Search

Background Lactic acid for polymer applications must be optically pure to allow the final plastic properties to be controlled. We have isolated a strain of Lactobacillus plantarum capable of utilising a range of carbohydrates and tolerant to high sugar and organic acid concentrations. However, like most Lactobacillus plantarum, this strain produces D- and L-lactic acid. To improve the commercial application of this strain gene editing has been used to ensure only one isoform is produced. Methods Using two-step homologous recombination, ldhL was replaced with a truncated version interrupted by a chloramphenicol acetyltransferase resistance marker, then with an unmarked truncated version. The optical purity shift was quantified biochemically by enzymatic assay and HPLC and fermentation performance compared against the unmodified strain using enzymatically hydrolysed municipal solid waste pulp (MSW sugars) as a feedstock. Results The ldhL gene was successfully deleted, leading to a dramatic shift in the optical purity of lactate produced in both synthetic media and MSW sugars. The unmodified strain produced D-lactic acid with an optical purity of 40%, while the mutant achieved 94%. In MSW sugars, the modified strain performed as well as the unmodified control, consuming all available glucose in less than 48 hours with a volumetric productivity of 1.02 g/L/h. Conclusions Deletion of ldhL from our strain of Lactobacillus plantarum allowed exclusive production of D-lactic acid from MSW sugars. This provides a laboratory scale demonstration of the production of optically pure lactic acid from renewable sugars for use in the production of biodegradable plastics.

Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption. Coalescent theory is a popular class of evolutionary models that implements the molecular clock hypothesis to facilitate computational inference of dated phylogenies. Cancer and virus evolution are two areas where these methods are particularly important. Methodologically, phylogenetic inference methods require a tree space over which the inference is performed, and geometry of this space plays an important role in statistical and computational aspects of tree inference algorithms. It has recently been shown that molecular clock, and hence coalescent, trees possess a unique geometry, different from that of classical phylogenetic tree spaces which do not model mutation rates. Here we introduce and study a space of discrete coalescent trees, that is, we assume that time is discrete, which is inevitable in many computational formalisations. We establish several geometrical properties of the space and show how these properties impact various algorithms used in phylogenetic analyses. Our tree space is a discretisation of a known time tree space, called t-space, and hence our results can be used to approximate solutions to various open problems in t-space. Our tree space is also a generalisation of another known trees space, called the ranked nearest neighbour interchange space, hence our advances in this paper imply new and generalise existing results about ranked trees.

