Environmental cues and genes involved in establishment of the superinfective Pf4 phage of Pseudomonas aeruginosa

© 2014 Hui, Mai-Prochnow, Kjelleberg, McDougald and Rice. Biofilm development in Pseudomonas aeruginosa is in part dependent on a filamentous phage, Pf4, which contributes to biofilm maturation, cell death, dispersal and variant formation, e.g., small colony variants (SCVs). These biofilm phenotypes correlate with the conversion of the Pf4 phage into a superinfection (SI) variant that reinfects and kills the prophage carrying host, in contrast to other filamentous phage that normally replicate without killing their host. Here we have investigated the physiological cues and genes that may be responsible for this conversion. Flow through biofilms typically developed SI phage approximately days 4 or 5 of development and corresponded with dispersal. Starvation for carbon or nitrogen did not lead to the development of SI phage. In contrast, exposure of the biofilm to nitric oxide, H2O2 or the DNA damaging agent, mitomycin C, showed a trend of increased numbers of SI phage, suggesting that reactive oxygen or nitrogen species (RONS) played a role in the formation of SI phage. In support of this, mutation of oxyR, the major oxidative stress regulator in P. aeruginosa, resulted in higher level of and earlier superinfection compared to the wild-type (WT). Similarly, inactivation of mutS, a DNA mismatch repair gene, resulted in the early appearance of the SI phage and this was four log higher than the WT. In contrast, loss of recA, which is important for DNA repair and the SOS response, also resulted in a delayed and decreased production of SI phage. Treatments or mutations that increased superinfection also correlated with an increase in the production of morphotypic variants. The results suggest that the accumulation of RONS by the biofilm may result in DNA lesions in the Pf4 phage, leading to the formation of SI phage, which subsequently selects for morphotypic variants, such as SCVs

'Big things in small packages: The genetics of filamentous phage and effects on fitness of their host'

© FEMS 2015. This review synthesizes recent and past observations on filamentous phages and describes how these phages contribute to host phentoypes. For example, the CTXφ phage of Vibrio cholerae encodes the cholera toxin genes, responsible for causing the epidemic disease, cholera. The CTXφ phage can transduce non-toxigenic strains, converting them into toxigenic strains, contributing to the emergence of new pathogenic strains. Other effects of filamentous phage include horizontal gene transfer, biofilm development, motility, metal resistance and the formation of host morphotypic variants, important for the biofilm stress resistance. These phages infect a wide range of Gram-negative bacteria, including deep-sea, pressure-adapted bacteria. Many filamentous phages integrate into the host genome as prophage. In some cases, filamentous phages encode their own integrase genes to facilitate this process, while others rely on host-encoded genes. These differences are mediated by different sets of 'core' and 'accessory' genes, with the latter group accounting for some of the mechanisms that alter the host behaviours in unique ways. It is increasingly clear that despite their relatively small genomes, these phages exert signficant influence on their hosts and ultimately alter the fitness and other behaviours of their hosts

Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment

Background: Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions. Methodology/Principal Findings: To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions. Conclusions/Significance: The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associated community. We have also identified properties that could mediate interactions with surfaces other than its currently recognised hosts. This together with the detection of known virulence genes leads to the hypothesis that P. tunicata maintains a carefully regulated balance between beneficial and detrimental interactions with a range of host surfaces. © 2008 Thomas et al

Process disturbances in agricultural biogas production—causes, mechanisms and effects on the biogas microbiome: A review

