Project description:PARTIAL UPLOAD: Metaproteomic dataset pertaining to marine biofilms analysed after growth on low-density polyethylene (LDPE) for 3 (D3) and 7 (D7) days. Four replicates per condition.
Project description:The aim of this study was to investigate the plastic colonisation process, to identify the active taxa involved in biofilm formation and the mechanisms used to initiate colonisation. To achieve this, a marine plastisphere characterised by active hydrocarbonoclastic genera was used as the inoculum for a short-term microcosm experiment using virgin low-density polyethylene as the sole carbon source. Following incubation for 1 and 2 weeks (representing early and late colonisation, respectively), a taxonomic and comparative metaproteomic approach was used to explore shifts in diversity and function.
Project description:Environment shapes development through a phenomenon called developmental plasticity. Deciphering its genetic basis has potential to shed light on the origin of novel traits and adaptation to environmental change. However, molecular studies are scarce, and little is known about molecular mechanisms associated with plasticity. We investigated the gene regulatory network controlling predatory vs. non-predatory dimorphism in the nematode Pristionchus pacificus and found that it consists of genes of extremely different age classes. We isolated mutants in the conserved nuclear hormone receptor nhr-1 with previously unseen phenotypic effects. They disrupt mouth-form determination and result in animals combining features of both wild-type morphs. In contrast, mutants in another conserved nuclear hormone receptor nhr-40 display altered morph ratios, but no intermediate morphology. Despite divergent modes of control, NHR-1 and NHR-40 share transcriptional targets, which encode extracellular proteins that have no orthologs in Caenorhabditis elegans and result from lineage-specific expansions. An array of transcriptional reporters revealed co-expression of all tested targets in the same pharyngeal gland cell. Major morphological changes in this gland cell accompanied the evolution of teeth and predation, linking rapid gene turnover with morphological innovations. Thus, the origin of feeding plasticity involved novelty at the level of genes, cells and behavior.
Project description:Biofilms present a great challenge in antimicrobial therapy due to their inherent tolerance to conventional antibiotics, promoting the need for advanced drug delivery strategies that improve therapy. While various nanoparticles (NPs) have been reported for this purpose, DNA-based NPs remain a largely unexploited resource against biofilm-associated infections. To fill this gap and to lay the groundwork for their potential therapeutic exploitation, we investigated the diffusion, penetration, and retention behaviors of three DNA-based nanocarriers -plain or modified-within P. aeruginosa biofilms. Watson-Crick base pairing or hydrophobic interactions mediated the formation of the plain NPs whilst electrostatic interaction enabled optimization of coated NPs via microfluidic mixing. We assessed the interactions of the nanocarriers with biofilm structures via Single Plane Illumination Microscopy - Fluorescence Correlation Spectroscopy (SPIM-FCS) and Confocal Laser Scanning Microscopy (CLSM). We demonstrate the impact of microfluidic parameters on the physicochemical properties of the modified DNA NPs and their subsequent distinct behaviors in the biofilm. Our results show that single stranded DNA micelles (ssDNA micelle) and tetrahedral DNA nanostructures (TDN) had similar diffusion and penetration profiles, whereas chitosan-coated TDN (TDN-Chit) showed reduced diffusion and increased biofilm retention. This is attributable to the relatively larger size and positive surface charge of the TDN-Chit NPs. The study shows first and foremost that DNA can be used as building block in drug delivery for antibiofilm therapeutics. Moreover, the overall behavioral findings are pivotal for the strategic selection of therapeutic agents to be encapsulated within these structures, possibly affecting the treatment efficacy. This research not only highlights the underexplored potential of DNA-based NPs in antibiofilm therapy but also advocates for further studies using different optimization strategies to refine these nanocarrier systems for targeted treatments in biofilm-related infections.
Project description:Bacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid-bacteria coevolution is solely based on studies done in well-mixed liquid cultures, even though biofilms represent the main way of bacterial life on Earth and are responsible for most infections. The spatial structure and the heterogeneity provided by biofilms are known to lead to increased genetic diversity as compared with well-mixed liquids. Therefore, we expect that growth in this complex environment could affect the evolutionary trajectories of plasmid-host dyads. We experimentally evolved Shewanella oneidensis MR-1 with plasmid pBP136Gm in biofilms and chemostats and sequenced the genomes of clones and populations. Biofilm populations not only maintained a higher diversity of mutations than chemostat populations but contained a few clones with markedly more persistent plasmids that evolved via multiple distinct trajectories. These included the acquisition of a putative toxin-antitoxin transposon by the plasmid and chromosomal mutations. Some of these genetic changes resulted in loss of plasmid transferability or decrease in plasmid cost. Growth in chemostats led to a higher proportion of variants with decreased plasmid persistence, a phenomenon not detected in biofilms. We suggest that the presence of more stable plasmid-host dyads in biofilms reflects higher genetic diversity and possibly unknown selection pressures. Overall, this study underscores the importance of the mode of growth in the evolution of antibiotic-resistant bacteria.
