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How can genetic variability reduce Fagus sylvatica's vulnerability to climate change
No full textGeneral context: Intra-specific diversity plays a key role in species' response to climate change (CC) and their ability to adapt locally through plastic response and/or response to selection. However, the CC velocity is likely to exceed the natural adaptation potential of most species and populations. One solution is to use assisted migration to bring genetic diversity from a region already subject to the expected future climate and therefore able to survive in the new region. Objective: We investigate how the consideration of existing intra-specific variability (due to local adaptation and to plasticity) affects the past and future prediction of vulnerability in beech.
Methods: We used CASTANEA, a process-based model, able to simulate carbon and water fluxes for different species, to assess the vulnerability of beech stands across Europe. The simulation design include several climatic scenarios of the past and the future under CC, with or without within-stand trait variability, and one with assisted migration (allowing the whole range off variation everywhere). We accounted for the genetic variability in three major adaptive traits: (1) the date of budburst (TBB), related to vulnerability to late frosts, (2) the percentage of loss of conductance (PLC), related to vulnerability to cavitation and (3) water use efficiency (WUE), related to vulnerability to carbon starvation. Results: We found that the vulnerability of the optimal average tree in a stand with trait variation is lower than that of stands without variation. In addition, with intra-specific variability, the species distribution is larger, especially in the south of Europe. Finally, in the future under CC, migrated trees are able to grow under conditions further north of the area and contribute to reduce the expected vulnerability without assisted migration
Zucchini vein clearing disease is caused by several lineages within Pseudomonas syringae species complex.
No full textZucchini (Cucurbita pepo) is worldwide affected by Pseudomonas syringae inducing vein clearing, stunting and necroses during plantlet development. A collection of 58 P. syringae strains isolated from diseased zucchini plantlets was characterized by multilocus sequence analysis (MLSA). A subset of 23 strains responsible for vein clearing of zucchini (VCZ) was evaluated for pathogenicity on zucchini and their genomes were sequenced. Host range of six VCZ strains was evaluated on 11 cucurbit species. Most VCZ strains belong to clades 2a and 2b-a within phylogroup 2 of P. syringae species complex and are closely related to other strains previously isolated from cucurbits. Genome analyses revealed diversity among VCZ strains within each clade. One main cluster, once referred to by the invalid pathovar name [peponis], gathers VCZ strains presenting a narrow host range including zucchini and squashes. Other VCZ strains present a large host range including zucchini, squashes, cucumber, melons and in some cases watermelon. The VCZ strain pathogenic features are strongly associated with type III effector repertoires. Presence of avrRpt2 and absence of hopZ5 are associated with a narrow host range, while presence of hopZ5 and absence of avrRpt2 are most generally associated with a large host range. In order to better detect the different clusters identified with whole genome sequence and pathogenicity analyses, we used a specific-k-mers approach to refine the MLSA scheme. Using this novel MLSA scheme to type P. syringae isolates from diseased cucurbits would give insight into distribution of worldwide strains and origin of epidemics
Which recurrent selection scheme to improve mixtures of crop species? Theoretical expectations
No full textIn a context of increasing environmental challenges, there is an emerging demand for plant cultivars that are adapted to cultivation in species mixture. It is thus pressing to look for the optimization of selection schemes to grow species mixtures, and especially recurrent selection schemes which are at the core of the improvement of many plant species. We considered the case of two populations from different species to be improved by recurrent selection for their performances in mixture. We set up an analytical model of performances in mixture. We expressed the expected responses of the performances in mixture to one cycle of selection in the case of a Reciprocal Mixture Ability selection scheme and of two parallel selection schemes aiming to improve General Mixture Abilities or performances in pure stands. We numerically compared these selection schemes when half-sib or topcross progeny families of selection candidates are tested in mixture. Selection in pure stands appeared efficient within a limited range of genetic correlations between pure stand performance and mixture model effects. The Reciprocal Mixture Ability selection scheme was expected to be less efficient than parallel selections for General Mixture Ability in some situations. The last option enables to control the ratio of expected responses of species contributions to the mixture performance without bias when using selection indices. When more than two species are be improved for their performances in mixture, the advantage of parallel selections for General Mixture Ability is even more marked, providing that compensation trends between species are not too prevalent
Inference on extremal dependence in a latent Markov tree model attracted to a Hüsler–Reiss distribution
No full textA Markov tree is a probabilistic graphical model for a random vector by which
conditional independence relations between variables are encoded via an undirected tree
and each node corresponds to a variable. One possible max-stable attractor for such a
model is a Hüsler–Reiss extreme value distribution whose variogram matrix inherits its
structure from the tree, each edge contributing one free dependence parameter. Even if
some of the variables are latent, as can occur on junctions or splits in a river network, the
underlying model parameters are still identifiable if and only if every node corresponding
to a missing variable has degree at least three. Three estimation procedures, based on the
method of moments, maximum composite likelihood, and pairwise extremal coefficients,
are proposed for usage on multivariate peaks over thresholds data. The model and the
methods are illustrated on a dataset of high water levels at several locations on the Seine
network. The structured Hüsler–Reiss distribution is found to fit the observed extremal
dependence well, and the fitted model confirms the importance of flow-connectedness
for the strength of dependence between high water levels, even for locations at large
distance apart
How lactic acid bacteria can improve organoleptic properties of plant-based food through fermentation ?
