Kernel methods for phenotyping complex plant architecture

The Quantitative Trait Loci (QTL) mapping of plant architecture is a critical step for understanding the genetic determinism of plant architecture. Previous studies adopted simple measurements, such as plant-height, stem-diameter and branching-intensity for QTL mapping of plant architecture. Many of these quantitative traits were generally correlated to each other, which give rise to statistical problem in the detection of QTL. We aim to test the applicability of kernel methods to phenotyping inflorescence architecture and its QTL mapping. We first test Kernel Principal Component Analysis (KPCA) and Support Vector Machines (SVM) over an artificial dataset of simulated inflorescences with different types of flower distribution, which is coded as a sequence of flower-number per node along a shoot. The ability of discriminating the different inflorescence types by SVM and KPCA is illustrated. We then apply the KPCA representation to the real dataset of rose inflorescence shoots (n=1460) obtained from a 98 F1 hybrid mapping population. We find kernel principal components with high heritability (>0.7), and the QTL analysis identifies a new QTL, which was not detected by a trait-by-trait analysis of simple architectural measurements. The main tools developed in this paper could be use to tackle the general problem of QTL mapping of complex (sequences, 3D structure, graphs) phenotypic traits

Ritmos biológicos y uso del tiempo en una comunidad mapuche aislada

Este proyecto persigue establecer la influencia de factores ambientales y culturales sobre los patrones temporales de poblaciones humanas. Estudiamos la comunidad mapuche de Milaín Currical (Neuquén) en distintas estaciones, registrando el ciclo diario sueño-vigilia y otros parámetros relacionados con cambios cíclicos en el comportamiento y la fisiología de los habitantes. El objetivo es lograr una explicación englobadora del uso del tiempo en poblaciones bajo distintas condiciones ambientales. Asimismo, se registró la variación estacional en los procesos migratorios y en variables epidemiológicas. Las variables ambientales (fotoperíodo, temperatura, lluvias) exhibieron ciclos anuales de gran amplitud. La comunidad presenta variaciones estacionales con claras diferencias entre verano e invierno, incluyendo cambios de horario de sus actividades y del ciclo sueño-vigilia, que correlacionan con variaciones ambientales. Las consultas médicas tuvieron un pico hacia el final del invierno. La comunidad realiza una migración anual entre las tierras de veranada y de invernada, que puede ser correlacionada con las variables ambientales, en particular el fotoperíodo. El estudio de comunidades sujetas a cambios temporales profundos en el ambiente (sin sincronizadores artificiales) ofrece un excelente modelo para la investigación del sistema cronobiológico humano.Asociación de Antropología Biológica de la República Argentin

Ritmos biológicos y uso del tiempo en una comunidad mapuche aislada

Este proyecto persigue establecer la influencia de factores ambientales y culturales sobre los patrones temporales de poblaciones humanas. Estudiamos la comunidad mapuche de Milaín Currical (Neuquén) en distintas estaciones, registrando el ciclo diario sueño-vigilia y otros parámetros relacionados con cambios cíclicos en el comportamiento y la fisiología de los habitantes. El objetivo es lograr una explicación englobadora del uso del tiempo en poblaciones bajo distintas condiciones ambientales. Asimismo, se registró la variación estacional en los procesos migratorios y en variables epidemiológicas. Las variables ambientales (fotoperíodo, temperatura, lluvias) exhibieron ciclos anuales de gran amplitud. La comunidad presenta variaciones estacionales con claras diferencias entre verano e invierno, incluyendo cambios de horario de sus actividades y del ciclo sueño-vigilia, que correlacionan con variaciones ambientales. Las consultas médicas tuvieron un pico hacia el final del invierno. La comunidad realiza una migración anual entre las tierras de veranada y de invernada, que puede ser correlacionada con las variables ambientales, en particular el fotoperíodo. El estudio de comunidades sujetas a cambios temporales profundos en el ambiente (sin sincronizadores artificiales) ofrece un excelente modelo para la investigación del sistema cronobiológico humano.Asociación de Antropología Biológica de la República Argentin

Wnt signaling is boosted during intestinal regeneration by a CD44-positive feedback loop

Enhancement of Wnt signaling is fundamental for stem cell function during intestinal regeneration. Molecular modules control Wnt activity by regulating signal transduction. CD44 is such a positive regulator and a Wnt target gene. While highly expressed in intestinal crypts and used as a stem cell marker, its role during intestinal homeostasis and regeneration remains unknown. Here we propose a CD44 positive-feedback loop that boosts Wnt signal transduction, thus impacting intestinal regeneration. Excision of Cd44 in Cd44$^{fl/fl}$;VillinCreER$^{T2}$ mice reduced Wnt target gene expression in intestinal crypts and affected stem cell functionality in organoids. Although the integrity of the intestinal epithelium was conserved in mice lacking CD44, they were hypersensitive to dextran sulfate sodium, and showed more severe inflammation and delayed regeneration. We localized the molecular function of CD44 at the Wnt signalosome, and identified novel DVL/CD44 and AXIN/CD44 complexes. CD44 thus promotes optimal Wnt signaling during intestinal regeneration

