Multi-channel microfluidic biosensor platform applied for online monitoring and screening of biofilm formation and activity

Bacterial colonization of surfaces and interfaces has a major impact on various areas including biotechnology, medicine, food industries, and water technologies. In most of these areas biofilm development has a strong impact on hygiene situations, product quality, and process efficacies. In consequence, biofilm manipulation and prevention is a fundamental issue to avoid adverse impacts. For such scenario online, non-destructive biofilm monitoring systems become important in many technical and industrial applications. This study reports such a system in form of a microfluidic sensor platform based on the combination of electrical impedance spectroscopy and amperometric current measurement, which allows sensitive online measurement of biofilm formation and activity. A total number of 12 parallel fluidic channels enable real-time online screening of various biofilms formed by different Pseudomonas aeruginosa and Stenotrophomonas maltophilia strains and complex mixed population biofilms. Experiments using disinfectant and antibiofilm reagents demonstrate that the biofilm sensor is able to discriminate between inactivation/killing of bacteria and destabilization of biofilm structures. The impedance and amperometric sensor data demonstrated the high dynamics of biofilms as a consequence of distinct responses to chemical treatment strategies. Gene expression of flagellar and fimbrial genes of biofilms grown inside the microfluidic system supported the detected biofilm growth kinetics. Thus, the presented biosensor platform is a qualified tool for assessing biofilm formation in specific environments and for evaluating the effectiveness of antibiofilm treatment strategies

Playing and Listening to Tailor-Made Notched Music: Cortical Plasticity Induced by Unimodal and Multimodal Training in Tinnitus Patients

Background. The generation and maintenance of tinnitus are assumed to be based on maladaptive functional cortical reorganization. Listening to modified music, which contains no energy in the range of the individual tinnitus frequency, can inhibit the corresponding neuronal activity in the auditory cortex. Music making has been shown to be a powerful stimulator for brain plasticity, inducing changes in multiple sensory systems. Using magnetoencephalographic (MEG) and behavioral measurements we evaluated the cortical plasticity effects of two months of (a) active listening to (unisensory) versus (b) learning to play (multisensory) tailor-made notched music in nonmusician tinnitus patients. Taking into account the fact that uni- and multisensory trainings induce different patterns of cortical plasticity we hypothesized that these two protocols will have different affects. Results. Only the active listening (unisensory) group showed significant reduction of tinnitus related activity of the middle temporal cortex and an increase in the activity of a tinnitus-coping related posterior parietal area. Conclusions. These findings indicate that active listening to tailor-made notched music induces greater neuroplastic changes in the maladaptively reorganized cortical network of tinnitus patients while additional integration of other sensory modalities during training reduces these neuroplastic effects

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study.

Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories

Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen.

Funder: Raymond and Beverly Sackler FoundationFunder: Isaac Newton TrustFunder: Newnham College, University of CambridgeFunder: Medical Research CouncilMutation rates vary both within and between bacterial species, and understanding what drives this variation is essential for understanding the evolutionary dynamics of bacterial populations. In this study, we investigate two factors that are predicted to influence the mutation rate: ecology and genome size. We conducted mutation accumulation experiments on eight strains of the emerging zoonotic pathogen Streptococcus suis. Natural variation within this species allows us to compare tonsil carriage and invasive disease isolates, from both more and less pathogenic populations, with a wide range of genome sizes. We find that invasive disease isolates have repeatedly evolved mutation rates that are higher than those of closely related carriage isolates, regardless of variation in genome size. Independent of this variation in overall rate, we also observe a stronger bias towards G/C to A/T mutations in isolates from more pathogenic populations, whose genomes tend to be smaller and more AT-rich. Our results suggest that ecology is a stronger correlate of mutation rate than genome size over these timescales, and that transitions to invasive disease are consistently accompanied by rapid increases in mutation rate. These results shed light on the impact that ecology can have on the adaptive potential of bacterial pathogens

The Structural and Mechanical Basis for Passive‐Hydraulic Pine Cone Actuation

The opening and closing of pine cones is based on the hygroscopic behavior of the individual seed scales around the cone axis, which bend passively in response to changes in environmental humidity. Although prior studies suggest a bilayer architecture consisting of lower actuating (swellable) sclereid and upper restrictive (non‐ or lesser swellable) sclerenchymatous fiber tissue layers to be the structural basis of this behavior, the exact mechanism of how humidity changes are translated into global movement are still unclear. Here, the mechanical and hydraulic properties of each structural component of the scale are investigated to get a holistic picture of their functional interplay. Measurements of the wetting behavior, water uptake, and mechanical measurements are used to analyze the influence of hydration on the different tissues of the cone scales. Furthermore, their dimensional changes during actuation are measured by comparative micro‐computed tomography (µ‐CT) investigations of dry and wet scales, which are corroborated and extended by 3D‐digital image correlation‐based displacement and strain analyses, biomechanical testing of actuation force, and finite element simulations. Altogether, a model allowing a detailed mechanistic understanding of pine cone actuation is developed, which is a prime concept generator for the development of biomimetic hygromorphic systems

