1,968 research outputs found
Up-dating the Cholodny method using PET films to sample microbial communities in soil
The aim of this work was to investigate the use of PET (polyethylene terephtalate) films as a modern development of Cholodnyβs glass slides, to enable microscopy and molecular-based analysis of soil communities where spatial detail at the scale of microbial habitats is essential to understand microbial associations and interactions in this complex environment. Methods. Classical microbiological methods; attachment assay; surface tension measurements; molecular techniques: DNA extraction, PCR; confocal laser scanning microscopy (CLSM); micro- focus X-ray computed tomography (ΞΌCT). Results. We first show, using the model soil and rhizosphere bacteria Pseudomonas fluorescens SBW25 and P. putida KT2440, that bacteria are able to attach and detach from PET films, and that pre-conditioning with a filtered soil suspension improved the levels of attachment. Bacteria attached to the films were viable and could develop substantial biofilms. PET films buried in soil were rapidly colonised by microorganisms which could be investigated by CLSM and recovered onto agar plates. Secondly, we demonstrate that ΞΌCT can be used to non-destructively visualise soil aggregate contact points and pore spaces across the surface of PET films buried in soil. Conclusions. PET films are a successful development of Cholodnyβs glass slides and can be used to sample soil communities in which bacterial adherence, growth, biofilm and community development can be investigated. The use of these films with ΞΌCT imaging in soil will enable a better understanding of soil micro-habitats and the spatially-explicit nature of microbial interactions in this complex environment
Rapid compensatory evolution promotes the survival of conjugative plasmids
