scholarly journals A Distinguishable Role of eDNA in the Viscoelastic Relaxation of Biofilms

mBio ◽  
2013 ◽  
Vol 4 (5) ◽  
Author(s):  
Brandon W. Peterson ◽  
Henny C. van der Mei ◽  
Jelmer Sjollema ◽  
Henk J. Busscher ◽  
Prashant K. Sharma
Keyword(s):  
Relaxation Time ◽  
Stress Relaxation ◽  
Time Constant ◽  
Extracellular Polymeric Substances ◽  
Principal Component ◽  
Mechanical Stresses ◽  
Extracellular Dna ◽  
Viscoelastic Relaxation ◽  
Content Type ◽  
Relaxation Time Constants

ABSTRACTBacteria in the biofilm mode of growth are protected against chemical and mechanical stresses. Biofilms are composed, for the most part, of extracellular polymeric substances (EPSs). The extracellular matrix is composed of different chemical constituents, such as proteins, polysaccharides, and extracellular DNA (eDNA). Here we aimed to identify the roles of different matrix constituents in the viscoelastic response of biofilms.Staphylococcus aureus,Staphylococcus epidermidis,Streptococcus mutans, andPseudomonas aeruginosabiofilms were grown under different conditions yielding distinct matrix chemistries. Next, biofilms were subjected to mechanical deformation and stress relaxation was monitored over time. A Maxwell model possessing an average of four elements for an individual biofilm was used to fit the data. Maxwell elements were defined by a relaxation time constant and their relative importance. Relaxation time constants varied widely over the 104 biofilms included and were divided into seven ranges (<1, 1 to 5, 5 to 10, 10 to 50, 50 to 100, 100 to 500, and >500 s). Principal-component analysis was carried out to eliminate related time constant ranges, yielding three principal components that could be related to the known matrix chemistries. The fastest relaxation component (<3 s) was due to the presence of water and soluble polysaccharides, combined with the absence of bacteria, i.e., the heaviest masses in a biofilm. An intermediate component (3 to 70 s) was related to other EPSs, while a distinguishable role was assigned to intact eDNA, which possesses a unique principal component with a time constant range (10 to 25 s) between those of EPS constituents. This implies that eDNA modulates its interaction with other matrix constituents to control its contribution to viscoelastic relaxation under mechanical stress.IMPORTANCEThe protection offered by biofilms to organisms that inhabit it against chemical and mechanical stresses is due in part to its matrix of extracellular polymeric substances (EPSs) in which biofilm organisms embed themselves. Mechanical stresses lead to deformation and possible detachment of biofilm organisms, and hence, rearrangement processes occur in a biofilm to relieve it from these stresses. Maxwell analysis of stress relaxation allows the determination of characteristic relaxation time constants, but the biofilm components and matrix constituents associated with different stress relaxation processes have never been identified. Here we grew biofilms with different matrix constituents and used principal-component analysis to reveal that the presence of water and soluble polysaccharides, together with the absence of bacteria, is associated with the fastest relaxation, while other EPSs control a second, slower relaxation. Extracellular DNA, as a matrix constituent, had a distinguishable role with its own unique principal component in stress relaxation with a time constant range between those of other EPSs.

scholarly journals Floc Formation Reduces the pH Stress Experienced by Microorganisms Living in Alkaline Environments

2017 ◽  
Vol 83 (6) ◽  
Author(s):  
C. J. Charles ◽  
S. P. Rout ◽  
K. A. Patel ◽  
S. Akbar ◽  
A. P. Laws ◽  
...  
Keyword(s):  
Extracellular Polymeric Substances ◽  
Complex Mixture ◽  
Thick Layer ◽  
Cementitious Materials ◽  
Radioactive Wastes ◽  
Extracellular Dna ◽  
Geological Disposal ◽  
Content Type ◽  
Ph Values ◽  
Disposal Facility

