Sequence analysis of enzymes of the shikimate pathway: Development of a novel multiple sequence alignment algorithm

The possibility of homology modelling the shikimate pathway enzymes, 3-dehydroquinate synthase (el), 3-dehydroquinase (e2), shikimate dehydrogenase (e3), shikimate kinase (e4) and 5-enolpyruvylshikimate 3 -phosphate (EPSP) synthase (e5) is investigated. The sequences of these enzymes are analysed and the results found indicate that for four of these proteins, el, e2, e3, and e5, no structural homologues exist. Developing a model structure by homology modelling is therefore not possible. For shikimate kinase, statistically significant alignments are found to two proteins with known structures, adenylate kinase and H-ras p21 protein. These are also judged to be biologically significant alignments. However, the alignments obtained show too little sequence identity to permit homology modelling based on primary sequence data alone. An ab initio based methodology is next applied, with the initial step being careful evaluation of multiple sequence alignments of the shikimate pathway enzymes. Altering the parameters of the available multiple sequence alignment algorithms, produces a large range of differing alignments, with no objective way to choose a single alignment or construct a composite from the many produced for each shikimate pathway enzyme. This problem with obtaining a reliable alignment for the shikimate pathway enzyme will occur in other low sequence identity protein families, and is addressed by the development of a novel multiple sequence alignment method, Mix'n'Match. Mix'n'Match is based on finding alternating Strongly Conserved Regions (SCRs) and Loosely Conserved Regions (LCRs) in the protein sequences. The SCRs are used as 'anchors' in the alignment and are calculated from analysis of several different multiple alignments, made using varying criteria. After divided the sequences into Strongly Conserved Regions (SCRs) and Loosely Conserved Regions (LCRs), the 'best' alignment for each LCR is chosen, independently of the other LCRs, from a selection of possibilities in the multiple alignments. To help make this choice for each LCR, the secondary structure is predicted and sliown alongside each different possible alignment. One advantage of this method over automatic, non-interactive, methods, is that the final alignment is not dependent on the choice of a single set of scoring parameters. Another is that, by allowing interactive choice and by taking account of secondary structural information, the final alignment is based more on biological, rather than mathematical factors. This method can produce better alignments than any of the initial automatic multiple alignment methods used. The SCRs identified by Mix'n'Match, are found to show good correlation with the actual secondary structural elements present in the enzyme families used to test the method. Analysis of the Mix'n'Match alignment and consensus secondary structure predictions for shikimate kinase, suggest a closer match with the actual secondary structure of adenylate kinase, than is found between their amino acid sequences. These proteins appear to share functional, sequence and secondary structural homology. The proposal is made that a model structure of shikimate kinase, based on the structure of adenylate kinase, could be constructed using homology modelling techniques

Isisfordia molnari sp. nov., a new basal eusuchian from the mid-Cretaceous of Lightning Ridge, Australia

The Australian Mesozoic crocodyliform record is sparse in comparison to other Gondwanan localities. A single formally-named taxon is known from this interval; Isisfordia duncani (Winton Formation, Albian–Turonian, Queensland). We present a previously undescribed crocodyliform braincase from the Griman Creek Formation (Cenomanian), New South Wales, which we assign to Isisfordia molnari sp. nov. Assignment to the genus is based on the possession of a newly-defined autapomorphy of Isisfordia: a broadly exposed prootic within the supratemporal foramen. A second autapomorphy of I. duncani (maximum diameter of the caudal aperture of the cranioquadrate siphonium approximately one-third the mediolateral width of the foramen magnum, with the lateral wall of the caudal aperture formed exclusively by the quadrate) may also be present in I. molnari; however, definitive recognition of this feature is marred by incomplete preservation. The new taxon is differentiated from I. duncani based on the absence of a median ridge on the parietal, and the lack of characteristic ridges on the parietal that form the medial margin of the supratemporal foramina. Reanalysis of a second specimen (the former holotype of the nomen dubium,‘Crocodylus (Bottosaurus) selaslophensis’) allows for its referral to the genus Isisfordia. Crucial to this reappraisal is the reinterpretation of the specimen as a partial maxilla, not the dentary as previously thought. This maxillary fragment possesses specific characteristics shared only with I. duncani; namely an alveolar groove. However, several key features differentiate the maxillary fragment from I. duncani, specifically the presence of continuous alveolar septa, the thickening of the medial alveolar rim, and the alveolar and crown base morphology. These findings constitute the first evidence of Isisfordia outside of the type locality and indicate its widespread occurrence on the freshwater floodplains along the eastern margin of the epeiric Eromanga Sea during the Albian–Cenomanian