El objetivo principal de este proyecto de grado es desarrollar un sistema de visión por computador embebido para dotar a un cuadricóptero con la capacidad de detectar y hacer el seguimiento autónomo de un objeto móvil terrestre visto desde la plataforma aérea no tripulada (Unmanned Aerial Vehicle (UAV)), utilizando ROS. La detección y el seguimiento de objetos en movimiento usando plataformas UAV, son consideradas tareas difíciles para los sistemas de visión por computador y su implementación requiere superar varios desafíos. Los modelos y algoritmos de visión expuestos en este trabajo de grado están basados en el uso de técnicas de deep learning para el procesamiento de imágenes, a través de los cuales se busca resolver varios de los desafíos asociados a la detección y el seguimiento visual de objetos en movimiento. Este proyecto utilizó ROS como entorno de trabajo estandarizado para el desarrollo de la aplicación robótica, se diseñó e implementó un entorno de simulación Hardware-in-the-loop (HIL) de forma que el sistema embebido no controla un UAV real sino uno simulado. Para validar el funcionamiento del sistema, se implementó una interfaz en ROS que permite comunicar el sistema de visión por computador embebido y un cuadricóptero. Se empleó el paquete de ROS hector quadrotor, el cual ofrece un modelo 3D de un cuadricóptero, con dinámicas de vuelo realistas, cámaras y sensores integrados. Una vez conformado el ambiente de simulación se realizaron diferentes vuelos, experimentos y pruebas con la ayuda de herramientas de visualización como Rviz (ROS Visualization) y Gazebo que se integran con ROS. Este trabajo de grado concluye que los sensores ópticos proporcionan una fuente de información confiable y su procesamiento constituye una herramienta de navegación para las tareas comunes de los UAV. Los detectores de objetos entrenados con Single Shot Multibox Detector (SSD) presentan el mejor equilibrio entre las métricas evaluadas, con un rendimiento de 18.1 ∼ 18.4 FPS y una precisión entre 84.97 % ∼ 94.44 %. Los resultados obtenidos en las diferentes simulaciones realizadas demuestran que el cuadricóptero es capaz de detectar y seguir de forma autónoma un carro de radio control que se mueve en tierra., The main objective of this degree project is to develop an embedded computer vision system to equip a quadcopter with the capability of autonomously detect and track a ground moving object viewed from the Unmanned Aerial Vehicle (UAV) platform using ROS. Detection and tracking of moving objects using UAV platforms are difficult tasks for computer vision systems and their implementation requires overcoming several challenges. The vision models and algorithms presented are based on the use of deep learning techniques for image processing, through which we seek to solve several of the challenges associated with the detection and visual tracking of moving objects. This project used ROS as a standardized work environment for the development of the robotic application, a Hardware-in-the-loop (HIL) simulation environment was designed and implemented so that the embedded system does not control a real UAV but a simulated one. An interface in ROS was implemented to validate the operation of the system, which serves as communication between the embedded computer vision system and a quadcopter. The ROS package hector quadrotor was used, which offers a 3D model of a quadcopter, with realistic flight dynamics, cameras and integrated sensors. The system was validated with different flights, experiments and tests with the help of visualization tools such as RViz (ROS Visualization) and Gazebo that integrate with ROS. This degree work concludes that optical sensors provide a reliable source of information and their processing makes up a navigation tool for common UAV tasks. Object detectors trained with Single Shot Multibox Detector (SSD) present the best balance among the evaluated metrics, with a performance of 18.1 ∼ 18.4 FPS and an accuracy between 84.97% ∼ 94.44%. The results obtained in the different simulations performed show that the quadcopter can autonomously detect and track a radio-controlled car moving on the ground., Maestría, Magíster en Ingeniería Electrónica

Diversities are a generalization of metric spaces, where instead of the non-negative function being defined on pairs of points, it is defined on arbitrary finite sets of points. Diversities have a well-developed theory. This includes the concept of a diversity tight span that extends the metric tight span in a natural way. Here we explore the generalization of diversities to lattices. Instead of defining diversities on finite subsets of a set we consider diversities defined on members of an arbitrary lattice (with a 0). We show that many of the basic properties of diversities continue to hold. However, the natural map from a lattice diversity to its tight span is not a lattice homomorphism, preventing the development of a complete tight span theory as in the metric and diversity cases., 18 pages, 4 figures

Gene tree discordance is now recognized as a major source of biological heterogeneity. How to deal with this heterogeneity is an unsolved problem, as the accurate inference of individual gene tree topologies is difficult. One solution has been to simply concatenate all of the data together, ignoring the underlying heterogeneity. Another approach infers gene tree topologies separately and combines the individual estimates in order to explicitly model this heterogeneity. Here we discuss the advantages and disadvantages of both approaches-using the gene trees singly or in concatenation-paying special attention to the sources of variance and implicit assumptions. We make it clear that all methods are likely to have their assumptions violated, though the consequence of these violations differs in different parts of parameter space. The main conclusion of our review is that different sources of error are more or less important in different settings, such that phylogenetics researchers should be using the methods most appropriate to their problems rather than stick to one dogmatically.

Gene tree discordance is now recognized as a major source of biological heterogeneity. How to deal with this heterogeneity is an unsolved problem, as the accurate inference of individual gene tree topologies is difficult. One solution has been to simply concatenate all of the data together, ignoring the underlying heterogeneity. Another approach infers gene tree topologies separately and combines the individual estimates in order to explicitly model this heterogeneity. Here we discuss the advantages and disadvantages of both approaches-using the gene trees singly or in concatenation-paying special attention to the sources of variance and implicit assumptions. We make it clear that all methods are likely to have their assumptions violated, though the consequence of these violations differs in different parts of parameter space. The main conclusion of our review is that different sources of error are more or less important in different settings, such that phylogenetics researchers should be using the methods most appropriate to their problems rather than stick to one dogmatically.