Disturbances of the anaerobic digestion process reduce the economic and environmental performance of biogas systems. A better understanding of the highly complex process is of crucial importance in order to avoid disturbances. This review defines process disturbances as significant changes in the functionality within the microbial community leading to unacceptable and severe decreases in biogas production and requiring an active counteraction to be overcome. The main types of process disturbances in agricultural biogas production are classified as unfavorable process temperatures, fluctuations in the availability of macro- and micronutrients (feedstock variability), overload of the microbial degradation potential, process-related accumulation of inhibiting metabolites such as hydrogen (H 2 ), ammonium/ammonia (NH 4 + /NH 3 ) or hydrogen sulphide (H 2 S) and inhibition by other organic and inorganic toxicants. Causes, mechanisms and effects on the biogas microbiome are discussed. The need for a knowledge-based microbiome management to ensure a stable and efficient production of biogas with low susceptibility to disturbances is derived and an outlook on potential future process monitoring and control by means of microbial indicators is provided

Process disturbances in agricultural biogas production—causes, mechanisms and effects on the biogas microbiome: A review

Disturbances of the anaerobic digestion process reduce the economic and environmental performance of biogas systems. A better understanding of the highly complex process is of crucial importance in order to avoid disturbances. This review defines process disturbances as significant changes in the functionality within the microbial community leading to unacceptable and severe decreases in biogas production and requiring an active counteraction to be overcome. The main types of process disturbances in agricultural biogas production are classified as unfavorable process temperatures, fluctuations in the availability of macro- and micronutrients (feedstock variability), overload of the microbial degradation potential, process-related accumulation of inhibiting metabolites such as hydrogen (H 2 ), ammonium/ammonia (NH 4 + /NH 3 ) or hydrogen sulphide (H 2 S) and inhibition by other organic and inorganic toxicants. Causes, mechanisms and effects on the biogas microbiome are discussed. The need for a knowledge-based microbiome management to ensure a stable and efficient production of biogas with low susceptibility to disturbances is derived and an outlook on potential future process monitoring and control by means of microbial indicators is provided

Rheophysics of dense granular materials : Discrete simulation of plane shear flows

We study the steady plane shear flow of a dense assembly of frictional, inelastic disks using discrete simulation and prescribing the pressure and the shear rate. We show that, in the limit of rigid grains, the shear state is determined by a single dimensionless number, called inertial number I, which describes the ratio of inertial to pressure forces. Small values of I correspond to the quasi-static regime of soil mechanics, while large values of I correspond to the collisional regime of the kinetic theory. Those shear states are homogeneous, and become intermittent in the quasi-static regime. When I increases in the intermediate regime, we measure an approximately linear decrease of the solid fraction from the maximum packing value, and an approximately linear increase of the effective friction coefficient from the static internal friction value. From those dilatancy and friction laws, we deduce the constitutive law for dense granular flows, with a plastic Coulomb term and a viscous Bagnold term. We also show that the relative velocity fluctuations follow a scaling law as a function of I. The mechanical characteristics of the grains (restitution, friction and elasticity) have a very small influence in this intermediate regime. Then, we explain how the friction law is related to the angular distribution of contact forces, and why the local frictional forces have a small contribution to the macroscopic friction. At the end, as an example of heterogeneous stress distribution, we describe the shear localization when gravity is added.Comment: 24 pages, 19 figure

Status of the LEP2 Spectrometer Project

The LEP spectrometer has been conceived to provide a determination of the beam energy with a relative accuracy of 10-4 in the LEP2 physics region where insufficient polarisation levels prevent the application of the resonant depolarisation method. The setup consists of a steel bending magnet flanked by a triplet of Beam Position Monitors (BPM) at each side providing a measurement of changes in the bending angle when the beams are accelerated to physics energies. The goal for a 100 ppm relative precision on the beam energy involves a ± 1 micron BPM resolution and the calibration of the dipole bending strength to a 30 ppm accuracy. This paper reports on the results of the commissioning of the Spectrometer during the 1999 LEP Run and on the experience acquired on the behaviour of the several sub-systems with circulating beams

The Spread and Utility of Social Network Analysis across a Group of Health Behavior Researchers

