The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International ...Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.
Abstract
Every evening, chimpanzees build sleeping “nests” in trees. In some studied communities, individuals appear to be selective about the tree species used, which has led researchers to ...hypothesize whether chimpanzees prefer trees that repel troublesome insects or/and that provide comfortable and stable structures. We investigate these hypotheses, or a trade-off between both, though study of tree species preference based on their biomechanical and/or biochemical properties in the Sebitoli chimpanzee community in Kibale National Park, Uganda. The ten tree species most frequently used for nesting were compared with ten abundant in their environment but not preferred for nesting. For these 20 tree species, we determined their biomechanical and morphological characteristics such as foliar density, foliar units form (shape and size) and branch rigidity. Their spatial repellent activity, previously tested against
Anopheles gambiae
was incorporated into the analysis. Chimpanzees chose tree species with medium-sized and elongated foliar units, high foliar density and branch with stiffer wood. In addition, most tree species with such mechanical and morphological properties also have mosquito repellent activity. These tree properties may provide a comfortable sleeping environment enhancing sleep quality. Finally, a comparison across chimpanzee communities would be relevant to understand whether these choices are not only ecological but also cultural.
Antiretroviral (ARV) drugs have, for many years, been studied and administered in the prevention and treatment of human immunodeficiency virus (HIV). Intramuscular (IM) injection of long acting (LA) ...ARVs are in clinical development, but injectable formulations require regular access to healthcare facilities and disposal facilities for sharps. The development of a discrete, self‐administered, and self‐disabling vehicle to deliver ARVs could obviate these issues. This study describes the formulation, mechanical characterization, and in vivo evaluation of dissolving microarray patches (MAPs) containing a LA nanosuspension of the ARV, rilpivirine (RPV, RPV LA), for vaginal delivery. This is the first study to apply MAPs into vaginal tissue. The RPV LA MAPs penetrate ex vivo skin and a synthetic vaginal skin model and withstand the effects of potential dragging motion across synthetic vaginal epithelium. In in vivo studies, the mean plasma concentration of RPV in rats at the 56 day endpoint (116.5 ng mL−1) is comparable to that achieved in the IM control cohort (118.9 ng mL−1). RPV is detected systemically, in lymph and vaginal tissue, indicating the potential to deliver RPV LA to primary sites of viral challenge and replication. This innovative research has future potential for patients and healthcare workers, particularly in low‐resource settings.
A study describing the design, formulation and characterisation of novel dissolving microarray patches (MAP) for vaginal delivery of a long acting nanosuspension of the antiretroviral (ARV) drug, rilpivirine (RPV). In an in vivo model, RPV is detected systemically, in lymph and vaginal tissue. This innovative delivery system could have wide ranging benefits for patients and healthcare workers in the future.
People with trisomy 21 (T21) are predisposed to developing hematological tumors, but have significantly lower-than-expected age-adjusted incidence rates of having a solid tumor.
To identify novel ...genetic factors implicated in the lower breast cancer (BC) frequency observed in women with T21 than in the general population, we compared the transcriptome pattern of women with a homogeneous T21, aged more than 30 years, with or without BC, and tumoral BC tissue of control women with a normal karyotype from the study of Varley et al. (2014).
Differential analysis of gene expression between the 15 women in the T21 without BC group and BC patients in the other groups (two women with T21 and fifteen control women, respectively) revealed 154 differentially expressed genes, of which 63 were found to have similar expression profile (up- or downregulated). Of those 63 genes, four were in the same family, namely GIMAP4, GIMAP6, GIMAP7 and GIMAP8, and were strongly upregulated in the T21 without BC group compared to the other groups. A significant decrease in mRNA levels of these genes in BC tissues compared to non-tumor breast tissues was also noted.