ABSTRACT The survival of microorganisms within a cementitious geological disposal facility for radioactive wastes heavily depends on their ability to survive the calcium-dominated, hyperalkaline conditions resulting from the dissolution of the cementitious materials. The results from this study show that the formation of flocs, composed of a complex mixture of extracellular polymeric substances (EPS), provides protection against alkaline pH values up to 13.0. The flocs were dominated by Alishewanella and Dietzia spp., producing a mannose-rich carbohydrate fraction incorporating extracellular DNA, resulting in Ca2+ sequestration. EPS provided a ∼10-μm thick layer around the cells within the center of the flocs, which were capable of growth at pH values of 11.0 and 11.5, maintaining internal pH values of 10.4 and 10.7, respectively. Microorganisms survived at a pH of 12.0, where an internal floc pH of 11.6 was observed, as was a reduced associated biomass. We observed limited floc survival (<2 weeks) at a pH of 13.0. This study demonstrates that flocs maintain lower internal pHs in response to the hyperalkaline conditions expected to occur within a cementitious geological disposal facility for radioactive wastes and indicates that floc communities within such a facility can survive at pHs up to 12.0. IMPORTANCE The role of extracellular polymeric substances (EPS) in the survival of microorganisms in hyperalkaline conditions is poorly understood. Here, we present the taxonomy, morphology, and chemical characteristics of an EPS-based microbial floc, formed by a consortium isolated from an anthropogenic hyperalkaline site. Short-term (<2 weeks) survival of the flocs at a pH of 13 was observed, with indefinite survival observed at a pH of 12.0. Measurements from micro-pH electrodes (10-μm-diameter tip) demonstrated that flocs maintain lower internal pHs in response to hyperalkaline conditions (pH 11.0, 11.5, and 12.0), demonstrating that floc formation and EPS production are survival strategies under hyperalkaline conditions. The results indicate how microbial communities may survive and propagate within the hyperalkaline environment that is expected to prevail in a cementitious geological disposal facility for radioactive wastes; the results are also relevant to the wider extremophile community.

Comments on “Mechanical relaxation time scales in a Zr-Ti-Ni-Cu-Be bulk metallic glass” by Daewoong Suh and Reinhold H. Dauskardt [J. Mater. Res. 17, 1254 (2002)]

2003 ◽  
Vol 18 (8) ◽  
pp. 1998-1999 ◽  
Author(s):  
K. Schröter
Keyword(s):  
Relaxation Time ◽  
Glass Transition ◽  
Transition Temperature ◽  
Glass Transition Temperature ◽  
Stress Relaxation ◽  
Metallic Glass ◽  
Bulk Metallic Glass ◽  
Time Scales ◽  
Mechanical Relaxation ◽  
Viscoelastic Relaxation

The stress relaxation results below the glass-transition temperatureTgare a continuation of the viscoelastic relaxation aboveTg. This means that the dynamic glass transition and not a secondary relaxation is the reason for the observed effects.

scholarly journals Multiple holins contribute to extracellular DNA release in Pseudomonas aeruginosa biofilms

Microbiology ◽  
2021 ◽  
Author(s):  
Amelia L. Hynen ◽  
James J. Lazenby ◽  
George M. Savva ◽  
Laura C. McCaughey ◽  
Lynne Turnbull ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Type Species ◽  
Extracellular Polymeric Substances ◽  
Bacterial Population ◽  
Extracellular Dna ◽  
Bacterial Biofilms ◽  
Content Type ◽  
Link Type ◽  
Dna Release ◽  
Biofilm Development

Bacterial biofilms are composed of aggregates of cells encased within a matrix of extracellular polymeric substances (EPS). One key EPS component is extracellular DNA (eDNA), which acts as a ‘glue’, facilitating cell–cell and cell–substratum interactions. We have previously demonstrated that eDNA is produced in Pseudomonas aeruginosa biofilms via explosive cell lysis. This phenomenon involves a subset of the bacterial population explosively lysing, due to peptidoglycan degradation by the endolysin Lys. Here we demonstrate that in P. aeruginosa three holins, AlpB, CidA and Hol, are involved in Lys-mediated eDNA release within both submerged (hydrated) and interstitial (actively expanding) biofilms, albeit to different extents, depending upon the type of biofilm and the stage of biofilm development. We also demonstrate that eDNA release events determine the sites at which cells begin to cluster to initiate microcolony formation during the early stages of submerged biofilm development. Furthermore, our results show that sustained release of eDNA is required for cell cluster consolidation and subsequent microcolony development in submerged biofilms. Overall, this study adds to our understanding of how eDNA release is controlled temporally and spatially within P. aeruginosa biofilms.