International audience

International audience

The general theory developed by Ben Yaacov for metric structures provides Fra\"iss\'e limits which are approximately ultrahomogeneous. We show here that this result can be strengthened in the case of relational metric structures. We give an extra condition that guarantees exact ultrahomogenous limits. The condition is quite general. We apply it to stochastic processes, the class of diversities, and its subclass of $L_1$ diversities., Comment: 22 pages

The general theory developed by Ben Yaacov for metric structures provides Fra��ss�� limits which are approximately ultrahomogeneous. We show here that this result can be strengthened in the case of relational metric structures. We give an extra condition that guarantees exact ultrahomogenous limits. The condition is quite general. We apply it to stochastic processes, the class of diversities, and its subclass of $L_1$ diversities., 22 pages

Fibroblast growth factor receptors (FGFRs) are a family of receptor tyrosine kinases that control a diverse range of biological processes during development and in adult tissues. We recently reported that somatic FGFR2 mutations are associated with shorter survival in endometrial cancer. However, little is known about how these FGFR2 mutations contribute to endometrial cancer metastasis. Here, we report that expression of the activating mutations FGFR2N550K and FGFR2Y376C in an endometrial cancer cell model induce Golgi fragmentation, and loss of polarity and directional migration. In mutant FGFR2-expressing cells, this was associated with an inability to polarise intracellular pools of FGFR2 towards the front of migrating cells. Such polarization defects were exacerbated in three-dimensional culture, where FGFR2 mutant cells were unable to form well-organised acini, instead undergoing exogenous ligand-independent invasion. Our findings uncover collective cell polarity and invasion as common targets of disease-associated FGFR2 mutations that lead to poor outcome in endometrial cancer patients.

Smoothing splines can be thought of as the posterior mean of a Gaussian process regression in a certain limit. By constructing a reproducing kernel Hilbert space with an appropriate inner product, the Bayesian form of the V-spline is derived when the penalty term is a fixed constant instead of a function. An extension to the usual generalized cross-validation formula is utilized to find the optimal V-spline parameters., Comment: a draft. not peer-reviewed yet

Diversities are a generalization of metric spaces in which a non-negative value is assigned to all finite subsets of a set, rather than just to pairs of points. Here we provide an analogue of the theory of negative type metrics for diversities. We introduce negative type diversities, and show that, as in the metric space case, they are a generalization of $L_1$-embeddable diversities. We provide a number of characterizations of negative type diversities, including a geometric characterisation. Much of the recent interest in negative type metrics stems from the connections between metric embeddings and approximation algorithms. We extend some of this work into the diversity setting, showing that lower bounds for embeddings of negative type metrics into $L_1$ can be extended to diversities by using recently established extremal results on hypergraphs.

The Minimal Ancestral Deviation (MAD) method is a recently introduced procedure for estimating the root of a phylogenetic tree, based only on the shape and branch lengths of the tree. The method is loosely derived from the midpoint rooting method, but, unlike its predecessor, makes use of all pairs of OTUs when positioning the root. In this note we establish properties of this method and then describe a fast and memory efficient algorithm. As a proof of principle, we use our algorithm to determine the MAD roots for simulated phylogenies with up to 100,000 OTUs. The calculations take a few minutes on a standard laptop.

Trajectory reconstruction is the process of inferring the path of a moving object between successive observations. In this paper, we propose a smoothing spline -- which we name the V-spline -- that incorporates position and velocity information and a penalty term that controls acceleration. We introduce a particular adaptive V-spline designed to control the impact of irregularly sampled observations and noisy velocity measurements. A cross-validation scheme for estimating the V-spline parameters is given and we detail the performance of the V-spline on four particularly challenging test datasets. Finally, an application of the V-spline to vehicle trajectory reconstruction in two dimensions is given, in which the penalty term is allowed to further depend on known operational characteristics of the vehicle., Comment: 25 pages, submitted

In the case of a linear state space model, we implement an MCMC sampler with two phases. In the learning phase, a self-tuning sampler is used to learn the parameter mean and covariance structure. In the estimation phase, the parameter mean and covariance structure informs the proposed mechanism and is also used in a delayed-acceptance algorithm. Information on the resulting state of the system is given by a Gaussian mixture. In on-line mode, the algorithm is adaptive and uses a sliding window approach to accelerate sampling speed and to maintain appropriate acceptance rates. We apply the algorithm to joined state and parameter estimation in the case of irregularly sampled GPS time series data., Comment: adaptive MCMC method application. need further work