We found that the expression of some GIMAPs is significantly higher in women with T21 without BC than in patients with sporadic BC. Our findings support the hypothesis that GIMAPs may play a tumor-suppressive role against BC, and open the possibility that they may also have the same role for other solid tumors in T21 patients. The search for new prognostic factors and hopefully new therapeutic or preventive strategies against BC are discussed.
Abstract
Background
Every evening, chimpanzees (
Pan troglodytes
) build a sleeping platform so called “nest” by intertwining branches of tree. Most of chimpanzees’ communities studied have a ...preference for tree species in which they nest. As female mosquitoes are feeding on the blood of their host at nighttime, chimpanzees may prevent being disturbed and bitten by mosquitoes by selecting tree species having properties to repel them.
Methods
To test the hypothesis that chimpanzees choose tree species for their aromatic properties, data related to 1,081 nesting trees built between 2017 and 2019 in the Sebitoli community of Kibale National Park (Uganda) were analysed. The 10 most used trees were compared to the 10 most common trees in the habitat that were not preferred for nesting. Leaves from the 20 trees species were collected and hydro-distillated to obtain essential oils and one of the by-products for behavioural bioassays against females of the African mosquito,
Anopheles gambiae
.
Results
Sebitoli chimpanzees showed tree preferences: 10 species correspond to more than 80% of the nesting trees. Out of the essential oil obtained from the 10 nesting trees, 7 extracts for at least one concentration tested showed spatial repellency, 7 were irritant by contact and none were toxic. In the other hand, for the abundant trees in their habitat not used by chimpanzees, only 3 were repellent and 5 irritants.
Discussion and conclusion
This study contributes to evidence that chimpanzees, to avoid annoying mosquitoes, may select their nesting trees according to their repellent properties (linked to chemical parameters), a potential inspiration for human health.
In the frame of the second French Total Diet Study (TDS), the 15+1 EU priority polycyclic aromatics hydrocarbons (PAHs) were analyzed in 725 foodstuffs habitually consumed by the French population, ...using gas chromatography coupled to tandem mass spectrometry, after pressurized liquid extraction and purification on PS-DVB stationary phase. The highest PAH concentrations recovered in foodstuffs corresponded to the following contributors: chrysene (25.7%), benzobfluoranthene (15.0%) and benzaanthracene (9.0%) whereas the lowest concentrations were those of dibenza,hanthracene, 5 methylchrysene and dibenzoa,hpyrene (below 2.0%). By food groups, the current highest levels of total PAH were detected in mollusks and crustaceans, followed by the different oil based products. To estimate French population's exposure, contamination data were combined with national individual food consumption data. Mean daily exposure to the sum of benzoapyrene, benzaanthracene, chrysene and benzobfluoranthene (PAH4) was estimated to be 1.48ng/kgbw/day in adults and 2.26ng/kgbw/day in children. The main contributors to PAH exposure for adults are fats, bread and dried bread products followed by crustaceans and mollusks. The margin of exposure (MOE) approach indicates that exposure to PAHs through food is not a major health problem for French consumers.
► We analyzed PAHs in 725 foodstuffs for the French Total Diet Study. ► Highest levels of total PAH were found in mollusks and crustaceans. ► Mean daily exposure to PAH4 is 1.48ng/kgbw/day for adults. ► We found fats and breads as major contributors to the PAHs exposure. ► The margin of exposure (MOE) indicates that PAHs in food is not an issue in France
Down Syndrome (DS) is the most common chromosome anomaly in humans and occurs due to an extra copy of chromosome 21. The malignancy profile in DS is unique, since DS patients have a low risk of ...developing solid tumors such as breast cancer however they are at higher risk of developing acute myeloid leukemia and acute lymphoblastic leukemia.
In this study, we investigated DNA methylation signatures and epigenetic aging in DS individuals with and without breast cancer. We analyzed DNA methylation patterns in Trisomy 21 (T21) individuals without breast cancer (T21-BCF) and DS individuals with breast cancer (T21-BC), using the Infinium Methylation EPIC BeadChip array.
