Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont.

Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain

Self-Calibration of Cameras with Euclidean Image Plane in Case of Two Views and Known Relative Rotation Angle

The internal calibration of a pinhole camera is given by five parameters that are combined into an upper-triangular $3\times 3$ calibration matrix. If the skew parameter is zero and the aspect ratio is equal to one, then the camera is said to have Euclidean image plane. In this paper, we propose a non-iterative self-calibration algorithm for a camera with Euclidean image plane in case the remaining three internal parameters --- the focal length and the principal point coordinates --- are fixed but unknown. The algorithm requires a set of $N \geq 7$ point correspondences in two views and also the measured relative rotation angle between the views. We show that the problem generically has six solutions (including complex ones). The algorithm has been implemented and tested both on synthetic data and on publicly available real dataset. The experiments demonstrate that the method is correct, numerically stable and robust.Comment: 13 pages, 7 eps-figure

Gravitational Collapse and Fragmentation in Molecular Clouds with Adaptive Mesh Refinement

We describe a powerful methodology for numerical solution of 3-D self-gravitational hydrodynamics problems with extremely high resolution. Our method utilizes the technique of local adaptive mesh refinement (AMR), employing multiple grids at multiple levels of resolution. These grids are automatically and dynamically added and removed as necessary to maintain adequate resolution. This technology allows for the solution of problems in a manner that is both more efficient and more versatile than other fixed and variable resolution methods. The application of AMR to simulate the collapse and fragmentation of a molecular cloud, a key step in star formation, is discussed. Such simulations involve many orders of magnitude of variation in length scale as fragments form. In this paper we briefly describe the methodology and present an illustrative application for nonisothermal cloud collapse. We describe the numerical Jeans condition, a criterion for stability of self-gravitational hydrodynamics problems. We show the first well-resolved nonisothermal evolutionary sequence beginning with a perturbed dense molecular cloud core that leads to the formation of a binary system consisting of protostellar cores surrounded by distinct protostellar disks. The scale of the disks, of order 100 AU, is consistent with observations of gaseous disks surrounding single T-Tauri stars and debris disks surrounding systems such as $\beta$ Pictoris.Comment: 10 pages, 6 figures (color postscript). To appear in the proceedings of Numerical Astrophysics 1998, Tokyo, March 10-13, 199

Effective-Range Expansion of the Neutron-Deuteron Scattering Studied by a Quark-Model Nonlocal Gaussian Potential

The S-wave effective range parameters of the neutron-deuteron (nd) scattering are derived in the Faddeev formalism, using a nonlocal Gaussian potential based on the quark-model baryon-baryon interaction fss2. The spin-doublet low-energy eigenphase shift is sufficiently attractive to reproduce predictions by the AV18 plus Urbana three-nucleon force, yielding the observed value of the doublet scattering length and the correct differential cross sections below the deuteron breakup threshold. This conclusion is consistent with the previous result for the triton binding energy, which is nearly reproduced by fss2 without reinforcing it with the three-nucleon force.Comment: 21 pages, 6 figures and 6 tables, submitted to Prog. Theor. Phy

Layering genetic circuits to build a single cell, bacterial half adder

Background: Gene regulation in biological systems is impacted by the cellular and genetic context-dependent effects of the biological parts which comprise the circuit. Here, we have sought to elucidate the limitations of engineering biology from an architectural point of view, with the aim of compiling a set of engineering solutions for overcoming failure modes during the development of complex, synthetic genetic circuits. Results: Using a synthetic biology approach that is supported by computational modelling and rigorous characterisation, AND, OR and NOT biological logic gates were layered in both parallel and serial arrangements to generate a repertoire of Boolean operations that include NIMPLY, XOR, half adder and half subtractor logics in a single cell. Subsequent evaluation of these near-digital biological systems revealed critical design pitfalls that triggered genetic context-dependent effects, including 5′ UTR interferences and uncontrolled switch-on behaviour of the supercoiled σ54 promoter. In particular, the presence of seven consecutive hairpins immediately downstream of the promoter transcription start site severely impeded gene expression. Conclusions: As synthetic biology moves forward with greater focus on scaling the complexity of engineered genetic circuits, studies which thoroughly evaluate failure modes and engineering solutions will serve as important references for future design and development of synthetic biological systems. This work describes a representative case study for the debugging of genetic context-dependent effects through principles elucidated herein, thereby providing a rational design framework to integrate multiple genetic circuits in a single prokaryotic cell.Published versio

