Development of real-time NASBA assays with molecular beacon detection to quantify mRNA coding for HHV-8 lytic and latent genes

BACKGROUND: Human herpesvirus-8 (HHV-8) is linked to the pathogenesis of Kaposi's sarcoma (KS), and the HHV-8 DNA load in peripheral blood mononuclear cells (PBMC) is associated with the clinical stage of KS. To examine the expression of HHV-8 in PBMC, four HHV-8 mRNA specific NASBA assays were developed METHODS: We have developed four quantitative nucleic acid sequence-based amplification assays (NASBA-QT) specifically to detect mRNA coding for ORF 73 (latency-associated nuclear antigen, LANA), vGCR (a membrane receptor), vBcl-2 (a viral inhibitor of apoptosis) and vIL-6 (a viral growth factor). The NASBA technique amplifies nucleic acids without thermocycling and mRNA can be amplified in a dsDNA background. A molecular beacon is used during amplification to enable real-time detection of the product. The assays were tested on PBMC samples of two AIDS-KS patients from the Amsterdam Cohort. RESULTS: For all four assays, the limit of detection (LOD) of 50 molecules and the limit of quantification (LOQ) of 100 molecules were determined using in vitro transcribed RNA. The linear dynamic range was 50 to 10(7) molecules of HHV-8 mRNA. We found HHV-8 mRNA expression in 9 out of the 10 tested samples. CONCLUSION: These real-time NASBA assays with beacon detection provide tools for further study of HHV-8 expression in patient material

How variation in head pitch could affect image matching algorithms for ant navigation

Desert ants are a model system for animal navigation, using visual memory to follow long routes across both sparse and cluttered environments. Most accounts of this behaviour assume retinotopic image matching, e.g. recovering heading direction by finding a minimum in the image difference function as the viewpoint rotates. But most models neglect the potential image distortion that could result from unstable head motion. We report that for ants running across a short section of natural substrate, the head pitch varies substantially: by over 20 degrees with no load; and 60 degrees when carrying a large food item. There is no evidence of head stabilisation. Using a realistic simulation of the ant’s visual world, we demonstrate that this range of head pitch significantly degrades image matching. The effect of pitch variation can be ameliorated by a memory bank of densely sampled along a route so that an image sufficiently similar in pitch and location is available for comparison. However, with large pitch disturbance, inappropriate memories sampled at distant locations are often recalled and navigation along a route can be adversely affected. Ignoring images obtained at extreme pitches, or averaging images over several pitches, does not significantly improve performance

K13 blocks KSHV lytic replication and deregulates vIL6 nad hIL6 expression: A model of lytic replication induced clonal selection in viral oncogenesis

Background. Accumulating evidence suggests that dysregulated expression of lytic genes plays an important role in KSHV (Kaposi's sarcoma associated herpesvirus) tumorigenesis. However, the molecular events leading to the dysregulation of KSHV lytic gene expression program are incompletely understood. Methodoloxy/Principal Findings. We have studied the effect of KSHV-encoded latent protein vFLIP K13, a potent activator of the NF-κB pathway, on lytic reactivation of the virus. We demonstrate that K13 antagonizes RTA, the KSHV lytic-regulator, and effectively blocks the expression of lytic proteins, production of infectious virions and death of the infected cells. Induction of lytic replication selects for clones with increased K13 expression and NF-κB activity, while siRNA-mediated silencing of K13 induces the expression of lytic genes. However, the suppressive effect of K13 on RTA-induced lytic genes is not uniform and it falls to block RTA-induced viral IL6 secretion and cooperates with RTA to enhance cellular IL-6 production, thereby dysregulating the lytic gene expression program. Conclusions/Significance. Our results support a model in which ongoing KSHV, lytic replication selects for clones with progressively higher levels of K13 expression and NF-κB activity, which in turn drive KSHV tumorigenesis by not only directly stimulating cellular survival and proliferation, but also indirectly by dysregulating the viral lytic gene program and allowing non-lytic production of growth-promoting viral and cellular genes. Lytic Replication-Induced Clonal Selection (LyRICS) may represent a general mechanism in viral oncogenesis. 2007 Zhao et al

Autonomous visual navigation of an indoor environment using a parsimonious, insect inspired familiarity algorithm