Impacts of climate change on plant diseases – opinions and trends

There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases in the coming decades. This review addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health. Sudden Oak Death is used as an introductory case study: Californian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronicity between host cambium activity and pathogen colonization rate. A summary of observed and predicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Prediction and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertainty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to interdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in mountain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (including our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycorrhiza, using long-term and large-scale datasets and considering various plant disease control methods

Temperature extremes of 2022 reduced carbon uptake by forests in Europe

The year 2022 saw record breaking temperatures in Europe during both summer and fall. Similar to the recent 2018 drought, close to 30% (3.0 million km2) of the European continent was under severe summer drought. In 2022, the drought was located in central and southeastern Europe, contrasting the Northern-centered 2018 drought. We show, using multiple sets of observations, a reduction of net biospheric carbon uptake in summer (56-62 TgC) over the drought area. Specific sites in France even showed a widespread summertime carbon release by forests, additional to wildfires. Partial compensation (32%) for the decreased carbon uptake due to drought was offered by a warm autumn with prolonged biospheric carbon uptake. The severity of this second drought event in 5 years suggests drought-induced reduced carbon uptake to no longer be exceptional, and important to factor into Europe’s developing plans for net-zero greenhouse gas emissions that rely on carbon uptake by forests

Observation of an Excited Bc+ State

Using pp collision data corresponding to an integrated luminosity of 8.5 fb-1 recorded by the LHCb experiment at center-of-mass energies of s=7, 8, and 13 TeV, the observation of an excited Bc+ state in the Bc+π+π- invariant-mass spectrum is reported. The observed peak has a mass of 6841.2±0.6(stat)±0.1(syst)±0.8(Bc+) MeV/c2, where the last uncertainty is due to the limited knowledge of the Bc+ mass. It is consistent with expectations of the Bc∗(2S31)+ state reconstructed without the low-energy photon from the Bc∗(1S31)+→Bc+γ decay following Bc∗(2S31)+→Bc∗(1S31)+π+π-. A second state is seen with a global (local) statistical significance of 2.2σ (3.2σ) and a mass of 6872.1±1.3(stat)±0.1(syst)±0.8(Bc+) MeV/c2, and is consistent with the Bc(2S10)+ state. These mass measurements are the most precise to date

Genetic analysis of the flowering date and number of petals in rose

Rose is the ornamental species with the highest financial impact. Floral traits such as the number of petals and the date of flowering are major characteristics of ornamental plants. Our objective is to study the genetic determinism of floral traits: date of flowering and number of petals, which are a major issue for rose breeders. The study was conducted on two interspecific populations interconnected by the male parent: H190 x hybrid of Rosa wichurana (referred to as HW) and “The Fairy” x hybrid of Rosa wichurana (referred to as FW). The number of petals and the date of flowering were scored over 2 and 8 years, respectively. A new HW genetic map covering 468 cM and the already available genetic map of the FW population (Kawamura et al. TAG Theor Appl Genet 122:661–675, 2011) were used for the genetic determinism studies. In each population, half of the hybrids exhibited single flowers (less than 10 petals), whereas the other half revealed double flowers. The number of petals is controlled by the NP gene located on LG3. Additionally, we detected two new major quantitative trait loci (QTLs) on LG2 and LG5, close to RoAP1b and RoRAG, respectively, two genes involved in the control of floral identity. For the date of flowering, three QTLs with a major effect and high stability between years were found on linkage groups 3, 4, and 6, indicating a high stability of QTLs to the changing environment. Candidate genes underlying these QTLs were investigated and key genes were identified. These major QTLs were linked to candidate genes, i.e., the identified QTL on LG4 was linked to RoFT, the one on LG3 to genes involved in gibberellin pathways, and the one on LG6 to RoFD. These QTLs, which are very stable over time, are good candidates to develop markers applicable in marker-assisted selection (MAS)

Atmospheric deposition, CO2, and change in the land carbon sink

Concentrations of atmospheric carbon dioxide (CO2) have continued to increase whereas atmospheric deposition of sulphur and nitrogen has declined in Europe and the USA during recent decades. Using time series of flux observations from 23 forests distributed throughout Europe and the USA, and generalised mixed models, we found that forest-level net ecosystem production and gross primary production have increased by 1% annually from 1995 to 2011. Statistical models indicated that increasing atmospheric CO2 was the most important factor driving the increasing strength of carbon sinks in these forests. We also found that the reduction of sulphur deposition in Europe and the USA lead to higher recovery in ecosystem respiration than in gross primary production, thus limiting the increase of carbon sequestration. By contrast, trends in climate and nitrogen deposition did not significantly contribute to changing carbon fluxes during the studied period. Our findings support the hypothesis of a general CO2-fertilization effect on vegetation growth and suggest that, so far unknown, sulphur deposition plays a significant role in the carbon balance of forests in industrialized regions. Our results show the need to include the effects of changing atmospheric composition, beyond CO2, to assess future dynamics of carbon-climate feedbacks not currently considered in earth system/climate modelling.Peer reviewe