Conjugative plasmids play a vital role in bacterial adaptation through horizontal gene transfer. Explaining how plasmids persist in host populations however is difficult, given the high costs often associated with plasmid carriage. Compensatory evolution to ameliorate this cost can rescue plasmids from extinction. In a recently published study we showed that compensatory evolution repeatedly targeted the same bacterial regulatory system, GacA/GacS, in populations of plasmid-carrying bacteria evolving across a range of selective environments. Mutations in these genes arose rapidly and completely eliminated the cost of plasmid carriage. Here we extend our analysis using an individual based model to explore the dynamics of compensatory evolution in this system. We show that mutations which ameliorate the cost of plasmid carriage can prevent both the loss of plasmids from the population and the fixation of accessory traits on the bacterial chromosome. We discuss how dependent the outcome of compensatory evolution is on the strength and availability of such mutations and the rate at which beneficial accessory traits integrate on the host chromosome
Examining c-di-GMP and possible quorum sensing regulation in Pseudomonas fluorescens SBW25:links between intra and inter-cellular regulation benefits community cooperative activities such as biofilm formation
Bacterial success in colonizing complex environments requires individual response to micro-scale conditions as well as community-level cooperation to produce large-scale structures such as biofilms. Connecting individual and community responses could be achieved by linking the intracellular sensory and regulatory systems mediated by bis-(3β²-5β²)-cyclic dimeric guanosine monophosphate (c-di-GMP) and other compounds of individuals with intercellular quorum sensing (QS) regulation controlling populations. There is growing evidence to suggest that biofilm formation by many pseudomonads is regulated by both intra and intercellular systems, though in the case of the model Pseudomonas fluorescens SBW25 Wrinkly Spreader in which mutations increasing c-di-GMP levels result in the production of a robust cellulose-based air-liquid interface biofilm, no evidence for the involvement of QS regulation has been reported. However, our recent review of the P. fluorescens SBW25 genome has identified a potential QS regulatory pathway and other QSβassociated genes linked to c-di-GMP