Objectives To test the hypothesis that somatic phosphatidylinositol-4,5-bisphospate 3-kinase, catalytic subunit alpha ( PIK3CA ) mutations would be found in patients with more common disorders ...including isolated lymphatic malformation (LM) and Klippel-Trenaunay syndrome (KTS). Study design We used next generation sequencing, droplet digital polymerase chain reaction, and single molecule molecular inversion probes to search for somatic PIK3CA mutations in affected tissue from patients seen at Boston Children's Hospital who had an isolated LM (n = 17), KTS (n = 21), fibro-adipose vascular anomaly (n = 8), or congenital lipomatous overgrowth with vascular, epidermal, and skeletal anomalies syndrome (n = 33), the disorder for which we first identified somatic PIK3CA mutations. We also screened 5 of the more common PIK3CA mutations in a second cohort of patients with LM (n = 31) from Seattle Children's Hospital. Results Most individuals from Boston Children's Hospital who had isolated LM (16/17) or LM as part of a syndrome, such as KTS (19/21), fibro-adipose vascular anomaly (5/8), and congenital lipomatous overgrowth with vascular, epidermal, and skeletal anomalies syndrome (31/33) were somatic mosaic for PIK3CA mutations, with 5 specific PIK3CA mutations accounting for ∼80% of cases. Seventy-four percent of patients with LM from Seattle Children's Hospital also were somatic mosaic for 1 of 5 specific PIK3CA mutations. Many affected tissue specimens from both cohorts contained fewer than 10% mutant cells. Conclusions Somatic PIK3CA mutations are the most common cause of isolated LMs and disorders in which LM is a component feature. Five PIK3CA mutations account for most cases. The search for causal mutations requires sampling of affected tissues and techniques that are capable of detecting low-level somatic mosaicism because the abundance of mutant cells in a malformed tissue can be low.
In 1989 we reported that the white-rot basidiomycete fungus
Trametes versicolor could delignify and substantially brighten unbleached kraft pulps. Since that time, considerable effort has been ...dedicated to understanding the biological mechanisms of this efficient delignification system in the hope that part or all of the system can be applied industrially. Early work indicated that all components necessary for extensive kraft pulp bleaching and delignification are secreted by the fungus, but that one or more of these components must be constantly replaced or renewed.
T. versicolor can bleach O
2-delignified and extended-cooking pulps as well as conventional hardwood and softwood kraft pulps. The fungus demethylates and solubilizes the residual lignin in the pulps, seemingly without depolymerization. Enzyme families secreted by
T. versicolor which may be involved in delignification include lignin peroxidases (LiP), manganese peroxidases (MnP), laccases, and cellobiose dehydrogenases (CDH). Each of these families has been investigated for its interactions with kraft pulp lignin. Two laccase isozymes (laccase I and II) have been purified. The reactivities of the two isozymes on all substrates tested, including kraft lignin, were similar, with no evidence of lignin depolymerization by either enzyme. However the presence of the mediator 2,2′-azinobis (3-ethylbenzthiazoline-6-sulphonate) (ABTS) prevented and reversed the polymerization of kraft lignin by either laccase. Both laccases were able to delignify kraft pulp, but only in the presence of the mediator. Secreted MnP activity and the presence of substantial available Mn(II) ions appear necessary for delignification and pulp brightening by
T. versicolor. Mutants unable to secrete MnP cannot delignify. Purified MnP substantially delignifies pulp when supplied with Mn (II), H
2O
2 and Mn (II)-complexing agents. Furthermore, the resulting pulp is made easier to bleach to high brightness with alkaline hydrogen peroxide. LiP, while produced under secondary metabolic conditions, appears to play no role in the delignification of kraft pulp by
T. versicolor. White-rot fungi typically carry out net oxidation of the lignin and hydrolytic depolymerization of the carbohydrate in wood. Is there likely to be a significant role in delignification for enzymes which oxidize wood carbohydrates and reduce lignin? The family of carbohydrate-oxidizing, quinone-, metal ion- and organic free radical-reducing enzymes known as the cellobiose oxidases and cellobiose dehydrogenases (CBO, CDH, formerly CBQase) are reported to occur in a number of wood-degrading fungi. A CDH from
T. versicolor has been purified, characterized and shown to decolorize and prevent laccase-mediated lignin polymerization. It can help supply MnP with chelator, hydrogen peroxide, and manganese. The rate of diffusion of enzymes or mediators in the kraft fiber wall may be a limiting factor for delignification. In order to visualize these diffusion bottlenecks we have built a model of the secondary wall and compared the pore sizes in the wall with the sizes of potential diffusible delignification agents.
CLCN5 chloride-channel mutations in six new North American families with X-linked nephrolithiasis.
X-linked nephrolithiasis, or Dent's disease, encompasses several clinical syndromes of low molecular ...weight (LMW) proteinuria, hypercalciuria, nephrocalcinosis, nephrolithiasis, and renal failure, and is associated with mutations in the CLCN5 gene encoding a kidney-specific voltage-gated chloride channel. Some patients from Europe have rickets, and all symptomatic patients confirmed by mutation analysis have been male.
We analyzed the CLCN5 DNA sequence in six new families with this disease.
In three probands, a single-base substitution yielded a nonsense triplet at codons 28, 34, and 343, respectively, and in two families, one of which was Hispanic, we found single-base deletions at codons 40 and 44, leading to premature termination of translation. In the sixth family, a single-base change from C to T predicted substitution of leucine for serine at codon 244, previously reported in two European families with prominent rickets, though this patient of Ashkenazi origin did not have rickets. Each of these mutations was confirmed by restriction endonuclease analysis, or repeat sequencing and CFLP. The R34X mutation occurred in a Canadian infant with severe rickets. The family with the R28X nonsense mutation included one woman with recurrent kidney stones and another woman with glomerular sclerosis. In another family, a woman heterozygous for the W343X mutation also had nephrolithiasis.
