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 Cholodny’s 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 (μCT). 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 μCT 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 Cholodny’s 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 μCT imaging in soil will enable a better understanding of soil micro-habitats and the spatially-explicit nature of microbial interactions in this complex environment

Quorum-quenching activity of the AHL-lactonase from <i>Bacillus licheniformis</i> DAHB1 inhibits vibrio biofilm formation in vitro and reduces shrimp intestinal colonisation and mortality

Vibrio parahaemolyticus is a significant cause of gastroenteritis resulting from the consumption of undercooked sea foods and often cause significant infections in shrimp aquaculture. Vibrio virulence is associated with biofilm formation and is regulated by N-acylated homoserine lactone (AHL)-mediated quorum sensing. In an attempt to reduce vibrio colonisation of shrimps and mortality, we screened native intestinal bacilli from Indian white shrimps (Fenneropenaeus indicus) for an isolate which showed biofilm-inhibitory activity (quorum quenching) against the pathogen V. parahaemolyticus DAHP1. The AHL-lactonase (AiiA) expressed by one of these, Bacillus licheniformis DAHB1, was characterised as having a broad-spectrum AHL substrate specificity and intrinsic resistance to the acid conditions of the shrimp intestine. Purified recombinant AiiA inhibited vibrio biofilm development in a cover slip assay and significantly attenuated infection and mortality in shrimps reared in a recirculation aquaculture system. Investigation of intestinal samples also showed that AiiA treatment also reduced vibrio viable counts and biofilm development as determined by confocal laser scanning microscopy (CLSM) imaging. These findings suggest that the B. licheniformis DAHB1 quorum-quenching AiiA might be developed for use as a prophylactic treatment to inhibit or reduce vibrio colonisation and mortality of shrimps in aquaculture

Parallel compensatory evolution stabilizes plasmids across the parasitism-mutualism continuum

Plasmids drive genomic diversity in bacteria via horizontal gene transfer [1 and 2]; nevertheless, explaining their survival in bacterial populations is challenging [3]. Theory predicts that irrespective of their net fitness effects, plasmids should be lost: when parasitic (costs outweigh benefits), plasmids should decline due to purifying selection [4, 5 and 6], yet under mutualism (benefits outweigh costs), selection favors the capture of beneficial accessory genes by the chromosome and loss of the costly plasmid backbone [4]. While compensatory evolution can enhance plasmid stability within populations [7, 8, 9, 10, 11, 12, 13, 14 and 15], the propensity for this to occur across the parasitism-mutualism continuum is unknown. We experimentally evolved Pseudomonas fluorescens and its mercury resistance mega-plasmid, pQBR103 [ 16], across an environment-mediated parasitism-mutualism continuum. Compensatory evolution stabilized plasmids by rapidly ameliorating the cost of plasmid carriage in all environments. Genomic analysis revealed that, in both parasitic and mutualistic treatments, evolution repeatedly targeted the gacA/gacS bacterial two-component global regulatory system while leaving the plasmid sequence intact. Deletion of either gacA or gacS was sufficient to completely ameliorate the cost of plasmid carriage. Mutation of gacA/gacS downregulated the expression of ∼17% of chromosomal and plasmid genes and appears to have relieved the translational demand imposed by the plasmid. Chromosomal capture of mercury resistance accompanied by plasmid loss occurred throughout the experiment but very rarely invaded to high frequency, suggesting that rapid compensatory evolution can limit this process. Compensatory evolution can explain the widespread occurrence of plasmids and allows bacteria to retain horizontally acquired plasmids even in environments where their accessory genes are not immediately useful

