Telomeric expression sites are highly conserved in trypanosoma brucei

Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs) of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs). The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs) were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology

Parametric inference of recombination in HIV genomes

Recombination is an important event in the evolution of HIV. It affects the global spread of the pandemic as well as evolutionary escape from host immune response and from drug therapy within single patients. Comprehensive computational methods are needed for detecting recombinant sequences in large databases, and for inferring the parental sequences. We present a hidden Markov model to annotate a query sequence as a recombinant of a given set of aligned sequences. Parametric inference is used to determine all optimal annotations for all parameters of the model. We show that the inferred annotations recover most features of established hand-curated annotations. Thus, parametric analysis of the hidden Markov model is feasible for HIV full-length genomes, and it improves the detection and annotation of recombinant forms. All computational results, reference alignments, and C++ source code are available at http://bio.math.berkeley.edu/recombination/.Comment: 20 pages, 5 figure

Smart environment monitoring through micro unmanned aerial vehicles

In recent years, the improvements of small-scale Unmanned Aerial Vehicles (UAVs) in terms of flight time, automatic control, and remote transmission are promoting the development of a wide range of practical applications. In aerial video surveillance, the monitoring of broad areas still has many challenges due to the achievement of different tasks in real-time, including mosaicking, change detection, and object detection. In this thesis work, a small-scale UAV based vision system to maintain regular surveillance over target areas is proposed. The system works in two modes. The first mode allows to monitor an area of interest by performing several flights. During the first flight, it creates an incremental geo-referenced mosaic of an area of interest and classifies all the known elements (e.g., persons) found on the ground by an improved Faster R-CNN architecture previously trained. In subsequent reconnaissance flights, the system searches for any changes (e.g., disappearance of persons) that may occur in the mosaic by a histogram equalization and RGB-Local Binary Pattern (RGB-LBP) based algorithm. If present, the mosaic is updated. The second mode, allows to perform a real-time classification by using, again, our improved Faster R-CNN model, useful for time-critical operations. Thanks to different design features, the system works in real-time and performs mosaicking and change detection tasks at low-altitude, thus allowing the classification even of small objects. The proposed system was tested by using the whole set of challenging video sequences contained in the UAV Mosaicking and Change Detection (UMCD) dataset and other public datasets. The evaluation of the system by well-known performance metrics has shown remarkable results in terms of mosaic creation and updating, as well as in terms of change detection and object detection

Mosaicing Tool for Aerial Imagery from a Lidar Bathymetry Survey

Aerial imagery collected during lidar bathymetry surveying provides an independent reference dataset for ground truth. Mosaicing of aerial imagery requires some manual involvement by the operator, which is time consuming. This paper presents an automatic mosaicing procedure that creates a continuous and visually consistent photographic map of the imaged area. This study aimed to use only the frames from the aerial camera without additional information. A comparison between the features in the resultant mosaic and a reference chart shows that the mosaic is visually consistent and there is good spatial-geometric correlation of features.Las imagenes aereas recogidas durante los levantamientos batimetricos efectuados con el lfdar proporcionan una coleccion de datos de referencia independientes para la validacion en el terreno. La composicion de las imagenes aereas en forma de mosaico requiere una cierta implicacion manual par parte del operador, to que toma mucho tiempo. Este articulo presenta un procedimiento para la composicion automatica en forma de mosaico, que crea un mapa fotografico continuo y visuatmente coherente de la zona representada en la imagen. El objetivo de este estudio es utilizar solo los marcos de la camara aerea sin informacion adicional. Una comparacion entre las caracterfsticas del mosaico resultante y una carta de referencia muestra que el mosaico es visualmente coherente y que hay una buena correlacion geometrico-espacial de las caracteristicas.L'imagerie aerienne effectuee pendant les leves bathymetriques lidar constitue un ensemble de donnees de reference independant, pour la realite de terrain. Le mosaiiquage de l'imagerie aerienne requiert une intervention manuelle de l'operateur, laquelle prend beaucoup de temps. Cet article presente une procedure de mosaiiquage automatique qui permet d'obtenir une carte photographique continue et visuellement coherente de la zone couverte. L'objectif de cette etude consiste a utiliser seulement les images de la camera aerienne sans informations supptementaires. Une comparaison entre tes elements dans la mosaique resultante et une carte de reference montre que la mosaique est visuellement coherente et qu'il existe une bonne correlation geometrique-spatiale des elements

Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species

Antigenic variation enables pathogens to avoid the host immune response by continual switching of surface proteins. The protozoan blood parasite Trypanosoma brucei causes human African trypanosomiasis ("sleeping sickness") across sub-Saharan Africa and is a model system for antigenic variation, surviving by periodically replacing a monolayer of variant surface glycoproteins (VSG) that covers its cell surface. We compared the genome of Trypanosoma brucei with two closely related parasites Trypanosoma congolense and Trypanosoma vivax, to reveal how the variant antigen repertoire has evolved and how it might affect contemporary antigenic diversity. We reconstruct VSG diversification showing that Trypanosoma congolense uses variant antigens derived from multiple ancestral VSG lineages, whereas in Trypanosoma brucei VSG have recent origins, and ancestral gene lineages have been repeatedly co-opted to novel functions. These historical differences are reflected in fundamental differences between species in the scale and mechanism of recombination. Using phylogenetic incompatibility as a metric for genetic exchange, we show that the frequency of recombination is comparable between Trypanosoma congolense and Trypanosoma brucei but is much lower in Trypanosoma vivax. Furthermore, in showing that the C-terminal domain of Trypanosoma brucei VSG plays a crucial role in facilitating exchange, we reveal substantial species differences in the mechanism of VSG diversification. Our results demonstrate how past VSG evolution indirectly determines the ability of contemporary parasites to generate novel variant antigens through recombination and suggest that the current model for antigenic variation in Trypanosoma brucei is only one means by which these parasites maintain chronic infections

