Biology subjects

Sikorski, P.

Publications and source records attributed to Sikorski, P..

18 recordsLinked to original sources

bioRxiv2026

Ultra-structural analysis of mineralized extracellular matrix in osteogenic monolayers and spheroids: comparison of sample preparation methods

Accurate evaluation of extracellular matrix (ECM) mineralization at the nano-scale is essential for establishing relevant in vitro bone models. This is particularly important with the development and increased application of three-dimensional (3D) cell models for biological research. Transmission electron microscopy (TEM) allows to perform ultra-structural analysis of cells and ECM organization, but its application in in vitro bone models remains limited, due to the potential alteration or loss of the mineral phase during sample preparation. In this study, we compared two TEM sample preparation methods the conventional chemical fixation and the anhydrous methods to evaluate their ability to preserve the mineralized ECM in MC3T3-E1 cells cultured as monolayers and as alginate-encapsulated bone spheroids. Chemical fixation preserved cellular ultra-structure and collagen organization, allowing for detailed assessment of cells and ECM organization. Although mineral deposits were detected and their needle-like morphology assessed, characterization of more immature deposits was partially limited by the effects of uranyl acetate and the overall sample preparation process, which could lead to alteration or loss of less stable mineral phases. The anhydrous preparation method resulted in limited preservation of cellular and ECM morphology and did not allow reliable identification of mineral deposits. When applied to spheroids, the chemical fixation method preserved the 3D architecture, collagen-rich ECM and inner mineral deposits, confirming spheroids as a relevant model for bone studies. Overall, these results highlight the need for optimized sample preparation strategies that preserve both ultra-structure and mineral components for accurate nano-scale characterization of bone mineralization.

biophysics↗

bioRxiv2026

Label-free imaging of matrix mineralization in alginate-encapsulated bone spheroids using Coherent Raman Scattering microscopy

Three-dimensional (3D) cell cultures, such as spheroids, are increasingly used to perform advanced studies on bone matrix mineralization. However, their full characterization remains challenging. Traditional colorimetric and fluorescent assays using dyes, such as Alizarin Red S (ARS) and calcein, are effective in monolayer cell cultures, but fail to provide reliable information when used in complex 3D cell constructs. In this study, we investigated the application of Coherent Raman Scattering microscopy for label-free, comprehensive characterization of extracellular matrix (ECM) mineralization in alginate-encapsulated bone spheroids. After confirming that traditional staining techniques are unreliable for mineral detection in spheroids, Stimulated Raman Scattering (SRS) microscopy was used to detect phosphate-rich mineral deposits at a Raman shift of 960 cm-1, while Second Harmonic Generation (SHG) microscopy was used in association with SRS to provide complementary information on the deposition and organization of the collagenous matrix. SRS was used to detect lipid-rich regions at a Raman shift of 2857 cm-1 to perform cell localization. SRS imaging revealed the presence of phosphate-rich regions in the spheroids, including the core regions, usually challenging to characterize in intact 3D constructs. Raman spectral scans on SRS-positive regions confirmed the specificity of the phosphate signal. In addition, comparison of SRS and Coherent Anti-Stokes Raman Scattering (CARS) demonstrated the advantage of SRS in terms of reduced background compared to CARS for lipid imaging. Taken together, our results demonstrated that SRS, in combination with SHG, provides a promising and powerful approach to perform label-free, chemically specific characterization of intact 3D bone models.

biophysics↗

bioRxiv2025

Characterization of ECM produced by MC3T3-E1 cellular spheroids encapsulated in alginate hydrogel

