Identification de génotypes-S chez les descendances d’amandiers par les méthodes NEPHGE et PCR

Almond (P. amygdalus Batsch) shows a gametophytic self-incompatibility system controlled by a multiallelic locus, known as the locus S. Self-compatibility has been related to Sf allele presence and this trait has become a priority in the main almond breeding programs and the search for new cultivars is focused on the evaluation of desirable traits in autogamous seedlings. Traditionally, self-compatibility has been assessed in almond by laborious and time consuming methods, such as determination of fruit set in bagged branches or microscopic observation of pollen tube growth after self-pollination in laboratory conditions. Recently, molecular methods have been developed to assess the S-genotype, such as the identification of stylar S-RNases by NEPHGE (non equilibrium pH gradient electro focusing) and the use of conserved and specific PCR primers for the amplification of fragments from the different S alleles. In this research we applied these molecular methods for the S-genotype assessment in two almond breeding progenies, from the crosses of the self-compatible elite selection 'G-2-25' (S11Sf) of the CITA, as female parent, with two self-incompatible cultivars, 'Desmayo Largueta' (S1S25) and 'Marcona' (S11S12), as male parents. Although no discrepancies were found between the two methods, PCR was more suitable than NEPHGE for S-genotype assessment. PCR is easier to optimize, cheaper, more precise and reliable. It is also possible to assess the genotype sooner than with NEPHGE, as flowers are not required for the determination, allowing an earlier elimination of the seedlings. In the 'G-2-25' (S11Sf) x 'Marcona' (S11S12) progeny, the ratio of genotypes was 42% S11S12 and 58% SfS12, approaching the Mendelian laws of transmission in spite of the slightly higher proportion of self-compatible seedlings. In the other family, 'G-2-25' (S11Sf) x 'Desmayo Largueta' (S1S25), four S-genotypes are possible, but the ratios obtained were 21% S1S11, 53% S1Sf, 0% S11S25, and 26% SfS25. These results showed that pollen carrying the S25 allele had only a 26% fertilization success as compared to 73 of pollen carrying the S1 allele. The absence of S11S25 seedlings may imply the expression of a homozygous lethal trait in these zygotes and the distortion of the Mendelian ratiosL’amandier (P. amygdalus Batsch) montre un système d’auto-incompatibilité gamétophytique contrôlé par un locus multiallélique, connu comme locus S. L’auto-compatibilité a été reliée à la présence de l’allèle Sf et cette caractéristique est devenue une priorité pour les principaux programmes d’amélioration de l’amandier, et ainsi la recherche de nouveaux cultivars se focalise sur l’évaluation des caractères désirables pour les plants autogames. Traditionnellement, l’auto-compatibilité a été évaluée chez les amandiers par des méthodes laborieuses et prenant beaucoup de temps, telles que la détermination de la nouaison pour les branches ensachées ou l’observation microscopique de la croissance des tubes de pollen après auto-pollinisation en conditions de laboratoire. Récemment, des méthodes moléculaires ont été développées pour évaluer le génotype-S, telles que l’identification de S-RNases stylaires par NEPHGE (non equilibrium pH gradient electro-focusing) et l’utilisation d’amorces PCR conservées et spécifiques pour l’amplification de fragments provenant de différents allèles-S. Pour cette recherche nous avons appliqué ces méthodes moléculaires pour l’évaluation du génotype-S chez les descendances améliorées de deux amandiers, à partir des croisements d’une sélection d’élite auto-compatible 'G-2-25' (S11Sf) du CITA, comme parent femelle, avec deux cultivars auto-incompatibles, 'Desmayo Largueta' (S1S25) et 'Marcona' (S11S12), comme parents mâles. Bien que l’on n’ait pas trouvé de divergences entre les deux méthodes, la PCR était plus adéquate que NEPHGE pour l’évaluation du génotype-S. La PCR est plus facile à optimiser, moins onéreuse, plus précise et fiable. Il est également possible d’évaluer le génotype plus tôt qu’avec NEPHGE, étant donné qu’il n’est pas nécessaire d’obtenir des fleurs pour la détermination, permettant ainsi une élimination précoce des plants. Dans la descendance de 'G-2-25' (S11Sf) 'Marcona' (S11S12), le quotient des génotypes était de 42% S11S12 et de 58% SfS12, se rapprochant des lois mendéliennes de transmission malgré la proportion légèrement plus élevée de plants auto-compatibles. Pour l’autre famille, 'G-2-25' (S11Sf) 'Desmayo Largueta' (S1S25), quatre génotypes-S sont possibles, mais les quotients obtenus étaient de 21% S1S11, 53% S1Sf, 0% S11S25, et 26% SfS25. Ces résultats montrent que le pollen portant l’allèle S25 avait une réussite de fertilisation d’uniquement 26% comparée à 73 pour le pollen portant l'allèle S1. L’absence de plants S11S25 pourrait faire penser à l’expression d’un caractère létal homozygote chez ces zygotes et à la distortion des quotients mendélien

