Evolution and developmental expression of nuclear receptor genes in the ascidian Herdmania

Nuclear receptors are a superfamily of metazoan transcription factors that have been shown to be involved in a wide range of developmental and physiological processes. A PCR-based survey of genomic DNA and developmental cDNAs from the ascidian Herdmania identifies eight members of this multigene family. Sequence comparisons and phylogenetic analyses reveal that these ascidian nuclear receptors are representative of five of the six previously defined nuclear receptor subfamilies and are apparent homologues of retinoic acid [NR1B], retinoid X [NR2B], peroxisome proliferator-activated [NR1C], estrogen related [NR3B], neuron-derived orphan (NOR) [NR4A3], nuclear orphan [NR4A], TR2 orphan [NR2C1] and COUP orphan [NR2F3] receptors. Phylogenetic analyses that include the ascidian genes produce topologically distinct trees that suggest a redefinition of some nuclear receptor subfamilies. These trees also suggest that extensive gene duplication occurred after the vertebrates split from invertebrate chordates. These ascidian nuclear receptor genes are expressed differentially during embryogenesis and metamorphosis.

Linkage of Paget disease of bone to a novel region on human chromosome 18q23

Paget disease of bone (PDB) is characterized by increased osteoclast activity and localized abnormal bone remodeling. PDB has a significant genetic component, with evidence of linkage to chromosomes 6p21.3 (PDB1) and 18q21-22 (PDB2) in some pedigrees. There is evidence of genetic heterogeneity, with other pedigrees showing negative linkage to these regions. TNFRSF11A, a gene that is essential for osteoclast formation and that encodes receptor activator of nuclear factor-kappa B (RANK), has been mapped to the PDB2 region. TNFRSF11A mutations that segregate in pedigrees with either familial expansile osteolysis or familial PDB have been identified; however, linkage studies and mutation screening have excluded the involvement of RANK in the majority of patients with PDB. We have excluded linkage, both to PDB1 and to PDB2, in a large multigenerational pedigree with multiple family members affected by PDB. We have conducted a genomewide scan of this pedigree, followed by fine mapping and multipoint analysis in regions of interest. The peak two-point LOD scores from the genomewide scan were 2.75, at D7S507, and 1.76, at D18S70. Multipoint and haplotype analysis of markers flanking D7S507 did not support linkage to this region. Haplotype analysis of markers flanking D18S70 demonstrated a haplotype segregating with PDB in a large subpedigree. This subpedigree had a significantly lower age at diagnosis than the rest of the pedigree (51.2 +/- 8.5 vs. 64.2 +/- 9.7 years; P = .0012). Linkage analysis of this subpedigree demonstrated a peak two-point LOD score of 4.23, at marker D18S1390 (theta = 0), and a peak multipoint LOD score of 4.71, at marker D18S70. Our data are consistent with genetic heterogeneity within the pedigree and indicate that 18q23 harbors a novel susceptibility gene for PDB.

Read-only-memory-based quantum computation: Experimental explorations using nuclear magnetic resonance and future prospects

Read-only-memory-based (ROM-based) quantum computation (QC) is an alternative to oracle-based QC. It has the advantages of being less magical, and being more suited to implementing space-efficient computation (i.e., computation using the minimum number of writable qubits). Here we consider a number of small (one- and two-qubit) quantum algorithms illustrating different aspects of ROM-based QC. They are: (a) a one-qubit algorithm to solve the Deutsch problem; (b) a one-qubit binary multiplication algorithm; (c) a two-qubit controlled binary multiplication algorithm; and (d) a two-qubit ROM-based version of the Deutsch-Jozsa algorithm. For each algorithm we present experimental verification using nuclear magnetic resonance ensemble QC. The average fidelities for the implementation were in the ranges 0.9-0.97 for the one-qubit algorithms, and 0.84-0.94 for the two-qubit algorithms. We conclude with a discussion of future prospects for ROM-based quantum computation. We propose a four-qubit algorithm, using Grover's iterate, for solving a miniature real-world problem relating to the lengths of paths in a network.

Comparative analysis of genetic diversity in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae) detected by AFLPs and SSRs