The application of cellular spheroids in bone tissue engineering research has gained significant interest in the last decade. Compared to monolayer cell cultures, the 3D architecture allows for more physiological cell-cell and cell-extracellular matrix (ECM) interactions that make cellular spheroids a suitable model system to investigate bone ECM in vitro. The use of 3D model systems requires fine-tuning of experimental methods used to study cell morphology, ECM deposition and mineralization, and cell-ECM interactions. In this study, we use MC3T3-E1 cellular spheroids encapsulated in an alginate hydrogel to study and characterize the deposited ECM. Spheroid shape and structure were evaluated using confocal microscopy. The deposited collagenous ECM was characterized using quantitative assay and microscopy, in particular Second Harmonic Imaging Microscopy (SHIM), hydroxyproline (HYP) assay and Transmission Electron Microscopy (TEM). The use of hydrogel constructs allows easy handling and imaging of the samples and helps to preserve the spheroids stability by preventing cells from adhering to the culture dish surface. We use a non-modified alginate hydrogel that does not facilitate cell attachment and therefore functions as an inert encapsulating scaffold. Constructs were cultured for up to 4 weeks. SHIM, HYP assay and TEM confirmed the deposition of collagenous matrix by the spheroid, with most of it taking place between week 2 and 4. We demonstrated that alginate encapsulated bone spheroids are a promising model for studying bone ECM in vitro.

bioengineering↗

bioRxiv2024

Nanoporous Platinum Microelectrode Arrays for Neuroscience Applications

Microelectrode arrays are invaluable tools for investigating the electrophysiological behaviour of neuronal networks with high spatiotemporal precision. In recent years, it has become increasingly common to functionalize such electrodes with highly porous platinum to increase their effective surface area, and hence their signal-to-noise ratio. Although such functionalization significantly improves the electrochemical performance of the electrodes, the impact of various electrode morphologies on biocompatibility and electrophysiological performance in cell cultures remains poorly understood. In this study, we introduce reproducible protocols for depositing highly porous platinum with varying morphologies on microelectrodes designed for neural cell cultures. We also evaluate the impact of morphology and electrode size on the signal-to-noise ratio in recordings from rat cortical neurons cultured on these electrodes. Our results indicate that electrodes with a uniform layer of highly nanoporous platinum offer the best trade-off between biocompatibility, electrochemical, and electrophysiological performance. While more microporous electrodes exhibited lower impedance, nanoporous electrodes detected higher extracellular signal amplitudes from neurons, suggesting reduced distance between perisomatic neuronal areas and the electrodes. Additionally, these nanoporous electrodes showed fewer thickness variations at their edges compared to the more porous electrodes. Such edges can be mechanically broken off during cell culturing and contribute to long-term cytotoxic effects, which is highly undesirable. We hope this work will contribute to better standardization in creating and utilizing nanoporous platinum microelectrodes for neuroscience applications. Improving the accessibility and reproducibility of this technology is crucial for enhancing the quality of electrophysiological data and advancing our understanding of neuronal network function and dysfunction.

neuroscience↗

bioRxiv2024

Engineered Cortical Microcircuits for Investigations of Neuroplasticity

Recent advances in neural engineering have opened new ways to investigate the impact of topology on neural network function. Leveraging microfluidic technologies, it is possible to establish modular circuit motifs that promote both segregation and integration of information processing in the engineered neural networks, similar to those observed in vivo. However, the impact of the underlying topologies on network dynamics and response to pathological perturbation remains largely unresolved. In this work, we demonstrate the utilization of microfluidic platforms with 12 interconnected nodes to structure modular, cortical engineered neural networks. By implementing geometrical constraints inspired by a Tesla valve within the connecting microtunnels, we additionally exert control over the direction of axonal outgrowth between the nodes. Interfacing these platforms with nanoporous microelectrode arrays reveals that the resulting laminar cortical networks exhibit pronounced segregated and integrated functional dynamics across layers, mirroring key elements of the feedforward, hierarchical information processing observed in the neocortex. The multi-nodal configuration also facilitates selective perturbation of individual nodes within the networks. To illustrate this, we induced hypoxia, a key factor in the pathogenesis of various neurological disorders, in well-connected nodes within the networks. Our findings demonstrate that such perturbations induce ablation of information flow across the hypoxic node, while enabling the study of plasticity and information processing adaptations in neighboring nodes and neural communication pathways. In summary, our presented model system recapitulates fundamental attributes of the microcircuit organization of neocortical neural networks, rendering it highly pertinent for preclinical neuroscience research. This model system holds promise for yielding new insights into the development, topological organization, and neuroplasticity mechanisms of the neocortex across the micro- and mesoscale level, in both healthy and pathological conditions.