No full textA Western diet containing 50% of plant-based protein is healthier and would help to reduce the environmental
impacts of food systems to contribute to meeting worldwide protein needs. However, few consumers do like plant-based protein food, 25% of consumers do like taste of soy products. Fermentation by lactic acid bacteria (LAB) is a sustainable and an inexpensive process for the preservation or raw material that can also modify taste. In this work, we screened 278 LAB in order to select strains of interest to ferment soy juice. Our findings showed that the ability of LAB to ferment soy juice is both species- and strain-dependent. We also found that some strains can improve organoleptic properties of fermented soy juices, and the study highlights the diversity of metabolic profiles of LAB in soy juice fermentation. In conclusion, specific LAB can improve plant-based product fermentation rates, organoleptic properties and thus help to promote plant-based proteins in our diet
Relationship between sensory liking for fat, sweet or salt and cardiometabolic diseases: mediating effects of diet and weight status
No full textPurpose[br/]
Previous works have been suggested that individual sensory liking is a predictor of dietary intake and weight status, and may consequently influence development of cardiometabolic diseases (CMDs). We investigated the association between sensory liking for fat-and-salt, fat-and-sweet, sweet or salt and the onset of hypertension, diabetes and cardiovascular diseases (CVDs) over 6 years in adults, and the mediating effects of dietary intake and body mass index (BMI).[br/]
Methods[br/]
We examined the CMDs risk among 41,332 (for CVD and diabetes) and 37,936 (for hypertension) French adults (NutriNet-Santé cohort). Liking scores, individual characteristics, diet and anthropometry were assessed at baseline using questionnaires. Health events were collected during 6 years. Associations between sensory liking and CMDs risk, and the mediating effect of diet and BMI, were assessed using Cox proportional hazards models.[br/]
Results[br/]
Sensory liking for fat-and-salt was associated with an increased risk of diabetes, hypertension and CVD [hazard ratios (HR) for 1-point increment of the sensory score: HR 1.30 (95% CI 1.18, 1.43), HR 1.08 (1.04, 1.13) and HR 1.10 (1.02, 1.19), respectively]. BMI and dietary intake both explained 93%, 98% and 70%, of the overall variation of liking for fat-and-salt liking in diabetes, hypertension and CVD, respectively. Liking for fat-and-sweet and liking for salt were also associated with an increased risk of diabetes [HR 1.09 (1.01, 1.17) and HR 1.09 (1.01, 1.18), respectively], whereas liking for sweet was associated with a decreased risk [HR 0.76 (0.69, 0.84)].[br/]
Conclusions[br/]
Higher liking for fat-and-salt is significantly associated with CMDs risk, largely explained by dietary intake and BMI. Our findings may help to guide effective targeted measures in prevention
Diversity of the metabolic profiles of a broad range of lactic acid bacteria in soy juice fermentation
No full textThis study explores the ability of lactic acid bacteria (LAB) to ferment soy juice. The ability of 276 LAB strains
from 25 species to ferment the principal soy carbohydrates, sucrose, raffinose or stachyose was tested in synthetic media and a soy juice. Fermented soy juices (FSJs) were characterized for their odor. Selected FSJs were characterized by targeted metabolomics. All Streptococcus, 83% of Leuconostoc and Lactobacillus and 41% of Lactococcus strains were sucrose-positive, while only 36% of all the LAB strains tested were raffinose-positive and 6% stachyose-positive. Nearly all (97%) the sucrose-positive strains fermented soy juice, indicating that an ability to use sucrose is a good criterion to select strains for soy juice fermentation. Among the most efficient acidifying strains, 46 FSJs had an odor deemed to be acceptable. FSJ composition was dependent on both species and strains: 17/46 strains deglycosylated soy juice isoflavones, the 27 S. thermophilus strains converted a mean 4.4 ± 0.1 g/L of sucrose into 3.0 ± 0.1 g/L of lactic acid versus 5.2 ± 0.1 g/L into 2.2 ± 0.1 g/L for the 18 Lactobacillus and one Lactococcus strains. This study highlights the diversity of the metabolic profiles of LAB strains in soy juice fermentation
