scholarly journals Gut bacterial aggregates as living gels

2021 ◽  
Author(s):  
Brandon H Schlomann ◽  
Raghuveer Parthasarathy
Keyword(s):  
Large Scale ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Intestinal Transport ◽  
Power Laws ◽  
Soft Materials ◽  
Dependent Manner ◽  
Bacterial Strains ◽  
Host Microbe Interactions ◽  
Bacterial Aggregates

The spatial organization of gut microbiota influences both microbial abundances and host-microbe interactions, but the underlying rules relating bacterial dynamics to large-scale structure remain unclear. To this end we studied experimentally and theoretically the formation of three-dimensional bacterial clusters, a key parameter controlling susceptibility to intestinal transport and access to the epithelium. Inspired by models of structure formation in soft materials, we sought to understand how the distribution of gut bacterial cluster sizes emerges from bacterial-scale kinetics. Analyzing imaging-derived data on cluster sizes for eight different bacterial strains in the larval zebrafish gut, we find a common family of size distributions that decay approximately as power laws with exponents close to -2, becoming shallower for large clusters in a strain-dependent manner. We show that this type of distribution arises naturally from a Yule-Simons-type process in which bacteria grow within clusters and can escape from them, coupled to an aggregation process that tends to condense the system toward a single massive cluster, reminiscent of gel formation. Together, these results point to the existence of general, biophysical principles governing the spatial organization of the gut microbiome that may be useful for inferring fast-timescale dynamics that are experimentally inaccessible.

scholarly journals Gut bacterial aggregates as living gels

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Brandon H Schlomann ◽  
Raghuveer Parthasarathy
Keyword(s):  
Large Scale ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Intestinal Transport ◽  
Power Laws ◽  
Soft Materials ◽  
Dependent Manner ◽  
Bacterial Strains ◽  
Host Microbe Interactions ◽  
Bacterial Aggregates

The spatial organization of gut microbiota influences both microbial abundances and host-microbe interactions, but the underlying rules relating bacterial dynamics to large-scale structure remain unclear. To this end we studied experimentally and theoretically the formation of three-dimensional bacterial clusters, a key parameter controlling susceptibility to intestinal transport and access to the epithelium. Inspired by models of structure formation in soft materials, we sought to understand how the distribution of gut bacterial cluster sizes emerges from bacterial-scale kinetics. Analyzing imaging-derived data on cluster sizes for eight different bacterial strains in the larval zebrafish gut, we find a common family of size distributions that decay approximately as power laws with exponents close to -2, becoming shallower for large clusters in a strain-dependent manner. We show that this type of distribution arises naturally from a Yule-Simons-type process in which bacteria grow within clusters and can escape from them, coupled to an aggregation process that tends to condense the system toward a single massive cluster, reminiscent of gel formation. Together, these results point to the existence of general, biophysical principles governing the spatial organization of the gut microbiome that may be useful for inferring fast-timescale dynamics that are experimentally inaccessible.

scholarly journals Integrated Genomic and Metabolomic Approach to the Discovery of Potential Anti-Quorum Sensing Natural Products from Microbes Associated with Marine Samples from Singapore

Marine Drugs ◽  
2019 ◽  
Vol 17 (1) ◽  
pp. 72 ◽  
Author(s):  
Ji Ong ◽  
Hui Goh ◽  
Swee Lim ◽  
Li Pang ◽  
Joyce Chin ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Quorum Sensing ◽  
Large Scale ◽  
Marine Ecosystem ◽  
Gene Clusters ◽  
Integrated Approach ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Bacterial Strains ◽  
Reporter System

With 70% of the Earth’s surface covered in water, the marine ecosystem offers immense opportunities for drug discovery and development. Due to the decreasing rate of novel natural product discovery from terrestrial sources in recent years, many researchers are beginning to look seaward for breakthroughs in new therapeutic agents. As part of an ongoing marine drug discovery programme in Singapore, an integrated approach of combining metabolomic and genomic techniques were initiated for uncovering novel anti-quorum sensing molecules from bacteria associated with subtidal samples collected in the Singapore Strait. Based on the culture-dependent method, a total of 102 marine bacteria strains were isolated and the identities of selected strains were established based on their 16S rRNA gene sequences. About 5% of the marine bacterial organic extracts showed quorum sensing inhibitory (QSI) activity in a dose-dependent manner based on the Pseudomonas aeruginosa QS reporter system. In addition, the extracts were subjected to mass spectrometry-based molecular networking and the genome of selected strains were analysed for known as well as new biosynthetic gene clusters. This study revealed that using integrated techniques, coupled with biological assays, can provide an effective and rapid prioritization of marine bacterial strains for downstream large-scale culturing for the purpose of isolation and structural elucidation of novel bioactive compounds.

