Showing papers by "University of Exeter published in 2001"

Use of TLS parameters to model anisotropic displacements in macromolecular refinement

Abstract: An essential step in macromolecular refinement is the selection of model parameters which give as good a description of the experimental data as possible while retaining a realistic data-to-parameter ratio. This is particularly true of the choice of atomic displacement parameters, where the move from individual isotropic to individual anisotropic refinement involves a sixfold increase in the number of required displacement parameters. The number of refinement parameters can be reduced by using collective variables rather than independent atomic variables and one of the simplest examples of this is the TLS parameterization for describing the translation, libration and screw-rotation displacements of a pseudo-rigid body. This article describes the implementation of the TLS parameterization in the macromolecular refinement program REFMAC. Derivatives of the residual with respect to the TLS parameters are expanded in terms of the derivatives with respect to individual anisotropic U values, which in turn are calculated using a fast Fourier transform technique. TLS refinement is therefore fast and can be used routinely. Examples of TLS refinement are given for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a transcription activator GerE, for both of which there is data to only 2.0 A, so that individual anisotropic refinement is not feasible. GAPDH has been refined with between one and four TLS groups in the asymmetric unit and GerE with six TLS groups. In both cases, inclusion of TLS parameters gives improved refinement statistics and in particular an improvement in R and free R values of several percent. Furthermore, GAPDH and GerE have two and six molecules in the asymmetric unit, respectively, and in each case the displacement parameters differ significantly between molecules. These differences are well accounted for by the TLS parameterization, leaving residual local displacements which are very similar between molecules and to which NCS restraints can be applied.

Electrochromic Systems and the Prospects for Devices

Abstract: Many inorganic and organic materials exhibit redox states with distinct electronic (UV-vis) absorption bands. When the switching of redox states generates new or different visible region bands, the material is electrochromic. Electrochromic materials are currently attracting much interest in academia and industry for both their fascinating spectroelectrochemical properties and their commercial applications. In this review some of the most important examples from the major classes of electrochromic materials are highlighted. Examples of their use in both prototype and commercial electrochromic devices are illustrated including car mirrors, windows and sun-roofs of cars, windows of buildings, displays (see Figure), printing, and frozen-food monitoring.

Overexpression of petunia chalcone isomerase in tomato results in fruit containing increased levels of flavonols.

Abstract: Tomatoes are an excellent source of the carotenoid lycopene, a compound that is thought to be protective against prostate cancer. They also contain small amounts of flavonoids in their peel (∼5–10 mg/kg fresh weight), mainly naringenin chalcone and the flavonol rutin, a quercetin glycoside. Flavonols are very potent antioxidants, and an increasing body of epidemiological data suggests that high flavonoid intake is correlated with a decreased risk for cardiovascular disease. We have upregulated flavonol biosynthesis in the tomato in order to generate fruit with increased antioxidant capacity and a wider range of potential health benefit properties. This involved transformation of tomato with the Petunia chi-a gene encoding chalcone isomerase. Resulting transgenic tomato lines produced an increase of up to 78 fold in fruit peel flavonols, mainly due to an accumulation of rutin. No gross phenotypical differences were observed between high-flavonol transgenic and control lines. The phenotype segregated with the transgene and demonstrated a stable inheritance pattern over four subsequent generations tested thus far. Whole-fruit flavonol levels in the best of these lines are similar to those found in onions, a crop with naturally high levels of flavonol compounds. Processing of high-flavonol tomatoes demonstrated that 65% of flavonols present in the fresh fruit were retained in the processed paste, supporting their potential as raw materials for tomato-based functional food products.

Structural colour. Now you see it--now you don't.

Abstract: The dazzling iridescence seen in some hummingbirds1 and tropical butterflies2 arises from natural optical phenomena, the brightest of which originate in nanoscale structures that produce ultra-high reflectivity and narrow-band spectral purity3. Here we investigate the coloration of male Ancyluris meliboeus Fabricius butterflies4, which have patches of unusual microstructure on their ventral wing scales. We find that this highly tilted, multilayered arrangement produces a bright iridescence of broad wavelength range and generates a strong flicker contrast from minimal wing movement.

Surface attachment and pre-penetration stage development by plant pathogenic fungi.

