A pilot study of the use of the oral and faecal microbiota for the diagnosis of ulcerative colitis and Crohn's disease in a paediatric population.

Crohn's disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBD) that affect the gastrointestinal tract. Changes in the microbiome and its interaction with the immune system are thought to play a key role in their development. The aim of this study was to determine whether metagenomic analysis is a feasible non-invasive diagnostic tool for IBD in paediatric patients. A pilot study of oral and faecal microbiota was proposed with 36 paediatric patients divided in three cohorts [12 with CD, 12 with UC and 12 healthy controls (HC)] with 6 months of follow-up. Finally, 30 participants were included: 13 with CD, 11 with UC and 8 HC (6 dropped out during follow-up). Despite the small size of the study population, a differential pattern of microbial biodiversity was observed between IBD patients and the control group. Twenty-one bacterial species were selected in function of their discriminant accuracy, forming three sets of potential markers of IBD. Although IBD diagnosis requires comprehensive medical evaluation, the findings of this study show that faecal metagenomics or a reduced set of bacterial markers could be useful as a non-invasive tool for an easier and earlier diagnosis.

Daily intake of probiotic strain Bacillus subtilis DE111 supports a healthy microbiome in children attending day-care.

There is ample evidence suggesting that modulations in gut microbiota play an important role in inflammation and immunity. In particular, the microbiota of children is highly susceptible to environment influences, such as infections. Consequently, probiotics and their ability to promote and support a healthy microbiome have been increasingly studied. This study aimed at investigating the effects of a probiotic supplement (Bacillus subtilis DE111) on the microbiome composition of preschool aged children attending day care. Healthy children aged 2-6 years old were randomised to receive either probiotic or placebo once a day for 8 weeks. No significant changes of the overall microbiome equilibrium were seen in between the two groups or from baseline to week 8. However, alpha diversity was increased in the probiotic group from baseline to week 8 (P<0.05), with no change in the placebo group. A decrease in the Firmicutes/Bacteroidetes ratio following probiotic supplementation (P<0.05) was also observed. Differential abundance analysis revealed an increase in Alistepes (P<0.01), Bacteroides (P<0.05), Parabacteroides (P<0.01), Odoribacter (P<0.001) and Rikenellaceae (P<0.001) in the probiotic group, most of which are involved in inflammation reduction. In addition, a decrease in Eisenbergiella (P<0.001), Lactobacillales (P<0.01) and Streptococcaceae (P<0.01), which is considered pro-inflammatory, were also observed in the probiotic group. Together with a reduction of the F/B ratio observed in the probiotic group, these results suggest probiotic supplementation with Bacillus subtilis DE111 introduce subtle but positive changes in the microbiome of children aged 2-6 years old.

Complex migration history is revealed by genetic diversity of tomato samples collected in Italy during the eighteenth and nineteenth centuries.

Native to South America, the tomato is now grown almost worldwide. During its domestication and improvement, important selection signatures were fixed in certain agronomic and adaption traits. Such traits include fruit morphology, which became a major target for selection over the centuries. However, little is known about precisely when some mutations arose and how they spread through the germplasm. For instance, elongated fruit variants, originating both via mutations in SUN and OVATE genes, may have arisen prior to domestication or during tomato cultivation in Europe. To gain insights into the tomato admixture and selection pattern, the genome of two tomato herbarium specimens conserved in the Herbarium Porticense (PORUN) was sequenced. Comparison of the DNA of herbarium samples collected in Italy between 1750 and 1890 with that of living tomato accessions yielded insights into the history of tomato loci selection. Interestingly, the genotype of the more recent sample (LEO90), classified in 1890 as the oblungum variety, shows several private variants in loci implicated in fruit shape determination, also present also in wild tomato samples. In addition, LEO90, sampled in the nineteenth century, is genetically more distant from cultivated varieties than the SET17 genotype, collected in the eighteenth century, suggesting that elongated tomato varieties may originate from a cross between a landrace and a wild ancestor. Findings from our study have major implications for the understanding of tomato migration patterns and for the conservation of allelic diversity and loci recovery.

LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells.

Oxidation of H3 at lysine 4 (H3K4ox) by lysyl oxidase-like 2 (LOXL2) generates an H3 modification with an unknown physiological function. We find that LOXL2 and H3K4ox are higher in triple-negative breast cancer (TNBC) cell lines and patient-derived xenografts (PDXs) than those from other breast cancer subtypes. ChIP-seq revealed that H3K4ox is located primarily in heterochromatin, where it is involved in chromatin compaction. Knocking down LOXL2 reduces H3K4ox levels and causes chromatin decompaction, resulting in a sustained activation of the DNA damage response (DDR) and increased susceptibility to anticancer agents. This critical role that LOXL2 and oxidized H3 play in chromatin compaction and DDR suggests that functionally targeting LOXL2 could be a way to sensitize TNBC cells to conventional therapy.

A semi-automated protocol for NGS metabarcoding and fungal analysis in forensic.

