Bionemo (http://bionemo.bioinfo.cnio.es) stores manually curated information about proteins and genes directly implicated in the Biodegradation metabolism. When possible, the database includes information on sequence, domains and structures for proteins; and sequence, regulatory elements and transcription units for genes. Thus, Bionemo is a unique resource that complements other biodegradation databases such as the University of Minessota Biocatalysis/Biodegradation Database, or Metarouter, which focus more on the biochemical aspects of biodegradation than in the nature of the biomolecules carrying out the reactions. Bionemo has been built by manually associating sequences database entries to biodegradation reactions, using the information extracted from published articles. Information on transcription units and their regulation was also extracted from the literature for biodegradation genes, and linked to the underlying biochemical network. In its current version, Bionemo contains sequence information for 324 reactions and transcription regulation information for more than 100 promoters and 100 transcription factors. The information in the Bionemo database is available via a web server and the full database is also downloadable as a PostgresSQL dump. To facilitate the programmatic use of the information contained in the database, an object-oriented Perl API is also provided.

Biodegradation, the ability of microorganisms to remove complex chemicals from the environment, is a multifaceted process in which many biotic and abiotic factors are implicated. The recent accumulation of knowledge about the biochemistry and genetics of the biodegradation process, and its categorization and formalization in structured databases, has recently opened the door to systems biology approaches, where the interactions of the involved parts are the main subject of study, and the system is analysed as a whole. The global analysis of the biodegradation metabolic network is beginning to produce knowledge about its structure, behaviour and evolution, such as its free-scale structure or its intrinsic robustness. Moreover, these approaches are also developing into useful tools such as predictors for compounds' degradability or the assisted design of artificial pathways. However, it is the environmental application of high-throughput technologies from the genomics, metagenomics, proteomics and metabolomics that harbours the most promising opportunities to understand the biodegradation process, and at the same time poses tremendous challenges from the data management and data mining point of view.

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Background Recent studies have applied single-cell RNA sequencing (sc-RNAseq) of the human intestine to resolve the cellular complexity and heterogeneity characteristic of inflammatory bowel disease (IBD). Nonetheless, an in-depth analysis of the myeloid mucosal compartment, a crucial player in gut immune responses, has not yet been conducted. Methods Colonic biopsies from healthy controls (HC, n=6), endoscopically active Crohn’s disease (CD, n=5) or ulcerative colitis (UC, n=6) patients were collected and immediately disaggregated. Single-cell suspensions were processed using the 10x Genomics Next-GEM Single Cell kit assays (Chromium 3’ v3.0) and the resulting libraries sequenced (NovaSeq 6000 S1, Illumina). Data from 3452 myeloid cells was separated in silico and analyzed using Cell Ranger v3.1.0 and the R package Seurat. Results In HC, mast cells, CD1c+ dendritic cells (DCs) and resident macrophages (RMΦ) in different transcriptional states were identified. All RMΦ clusters were HLA-IIhi and expressed C1Q genes, SELENOP, CD74 and LYZ. Within RMΦ, a distinct cluster of M2-like cells characterized by high expression of CD209, CD163L1, LILRB5, AXL and MRC1 formed an independent cluster. IBD showed a marked increase in both the number of cells and heterogeneity within the myeloid compartment compared to HC. While RMΦ and M2 macrophages were decreased, we observed an infiltration of inflammatory monocytes and M1-like macrophages expressing the monocyte markers VCAN and CD300E. A cluster of TNIP3-expressing M1 macrophages that co-expressed ACOD1, KYNU, TRAF1, MMP19, IRAK2, TNF and IL1B was present in most UC and CD samples. Additional M1-like macrophage subsets, including a cluster characterized by high expression of CXCL5, HTRA1, SPP1, INHBA, MMP9, MMP14 and MMP10, or a cluster of NRG1, RETN, EREG, HBEGF, TGFB1 and VEGFA-expressing macrophages were identified in UC. Furthermore, IBD samples presented an additional cluster of mature DCs expressing CCL22, CCL17, CCL19 and CCR7. Importantly, our study is the first to capture infiltrating granulocytes in IBD patients by scRNA-seq; specifically, eosinophils expressing CLC, IL4 and IL13, and 3 neutrophil states, expressing FCGR2B, CMTM2, S100A8 and CXCL8. Conclusion We describe an unbiased approach for the identification of intestinal myeloid cells that revealed previously undescribed macrophage subpopulations. In addition, we discovered a marked heterogeneity within intestinal inflammatory macrophages that showed high patient-to-patient variability. We suggest that the diverse macrophage states in mucosal lesions could explain important differences in disease pathophysiology and contribute to the observed diversity in patient behavior.

Background Janus Kinases (JAK), including JAK1, JAK2, JAK3 and TYK2, have garnered increasing interest as therapeutic targets for several chronic inflammatory diseases such as inflammatory bowel disease (IBD). Although oral small molecule JAK inhibitors are being used in the clinics as an effective treatment for moderate-to-severe ulcerative colitis, nonethelessthey can lead to severe systemic immunosuppression, which is associated with an increased risk of infections. Our project aimed to develop a nanomedicine that induced JAK1 mRNA degradation within the intestinal mucosa with little systemic distribution. Methods The NEWDEAL project (H2020) developed both potent small interfering RNAs (siRNA) specific for JAK1 (siJAK1) or TNF (siTNF), and lipid nanoparticles (CL40) as nano-vectors. Their biodistribution in a mice colitis model was analyzed using labeled AF488-siJAK1 complexed to CL40 and given intrarectally (IR) for 3 consecutive days. In vivo cellular uptake was determined by FACS analysis. To induce colitis, C57/Bl6 mice received 2.5% dextrate sulfate sodium (DSS) in drinking water for 5 days. To determine efficacy of siRNAs, mice started DSS on day 0 and received IR administrations of siRNAs alone or complexed with CL40 nanoparticles on days -3, -2, -1, 1, 3, 5 and 7. On day 9, mice were sacrificed and disease activity index (DAI), histological score, fecal inflammatory markers and qPCR of targeted genes were analyzed. Results Colonic phagocytic cells - such as macrophages, neutrophils and monocytes - are the main targets cells of the siRNA-CL40 nanocomplexes following IR administration. A small percentage of cells in the draining lymph nodes captured siRNA CL40 nanocomplexes, remaining almost undetectable in spleen. This suggests a localized effect of the siRNA nanocomplexes after IR administration. While siJAK1-alone effectively reduced JAK1 mRNA expression in the distal colon, it did not improve intestinal inflammation induced by administering DSS. siTNF-CL40 treatment, though not siTNF-alone, significantly decreased intestinal inflammation in the DSS colitis model of treated mice, revealing significant protection from weight loss, lower histological scores, and reduced production of fecal lipocalin. Conclusion In summary, these results show that despite effectively reducing JAK1 mRNA expression, siJAK1 administration does not ameliorate colitis in a DSS mice model. However, we showed that a locally delivered siTNF-nanocomplex has the capacity to improve clinical, macroscopic and histological symptoms as well as fecal biomarkers in DSS colitic mice. We conclude not only that siRNA-CL40 target delivery is a good therapeutic strategy, but also that siTNF-CL40 is effective in locally treating intestinal inflammation.