Abstract: Fungal pathogens cause many of the most serious crop diseases. One of the principal reasons for the success of this group is their ability to locate and perceive appropriate host surfaces and then to elaborate specialized infection structures. Here we review the processes implicated in surface attachment, germ tube elongation, and development of appressoria. The involvement of surface-acting proteins such as fungal hydrophobins and integrins in these processes is evaluated, along with a description of studies that have revealed the existence of conserved signaling pathways that regulate appressorium formation. Finally, we anticipate the prospect of genome-level analysis of fungal pathogens and the key research questions that will need to be addressed.

Rebels with a Cause: Group Identification as a Response to Perceived Discrimination from the Mainstream

Abstract: Two studies involving people with body piercings tested the hypothesis that perceived discrimination increases group identification. In Study 1, group identification mediated the positive relationship between perceived discrimination and attempts to differentiate the ingroup from the mainstream. In Study 2, perceived discrimination against people with body piercings was manipulated and was found to increase group identification. Support was found for the prediction that group identification mediates the relation-ship between perceptions of discrimination and collective self-esteem. Results demonstrate the importance of group identification for both the meaning of group membership and its consequences for well-being among members of disadvantaged groups.

Adverse events following acupuncture: prospective survey of 32 000 consultations with doctors and physiotherapists.

Abstract: Acupuncture is increasingly popular, but it is not free from risk for the patient.1 Safety is best established with prospective surveys. Our aim was to ascertain the incidence of adverse events related to acupuncture treatment, as currently practised in Britain by doctors and physiotherapists. Volunteer acupuncture practitioners were recruited through journals circulated to members of the British Medical Acupuncture Society and the Acupuncture Association of Chartered Physiotherapists (approximately 2750 members).2 A prospective survey was undertaken using forms for intensive event monitoring that had been piloted previously.3 Minor adverse events were defined as “any ill-effect, no matter how small, that is unintended and non-therapeutic, even if not unexpected.” These events were reported every month, along with the total number of consultations. Minor or serious events that were considered to be “significant”—“unusual, novel, dangerous, significantly inconvenient, or requiring further information”—were reported on separate forms when they occurred. Anonymous reporting was accepted. A sample size of …

A Score Test for Testing a Zero‐Inflated Poisson Regression Model Against Zero‐Inflated Negative Binomial Alternatives

Abstract: Count data often show a higher incidence of zero counts than would be expected if the data were Poisson distributed. Zero-inflated Poisson regression models are a useful class of models for such data, but parameter estimates may be seriously biased if the nonzero counts are overdispersed in relation to the Poisson distribution. We therefore provide a score test for testing zero-inflated Poisson regression models against zero-inflated negative binomial alternatives.

Growth and detachment of cell clusters from mature mixed-species biofilms.

Abstract: Detachment from biofilms is an important consideration in the dissemination of infection and the contamination of industrial systems but is the least-studied biofilm process. By using digital time-lapse microscopy and biofilm flow cells, we visualized localized growth and detachment of discrete cell clusters in mature mixed-species biofilms growing under steady conditions in turbulent flow in situ. The detaching biomass ranged from single cells to an aggregate with a diameter of approximately 500 μm. Direct evidence of local cell cluster detachment from the biofilms was supported by microscopic examination of filtered effluent. Single cells and small clusters detached more frequently, but larger aggregates contained a disproportionately high fraction of total detached biomass. These results have significance in the establishment of an infectious dose and public health risk assessment.

Advantageous Selection in Insurance Markets

Abstract: This article reverses the standard conclusion that asymmetric information plus competition results in insufficient insurance provision. Risk-tolerant individuals take few precautions and are disinclined to insure, but they are drawn into a pooling equilibrium by the low premiums created by the presence of safer, more risk-averse types. Taxing insurance drives out the reckless clients, allowing a strict Pareto gain. This result depends on administrative costs in processing claims and issuing policies, as does the novel finding of a pure-strategy, partial-pooling, subgame-perfect Nash equilibrium in the insurance market. Copyright 2001 by the RAND Corporation.

Patterns of Ring Currents in Conjugated Molecules: A Few-Electron Model Based on Orbital Contributions

Abstract: In the CTOCD-DZ (continuous transformation of origin of current density-diamagnetic zero) formulation of coupled Hartree−Fock theory for magnetic response of closed-shell systems, induced current density at each point is calculated with the gauge origin at that point. In addition to its economy and accuracy for total current maps, CTOCD-DZ is shown to yield a unique and physically motivated definition of, and symmetry criteria for, orbital contributions to current density. This leads to a few-electron interpretation of ring currents. Only the four HOMO electrons of an aromatic (4n+2)-electron monocycle contribute significantly to the ring current, and in general only a small subset of the high-lying π electrons dominate the more complex patterns of current in polycyclic π systems. Benzene, naphthalene, hexacene, pyracylene, coronene, and corannulene are treated as examples.