Avicennia marina is an important mangrove species with a wide geographical and climatic distribution which suggests that large amounts of genetic diversity are available for conservation and breeding programs. In this study we compare the informativeness of AFLPs and SSRs for assessing genetic diversity within and among individuals, populations and subspecies of A. marina in Australia. Our comparison utilized three SSR loci and three AFLP primer sets that were known to be polymorphic, and could be run in a single analysis on a capillary electrophoresis system, using different-colored fluorescent dyes. A total of 120 individuals representing six populations and three subspecies were samplcd. At the locus level, SSRs were considerably more variable than AFLPs, with a total of 52 alleles and an average heterozygosity of 0.78. Average heterozygosity for AFLPs was 0.193, but all of the 918 bands scored were polymorphic. Thus, AFLPs were considerably more efficient at revealing polymorphic loci than SSRs despite lower average heterozygosities. SSRs detected more genetic differentiation between populations (19 vs 9%) and subspecies (35 vs 11%) than AFLPs. Principal co-ordinate analysis revealed congruent patterns of genetic relationships at the individual, population and subspecific levels for both data sets. Mantel testing confirmed congruence between AFLP and SSR genetic distances among, but not within, population comparisons, indicating that the markers were segregating inde- pendently but that evolutionary groups (populations and subspecies) were similar. Three genetic criteria of importance for defining priorities for ex situ collections or in situ conservation programs (number of alleles, number of locally common alleles and number of private alleles) were correlated between the AFLP and SSR data sets. The congruence between AFLP and SSR data sets suggest that either method, or a combination, is applicable to expanded genetic studies of mangroves. The codominant nature of SSRs makes them ideal for further population-based investigations, such as mating-system analyses, for which the dominant AFLP markers are less well suited. AFLPs may be particularly useful for monitoring propagation programs and identifying duplicates within collections, since a single PCR assay can reveal many loci at once.

Reversible luminescence thermochromism in dipotassiumsodium tris[dicyanoargentate(I)] and the role of structural phase transitions

As a function of temperature, the layered compound K2Na[Ag(CN)213 displays dramatic variations in luminescence thermochromism with major trend changes occurring around 80 K. In order to understand these interesting optical properties, high-resolution neutron diffraction investigations were performed on a polycrystalline sample of this material in the temperature range from 1.5 to 300 K, and previous synchrotron X-ray data of Larochelle et al. (Solid State Commun. 114, 155 (2000)) were reinterpreted. The corresponding significant structural changes were found to be continuous with an anomalous increase of the monoclinic c-lattice parameter with decreasing temperature, associated with slight reorientations of two inequivalent, approximately linear N-C-Ag-C-N units. In the whole temperature range, the crystal structure is monoclinic with the space group C2/m. Based on the structural results, the major luminescence thermochromism changes around 80 K are attributed to the dominance of a back energy transfer process from low- to high-energy excitons at high temperatures. (E) 2002 Elsevier Science (USA).

Testing insect movement theory: empirical analysis of pest data routinely collected from agricultural crops

Observations of an insect's movement lead to theory on the insect's flight behaviour and the role of movement in the species' population dynamics. This theory leads to predictions of the way the population changes in time under different conditions. If a hypothesis on movement predicts a specific change in the population, then the hypothesis can be tested against observations of population change. Routine pest monitoring of agricultural crops provides a convenient source of data for studying movement into a region and among fields within a region. Examples of the use of statistical and computational methods for testing hypotheses with such data are presented. The types of questions that can be addressed with these methods and the limitations of pest monitoring data when used for this purpose are discussed. (C) 2002 Elsevier Science B.V. All rights reserved.

Characterization of mouse profilaggrin: Evidence for nuclear engulfment and translocation of the profilaggrin B-domain during epidermal differentiation

Filaggrin is a keratin filament associated protein that is expressed in granular layer keratinocytes and derived by sequential proteolysis from a polyprotein precursor termed profilaggrin. Depending on the species, each profilaggrin molecule contains between 10 and 20 filaggrin subunits organized as tandem repeats with a calcium-binding domain at the N-terminal end. We now report the characterization of the complete mouse gene. The structural organization of the mouse gene is identical to the human profilaggrin gene and consists of three exons with a 4 kb intron within the 5' noncoding region and a 1.7 kb intron separating the sequences encoding the calcium-binding EF-hand motifs. A processed pseudogene was found embedded within the second intron. The third and largest exon encodes the second EF-hand, a basic domain (designated the B-domain) followed by 12 filaggrin repeats and a unique C-terminal tail domain. A polyclonal anti-body raised against the conceptually translated sequence of the B-domain specifically stained keratohyalin granules and colocalized with a filaggrin antibody in granular layer cells. In upper granular layer cells, B-domain containing keratohyalin granules were in close apposition to the nucleus and, in some cells, appeared to be completely engulfed by the nucleus. In transition layer cells, B-domain staining was evident in the nucleus whereas filaggrin staining remained cytoplasmic. Nuclear staining of the B-domain was also observed in primary mouse keratinocytes induced to differentiate. This study has also revealed significant sequence homology between the mouse and human promoter sequences and in the calcium-binding domain but the remainder of the protein-coding region shows substantial divergence.