Metabarcoding through Next Generation Sequencing (NGS) has revolutionized environmental biological studies. The availability of this technical approach has opened the opportunity for a systematic implementation of fungal metabarcoding analysis in forensics, where standardized, sensitive and reproducible protocols are highly desirable. In the present paper, a pipeline including a semi-automated molecular protocol and user-friendly bioinformatics tools are applied to several kinds of environmental samples and forensic caseworks. The identification of fungi that characterize specific environments (like Aspergillus for indoor walls, or Penicillium, Debaryomices and Wickerhamomyces for food storage) can be informative for the provenance of samples. In some situations, fungal analysis cannot allow the identification of a defined environment but seems useful to cluster samples with similar provenance. Based on these considerations, fungal analysis can be included in a wider process of non-human DNA identification in order to provide clues on sample provenance.

Pentatricopeptide repeat 336 as the candidate gene for paternal sorting of mitochondria (Psm) in cucumber.

KEY MESSAGE: Pentatricopeptide repeat (PPR) 336 was identified as the candidate gene for Paternal Sorting of Mitochondria ( Psm ), a nuclear locus that affects the predominant mitochondria transmitted to progenies. Cucumber (Cucumis sativus L.) is a useful plant to study organellar-nuclear interactions because its organelles show differential transmission, maternal for chloroplasts and paternal for mitochondria. The mitochondrial DNA (mtDNA) of cucumber is relatively large due in part to accumulation of repetitive DNAs and recombination among these repetitive regions produces structurally polymorphic mtDNAs associated with paternally transmitted mosaic (MSC) phenotypes. The mitochondrial mutant MSC16 possesses an under-representation of ribosomal protein S7 (rps7), a key component of the small ribosomal subunit in the mitochondrion. A nuclear locus, Paternal Sorting of Mitochondria (Psm), affects the predominant mitochondria transmitted to progenies generated from crosses with MSC16 as the male parent. Using single nucleotide polymorphisms, Psm was mapped to a 170 kb region on chromosome 3 of cucumber and pentatricopeptide repeat (PPR) 336 was identified as the likely candidate gene. PPR336 stabilizes mitochondrial ribosomes in Arabidopsis thaliana and because MSC16 shows reduced transcription of rps7, the cucumber homolog of PPR336 (CsPPR336) as the candidate for Psm is consistent with a nuclear effect on ribosome assembly or stability in the mitochondrion. We used polymorphisms in CsPPR336 to genotype progenies segregating at Psm and recovered only one Psm -/- plant with the MSC phenotype, indicating that the combination of the Psm- allele with mitochondria from MSC16 is almost always lethal. This research illustrates the usefulness of the MSC mutants of cucumber to reveal and study unique interactions between the mitochondrion and nucleus.

Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics.

To investigate the genome-wide spatial arrangement of R loci, a complete catalogue of tomato (Solanum lycopersicum) and potato (Solanum tuberosum) nucleotide-binding site (NBS) NBS, receptor-like protein (RLP) and receptor-like kinase (RLK) gene repertories was generated. Candidate pathogen recognition genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution. NBS genes frequently occur in clusters of related gene copies that also include RLP or RLK genes. This scenario is compatible with the existence of selective pressures optimizing coordinated transcription. A number of duplication events associated with lineage-specific evolution were discovered. These findings suggest that different evolutionary mechanisms shaped pathogen recognition gene cluster architecture to expand and to modulate the defence repertoire. Analysis of pathogen recognition gene clusters associated with documented resistance function allowed the identification of adaptive divergence events and the reconstruction of the evolution history of these loci. Differences in candidate pathogen recognition gene number and organization were found between tomato and potato. Most candidate pathogen recognition gene orthologues were distributed at less than perfectly matching positions, suggesting an ongoing lineage-specific rearrangement. Indeed, a local expansion of Toll/Interleukin-1 receptor (TIR)-NBS-leucine-rich repeat (LRR) (TNL) genes in the potato genome was evident. Taken together, these findings have implications for improved understanding of the mechanisms of molecular adaptive selection at Solanum R loci.

Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects.

Tomato (Solanum lycopersicum) is one of the world's most important vegetable crops. Managing the health of this crop can be particularly challenging; crop resistance may be overcome by new pathogen races while new pathogens have been introduced by global agricultural markets. Tomato is extensively used as a model plant for resistance studies and much has been attained through both genetic and biotechnological approaches. In this paper, we illustrate genomic methods currently employed to preserve resistant germplasm and to facilitate the study and transfer of resistance genes, and we describe the genomic organization of R-genes. Patterns of gene activation during disease resistance response, identified through functional approaches, are depicted. We also describe the opportunities offered by the use of new genomic technologies, including high-throughput DNA sequencing, large-scale expression data production and the comparative hybridization technique, whilst reporting multifaceted approaches to achieve genetic tomato disease control. Future strategies combining the huge amount of genomic and genetic data will be able to accelerate development of novel resistance varieties sustainably on a worldwide basis. Such strategies are discussed in the context of the latest insights obtained in this field.