Herb-drug interactions: review and assessment of report reliability.

Abstract: Aims The aim of this systematic review was to assess the published clinical evidence on interactions between herbal and conventional drugs.

Reproductive effects of long-term exposure to Bisphenol A in the fathead minnow (Pimephales promelas).

Abstract: Bisphenol A (BPA), a high-volume chemical used to make polycarbonate plastic, epoxy resins, and other chemicals has been reported to be weakly estrogenic. To investigate the effects of long-term exposure to Bisphenol A, a multigeneration study was conducted in which fathead minnows (Pimephales promelas) were exposed to water concentrations of BPA in the range from 1 to 1280 micrograms/L. In this paper, we report the growth and reproductive effects of BPA on sexually mature adults in the F0 generation (after 43, 71, and 164 d of exposure) and the effects on hatchability in the F1 generation. Mean measured concentrations of BPA in the water for all doses, over a 164-d exposure period, were between 70% and 96% of nominal. An inhibitory effect of BPA on somatic growth (length and weight) occurred in adult male fish exposed to 640 and 1280 micrograms/L (after 71 and 164 d). BPA induced vitellogenin synthesis (VTG; a biomarker for estrogen exposure) in males at concentrations of 640 and 1280 micrograms/L after 43 d and 160 micrograms/L after 71 d. In females, plasma VTG concentrations were elevated above controls only after 164-d exposure to 640 micrograms/L. Inhibition of gonadal growth (as measured by the gonadosomatic index) occurred in both males and females at concentrations of 640 and 1280 micrograms/L after 164 d. In males, a concentration of 16 micrograms/L altered the proportion of sex cell types in the testis, suggesting inhibition of spermatogenesis. Concentrations of BPA that induced VTG synthesis and affected gonadal development were lower than those that resulted in discernible effects on reproductive output. Egg production was inhibited at a BPA concentration of 1280 micrograms/L, and hatchability in the F1 generation was reduced at a BPA concentration of 640 micrograms/L (there were not enough eggs spawned in the 1280 micrograms/L group for hatchability studies to be conducted). The results demonstrate that BPA acts as a weak estrogen to fish when administered via the water, with effects on breeding at and above 640 micrograms/L.

A Genomewide Scan for Loci Predisposing to Type 2 Diabetes in a U.K. Population (The Diabetes UK Warren 2 Repository): Analysis of 573 Pedigrees Provides Independent Replication of a Susceptibility Locus on Chromosome 1q

Abstract: Improved molecular understanding of the pathogenesis of type 2 diabetes is essential if current therapeutic and preventative options are to be extended. To identify diabetes-susceptibility genes, we have completed a primary (418-marker, 9-cM) autosomal-genome scan of 743 sib pairs (573 pedigrees) with type 2 diabetes who are from the Diabetes UK Warren 2 repository. Nonparametric linkage analysis of the entire data set identified seven regions showing evidence for linkage, with allele-sharing LOD scores ⩾1.18 ( P ≤.01). The strongest evidence was seen on chromosomes 8p21-22 (near D8S258 [LOD score 2.55]) and 10q23.3 (near D10S1765 [LOD score 1.99]), both coinciding with regions identified in previous scans in European subjects. This was also true of two lesser regions identified, on chromosomes 5q13 (D5S647 [LOD score 1.22] and 5q32 (D5S436 [LOD score 1.22]). Loci on 7p15.3 (LOD score 1.31) and 8q24.2 (LOD score 1.41) are novel. The final region showing evidence for linkage, on chromosome 1q24-25 (near D1S218 [LOD score 1.50]), colocalizes with evidence for linkage to diabetes found in Utah, French, and Pima families and in the GK rat. After dense-map genotyping (mean marker spacing 4.4 cM), evidence for linkage to this region increased to a LOD score of 1.98. Conditional analyses revealed nominally significant interactions between this locus and the regions on chromosomes 10q23.3 ( P =.01) and 5q32 ( P =.02). These data, derived from one of the largest genome scans undertaken in this condition, confirm that individual susceptibility-gene effects for type 2 diabetes are likely to be modest in size. Taken with genome scans in other populations, they provide both replication of previous evidence indicating the presence of a diabetes-susceptibility locus on chromosome 1q24-25 and support for the existence of additional loci on chromosomes 5, 8, and 10. These data should accelerate positional cloning efforts in these regions of interest.

