Florence Mompart

Differences in Frequency, Level, and Duration of Cecal Carriage Between Four Outbred Chicken Lines Infected Orally with Salmonella enteritidis

Four chicken lines, L2, B13, PA12 (egg-type), and Y11 (meat-type), were tested for experimental carrier state of Salmonella enteritidis (SE) in two identical trials. After oral inoculation of SE at 1 wk of age with 5 x 10(4) SE colony-forming units (CFU), 10 chickens per line were necropsied weekly for 6 wk and then every 8 or 15 days until the 12th week postinoculation (PI). Liver, spleen, ovary, and ceca were examined for level of SE colonization. Numbers of positive livers and spleens and levels of the challenge strain in these organs differed little between the four chicken lines. Only three positive ovaries were detected. According to the chicken line, ceca exhibited generally significant (P < 0.05) differences in the number of positive organs during weeks 5-11 PI, in the SE CFU levels (P < 0.05) in the first 5 wk PI and during weeks 8 and 10 PI, and in the duration of colonization. L2 and B13 chickens generally carried SE in their ceca at higher levels, in more animals, and for a longer time than PA12 and Y11 chickens. Y11 chickens were the most resistant to SE cecal colonization.

NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments

UNLABELLED Three-dimensional fluorescence in situ hybridization (3D-FISH) is used to study the organization and the positioning of chromosomes or specific sequences such as genes or RNA in cell nuclei. Many different programs (commercial or free) allow image analysis for 3D-FISH experiments. One of the more efficient open-source programs for automatically processing 3D-FISH microscopy images is Smart 3D-FISH, an ImageJ plug-in designed to automatically analyze distances between genes. One of the drawbacks of Smart 3D-FISH is that it has a rather basic user interface and produces its results in various text and image files thus making the data post-processing step time consuming. We developed a new Smart 3D-FISH graphical user interface, NEMO, which provides all information in the same place so that results can be checked and validated efficiently. NEMO gives users the ability to drive their experiments analysis in either automatic, semi-automatic or manual detection mode. We also tuned Smart 3D-FISH to better analyze chromosome territories. AVAILABILITY NEMO is a stand-alone Java application available for Windows and Linux platforms. The program is distributed under the creative commons licence and can be freely downloaded from https://www-lgc.toulouse.inra.fr/nemo

Antibody responses in the serum and gut of chicken lines differing in cecal carriage of Salmonella enteritidis

Salmonella frequently causes human foodborne infections. Contaminated products from poultry infected with Salmonella enteritidis are mainly involved. This serovar is able to colonize the gastrointestinal tract and generally produces a chronic asymptomatic carrier state in poultry, except in very young birds. We have developed a model of S. enteritidis carriage in chicks and found that four chicken lines, B13, L2, PA12 and Y11 differ in their cecal colonization by S. enteritidis, whereas their systemic organs are similarly infected. We have monitored the serum and gut antibody responses of these four lines to S. enteritidis for 9 weeks post inoculation (pi). We confirm that S. enteritidis infected the spleens of the four chicken lines similarly, and that it often colonized the ceca at levels significantly higher in B13 and L2 chicks than those of the PA12 and Y11 chicks. The serum IgM and IgG antibody responses were high and the serum IgA antibody responses low. In contrast, the intestinal secretions contained mostly IgA antibodies. The serum IgM antibody values of the four chicken lines were similar. However, the B13 and L2 chicks often had significantly higher serum IgG and IgA antibody responses than PA12 and Y11 chicks. Only the B13 and L2 chicks showed high, persistent levels of IgA antibody in intestinal secretions. These results suggest that most antibody responses are related to cecal colonization by S. enteritidis. They also indicate that factors other than the antibody levels are involved in the control of this colonization.