Strong MHD helical turbulence and the nonlinear dynamo effect

1976 ◽  
Vol 77 (2) ◽  
pp. 321-354 ◽  
Author(s):  
A. Pouquet ◽  
U. Frisch ◽  
J. Léorat
Keyword(s):  
Large Scale ◽  
Magnetic Energy ◽  
Three Dimensional ◽  
Power Laws ◽  
Inertial Range ◽  
Small Scale ◽  
Mhd Turbulence ◽  
Inverse Cascade ◽  
Small Scales ◽  
Dynamo Effect

To understand the turbulent generation of large-scale magnetic fields and to advance beyond purely kinematic approaches to the dynamo effect like that introduced by Steenbeck, Krause & Radler (1966)’ a new nonlinear theory is developed for three-dimensional, homogeneous, isotropic, incompressible MHD turbulence with helicity, i.e. not statistically invariant under plane reflexions. For this, techniques introduced for ordinary turbulence in recent years by Kraichnan (1971 a)’ Orszag (1970, 1976) and others are generalized to MHD; in particular we make use of the eddy-damped quasi-normal Markovian approximation. The resulting closed equations for the evolution of the kinetic and magnetic energy and helicity spectra are studied both theoretically and numerically in situations with high Reynolds number and unit magnetic Prandtl number.Interactions between widely separated scales are much more important than for non-magnetic turbulence. Large-scale magnetic energy brings to equipartition small-scale kinetic and magnetic excitation (energy or helicity) by the ‘Alfvén effect’; the small-scale ‘residual’ helicity, which is the difference between a purely kinetic and a purely magnetic helical term, induces growth of large-scale magnetic energy and helicity by the ‘helicity effect’. In the absence of helicity an inertial range occurs with a cascade of energy to small scales; to lowest order it is a −3/2 power law with equipartition of kinetic and magnetic energy spectra as in Kraichnan (1965) but there are −2 corrections (and possibly higher ones) leading to a slight excess of magnetic energy. When kinetic energy is continuously injected, an initial seed of magnetic field will grow to approximate equipartition, at least in the small scales. If in addition kinetic helicity is injected, an inverse cascade of magnetic helicity is obtained leading to the appearance of magnetic energy and helicity in ever-increasing scales (in fact, limited by the size of the system). This inverse cascade, predicted by Frischet al.(1975), results from a competition between the helicity and Alféh effects and yields an inertial range with approximately — 1 and — 2 power laws for magnetic energy and helicity. When kinetic helicity is injected at the scale linjand the rate$\tilde{\epsilon}^V$(per unit mass), the time of build-up of magnetic energy with scaleL[Gt ] linjis$t \approx L(|\tilde{\epsilon}^V|l^2_{\rm inj})^{-1/3}.$

Very-large-scale motions in a turbulent boundary layer

2011 ◽  
Vol 673 ◽  
pp. 80-120 ◽  
Author(s):  
JAE HWA LEE ◽  
HYUNG JIN SUNG
Keyword(s):  
Boundary Layer ◽  
Shear Stress ◽  
Turbulent Boundary Layer ◽  
Large Scale ◽  
Spatial Organization ◽  
Reynolds Shear Stress ◽  
Three Dimensional ◽  
Hairpin Vortices ◽  
Extraction Algorithm ◽  
Normal Distance

Direct numerical simulation of a turbulent boundary layer was performed to investigate the spatially coherent structures associated with very-large-scale motions (VLSMs). The Reynolds number was varied in the range Reθ = 570–2560. The main simulation was conducted by using a computational box greater than 50δo in the streamwise domain, where δo is the boundary layer thickness at the inlet, and inflow data was obtained from a separate inflow simulation based on Lund's method. Inspection of the three-dimensional instantaneous fields showed that groups of hairpin vortices are coherently arranged in the streamwise direction and that these groups create significantly elongated low- and high-momentum regions with large amounts of Reynolds shear stress. Adjacent packet-type structures combine to form the VLSMs; this formation process is attributed to continuous stretching of the hairpins coupled with lifting-up and backward curling of the vortices. The growth of the spanwise scale of the hairpin packets occurs continuously, so it increases rapidly to double that of the original width of the packets. We employed the modified feature extraction algorithm developed by Ganapathisubramani, Longmire & Marusic (J. Fluid Mech., vol. 478, 2003, p. 35) to identify the properties of the VLSMs of hairpin vortices. In the log layer, patches with the length greater than 3δ–4δ account for more than 40% of all the patches and these VLSMs contribute approximately 45% of the total Reynolds shear stress included in all the patches. The VLSMs have a statistical streamwise coherence of the order of ~6δ; the spatial organization and coherence decrease away from the wall, but the spanwise width increases monotonically with the wall-normal distance. Finally, the application of linear stochastic estimation demonstrated the presence of packet organization in the form of a train of packets in the log layer.