scholarly journals Stress relaxation amplitude of hydrogels determines migration, proliferation, and morphology of cells in 3-D

2021 ◽  
Author(s):  
Jonas Hazur ◽  
Nadine Endrizzi ◽  
Dirk W. Schubert ◽  
Aldo R. Boccaccini ◽  
Ben Fabry
Keyword(s):  
Relaxation Time ◽  
Stress Relaxation ◽  
Time Constant ◽  
3D Culture ◽  
Viscoelastic Behavior ◽  
Model Systems ◽  
Cell Behavior ◽  
Relaxation Time Constant ◽  
Young’S Moduli ◽  
The Matrix

The viscoelastic behavior of hydrogel matrices sensitively influences the cell behavior in 3D culture and biofabricated tissue model systems. Previous reports have demonstrated that cells tend to adhere, spread, migrate and proliferate better in hydrogels with pronounced stress relaxation. However, it is currently unknown if cells respond more sensitively to the amplitude of stress relaxation, or to the relaxation time constant. To test this, we compare the behavior of fibroblasts cultured for up to 10 days in alginate and oxidized alginate hydrogels with similar Young's moduli but diverging stress relaxation behavior. We find that fibroblasts elongate, migrate and proliferate better in hydrogels that display a higher stress relaxation amplitude. By contrast, the cells' response to the relaxation time constant was less pronounced and less consistent. Together, these data suggest that it is foremost the stress relaxation amplitude of the matrix that determines the ability of cells to locally penetrate and remodel the matrix, which subsequently leads to better spreading, faster migration, and higher cell proliferation. We conclude that the stress relaxation amplitude is a central design parameter for optimizing cell behavior in 3-D hydrogels.

scholarly journals Competence-Stimulating-Peptide-Dependent Localized Cell Death and Extracellular DNA Production in Streptococcus mutans Biofilms

2020 ◽  
Vol 86 (23) ◽  
Author(s):  
Ryo Nagasawa ◽  
Tatsuya Yamamoto ◽  
Andrew S. Utada ◽  
Nobuhiko Nomura ◽  
Nozomu Obana
Keyword(s):  
Cell Death ◽  
Single Cell ◽  
Streptococcus Mutans ◽  
Structural Stability ◽  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Imaging Techniques ◽  
Extracellular Dna ◽  
Content Type ◽  
Cariogenic Bacterium

ABSTRACT Extracellular DNA (eDNA) is a biofilm component that contributes to the formation and structural stability of biofilms. Streptococcus mutans, a major cariogenic bacterium, induces eDNA-dependent biofilm formation under specific conditions. Since cell death can result in the release and accumulation of DNA, the dead cells in biofilms are a source of eDNA. However, it remains unknown how eDNA is released from dead cells and is localized within S. mutans biofilms. We focused on cell death induced by the extracellular signaling peptide called competence-stimulating peptide (CSP). We demonstrate that nucleic acid release into the extracellular environment occurs in a subpopulation of dead cells. eDNA production induced by CSP was highly dependent on the lytF gene, which encodes an autolysin. Although lytF expression was induced bimodally by CSP, lytF-expressing cells further divided into surviving cells and eDNA-producing dead cells. Moreover, we found that lytF-expressing cells were abundant near the bottom of the biofilm, even when all cells in the biofilm received the CSP signal. Dead cells and eDNA were also abundantly present near the bottom of the biofilm. The number of lytF-expressing cells in biofilms was significantly higher than that in planktonic cultures, which suggests that adhesion to the substratum surface is important for the induction of lytF expression. The deletion of lytF resulted in reduced adherence to a polystyrene surface. These results suggest that lytF expression and eDNA production induced near the bottom of the biofilm contribute to a firmly attached and structurally stable biofilm. IMPORTANCE Bacterial communities encased by self-produced extracellular polymeric substances (EPSs), known as biofilms, have a wide influence on human health and environmental problems. The importance of biofilm research has increased, as biofilms are the preferred bacterial lifestyle in nature. Furthermore, in recent years it has been noted that the contribution of phenotypic heterogeneity within biofilms requires analysis at the single-cell or subpopulation level to understand bacterial life strategies. In Streptococcus mutans, a cariogenic bacterium, extracellular DNA (eDNA) contributes to biofilm formation. However, it remains unclear how and where the cells produce eDNA within the biofilm. We focused on LytF, an autolysin that is induced by extracellular peptide signals. We used single-cell level imaging techniques to analyze lytF expression in the biofilm population. Here, we show that S. mutans generates eDNA by inducing lytF expression near the bottom of the biofilm, thereby enhancing biofilm adhesion and structural stability.