homeostasis, and QS signal molecules have also been identified in culture supernatants. These findings suggest a possible link between c-di-GMP and QS regulation in P. fluorescens SBW25 which might allow a more sophisticated and responsive control of cellulose production and biofilm formation when colonising the soil and plant-associated environments P. fluorescens SBW25 normally inhabits.ΠΠ½Π°Π»ΠΈΠ· Ρ-Π΄ΠΈ-ΠΠΠ€ ΠΈ Π²ΠΎΠ·ΠΌΠΎΠΆΠ½ΠΎΠ³ΠΎ ΡΡΠ²ΡΡΠ²Π° ΠΊΠ²ΠΎΡΡΠΌΠ° Ρ Pseudomonas fluorescens SBW 25: ΡΠ²ΡΠ·Ρ ΠΌΠ΅ΠΆΠ΄Ρ Π²Π½ΡΡΡΠΈ ΠΈ ΠΌΠ΅ΠΆΠΊΠ»Π΅ΡΠΎΡΠ½ΠΎΠΉ ΡΠ΅Π³ΡΠ»ΡΡΠΈΠ΅ΠΉ ΡΠΏΠΎΡΠΎΠ±ΡΡΠ²ΡΠ΅Ρ ΠΊΠΎΠΎΠΏΠ΅ΡΠ°ΡΠΈΠ²Π½ΠΎΠΌΡ ΠΏΠΎΠ²Π΅Π΄Π΅Π½ΠΈΡ Π² ΡΠΎΠΎΠ±ΡΠ΅ΡΡΠ²Π΅ ΠΈ ΡΠΎΡΠΌΠΈΡΠΎΠ²Π°Π½ΠΈΡ Π±ΠΈΠΎΠΏΠ»ΡΠ½ΠΊΠΈΠ£ΡΠΏΠ΅ΡΠ½ΠΎΡΡΡ Π±Π°ΠΊΡΠ΅ΡΠΈΠ°Π»ΡΠ½ΠΎΠΉ ΠΊΠΎΠ»ΠΎΠ½ΠΈΠ·Π°ΡΠΈΠΈ ΡΠ»ΠΎΠΆΠ½ΡΡ
ΡΠΊΠΎΠ½ΠΈΡ ΡΡΠ΅Π±ΡΠ΅Ρ ΠΈΠ½Π΄ΠΈΠ²ΠΈΠ΄ΡΠ°Π»ΡΠ½ΠΎΠ³ΠΎ ΠΎΡΠ²Π΅ΡΠ° Π½Π° ΠΈΠ·ΠΌΠ΅Π½Π΅Π½ΠΈΡ ΡΡΠ»ΠΎΠ²ΠΈΠΉ Π½Π° ΠΌΠΈΠΊΡΠΎΡΡΠΎΠ²Π½Π΅ ΡΠ°Π²Π½ΠΎ ΠΊΠ°ΠΊ ΠΈ ΠΊΠΎΠΎΠΏΠ΅ΡΠ°ΡΠΈΠΈ Π½Π° ΡΡΠΎΠ²Π½Π΅ ΡΠΎΠΎΠ±ΡΠ΅ΡΡΠ²Π° Π΄Π»Ρ ΠΏΡΠΎΠ΄ΡΠΊΡΠΈΠΈ ΡΠ°ΠΊΠΈΡ
ΠΊΡΡΠΏΠ½ΠΎ ΠΌΠ°ΡΡΡΠ°Π±Π½ΡΡ
ΡΡΡΡΠΊΡΡΡ ΠΊΠ°ΠΊ Π±ΠΈΠΎΠΏΠ»ΡΠ½ΠΊΠΈ. ΠΠΎΠΎΡΠ΄ΠΈΠ½Π°ΡΠΈΡ ΠΈΠ½Π΄ΠΈΠ²ΠΈΠ΄ΡΠ°Π»ΡΠ½ΡΡ
ΠΎΡΠ²Π΅Ρ ΠΎΠ² ΠΈ ΠΎΡΠ²Π΅ΡΠΎΠ² ΡΠΎΠΎΠ±ΡΠ΅ΡΡΠ²Π° ΠΌΠΎΠΆΠ΅Ρ Π±ΡΡΡ Π΄ΠΎΡΡΠΈΠ³Π½ΡΡΠ° ΠΏΡΡΠ΅ΠΌ ΡΠ²ΡΠ·ΡΠ²Π°Π½ΠΈΡ Π²Π½ΡΡΡΠΈΠΊΠ»Π΅ΡΠΎΡΠ½ΡΡ
ΡΠ΅Π½ΡΠΎΡΠ½ΡΡ
ΠΈ ΡΠ΅Π³ΡΠ»ΡΡΠΎΡΠ½ΡΡ
ΡΠΈΡΡΠ΅ΠΌ, ΠΎΠΏΠΎΡΡΠ΅Π΄ΡΠ΅ΠΌΡΡ
Π±ΠΈΡ-(3',5')-ΡΠΈΠΊΠ»ΠΈΡΠ΅ΡΠΊΠΈΠΌ Π΄ΠΈΠΌΠ΅ΡΠ½ΡΠΌ Π³ΡΠ°Π½ΠΎΠ·ΠΈΠ½ΠΌΠΎΠ½ΠΎΡΠΎΡΡΠ°ΡΠΎΠΌ (Ρ-Π΄ΠΈ-ΠΠΠ€) ΠΈ Π΄ΡΡΠ³ΠΈΠΌΠΈ ΡΠΎΠ΅Π΄ΠΈΠ½Π΅Π½ΠΈΡΠΌΠΈ ΠΈΠ½Π΄ΠΈΠ²ΠΈΠ΄ΡΡΠΌΠΎΠ² Ρ ΠΌΠ΅ΠΆΠΊΠ»Π΅ΡΠΎΡΠ½ΠΎΠΉ ΡΠ΅Π³ΡΠ»ΡΡΠΈΠ΅ΠΉ - ΡΡΠ²ΡΡΠ²ΠΎΠΌ ΠΊΠ²ΠΎΡΡΠΌΠ° (Π§Π), ΠΊΠΎΠ½ΡΡΠΎΠ»ΠΈΡΡΡΡΠ΅ΠΌ ΠΏΠΎΠΏΡΠ»ΡΡΠΈ Ρ. ΠΠ°ΠΊΠ°ΠΏΠ»ΠΈΠ²Π°Π΅ΡΡΡ Π²ΡΡ Π±ΠΎΠ»ΡΡΠ΅ Π΄ΠΎΠΊΠ°Π·Π°ΡΠ΅Π»ΡΡΡΠ² ΡΠΎΠ³ΠΎ, ΡΡΠΎ ΡΠΎΡΠΌΠΈΡΠΎΠ²Π°Π½ΠΈΠ΅ Π±ΠΈΠΎΠΏΠ»Π΅Π½ΠΊΠΈ ΠΌΠ½ΠΎΠ³ΠΈΠΌΠΈ ΠΏΡΠ΅Π²Π΄ΠΎΠΌΠΎΠ½Π°Π΄Π°ΠΌΠΈ ΡΠ΅Π³ΡΠ»ΠΈΡΡΠ΅ΡΡΡ ΠΊΠ°ΠΊ Π²Π½ΡΡΡΠΈ ΠΊΠ»Π΅ΡΠΎΡΠ½ΡΠΌΠΈ, ΡΠ°ΠΊ ΠΈ ΠΌΠ΅ΠΆ ΠΊΠ»Π΅ΡΠΎΡΠ½ΡΠΌΠΈ ΡΠ΅Π³ΡΠ»ΡΡΠΎΡΠ½ΡΠΌΠΈ ΡΠΈΡΡΠ΅ΠΌΠ°ΠΌΠΈ, Ρ
ΠΎΡΡ Π² ΡΠ»ΡΡΠ°Π΅ ΠΌΠΎΠ΄Π΅Π»ΡΠ½ΠΎΠΉ Pseudomonas fluorescens SBW25 Wrinkly Spreader, Ρ ΠΊΠΎΡΠΎΡΠΎΠΉ ΠΌΡΡΠ°ΡΠΈΠΈ, ΠΏΠΎΠ²ΡΡΠ°ΡΡ ΠΈΠ΅ ΡΡΠΎΠ²Π½ΠΈ Ρ-Π΄ΠΈ-ΠΠΠ€, ΠΏΡΠΈΠ²ΠΎΠ΄ΡΡ ΠΊ ΡΠΎΠ·Π΄Π°Π½ΠΈΡ ΠΏΡΠΎΡΠ½ΠΎΠΉ ΡΠ΅Π»Π»ΡΠ»ΠΎΠ·Π½ΠΎΠΉ Π±ΠΈΠΎΠΏΠ»ΡΠ½ΠΊΠΈ Π½Π° Π³ΡΠ°Π½ΠΈΡΠ΅ ΡΠ°Π·Π΄Π΅Π»Π° ΡΠ°Π· Π²ΠΎΠ·Π΄ΡΡ