Phase variation in meningococcal lipooligosaccharide biosynthesis genes

Neisseria meningitidis expresses a range of lipooligosaccharide (LOS) structures, comprising of at least 13 immunotypes (ITs). Meningococcal LOS is subject to phase variation of its terminal structures allowing switching between ITs, which is proposed to have functional significance in disease. The objectives of this study were to investigate the repertoire of structures that can be expressed in clinical isolates, and to examine the role of phase-variable expression of LOS genes during invasive disease. Southern blotting was used to detect the presence of LOS biosynthetic genes in two collections of meningococci, a global set of strains previously assigned to lineages of greater or lesser virulence, and a collection of local clinical isolates which included paired throat and blood isolates from individual patients. Where the phase-variable genes lgtA, lgtC or IgtG were identified, they were amplified by PCR and the homopolymeric tracts, responsible for their phase-variable expression, were sequenced. The results revealed great potential for variation between alternate LOS structures in the isolates studied, with most strains capable of expressing several alternative terminal structures. The structures predicted to be currently expressed by the genotype of the strains agreed well with conventional immunotyping. No correlation was observed between the structural repertoire and virulence of the isolate. Based on the potential for LOS phase variation in the clinical collection and observations with the paired patient isolates, our data suggest that phase variation of LOS structures is not required for translocation between distinct compartments in the host. (C) 2002 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Work domain analysis and sensors I: principles and simple example

In this paper we establish a foundation for understanding the instrumentation needs of complex dynamic systems if ecological interface design (EID)-based interfaces are to be robust in the face of instrumentation failures. EID-based interfaces often include configural displays which reveal the higher-order properties of complex systems. However, concerns have been expressed that such displays might be misleading when instrumentation is unreliable or unavailable. Rasmussen's abstraction hierarchy (AH) formalism can be extended to include representations of sensors near the functions or properties about which they provide information, resulting in what we call a sensor-annotated abstraction hierarchy. Sensor-annotated AHs help the analyst determine the impact of different instrumentation engineering policies on higher-order system information by showing how the data provided from individual sensors propagates within and across levels of abstraction in the AH. The use of sensor-annotated AHs with a configural display is illustrated with a simple water reservoir example. We argue that if EID is to be effectively employed in the design of interfaces for complex systems, then the information needs of the human operator need to be considered at the earliest stages of system development while instrumentation requirements are being formulated. In this way, Rasmussen's AH promotes a formative approach to instrumentation engineering. (C) 2002 Elsevier Science Ltd. All rights reserved.

Phase equilibrium data and liquidus for the system "MnO"-CaO-(Al2O3+SiO2) at Al2O3/SiO2 of 0.41

Phase-equilibrium data and the liquidus for the system. "MnO"-CaO-(Al2O3-SiO2) at a manganese-rich alloy saturation have been determined in the temperature range from 1423 to 1723 K. The results are presented in the form of a pseudoternary section "MnO"-CaO-(Al2O3 + SiO2) with an Al2O3/SiO2 weight ratio of 0.41. The following primary phases are present in the range of conditions investigated:, 3Al(2)O(3).2SiO(2); SiO2; MnO.Al2O3-2SiO(2); (Mn,Ca)O.SiO2; 2(Mn,Ca)O.SiO2; MnO.Al2O3; (Mn,Ca)O; alpha-2CaO.SiO2; alpha'-2CaO.SiO2; 2CaO.Al2O3.SiO2; CaO.SiO2, and CaO.Al2O3.2SiO(2). The presence of alumina in this system is shown to have a significant effect on the liquidus compared to the system "MnO"-CaO-SiO2, leading to, the stabilization of the anorthite and gehlenite phases.

Mineral chemistry, whole-rock compositions, and petrogenesis of leg 176 gabbros: Data and discussion

We report mineral chemistry, whole-rock major element compositions, and trace element analyses on Hole 735B samples drilled and selected during Leg 176. We discuss these data, together with Leg 176 shipboard data and Leg 118 sample data from the literature, in terms of primary igneous petrogenesis. Despite mineral compositional variation in a given sample, major constituent minerals in Hole 735B gabbroic rocks display good chemical equilibrium as shown by significant correlations among Mg# (= Mg/[Mg+Fe2+]) of olivine, clinopyroxene, and orthopyroxene and An (=Ca/[Ca+Na]) of plagioclase. This indicates that the mineral assemblages olivine + plagioclase in troctolite, plagioclase + clinopyroxene in gabbro, plagioclases + clinopyroxene + olivine in olivine gabbro, and plagioclase + clinopyroxene + olivine + orthopyroxene in gabbronorite, and so on, have all coprecipitated from their respective parental melts. Fe-Ti oxides (ilmenite and titanomagnetite), which are ubiquitous in most of these rocks, are not in chemical equilibrium with olivine, clinopyroxene, and plagioclase, but precipitated later at lower temperatures. Disseminated oxides in some samples may have precipitated from trapped Fe-Ti–rich melts. Oxides that concentrate along shear bands/zones may mark zones of melt coalescence/transport expelled from the cumulate sequence as a result of compaction or filter pressing. Bulk Hole 735B is of cumulate composition. The most primitive olivine, with Fo = 0.842, in Hole 735B suggests that the most primitive melt parental to Hole 735B lithologies must have Mg# ≤ 0.637, which is significantly less than Mg# = 0.714 of bulk Hole 735B.