Prescottia equi gen. nov., comb. nov.: a new home for an old pathogen

The taxonomic status of Rhodococcus equi, originally isolated from foal specimens, has been the subject of discussion for a number of years. The chequered history of the taxon has prompted this polyphasic analysis of R. equi strains, close members of the genus Rhodococcus and representatives of other genera classified in the order Corynebacteriales, to establish the taxonomic position of this taxon. Thirty one R. equi strains, including the type strain, were examined for genotypic and numerical taxonomic properties. The resultant data are consistent with their classification in the order Corynebacteriales but the R. equi strains formed a distinct phyletic clade away from representatives of other members of the genus Rhodococcus in the 16S rRNA gene tree. Representatives of this clade shared their highest pairwise 16S rRNA gene sequence similarities with the type strain of Rhodococcus kunmingensis (95.2–98.1 %). However, the R. equi taxon was readily distinguished from R. kunmingensis and from the other members of the order Corynebacteriales using a combination of genotypic, chemotypic and phenotypic properties. On the basis of these data the R. equi strains are considered to represent a new genus. The name proposed for this taxon is Prescottia gen. nov., with Prescottia equi comb. nov. as the type species containing the type strain, C 7T (= ATCC 25729T = ATCC 6939T = CCUG 892T = CIP 54.72T = DSM 20307T = HAMBI 2061T = NBRC 14956T = JCM 1311T = JCM 3209T = LMG 18452T = NBRC 101255T = NCTC 1621T = NRRL B-16538T = VKM Ac-953T)

The 5' → 3' exoribonuclease XRN1/Pacman and its functions in cellular processes and development

XRN1 is a 5' → 3' processive exoribonuclease that degrades mRNAs after they have been decapped. It is highly conserved in all eukaryotes, including homologs in Drosophila melanogaster (Pacman), Caenorhabditis elegans (XRN1), and Saccharomyces cerevisiae (Xrn1p). As well as being a key enzyme in RNA turnover, XRN1 is involved in nonsense-mediated mRNA decay and degradation of mRNAs after they have been targeted by small interfering RNAs or microRNAs. The crystal structure of XRN1 can explain its processivity and also the selectivity of the enzyme for 5' monophosphorylated RNA. In eukaryotic cells, XRN1 is often found in particles known as processing bodies (P bodies) together with other proteins involved in the 5' → 3' degradation pathway, such as DCP2 and the helicase DHH1 (Me31B). Although XRN1 shows little specificity to particular 5' monophosphorylated RNAs in vitro, mutations in XRN1 in vivo have specific phenotypes suggesting that it specifically degrades a subset of RNAs. In Drosophila, mutations in the gene encoding the XRN1 homolog pacman result in defects in wound healing, epithelial closure and stem cell renewal in testes. We propose a model where specific mRNAs are targeted to XRN1 via specific binding of miRNAs and/or RNA-binding proteins to instability elements within the RNA. These guide the RNA to the 5' core degradation apparatus for controlled degradation

Explicit tracking of uncertainty increases the power of quantitative rule-of-thumb reasoning in cell biology

"Back-of-the-envelope" or "rule-of-thumb" calculations involving rough estimates of quantities play a central scientific role in developing intuition about the structure and behaviour of physical systems, for example in so-called `Fermi problems' in the physical sciences. Such calculations can be used to powerfully and quantitatively reason about biological systems, particularly at the interface between physics and biology. However, substantial uncertainties are often associated with values in cell biology, and performing calculations without taking this uncertainty into account may limit the extent to which results can be interpreted for a given problem. We present a means to facilitate such calculations where uncertainties are explicitly tracked through the line of reasoning, and introduce a `probabilistic calculator' called Caladis, a web tool freely available at www.caladis.org, designed to perform this tracking. This approach allows users to perform more statistically robust calculations in cell biology despite having uncertain values, and to identify which quantities need to be measured more precisely in order to make confident statements, facilitating efficient experimental design. We illustrate the use of our tool for tracking uncertainty in several example biological calculations, showing that the results yield powerful and interpretable statistics on the quantities of interest. We also demonstrate that the outcomes of calculations may differ from point estimates when uncertainty is accurately tracked. An integral link between Caladis and the Bionumbers repository of biological quantities further facilitates the straightforward location, selection, and use of a wealth of experimental data in cell biological calculations.Comment: 8 pages, 3 figure

A system for gaze-contingent image analysis and multi-sensorial image display

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Foot and Mouth Epidemic Reduces Cases of Human Cryptosporidiosis in Scotland.

