Project description:Beneficial microbial symbionts are often horizontally acquired by their animal hosts from environmental sources, requiring the symbionts to complete a lifestyle transition from free-living in the environment to association with host tissues. In the model symbiosis between the Hawaiian bobtail squid and its microbial symbiont Vibrio fischeri, one mechanism used to make this transition during host colonization is the formation of biofilm-like aggregates on host mucosa. Extensive work has previously been conducted to isolate the critical factors controlling V. fischeri biofilm formation, yet much remains unknown regarding the full breadth of the biofilm-associated regulon. Here, we probed in vitro models of biofilm formation using transcriptomics, to identify novel regulatory pathways active within biofilms of the V. fischeri type strain ES114. Through comparing the gene-sets which became differentially regulated in multiple biofilm models, we discovered a shared set of 232 genes which demonstrated similar patterns in expression relative to uninduced controls. These genes contained representatives of multiple exopolysaccharide loci, genes involved in flagellar motility, and a diverse collection of other genes. Follow-up analysis suggested that these transcriptomic changes reflected true phenotypic effects, including changes in motility and cyclic-di-GMP production in biofilm-induced backgrounds. Beyond characterizing the shared biofilm response, we additionally profiled the regulatory activity of the sensor kinase RscS. This sensor kinase has previously been characterized to function as a phospho-donor within an established biofilm-inducing phospho-relay, yet our data suggests that RscS moonlights in at least one other phospho-relay that integrates downstream signaling from a homolog of the Vibrio cholerae response regulator VpsR, without a need for its established signaling partners. Overall, this study adds to our understanding of the genes involved in V. fischeri biofilm regulation, while revealing new regulatory pathways branching from previously characterized signaling networks.
Project description:Metabolic signature of HepaRG cells exposed to ethanol and tumor necrosis factor alpha to study ethanol-induced hepatotoxicity by LC-MS-based untargeted metabolomics.
Dataset contains .mzML files originating from an LC-QTOF (6530 for metabolomics & 6560 for lipidomics). HepaRG samples were exposed to ethanol, ethanol & TNF-alpha or no ethanol and TNF-alpha (i.e. negative control). In addition, data from extraction blanks and QC pooled samples are available. Both intracellular and extracellular extracts were analyzed on four different platforms (metabolomics in ESI+ and ESI- and lipidomics in ESI+ and ESI-).
Project description:Early-life adversities increase vulnerability to substance use disorders, which are characterized by persistent, uncontrollable drive to seek drugs, often leading to relapse. Previously, we reported that early social isolation (ESI) during adolescence potentiates heroin-seeking in mice. However, the underlying neurobiology remains unknown. Here, we found that ESI aggravated heroin-induced neuronal dysfunction in prelimbic cortex (PrL) to ventral tegmental area (VTA) projecting neurons. Activating PrL->VTA projection attenuated ESI-potentiated heroin seeking, alongside normalized neuronal function. RNA-seq revealed that ESI and heroin convergently altered genes regulating morphogenesis and metabolism, with Tmsb4x (thymosin β4) as a key gene. ESI and heroin interaction affected genes regulating cell cycle and DNA damage response, with Mcm3 and Mcm7 (minichromosome maintenance proteins 3/7) as hubs. PrL thymosin β4 infusion or CRISPR-Cas9-mediated PrL->VTA projection-specific Mcm3/7 knockdown attenuated ESI-potentiated heroin-seeking and neuronal hypofunction. Our study suggests that ESI-potentiated heroin relapse is associated with neuronal and transcriptional alterations in PrL->VTA projection.
Project description:Raw data and Metabolomics of hemocytes from the Hawaiian bobtail squid E. scolopes exposed to Vibrio fischeri and magnetic nanoparticles
Project description:Mass spectrometry imaging (MSI) allows investigating the spatial distribution of chemical compounds directly in biological tissues. As the analytical depth of MSI is limited, MSI needs to be coupled to more sensitive local extraction-based omics approaches to achieve a comprehensive molecular characterization. For this it is important to retain the spatial information provided by MSI for follow-up omics studies. It has been shown that regiospecific MSI data can be used to guide a laser microdissection system (LMD) for ultra-sensitive LC-MS analyses. So far, this combination has required separate and specialized MS instrumentation. Recent advances in dual-source instrumentation, harboring both MALDI and ESI sources, promise state-of-the-art MSI and liquid-based proteomic capabilities on the same MS instrument. In this study, we demonstrate that such an instrument can offer both, fast lipid-based MSI at high mass- and high lateral resolution, and sensitive LC-MS on local protein extracts from the exact same tissue section.
Project description:This dataset provides a comprehensive proteomic characterization of a defined five-strain human gut bacterial consortium, including Bifidobacterium and Roseburia species. The consortium was grown on different carbohydrate sources, human milk oligosaccharides, dietary fibers, or a combination of both, to investigate how substrate availability influences microbial protein expression and metabolic activity. The resulting data captures functional responses and interactions within the community, offering insights into carbohydrate utilization, cross-feeding dynamics, and gut microbial ecology. This resource can support studies of microbiome function, microbial interactions, and dietary modulation of gut microbiota.
Project description:Bacterial outer-membrane vesicles (OMVs) and the cargo they carry are increasingly recognized as a means of communication between microbial symbionts and the cells of their host. However, few studies have focused on the biochemical and molecular mechanisms underlying OMV-signaling during symbiosis onset and development. We show here that SypC, an OMV protein of the bioluminescent symbiont Vibrio fischeri, is taken up by cells of the squid host Euprymna scolopes where it assumes a new function, i.e., the facilitation of symbiont-induced light-organ morphogenesis. SypC is a Wza-like outer-membrane protein found in host-associated Vibrionaceae, and is essential for V. fischeri biofilm formation. Colonization or direct treatment with V. fischeri OMVs triggers host development, which is reduced or delayed if the host is instead exposed to a sypC mutant or its OMVs. RNA-seq analyses comparing light-organs colonized by the mutant versus its parent strain revealed differential expression of host genes involved in immune responses and tissue morphogenesis. Immunocytochemical imaging revealed that, within the light-organ crypts, SypC-bearing OMVs are taken up by the host’s macrophage-like cells, revealing the mechanism by which SypC travels throughout the tissue to trigger morphogenesis. Taken together, the data show that, in addition to its role in biofilm formation, SypC has a second function promoting colonization and the induction of symbiotic-tissue development. These findings provide a critical piece of a puzzle whereby a rich array of host and symbiont molecules work in concert to orchestrate normal symbiont colonization and host development within the first hours to days of symbiosis.
Project description:The bioluminescent bacterium Vibrio fischeri initiates a specific, persistent symbiosis in the light organ of the squid Euprymna scolopes. During the early stages of colonization, V. fischeri is exposed to host-derived nitric oxide (NO). While NO can be both an antimicrobial component of innate immunity and a common signaling molecule of eukaryotes, its roles in beneficial host-microbe associations remain undescribed. V. fischeri encodes HnoX, a member of a family of bacterial NO-binding proteins of unknown function. We hypothesized that HnoX acts as a NO sensor that is involved in regulating symbiosis-related genes during initiation of symbiosis. With an aim to discover the genes whose regulations respond to NO signal, and in an HnoX-mediated fashion in particular, we carried out a whole-genome expression study on the wild-type and an insertional mutant of hnoX.