Local group star formation in warm and self-interacting dark matter cosmologies

The nature of the dark matter can affect the collapse time of dark matter haloes, and can therefore be imprinted in observables such as the stellar population ages and star formation histories of dwarf galaxies. In this paper, we use high-resolution hydrodynamical simulations of Local Group-analogue (LG) volumes in cold dark matter (CDM), sterile neutrino warm dark matter (WDM) and self-interacting dark matter (SIDM) models with the EAGLE galaxy formation code to study how galaxy formation times change with dark matter model. We are able to identify the same haloes in different simulations, since they share the same initial density field phases. We find that the stellar mass of galaxies depends systematically on resolution, and can differ by as much as a factor of 2 in haloes of a given dark matter mass. The evolution of the stellar populations in SIDM is largely identical to that of CDM, but in WDM early star formation is instead suppressed. The time at which LG haloes can begin to form stars through atomic cooling is delayed by ∼200 Myr in WDM models compared to CDM. It will be necessary to measure stellar ages of old populations to a precision of better than 100 Myr, and to address degeneracies with the redshift of reionization – and potentially other baryonic processes – in order to use these observables to distinguish between dark matter models

Candidemia and its risk factors in neonates and children

Objectives: The present study was conducted to raise attention to the frequency of Candida spp. and evaluation of risk factors of candidemia in hospitalized neonates and children. Methods: Identification of Candida at species level was done using the PCR-RFLP method. The Candida albicans complex and Candida parapsilosis complex were differentiated using the HWP1 gene amplification and PCR-RFLP with NlaIII restriction enzyme, respectively. Results: Out of 75 blood culture specimens, 42 (84) cases were positive for Candida spp. of whom 30 (71.42) and 12 (28.57) cases were female and male, respectively. Thirty-two (76) candidemia were presented in pediatrics with 6 years up to 12 years, 10 (23.80) in neonates of one month or less. In the present study, Candida parapsilosis (n =25; 59.52) was the most prevalent isolated species followed by C. albicans (n =11; 26.19), C. tropicalis (n =4; 9.52), and Candida glabrata (n =2; 4.76). Conclusions: According to potentially dangerous complications of bloodstream infection by Candida spp. in neonates and children, it is necessary to identify and eliminate the underlying conditions and risk factors of this disease. © 2020, Author(s)

Epidermal neural crest stem cell transplantation as a promising therapeutic strategy for ischemic stroke

