Predatory Bdellovibrio bacteria use gliding motility to scout for prey on surfaces

Bdellovibrio bacteriovorus is a famously fast, flagellate predatory bacterium, preying upon Gram-negative bacteria in liquids; how it interacts with prey on surfaces such as in medical biofilms is unknown. Here we report that Bdellovibrio bacteria "scout" for prey bacteria on solid surfaces, using slow gliding motility that is present in flagellum-negative and pilus-negative strains.

Roles of multiple flagellins in flagellar formation and flagellar growth post bdelloplast lysis in Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus cells have a single polar flagellum whose helical pitch and diameter characteristically change near the midpoint, resulting in a tapered wave. There are six flagellin genes in the genome: fliC1 to fliC6. Accordingly, the flagellar filament is composed of several similar flagellin species. We have used knockout mutants of each gene and analyzed the mutational effects on the filament length and on the composition and localization of each flagellin species in the filament by electron microscopy and one- and two-dimensional polyacrylamide gel electrophoresis. The location and amounts of flagellins in a filament were determined to be as follows: a small amount of FliC3 at the proximal end, followed by a large amount of FliC5, a large amount of FliC1, a small amount of FliC2 in this order, and a large amount of FliC6 at the distal end. FliC4 was present at a low level, but the location was not determined. Filament lengths of newly born progeny cells increased during prolonged incubation in nutrient-deficient buffer. The newly formed part of the elongated filament was composed of mainly FliC6. Reverse transcription PCR analysis of flagellar gene expression over 5 days in buffer showed that fliC gene expression tailed off over 5 days in the wild-type cells, but in the fliC5 mutant, expression of the fliC2, fliC4, and fliC6 genes was elevated on day 5, suggesting that they may be expressed to compensate for the absence of a major component, FliC5.

A predatory patchwork:membrane and surface structures of Bdellovibrio bacteriovorus

Predatory Bdellovibrio bacteriovorus bacteria are remarkable in that they attach to, penetrate and digest other Gram-negative bacteria, living and replicating within them until all resources are exhausted, when they escape the prey ghost to invade fresh prey. Remarkable remodeling of both predator and prey cell occurs during this process to allow the Bdellovibrio to exploit the intracellular niche they have worked so hard to enter, keeping the prey "bdelloplast" intact until the end of predatory growth. If one views motile non-predatory bacteria in a light microscope, one is immediately struck by how rare it is for bacteria to collide. This highlights how the cell surface of Bdellovibrio must be specialized and adapted to allow productive collisions and further to allow entry into the prey periplasm and subsequent secretion of hydrolytic enzymes to digest it. Bdellovibrio can, however, also be made to grow artificially without prey; thus, they have a large genome containing both predatory genes and genes for saprophytic heterotrophic growth. Thus, the membrane and outer surface layers are a patchwork of proteins encompassing not only those that have a sole purpose in heterotrophic growth but also many more that are specialized or employed to attach to, enter, remodel, kill and ultimately digest prey cells. There is much that is as yet not understood, but molecular genetic and post-genomic approaches to microbial physiology have enhanced the pioneering biochemical work of four decades ago in characterizing some of the key events and surface protein requirements for prey attack.

Characterizing the flagellar filament and the role of motility in bacterial prey-penetration by Bdellovibrio bacteriovorus

The predatory bacterium Bdellovibrio bacteriovorus swims rapidly by rotation of a single, polar flagellum comprised of a helical filament of flagellin monomers, contained within a membrane sheath and powered by a basal motor complex. Bdellovibrio collides with, enters and replicates within bacterial prey, a process previously suggested to firstly require flagellar motility and then flagellar shedding upon prey entry. Here we show that flagella are not always shed upon prey entry and we study the six fliC flagellin genes of B. bacteriovorus, finding them all conserved and expressed in genome strain HD100 and the widely studied lab strain 109J. Individual inactivation of five of the fliC genes gave mutant Bdellovibrio that still made flagella, and which were motile and predatory. Inactivation of the sixth fliC gene abolished normal flagellar synthesis and motility, but a disordered flagellar sheath was still seen. We find that this non-motile mutant was still able to predate when directly applied to lawns of YFP-labelled prey bacteria, showing that flagellar motility is not essential for prey entry but important for efficient encounters with prey in liquid environments.

