A registry-based population study of the HLA in Québec, Canada.

As part of the worldwide effort to better characterize HLA diversity in populations, we have studied the population of Québec in Canada. This province has been defined by a complex history with multiple founder effects and migration patterns. We analyzed the typing data of 3806 individuals registered in Héma-Québec's Registry, which covered most administrative regions in Québec. Typing information was resolved at the second field level of resolution by next-generation sequencing (NGS) or by Sanger sequencing. We used the HLA-net.eu GENE[RATE] tools to estimate allele and two-locus haplotype frequencies for HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1, as well as Hardy-Weinberg equilibrium (HWE), selective neutrality, and linkage disequilibrium. The chord genetic distance was also calculated between administrative regions and was visualized using non-metric multidimensional scaling (NMDS) analysis. While most individual regions were in HWE, HWE was rejected for the province considered as a whole. Some regions exhibited signatures of selection, mostly toward an excess of heterozygotes. Allele and haplotype frequencies revealed outlier regions that strongly differed from the other regions. NMDS plots also showed differences between regions. The administrative regions of the province of Québec displayed heterogeneity in their HLA profiles. This heterogeneity was attributable to differing allele and haplotype specificities by region. In particular, regions 02-Saguenay-Lac-Saint-Jean and 01-Bas-St-Laurent diverged from the rest of the regions. The urban regions 06-Montréal and 13-Laval were very diversified in their HLA profiles. Together, these results will help optimize donor recruitment strategies in Québec.

Medium-Term Effects of Sprinkler Irrigation Combined with a Single Compost Application on Water and Rice Productivity and Food Safety.

Traditional rice (Oryza sativa L.) management (tillage and flooding) is unsustainable due to soil degradation and the large amount of irrigation water used, an issue which is exacerbated in the Mediterranean region. Therefore, there is a need to explore rice management strategies in order to improve water-use efficiency and ensure its sustainability. Thus, field experiments were conducted to determine the medium-term effects of different irrigation and tillage methods combined with a single compost application on water and rice productivity, as well as food safety in a semiarid Mediterranean region. The management systems evaluated were: sprinkler irrigation in combination with no-tillage (SNT), sprinkler irrigation in combination with conventional tillage (ST), which were implemented in 2015, and flooding irrigation in combination with conventional tillage (FT), and their homologues (SNT-C, ST-C, and FT-C) with single compost application in 2015. In reference to rice grain yield, the highest values were observed under ST treatment with 10 307 and 11 625 kg ha-1 in 2018 and 2019 respectively; whereas between FT and SNT there were no significant differences, with 8 140 kg ha-1 as mean value through the study. Nevertheless, sprinkler irrigation allowed saving 55% of the total amount of water applied in reference to flooding irrigation. Furthermore, the highest arsenic concentration in grains was found under FT but it decreased with compost application (FT-C) and especially with sprinkler irrigation, regardless of tillage management systems. However, sprinkler irrigation favors the cadmium uptake by plants, although this process was reduced under SNT in reference to ST, and especially under amended compost treatments. Therefore, our results suggested that a combination of sprinkler irrigation and compost application, regardless of the tillage system, could be an excellent strategy for rice management for the Mediterranean environment in terms of water and crop productivity as well as food safety.

Combined use of biochar and alternative management systems for imazamox induced pollution control in rice growing environments.

Imazamox (IMZX) is a persistent herbicide having probable risks for non-target organisms in the environment and water contamination. Alternatives to conventional flooding rice production, including biochar amendment, may induce changes in soil properties which can greatly modify the environmental fate of IMZX. This two-year study is the first to evaluate how tillage and irrigation practices, with or without fresh or aged biochar (Bc), that are alternatives to conventional rice production impact IMZX's environmental fate. The treatments were: conventional tillage and flooding irrigation (CTFI), conventional tillage and sprinkler irrigation (CTSI), no-tillage and sprinkler irrigation (NTSI), and the corresponding Bc-amendment treatments (CTFI-Bc, CTSI-Bc, and NTSI-Bc). Fresh and aged Bc amendment decreased IMZX's sorption onto the soil in tillage treatments, with Kf values decreasing 3.7 and 4.2-fold (fresh case) and 1.5 and 2.6-fold (aged case) for CTSI-Bc and CTFI-Bc, respectively. The transition to sprinkler irrigation reduced IMZX persistence. Overall, Bc amendment also reduced chemical persistence with half-life values decreasing 1.6 and 1.5-fold for CTFI and CTSI (fresh year) and 1.1, 1.1, and 1.3-fold for CTFI, CTSI, and NTSI (aged year), respectively. Sprinkler irrigation reduced IMZX leaching by up to a factor of 2.2. The use of Bc as amendment led to a significant decrease in IMZX leaching only under tillage conditions, but notable in particular for the CTFI case where leaching losses were reduced in the fresh year from 80% to 34% and, in the aged year, from 74% to 50%. Hence the change in irrigation from flooding to sprinkler either alone or in combination with the use of Bc (fresh or aged) amendment could be considered an effective way to sharply mitigate IMZX contamination of water in environments where rice is grown, particularly in those managed with tillage.