Negative frequency-dependent selection maintains a dramatic flower color polymorphism in the rewardless orchid Dactylorhiza sambucina (L.) Soo.

Abstract: The orchid Dactylorhiza sambucina shows a stable and dramatic flower-color polymorphism, with both yellow- and purple-flowered individuals present in natural populations throughout the range of the species in Europe. The evolutionary significance of flower-color polymorphisms found in many rewardless orchid species has been discussed at length, but the mechanisms responsible for their maintenance remain unclear. Laboratory experiments have suggested that behavioral responses by pollinators to lack of reward availability might result in a reproductive advantage for rare-color morphs. Consequently, we performed an experiment varying the relative frequency of the two color morphs of D. sambucina to test whether rare morph advantage acted in the natural habitat of the species. We show here clear evidence from this manipulative experiment that rare-color morphs have reproductive advantage through male and female components. This is the first demonstration, to our knowledge, that negative frequency-dependent selection through pollinator preference for rare morphs can cause the maintenance of a flower-color polymorphism.

Assessing the biological potency of binary mixtures of environmental estrogens using vitellogenin induction in juvenile rainbow trout (Oncorhynchus mykiss).

Abstract: Experiments were conducted to assess the in vivo potency of binary mixtures of estrogenic chemicals using plasma vitellogenin (VTG) concentrations in juvenile rainbow trout (Oncorhynchus mykiss) as the endpoint. The estrogenic potencies of estradiol-17beta (E2), 4-tertnonylphenol (NP), and methoxychlor (MXC) were determined following 14 day exposures to the individual chemicals and binary mixtures of these chemicals. E2, NP, and MXC all induced concentration dependent increases in plasma VTG, with lowest observed effect concentrations of 4.7 and 7.9 ng L(-1) for E2, 6.1 and 6.4 microg L(-1) for NP, and 4.4 and 6.5 microg L(-1) for MXC. Concentration-response curves for fixed ratio binary mixtures of E2 and NP (1:1000), E2 and MXC (1:1000), and NP and MXC (1:1) were compared to those obtained for the individual chemicals, using the model of concentration addition. Mixtures of E2 and NP were additive at the concentrations tested, but mixtures of E2 and MXC were less than additive. This suggests that while NP probably acts via the same mechanism as E2 in inducing VTG synthesis, MXC may be acting via a different mechanism(s), possibly as a result of its conversion to HPTE which is an estrogen receptor alpha agonist and an estrogen receptor beta antagonist. It was not possible to determine whether mixtures of MXC and NP were additive using VTG induction, because the toxicity of MXC restricted the effect range forwhich the expected response curve forthe binary mixture could be calculated. The data presented illustrate that the model of concentration addition can accurately predict effects on VTG induction, where we know that both chemicals act via the same mechanism in mediating a vitellogenic response.

Mutations in the Hepatocyte Nuclear Factor-1β Gene Are Associated with Familial Hypoplastic Glomerulocystic Kidney Disease

Abstract: Familial glomerulocystic kidney disease (GCKD) is a dominantly inherited condition characterized by glomerular cysts and variable renal size and function; the molecular genetic etiology is unknown. Mutations in the gene encoding hepatocyte nuclear factor (HNF)–1β have been associated with early-onset diabetes and nondiabetic renal disease—particularly renal cystic disease. We investigated a possible role for the HNF-1β gene in four unrelated GCKD families and identified mutations in two families: a nonsense mutation in exon 1 (E101X) and a frameshift mutation in exon 2 (P159fsdelT). The family members with HNF-1β gene mutations had hypoplastic GCKD and early-onset diabetes or impaired glucose tolerance. We conclude that there is genetic heterogeneity in familial GCKD and that the hypoplastic subtype is a part of the clinical spectrum of the renal cysts and diabetes syndrome that is associated with HNF-1β mutations.

beta-cell genes and diabetes: molecular and clinical characterization of mutations in transcription factors