Equilibrium and dynamical properties of two dimensional self-gravitating systems

A system of N classical particles in a 2D periodic cell interacting via long-range attractive potential is studied. For low energy density $U$ a collapsed phase is identified, while in the high energy limit the particles are homogeneously distributed. A phase transition from the collapsed to the homogeneous state occurs at critical energy U_c. A theoretical analysis within the canonical ensemble identifies such a transition as first order. But microcanonical simulations reveal a negative specific heat regime near $U_c$. The dynamical behaviour of the system is affected by this transition : below U_c anomalous diffusion is observed, while for U > U_c the motion of the particles is almost ballistic. In the collapsed phase, finite $N$-effects act like a noise source of variance O(1/N), that restores normal diffusion on a time scale diverging with N. As a consequence, the asymptotic diffusion coefficient will also diverge algebraically with N and superdiffusion will be observable at any time in the limit N \to \infty. A Lyapunov analysis reveals that for U > U_c the maximal exponent \lambda decreases proportionally to N^{-1/3} and vanishes in the mean-field limit. For sufficiently small energy, in spite of a clear non ergodicity of the system, a common scaling law \lambda \propto U^{1/2} is observed for any initial conditions.Comment: 17 pages, Revtex - 15 PS Figs - Subimitted to Physical Review E - Two column version with included figures : less paper waste

Activation of the GLP-1 receptor by a non-peptidic agonist

Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, including diabetes and obesity1. Structures of active receptors reveal peptide agonists engage deep within the receptor core, leading to an outward movement of extracellular loop 3 and the tops of transmembrane helices 6 and 7, an inward movement of transmembrane helix 1, reorganization of extracellular loop 2 and outward movement of the intracellular side of transmembrane helix 6, resulting in G-protein interaction and activation2,3,4,5,6. Here we solved the structure of a non-peptide agonist, TT-OAD2, bound to the glucagon-like peptide-1 (GLP-1) receptor. Our structure identified an unpredicted non-peptide agonist-binding pocket in which reorganization of extracellular loop 3 and transmembrane helices 6 and 7 manifests independently of direct ligand interaction within the deep transmembrane domain pocket. TT-OAD2 exhibits biased agonism, and kinetics of G-protein activation and signalling that are distinct from peptide agonists. Within the structure, TT-OAD2 protrudes beyond the receptor core to interact with the lipid or detergent, providing an explanation for the distinct activation kinetics that may contribute to the clinical efficacy of this compound series. This work alters our understanding of the events that drive the activation of class B receptors

Oral cancer awareness of undergraduate medical and dental students

<p>Abstract</p> <p>Background</p> <p>The incidence of oral cancer is increasing in the United Kingdom. Early detection of oral cancers makes them more amenable to treatment and allows the greatest chance of cure. Delay in presentation and/or referral has a significant effect on the associated morbidity and mortality. Lack of general medical practitioner and general dental practitioner oral cancer knowledge has been shown to contribute to delays in referral and treatment. The aim of this study was to investigate the oral cancer awareness of future general medical and general dental practitioners by assessing undergraduate medical and dental students' knowledge of prevention and early detection of oral cancer.</p> <p>Method</p> <p>Questionnaires were delivered to undergraduate medical and dental students at the University of Dundee, assessing oral examination habits, delivery of advice on oral cancer risk factors, knowledge of oral cancer risk factors and clinical appearance, preferred point of referral and requests for further information.</p> <p>Results</p> <p>Undergraduate medical students were less likely to examine patients' oral mucosa routinely and less likely to advise patients about risk factors for oral cancer. Medical students identified fewer oral cancer risk factors. In particular alcohol use was identified poorly. Medical students also identified fewer oral changes associated with oral cancer. Erythroplakia and erythroleukoplakia were identified poorly. Medical students felt less well informed regarding oral cancer. 86% and 92% of undergraduate medical and dental students respectively requested further information about oral cancer.</p> <p>Conclusion</p> <p>This study highlights the need for improved education of undergraduate medical and dental students regarding oral cancer.</p

