A unique homologue of the eukaryotic protein-modifier ubiquitin present in the bacterium Bacteroides fragilis, a predominant resident of the human gastrointestinal tract

In the complete genome sequences of Bacteroides fragilis NCTC9343 and 638R, we have discovered a gene, ubb, the product of which has 63 % identity to human ubiquitin and cross-reacts with antibodies raised against bovine ubiquitin. The sequence of ubb is closest in identity (76 %) to the ubiquitin gene from a migratory grasshopper entomopoxvirus, suggesting acquisition by inter-kingdom horizontal gene transfer. We have screened clinical isolates of B. fragilis from diverse geographical regions and found that ubb is present in some, but not all, strains. The gene is transcribed and the mRNA is translated in B. fragilis, but deletion of ubb did not have a detrimental effect on growth. BfUbb has a predicted signal sequence; both full-length and processed forms were detected in whole-cell extracts, while the processed form was found in concentrated culture supernatants. Purified recombinant BfUbb inhibited in vitro ubiquitination and was able to covalently bind the human E1 activating enzyme, suggesting it could act as a suicide substrate in vivo. B. fragilis is one of the predominant members of the normal human gastrointestinal microbiota with estimates of up to >1011 cells per g faeces by culture. These data indicate that the gastro-intestinal tract of some individuals could contain a significant amount of aberrant ubiquitin with the potential to inappropriately activate the host immune system and/or interfere with eukaryotic ubiquitin activity. This discovery could have profound implications in relation to our understanding of human diseases such as inflammatory bowel and autoimmune diseases

Removal of a frameshift between the hsdM and hsdS genes of the EcoKI Type IA DNA restriction and modification system produces a new type of system and links the different families of Type I systems

The EcoKI DNA methyltransferase is a trimeric protein comprised of two modification subunits (M) and one sequence specificity subunit (S). This enzyme forms the core of the EcoKI restriction/modification (RM) enzyme. The 3′ end of the gene encoding the M subunit overlaps by 1 nt the start of the gene for the S subunit. Translation from the two different open reading frames is translationally coupled. Mutagenesis to remove the frameshift and fuse the two subunits together produces a functional RM enzyme in vivo with the same properties as the natural EcoKI system. The fusion protein can be purified and forms an active restriction enzyme upon addition of restriction subunits and of additional M subunit. The Type I RM systems are grouped into families, IA to IE, defined by complementation, hybridization and sequence similarity. The fusion protein forms an evolutionary intermediate form lying between the Type IA family of RM enzymes and the Type IB family of RM enzymes which have the frameshift located at a different part of the gene sequence

Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI–DNA complexes

DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 Å resolution. From time-resolved fluorescence measurements of these single crystals, we have established that the fluorescence decay function of AP shows a pronounced, characteristic response to base flipping: the loss of the very short (∼100 ps) decay component and the large increase in the amplitude of the long (∼10 ns) component. When AP is positioned at sites other than the target site, this response is not seen. Most significantly, we have shown that the same clear response is apparent when M.HhaI complexes with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA–enzyme complexes that cannot be discerned from the present X-ray structures

Photo-elicitation and time-lining to enhance the research interview: Exploring the quarterlife crisis of young adults in India and the UK

The aim of this article is to convey our experience of using photo-elicitation along with time-lining to enhance the research interview. We reflect on a study on the ‘quarterlife crisis’ in India and the UK. Participants were aged 22-30 years and self-defined as having experienced difficulties ‘finding their place in the world.’ There were 16 British (8 women, 8 men) and 8 Indian participants (4 women; 4 men). First, we consider how photo-elicitation proved highly compatible with our method of analysis – interpretative phenomenological analysis – through affording a deep connection with participant experience. Second, we explore how participants engaged with photo-elicitation and time-lining, providing examples of image content (events and feelings), image form (literal and symbolic), and creative use of timelines. Third, we reflect on how photo-elicitation and time-lining appeared to enhance participant agency, and to have a therapeutic value for participants, as well as providing particularly rich material for analysis

Building and Testing a Statistical Shape Model of the Human Ear Canal

Abstract. Today the design of custom in-the-ear hearing aids is based on personal experience and skills and not on a systematic description of the variation of the shape of the ear canal. In this paper it is described how a dense surface point distribution model of the human ear canal is built based on a training set of laser scanned ear impressions and a sparse set of anatomical landmarks placed by an expert. The landmarks are used to warp a template mesh onto all shapes in the training set. Using the vertices from the warped meshes, a 3D point distribution model is made. The model is used for testing for gender related differences in size and shape of the ear canal.