The navigation of bees and ants from hive to food and back has captivated people for more than a century. Recently, the Navigation by Scene Familiarity Hypothesis (NSFH) has been proposed as a parsimonious approach that is congruent with the limited neural elements of these insects’ brains. In the NSFH approach, an agent completes an initial training excursion, storing images along the way. To retrace the path, the agent scans the area and compares the current scenes to those previously experienced. By turning and moving to minimize the pixel-by-pixel differences between encountered and stored scenes, the agent is guided along the path without having memorized the sequence. An important premise of the NSFH is that the visual information of the environment is adequate to guide navigation without aliasing. Here we demonstrate that an image landscape of an indoor setting possesses ample navigational information. We produced a visual landscape of our laboratory and part of the adjoining corridor consisting of 2816 panoramic snapshots arranged in a grid at 12.7-cm centers. We show that pixel-by-pixel comparisons of these images yield robust translational and rotational visual information. We also produced a simple algorithm that tracks previously experienced routes within our lab based on an insect-inspired scene familiarity approach and demonstrate that adequate visual information exists for an agent to retrace complex training routes, including those where the path’s end is not visible from its origin. We used this landscape to systematically test the interplay of sensor morphology, angles of inspection, and similarity threshold with the recapitulation performance of the agent. Finally, we compared the relative information content and chance of aliasing within our visually rich laboratory landscape to scenes acquired from indoor corridors with more repetitive scenery.The authors received funding from a Research Council Faculty Investment Grant from the University of Oklahoma.Ye

Pre-Micro RNA Signatures Delineate Stages of Endothelial Cell Transformation in Kaposi Sarcoma

MicroRNAs (miRNA) have emerged as key regulators of cell lineage differentiation and cancer. We used precursor miRNA profiling by a novel real-time QPCR method (i) to define progressive stages of endothelial cell transformation cumulating in Kaposi sarcoma (KS) and (ii) to identify specific miRNAs that serve as biomarkers for tumor progression. We were able to compare primary patient biopsies to well-established culture and mouse tumor models. Loss of mir-221 and gain of mir-15 expression demarked the transition from merely immortalized to fully tumorigenic endothelial cells. Mir-140 and Kaposi sarcoma–associated herpesvirus viral miRNAs increased linearly with the degree of transformation. Mir-24 emerged as a biomarker specific for KS

Omnidirectional vision with frontal stereo

This study describes a novel imaging system that can be used as a front end for a vision system for guidance of unmanned aerial vehicles. A single camera and a combination of three specially designed reflecting surfaces axe used to provide (a) complete onmidirectional vision with no frontal blind zone and (b) stereo range within a frontal field. Important features are (i) the use of a single camera, which, apart from minimising cost, eliminates the need for alignment and calibration of multiple cameras; and (ii) a novel approach to stereoscopic range computation that uses a single camera and a circular baseline to overcome potential aperture problems

Relocalization with Submaps: Multi-Session Mapping for Planetary Rovers Equipped with Stereo Cameras

To enable long term exploration of extreme environments such as planetary surfaces, heterogeneous robotic teams need the ability to localize themselves on previously built maps. While the Localization and Mapping problem for single sessions can be efficiently solved with many state of the art solutions, place recognition in natural environments still poses great challenges for the perception system of a robotic agent. In this paper we propose a relocalization pipeline which exploits both 3D and visual information from stereo cameras to detect matches across local point clouds of multiple SLAM sessions. Our solution is based on a Bag of Binary Words scheme where binarized SHOT descriptors are enriched with visual cues to recall in a fast and efficient way previously visited places. The proposed relocalization scheme is validated on challenging datasets captured using a planetary rover prototype on Mount Etna, designated as a Moon analogue environment

Gaussian Process Gradient Maps for Loop-Closure Detection in Unstructured Planetary Environments

The ability to recognize previously mapped locations is an essential feature for autonomous systems. Unstructured planetary-like environments pose a major challenge to these systems due to the similarity of the terrain. As a result, the ambiguity of the visual appearance makes state-of-the-art visual place recognition approaches less effective than in urban or man-made environments. This paper presents a method to solve the loop closure problem using only spatial information. The key idea is to use a novel continuous and probabilistic representations of terrain elevation maps. Given 3D point clouds of the environment, the proposed approach exploits Gaussian Process (GP) regression with linear operators to generate continuous gradient maps of the terrain elevation information. Traditional image registration techniques are then used to search for potential matches. Loop closures are verified by leveraging both the spatial characteristic of the elevation maps (SE(2) registration) and the probabilistic nature of the GP representation. A submap-based localization and mapping framework is used to demonstrate the validity of the proposed approach. The performance of this pipeline is evaluated and benchmarked using real data from a rover that is equipped with a stereo camera and navigates in challenging, unstructured planetary-like environments in Morocco and on Mt. Etna.Comment: This work is accepted for presentation at the 2020 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS). Please find IEEE's copyright statement at the bottom of the first page. Cedric Le Gentil and Mallikarjuna Vayugundla share the first authorship of this pape

Debundling, selection and release of SWNTs using fluorene-based photocleavable polymers

Photocleavable polymers based on 9,9-dialkylfluorene backbone and o-nitrobenzylether were designed and synthesized to obtain stable (n,m) enriched suspensions of semiconducting SWNTs in toluene. Photoirradiation of the suspensions triggered the precipitation of the SWNTs and TEM images indicate close packing of SWNTs pointing at partial removal of the coating polymer