In Scotland, rates of cryptosporidiosis infection in humans peak during the spring, a peak that is coincident with the peak in rates of infection in farm animals (during lambing and calving time). Here we show that, during the outbreak of foot and mouth disease (FMD) in 2001, there was a significant reduction in human cases of cryptosporidiosis infection in southern Scotland, where FMD was present, whereas, in the rest of Scotland, there was a reduction in cases that was not significant. We associate the reduction in human cases of cryptosporidiosis infection with the reduction in the number of young farm animals, together with restrictions on movement of both farm animals and humans, during the outbreak of FMD in 2001. We further show that, during 2002, there was recovery in the rate of cryptosporidiosis infection in humans throughout Scotland, particularly in the FMD-infected area, but that rates of infection remained lower, though not significantly, than pre-2001 levels

Genomic analyses confirm close relatedness between Rhodococcus defluvii and Rhodococcus equi (Rhodococcus hoagii)

Rhodococcus defluvii strain Ca11T was isolated from a bioreactor involved in extensive phosphorus removal. We have sequenced the whole genome of this strain and our comparative genomic and phylogenetic analyses confirm its close relatedness with Rhodococcus equi (Rhodococcus hoagii) strains, which share >80% of the gene content. The R. equi virulence plasmid is absent though most of the chromosomal R. equi virulence-associated genes are present in R. defluvii Ca11T. These data suggest that although R. defluvii is an environmental organism, it has the potential to colonise animal hosts

Characterisation of Nature-Based Solutions for the Built Environment

Nature has provided humankind with food, fuel, and shelter throughout evolutionary history. However, in contemporary cities, many natural landscapes have become degraded and replaced with impermeable hard surfaces (e.g., roads, paving, car parks and buildings). The reversal of this trend is dynamic, complex and still in its infancy. There are many facets of urban greening initiatives involving multiple benefits, sensitivities and limitations. The aim of this paper is to develop a characterisation method of nature based solutions for designing and retrofitting in the built environment, and to facilitate knowledge transfer between disciplines and for design optimisation. Based on a review of the literature across disciplines, key characteristics could be organised into four groups: policy and community initiatives, multiple benefits assessment, topology, and design options. Challenges and opportunities for developing a characterisation framework to improve the use of nature based solutions in the built environment are discussed

Analysis of Information Remaining on Hand Held Devices Offered for Sale on the Second Hand

The ownership and use of mobile phones, Personal Digital Assistants and other hand held devices is now ubiquitous both for home and business use. The majority of these devices have a high initial cost, a relatively short period before they become obsolescent and a relatively low second hand value. As a result of this, when the devices are replaced, there are indications that they tend to be discarded. As technology has continued to develop, it has led to an increasing diversity in the number and type of devices that are available, and the processing power and the storage capacity of the digital storage in the device. All organisations, whether in the public or private sector increasingly use hand held devices that contain digital media for the storage of information relating to their business, their employees or their customers. Similarly, individual private users increasingly use hand held devices containing digital media for the storage of information relating to their private lives. The research revealed that a significant number of organisations and private users are ignorant or misinformed about the volume and type of information that is stored on the hand held devices and the media on which it is stored. It is apparent that they have either not considered, or are unaware of, the potential impact of this information becoming available to their competitors or those with criminal intent. This main purpose of this study was to gain an understanding of the volume and type of information that may remain on hand held devices that are offered for sale on the second hand market. A second aim of the research was to determine the level of damage that could, potentially be caused, if the information that remains on the devices fell into the wrong hands. The study examined a number of hand held devices that had been obtained from sources in the UK and Australia that ranged from internet auction sites, to private sales and commercial resellers. The study was carried out by the security research team at the BT IT Futures Centre in conjunction with Edith Cowan University in Australia and the University of Glamorgan in the UK. The basis of the research was to acquire a number of second hand hand held devices from a diverse range of sources and then determine whether they still contained information relating to a previous owner or whether the information had been effectively removed. The devices that were obtained for the research were supplied blind to the researchers through a third party. The ‘blind’ supply of the devices meant that the people undertaking the research were provided with no information about the device and that the source of the devices and any external markings were hidden from them. This process was put in place to ensure that any findings of the research were based solely on the information that could be recovered from the digital storage media that was contained within the device. The underlying methodology that was used in the research was based on the forensic imaging of the devices. A forensic image of a device is a copy of the digital media that has been created in a scientifically sound manner to a standard that is acceptable to the courts. This procedure was implemented to ensure that the evidential integrity of the devices was maintained, with the devices also then being stored in a secure manner. All subsequent research was then conducted on the image of the device. This was considered to be a sensible precaution against the possibility that information discovered on a device might indicate criminal activity and require the involvement of law enforcement. Following the forensic imaging of the devices, the images that were created were then analysed to determine whether any information remained and whether it could be easily recovered using commonly available tools and techniques that anyone who had purchased the device could acquire