Introduction: Cell-based therapy is considered as promising strategy to cure stroke. However, employing appropriate type of stem cell to fulfill many therapeutic needs of cerebral ischemia is still challenging. In this regard, the current study was designed to elucidate therapeutic potential of epidermal neural crest stem cells (EPI-NCSCs) compared to bone marrow mesenchymal stem cells (BM-MSCs) in rat model of ischemic stroke. Methods: Ischemic stroke was induced by middle cerebral artery occlusion (MCAO) for 45 minutes. Immediately after reperfusion, EPI-NCSCs or BM-MSCs were transplanted via intra-arterial or intravenous route. A test for neurological function was performed before ischemia and 1, 3, and 7 days after MCAO. Also, infarct volume ratio and relative expression of 15 selected target genes were evaluated 7 days after transplantation. Results: EPI-NCSCs transplantation (both intra-arterial and intravenous) and BM-MSCs transplantation (only intra-arterial) tended to result in a better functional outcome, compared to the MCAO group; however, this difference was not statistically significant. The infarct volume ratio significantly decreased in NCSC-intra-arterial, NCSC-intravenous and MSC-intra-arterial groups compared to the control. EPI-NCSCs interventions led to higher expression levels of Bdnf, nestin, Sox10, doublecortin, β-III tubulin, Gfap, and interleukin-6, whereas neurotrophin-3 and interleukin-10 were decreased. On the other hand, BM-MSCs therapy resulted in upregulation of Gdnf, β-III tubulin, and Gfap and down-regulation of neurotrophin-3, interleukin-1, and interleukin-10. Conclusion: These findings highlight the therapeutic effects of EPI-NCSCs transplantation, probably through simultaneous induction of neuronal and glial formation, as well as Bdnf over-expression in a rat model of ischemic strok

Genetics of intellectual disability in consanguineous families

Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence

Mapping subnational HIV mortality in six Latin American countries with incomplete vital registration systems

BackgroundHuman immunodeficiency virus (HIV) remains a public health priority in Latin America. While the burden of HIV is historically concentrated in urban areas and high-risk groups, subnational estimates that cover multiple countries and years are missing. This paucity is partially due to incomplete vital registration (VR) systems and statistical challenges related to estimating mortality rates in areas with low numbers of HIV deaths. In this analysis, we address this gap and provide novel estimates of the HIV mortality rate and the number of HIV deaths by age group, sex, and municipality in Brazil, Colombia, Costa Rica, Ecuador, Guatemala, and Mexico.MethodsWe performed an ecological study using VR data ranging from 2000 to 2017, dependent on individual country data availability. We modeled HIV mortality using a Bayesian spatially explicit mixed-effects regression model that incorporates prior information on VR completeness. We calibrated our results to the Global Burden of Disease Study 2017.ResultsAll countries displayed over a 40-fold difference in HIV mortality between municipalities with the highest and lowest age-standardized HIV mortality rate in the last year of study for men, and over a 20-fold difference for women. Despite decreases in national HIV mortality in all countries-apart from Ecuador-across the period of study, we found broad variation in relative changes in HIV mortality at the municipality level and increasing relative inequality over time in all countries. In all six countries included in this analysis, 50% or more HIV deaths were concentrated in fewer than 10% of municipalities in the latest year of study. In addition, national age patterns reflected shifts in mortality to older age groups-the median age group among decedents ranged from 30 to 45years of age at the municipality level in Brazil, Colombia, and Mexico in 2017.ConclusionsOur subnational estimates of HIV mortality revealed significant spatial variation and diverging local trends in HIV mortality over time and by age. This analysis provides a framework for incorporating data and uncertainty from incomplete VR systems and can help guide more geographically precise public health intervention to support HIV-related care and reduce HIV-related deaths.Peer reviewe

Anemia prevalence in women of reproductive age in low- and middle-income countries between 2000 and 2018

Anemia is a globally widespread condition in women and is associated with reduced economic productivity and increased mortality worldwide. Here we map annual 2000–2018 geospatial estimates of anemia prevalence in women of reproductive age (15–49 years) across 82 low- and middle-income countries (LMICs), stratify anemia by severity and aggregate results to policy-relevant administrative and national levels. Additionally, we provide subnational disparity analyses to provide a comprehensive overview of anemia prevalence inequalities within these countries and predict progress toward the World Health Organization’s Global Nutrition Target (WHO GNT) to reduce anemia by half by 2030. Our results demonstrate widespread moderate improvements in overall anemia prevalence but identify only three LMICs with a high probability of achieving the WHO GNT by 2030 at a national scale, and no LMIC is expected to achieve the target in all their subnational administrative units. Our maps show where large within-country disparities occur, as well as areas likely to fall short of the WHO GNT, offering precision public health tools so that adequate resource allocation and subsequent interventions can be targeted to the most vulnerable populations.Peer reviewe