Anaplasma phagocytophilum in White-tailed Deer

We examined the reservoir potential of white-tailed deer for Anaplasma phagocytophilum. Results suggest that white-tailed deer harbor a variant strain not associated with human infection, but contrary to published reports, white-tailed deer are not a reservoir for strains that cause human disease. These results will affect surveillance studies of vector and reservoir populations

Evaluation of fluralaner and afoxolaner treatments to control flea populations, reduce pruritus and minimize dermatologic lesions in naturally infested dogs in private residences in west central Florida USA

Citation: Dryden, M. W., Canfield, M. S., Kalosy, K., Smith, A., Crevoiserat, L., McGrady, J. C., . . . Sun, F. (2016). Evaluation of fluralaner and afoxolaner treatments to control flea populations, reduce pruritus and minimize dermatologic lesions in naturally infested dogs in private residences in west central Florida USA. Parasites & Vectors, 9, 11. doi:10.1186/s13071-016-1654-7Background: A study was conducted to evaluate and compare the effectiveness of two different oral flea and tick products to control flea infestations, reduce pruritus and minimize dermatologic lesions over a 12 week period on naturally infested dogs in west central FL USA. Methods: Thirty-four dogs with natural flea infestations living in 17 homes were treated once with a fluralaner chew on study day 0. Another 27 dogs living in 17 different homes were treated orally with an afoxolaner chewable on day 0, once between days 28-30 and once again between days 54-60. All products were administered according to label directions by study investigators. Flea populations on pets were assessed using visual area counts and premise flea infestations were assessed using intermittent-light flea traps on days 0, 7, 14, 21, and once between days 28-30, 40-45, 54-60 and 82-86. Dermatologic assessments were conducted on day 0 and once monthly. Pruritus assessments were conducted by owners throughout the study. No concurrent treatments for existing skin disease (antibiotics, anti-inflammatories, anti-fungals) were allowed. Results: Following the first administration of fluralaner or afoxolaner, flea populations on pets were reduced by 99.0 % and 99.3 %, respectively within 7 days. Flea populations on the fluralaner treated dogs were 0 (100 % efficacy) on days 54-60 and 82-86 after the administration of a single dose on day 0. Administration of 3 monthly doses of afoxolaner reduced flea populations by 100 % on days 82-86. Flea numbers in indoor-premises were markedly reduced in both treatment groups by days 82-86, with 100 % and 98.9 % reductions in flea trap counts in the fluralaner and afoxolaner treatment groups, respectively. Marked improvement was observed in FAD lesion scoring, Atopic Dermatitis lesions scoring (CADESI-4) and pruritus scores with both formulations. Conclusions: In a clinical field investigation conducted during the summer of 2015 in subtropical Florida, a single administration of an oral fluralaner chew completely eliminated dog and premises flea infestations and markedly reduced dermatology lesions and pruritus. Three monthly doses of the afoxolaner chewable also eliminated flea infestations in dogs, markedly reduced premises' flea populations and similarly improved dermatology lesions and pruritus

Psychotherapy in historical perspective

This article will briefly explore some of the ways in which the past has been used as a means to talk about psychotherapy as a practice and as a profession, its impact on individuals and society, and the ethical debates at stake. It will show how, despite the multiple and competing claims about psychotherapy’s history and its meanings, historians themselves have, to a large degree, not attended to the intellectual and cultural development of many therapeutic approaches. This absence has the potential consequence of implying that therapies have emerged as value-free techniques, outside of a social, economic and political context. The relative neglect of psychotherapy, by contrast with the attention historians have paid to other professions, particularly psychiatry, has also underplayed its societal impact. This article will foreground some of the instances where psychotherapy has become an object of emerging historical interest, including the new research that forms the substance of this special issue of History of the Human Sciences

Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance

The ardA gene, found in many prokaryotes including important pathogenic species, allows associated mobile genetic elements to evade the ubiquitous Type I DNA restriction systems and thereby assist the spread of resistance genes in bacterial populations. As such, ardA contributes to a major healthcare problem. We have solved the structure of the ArdA protein from the conjugative transposon Tn916 and find that it has a novel extremely elongated curved cylindrical structure with defined helical grooves. The high density of aspartate and glutamate residues on the surface follow a helical pattern and the whole protein mimics a 42-base pair stretch of B-form DNA making ArdA by far the largest DNA mimic known. Each monomer of this dimeric structure comprises three alpha–beta domains, each with a different fold. These domains have the same fold as previously determined proteins possessing entirely different functions. This DNA mimicry explains how ArdA can bind and inhibit the Type I restriction enzymes and we demonstrate that 6 different ardA from pathogenic bacteria can function in Escherichia coli hosting a range of different Type I restriction systems

The Development and Initial Validation of the Irrational Performance Beliefs Inventory (iPBI)

© 2016 Hogrefe Publishing. The growing use of Rational Emotive Behavior Therapy (REBT) in performance contexts (e.g., business, sport) has highlighted the absence of a contextually valid and reliable measure of irrational beliefs. This paper reports the development and initial validation of the Irrational Performance Beliefs Inventory (iPBI). The iPBI was developed to provide a validated measure of the four core irrational beliefs of REBT theory. Item development was completed in three stages comprising two expert panels and one novice panel, reducing and refining 176 items to 133. Then, exploratory and confirmatory factor analyses were used to refine the measure and reduce the number of items. A total of 665 business professionals completed the 133-item scale, alongside an established measure of irrational beliefs and a measure of negative emotion. A 28-item measure was developed (the iPBI) that showed an acceptable fit to the four-factor REBT structure. The iPBI correlated well with the established irrational beliefs measure, and with anxiety, depression, and anger, demonstrating concurrent and predictive validity. Further validation efforts are required to assess the validity and reliability of the iPBI in alternative samples in other performance-related contexts