Transcriptomic and nuclear architecture of immune cells after LPS activation

Changes in the nuclear positioning of specific genes, depending on their expression status, have been observed in a large diversity of physiological processes. However, gene position is poorly documented for immune cells which have been subjected to activation following bacterial infection. Using a pig model, we focused our study on monocyte-derived macrophages and neutrophils, as they are the first lines of defence against pathogens. We examined whether changes in gene expression due to LPS activation imply that genes have repositioned in the nuclear space. We first performed a transcriptomic analysis to identify the differentially expressed genes and then analysed the networks involved during lypopolysaccharide/interferon gamma activation in monocyte-derived macrophages. This allowed us to select four up-regulated (IL1β, IL8, CXCL10 and TNFα) and four down-regulated (VIM, LGALS3, TUBA3 and IGF2) genes. Their expression statuses were verified by quantitative real-time RT-PCR before studying their behaviour in the nuclear space during macrophage activation by means of 3D fluorescence in situ hybridization. No global correlation was found between gene activity and radial positioning. Only TNFα belonging to the highly transcribed MHC region on chromosome 7 became more peripherally localized in relation to the less decondensed state of its chromosome territory (CT) in activated macrophages. The analysis of gene positioning towards their CT revealed that IL8 increases significantly its tendency to be outside its CT during the activation process. In addition, the gene to CT edge distances increase for the three up-regulated genes (IL8, CXCL10 and TNFα) among the four analysed. Contrarily, the four down-regulated genes did not change their position. The analysis of gene behaviour towards their CT was extended to include neutrophils for three (TNFα, IL8 and IL1β) up- and two (IGF2 and TUBA3) down-regulated genes, and similar results were obtained. The analysis was completed by studying the four up-regulated genes in fibroblasts, not involved in immune response. Our data suggest that relocation in the nuclear space of genes that are differentially expressed in activated immune cells is gene and cell type specific but also closely linked to the entire up-regulation status of their chromosomal regions.

Nuclear architecture of resting and LPS-stimulated porcine neutrophils by 3D FISH

Neutrophils are essential components of the innate immune system due to their ability to kill and phagocytose invading microbes. They possess a lobulated nucleus and are capable of extensive and complex changes in response to bacterial stimulation. The aim of our study was to investigate whether the 3D nuclear organization of porcine neutrophils was modified upon stimulation. The organization of centromeres, telomeres, and chromosome territories (chromosomes 2, 3, 7, 8, 12, 13, and 17) was studied on structurally preserved nuclei using 3D fluorescence in situ hybridization, confocal microscopy, and image analysis. By differential labeling of centromeres of acrocentric and metacentric/submetacentric chromosomes, we showed that centromeres associated to form chromocenters but did so preferentially between chromosomes with the same morphology. Upon activation, some of these chromocenters dispersed. Telomeres were also found to form clusters, but their number remained unchanged in lipopolysaccharide-stimulated neutrophils. The analysis of the position of chromocenters and telomere clusters showed a more internal location of the latter compared to the former. The analysis of chromosome territories revealed that homologs were distributed randomly among lobes whatever the cell’s status. The volume of these territories was not proportional to chromosome length, and some chromosomes (chr 3, 12, 13, and 17) were more prone to decondensation when neutrophils were stimulated. Thus, our study demonstrated that activation of neutrophils resulted in several modifications of their nuclear architecture: a decrease in the number of non-acrocentric chromocenters and the decondensation of several chromosomes.

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.

Background Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims at profiling the landscape of transcription (RNA-seq) and chromatin accessibility and conformation (ATAC-seq and Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Results Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species. RNA-seq assays considerably extended the available catalog of protein-coding and non-coding transcripts. Gene expression profiles were consistent with known metabolic/immune functions and revealed differentially expressed transcripts with unknown function, including new lncRNAs in syntenic regions. The majority of ATAC-seq peaks of chromatin accessibility mapped to putative regulatory regions, with an enrichment of predicted transcription factor binding sites in differentially accessible peaks. Hi-C provided the first set of genome-wide maps of three-dimensional interactions across livestock and showed consistency with results from gene expression and chromatin accessibility in topological compartments of the genomes. Conclusions We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project. The global consistency between gene expression and chromatin structure data in these four livestock species confirms previous findings in model animals. Overall, these results emphasize the value of FAANG for research on domesticated animals and strengthen the importance of future meta-analyses of the reference datasets being generated by this community on different species.Abstract Background Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project (http://www.fragencode.org) aimed to profile the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Results RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically Associating Domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. Conclusions We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing

Reciprocal translocations are the most frequently occurring constitutional structural rearrangements in mammalian genomes. In phenotypically normal pigs, an incidence of 1/200 is estimated for such rearrangements. Even if constitutional translocations do not necessarily induce defects and diseases, they are responsible for significant economic losses in domestic animals due to reproduction failures. Over the last 30 years, advances in molecular and cytogenetic technologies have led to major improvements in the resolution of the characterization of translocation events. Characterization of translocation breakpoints helps to decipher the mechanisms that lead to such rearrangements and the functions of the genes that are involved in the translocation. Here, we describe the fine characterization of a reciprocal translocation t(3;4) (p1.3;q1.5) detected in a pig line. The breakpoint was identified at the base-pair level using a positional cloning and chromosome walking strategy in somatic cell hybrids that were generated from an animal that carries this translocation. We show that this translocation occurs within the ADAMTSL4 gene and results in a loss of expression in homozygous carriers. In addition, by taking this translocation as a model, we used a whole-genome next-generation mate-pair sequencing approach on pooled individuals to evaluate this strategy for high-throughput screening of structural rearrangements.

3D nuclear organization of the CMH complex in control and LPS-activated porcine macrophages

Chromosomal abnormalities in secondary bovine oocytes matured in vitro up to 48 hours Abstract Chromosomal abnormalities in secondary bovine oocytes matured in vitro up to 48 hours. 21st International Colloquium on Animal Cytogenetics and Gene Mapping Rubessa M., Pauciullo A., Peretti V., Iannuzzi L., Ramunno L., Di Berardino D.Edited by: L. Iannuzzi, A. Perucatti, A. Iannuzzi, A. Pauciullo, V. Genualdo, D. Incarnato, L. Keller (CNRISPAAM, Naples, Italy)Sister Chromatid exchange (SCE) test in river buffalo cells treated with Furocoumarins. / Iannuzzi A.; Perucatti A.; Genualdo V.; Pauciullo A.; Pucciarelli L.; Incarnato D.; Melis R.; Porqueddu C.; Marchetti M.; Iannuzzi L.. In: CHROMOSOME RESEARCH. ISSN 0967-3849. 22(2014), pp. 421-421. Original Citation: Sister Chromatid exchange (SCE) test in river buffalo cells treated with Furocoumarins.Comparative FISH-mapping of TNF, STAT5A and MNTR1A fecundity genes on river buffalo, cattle, sheep and goat. / Iannuzzi A.; Perucatti A.; Pauciullo A.; Genualdo V.; Incarnato D.; Pucciarelli L.; De Lorenzi L.; Parma P.; Iannuzzi L.. In: CHROMOSOME RESEARCH. ISSN 0967-3849. 22(2014), pp. 418-418. Original Citation: Comparative FISH-mapping of TNF, STAT5A and MNTR1A fecundity genes on river buffalo, cattle, sheep and goat.Multicolor FISH with 10 specific painting probes for the rapid identification of the sub-metacentric river buffalo autosomes (Bubalus bubalis, 2n=50) / Pauciullo A.; Perucatti A.; Iannuzzi A.; Incarnato D.; Genualdo V.; Pucciarelli L.; Di Berardino D.; Iannuzzi L.. In: CHROMOSOME RESEARCH. ISSN 0967-3849. 22(2014), pp. 410-410. Original Citation: Multicolor FISH with 10 specific painting probes for the rapid identification of the sub-metacentric river buffalo autosomes (Bubalus bubalis, 2n=50)