Effects of Combined Use of Olive Mill Waste Compost and Sprinkler Irrigation on GHG Emissions and Net Ecosystem Carbon Budget under Different Tillage Systems.

Traditional rice (Oryza sativa L.) production by flooding is a source of greenhouse gases (GHG), especially methane. The high consumption of water, as well as the chemical and physical degradation caused by these traditional practices in rice soils, is promoting a decrease in rice production in the Mediterranean area. The aim of this study was to monitor GHG emissions and the net ecosystem carbon balance (NECB) from rice produced with sprinkler irrigation techniques and also assess the impact of olive mill waste compost (C-OW) application and tillage on GHG emissions and the NECB. A field experiment for irrigated rice production was implemented by considering four different treatments: (1) tillage (T); (2) no tillage-direct seeding techniques (DS); (3) application of C-OW followed by tillage (TC); and (4) application of C-OW followed by direct seeding (DSC). The C-OW was only applied in the first year at a dose of 80 Mg ha-1. GHG emissions were monitored over three years in these four treatments in order to estimate the direct (first year) and residual (third year) effects of such practices. The application of C-OW caused an increase of 1.85 times the emission of CO2-C in the TC-DSC compared to the T-DS in the first year. It is noteworthy that the TC treatment was the only one that maintained an emission of CO2-C that was 42% higher than T in the third year. Regardless of the treatments and year of the study, negative values for the cumulative CH4 were found, suggesting that under sprinkler irrigation, CH4 oxidation was the dominant process. A decrease in N2O emissions was observed under direct seeding relative to the tillage treatments, although without significant differences. Tillage resulted in an increase in the global warming potential (GWP) of up to 31% with respect to direct seeding management in the third year, as a consequence of the greater carbon oxidation caused by intensive tillage. DS presented a positive NECB in the accumulation of C in the soil; therefore, it provided a greater ecological benefit to the environment. Thus, under Mediterranean conditions, rice production through a sprinkler irrigation system in combination with direct seeding techniques may be a sustainable alternative for rice crops, reducing their GWP and resulting in a lower carbon footprint. However, the use of C-OW as an organic amendment could increase the GHG emissions from rice fields irrigated by sprinklers, especially under tillage conditions.

Environmental fate and efficiency of bispyribac­sodium in rice soils under conventional and alternative production systems affected by fresh and aged biochar amendment.

Irrigation and tillage practice alternatives to conventional flooding production, with or without organic amendments, are attracting great interest to adapt rice cultivation to climate change. However, they can alter the behaviour of pesticides and their efficiency against weeds. A two-year field experiment was conducted to investigate how the environmental fate and the weed control efficiency (WCE) of bispyribac­sodium (BS) were influenced by biochar produced from holm oak prunings (BHO) testing both the fresh and the aged effects. The treatments were: flooding irrigation and tillage (FT), sprinkler irrigation and tillage (ST), sprinkler irrigation and no-tillage (SNT), and the corresponding homologues with BHO addition (FT-BHO, ST-BHO, and SNT-BHO, respectively). Fresh BHO amendment decreased the sorption of BS onto the soil in all treatments, while, after aging, it also decreased sorption in FT-BHO (1.3-fold) but increased it in SNT-BHO and ST-BHO (1.1-fold). BHO addition reduced BS persistence under non-flooding and flooding incubation conditions, except for FT under the former condition for which t1/2 increased ≈1.5-fold in both years. The addition of BHO led to a decrease in BS leaching from 58.3 % and 44.6 % and from 70.4 % and 58.1 % in ST and FT to 50.1 % and 38.3 % and 63.6 % and 50.3 % in the homologue amended soils for the fresh and aged years, respectively. While fresh BHO addition decreased the WCE of BS in SNT-BHO, ST-BHO, and FT-BHO on average by a factor of 1.5, with aged BHO there was only such a decrease (by a factor of 1.4) in FT-BHO. The use of BHO could be effective for reducing water contamination by BS in flooding or sprinkler irrigation rice farming as long as conventional tillage is used. But it may also contribute to greatly reducing the herbicide's efficiency, although with time to allow aging, this reduction would only persist under conventional flooding production.