The Application of Digital Photogrammetric Techniques and Aerial Photography to the Preservation of Archaeological Detail. Case Study: The Copney Stone Circle Complex, Co. Tyrone, N. Ireland

The Copney Stone Circle Complex, Co. Tyrone, N. Ireland, is an important Bronze Age site forming part of the Mid-Ulster Stone Circle Complex. The Environment Service: Historic Monuments and Buildings (ESHMB) initiated a program of bog-clearance in August 1994 to excavate the stone circles. This work was completed by October 1994 and the excavated site was surveyed in August 1995. Almost immediately, the rate at which the stones forming the circles were breaking down was noted and a program of study initiated to make recommendations upon the conservation of this important site. Digital photogrammetric techniques were applied to aerial images of the stone circles and digital terrain models created from the images at a range of scales. These provide base data sets for comparison with identical surveys to be completed in successive years and will allow the rate of deterioration, and the areas most affected, of the circles to be determined. In addition, a 2D analysis of the stones provides an accurate analysis of the absolute 2D dimensions of the stones for rapid desktop computer analysis by researchers remote from the digital photogrammetric workstation used in the survey.

The products of this work are readily incorporated into web sites, educational packages and databases. The technique provides a rapid and user friendly method of presentation of a large body of information and measurements, and a reliable method of storage of the information from Copney should it become necessary to re-cover the site.

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.

Rethinking Rice Preparation for Highly Efficient Removal of Inorganic Arsenic Using Percolating Cooking Water

A novel way of cooking rice to maximize the removal of the carcinogen inorganic arsenic (Asi) is presented here. In conventional rice cooking water and grain are in continuous contact, and it is known that the larger the water:rice cooking ratio, the more Asi removed by cooking, suggesting that the Asi in the grain is mobile in water. Experiments were designed where rice is cooked in a continual stream of percolating near boiling water, either low in Asi, or Asi free. This has the advantage of not only exposing grain to large volumes of cooking water, but also physically removes any Asi leached from the grain into the water receiving vessel. The relationship between cooking water volume and Asi removal in conventional rice cooking was demonstrated for the rice types under study. At a water-to-rice cooking ratio of 12:1, 57±5% of Asi could be removed, average of 6 wholegrain and 6 polished rice samples. Two types of percolating technology were tested, one where the cooking water was recycled through condensing boiling water steam and passing the freshly distilled hot water through the grain in a laboratory setting, and one where tap water was used to cook the rice held in an off-the-shelf coffee percolator in a domestic setting. Both approaches proved highly effective in removing Asi from the cooking rice, with up to 85% of Asi removed from individual rice types. For the recycled water experiment 59±8% and 69±10% of Asi was removed, on average, compared to uncooked rice for polished (n=27) and wholegrain (n=13) rice, respectively. For coffee percolation there was no difference between wholegrain and polished rice, and the effectiveness of Asi removal was 49±7% across 6 wholegrain and 6 polished rice samples. The manuscript explores the potential applications and further optimization of this percolating cooking water, high Asi removal, discovery.

Moving from Batch to Continuous Operation for the Liquid Phase Dehydrogenation of Tetrahydrocarbazole

Despite the numerous advantages of continuous processing, high-value chemical production is still dominated by batch techniques. In this paper, we investigate options for the continuous dehydrogenation of 1,2,3,4- tetrahydrocarbazole using a trickle bed reactor operating under realistic liquid velocities with and without the addition of a hydrogen acceptor. Here, a commercial 5 wt % Pd/Al₂O₃ catalyst was observed to slowly deactivate, hence proving unsuitable for continuous use. This deactivation was attributed to the strong adsorption of a byproduct on the surface of the support. Application of a base washing technique resolved this issue and a stable continuous reaction has been demonstrated. As was previously shown for the batch reaction, the addition of a hydrogen acceptor gas (propene) can increase the overall catalytic activity of the system. 

Predator-free space, functional responses and invasions.