Social network analysis (SNA), both as theory and methodology, is a powerful framework for delimiting and studying health behaviors. Using SNA allows scholars to answer new research questions, innovatively investigate the social and systemic contexts of health and behavior, and collaborate on multi- or inter-disciplinary projects. As a result, SNA is growing in popularity within health behavior research and practice. Despite SNA’s contribution and appeal, few health behavior researchers and practitioners have access to formal SNA education; much of the current training efforts occur outside degree-granting curricula. Therefore, the aims of this paper were to: 1) assess the diffusion of SNA, over time, among scholars presenting at AAHB annual meetings; and 2) determine whether AAHB can function as a professional venue for fostering development of SNA-related skills, especially by capitalizing on mentoring relationships. To assess the “spread” of SNA among AAHB scholars, we conducted a network analysis to capture the connections among those presenting research posters between 2016 and 2019. Results indicated sizeable increases in adoption of, and exposure to SNA within this network. Based on these findings, we recommend responding to the growing trends of SNA use by providing conference-based training and education in SNA. We also propose utilizing mentorship ties as leverage points in diffusing SNA within a system of professional scholars and, as a result, advancing health behavior research and practice

Water footprint analysis for the assessment of milk production in Brandenburg (Germany)

The working group "Adaptation to Climate Change" at the Leibniz-Institute for Agricultural Engineering Potsdam-Bornim (ATB) is introduced. This group calculates the water footprint for agricultural processes and farms, distinguished into green water footprint, blue water footprint, and dilution water footprint. The green and blue water demand of a dairy farm plays a pivotal role in the regional water balance. Considering already existing and forthcoming climate change effects there is a need to determine the water cycle in the field and in housing for process chain optimisation for the adaptation to an expected increasing water scarcity. Resulting investments to boost water productivity and to improve water use efficiency in milk production are two pathways to adapt to climate change effects. In this paper the calculation of blue water demand for dairy farming in Brandenburg (Germany) is presented. The water used for feeding, milk processing, and servicing of cows over the time period of ten years was assessed in our study. The preliminary results of the calculation of the direct blue water footprint shows a decreasing water demand in the dairy production from the year 1999 with 5.98×109 L/yr to a water demand of 5.00×109 L/yr in the year 2008 in Brandenburg because of decreasing animal numbers and an improved average milk yield per cow. Improved feeding practices and shifted breeding to greater-volume producing Holstein-Friesian cow allow the production of milk in a more water sustainable way. The mean blue water consumption for the production of 1 kg milk in the time period between 1999 to 2008 was 3.94±0.29 L. The main part of the consumed water seems to stem from indirect used green water for the production of feed for the cows

Subliminal versus supraliminal stimuli activate neural responses in anterior cingulate cortex, fusiform gyrus and insula:a meta-analysis of fMRI studies

Background: Non-conscious neural activation may underlie various psychological functions in health and disorder. However, the neural substrates of non-conscious processing have not been entirely elucidated. Examining the differential effects of arousing stimuli that are consciously, versus unconsciously perceived will improve our knowledge of neural circuitry involved in non-conscious perception. Here we conduct preliminary analyses of neural activation in studies that have used both subliminal and supraliminal presentation of the same stimulus. Methods: We use Activation Likelihood Estimation (ALE) to examine functional Magnetic Resonance Imaging (fMRI) studies that uniquely present the same stimuli subliminally and supraliminally to healthy participants during functional magnetic resonance imaging (fMRI). We included a total of 193 foci from 9 studies representing subliminal stimulation and 315 foci from 10 studies representing supraliminal stimulation. Results: The anterior cingulate cortex is significantly activated during both subliminal and supraliminal stimulus presentation. Subliminal stimuli are linked to significantly increased activation in the right fusiform gyrus and right insula. Supraliminal stimuli show significantly increased activation in the left rostral anterior cingulate. Conclusions: Non-conscious processing of arousing stimuli may involve primary visual areas and may also recruit the insula, a brain area involved in eventual interoceptive awareness. The anterior cingulate is perhaps a key brain region for the integration of conscious and non-conscious processing. These preliminary data provide candidate brain regions for further study in to the neural correlates of conscious experience