Combined use of olive mill waste compost and sprinkler irrigation to decrease the risk of As and Cd accumulation in rice grain.

Sprinkler irrigation has been successfully introduced in rice production as an alternative to the traditional flooding system, allowing water savings and the reduction of As accumulation in the grain. However, the same conditions can increase Cd mobility and grain accumulation, an effect that needs to be countered. A 3-year field experiment was set-up in a Mediterranean region (Extremadura, Spain), to evaluate how the application of compost from olive mill waste (single application, 80 t ha-1), influences the accumulation of As and Cd in the grain under different irrigation regimes. Accumulation of As in the grain was always lower in the sprinkler irrigation when compared with the flooding irrigation, reaching a 5-fold difference in the third year. Compost application did not evidence a clear effect on the As accumulation in the rice grain, but highly significant negative correlations (p < 0.001) were obtained between As content in the grain (total, inorganic, and organic) and the humification parameters in the soil, evidencing the importance of using a mature and stable organic amendment to avoid As accumulation in the grain. Cadmium accumulation in the rice grain decreased in each treatment where compost was applied, relatively to the non-treated counterpart (e.g., from 0.080 to <0.010 mg kg-1, in direct seeding with sprinkler irrigation, in the third year). There were no significant differences in the total inorganic As between treatments with or without compost application, but it was possible to observe an increase in the predominance of the organic As over the more toxic inorganic As, when compost was applied, allowing a decrease in the risk associated to As accumulation. Therefore, the aerobic cultivation of rice, with the simultaneous application of an adequate source of organic matter, can be considered a good solution to cope with the risk of accumulation of As and Cd in the rice grain.

Challenging Ancient DNA Results About Putative HLA Protection or Susceptibility to Yersinia pestis.

In a recent article, Immel et al. (Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, et al. 2021. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol. 38:4059-4076) extracted DNA from 36 individuals dead from plague in Ellwangen, Southern Germany, during the 16th century. By comparing their human leukocyte antigen (HLA) genotypes with those of 50 present-day Ellwangen inhabitants, the authors reported a significant decrease of HLA-B*51:01 and HLA-C*06:02 and a significant increase of HLA-DRB1*13:01/13:02 frequencies from ancient to modern populations. After comparing these frequencies with a larger sample of 8,862 modern Germans and performing simulations of natural selection, they concluded that these changes had been driven by natural selection. In an attempt to provide more evidence on such stimulating results, we explored the HLA frequency patterns over all of Europe, we predicted binding affinities of HLA-B/C/DRB1 alleles to 106,515 Yersinia pestis-derived peptides, and we performed forward simulations of HLA genetic profiles under neutrality. Our analyses do not sustain the conclusions of HLA protection or susceptibility to plague based on ancient DNA.

Paradoxical neuronal hyperexcitability in a mouse model of mitochondrial pyruvate import deficiency.

Neuronal excitation imposes a high demand of ATP in neurons. Most of the ATP derives primarily from pyruvate-mediated oxidative phosphorylation, a process that relies on import of pyruvate into mitochondria occuring exclusively via the mitochondrial pyruvate carrier (MPC). To investigate whether deficient oxidative phosphorylation impacts neuron excitability, we generated a mouse strain carrying a conditional deletion of MPC1, an essential subunit of the MPC, specifically in adult glutamatergic neurons. We found that, despite decreased levels of oxidative phosphorylation and decreased mitochondrial membrane potential in these excitatory neurons, mice were normal at rest. Surprisingly, in response to mild inhibition of GABA mediated synaptic activity, they rapidly developed severe seizures and died, whereas under similar conditions the behavior of control mice remained unchanged. We report that neurons with a deficient MPC were intrinsically hyperexcitable as a consequence of impaired calcium homeostasis, which reduced M-type potassium channel activity. Provision of ketone bodies restored energy status, calcium homeostasis and M-channel activity and attenuated seizures in animals fed a ketogenic diet. Our results provide an explanation for the seizures that frequently accompany a large number of neuropathologies, including cerebral ischemia and diverse mitochondriopathies, in which neurons experience an energy deficit.