Mosaicing Tool for Aerial Imagery from a Lidar Bathymetry Survey

Aerial imagery collected during lidar bathymetry surveying provides an independent reference dataset for ground truth. Mosaicing of aerial imagery requires some manual involvement by the operator, which is time consuming. This paper presents an automatic mosaicing procedure that creates a continuous and visually consistent photographic map of the imaged area. This study aimed to use only the frames from the aerial camera without additional information. A comparison between the features in the resultant mosaic and a reference chart shows that the mosaic is visually consistent and there is good spatial-geometric correlation of features.Las imagenes aereas recogidas durante los levantamientos batimetricos efectuados con el lfdar proporcionan una coleccion de datos de referencia independientes para la validacion en el terreno. La composicion de las imagenes aereas en forma de mosaico requiere una cierta implicacion manual par parte del operador, to que toma mucho tiempo. Este articulo presenta un procedimiento para la composicion automatica en forma de mosaico, que crea un mapa fotografico continuo y visuatmente coherente de la zona representada en la imagen. El objetivo de este estudio es utilizar solo los marcos de la camara aerea sin informacion adicional. Una comparacion entre las caracterfsticas del mosaico resultante y una carta de referencia muestra que el mosaico es visualmente coherente y que hay una buena correlacion geometrico-espacial de las caracteristicas.L'imagerie aerienne effectuee pendant les leves bathymetriques lidar constitue un ensemble de donnees de reference independant, pour la realite de terrain. Le mosaiiquage de l'imagerie aerienne requiert une intervention manuelle de l'operateur, laquelle prend beaucoup de temps. Cet article presente une procedure de mosaiiquage automatique qui permet d'obtenir une carte photographique continue et visuellement coherente de la zone couverte. L'objectif de cette etude consiste a utiliser seulement les images de la camera aerienne sans informations supptementaires. Une comparaison entre tes elements dans la mosaique resultante et une carte de reference montre que la mosaique est visuellement coherente et qu'il existe une bonne correlation geometrique-spatiale des elements

Advances in Simultaneous Localization and Mapping in Confined Underwater Environments Using Sonar and Optical Imaging.

This thesis reports on the incorporation of surface information into a probabilistic simultaneous localization and mapping (SLAM) framework used on an autonomous underwater vehicle (AUV) designed for underwater inspection. AUVs operating in cluttered underwater environments, such as ship hulls or dams, are commonly equipped with Doppler-based sensors, which---in addition to navigation---provide a sparse representation of the environment in the form of a three-dimensional (3D) point cloud. The goal of this thesis is to develop perceptual algorithms that take full advantage of these sparse observations for correcting navigational drift and building a model of the environment. In particular, we focus on three objectives. First, we introduce a novel representation of this 3D point cloud as collections of planar features arranged in a factor graph. This factor graph representation probabalistically infers the spatial arrangement of each planar segment and can effectively model smooth surfaces (such as a ship hull). Second, we show how this technique can produce 3D models that serve as input to our pipeline that produces the first-ever 3D photomosaics using a two-dimensional (2D) imaging sonar. Finally, we propose a model-assisted bundle adjustment (BA) framework that allows for robust registration between surfaces observed from a Doppler sensor and visual features detected from optical images. Throughout this thesis, we show methods that produce 3D photomosaics using a combination of triangular meshes (derived from our SLAM framework or given a-priori), optical images, and sonar images. Overall, the contributions of this thesis greatly increase the accuracy, reliability, and utility of in-water ship hull inspection with AUVs despite the challenges they face in underwater environments. We provide results using the Hovering Autonomous Underwater Vehicle (HAUV) for autonomous ship hull inspection, which serves as the primary testbed for the algorithms presented in this thesis. The sensor payload of the HAUV consists primarily of: a Doppler velocity log (DVL) for underwater navigation and ranging, monocular and stereo cameras, and---for some applications---an imaging sonar.PhDElectrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/120750/1/paulozog_1.pd

Evidence of animal mtDNA recombination between divergent populations of the potato cyst nematode Globodera pallida

Recombination is typically assumed to be absent in animal mitochondrial genomes (mtDNA). However, the maternal mode of inheritance means that recombinant products are indistinguishable from their progenitor molecules. The majority of studies of mtDNA recombination assess past recombination events, where patterns of recombination are inferred by comparing the mtDNA of different individuals. Few studies assess contemporary mtDNA recombination, where recombinant molecules are observed as direct mosaics of known progenitor molecules. Here we use the potato cyst nematode, Globodera pallida, to investigate past and contemporary recombination. Past recombination was assessed within and between populations of G. pallida, and contemporary recombination was assessed in the progeny of experimental crosses of these populations. Breeding of genetically divergent organisms may cause paternal mtDNA leakage, resulting in heteroplasmy and facilitating the detection of recombination. To assess contemporary recombination we looked for evidence of recombination between the mtDNA of the parental populations within the mtDNA of progeny. Past recombination was detected between a South American population and several UK populations of G. pallida, as well as between two South American populations. This suggests that these populations may have interbred, paternal mtDNA leakage occurred, and the mtDNA of these populations subsequently recombined. This evidence challenges two dogmas of animal mtDNA evolution; no recombination and maternal inheritance. No contemporary recombination between the parental populations was detected in the progeny of the experimental crosses. This supports current arguments that mtDNA recombination events are rare. More sensitive detection methods may be required to adequately assess contemporary mtDNA recombination in animals