Estrutura e dinâmica do tecido ósseo

O tecido ósseo é uma forma especializada de tecido conjuntivo constituído por uma fase mineral, formada essencialmente por cristais de fosfato de cálcio, sob a forma de hidroxiapatite, que assenta numa organizada matriz colagénica. A combinação da fase mineral e da fase orgânica confere ao tecido ósseo propriedades únicas, que o tornam muito resistente às solicitações mecânicas. Apesar seu aspeto aparentemente inerte, os ossos são estruturas plásticas altamente dinâmicas que, durante toda a vida do organismo, estão em permanente remodelação, por forma a manter as suas propriedades mecânicas e capacidades metabólicas. Quando lesados têm capacidade regenerativa, isto é, o processo de reparação óssea é efetuado através da formação de osso novo e não pela formação de tecido fibroso. As células do tecido ósseo podem ser agrupadas em duas séries diferentes: células da linha osteoblástica, responsáveis pelo processo de formação e mineralização da matriz óssea e células da linha osteoclástica, relacionadas com a sua reabsorção. O processo de diferenciação das células da linha osteoclástica está muito controlado pelas células da linha osteoblástica, através de um eixo de regulação comum, vulgarmente conhecido por RANKL/RANK/OPG. O equilíbrio entre formação e reabsorção óssea está na dependência das flutuações locais do rácio RANKL/OPG. A remodelação óssea consiste num mecanismo de substituição, ou de reconstrução, de áreas de tecido ósseo de modo a preservar a integridade, otimizar a função e prevenir a degradação ósseas. No processo de remodelação intervêm duas atividades opostas, mas complementares: a formação e a reabsorção do tecido ósseo a cargo das células das linhas osteoblástica e osteoclástica. Desta forma, elimina-se uma porção de osso velho, substituindo-o por osso novo, com pouca ou nenhuma alteração da massa óssea e assegura-se, também, a substituição de osso imaturo por osso lamelar. O ciclo celular da remodelação compreende uma série ordenada de eventos que vão converter uma superfície em repouso numa zona em remodelação, seguindo uma sequência imutável de ativação - reabsorção - formação. As equipas celulares responsáveis por estas múltiplas atividades incluem não só células específicas do tecido ósseo, como também células do sistema imunitário e células endoteliais. O objetivo da remodelação parece incluir duas perspetivas diferentes: uma de índole mecânica dirigida para a reparação e adaptação da estrutura óssea ao meio e a outra metabólica, participando na homeostasia do cálcio plasmático O tecido ósseo constitui um notável material de construção, de natureza biológica, com a singular capacidade de edificar estruturas muito resistentes que se remodelam e reparam a si próprias

A multi-exon deletion within WWOX is associated with a 46,XY disorder of sex development

Disorders of sex development (DSD) are congenital conditions where chromosomal, gonad or genital development is atypical. In a significant proportion of 46,XY DSD cases it is not possible to identify a causative mutation, making genetic counseling difficult and potentially hindering optimal treatment. Here, we describe the analysis of a 46,XY DSD patient that presented at birth with ambiguous genitalia. Histological analysis of the surgically removed gonads showed bilateral undifferentiated gonadal tissue and immature testis, both containing malignant germ cells. We screened genomic DNA from this patient for deletions and duplications using an Illumina whole-genome SNP microarray. This analysis revealed a heterozygous deletion within the WWOX gene on chromosome 16, removing exons 6-8. Analysis of parental DNA showed that the deletion was inherited from the mother. cDNA analysis confirmed that the deletion maintained the reading frame, with exon 5 being spliced directly onto exon 9. This deletion is the first description of a germline rearrangement affecting the coding sequence of WWOX in humans. Previously described Wwox knockout mouse models showed gonadal abnormalities, supporting a role for WWOX in human gonad development

Collapses and revivals of exciton emission in a semiconductor microcavity: detuning and phase-space filling effects

We investigate exciton emission of quantum well embedded in a semiconductor microcavity. The analytical expressions of the light intensity for the cases of excitonic number state and coherent state are presented by using secular approximation. Our results show that the effective exciton-exciton interaction leads to the appearance of collapse and revival of the light intensity. The revival time is twice compared the coherent state case with that of the number state. The dissipation of the exciton-polariton lowers the revival amplitude but does not alter the revival time. The influences of the detuning and the phase-space filling are studied. We find that the effect of the higher-order exciton-photon interaction may be removed by adjusting the detuning.Comment: 7 pages, 3 figure

First report of bacterial spot caused by Xanthomonas cucurbitae on pumpkin in Italy

In 2018, a disease outbreak was observed on pumpkin (Cucurbita moschata cv. Violina) in the municipality of Reggio Emilia (Northern Italy). Symptoms were observed on leaves and fruits