Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop

BACKGROUND: Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10-13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. RESULTS: Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2-6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 "subgenomes" after their divergence approximately 3.8-4.6 million years ago and reveals single-nucleotide variants that may underlie their differences. CONCLUSIONS: This assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production

Euclid preparation TBD. The effect of baryons on the Halo Mass Function

The Euclid photometric survey of galaxy clusters stands as a powerful cosmological tool, with the capacity to significantly propel our understanding of the Universe. Despite being sub-dominant to dark matter and dark energy, the baryonic component in our Universe holds substantial influence over the structure and mass of galaxy clusters. This paper presents a novel model to precisely quantify the impact of baryons on galaxy cluster virial halo masses, using the baryon fraction within a cluster as proxy for their effect. Constructed on the premise of quasi-adiabaticity, the model includes two parameters calibrated using non-radiative cosmological hydrodynamical simulations and a single large-scale simulation from the Magneticum set, which includes the physical processes driving galaxy formation. As a main result of our analysis, we demonstrate that this model delivers a remarkable one percent relative accuracy in determining the virial dark matter-only equivalent mass of galaxy clusters, starting from the corresponding total cluster mass and baryon fraction measured in hydrodynamical simulations. Furthermore, we demonstrate that this result is robust against changes in cosmological parameters and against varying the numerical implementation of the sub-resolution physical processes included in the simulations. Our work substantiates previous claims about the impact of baryons on cluster cosmology studies. In particular, we show how neglecting these effects would lead to biased cosmological constraints for a Euclid-like cluster abundance analysis. Importantly, we demonstrate that uncertainties associated with our model, arising from baryonic corrections to cluster masses, are sub-dominant when compared to the precision with which mass-observable relations will be calibrated using Euclid, as well as our current understanding of the baryon fraction within galaxy clusters

Euclid preparation: XXIV. Calibration of the halo mass function in (?)CDM cosmologies

Euclid s photometric galaxy cluster survey has the potential to be a very competitive cosmological probe. The main cosmological probe with observations of clusters is their number count, within which the halo mass function (HMF) is a key theoretical quantity. We present a new calibration of the analytic HMF, at the level of accuracy and precision required for the uncertainty in this quantity to be subdominant with respect to other sources of uncertainty in recovering cosmological parameters from Euclid cluster counts. Our model is calibrated against a suite of N-body simulations using a Bayesian approach taking into account systematic errors arising from numerical effects in the simulation. First, we test the convergence of HMF predictions from different N-body codes, by using initial conditions generated with different orders of Lagrangian Perturbation theory, and adopting different simulation box sizes and mass resolution. Then, we quantify the effect of using different halo finder algorithms, and how the resulting differences propagate to the cosmological constraints. In order to trace the violation of universality in the HMF, we also analyse simulations based on initial conditions characterised by scale-free power spectra with different spectral indexes, assuming both Einsteinde Sitter and standard CDM expansion histories. Based on these results, we construct a fitting function for the HMF that we demonstrate to be sub-percent accurate in reproducing results from 9 different variants of the CDM model including massive neutrinos cosmologies. The calibration systematic uncertainty is largely sub-dominant with respect to the expected precision of future massobservation relations; with the only notable exception of the effect due to the halo finder, that could lead to biased cosmological inference

Euclid preparation. XXIV. Calibration of the halo mass function in Λ(ν)\Lambda(\nu)CDM cosmologies

Euclid's photometric galaxy cluster survey has the potential to be a very competitive cosmological probe. The main cosmological probe with observations of clusters is their number count, within which the halo mass function (HMF) is a key theoretical quantity. We present a new calibration of the analytic HMF, at the level of accuracy and precision required for the uncertainty in this quantity to be subdominant with respect to other sources of uncertainty in recovering cosmological parameters from Euclid cluster counts. Our model is calibrated against a suite of N-body simulations using a Bayesian approach taking into account systematic errors arising from numerical effects in the simulation. First, we test the convergence of HMF predictions from different N-body codes, by using initial conditions generated with different orders of Lagrangian Perturbation theory, and adopting different simulation box sizes and mass resolution. Then, we quantify the effect of using different halo-finder algorithms, and how the resulting differences propagate to the cosmological constraints. In order to trace the violation of universality in the HMF, we also analyse simulations based on initial conditions characterised by scale-free power spectra with different spectral indexes, assuming both Einstein--de Sitter and standard $\Lambda$CDM expansion histories. Based on these results, we construct a fitting function for the HMF that we demonstrate to be sub-percent accurate in reproducing results from 9 different variants of the $\Lambda$CDM model including massive neutrinos cosmologies. The calibration systematic uncertainty is largely sub-dominant with respect to the expected precision of future mass-observation relations; with the only notable exception of the effect due to the halo finder, that could lead to biased cosmological inference.Comment: 24 pages, 21 figures, 5 tables, 3 appendixes