1. Predator–prey interactions are mediated by the structural complexity of habitats, but disentangling the many facets of structure that contribute to this mediation remains elusive. In a world replete with altered landscapes and biological invasions, determining how structure mediates the interactions between predators and novel prey will contribute to our understanding of invasions and predator–prey dynamics in general.
2. Here, using simplified experimental arenas, we manipulate predator-free space, whilst holding surface area and volume constant, to quantify the effects on predator–prey interactions between two resident gammarid predators and an invasive prey, the Ponto-Caspian corophiid Chelicorophium curvispinum.
3. Systematically increasing predator-free space alters the functional responses (the relationship between prey density and consumption rate) of the amphipod predators by reducing attack rates and lengthening handling times. Crucially, functional response shape also changes subtly from destabilizing Type II towards stabilizing Type III, such that small increases in predator-free space to result in significant reductions in prey consumption at low prey densities.
4. Habitats with superficially similar structural complexity can have considerably divergent consequences for prey population stability in general and, particularly, for invasive prey establishing at low densities in novel habitats.

A study protocol for a pilot randomised trial of a structured education programme for the self-management of type 2 diabetes for adults with intellectual disabilities

BACKGROUND: The need for structured education programmes for type 2 diabetes is a high priority for many governments around the world. One such national education programme in the United Kingdom is the DESMOND Programme, which has been shown to be robust and effective for patients in general. However, these programmes are not generally targeted to people with intellectual disabilities (ID), and robust evidence on their effects for this population is lacking. We have adapted the DESMOND Programme for people with ID and type 2 diabetes to produce an amended programme known as DESMOND-ID. This protocol is for a pilot trial to determine whether a large-scale randomised trial is feasible, to test if DESMOND-ID is more effective than usual care in adults with ID for self-management of their type 2 diabetes, in particular as a means to reduce glycated haemoglobin (Hb1Ac), improve psychological wellbeing and quality of life and promote a healthier lifestyle. This protocol describes the rationale, methods, proposed analysis plan and organisational and administrative details.

METHODS/DESIGN: This trial is a two arm, individually randomised, pilot trial for adults with ID and type 2 diabetes, and their family and/or paid carers. It compares the DESMOND-ID programme with usual care. Approximately 36 adults with mild to moderate ID will be recruited from three countries in the United Kingdom. Family and/or paid carers may also participate in the study. Participants will be randomly assigned to one of two conditions using a secure computerised system with robust allocation concealment. A range of data will be collected from the adults with ID (biomedical, psychosocial and self-management strategies) and from their carers. Focus groups with all the participants will assess the acceptability of the intervention and the trial.

DISCUSSION: The lack of appropriate structured education programmes and educational materials for this population leads to secondary health conditions and may lead to premature deaths. There are significant benefits to be gained globally, if structured education programmes are adapted and shown to be successful for people with ID and other cognitive impairments.

TRIAL REGISTRATION: Registered with International Standard Randomised Controlled Trial (identifier: ISRCTN93185560 ) on 10 November 2014.

Power Capping: What Works, What Does Not

Peak power consumption is the first order design constraint of data centers. Though peak power consumption is rarely, if ever, observed, the entire data center facility must prepare for it, leading to inefficient usage of its resources. The most prominent way for addressing this issue is to limit the power consumption of the data center IT facility far below its theoretical peak value. Many approaches have been proposed to achieve that, based on the same small set of enforcement mechanisms, but there has been no corresponding work on systematically examining the advantages and disadvantages of each such mechanism. In the absence of such a study,it is unclear what is the optimal mechanism for a given computing environment, which can lead to unnecessarily poor performance if an inappropriate scheme is used. This paper fills this gap by comparing for the first time five widely used power capping mechanisms under the same hardware/software setting. We also explore possible alternative power capping mechanisms beyond what has been previously proposed and evaluate them under the same setup. We systematically analyze the strengths and weaknesses of each mechanism, in terms of energy efficiency, overhead, and predictable behavior. We show how these mechanisms can be combined in order to implement an optimal power capping mechanism which reduces the slow down compared to the most widely used mechanism by up to 88%. Our results provide interesting insights regarding the different trade-offs of power capping techniques, which will be useful for designing and implementing highly efficient power capping in the future.