Our results revealed several differentially methylated sites and regions in the T21-BC patients that were associated with changes in gene expression. The differentially methylated CpG sites were enriched for processes related to serine-type peptidase activity, epithelial cell development, GTPase activity, bicellular tight junction, Ras protein signal transduction, etc. On the other hand, the epigenetic age acceleration analysis showed no difference between T21-BC and T21-BCF patients.
This is the first study to investigate DNA methylation changes in Down syndrome women with and without breast cancer and it could help shed light on factors that protect against breast cancer in DS.
Persian walnut (Juglans regia L.), the walnut species cultivated for nut production, is grown worldwide in temperate areas. In this work, chronological phenotypic data have been collected regarding a ...part of the walnut genetic resources of the French National Institute for Agricultural Research (INRA) of Bordeaux. Using a well described ontology, these data have been collected in order to assess the phenotypic variations among the accessions, and to better manage the germplasm collection. These data can also be helpful for any breeding program as they provide a clear phenotypic characterization of the main cultivars.
This paper introduces a dataset collected for 150 J. regia accessions for a period from 1965 to 2016, and for 3 observation sites, released as comma separated value spreadsheet. It includes observations about phenological traits (e.g. flowering dates), traits related to in-shell walnut (e.g. weight and size), and traits related to kernel (e.g. color). It can be used by other researchers particularly for multi-site phenological studies in the context of climate change since climate data files are also available. In addition, a complete walnut ontology was deposited in this repository and can assist to standardize the management of any walnut germplasm collection.
Down syndrome (DS) is a complex genetic condition due to an additional copy of human chromosome 21, which results in the deregulation of many genes. In addition to the intellectual disability ...associated with DS, adults with DS also have an ultrahigh risk of developing early onset Alzheimer’s disease dementia. DYRK1A, a proline-directed serine/threonine kinase, whose gene is located on chromosome 21, has recently emerged as a promising plasma biomarker in patients with sporadic Alzheimer’s disease (AD). The protein DYRK1A is truncated in symptomatic AD, the increased truncated form being associated with a decrease in the level of full-length form. Activity-dependent neuroprotective protein (ADNP), a key protein for the brain development, has been demonstrated to be a useful marker for symptomatic AD and disease progression. In this study, we evaluated DYRK1A and ADNP in CSF and plasma of adults with DS and explored the relationship between these proteins. We used mice models to evaluate the effect of DYRK1A overexpression on ADNP levels and then performed a dual-center cross-sectional human study in adults with DS in Barcelona (Spain) and Paris (France). Both cohorts included adults with DS at different stages of the continuum of AD: asymptomatic AD (aDS), prodromal AD (pDS), and AD dementia (dDS). Non-trisomic controls and patients with sporadic AD dementia were included for comparison. Full-form levels of DYRK1A were decreased in plasma and CSF in adults with DS and symptomatic AD (pDS and dDS) compared to aDS, and in patients with sporadic AD compared to controls. On the contrary, the truncated form of DYRK1A was found to increase both in CSF and plasma in adults with DS and symptomatic AD and in patients with sporadic AD with respect to aDS and controls. ADNP levels showed a more complex structure. ADNP levels increased in aDS groups vs. controls, in agreement with the increase in levels found in the brains of mice overexpressing DYRK1A. However, symptomatic individuals had lower levels than aDS individuals. Our results show that the comparison between full-length and truncated-form levels of DYRK1A coupled with ADNP levels could be used in trials targeting pathophysiological mechanisms of dementia in individuals with DS.
Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can ...generate lots of heterogeneous and unrelated data. The challenge is to integrate this information with other publicly available data. Nucleotide sequencing throughput has been improved with new technologies; this increases the need for powerful information systems able to store, manage and explore data. GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. Here, we illustrate its use. Database URL: http://urgi.versailles.inra.fr/gnpis.
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