings in perspective.

The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana.

Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudofunctionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. Although such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here, we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions that included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently coexist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.

Interaction between photoperiod and variation in circadian rhythms in tomato.

BACKGROUND: Many biological processes follow circadian rhythmicity and are controlled by the circadian clock. Predictable environmental changes such as seasonal variation in photoperiod can modulate circadian rhythms, allowing organisms to adjust the timing of their biological processes to the time of the year. In some crops such as rice, barley or soybean, mutations in circadian clock genes have altered photoperiod sensitivity, enhancing their cultivability in specific seasons and latitudes. However, how changes in circadian rhythms interact with the perception of photoperiod in crops remain poorly studied. In tomato, the appearance during domestication of mutations in EMPFINDLICHER IM DUNKELROTEN LICHT 1 (EID1, Solyc09g075080) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED GENE 2 (LNK2, Solyc01g068560) delayed both the phase and period of its circadian rhythms. The fact that variation in period and phase are separated in tomato provides an optimal tool to study how these factors affect the perception of photoperiod. RESULTS: Here we develop tomato near isogenic lines carrying combinations of wild alleles of EID1 and LNK2 and show that they recreate the changes in phase and period that occurred during its domestication. We perform transcriptomic profiling of these near isogenic lines under two different photoperiods, and observe that EID1, but not LNK2, has a large effect on how the tomato transcriptome responds to photoperiod. This large effect of EID1 is likely a consequence of the global phase shift elicited by this gene in tomato's circadian rhythms. CONCLUSIONS: Our study shows that changes in phase that occurred during tomato domestication determine photoperiod perception in this species, while changes in period have little effect.

The SCOOP12 peptide regulates defense response and root elongation in Arabidopsis thaliana.

Small secreted peptides are important players in plant development and stress response. Using a targeted in silico approach, we identified a family of 14 Arabidopsis genes encoding precursors of serine-rich endogenous peptides (PROSCOOP). Transcriptomic analyses revealed that one member of this family, PROSCOOP12, is involved in processes linked to biotic and oxidative stress as well as root growth. Plants defective in this gene were less susceptible to Erwinia amylovora infection and showed an enhanced root growth phenotype. In PROSCOOP12 we identified a conserved motif potentially coding for a small secreted peptide. Exogenous application of synthetic SCOOP12 peptide induces various defense responses in Arabidopsis. Our findings show that SCOOP12 has numerous properties of phytocytokines, activates the phospholipid signaling pathway, regulates reactive oxygen species response, and is perceived in a BAK1 co-receptor-dependent manner.

Natural variation at the FRD3 MATE transporter locus reveals cross-talk between Fe homeostasis and Zn tolerance in Arabidopsis thaliana.

Zinc (Zn) is essential for the optimal growth of plants but is toxic if present in excess, so Zn homeostasis needs to be finely tuned. Understanding Zn homeostasis mechanisms in plants will help in the development of innovative approaches for the phytoremediation of Zn-contaminated sites. In this study, Zn tolerance quantitative trait loci (QTL) were identified by analyzing differences in the Bay-0 and Shahdara accessions of Arabidopsis thaliana. Fine-scale mapping showed that a variant of the Fe homeostasis-related FERRIC REDUCTASE DEFECTIVE3 (FRD3) gene, which encodes a multidrug and toxin efflux (MATE) transporter, is responsible for reduced Zn tolerance in A. thaliana. Allelic variation in FRD3 revealed which amino acids are necessary for FRD3 function. In addition, the results of allele-specific expression assays in F1 individuals provide evidence for the existence of at least one putative metal-responsive cis-regulatory element. Our results suggest that FRD3 works as a multimer and is involved in loading Zn into xylem. Cross-homeostasis between Fe and Zn therefore appears to be important for Zn tolerance in A. thaliana with FRD3 acting as an essential regulator.

The HSP90/R2TP assembly chaperone promotes cell proliferation in the intestinal epithelium.

