Sequence variability of Campylobacter temperate bacteriophages

<p>Abstract</p> <p>Background</p> <p>Prophages integrated within the chromosomes of <it>Campylobacter jejuni </it>isolates have been demonstrated very recently. Prior work with <it>Campylobacter </it>temperate bacteriophages, as well as evidence from prophages in other enteric bacteria, suggests these prophages might have a role in the biology and virulence of the organism. However, very little is known about the genetic variability of <it>Campylobacter </it>prophages which, if present, could lead to differential phenotypes in isolates carrying the phages versus those that do not. As a first step in the characterization of <it>C. jejuni </it>prophages, we investigated the distribution of prophage DNA within a <it>C. jejuni </it>population assessed the DNA and protein sequence variability within a subset of the putative prophages found.</p> <p>Results</p> <p>Southern blotting of <it>C. jejuni </it>DNA using probes from genes within the three putative prophages of the <it>C. jejuni </it>sequenced strain RM 1221 demonstrated the presence of at least one prophage gene in a large proportion (27/35) of isolates tested. Of these, 15 were positive for 5 or more of the 7 <it>Campylobacter </it>Mu-like phage 1 (CMLP 1, also designated <it>Campylobacter jejuni </it>integrated element 1, or CJIE 1) genes tested. Twelve of these putative prophages were chosen for further analysis. DNA sequencing of a 9,000 to 11,000 nucleotide region of each prophage demonstrated a close homology with CMLP 1 in both gene order and nucleotide sequence. Structural and sequence variability, including short insertions, deletions, and allele replacements, were found within the prophage genomes, some of which would alter the protein products of the ORFs involved. No insertions of novel genes were detected within the sequenced regions. The 12 prophages and RM 1221 had a % G+C very similar to <it>C. jejuni </it>sequenced strains, as well as promoter regions characteristic of <it>C. jejuni</it>. None of the putative prophages were successfully induced and propagated, so it is not known if they were functional or if they represented remnant prophage DNA in the bacterial chromosomes.</p> <p>Conclusion</p> <p>These putative prophages form a family of phages with conserved sequences, and appear to be adapted to <it>Campylobacter</it>. There was evidence for recombination among groups of prophages, suggesting that the prophages had a mosaic structure. In many of these properties, the Mu-like CMLP 1 homologs characterized in this study resemble temperate bacteriophages of enteric bacteria that are responsible for contributions to virulence and host adaptation.</p

"Am iz kwiin" (I'm his queen): Combining interpretative phenomenological analysis with a feminist approach to work with gems in a resource-constrained setting

This article focuses on working with gems using a feminist approach to interpretative phenomenological analysis (IPA) in a resource-constrained setting. The research explores the experiences of maternal disclosure of HIV to children of HIV positive mothers in Kingston, Jamaica. A feminist approach helps recognise power imbalances within research relationships and the women’s lived experiences. We present three “gems” which illuminate women’s lived experiences and explore how popularised representations of women’s sexuality and mothering influence disclosure discourses. We use emotion work as a conceptual resource to structure the women’s narratives and challenge existing policy discourses, which arguably represent disclosure within a binary, rationalist, decision-making framework. This article adds to global literature on maternal HIV disclosure and problematises policy discourses by bringing into relief the emotion work women engage in when deciding if and how to communicate their HIV status to their children. It adds to the body of research using IPA, particularly in resource-constrained settings where IPA has thus far had little application