Robust-PCA-based hierarchical plane extraction for application to geometric 3D indoor mapping

2014 ◽  
Vol 41 (2) ◽  
pp. 203-212 ◽  
Author(s):  
Suyong Yeon ◽  
ChangHyun Jun ◽  
Hyunga Choi ◽  
Jaehyeon Kang ◽  
Youngmok Yun ◽  
...  
Keyword(s):  
Principal Component ◽  
Point Clouds ◽  
Previous Method ◽  
Divide And Conquer ◽  
Sensor Data ◽  
Estimation Accuracy ◽  
Content Type ◽  
Extraction Algorithm ◽  
Plane Extraction ◽  
Scan Data

Purpose – The authors aim to propose a novel plane extraction algorithm for geometric 3D indoor mapping with range scan data. Design/methodology/approach – The proposed method utilizes a divide-and-conquer step to efficiently handle huge amounts of point clouds not in a whole group, but in forms of separate sub-groups with similar plane parameters. This method adopts robust principal component analysis to enhance estimation accuracy. Findings – Experimental results verify that the method not only shows enhanced performance in the plane extraction, but also broadens the domain of interest of the plane registration to an information-poor environment (such as simple indoor corridors), while the previous method only adequately works in an information-rich environment (such as a space with many features). Originality/value – The proposed algorithm has three advantages over the current state-of-the-art method in that it is fast, utilizes more inlier sensor data that does not become contaminated by severe sensor noise and extracts more accurate plane parameters.

Aspects of project learning in construction: a socio-technical model

2014 ◽  
Vol 14 (2) ◽  
pp. 229-244 ◽  
Author(s):  
Ali Mohammed Alashwal ◽  
Hamzah Abdul-Rahman
Keyword(s):  
Latent Variable ◽  
Construction Projects ◽  
Team Building ◽  
Principal Component ◽  
Measurement Model ◽  
Survey Method ◽  
Path Modeling ◽  
Content Type ◽  
Measurement Models ◽  
Project Learning

Purpose – The purpose of this paper is to determine the measurement constructs of learning within construction projects' milieu. The literature indicated some mechanisms of learning in projects under four aspects, namely knowledge sharing, knowledge creation, team action to learn, and learning support. The empirical study attempts to verify whether intra-project learning can be measured through these aspects. Design/methodology/approach – The study used a survey method to collect the data from 36 mega-sized building projects in Malaysia. In total, 203 questionnaires were collected from professionals working in the sites of these projects. The data were analysed using principal component analysis (PCA) to determine the constructs of intra-project learning. Partial least squares-path modeling was used then to confirm the results of PCA and determine the contribution of each construct to intra-project learning. Findings – The results affirmed two constructs of intra-project learning, named, social and technical and each consisted of four indicators of learning. Originality/value – The paper emphasized the socio-technical perspective of learning and contributed to developing a hierarchical measurement model of learning in construction project. A project manager can propose new initiatives in response to the new perspective of learning for team building and continuous development. Lastly, the paper provides a comprehensive presentation of how to estimate the hierarchical measurement models of project learning as a latent variable.

