Publications by authors named "Marie-Agnes Dillies"

Background: Advances in high-throughput technologies have originated an ever-increasing availability of omics datasets. The integration of multiple heterogeneous data sources is currently an issue for biology and bioinformatics. Multiple kernel learning (MKL) has shown to be a flexible and valid approach to consider the diverse nature of multi-omics inputs, despite being an underused tool in genomic data mining.

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Background: Kernel methods have been proven to be a powerful tool for the integration and analysis of high-throughput technologies generated data. Kernels offer a nonlinear version of any linear algorithm solely based on dot products. The kernelized version of principal component analysis is a valid nonlinear alternative to tackle the nonlinearity of biological sample spaces.

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  • The text discusses a genus of Amoebozoa that includes harmful species found in the intestines, focusing on gene regulation from an evolutionary viewpoint.
  • Research involved profiling transcriptomes of closely related species, identifying transcription start sites (TSS) and polyadenylation sites (PAS) to analyze gene regulatory sequences.
  • A key finding was the prevalence of antisense transcription within gene coding sequences, particularly in genes related to processes critical for species that infect the human intestine, hinting at a conserved gene regulatory system.
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  • Epstein-Barr virus (EBV) establishes a latent infection in B-cells and is linked to cancer development, particularly in immunocompromised individuals, such as those with ataxia telangiectasia (AT)—a genetic disorder leading to immune deficiency.
  • Research using RNA sequencing shows that AT patients exhibit deregulated cellular signaling pathways related to transcription, translation, and immune regulation, indicating potential ribosomal defects contributing to the disease.
  • The findings suggest that the deficiency of the ATM gene in AT patients may disrupt the regulation of EBV's latent genes, enhancing the virus's oncogenic potential and aiding in the understanding of both EBV and AT pathogenesis.
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Lassa virus (LASV) is endemic in West Africa and induces a viral hemorrhagic fever (VHF) with up to 30% lethality among clinical cases. The mechanisms involved in control of Lassa fever or, in contrast, the ensuing catastrophic illness and death are poorly understood. We used the cynomolgus monkey model to reproduce the human disease with asymptomatic to mild or fatal disease.

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  • The study investigates natural antisense transcripts (NAT) in the unicellular parasite Entamoeba histolytica, revealing that about 28% of its protein-coding genes show significant transcription on the opposite strand.
  • It finds that the location of transcription start and polyadenylation sites for these NATs is influenced by specific motifs encoded on the opposite strand, suggesting a compact regulatory system for gene expression.
  • Additionally, NATs are shown to be up-regulated under multiple environmental stresses, indicating a potential regulatory role in the gene expression of E. histolytica that requires further exploration.
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Spontaneous control of human immunodeficiency virus (HIV) is generally associated with an enhanced capacity of CD8 T cells to eliminate infected CD4 T cells, but the molecular characteristics of these highly functional CD8 T cells are largely unknown. In the present study, using single-cell analysis, it was shown that HIV-specific, central memory CD8 T cells from spontaneous HIV controllers (HICs) and antiretrovirally treated non-controllers have opposing transcriptomic profiles. Genes linked to effector functions and survival are upregulated in cells from HICs.

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The intestinal microbiota modulates host physiology and gene expression via mechanisms that are not fully understood. Here we examine whether host epitranscriptomic marks are affected by the gut microbiota. We use methylated RNA-immunoprecipitation and sequencing (MeRIP-seq) to identify N6-methyladenosine (mA) modifications in mRNA of mice carrying conventional, modified, or no microbiota.

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Lassa fever is a major threat in Western Africa. The large number of people living at risk for this disease calls for the development of a vaccine against Lassa virus (LASV). We generated live-attenuated LASV vaccines based on measles virus and Mopeia virus platforms and expressing different LASV antigens, with the aim to develop a vaccine able to protect after a single shot.

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Lassa virus (LASV) causes a viral haemorrhagic fever in humans and is a major public health concern in West Africa. An efficient immune response to LASV appears to rely on type I interferon (IFN-I) production and T-cell activation. We evaluated the response of plasmacytoid dendritic cells (pDC) to LASV, as they are an important and early source of IFN-I.

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Background: Infectious diseases are still a leading cause of death and, with the emergence of drug resistance, pose a great threat to human health. New drugs and strategies are thus urgently needed to improve treatment efficacy and limit drug-associated side effects. Nanotechnology-based drug delivery systems are promising approaches, offering hope in the fight against drug resistant bacteria.