neuroscience↗

bioRxiv2024

Functional Complexity of Engineered Neural Networks Self-Organized on Novel 3D Interfaces

Engineered neural networks are indispensable tools for studying neural function and dysfunction in controlled microenvironments. In vitro, neurons self-organize into complex assemblies with structural and functional similarities to in vivo circuits. Traditionally, these models are established on planar interfaces, but studies suggest that the lack of a three-dimensional growth space affects neuronal organization and function. While methods supporting 3D growth exist, reproducible 3D neuroengineering techniques compatible with electrophysiological recording methods are still needed. In this study, we developed a novel biocompatible interface made of the polymer SU-8 to support 3D network development. Using electron microscopy and immunocytochemistry, we show that neurons utilize these 3D scaffolds to self-assemble into complex, multi-layered networks. Furthermore, interfacing the scaffolds with custom microelectrode arrays enabled characterizing of electrophysiological activity. Both planar control networks and 3D networks displayed complex interactions with integrated and segregated functional dynamics. However, control networks showed stronger functional interconnections, higher entropy, and increased firing rates. In summary, our interfaces provide a versatile approach for supporting neural networks with a 3D growth environment, compatible with assorted electrophysiology and imaging techniques. This system can offer new insights into the impact of 3D topologies on neural network organization and function.

neuroscience↗

bioRxiv2022

Structure-Function Dynamics of Engineered, Modular Neuronal Networks with Controllable Afferent-Efferent Connectivity

Microfluidic devices interfaced with microelectrode arrays have in recent years emerged as powerful platforms for studying and manipulating in vitro neuronal networks at the micro- and mesoscale. By segregating neuronal populations using microchannels only permissible to axons, neuronal networks can be designed to mimic the highly organized, modular topology of neuronal assemblies in the brain. However, little is known about how the underlying topological features of such engineered neuronal networks contribute to their functional profile. To start addressing this question, a key parameter is control of afferent or efferent connectivity within the network. In this study, we show that a microfluidic device featuring axon guiding channels with geometrical constraints inspired by a Tesla valve effectively promotes unidirectional axonal outgrowth between neuronal nodes, thereby enabling us to control afferent connectivity. Our results moreover indicate that these networks exhibit a more efficient network organization with higher modularity compared to single nodal controls. We verified this by applying designer viral tools to fluorescently label the neurons to visualize the structure of the networks, combined with extracellular electrophysiological recordings using embedded nanoporous microelectrodes to study the functional dynamics of these networks during maturation. We furthermore show that electrical stimulations of the networks induce signals selectively transmitted in a feedforward fashion between the neuronal populations. A key advantage with our microdevice is the ability to longitudinally study and manipulate both the structure and function of neuronal networks with high accuracy. This model system has the potential to provide novel insights into the development, topological organization, and neuroplasticity mechanisms of neuronal assemblies at the micro- and mesoscale in healthy and perturbed conditions.