The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts

BACKGROUND: The presence of Campylobacter jejuni temperate bacteriophages has increasingly been associated with specific biological effects. It has recently been demonstrated that the presence of the prophage CJIE1 is associated with increased adherence and invasion of C. jejuni isolates in cell culture assays. RESULTS: Quantitative comparative proteomics experiments were undertaken using three closely related isolates with CJIE1 and one isolate without CJIE1 to determine whether there was a corresponding difference in protein expression levels. Initial experiments indicated that about 2% of the total proteins characterized were expressed at different levels in isolates with or without the prophage. Some of these proteins regulated by the presence of CJIE1 were associated with virulence or regulatory functions. Additional experiments were conducted using C. jejuni isolates with and without CJIE1 grown on four different media: Mueller Hinton (MH) media containing blood; MH media containing 0.1% sodium deoxycholate, which is thought to result in increased expression of virulence proteins; MH media containing 2.5% Oxgall; and MHwithout additives. These experiments provided further evidence that CJIE1 affected protein expression, including virulence-associated proteins. They also demonstrated a general bile response involving a majority of the proteome and clearly showed the induction of almost all proteins known to be involved with iron acquisition. The data have been deposited to the ProteomeXchange with identifiers PXD000798, PXD000799, PXD000800, and PXD000801. CONCLUSION: The presence of the CJIE1 prophage was associated with differences in protein expression levels under different conditions. Further work is required to determine what genes are involved in causing this phenomenon

Testing Scalar-Tensor Gravity with Gravitational-Wave Observations of Inspiralling Compact Binaries

Observations of gravitational waves from inspiralling compact binaries using laser-interferometric detectors can provide accurate measures of parameters of the source. They can also constrain alternative gravitation theories. We analyse inspiralling compact %binaries in the context of the scalar-tensor theory of Jordan, Fierz, Brans and Dicke, focussing on the effect on the inspiral of energy lost to dipole gravitational radiation, whose source is the gravitational self-binding energy of the inspiralling bodies. Using a matched-filter analysis we obtain a bound on the coupling constant $\omega_{\rm BD}$ of Brans-Dicke theory. For a neutron-star/black-hole binary, we find that the bound could exceed the current bound of $\omega_{\rm BD}>500$ from solar-system experiments, for sufficiently low-mass systems. For a $0.7 M_\odot$ neutron star and a $3 M_\odot$ black hole we find that a bound $\omega_{\rm BD} \approx 2000$ is achievable. The bound decreases with increasing black-hole mass. For binaries consisting of two neutron stars, the bound is less than 500 unless the stars' masses differ by more than about $0.5 M_\odot$. For two black holes, the behavior of the inspiralling binary is observationally indistinguishable from its behavior in general relativity. These bounds assume reasonable neutron-star equations of state and a detector signal-to-noise ratio of 10.Comment: 10 pages, (3 figures upon request), WUGRAV-94-

Gravitational waveforms from inspiralling compact binaries to second-post-Newtonian order

The two independent ``plus" and ``cross" polarization waveforms associated with the gravitational waves emitted by inspiralling, non-spinning, compact binaries are presented, ready for use in the data analysis of signals received by future laser interferometer gravitational-wave detectors such as LIGO and VIRGO. The computation is based on a recently derived expression of the gravitational field at the second-post-Newtonian approximation of general relativity beyond the dominant (Newtonian) quadrupolar field. The use of these theoretical waveforms to make measurements of astrophysical parameters and to test the nature of relativistic gravity is discussed.Comment: 17 pages; To appear in Classical and Quantum Gravit

The potential of trading activity income to fund third sector organisations operating in deprived areas

In the United Kingdom, as in other countries, Third Sector Organisations (TSOs) have been drawn towards income sources associated with trading activities (Teasdale, 2010), but many remain reliant on grant funding to support such activities (Chell, 2007). Using a multivariate analysis approach and data from the National Survey of Charities and Social Enterprises (NSCSE), it is found that trading activities are used relatively commonly in deprived areas. These organisations are also more likely to attempt to access public sector funds. This suggests policy-makers need to consider the impact of funding cuts on TSOs in the most deprived areas as TSOs are unlikely achieve their objectives without continuing support