-ΠΆΠΈΠ΄ΠΊΠΎΡΡΡ, Π½Π΅ Π±ΡΠ»ΠΎ ΠΎΠ±Π½Π°ΡΡΠΆΠ΅Π½ΠΎ Π½ΠΈ ΠΊΠ° ΠΊΠΎΠ³ΠΎ ΡΠ²ΠΈΠ΄Π΅ΡΠ΅Π»ΡΡΡΠ²Π° Π²ΠΎΠ²Π»Π΅ΡΠ΅Π½ΠΈΡ ΠΊΠ²ΠΎΡΡΠΌ-Π·Π°Π²ΠΈΡΠΈΠΌΠΎΠΉ ΡΠ΅Π³ΡΠ»ΡΡΠΈΠΈ. ΠΠ΄Π½Π°ΠΊΠΎ Π½Π°Ρ Π½Π΅Π΄Π°Π²Π½ΠΈΠΉ ΠΎΠ±Π·ΠΎΡ Π³Π΅Π½ΠΎΠΌΠ° P. fluorescens SBW25 Π²ΡΡΠ²ΠΈΠ» ΠΏΠΎΡΠ΅Π½ΡΠΈΠ°Π»ΡΠ½ΡΠΉ Π§Π-Π·Π°Π²ΠΈΡΠΈΠΌΡΠΉ ΡΠ΅Π³ΡΠ»ΡΡΠΎΡΠ½ΡΠΉ ΠΏΡ ΡΡ ΠΈ Π΄ΡΡΠ³ΠΈΠ΅ Π§Π-Π·Π°Π²ΠΈΡΠΈΠΌΡΠ΅ Π³Π΅Π½Ρ, ΡΠ²ΡΠ·Π°Π½Π½ΡΠ΅ Ρ Π³ΠΎΠΌΠ΅ΠΎΡΡΠ°Π·ΠΎΠΌ Ρ-Π΄ΠΈ-ΠΠΠ€, Π° ΠΌΠΎΠ»Π΅ΠΊΡΠ»Ρ Π§Π-ΡΠΈΠ³Π½Π°Π»ΠΈΠ½Π³Π° Π±ΡΠ»ΠΈ ΠΈΠ΄Π΅Π½ΡΠΈΡΠΈΡΠΈΡΠΎΠ²Π°Π½Ρ Π² ΠΊΡΠ»ΡΡΡΡΠ΅. ΠΡΠΈ Π΄Π°Π½Π½ΡΠ΅ ΡΠ²ΠΈΠ΄Π΅ΡΠ΅Π»ΡΡΡΠ²ΡΡΡ ΠΎ Π²ΠΎΠ·ΠΌΠΎΠΆΠ½ΠΎΠΉ ΡΠ²ΡΠ·ΠΈ ΠΌΠ΅ΠΆΠ΄Ρ Ρ-Π΄ΠΈ-ΠΠΠ€-ΡΠ΅Π³ΡΠ»ΡΡΠΈΠ΅ΠΉ ΠΈ Π§Π Ρ P. fluorescens SBW25, ΡΡΠΎ ΠΏΠΎΠ·Π²ΠΎΠ»ΡΠ΅Ρ Π±ΠΎΠ»Π΅Π΅ ΡΠ»ΠΎΠΆΠ½ΡΠΉ ΠΈ Π³ΠΈΠ±ΠΊΠΈΠΉ ΠΊΠΎΠ½ΡΡΠΎΠ»Ρ Π½Π°Π΄ ΠΏΡΠΎΠ΄ΡΠΊΡΠΈΠ΅ΠΉ ΡΠ΅Π»Π»ΡΠ»ΠΎΠ·Ρ ΠΈ ΠΎΠ±ΡΠ°Π·ΠΎΠ²Π°Π½ΠΈ Π΅ΠΌ Π±ΠΈΠΎΠΏΠ»Π΅Π½ΠΊΠΈ ΠΏΡΠΈ ΠΊΠΎΠ»ΠΎΠ½ΠΈΠ·Π°ΡΠΈΠΈ ΠΏΠΎΡΠ² ΠΈ ΡΠΊΠΎΠ½ΠΈΡ, aΡΡΠΎΡΠΈΠΈΡΠΎΠ²Π°Π½Π½ΡΡ
Ρ ΡΠ°ΡΡΠ΅Π½ΠΈΡΠΌ ΠΈ, - Π΅ΡΡΠ΅ΡΡΠ²Π΅Π½Π½ΡΠΌΠΈ ΡΡΠ΅Π΄Π°ΠΌΠΈ ΠΎΠ±ΠΈΡΠ°Π½ΠΈΡ P. fluorescens SBW25
Priming winter wheat seeds with the bacterial quorum sensing signal N-hexanoyl-L-homoserine lactone (C6-HSL) shows potential to improve plant growth and seed yield
Several model plants are known to respond to bacterial quorum sensing molecules with altered root growth and gene expression patterns and induced resistance to plant pathogens. These compounds may represent novel elicitors that could be applied as seed primers to enhance cereal crop resistance to pathogens and abiotic stress and to improve yields. We investigated whether the acyl-homoserine lactone N-hexanoyl-L-homoserine lactone (C6-HSL) impacted winter wheat (Triticum aestivum L.) seed germination, plant development and productivity, using two Ukrainian varieties, Volodarka and Yatran 60, in both in vitro experiments and field trials. In vitro germination experiments indicated that C6-HSL seed priming had a small but significant positive impact on germination levels (1.2x increase, p < 0.0001), coleoptile and radicle development (1.4x increase, p < 0.0001). Field trials over two growing seasons (2015-16 and 2016-17) also demonstrated significant improvements in biomass at the tillering stage (1.4x increase, p < 0.0001), and crop structure and productivity at maturity including grain yield (1.4 β 1.5x increase, p < 0.0007) and quality (1.3x increase in good grain, p < 0.0001). In some cases variety effects were observed (p β€ 0.05) suggesting that the effect of C6-HSL seed priming might depend on plant genetics, and some benefits of priming were also evident in F1 plants grown from seeds collected the previous season (p β€ 0.05). These field-scale findings suggest that bacterial acyl-homoserine lactones such as C6-HSL could be used to improve cereal crop growth and yield and reduce reliance on fungicides and fertilisers to combat pathogens and stress
Invalid party wall awards and how to avoid them
Considers the reasons for the invalidity of party wall awards. Examines decided cases under earlier party wall legislation in the context of the Party Wall etc. Act 1996. Explains invalidity on the basis of an excess of the surveyorsβ statutory authority. Defines this authority in terms of jurisdiction and power. Demonstrates the limits of the surveyorsβ authority and emphasises the importance of strict compliance with statutory procedures. Concludes that surveyors should adopt an inquisitive and analytical approach to the scope of their authority to avoid the possibility of invalid awards. Echoes John Ansteyβs earlier warning that surveyors should avoid a broad-brush approach to their duties which will only leave them βcovered in sootβ
Study of diffusion weighted MRI as a predictive biomarker of response during radiotherapy for high and intermediate risk squamous cell cancer of the oropharynx: The MeRInO study
Introduction and background:
A significant proportion of patients with intermediate and high risk squamous cell cancer of the oropharynx (OPSCC) continue to relapse locally despite radical chemoradiotherapy (CRT). The toxicity of the current combination of intensified dose per fraction radiotherapy and platinum based chemotherapy limits further uniform intensification. If a predictive biomarker for outcomes from CRT can be identified during treatment then individualised and adaptive treatment strategies may be employed.