neuroscience↗

bioRxiv2020

Tailoring the assembly of collagen fibers in alginate microspheres

The application of microspheres instead of bulk hydrogels in cell-laden biomaterials offers multiple advantages such as a high surface-to-volume-ratio and, consequently, a better nutrition and oxygen transfer to and from cells. The preparation of inert alginate microspheres is facile, quick, and well-established and the fabrication of alginate-collagen microspheres has been previously reported. However, no detailed characterization of the collagen fibrillogenesis in the alginate matrix is available. We use second-harmonic imaging microscopy reflection microscopy and turbidity assay to study assembly of collagen in alginate microspheres. We show that the assembly of collagen fibers in a gelled alginate matrix is a complex process that can be aided by addition of small polar molecules, such as glycine and by a careful selection of the gelling buffer used to prepare alginate hydrogels. HighlightsO_LIIn situ characterization of collagen fiber assembly in a gelled alginate matrix using collagen-specific second harmonic generated microscopy C_LIO_LICollagen fibrillogenesis is positively influenced by the presence of small molecules in the solution prior microsphere preparation C_LIO_LIThe ratio and amount of calcium, sodium and chloride ions used for the alginate gelling has also a crucial impact on the development of a collagen fiber network C_LI

bioengineering↗

bioRxiv2020

Actin cytoskeletal and focal adhesion organisation in U2OS cells on polymer nanostructures

Cells in their natural environment are embedded in a complex surrounding consisting of biochemical and biomechanical cues directing cell properties and cell behaviour. Nonetheless, in vitro cell studies are typically performed on flat surfaces, with clear differences from the more complex situation cells experience in vivo. To increase the physiological relevance of these studies, a number of advanced cellular substrates for in vitro studies have been applied. One of these approaches include flat surfaces decorated with vertically aligned nanostructures. In this work, we explore how U2OS cells are affected by arrays of polymer nanopillars fabricated on flat glass surfaces. We focus on describing changes to the organisation of the actin cytoskeleton and in the location, number and shape of focal adhesions. From our findings we identify that the cells can be categorised into different regimes based on their spreading and adhesion behaviour on nanopillars. A quantitative analysis suggests that cells seeded on dense nanopillar arrays are suspended on top of the pillars with focal adhesions forming closer to the cell periphery compared to flat surfaces or sparse pillar arrays. This change is analogous to similar responses for cells seeded on soft substrates. Overall, we show that the combination of high throughput nanofabrication, advanced optical microscopy, molecular biology tools to visualise cellular processes and data analysis can be used to investigate how cells interact with nanostructured surfaces and will in the future help to create culture substrates that induce particular cell function.

biophysics↗

bioRxiv2020

Experimental study of microbial induced carbonate precipitation (MICP) in the presence of CaCO3 seeds

Microbial-induced calcium carbonate precipitation (MICP) is a biological process inducing biomineralization of CaCO3. This can be used to form a solid, concrete-like material. To be able to use MICP successfully for producing solid materials, it is important to understand the formation process of the material in detail. It is well known, that crystallization surfaces can influence the precipitation process. Therefore, we present in this contribution a systematic study investigating the influence of calcite seeds on the MICP processes. We focus on the pH changes during the crystallization process measured with absorption spectroscopy and on the optical density (OD) signal to analyze the precipitation process. Furthermore, optical microscopy was used to visualize the precipitation processes in the sample and connect them to changes in pH and OD. We show that there is a significant difference in the pH evolution between samples with and without calcite seeds present and that the shape of the pH evolution and the changes in OD can give detailed information about the mineral precipitation and transformations. In the presented experiments we show that amorphous calcium carbonate (ACC) can also precipitate in the presence of initial calcite seeds, which can have consequences for consolidated MICP materials.

biophysics↗

bioRxiv2020

Functional and LC-MS/MS analysis of in vitro transcribed mRNAs carrying phosphorothioate or boranophosphate moieties reveal polyA tail modifications that prevent deadenylation without compromising protein expression