Digging Deeper for Agricultural Resources, the Value of Deep Rooting
No full textIn the quest for sustainable intensification of crop production, we discuss the option of extending the root depth of crops to increase the volume of soil exploited by their root systems. We discuss the evidence that deeper rooting can be obtained by appropriate choice of crop species, by plant breeding, or crop management and its potential contributions to production and sustainable development goals. Many studies highlight the potentials of deeper rooting, but we evaluate its contributions to sustainable intensification of crop production, the causes of the limited research into deep rooting of crops, and the research priorities to fill the knowledge gap
Dysfunction of oskyddad causes harlequin-type ichthyosis-like defects in Drosophila Melanogaster
No full textPrevention of desiccation is a constant challenge for terrestrial organisms. Land insects have an extracellular coat, the cuticle, that plays a major role in protection against exaggerated water loss. Here, we report that the ABC transporter Oskyddad (Osy)-a human ABCA12 paralog-contributes to the waterproof barrier function of the cuticle in the fruit fly Drosophila melanogaster. We show that the reduction or elimination of Osy function provokes rapid desiccation. Osy is also involved in defining the inward barrier against xenobiotics penetration. Consistently, the amounts of cuticular hydrocarbons that are involved in cuticle impermeability decrease markedly when Osy activity is reduced. GFP-tagged Osy localises to membrane nano-protrusions within the cuticle, likely pore canals. This suggests that Osy is mediating the transport of cuticular hydrocarbons (CHC) through the pore canals to the cuticle surface. The envelope, which is the outermost cuticle layer constituting the main barrier, is unaffected in osy mutant larvae. This contrasts with the function of Snu, another ABC transporter needed for the construction of the cuticular inward and outward barriers, that nevertheless is implicated in CHC deposition. Hence, Osy and Snu have overlapping and independent roles to establish cuticular resistance against transpiration and xenobiotic penetration. The osy deficient phenotype parallels the phenotype of Harlequin ichthyosis caused by mutations in the human abca12 gene. Thus, it seems that the cellular and molecular mechanisms of lipid barrier assembly in the skin are conserved during evolution
Importance of the major histocompatibility complex (Swine Leukocyte Antigen) in swine health and biomedical Research
No full textIn pigs, the major histocompatibility complex (MHC), or swine leukocyte antigen (SLA) complex, maps to Sus scrofa chromosome 7. It consists of three regions, the class I and class III regions mapping to 7p1.1 and the class II region mapping to 7q1.1. The swine MHC is divided by the centromere, which is unique among mammals studied to date. The SLA complex spans between 2.4 and 2.7 Mb, depending on haplotype, and encodes approximately 150 loci, with at least 120 genes predicted to be functional. Here we update the whole SLA complex based on the Sscrofa11.1 build and annotate the organization for all recognized SLA genes and their allelic sequences. We present SLA nomenclature and typing methods and discuss the expression of SLA proteins, as well as their role in antigen presentation and immune, disease, and vaccine responses. Finally, we explore the role of SLA genes in transplantation and xenotransplantation and their importance in swine biomedical models