The prevalence of onchocerciasis in Africa and Yemen, 2000–2018: a geospatial analysis

Background Onchocerciasis is a disease caused by infection with Onchocerca volvulus, which is transmitted to humans via the bite of several species of black fly, and is responsible for permanent blindness or vision loss, as well as severe skin disease. Predominantly endemic in parts of Africa and Yemen, preventive chemotherapy with mass drug administration of ivermectin is the primary intervention recommended for the elimination of its transmission. Methods A dataset of 18,116 geo-referenced prevalence survey datapoints was used to model annual 2000–2018 infection prevalence in Africa and Yemen. Using Bayesian model-based geostatistics, we generated spatially continuous estimates of all-age 2000–2018 onchocerciasis infection prevalence at the 5 × 5-km resolution as well as aggregations to the national level, along with corresponding estimates of the uncertainty in these predictions. Results As of 2018, the prevalence of onchocerciasis infection continues to be concentrated across central and western Africa, with the highest mean estimates at the national level in Ghana (12.2%, 95% uncertainty interval [UI] 5.0–22.7). Mean estimates exceed 5% infection prevalence at the national level for Cameroon, Central African Republic, Democratic Republic of the Congo (DRC), Guinea-Bissau, Sierra Leone, and South Sudan. Conclusions Our analysis suggests that onchocerciasis infection has declined over the last two decades throughout western and central Africa. Focal areas of Angola, Cameroon, the Democratic Republic of the Congo, Ethiopia, Ghana, Guinea, Mali, Nigeria, South Sudan, and Uganda continue to have mean microfiladermia prevalence estimates exceeding 25%. At and above this level, the continuation or initiation of mass drug administration with ivermectin is supported. If national programs aim to eliminate onchocerciasis infection, additional surveillance or supervision of areas of predicted high prevalence would be warranted to ensure sufficiently high coverage of program interventions

Mapping subnational HIV mortality in six Latin American countries with incomplete vital registration systems

Background: Human immunodeficiency virus (HIV) remains a public health priority in Latin America. While the burden of HIV is historically concentrated in urban areas and high-risk groups, subnational estimates that cover multiple countries and years are missing. This paucity is partially due to incomplete vital registration (VR) systems and statistical challenges related to estimating mortality rates in areas with low numbers of HIV deaths. In this analysis, we address this gap and provide novel estimates of the HIV mortality rate and the number of HIV deaths by age group, sex, and municipality in Brazil, Colombia, Costa Rica, Ecuador, Guatemala, and Mexico. Methods: We performed an ecological study using VR data ranging from 2000 to 2017, dependent on individual country data availability. We modeled HIV mortality using a Bayesian spatially explicit mixed-effects regression model that incorporates prior information on VR completeness. We calibrated our results to the Global Burden of Disease Study 2017. Results: All countries displayed over a 40-fold difference in HIV mortality between municipalities with the highest and lowest age-standardized HIV mortality rate in the last year of study for men, and over a 20-fold difference for women. Despite decreases in national HIV mortality in all countries�apart from Ecuador�across the period of study, we found broad variation in relative changes in HIV mortality at the municipality level and increasing relative inequality over time in all countries. In all six countries included in this analysis, 50 or more HIV deaths were concentrated in fewer than 10 of municipalities in the latest year of study. In addition, national age patterns reflected shifts in mortality to older age groups�the median age group among decedents ranged from 30 to 45 years of age at the municipality level in Brazil, Colombia, and Mexico in 2017. Conclusions: Our subnational estimates of HIV mortality revealed significant spatial variation and diverging local trends in HIV mortality over time and by age. This analysis provides a framework for incorporating data and uncertainty from incomplete VR systems and can help guide more geographically precise public health intervention to support HIV-related care and reduce HIV-related deaths