ABSTRACTChemical modifications enable preparation of mRNAs with augmented stability and translational activity. In this study, we explored how chemical modifications of 5’,3’-phosphodiester bonds in the mRNA body and polyA tail influence the biological properties of eukaryotic mRNA. To obtain modified and unmodified in vitro transcribed mRNAs, we used ATP and ATP analogues modified at the α-phosphate (containing either O-to-S or O-to-BH3 substitutions) and three different RNA polymerases—SP6, T7 and polyA polymerase. To verify the efficiency of incorporation of ATP analogues in the presence of ATP, we developed a liquid chromatography–tandem mass spectrometry (LC-MS/MS) method for quantitative assessment of modification frequency based on exhaustive degradation of the transcripts to 5’-mononucleotides. The method also estimated the average polyA tail lengths, thereby providing a versatile tool for establishing a structure-biological property relationship for mRNA. We found that mRNAs containing phosphorothioate groups within the polyA tail were substantially less susceptible to degradation by 3’-deadenylase than unmodified mRNA and were efficiently expressed in cultured cells, which makes them useful research tools and potential candidates for future development of mRNA-based therapeutics.View Full Text

biochemistry↗

bioRxiv2020

Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution

Concrete is the second most consumed product by humans, after water. However, the production of cement, which is used as a binding material in concrete, causes more than 5% of anthropogenic CO2 emissions and has therefore a significant contribution to climate change and global warming. Due to increasing environmental awareness and international climate goals, there is a need for emission-reduced materials, that can replace conventional concrete in certain applications. One path to produce a solid, concrete-like construction material is microbial-induced calcium carbonate precipitation (MICP). As a calcium source in MICP, crushed limestone, which mainly consists out of CaCO3, can be dissolved with acids, for example lactic acid. The pH evolution during crystallization and dissolution processes provides important information about kinetics of the reactions. However, previous research on MICP has mainly been focused on macro-scale pH evolution and on characterization of the finished material. To get a better understanding of MICP it is important to be able to follow also local pH changes in a sample. In this work we present a new method to study processes of MICP at micro-scale in situ and in real time. We present two different methods to monitor the pH changes during the precipitation process of CaCO3. In the first method, the average pHs of small sample volumes are measured in real time, and pH changes are subsequently correlated with processes in the sample by comparing to optical microscope results. The second method is introduced to follow local pH changes at a grain scale in situ and in real time. Furthermore, local pH changes during the dissolution of CaCO3 crystals are monitored. We demonstrate that these two methods are powerful tools to investigate pH changes for both MICP precipitation and CaCO3 dissolution for knowledge-based improvement of MICP-based material properties. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/042168v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@dad9bcorg.highwire.dtl.DTLVardef@ce9fborg.highwire.dtl.DTLVardef@1d583b8org.highwire.dtl.DTLVardef@bab03a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2019

Electron beam lithography fabrication of SU-8 polymer structures for cell studies

Flat surfaces decorated with micro- and nanostructures are important tools in biomedical research used to control cellular shape, in studies of mechanotransduction, membrane mechanics, cell migration and cellular interactions with nanostructured surfaces. Existing methods to fabricate surface-bound nanostructures are typically limited either by resolution, aspect ratio or throughput. In this work, we explore electron beam lithography based structuring of the epoxy resist SU-8 on glass substrate. We focus on a systematic investigation of the process parameters and determine limits of the fabrication process, both in terms of spatial resolution, structure aspect ration and fabrication throughput. The described approach is capable of producing high-aspect ratio, surface bound nanostructures with height ranging from 100 nm to 4000 nm and with in-plane resolution below 100 nm directly on a transparent substrate. Fabricated nanostructured surfaces can be integrated with common techniques for biomedical research, such as high numerical aperture optical microscopy. Further more, we show how the described approach can be used to make nanostructures with multiple heights on the same surface, something which is not readily achievable using alternative fabrication approaches. Our research paves an alternative way of manufacturing nanostructured surfaces with applications in life science research.

biophysics↗

bioRxiv2019

Tunable Fibrin-Alginate Interpenetrating Network Hydrogels to Guide Cell Behavior