These studies expand the range of mutations identified in this disease, and broaden the phenotypic range to include clinically affected women and the first North American case with severe rickets.
We discuss the calibration of a laser triangulation range system mounted on a robot vehicle. Range sensing in general is briefly reviewed, followed by a description of the Oxford/NEL range finder, a ...sensor mounted on the Oxford AGV for use in object recognition and acquisition tasks. Calibration of the range sensor is achieved by modelling it as a projectivity between two planes: the plane of the light stripe and the plane of the camera's detector array. The vehicle is driven to a known location where there exists an arrangement of orthogonal planes whose equations expressed in world coordinates have been premeasured accurately. Known vehicle position relative to world coordinates, known sensor position relative to vehicle coordinates, and a set of world plane to image point correspondences lead to an overdetermined set of linear equations which can be solved to give the required eight unknown parameters of the projectivity.
Greater than 95% of acute promyelocytic leukemia (APL) cases are associated with the expression of PML-RARalpha. This chimeric protein has been strongly implicated in APL pathogenesis because of its ...interactions with growth suppressors (PML), retinoid signaling molecules (RXRalpha), and nuclear hormone transcriptional co-repressors (N-CoR and SMRT). A small number of variant APL translocations have also been shown to involve rearrangements that fuse RARalpha to partner genes other than PML, namely PLZF, NPM, and NuMA. We describe the molecular characterization of a t(5;17)(q35;q21) variant translocation involving the NPM gene, identified in a pediatric case of APL. RT-PCR, cloning, and sequence studies identified NPM as the RARalpha partner on chromosome 5, and both NPM-RARalpha and RARalpha-NPM fusion mRNAs were expressed in this patient. We further explored the effects of the NPM-RARalpha chimeric protein on the subcellular localization of PML, RXRalpha, NPM, and PLZF using immunofluorescent confocal microscopy. While PML remained localized to its normal 10-20 nuclear bodies, NPM nucleolar localization was disrupted and PLZF expression was upregulated in a microspeckled pattern in patient leukemic bone marrow cells. We also observed nuclear co-localization of NPM, RXRalpha, and NPM-RARalpha in these cells. Our data support the hypothesis that while deregulation of both the retinoid signaling pathway and RARalpha partner proteins are molecular consequences of APL translocations, APL pathogenesis is not dependent on disruption of PML nuclear bodies.
There is a need to identify better biomarkers to monitor diseases and/or assess therapeutic responses. For those with cancer, one can identify DNA fragments that contain somatic mutations originating ...in the tumor DNA in plasma or serum. There have been several early studies suggesting that advances in sequencing technologies will allow identification of somatic genomic alterations that can be used to monitor tumor dynamics. Dawson et al. investigated circulating cell-free DNA carrying tumor specific alterations in patients with breast cancer. The authors compared CT imaging from 30 women with metastatic breast cancer receiving treatment, using two assays for circulating tumor DNA, CA 15-3, and CTCs. Taken the two methods together circulating tumor DNA was detected in 29 or 30 women (97%) and 115 of 141 plasma samples (82%). Circulating tumor DNA levels showed a greater dynamic range and greater correlation with changes in tumor burden than did CA 15-3 or CTC. The relatively small study showed that circulating tumor DNA has a superior sensitivity to other circulating biomarkers and a dynamic range that correlates with tumor burden.
We report detailed measurements of the temperature dependence of muon-spin relaxation in sulfur. These complement measurements reported earlier I.D. Reid and S.F.J. Cox, Physica B 289–290 (2000) 620 ...and allow a fuller comparison with the observations of muoniated radicals seen in selenium I.D. Reid, et al., Physica B 326 (2003) 89.
This paper describes the theory and real-time implementation using an active camera platform of a method of planar trajectory recovery, and of the use of those trajectories to facilitate prediction ...over delays in the visual feedback loop. Image-based position and velocity demands for tracking are generated by detecting and segmenting optical flow within a central region of the image, and a projective construct is used to map the camera platform's joint angles into a Euclidean coordinate system within a plane, typically the ground plane, in the scene. A set of extended Kalman filters with different dynamics is implemented to analyze the trajectories, and these compete to provide the best description of the motion within an interacting multiple model. Prediction from the optimum motion model is used within the visual feedback loop to overcome visual latency. It is demonstrated that prediction from the 3D planar description gives better tracking performance than prediction based on a filtered description of observer-based 2D motion trajectories.
RoxAnn acoustic surveys of the inner Moray Firth, undertaken in September/October 1995 and January 1996, were used to map seabed habitat on the basis of two sediment characteristics, “roughness” (E1) ...and “hardness” (E2). The traditional analytical method of fitting a “box pattern” to E1 vs. E2 scatter plots was compared with a more objective method using False Colour Composite Image (FCCI) and cluster analysis. Although both methods produced similar maps, the latter provided greater between survey consistency. Six to seven sediment types were indicated by RoxAnn, however ordination analysis of sediment samples indicated that some of the FCCI clusters could not be separated on the basis of their particle size distributions. This may have been due to a degree of depth sensitivity, but it is also possible that RoxAnn was responding to other physical or biotic seabed features other than just particle size. After combining RoxAnn FCCI clusters where ground-truthing grab samples had shown the particle size distributions to be similar, it was evident that RoxAnn could distinguish three main sediment habitats with certainty. On this basis, the RoxAnn derived maps compared well with maps obtained from British Geological Survey data. Finally we examined the distributions of four flatfish species to determine whether these were in any way related to the different sediment habitats identified by RoxAnn.
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