The O28 Antigen Gene Clusters of Salmonella enterica

A 10 kb O-antigen gene cluster was sequenced from a Salmonella enterica subsp. enterica Dakar O28 reference strain and from two S. Pomona serogroup O28 isolates. The two S. Pomona O antigen gene clusters showed only moderate identity with the S. Dakar O28 gene cluster, suggesting that the O antigen oligosaccharides may contain one or more sugars conferring the O28 epitope but may otherwise be different. These novel findings are absolutely critical for the correct interpretation of molecular serotyping assays targeting genes within the O antigen gene clusters of these Salmonella serotypes and suggest the possibility that the O antigen gene clusters of other Salmonella serovars may also be heterogenous

Intravenous iron for heart failure, iron deficiency definitions, and clinical response:the IRONMAN trial

BACKGROUND AND AIMS: What is the relationship between blood tests for iron deficiency, including anaemia, and the response to intravenous iron in patients with heart failure?METHODS: In the IRONMAN trial, 1137 patients with heart failure, ejection fraction ≤ 45%, and either serum ferritin &lt; 100 µg/L or transferrin saturation (TSAT) &lt; 20% were randomized to intravenous ferric derisomaltose (FDI) or usual care. Relationships were investigated between baseline anaemia severity, ferritin and TSAT, to changes in haemoglobin from baseline to 4 months, Minnesota Living with Heart Failure (MLwHF) score and 6-minute walk distance achieved at 4 months, and clinical events, including heart failure hospitalization (recurrent) or cardiovascular death.RESULTS: The rise in haemoglobin after administering FDI, adjusted for usual care, was greater for lower baseline TSAT (Pinteraction &lt; .0001) and ferritin (Pinteraction = .028) and more severe anaemia (Pinteraction = .014). MLwHF scores at 4 months were somewhat lower (better) with FDI for more anaemic patients (overall Pinteraction = .14; physical Pinteraction = .085; emotional Pinteraction = .043) but were not related to baseline TSAT or ferritin. Blood tests did not predict difference in achieved walking distance for those randomized to FDI compared to control. The absence of anaemia or a TSAT ≥ 20% was associated with lower event rates and little evidence of benefit from FDI. More severe anaemia or TSAT &lt; 20%, especially when ferritin was ≥100 µg/L, was associated with higher event rates and greater absolute reductions in events with FDI, albeit not statistically significant.CONCLUSIONS: This hypothesis-generating analysis suggests that anaemia or TSAT &lt; 20% with ferritin &gt; 100 µg/L might identify patients with heart failure who obtain greater benefit from intravenous iron. This interpretation requires confirmation.</p

Developing a Personality Model for Speech-based Conversational Agents Using the Psycholexical Approach

We present the first systematic analysis of personality dimensions developed specifically to describe the personality of speech-based conversational agents. Following the psycholexical approach from psychology, we first report on a new multi-method approach to collect potentially descriptive adjectives from 1) a free description task in an online survey (228 unique descriptors), 2) an interaction task in the lab (176 unique descriptors), and 3) a text analysis of 30,000 online reviews of conversational agents (Alexa, Google Assistant, Cortana) (383 unique descriptors). We aggregate the results into a set of 349 adjectives, which are then rated by 744 people in an online survey. A factor analysis reveals that the commonly used Big Five model for human personality does not adequately describe agent personality. As an initial step to developing a personality model, we propose alternative dimensions and discuss implications for the design of agent personalities, personality-aware personalisation, and future research.Comment: 14 pages, 2 figures, 3 tables, CHI'2

Mind the gap!: Students' Understanding and Application of Social Work Values

This paper discusses a research project that explored the development of student social workers' values during the first year of professional education at one Scottish university. Questionnaires, based on a vignette, and focus groups established baseline information at the outset of the study. These methods were reapplied a year later to identify the extent to which students' values framework had developed, and the factors that had supported this. The study revealed that, by the end of that year, students could both identify and apply values to support them in their work with individuals to a greater extent than they could those to help them challenge structural discrimination. The study also highlighted the need for university-based teaching, and practice learning experiences, to provide more opportunities for reflection and discussion to support the development of values in student social workers