Euclid preparation TBD. The effect of baryons on the Halo Mass Function

The Euclid photometric survey of galaxy clusters stands as a powerful cosmological tool, with the capacity to significantly propel our understanding of the Universe. Despite being sub-dominant to dark matter and dark energy, the baryonic component in our Universe holds substantial influence over the structure and mass of galaxy clusters. This paper presents a novel model to precisely quantify the impact of baryons on galaxy cluster virial halo masses, using the baryon fraction within a cluster as proxy for their effect. Constructed on the premise of quasi-adiabaticity, the model includes two parameters calibrated using non-radiative cosmological hydrodynamical simulations and a single large-scale simulation from the Magneticum set, which includes the physical processes driving galaxy formation. As a main result of our analysis, we demonstrate that this model delivers a remarkable one percent relative accuracy in determining the virial dark matter-only equivalent mass of galaxy clusters, starting from the corresponding total cluster mass and baryon fraction measured in hydrodynamical simulations. Furthermore, we demonstrate that this result is robust against changes in cosmological parameters and against varying the numerical implementation of the sub-resolution physical processes included in the simulations. Our work substantiates previous claims about the impact of baryons on cluster cosmology studies. In particular, we show how neglecting these effects would lead to biased cosmological constraints for a Euclid-like cluster abundance analysis. Importantly, we demonstrate that uncertainties associated with our model, arising from baryonic corrections to cluster masses, are sub-dominant when compared to the precision with which mass-observable relations will be calibrated using Euclid, as well as our current understanding of the baryon fraction within galaxy clusters.Comment: 18 pages, 10 figures, 4 tables, 1 appendix, abstract abridged for arXiv submissio

Description d’un Systeme Informatique dans un Laboratoire d’Analyses Biologiques d’Urgence

Peer Reviewe

Allopregnanolone and mood disorders

Certain women experience negative mood symptoms during the menstrual cycle and progesterone addition in estrogen treatments. In women with PMDD increased negative mood symptoms related to allopregnanolone increase during the luteal phase of ovulatory menstrual cycles. In anovulatory cycles no symptom or sex steroid increase occurs. This is unexpected as positive modulators of the GABA-A receptor are generally increasing mood. This paradoxical effect has brought forward a hypothesis that the symptoms are provoked by allopregnanolone the GABA-A receptor system. GABA-A is the major inhibitory system in the brain. Positive modulators of the GABA-A receptor include the progesterone metabolites allopregnanolone and pregnanolone, benzodiazepines, barbiturates, and alcohol. GABA-A receptor modulators are known, in low concentrations to induce adverse, anxiogenic effects whereas in higher concentrations show beneficial, calming properties. Positive GABA-A receptor modulators induce strong paradoxical effects e.g. negative mood in 3-8% of those exposed, while up to 25% have moderate symptoms thus similar as the prevalence of PMDD, 3-8% among women in fertile ages, and up to 25% have moderate symptoms of premenstrual syndrome (PMS). The mechanism behind paradoxical reaction might be similar among them who react on positive GABA-A receptor modulators and in women with PMDD. In women the severity of these mood symptoms are related to the allopregnanolone serum concentrations in an inverted U-shaped curve. Negative mood symptoms occur when the serum concentration of allopregnanolone is similar to endogenous luteal phase levels, while low and high concentrations have less effect on mood. Low to moderate progesterone/allopregnanolone concentrations in women increases the activity in the amygdala (measured with fMRI) similar to the changes seen during anxiety reactions. Higher concentrations give decreased amygdala activity similar as seen during benzodiazepine treatment with calming anxiolytic effects. Patients with PMDD show decreased sensitivity in GABA-A receptor sensitivity to diazepam and pregnanolone while increased sensitivity to allopregnanolone. This agrees with findings in animals showing a relation between changes in alpha4 and delta subunits of the GABA-A receptor and anxiogenic effects of allopregnanolone. These findings suggest that negative mood symptoms in women with PMDD are caused by the paradoxical effect of allopregnanolone mediated via the GABA-A recepto

Allelism tests between the rust resistance gene present in common bean cultivar Ouro Negro and genes Ur-5 and Ur-11

The pathogenic variability of the fungus Uromyces appendiculatus is an obstacle for the creation of rust‐resistant common bean (Phaseolus vulgaris L.) varieties. Gene pyramiding is an alternative strategy for the development of varieties with durable resistance. However, to reach this goal it is important to identify different genes with ample resistance spectra. Cultivars Ouro Negro, Mexico 309 and Belmidak RR‐3 have been shown to be resistant to several rust races identified in the state of Minas Gerais, Brazil. Ouro Negro is the only rust resistance source being used in the BIOAGRO/Universidade Federal de Viçosa (UFV) breeding programme, which aims at pyramiding resistance genes in the ‘carioca‐type’ cultivar Rudá. It would be also interesting to use Mexico 309 (Ur‐5) and Belmidak RR‐3 (Ur‐11) in the breeding programme. However, there is no available information on the possible allelic relationships between the Ouro Negro resistance gene and Ur‐5 and Ur‐11. This work aimed at: (1) determining the allelic relationship between the Ouro Negro resistance gene and Ur‐5 and Ur‐11; and (2) evaluating a random amplified polymorphic DNA (RAPD) marker previously reported as being linked to Ur‐11, in populations from crosses between Belmidak RR‐3 and Rudá. The allelism tests confirmed that the Ouro Negro rust resistance gene is distinct from Ur‐5 and Ur‐11 and the molecular analyses confirmed that the RAPD marker can be used in our breeding programme to develop ‘carioca‐type’ cultivars with the Ur‐11 gene