Like Wings of a Bird: Functional Divergence and Complementarity between HLA-A and HLA-B Molecules.

Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all human populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence analysis and linear modeling) on 2,909 common and rare HLA-A, HLA-B, and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defense. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intraprotein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.

Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution.

BACKGROUND: Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations' survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. RESULTS: Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. CONCLUSIONS: We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations - like that ascribed to a viral epidemic - exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans' peopling history. We thus propose a model where chimpanzees' MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.

Correction: High-resolution HLA phased haplotype frequencies to predict the success of unrelated donor searches and clinical outcome following hematopoietic stem cell transplantation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

High-resolution HLA phased haplotype frequencies to predict the success of unrelated donor searches and clinical outcome following hematopoietic stem cell transplantation.

HLA matching is a critical factor for successful allogeneic hematopoietic stem cell transplantation. For unrelated donor searches, matching is usually based on high-resolution typing at five HLA loci, looking for a 10/10 match. Some studies have proposed that further matching at the haplotype level could be beneficial for clinical outcome. In this study, we determined the phased haplotypes of 291 patients using family members and segregation analysis. The sum of ranks of the haplotypes carried by patients was used as a surrogate predictor of a successful unrelated donor search. The putative impact of haplotypes was then analyzed in a cohort of 211 recipients transplanted with 10/10 matched unrelated donors. A logistic regression analysis showed a highly significant effect of the haplotypes in the outcome of a search, but we did not find any significant effect on overall survival, graft versus host disease or relapse/progression following HSCT. This study provides useful data for the optimization of unrelated bone marrow donor searches, but does not confirm previous reports that matching at the haplotype level has a clinical impact following HSCT. Due to the extreme polymorphism of HLA genes, further studies are warranted to better understand the many factors at play.

Does NGS typing highlight our understanding of HLA population diversity?: Some good reasons to say yes and a few to say be careful.

This paper discusses the advantages provided by next generation sequencing (NGS) compared to traditional typings or limited sequencing strategies for the characterization of HLA population diversity based on four documented examples. We also comment the limitations of this approach by highlighting pitfalls in interpreting NGS data.

Rif1 Binding and Control of Chromosome-Internal DNA Replication Origins Is Limited by Telomere Sequestration.

The Saccharomyces cerevisiae telomere-binding protein Rif1 plays an evolutionarily conserved role in control of DNA replication timing by promoting PP1-dependent dephosphorylation of replication initiation factors. However, ScRif1 binding outside of telomeres has never been detected, and it has thus been unclear whether Rif1 acts directly on the replication origins that it controls. Here, we show that, in unperturbed yeast cells, Rif1 primarily regulates late-replicating origins within 100 kb of a telomere. Using the chromatin endogenous cleavage ChEC-seq technique, we robustly detect Rif1 at late-replicating origins that we show are targets of its inhibitory action. Interestingly, abrogation of Rif1 telomere association by mutation of its Rap1-binding module increases Rif1 binding and origin inhibition elsewhere in the genome. Our results indicate that Rif1 inhibits replication initiation by interacting directly with origins and suggest that Rap1-dependent sequestration of Rif1 increases its effective concentration near telomeres, while limiting its action at chromosome-internal sites.

Correction to: HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection.

The above article originally published with an incomplete bibliographic information for Bitarello et al. (2016) and presented correctly in this article.

The HLA-B landscape of Africa: Signatures of pathogen-driven selection and molecular identification of candidate alleles to malaria protection.