Vocal Communications and the Maintenance of Population Specific Songs in a Contact Zone

Bird song has been hypothesized to play a role in several important aspects of the biology of songbirds, including the generation of taxonomic diversity by speciation; however, the role that song plays in speciation within this group may be dependent upon the ability of populations to maintain population specific songs or calls in the face of gene flow and external cultural influences. Here, in an exploratory study, we construct a spatially explicit model of population movement to examine the consequences of secondary contact of populations singing distinct songs. We concentrate on two broad questions: 1) will population specific songs be maintained in a contact zone or will they be replaced by shared song, and 2) what spatial patterns in the distribution of songs may result from contact? We examine the effects of multiple factors including song-based mating preferences and movement probabilities, oblique versus paternal learning of song, and both cultural and genetic mutations. We find a variety of conditions under which population specific songs can be maintained, particularly when females have preferences for their population specific songs, and we document many distinct patterns of song distribution within the contact zone, including clines, banding, and mosaics

Pharmacological and genetic characterisation of the canine P2X4 receptor

Background and Purpose: P2X4 receptors are emerging therapeutic targets for treating chronic pain and cardiovascular disease. Dogs are well-recognised natural models of human disease, but information regarding P2X4 receptors in dogs is lacking. To aid the development and validation of P2X4 receptor ligands, we have characterised and compared canine and human P2X4 receptors. Experimental Approach: Genomic DNA was extracted from whole blood samples from 101 randomly selected dogs and sequenced across the P2RX4 gene to identify potential missense variants. Recombinant canine and human P2X4 receptors tagged with Emerald GFP were expressed in 1321N1 and HEK293 cells and analysed by immunoblotting and confocal microscopy. In these cells, receptor pharmacology was characterised using nucleotide-induced Fura-2 AM measurements of intracellular Ca 2+ and known P2X4 receptor antagonists. P2X4 receptor-mediated inward currents in HEK293 cells were assessed by automated patch clamp. Key Results: No P2RX4 missense variants were identified in any canine samples. Canine and human P2X4 receptors were localised primarily to lysosomal compartments. ATP was the primary agonist of canine P2X4 receptors with near identical efficacy and potency at human receptors. 2′(3′)-O-(4-benzoylbenzoyl)-ATP, but not ADP, was a partial agonist with reduced potency for canine P2X4 receptors compared to the human orthologues. Five antagonists inhibited canine P2X4 receptors, with 1-(2,6-dibromo-4-isopropyl-phenyl)-3-(3-pyridyl)urea displaying reduced sensitivity and potency at canine P2X4 receptors. Conclusion and Implications: P2X4 receptors are highly conserved across dog pedigrees and display expression patterns and pharmacological profiles similar to human receptors, supporting validation and use of therapeutic agents for P2X4 receptor-related disease onset and management in dogs and humans

Realising the right to data portability for the domestic Internet of Things

There is an increasing role for the IT design community to play in regulation of emerging IT. Article 25 of the EU General Data Protection Regulation (GDPR) 2016 puts this on a strict legal basis by establishing the need for information privacy by design and default (PbD) for personal data-driven technologies. Against this backdrop, we examine legal, commercial and technical perspectives around the newly created legal right to data portability (RTDP) in GDPR. We are motivated by a pressing need to address regulatory challenges stemming from the Internet of Things (IoT). We need to find channels to support the protection of these new legal rights for users in practice. In Part I we introduce the internet of things and information PbD in more detail. We briefly consider regulatory challenges posed by the IoT and the nature and practical challenges surrounding the regulatory response of information privacy by design. In Part II, we look in depth at the legal nature of the RTDP, determining what it requires from IT designers in practice but also limitations on the right and how it relates to IoT. In Part III we focus on technical approaches that can support the realisation of the right. We consider the state of the art in data management architectures, tools and platforms that can provide portability, increased transparency and user control over the data flows. In Part IV, we bring our perspectives together to reflect on the technical, legal and business barriers and opportunities that will shape the implementation of the RTDP in practice, and how the relationships may shape emerging IoT innovation and business models. We finish with brief conclusions about the future for the RTDP and PbD in the IoT