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Lassa virus (LASV) is responsible for a viral hemorrhagic fever in humans and the death of 3,000 to 5,000 people every year. The immune response to LASV is poorly understood, but type I interferon (IFN-I) and T-cell responses appear to be critical for the host. We studied the response of myeloid dendritic cells (mDC) to LASV, as mDCs are involved in both IFN-I production and T-cell activation.

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Background: The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment.

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Dengue virus (DENV) causes more human infections than any other mosquito-borne virus. The current lack of antiviral strategies has prompted genome-wide screens for host genes that are required for DENV infectivity. Earlier transcriptomic studies that identified DENV host factors in the primary vector Aedes aegypti used inbred laboratory colonies and/or pools of mosquitoes that erase individual variation.

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  • Thiomonas bacteria are found in arsenic-contaminated waters like acid mine drainage and play a role in cleaning up arsenic through biofilm formation.
  • The study examined three Thiomonas strains, discovering that two favored biofilm formation while one preferred motility when exposed to arsenite.
  • Using RNA-seq, the research investigated gene expression related to biofilm formation in Thiomonas sp. CB2, enhancing understanding of how these bacteria adapt to extreme environments.
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Amoebiasis is a human infectious disease due to the amoeba parasite Entamoeba histolytica. The disease appears in only 20% of the infections. Diversity in phenotypes may occur within the same infectious strain in the gut; for instance, parasites can be commensal (in the intestinal lumen) or pathogenic (inside the tissue).

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Motivation: With the continued improvement of requisite mass spectrometers and UHPLC systems, Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) workflows are rapidly evolving towards the investigation of more challenging biological systems, including large protein complexes and membrane proteins. The analysis of such extensive systems results in very large HDX-MS datasets for which specific analysis tools are required to speed up data validation and interpretation.

Results: We introduce a web application and a new R-package named 'MEMHDX' to help users analyze, validate and visualize large HDX-MS datasets.

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The fungal cell wall is a rigid structure because of fibrillar and branched β-(1,3)-glucan linked to chitin. Softening of the cell wall is an essential phenomenon during fungal morphogenesis, wherein rigid cell wall structures are cleaved by glycosylhydrolases. During the search for glycosylhydrolases acting on β-(1,3)-glucan, we identified seven genes in the Aspergillus fumigatus genome coding for potential endo-β-(1,3)-glucanase.

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Background: Several R packages exist for the detection of differentially expressed genes from RNA-Seq data. The analysis process includes three main steps, namely normalization, dispersion estimation and test for differential expression. Quality control steps along this process are recommended but not mandatory, and failing to check the characteristics of the dataset may lead to spurious results.

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Listeria monocytogenes is responsible for gastroenteritis in healthy individuals and for a severe invasive disease in immunocompromised patients. Among the three identified L. monocytogenes evolutionary lineages, lineage I strains are overrepresented in epidemic listeriosis outbreaks, but the mechanisms underlying the higher virulence potential of strains of this lineage remain elusive.

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The RIG-I-like receptors (RLRs) play a major role in sensing RNA virus infection to initiate and modulate antiviral immunity. They interact with particular viral RNAs, most of them being still unknown. To decipher the viral RNA signature on RLRs during viral infection, we tagged RLRs (RIG-I, MDA5, LGP2) and applied tagged protein affinity purification followed by next-generation sequencing (NGS) of associated RNA molecules.

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Uropathogenic Escherichia coli (UPEC) is the leading cause of urinary tract infections (UTIs) worldwide, causing over 150 million clinical cases annually. There is currently no specific treatment addressing the asymptomatic carriage in the gut of UPEC before they initiate UTIs. This study investigates the efficacy of virulent bacteriophages to decrease carriage of gut pathogens.

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  • BAHD1 is a protein that contributes to heterochromatin formation and gene repression in human cells, particularly affecting DNA methylation patterns.
  • Research showed that increasing BAHD1 levels leads to hypermethylation on autosomes and hypomethylation on the inactive X chromosome in HEK293 cells.
  • The study identified over 91,000 regions with different DNA methylation patterns linked to BAHD1 and suggested that BAHD1 influences genome organization and spatial architecture through its effects on DNA methylation.
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Background And Aims: In cystic fibrosis (CF), Pseudomonas aeruginosa is not eradicated from the lower respiratory tract and is associated with epithelial inflammation that eventually causes tissue damage. To identify the molecular determinants of an effective response to P. aeruginosa infection, we performed a transcriptomic analysis of primary human bronchial epithelial cells from healthy donors (CTRL) 2, 4, and 6 h after induced P.

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