Genetic and physical mapping of DNA replication origins in Haloferax volcanii

The halophilic archaeon Haloferax volcanii has a multireplicon genome, consisting of a main chromosome, three secondary chromosomes, and a plasmid. Genes for the initiator protein Cdc6/Orc1, which are commonly located adjacent to archaeal origins of DNA replication, are found on all replicons except plasmid pHV2. However, prediction of DNA replication origins in H. volcanii is complicated by the fact that this species has no less than 14 cdc6/orc1 genes. We have used a combination of genetic, biochemical, and bioinformatic approaches to map DNA replication origins in H. volcanii. Five autonomously replicating sequences were found adjacent to cdc6/orc1 genes and replication initiation point mapping was used to confirm that these sequences function as bidirectional DNA replication origins in vivo. Pulsed field gel analyses revealed that cdc6/orc1-associated replication origins are distributed not only on the main chromosome (2.9 Mb) but also on pHV1 (86 kb), pHV3 (442 kb), and pHV4 (690 kb) replicons. Gene inactivation studies indicate that linkage of the initiator gene to the origin is not required for replication initiation, and genetic tests with autonomously replicating plasmids suggest that the origin located on pHV1 and pHV4 may be dominant to the principal chromosomal origin. The replication origins we have identified appear to show a functional hierarchy or differential usage, which might reflect the different replication requirements of their respective chromosomes. We propose that duplication of H. volcanii replication origins was a prerequisite for the multireplicon structure of this genome, and that this might provide a means for chromosome-specific replication control under certain growth conditions. Our observations also suggest that H. volcanii is an ideal organism for studying how replication of four replicons is regulated in the context of the archaeal cell cycle. © 2007 Norais et al

Directed evolution of Vibrio fischeri LuxR for improved response to butanoyl-homoserine lactone

LuxR is the 3-oxohexanoyl-homoserine lactone (3OC6HSL) dependent transcriptional activator of the prototypical acyl-homoserine lactone (AHL) quorum sensing system of Vibrio fischeri. Wild-type LuxR exhibits no response to butanoyl-HSL (C4HSL) in quantitative bioassays at concentrations of up to 1 µM; a previously described LuxR variant (LuxR-G2E) exhibits a broadened response to diverse AHLs, including pentanoyl-HSL (C5HSL), but not to C4HSL. Here, two rounds of directed evolution of LuxR-G2E generated variants of LuxR that responded to C4HSL at concentrations as low as 10 nM. One variant, LuxR-G4E, had only one change, I45F, relative to the parent LuxR-G2E, which itself differs from wild-type at three residues. Dissection of the four mutations within LuxR-G4E demonstrated that at least three of these changes were simultaneously required to achieve any measurable C4HSL response. The four changes improved both sensitivity and specificity towards C4HSL relative to any of the other 14 possible combinations of those residues. These data confirm that LuxR is evolutionarily pliable and suggest that LuxR is not intrinsically asymmetric in its response to quorum sensing signals with different acyl-side chain lengths

Postcard: Man Standing Next to a Stalk of Corn

This black and white photographic postcard features a number of corn stalks propped upright by a man\u27s hand. A man on the right of it is wearing a shirt, jacket and pants with a hat. There is handwriting on the back of the card.https://scholars.fhsu.edu/tj_postcards/1526/thumbnail.jp

Legal needs of adults with life-limiting illness: what are they and how are they managed? A qualitative multi-agency stakeholder exercise

Objective: Little is known about legal needs in the context of life-limiting illness, particularly the need for advice concerning legal arrangements, rights and entitlements. This UK-based multiagency stakeholder engagement exercise scoped legal needs associated with life-limiting illness and identified support structures, gaps and opportunities for practice improvement. / Method and analysis: Snowball sampling generated a stakeholder group from a wide range of regional and national organisations involved in care of people with life-limiting illness, spanning health, social care, legal support, advice, charities, prison services as well as patient and carer representatives. A coproduced survey of three open questions generated qualitative data, interpreted by thematic analysis. Results Stakeholders reported a broad spectrum of problems and needs raising legal issues, with no consistency of definition. A classification is proposed, identifying matters concerning rights and entitlements of patients/carers in day-to-day life and decisions around care, both immediate and in the future, as well as professional responsibilities in delivering personalised care. The support structures identified were predominantly online literature, although there was some availability of remote and face-to-face services. Limited awareness of the issues, variable service configuration, fragmentation of care and inequitable access were identified as barriers to support. Stakeholders recognised the need for education and closer multiagency working. / Conclusions: ‘Legal needs’ incorporate wide-ranging issues, but there is inconsistency in perceptions among stakeholders. Practice is variable, risking unmet need. Opportunities for improvement include more formal integration of social welfare legal services in the health context, generating clearer pathways for assessment and management

A survey of UV-excess AGNs in the South Galactic Pole

Spectra, position, magnitudes and colors are presented for 485 faint (B<20.5) emission line objects selected with the ultraviolet-excess (UVX) criterion on a area of 24.6 sq. deg in the South Galactic Pole. The objects were selected from the analysis of pixel-to-pixel stacking of COSMOS scans of UKST U, J and R plates. The candidates were observed with the Meudon-ESO Fiber Optics System (MEFOS) at the ESO 3.6m telescope. 429 type 1 AGNs have been identified (373 in the redshift range 0.3<z<2.2). This sample has allowed the measure of a difference on the QSO clustering evolution in comparison with that found for galaxies (La Franca et al 1998). The region is part of the ESO Imaging Survey (EIS) and of the 2dF QSO redshift survey.Comment: 32 pages, 19 figures. To appear on A&AS, revised after minor comment

Public geographies II: being organic

This second report on ‘public geographies' considers the diverse, emergent and shifting spaces of engaging with and in public/s. Taking as its focus the more ‘organic’ rather than ‘traditional’ approach to doing public geography, as discussed in the first report, it explores the multiple and unorthodox ways in which engagements across academic-public spheres play out, and what such engagements may mean for geography/ers. The report first explores the role of the internet in ‘enabling conversations', generating a range of opportunities for public geography through websites, wikis, blogs, file-sharing sites, discussion forums and more, thinking critically about how technologies may enable/disable certain kinds of publically engaged activities. It then considers issues of process and praxis: how collaborations with groups/communities/organizations beyond academia are often unplanned, serendipitous encounters that evolve organically into research/learning/teaching endeavours; but also that personal politics/positionality bring an agency to bear upon whether we, as academics, follow the leads we may stumble upon. The report concludes with a provocative question – given that many non-academics appear to be doing some amazing and inspiring projects and activities, thoughtful, critical and (arguably) examples of organic public geographies, what then is academia’s role

Causal structure of the entanglement renormalization ansatz

We show that the multiscale entanglement renormalization ansatz (MERA) can be reformulated in terms of a causality constraint on discrete quantum dynamics. This causal structure is that of de Sitter space with a flat spacelike boundary, where the volume of a spacetime region corresponds to the number of variational parameters it contains. This result clarifies the nature of the ansatz, and suggests a generalization to quantum field theory. It also constitutes an independent justification of the connection between MERA and hyperbolic geometry which was proposed as a concrete implementation of the AdS-CFT correspondence

The semantic effects of verb raising and its consequences in second language grammars

This article considers whether highly proficient second language speakers of English can distinguish meaning contrasts associated with constructions where there is a raising be, and constructions where there is a non-raising thematic verb, as illustrated in the difference between (1a) and (1b): 1a. Kim is reading a novel (`event-in-progress/existential ? interpretation