The R2TP chaperone cooperates with HSP90 to integrate newly synthesized proteins into multi-subunit complexes, yet its role in tissue homeostasis is unknown. Here, we generated conditional, inducible knock-out mice for Rpap3 to inactivate this core component of R2TP in the intestinal epithelium. In adult mice, Rpap3 invalidation caused destruction of the small intestinal epithelium and death within 10 days. Levels of R2TP substrates decreased, with strong effects on mTOR, ATM and ATR. Proliferative stem cells and progenitors deficient for Rpap3 failed to import RNA polymerase II into the nucleus and they induced p53, cell cycle arrest and apoptosis. Post-mitotic, differentiated cells did not display these alterations, suggesting that R2TP clients are preferentially built in actively proliferating cells. In addition, high RPAP3 levels in colorectal tumors from patients correlate with bad prognosis. Here, we show that, in the intestine, the R2TP chaperone plays essential roles in normal and tumoral proliferation.

Therapeutic Communities In Latin America: An International Descriptive Study In Different Countries Across Latin America.

OBJECTIVE: In Latin America is not known for certain the quantity or quality of therapeutic communities (TCs) available in the region. The objective of this study is to describe and quantify the quantity and quality of the existing TCs in 5 different countries. DESIGN: A multicenter quantitative description of the TCs was conducted in Argentina, Brazil, Colombia, Mexico and Peru. METHODS: A survey was realized through the TCs regulatory entities of each country that accepted to participate in the study. RESULTS: Of the 285 TCs identified in the 5 countries, 176 (62%) accepted to participate in this study. The TCs quality vas evaluated according to the scoring system stablished by De Leon, finding that 70% of the facilities have scores of 11/12 or 12/12 using these criteria. We also found that the majority of the De Leon criteria are known by more than 90% of the institutions, however, the dimensions of "separation of the community" and "encounter groups between residents" were the least known with 63 and 85% respectively. The main reasons for abandonment of TCs were "not accepting the rules of the institution", "lack of money" and "not feeling comfortable with the facilities". 98% of the TCs provided services to other substance abuse problems, 94% for alcohol and 40% for other types of substances. CONCLUSIONS: The majority of the TCs identified in our sample meet the quality criteria stablished by De Leon, mostly providing services for substance abuse. However, they should put in place additional policies to improve the unfulfilled conditions and investigate the reasons for the dissatisfaction and abandonment of these institutions.

Quality measurers of therapeutic communities for substance dependence: an international collaborative study survey in Latin America.

BACKGROUND: In Latin America, substance related disorders are highly prevalent and one of the treatment strategies is the Therapeutic Communities (TCs), however, in Latin America there is scarce data about this treatment strategies, their quality, drop-out rates and patient satisfaction. METHODS: Based on a previous study in 5 Latin American countries, the TCs who had a score equal or higher than 9 according to the De Leon criteria which are some fundamental items that the TCs should meet, were selected to carry out a descriptive and retrospective study of qualitative and quantitative characteristics of the TCs. RESULTS: Data from 58 TCs in 5 countries were included, with a sample of 1414 patients interviewed, of which most were single men, with no hospitalization history in a therapeutic community. Marijuana was the most commonly substance used in the 30 days prior to hospitalization, with 78% of interviewees referring alcohol consumption in the last 6 months and an average onset of psychoactive substances at 16 years of age. A 79% of the patients interviewed perceived some improvement during their stay in the TCs. The less fulfilled Quality Indicators by the TCs were "Requesting a professional qualification to former addicts that belonged to the program" and "Work as part of the therapeutic program". Among the reasons for discharge found in the database, 44% were due to therapeutic discharge with fulfillment of the treatment plan and 44% withdraws. CONCLUSION: The user satisfaction with TCs, in terms of infrastructure and quality are quite high, as the fulfillment of essential quality items, however, the follow up information to evaluate effectiveness of the treatment is poor or in some cases unknown.

Leaf fructose content is controlled by the vacuolar transporter SWEET17 in Arabidopsis.