Hydrogels are effective platforms for use as artificial extracellular matrices, cell carriers, and to present bioactive cues. Two common natural polymers, fibrin and alginate, are broadly used to form hydrogels and have numerous advantages over synthetic materials. Fibrin is a provisional matrix containing native adhesion motifs for cell engagement, yet the interplay between mechanical properties, degradation, and gelation rate is difficult to decouple. Conversely, alginate is highly tunable yet bioinert and requires modification to present necessary adhesion ligands. To address these challenges, we developed a fibrin-alginate interpenetrating network (IPN) hydrogel to combine the desirable adhesion and stimulatory characteristics of fibrin with the tunable mechanical properties of alginate. We tested its efficacy by examining capillary network formation with entrapped co-cultures of mesenchymal stromal cells (MSCs) and endothelial cells (ECs). We manipulated thrombin concentration and alginate crosslinking density independently to modulate the fibrin structure, mesh size, degradation, and biomechanical properties of these constructs. In IPNs of lower stiffness, we observed a significant increase in total cell area (1.72x105 {+/-} 7.9x104 m2) and circularity (0.56 {+/-} 0.03) compared to cells encapsulated in stiffer IPNs (3.98x104 {+/-} 1.49x104 m2 and 0.77 {+/-} 0.09, respectively). Fibrinogen content did not influence capillary network formation. However, higher fibrinogen content led to greater retention of these networks confirmed via increased spreading and presence of F-actin at 7 days. This is an elegant platform to decouple cell adhesion and hydrogel bulk stiffness that will be broadly useful for cell instruction and delivery.

bioengineering↗

bioRxiv2019

Nutritional Immunity and Antibiotic Drug Treatments Influence Microbial Composition but Fail to Eliminate Urethral Catheter Biofilms in Recurrently Catheterized Patients

Polymicrobial biofilms that form on indwelling urethral catheters used by neurogenic bladder patients are known to recur following catheter replacements. Uropathogens dominate in catheter biofilms (CBs), grow and disperse as multi-cellular aggregates. Their microbial complexity, the characteristics of host immune responses and the molecular crosstalk in this ecosystem are incompletely understood. By surveying eight patients over up to six months with meta-omics analysis methods, we shed new light on the longitudinal microbial dynamics in CBs and the microbial-host crosstalk. There was evidence of chronic innate immune responses in all patients. Pathogens dominated the microbial contents. Proteus mirabilis often out-competed other species in cases of salt encrustation of catheters. The examination of proteomes in CBs and associated urinary pellets revealed many abundant bacterial systems for transition metal ion (TMI) acquisition. TMIs are sequestered by effector proteins released by activated neutrophils and urothelial cells, such as lactotransferrin and calgranulins, which were abundant in the host proteomes. We identified positive quantitative correlations among systems responsible for siderophore biosynthesis, TMI/siderophore uptake and TMI cellular import in bacterial species, suggesting competition for TMIs to support their metabolism and growth in CBs. Enterococcus faecalis was prevalent as a cohabitant of CBs and expressed three lipoproteins with apparent TMI acquisition functions. Fastidious anaerobic bacteria such as Veillonella, Actinobaculum, and Bifidobacterium grew in CB communities that appeared to be oxygen starved. Finally, antibiotic drug treatments were shown to influence microbial composition of CBs but failed to prevent re-colonization of urethral catheters with persisting and/or drug-resistant newly emerging pathogens.

microbiology↗

bioRxiv2019

Influence of nanopillar arrays on fibroblast motility, adhesion and migration mechanisms

Surfaces decorated with high aspect ratio nanostructures are a promising tool to study cellular processes and design novel devices to control cellular behaviour, perform intracellular sensing or deliver effector molecules to cells in culture. However, little is known about the dynamics of cellular phenomenon such as adhesion, spreading and migration on such surfaces. In particular, how these are influenced by the surface properties. In this work, we investigate fibroblast behaviour on regular arrays of 1 micrometer high, polymer nanopillars with varying pillar to pillar distance (array pitch). NIH-3T3 fibroblasts spread on all arrays, and on contact with the substrate engulf nanopillars independently of the array pitch. As the cells start to spread, different behaviour is observed. On dense arrays which have the pitch equal or below 1 micrometer, cells are suspended on top of the nanopillars, making only sporadic contact with the glass support. Cells stay attached to the glass support and fully engulf nanopillars during spreading and migration on the sparse arrays which are characterized by a pitch of 2 micrometers and above. These alternate states have a profound effect on cell migration rates, which are strongly reduced on nanopillar sparse arrays. Dynamic actin puncta colocalize with nanopillars during cell spreading and migration. Strong membrane association with engulfed nanopillars might explain the reduced migration rates on sparse arrays. This work reveals several interesting phenomenon of dynamical cell behaviour on nanopillar arrays, and provides important perspectives on design and applications of high aspect ratio nanostructures.