Abstract: beta-Cell transcription factor genes are important in the pathophysiology of the beta-cell, with mutations in hepatocyte nuclear factor (HNF)-1alpha, HNF-4alpha, insulin promoter factor (IPF)-1, HNF-1beta, and NeuroD1/BETA2, all resulting in early-onset type 2 diabetes. We assessed the relative contribution of these genes to early-onset type 2 diabetes using linkage and sequencing analysis in a cohort of 101 families (95% U.K. Caucasian). The relative distribution of the 90 families fitting maturity-onset diabetes of the young (MODY) criteria was 63% HNF-1alpha, 2% HNF-4alpha, 0% IPF-1, 1% HNF-1beta, 0% NeuroD1/ BETA2, and 20% glucokinase. We report the molecular genetic and clinical characteristics of these patients including 29 new families and 8 novel HNF-1alpha gene mutations. Mutations in the transactivation domain are more likely to be protein truncating rather than result in amino acid substitutions, suggesting that a relatively severe disruption of this domain is necessary to result in diabetes. Mutations in the different transcription factors result in clinical heterogeneity. IPF-1 mutations are associated with a higher age at diagnosis (42.7 years) than HNF-1alpha (20.4 years), HNF-1beta (24.2 years), or HNF-4alpha (26.3 years) gene mutations. Subjects with HNF-1beta mutations, in contrast to the other transcription factors, frequently present with renal disease. A comparison of age at diagnosis between subjects with different types and locations of HNF-1alpha mutations did not reveal genotype-phenotype correlations. In conclusion, mutations in transcription factors expressed in the beta-cell are the major cause of MODY, and the phenotype clearly varies with the gene that is mutated. There is little evidence to indicate that different mutations within the same gene have different phenotypes.

The Past, Present and Future of School Improvement: Towards the Third Age

Abstract: The article outlines the three phases that school improvement has been through since the mid-1980s, paying particular attention to the characteristics of the recent 'third age' improvement paradigm. It is argued that these new models of improvement stand a chance of overcoming the difficulties that past improvement has had in affecting outcomes, and a number of areas of potential development for the paradigm are outlined for it to fulfil its promise, particularly in the areas of context specificity, focusing on learning in classrooms and concentrating on understanding 'the capacity for improvement'. The contributions of 'Third Age' school improvement to resolving a number of conundrums that have affected the field are also explored.

Counter‐Rotating Ring Currents in Coronene and Corannulene

Abstract: Explicit ab initio current-density maps contradict the annulene-within-an-annulene model of [n]circulenes: in both coronene and corannulene the expected diamagnetic current on the perimeter is opposed by the central, paramagnetic ring current

The molecular evolution of Trypanosomatidae.

Abstract: In the absence of a fossil record, theories relating to the evolution of protozoa have, for most of the twentieth century, been based on morphological and life cycle data despite their known limitations. However, recent advances in molecular methodology, notably the wide availability of accurate, automated DNA sequencing, have made it possible to deduce the evolutionary relationships of extant species from their genes. This paper focuses on new findings concerning the evolution of the Trypanosomatidae, based on the ever-expanding body of molecular data now available. Classically, the evolution of digenetic parasitism in kinetoplastids has centred around two opposing theories--invertebrate first or vertebrate first--depending on which was the original host of the monogenetic parasite. However, data supporting a close phylogenetic relationship between genera of monogenetic insect parasites and digenetic vertebrate parasites challenge the simplicity of these hypotheses and suggest that the transition may not have been a major evolutionary barrier. The implications of these observations for the evolution of parasitism within the group are discussed. Phylogenetic analysis of a diverse selection of trypanosomatid species suggests that the genus Trypanosoma is monophyletic and that the human parasites, T. brucei, T. cruzi and Leishmania spp., have fundamentally different patterns of evolution. T. brucei clusters with mammalian trypanosomes of African origin, suggesting an evolutionary history confined to Africa. T. cruzi shows association with trypanosomes from bats, T. rangeli, and trypanosomes from a range of South American mammals and an Australian kangaroo. The origins of most parasites within this clade lie in South America and Australia, suggesting an ancient southern super-continent origin for T. cruzi, possibly in marsupials. The divergence between the Leishmania and Trypanosoma lineages is also ancient. The topology of Leishmania phylogenies suggests an independent transition to digenetic parasitism, a neotropical origin and an early tertiary radiation of the parasite.