Human leukocyte antigen (HLA) genes play a key role in the immune response to infectious diseases, some of which are highly prevalent in specific environments, like malaria in sub-Saharan Africa. Former case-control studies showed that one particular HLA-B allele, B*53, was associated with malaria protection in Gambia, but this hypothesis was not tested so far within a population genetics framework. In this study, our objective was to assess whether pathogen-driven selection associated with malaria contributed to shape the HLA-B genetic landscape of Africa. To that aim, we first typed the HLA-A and -B loci in 484 individuals from 11 populations living in different environments across the Sahel, and we analysed these data together with those available for 29 other populations using several approaches including linear modelling on various genetic, geographic and environmental parameters. In addition to relevant signatures of populations' demography and migrations history in the genetic differentiation patterns of both HLA-A and -B loci, we found that the frequencies of three HLA alleles, B*53, B*78 and A*74, were significantly associated with Plasmodium falciparum malaria prevalence, suggesting their increase through pathogen-driven selection in malaria-endemic environments. The two HLA-B alleles were further identified, by high-throughput sequencing, as B*53:01:01 (in putative linkage disequilibrium with one HLA-C allele, C*04:01:01:01) and B*78:01 in all but one individuals tested, making them appropriate candidates to malaria protection. These results highlight the role of environmental factors in the evolution of the HLA polymorphism and open key perspectives for functional studies focusing on HLA peptide-binding properties.

Behaviour of bentazon as influenced by water and tillage management in rice-growing conditions.

Bentazon is a widely used herbicide in rice agroecosystems that has commonly been found in water resources. To assess how tillage and water regimes affect sorption/desorption, dissipation and leaching of bentazon in Mediterranean rice-growing conditions, field experiments were carried out using tillage and flooding (TF), tillage and sprinkler irrigation (TS), no-tillage and sprinkler irrigation (NTS) and long-term no-tillage and sprinkler irrigation (NTS7). After 3 years, the Kd values in TS were 2.3, 1.6 and 1.7 times lower than the values in NTS7, NTS and TF respectively. Greater sorption of bentazon was related to higher contents in total organic carbon and, although to a lesser extent, in humic acids and dissolved organic carbon. The persistence of bentazon was significantly greater under anaerobic (half-life DT50 = 94.1-135 days) than under aerobic (DT50 = 42.4-91.3 days) incubation conditions for all management regimes. Leaching losses of bentazon were reduced from 78 and 74% in TS and TF to 61 and 62% in NTS7 and NTS respectively. The mid- and long-term implementation of sprinkler irrigation in combination with no-tillage could be considered a management system that is effective at reducing water contamination by bentazon in Mediterranean rice-growing agroecosystems. © 2017 Society of Chemical Industry.

Fluorescence circadian imaging reveals a PDF-dependent transcriptional regulation of the Drosophila molecular clock.

Circadian locomotor behaviour is controlled by a pacemaker circuit composed of clock-containing neurons. To interrogate the mechanistic relationship between the molecular clockwork and network communication critical to the operation of the Drosophila circadian pacemaker circuit, we established new fluorescent circadian reporters that permit single-cell recording of transcriptional and post-transcriptional rhythms in brain explants and cultured neurons. Live-imaging experiments combined with pharmacological and genetic manipulations demonstrate that the neuropeptide pigment-dispersing factor (PDF) amplifies the molecular rhythms via time-of-day- and activity-dependent upregulation of transcription from E-box-containing clock gene promoters within key pacemaker neurons. The effect of PDF on clock gene transcription and the known role of PDF in enhancing PER/TIM stability occur via independent pathways downstream of the PDF receptor, the former through a cAMP-independent mechanism and the latter through a cAMP-PKA dependent mechanism. These results confirm and extend the mechanistic understanding of the role of PDF in controlling the synchrony of the pacemaker neurons. More broadly, our results establish the utility of the new live-imaging tools for the study of molecular-neural interactions important for the operation of the circadian pacemaker circuit.

Mapping the HLA diversity of the Iberian Peninsula.

The polymorphism of HLA genes can be used to reconstruct human peopling history. However, this huge diversity impairs successful matching in stem cell transplantation, a situation which has led to the recruitment of millions of donors worldwide. In parallel to the increase of recruitment, registries are progressively relying on information from population genetics to optimize their donor pools in terms of HLA variability. In this study, the HLA data of 65,000 Spanish bone marrow donors were analyzed together with 60,000 Portuguese individuals to provide a comprehensive HLA genetic map of the Iberian Peninsula. The frequencies of many alleles were shown to vary continuously across the Peninsula, either increasing or decreasing from the Mediterranean coast to the Atlantic domain or from the Strait of Gibraltar to the Pyrenees and Bay of Biscay. Similar patterns were observed for several haplotypes. In addition, within some regions neighboring provinces share a close genetic similarity. These results outline the genetic landscape of the Iberian Peninsula, and confirm that the analysis of the HLA polymorphism may reveal relevant signatures of past demographic events even when data from donor registries are used. This conclusion stimulates future developments of the Spanish registry, presented here for the first time.