biophysics↗

bioRxiv2019

Towards a low CO2 emission building material employing bacterial metabolism in a two-step process of limestone dissolution and recrystallization: The bacterial system and prototype production

The production of concrete for construction purposes is a major source of anthropogenic CO2 emissions. One promising avenue towards a more sustainable construction industry is to make use of naturally occurring mineral-microbe interactions, such as microbial-induced carbonate precipitation (MICP), to produce solid materials. In this paper, we present a new process where calcium carbonate in the form of powdered limestone is transformed to a binder material (termed BioZEment) through microbial dissolution and recrystallization. For the dissolution step, a suitable bacterial strain, closely related to Bacillus pumilus, was isolated from soil near a limestone quarry. We show that this strain produces organic acids from glucose, inducing the dissolution of calcium carbonate in an aqueous slurry of powdered limestone. In the second step, the dissolved limestone solution is used as the calcium source for MICP in sand packed syringe moulds. The amounts of acid produced and calcium carbonate dissolved are shown to depend on the amount of available oxygen as well as the degree of mixing. Precipitation is induced through the pH increase caused by the hydrolysis of urea, mediated by the enzyme urease, which is produced in situ by the bacterium Sporosarcina pasteurii DSM33. The degree of successful consolidation of sand by BioZEment was found to depend on both the amount of urea and the amount of glucose available in the dissolution reaction.

microbiology↗

bioRxiv2018

Longitudinal Surveys Show that Urethral Catheters Harbor Recurrent Polymicrobial Biofilms with Cooperative and Competitive Behaviors Among Cohabitating Pathogens

The analysis of catheter biofilms (CBs) from patients with neurogenic bladder disorders revealed persistent colonization by polymicrobial communities. The recurrence of bacterial species in the CBs of sequentially replaced catheters suggests urothelial reservoirs responsible for recolonization of the catheter surface. Proteomic data for CB samples were indicative of chronic inflammation in the patients urinary tracts via neutrophil and eosinophil infiltration and epithelial cell exfoliation. These host defense pathways, effective in killing pathogens during uncomplicated urinary tract infection, failed to eliminate CBs. Intermittent antibiotic drug treatment had different outcomes: either replacement of drug-susceptible by drug-tolerant bacteria or transient microbial biomass reduction followed by resurgence of the previously colonizing bacteria. Proteins that sequester iron and zinc such as lactotransferrin, lipocalin-2 and calprotectin were abundant in the patients CBs and urine sediments. Indicative of a host-pathogen battle for bivalent metal ions, acquisition and transport systems for such ions were highly expressed by many organisms residing in CBs. Species part of the Enterococcaceae and Aerococcaceae families, generally not well-characterized in their ability to synthesize siderophores, frequently cohabitated biofilms dominated by siderophore-producing Enterobacteriaceae. In support of metal acquisition cooperativity, we noticed positive abundance correlations for a Proteus mirabilis yersiniabactin-type siderophore system and two Enterococcus faecalis ABC transporters. Distinct bacterial strains highly expressed known or putative cytotoxins that appeared to compromise the survival of co-resident bacteria, e.g. a P. mirabilis hemolysin and Pseudomonas aeruginosa type 6 secretion and pyoverdin biosynthesis systems. In conclusion, there is support for cooperative and competitive behaviors among bacteria cohabitating CBs.

microbiology↗