A model of the large-scale organization of chromatin

2013 ◽  
Vol 41 (2) ◽  
pp. 508-512 ◽  
Author(s):  
Mariano Barbieri ◽  
Mita Chotalia ◽  
James Fraser ◽  
Liron-Mark Lavitas ◽  
Josée Dostie ◽  
...  
Keyword(s):  
Experimental Data ◽  
Present Article ◽  
Cell Nucleus ◽  
Large Scale ◽  
Spatial Organization ◽  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Polymer Physics ◽  
Self Organization ◽  
Dna Binding Factors

In the cell nucleus, chromosomes have a complex spatial organization, spanning several length scales, which serves vital functional purposes. It is unknown, however, how their three-dimensional architecture is orchestrated. In the present article, we review the application of a model based on classical polymer physics, the strings and binders switch model, to explain the molecular mechanisms of chromatin self-organization. We explore the scenario where chromatin architecture is shaped and regulated by the interactions of chromosomes with diffusing DNA-binding factors via thermodynamics mechanisms and compare it with available experimental data.

Space–time formation of very-large-scale motions in turbulent pipe flow

2019 ◽  
Vol 881 ◽  
pp. 1010-1047 ◽  
Author(s):  
Jae Hwa Lee ◽  
Hyung Jin Sung ◽  
Ronald J. Adrian
Keyword(s):  
Pipe Flow ◽  
Large Scale ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Streamwise Velocity ◽  
Turbulent Pipe Flow ◽  
Strain Component ◽  
Spatial Correlations ◽  
Correlation Pattern ◽  
Using Data

We examine the origin of very-large-scale motions (VLSMs) in fully developed turbulent pipe flow at friction Reynolds number, $\mathit{Re}_{\unicode[STIX]{x1D70F}}=934$, using data from a direct numerical simulation. The VLSMs and the packet-like large-scale motions (LSMs) found in this study are very similar to those found in earlier studies. Three-dimensional time-evolving instantaneous fields show that one component of the process leading to the large streamwise length of VLSMs is the concatenation of adjacent streamwise LSMs caused by the continuous elongation of LSMs due to the strain component of the mean shear. Spatial organization patterns of the VLSMs and LSMs and their properties are studied by separating auto-correlation of the streamwise velocity fluctuations into the components of the VLSM and the LSM defined by low-pass/high-pass filtering in the streamwise direction. The structures of the two-point spatial correlations of the streamwise velocity component of the VLSMs and the LSMs in the streamwise-azimuthal plane are characterized by multiple maxima and complex patterns that beg explanation in terms of patterned coherent arrangements of the LSMs. Using proper orthogonal decomposition (POD), it is found that the X-shape correlation pattern of the VLSMs results from the superposition of very long helically inclined structures and streamwise-aligned structures. Further explanation of the patterns in the correlations of the VLSMs and LSMs is provided through the study of synthetically constructed arrangements of simple hairpin packet models of the LSM. Head-to-tail alignment of the model packets along streamwise and helical directions suggested by the eigenvalues of the POD creates a pair of long roll-cells centred above the logarithmic layer, and bracketing the LSMs. These roll-cells are pure kinematic consequences of the induction within the LSM packets, but they may also serve to organize smaller packets.

scholarly journals Spatial Organization of Dual-Species Bacterial Aggregates on Leaf Surfaces

2005 ◽  
Vol 71 (9) ◽  
pp. 5484-5493 ◽  
Author(s):  
J.-M. Monier ◽  
S. E. Lindow
Keyword(s):  
Pseudomonas Syringae ◽  
Spatial Organization ◽  
Fluorescent Protein ◽  
Bacterial Species ◽  
Epifluorescence Microscopy ◽  
Bacterial Strains ◽  
Leaf Surfaces ◽  
Mixed Aggregates ◽  
Total Cell Population ◽  
Bacterial Aggregates

ABSTRACT The spatial organization of cells within bacterial aggregates on leaf surfaces was determined for pair-wise mixtures of three different bacterial species commonly found on leaves, Pseudomonas syringae, Pantoea agglomerans, and Pseudomonas fluorescens. Cells were coinoculated onto bean plants and allowed to grow under moist conditions, and the resulting aggregates were examined in situ by epifluorescence microscopy. Each bacterial strain could be localized because it expressed either the green or the cyan fluorescent protein constitutively, and the viability of individual cells was assessed by propidium iodide staining. Each pair of bacterial strains that was coinoculated onto leaves formed mixed aggregates. The degree of segregation of cells in mixed aggregates differed between the different coinoculated pairs of strains and was higher in mixtures of P. fluorescens A506 and P. agglomerans 299R and mixtures of P. syringae B728a and P. agglomerans 299R than in mixtures of two isogenic strains of P. agglomerans 299R. The fractions of the total cell population that were dead in mixed and monospecific aggregates of a gfp-marked strain of P. agglomerans 299R and a cfp-marked strain of P. agglomerans 299R, or of P. fluorescens A506 and P. agglomerans 299R, were similar. However, the proportion of dead cells in mixed aggregates of P. syringae B728a and P. agglomerans 299R was significantly higher (13.2% ± 8.2%) than that in monospecific aggregates of these two strains (1.6% ± 0.7%), and it increased over time. While dead cells in such mixed aggregates were preferentially found at the interface between clusters of cells of these strains, cells of these two strains located at the interface did not exhibit equal probabilities of mortality. After 9 days of incubation, about 77% of the P. agglomerans 299R cells located at the interface were dead, while only about 24% of the P. syringae B728a cells were dead. The relevance of our results to understanding bacterial interactions on leaf surfaces and the implications for biological control of pathogenic and other deleterious microorganisms is discussed.