Methods/design:
The MeRInO study is a prospective observational imaging study of patients with intermediate and high risk, locally advanced OPSCC receiving radical RT or concurrent CRT Patients undergo diffusion weighted MRI prior to treatment (MRI_1) and during the third week of RT (MRI_2). Apparent diffusion coefficient (ADC) measurements will be made on each scan for previously specified target lesions (primary and lymph nodes) and change in ADC calculated. Patients will be followed up and disease status for each target lesion noted. The primary aim of the MeRInO study is to determine the threshold change in ADC from baseline to week 3 of RT that may identify the sub-group of non-responders during treatment.
Discussion:
The use of DW-MRI as a predictive biomarker during RT for SCC H&N is in its infancy but studies to date have found that response to treatment may indeed be predicted by comparison of DW-MRI carried out before and during treatment. However, previous studies have included all sub-sites and biological sub-types. Establishing ADC thresholds that predict for local failure is an essential step towards using DW-MRI to improve the therapeutic ratio in treating SCC H&N. This would be done most robustly in a specific H&N sub-site and in sub-types with similar biological behaviour. The MeRInO study will help establish these thresholds in OPSCC
New metric reconstruction scheme for gravitational self-force calculations
Inspirals of stellar-mass objects into massive black holes will be important sources for the space-based gravitational-wave detector LISA. Modelling these systems requires calculating the metric perturbation due to a point particle orbiting a Kerr black hole. Currently, the linear perturbation is obtained with a metric reconstruction procedure that puts it in a "no-string" radiation gauge which is singular on a surface surrounding the central black hole. Calculating dynamical quantities in this gauge involves a subtle procedure of "gauge completion" as well as cancellations of very large numbers. The singularities in the gauge also lead to pathological field equations at second perturbative order. In this paper we re-analyze the point-particle problem in Kerr using the corrector-field reconstruction formalism of Green, Hollands, and Zimmerman (GHZ). We clarify the relationship between the GHZ formalism and previous reconstruction methods, showing that it provides a simple formula for the "gauge completion". We then use it to develop a new method of computing the metric in a more regular gauge: a Teukolsky puncture scheme. This scheme should ameliorate the problem of large cancellations, and by constructing the linear metric perturbation in a sufficiently regular gauge, it should provide a first step toward second-order self-force calculations in Kerr. Our methods are developed in generality in Kerr, but we illustrate some key ideas and demonstrate our puncture scheme in the simple setting of a static particle in Minkowski spacetime
Ringdowns for black holes with scalar hair: the large mass case
Deviations from General Relativity can alter the quasi-normal mode (QNM)
ringdown of perturbed black holes. It is known that a shift-symmetric (hence
massless) scalar can only introduce black hole hair if it couples to the
Gauss-Bonnet invariant, in which case the scalar charge is fixed with respect
to the black hole mass and controlled by the strength of that coupling. The
charge per unit mass decreases with the mass and can, therefore, be used as a
perturbative parameter for black holes that are sufficiently large with respect
to the scale suppressing the deviation from General Relativity or the Standard
model. We construct an effective field theory scheme for QNMs using this
perturbative parameter to capture deviations from Kerr for both the background
and the perturbations. We demonstrate that up to second order in the charge per
unit mass, QNMs can be calculated by solving standard linearised perturbation
equations for the Kerr metric with sources depending on solutions of the same
equations up to first order. It follows that corrections to the QNM frequencies
are heavily suppressed for sufficiently massive black holes, meaning that LISA
is very unlikely to detect any evidence of scalar hair in ringdown signals.Comment: 6 page
Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction
Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage SBW25Ο2 and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that, individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions
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