In higher plants, soluble sugars are mainly present as sucrose, glucose, and fructose. Sugar allocation is based on both source-to-sink transport and intracellular transport between the different organelles and depends on actual plant requirements. Under abiotic stress conditions, such as nitrogen limitation, carbohydrates accumulate in plant cells. Despite an increasing number of genetic studies, the genetic architecture determining carbohydrate composition is poorly known. Using a quantitative genetics approach, we determined that the carrier protein SWEET17 is a major factor controlling fructose content in Arabidopsis leaves. We observed that when SWEET17 expression is reduced, either by induced or natural variation, fructose accumulates in leaves, suggesting an enhanced storage capacity. Subcellular localization of SWEET17-GFP to the tonoplast and functional expression in Xenopus oocytes showed that SWEET17 is the first vacuolar fructose transporter to be characterized in plants. Physiological studies in planta provide evidence that SWEET17 acts to export fructose out of the vacuole. Overall, our results suggest that natural variation in leaf fructose levels is controlled by the vacuolar fructose transporter SWEET17. SWEET17 is highly conserved across the plant kingdom; thus, these findings offer future possibilities to modify carbohydrate partitioning in crops.

Therapeutic Communities In Latin America: An International Descriptive Study In Different Countries Across Latin America / Comunidades terapéuticas en Latinoamérica: un estudio descriptivo en varios países de Latinoamérica

ABSTRACT Objective: In Latin America is not known for certain the quantity or quality of therapeutic communities (TCs) available in the region. The objective of this study is to describe and quantify the quantity and quality of the existing TCs in 5 different countries. Design: A multicenter quantitative description of the TCs was conducted in Argentina, Brazil, Colombia, Mexico and Peru. Methods: A survey was realized through the TCs regulatory entities of each country that accepted to participate in the study. Results: Of the 285 TCs identified in the 5 countries, 176 (62%) accepted to participate in this study. The TCs quality vas evaluated according to the scoring system stablished by De Leon, finding that 70% of the facilities have scores of 11/12 or 12/12 using these criteria. We also found that the majority of the De Leon criteria are known by more than 90% of the institutions, however, the dimensions of "separation of the community" and "encounter groups between residents" were the least known with 63 and 85% respectively. The main reasons for abandonment of TCs were "not accepting the rules of the institution", "lack of money" and "not feeling comfortable with the facilities". 98% of the TCs provided services to other substance abuse problems, 94% for alcohol and 40% for other types of substances. Conclusions: The majority of the TCs identified in our sample meet the quality criteria stablished by De Leon, mostly providing services for substance abuse. However, they should put in place additional policies to improve the unfulfilled conditions and investigate the reasons for the dissatisfaction and abandonment of these institutions.

RESUMEN Objetivo: En Latinoamérica no se conoce a ciencia cierta la cantidad o la calidad de las comunidades terapéuticas disponibles en los distintos países de la región. El objetivo de este estudio es identificar y describir la cantidad y la calidad de las comunidades terapéuticas existentes en 5 países de la región. Diseño: Se realizó un estudio multicéntrico descriptivo cuantitativo de las comunidades terapéuticas en Argentina, Brasil, Colombia, México y Perú. Métodos: Mediante las entidades reguladoras de las comunidades terapéuticas de cada país, se realizó una encuesta a las que aceptaran participar en el estudio. Resultados: De las 285 comunidades terapéuticas identificadas en los 5 países, 176 (62%) aceptaron participar en el estudio. La calidad de las comunidades terapéuticas se evaluó por las puntuaciones establecidas con los criterios de De León; se encontró que el 70% de las instituciones tienen puntuaciones de 11/12 o 12/12 según estos criterios. También se encontró que cumplen la mayoría de los criterios de De León más del 90% de las instituciones; sin embargo, las dimensiones «separación de la comunidad¼ y «grupos de encuentro entre residentes¼ fueron los menos cumplidos (el 63 y el 85% de las comunidades respectivamente). Las principales razones de abandono de las comunidades terapéuticas fueron no aceptar las normas de la institución, falta de recursos económicos y no sentirse a gusto con ella. El 98% de las comunidades terapéuticas prestaban servicios para problemas de abuso de otras sustancias, el 94% para abuso de alcohol y el 40% para otros tipos de abusos. Conclusiones: La mayoría de las comunidades terapéuticas identificadas en nuestra muestra cumplen los criterios de calidad establecidos por De León, y en su gran mayoría prestan servicios para abuso de sustancias, pero deben instaurarse políticas para mejorar las condiciones no cumplidas e indagar los motivos de las disconformidades y el abandono de estas instituciones.