Project description:Tunicates have been extensively studied because of their crucial phylogenetic location (the closest living relatives of vertebrates) and particular developmental plan. Recent genome efforts have disclosed that tunicates are also remarkable in their genome organization and molecular evolutionary patterns. Here, we review these latter aspects, comparing the similarities and specificities of two model species of the group: Oikopleura dioica and Ciona intestinalis. These species exhibit great genome plasticity and Oikopleura in particular has undergone a process of extreme genome reduction and compaction that can be explained in part by gene loss, but is mostly due to other mechanisms such as shortening of intergenic distances and introns, and scarcity of mobile elements. In Ciona, genome reorganization was less severe being more similar to the other chordates in several aspects. Rates and patterns of molecular evolution are also peculiar in tunicates, being Ciona about 50% faster than vertebrates and Oikopleura three times faster. In fact, the latter species is considered as the fastest evolving metazoan recorded so far. Two processes of increase in evolutionary rates have taken place in tunicates. One of them is more extreme, and basically restricted to genes encoding regulatory proteins (transcription regulators, chromatin remodeling proteins, and metabolic regulators), and the other one is less pronounced but affects the whole genome. Very likely adaptive evolution has played a very significant role in the first, whereas the functional and/or evolutionary causes of the second are less clear and the evidence is not conclusive. The evidences supporting the incidence of increased mutation and less efficient negative selection are presented and discussed.
Project description:To characterize the taxonomic and functional diversity of biofilms on plastics in marine environments, plastic pellets (PE and PS, ø 3mm) and wooden pellets (as organic control) were incubated at three stations: at the Baltic Sea coast in Heiligendamm (coast), in a dead branch of the river Warnow in Warnemünde (inlet), and in the Warnow estuary (estuary). After two weeks of incubation, all pellets were frozen for subsequent metagenome sequencing and metaproteomic analysis. Biofilm communities in the samples were compared on multiple levels: a) between the two plastic materials, b) between the individual incubation sites, and c) between the plastic materials and the wooden control. Using a semiquantitative approach, we established metaproteome profiles, which reflect the dominant taxonomic groups as well as abundant metabolic functions in the respective samples.
Project description:Air pollution is the world's largest single environmental health risk (WHO). Particulate matter such as black carbon is one of the main components of air pollution. The effects of particulate matter on human health are well established however the effects on bacteria, organisms central to ecosystems in humans and in the natural environment, are poorly understood. We report here for the first time that black carbon drastically changes the development of bacterial biofilms, key aspects of bacterial colonisation and survival. Our data show that exposure to black carbon induces structural, compositional and functional changes in the biofilms of both S. pneumoniae and S. aureus. Importantly, the tolerance of the biofilms to multiple antibiotics and proteolytic degradation is significantly affected. Additionally, our results show that black carbon impacts bacterial colonisation in vivo. In a mouse nasopharyngeal colonisation model, black carbon caused S. pneumoniae to spread from the nasopharynx to the lungs, which is essential for subsequent infection. Therefore our study highlights that air pollution has a significant effect on bacteria that has been largely overlooked. Consequently these findings have important implications concerning the impact of air pollution on human health and bacterial ecosystems worldwide.
Project description:Exosomes, or extracellular vesicles, represent the latest cell-free addition to the regenerative medicine toolkit. In vitro preclinical studies have demonstrated the safety and efficacy of exosomes, which vary based on source and biomanufacturing, for a myriad of potential therapeutic applications relevant to skin and soft tissue reconstruction. Primary search was performed in September 2021 on the MEDLINE database via PubMed and Ovid, with focus on articles about therapeutic application of exosomes or extracellular vesicles. In total, 130 articles met criteria for applicability, including early-stage clinical trials, preclinical research studies with in vivo application, and articles applicable to plastic and reconstructive surgery and dermatology. Most studies used animal models of human disease processes, using either animal donor cells to isolate exosomes, or human donor cells in animal models. Exosome technology has catapulted as an acellular therapeutic vehicle with off-the-shelf accessibility. These features eliminate prior threshold for broad adoption of regenerative cell-based therapies into surgical and medical practice. To date, there are no exosome products approved by the US Food and Drug Administration. This review highlights exosomes as the new frontier in regenerative medicine and outlines its preclinical therapeutic applications for cutaneous repair and restoration.