The Effect of Active Site-inhibited Factor VIIa on Tissue Factor-initiated Coagulation Using Platelets before and after Aspirin Administration

1997 ◽  
Vol 78 (04) ◽  
pp. 1202-1208 ◽  
Author(s):  
Marianne Kjalke ◽  
Julie A Oliver ◽  
Dougald M Monroe ◽  
Maureane Hoffman ◽  
Mirella Ezban ◽  
...  
Keyword(s):  
Tissue Factor ◽  
Active Site ◽  
Large Scale ◽  
Thrombin Generation ◽  
Factor Viia ◽  
Dependent Manner ◽  
Antithrombotic Agent ◽  
Before And After ◽  
Ic50 Values

SummaryActive site-inactivated factor VIIa has potential as an antithrombotic agent. The effects of D-Phe-L-Phe-L-Arg-chloromethyl ketone-treated factor VIla (FFR-FVIIa) were evaluated in a cell-based system mimicking in vivo initiation of coagulation. FFR-FVIIa inhibited platelet activation (as measured by expression of P-selectin) and subsequent large-scale thrombin generation in a dose-dependent manner with IC50 values of 1.4 ± 0.8 nM (n = 8) and 0.9 ± 0.7 nM (n = 7), respectively. Kd for factor VIIa binding to monocytes ki for FFR-FVIIa competing with factor VIIa were similar (11.4 ± 0.8 pM and 10.6 ± 1.1 pM, respectively), showing that FFR-FVIIa binds to tissue factor in the tenase complex with the same affinity as factor VIIa. Using platelets from volunteers before and after ingestion of aspirin (1.3 g), there were no significant differences in the IC50 values of FFR-FVIIa [after aspirin ingestion, the IC50 values were 1.7 ± 0.9 nM (n = 8) for P-selectin expression, p = 0.37, and 1.4 ± 1.3 nM (n = 7) for thrombin generation, p = 0.38]. This shows that aspirin treatment of platelets does not influence the inhibition of tissue factor-initiated coagulation by FFR-FVIIa, probably because thrombin activation of platelets is not entirely dependent upon expression of thromboxane A2.

Phyto-fabrication of Iron Nanoparticles: Characterization and Antibacterial Capacity

2020 ◽  
Vol 16 ◽  
Author(s):  
Asma S. Algebaly ◽  
Afrah E. Mohammed ◽  
Mudawi M. Elobeid
Keyword(s):  
Electron Microscopy ◽  
Plant Extracts ◽  
Large Scale ◽  
Iron Nanoparticles ◽  
Ethanolic Extract ◽  
Green Technology ◽  
Resistant Bacteria ◽  
Scale Production ◽  
Bacterial Strains ◽  
Plant Sources

Introduction: Fabrication of iron nanoparticles (FeNPs) has recently gained a great concern for their varied applications in remediation technologies of the environment. Objective: The current study aimed to fabricate iron nanoparticles by green technology approach using different plant sources, Azadirachta indica leaf and Calligonum comosum root following two extraction methods. Methods: Currently, a mixture of FeCl2 and FeCl3 was used to react with the plant extracts which are considered as reducing and stabilizing agents for the generation of FeNPs in one step. Different techniques were used for FeNPs identification. Results: Immediately after mixing of the two reaction components, the color changed to dark brown as an indication of safe conversion of Fe ions to FeNPs, that later confirmed by zeta sizer, transmission electron microscopy (TEM) and scanning electron microscopy (SEM). FeNPs fabricated by C. comosum showed smaller size when compared by those fabricated by A. indica. Using both plant sources, FeNPs fabricated by the aqueous extract had smaller size in relation to those fabricated by ethanolic extract. Furthermore, antibacterial ability against two bacterial strains was approved. Conclusion: The current results indicated that, at room temperature plant extracts fabricated Fe ion to Fe nanoparticles, suggesting its probable usage for large scale production as well as its suitability against bacteria. It could also be recommended for antibiotic resistant bacteria.

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