The structural and mechanical basis for passive‐hydraulic pine cone actuation

The opening and closing of pine cones is based on the hygroscopic behavior of the individual seed scales around the cone axis, which bend passively in response to changes in environmental humidity. Although prior studies suggest a bilayer architecture consisting of lower actuating (swellable) sclereid and upper restrictive (non‐ or lesser swellable) sclerenchymatous fiber tissue layers to be the structural basis of this behavior, the exact mechanism of how humidity changes are translated into global movement are still unclear. Here, the mechanical and hydraulic properties of each structural component of the scale are investigated to get a holistic picture of their functional interplay. Measurements of the wetting behavior, water uptake, and mechanical measurements are used to analyze the influence of hydration on the different tissues of the cone scales. Furthermore, their dimensional changes during actuation are measured by comparative micro‐computed tomography (µ‐CT) investigations of dry and wet scales, which are corroborated and extended by 3D‐digital image correlation‐based displacement and strain analyses, biomechanical testing of actuation force, and finite element simulations. Altogether, a model allowing a detailed mechanistic understanding of pine cone actuation is developed, which is a prime concept generator for the development of biomimetic hygromorphic systems.Deutsche Bundesstiftung UmweltFreiburg Center for interactive Materials and Bioinspired Technologies, University of FreiburgJoint Research Network on Advanced Materials and Systems (JONAS), BASF SE, LudwigshafenCluster of Excellence livMatS, Deutsche ForschungsgemeinschaftMinisterium für Wissenschaft, Forschung und Kunst Baden‐Württember

Origins Of Heterospory And The Seed Habit: The Role Of Heterochrony

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149713/1/tax04577.pd

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs

The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs

The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized.This work was primarily funded by an EU Horizon 2020 grant “PIGSs” (727966) and a ZELS BBSRC award “Myanmar Pigs Partnership (MPP)” (BB/L018934/1). G.G.R.M., E.L.M., and L.A.W. were supported by a Sir Henry Dale Fellowship to L.A.W. jointly funded by the Wellcome Trust and the Royal Society (109385/Z/15/Z). N.H. was supported by a Challenge grant from the Royal Society (CH16011) and an Isaac Newton Trust Research Grant [17.24(u)]. G.G.R.M. was also supported by a Research Fellowship at Newnham College. S.B. is supported by the Medical Research Council (MR/V032836/1). PIC North America provided part of the funds for the sequencing of the isolates from the USA. A.J.B. and M.M. were funded by Medical Research Council and Biotechnology and Biological Sciences Research Council studentships respectively, and M.M. was co-funded by the Raymond and Beverly Sackler Fund. We would like to acknowledge Susanna Williamson at the APHA for providing samples, Oscar Cabezón for sampling of the wild boar population in Spain, Mark O’Dea for access to sequence data from Australian isolates, the PIGSs and MPP consortiums for providing samples and helpful discussions, Julian Parkhill and John Welch for helpful discussions, and two anonymous reviewers for their valuable suggestions for improving the manuscript. This research was funded in whole or in part by the Wellcome Trust. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.info:eu-repo/semantics/publishedVersio

Neuro-cognitive mechanisms of conscious and unconscious visual perception: From a plethora of phenomena to general principles

Psychological and neuroscience approaches have promoted much progress in elucidating the cognitive and neural mechanisms that underlie phenomenal visual awareness during the last decades. In this article, we provide an overview of the latest research investigating important phenomena in conscious and unconscious vision. We identify general principles to characterize conscious and unconscious visual perception, which may serve as important building blocks for a unified model to explain the plethora of findings. We argue that in particular the integration of principles from both conscious and unconscious vision is advantageous and provides critical constraints for developing adequate theoretical models. Based on the principles identified in our review, we outline essential components of a unified model of conscious and unconscious visual perception. We propose that awareness refers to consolidated visual representations, which are accessible to the entire brain and therefore globally available. However, visual awareness not only depends on consolidation within the visual system, but is additionally the result of a post-sensory gating process, which is mediated by higher-level cognitive control mechanisms. We further propose that amplification of visual representations by attentional sensitization is not exclusive to the domain of conscious perception, but also applies to visual stimuli, which remain unconscious. Conscious and unconscious processing modes are highly interdependent with influences in both directions. We therefore argue that exactly this interdependence renders a unified model of conscious and unconscious visual perception valuable. Computational modeling jointly with focused experimental research could lead to a better understanding of the plethora of empirical phenomena in consciousness research