A principal component analysis of the determinants of spatial disparity between rural and urban localities of Ghana

2017 ◽  
Vol 44 (6) ◽  
pp. 715-731 ◽  
Author(s):  
Ivy Drafor
Keyword(s):  
Principal Component Analysis ◽  
Rural Areas ◽  
Urban Areas ◽  
Principal Component ◽  
Component Analysis ◽  
Spatial Inequality ◽  
Necessary Condition ◽  
Spatial Disparity ◽  
Content Type ◽  
Rural And Urban

Purpose The purpose of this paper is to analyse the spatial disparity between rural and urban areas in Ghana using the Ghana Living Standards Survey’s (GLSS) rounds 5 and 6 data to advance the assertion that an endowed rural sector is necessary to promote agricultural development in Ghana. This analysis helps us to know the factors that contribute to the depravity of the rural sectors to inform policy towards development targeting. Design/methodology/approach A multivariate principal component analysis (PCA) and hierarchical cluster analysis were applied to data from the GLSS-5 and GLSS-6 to determine the characteristics of the rural-urban divide in Ghana. Findings The findings reveal that the rural poor also spend 60.3 per cent of their income on food, while the urban dwellers spend 49 per cent, which is an indication of food production capacity. They have low access to information technology facilities, have larger household sizes and lower levels of education. Rural areas depend a lot on firewood for cooking and use solar/dry cell energies and kerosene for lighting which have implications for conserving the environment. Practical implications Developing the rural areas to strengthen agricultural growth and productivity is a necessary condition for eliminating spatial disparities and promoting overall economic development in Ghana. Addressing rural deprivation is important for conserving the environment due to its increased use of fuelwood for cooking. Absence of alternatives to the use of fuelwood weakens the efforts to reduce deforestation. Originality/value The application of PCA to show the factors that contribute to spatial inequality in Ghana using the GLSS-5 and GLSS-6 data is unique. The study provides insights into redefining the framework for national poverty reduction efforts.

scholarly journals Control of Mucosal Candidiasis in the Zebrafish Swim Bladder Depends on Neutrophils That Block Filament Invasion and Drive Extracellular-Trap Production

2017 ◽  
Vol 85 (9) ◽  
Author(s):  
Remi L. Gratacap ◽  
Allison K. Scherer ◽  
Brittany G. Seman ◽  
Robert T. Wheeler
Keyword(s):  
Invasive Disease ◽  
Extracellular Dna ◽  
Epithelial Barrier ◽  
Infection Model ◽  
Swim Bladder ◽  
Spatiotemporal Resolution ◽  
Zebrafish Model ◽  
Content Type ◽  
Mucosal Candidiasis ◽  
Disease Pressure

ABSTRACT Candida albicans is a ubiquitous mucosal commensal that is normally prevented from causing acute or chronic invasive disease. Neutrophils contribute to protection in oral infection but exacerbate vulvovaginal candidiasis. To dissect the role of neutrophils during mucosal candidiasis, we took advantage of a new, transparent zebrafish swim bladder infection model. Intravital microscopic tracking of individual animals revealed that the blocking of neutrophil recruitment leads to rapid mortality in this model through faster disease progression. Conversely, artificial recruitment of neutrophils during early infection reduces disease pressure. Noninvasive longitudinal tracking showed that mortality is a consequence of C. albicans breaching the epithelial barrier and invading surrounding tissues. Accordingly, we found that a hyperfilamentous C. albicans strain breaches the epithelial barrier more frequently and causes mortality in immunocompetent zebrafish. A lack of neutrophils at the infection site is associated with less fungus-associated extracellular DNA and less damage to fungal filaments, suggesting that neutrophil extracellular traps help to protect the epithelial barrier from C. albicans breach. We propose a homeostatic model where C. albicans disease pressure is balanced by neutrophil-mediated damage of fungi, maintaining this organism as a commensal while minimizing the risk of damage to host tissue. The unequaled ability to dissect infection dynamics at a high spatiotemporal resolution makes this zebrafish model a unique tool for understanding mucosal host-pathogen interactions.

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