Familiarity expands space and contracts time

When humans draw maps, or make judgments about travel-time, their responses are rarely accurate and are often systematically distorted. Distortion effects on estimating time to arrival and the scale of sketch-maps reveal the nature of mental representation of time and space. Inspired by data from rodent entorhinal grid cells, we predicted that familiarity to an environment would distort representations of the space by expanding the size of it. We also hypothesized that travel-time estimation would be distorted in the same direction as space-size, if time and space rely on the same cognitive map. We asked international students, who had lived at a college in London for 9 months, to sketch a south-up map of their college district, estimate travel-time to destinations within the area, and mark their everyday walking routes. We found that while estimates for sketched space were expanded with familiarity, estimates of the time to travel through the space were contracted with familiarity. Thus, we found dissociable responses to familiarity in representations of time and space. © 2016 The Authors Hippocampus Published by Wiley Periodicals, Inc

Waiting for a kidney from a deceased donor: an interpretative phenomenological analysis

Demand for kidneys from deceased donors far outstrips supply. Despite this, there appears to be little research that focuses solely on the experience of waiting for a kidney from a deceased donor. This study uses the qualitative methodology Interpretative Phenomenological Analysis (IPA) to explore the lives of 10 people on the transplant list, with the aims of illuminating the potential psychological challenges those on the list may face during this time, and providing information to help clinicians more fully support such people in the future. Two themes connected to the experience of waiting – adjustment to the uncertainty of waiting and thinking about receiving a kidney from a living donor – are presented here. Participants describe a sense of confusion and uncertainty around life on the list, and discuss their strategies for dealing with this. Novel complexities around the ambiguous challenge of receiving an organ from a deceased donor are revealed. It is recommended that healthcare teams provide a forum for this patient group to work through these feelings of confusion and ambiguity

Sleep enhances a spatially mediated generalization of learned values

Sleep is thought to play an important role in memory consolidation. Here we tested whether sleep alters the subjective value associated with objects located in spatial clusters that were navigated to in a large-scale virtual town. We found that sleep enhances a generalization of the value of high-value objects to the value of locally clustered objects, resulting in an impaired memory for the value of high-valued objects. Our results are consistent with (a) spatial context helping to bind items together in long-term memory and serve as a basis for generalizing across memories and (b) sleep mediating memory effects on salient/reward-related items

Transparent soil for imaging the rhizosphere

Understanding of soil processes is essential for addressing the global issues of food security, disease transmission and climate change. However, techniques for observing soil biology are lacking. We present a heterogeneous, porous, transparent substrate for in situ 3D imaging of living plants and root-associated microorganisms using particles of the transparent polymer, Nafion, and a solution with matching optical properties. Minerals and fluorescent dyes were adsorbed onto the Nafion particles for nutrient supply and imaging of pore size and geometry. Plant growth in transparent soil was similar to that in soil. We imaged colonization of lettuce roots by the human bacterial pathogen Escherichia coli O157:H7 showing micro-colony development. Micro-colonies may contribute to bacterial survival in soil. Transparent soil has applications in root biology, crop genetics and soil microbiology

Quantifying prosthetic and intact limb use in upper limb amputees via egocentric video: an unsupervised, at-home study

Analysis of the manipulation strategies employed by upper-limb prosthetic device users can provide valuable insights into the shortcomings of current prosthetic technology or therapeutic interventions. Typically, this problem has been approached with survey or lab-based studies, whose prehensile-grasp-focused results do not necessarily give accurate representations of daily activity. In this work, we capture prosthesis-user behavior in the unstructured and familiar environments of the participants own homes. Compact head-mounted video cameras recorded ego-centric views of the hands during self-selected household chores. Over 60 hours of video was recorded from 8 persons with unilateral amputation or limb difference (6 transradial, 1 transhumeral, 1 shoulder). Of this, almost 16 hours of video data was analyzed by human experts using the 22-category ‘TULIP’ custom manipulation taxonomy, producing the type and duration of over 27,000 prehensile and non-prehensile manipulation tags on both upper limbs, permitting a level of objective analysis not previously possible with this population. Our analysis included unique observations on non-prehensile manipulations occurrence, determining that 79% of transradial body-powered device manipulations were non-prehensile, compared to 60% for transradial myoelectric devices. Conversely, only 16-19% of intact limb activity was non-prehensile. Additionally, multi-grasp terminal devices did not lead to increased activity compared to 1DOF devices