We define a set inner product to be a function on pairs of convex bodies which is symmetric, Minkowski linear in each dimension, positive definite, and satisfies the natural analogue of the Cauchy-Schwartz inequality (which is not implied by the other conditions). We show that any set inner product can be embedded into an inner product space on the associated support functions, thereby extending fundamental results of Hormander and Radstrom. The set inner product provides a geometry on the space of convex bodies. We explore some of the properties of that geometry, and discuss an application of these ideas to the reconstruction of ancestral ecological niches in evolutionary biology.

David Bryant studied music composition and biological science at the University of Queensland, Brisbane, Australia, and graduated with a BSc in biochemistry. He pursued his PhD in the laboratory of Jennifer Stow at the Institute for Molecular Bioscience with a focus on cellular trafficking mechanisms for E-cadherin. David then moved to San Francisco for his postdoctoral work on apical polarity establishment in a three-dimensional context in the laboratory of Keith Mostov. After an NIH Pathway to Independence (PI) award in 2012, David moved to the University of Glasgow, where he established his own research group in 2014 at the Cancer Research UK Beatson Institute. His work focuses on collective cell polarity in 3D tumours, and how the gain and loss of polarity influences development, as well as cancer invasion and progression.

In many types of tubules, continuity of the lumen is paramount to tubular function, yet how tubules generate lumen continuity in vivo is not known. We recently found that the F-actin-binding protein afadin is required for lumen continuity in developing renal tubules, though its mechanism of action remains unknown. Here, we demonstrate that afadin is required for lumen continuity by orienting the mitotic spindle during cell division. Using an in vitro 3D cyst model, we find that afadin localizes to the cell cortex adjacent to the spindle poles and orients the mitotic spindle. In tubules, cell division may be oriented relative to two axes: longitudinal and apical-basal. Unexpectedly, in vivo examination of early-stage developing nephron tubules reveals that cell division is not oriented in the longitudinal (or planar-polarized) axis. However, cell division is oriented perpendicular to the apical-basal axis. Absence of afadin in vivo leads to misorientation of apical-basal cell division in nephron tubules. Together, these results support a model whereby afadin determines lumen placement by directing apical-basal spindle orientation, resulting in a continuous lumen and normal tubule morphogenesis.

The Company of Biologists held the workshop 'Intercellular interactions in context: towards a mechanistic understanding of cells in organs' at historic Wiston House in West Sussex, UK, 5-8 February 2017. The meeting brought together around 30 scientists from disparate backgrounds - yet with a common interest of how tissue morphogenesis occurs and its dysregulation leads to pathologies - to intensively discuss their latest research, the current state of the field, as well as any challenges for the future. This report summarises the concepts and challenges that arose as key questions for the fields of cell, cancer and developmental biology. By design of the organizers - Andrew Ewald (John Hopkins University, MA), John Wallingford (University of Texas at Austin, TX) and Peter Friedl (Radboud University, Nijmegen, The Netherlands) - the attendee makeup was cross-sectional: both in terms of career stage and scientific background. This intermingling was mirrored in the workshop format; all participants - irrespective of career stage - were given equal speaking and question time, and all early-career researchers also chaired a session, which promoted an atmosphere for discussions that were open, egalitarian and supportive. This was particularly evident in the scheduled 'out-of-the-box' sessions, which provided an avenue for participants to raise ideas and concepts or to discuss specific problems they wanted feedback or clarification on. In the following, rather than act as court reporters and convey chronological accounting of presentations, we present the questions that arose from the workshop and should be posed to the field at large, by discussing the presentations as they relate to these concepts.

Pathogens can alter epithelial polarity by recruiting polarity proteins to the apical membrane, but how a change in protein localization is linked to polarity disruption is not clear. In this study, we used chemically induced dimerization to rapidly relocalize proteins from the cytosol to the apical surface. We demonstrate that forced apical localization of Par3, which is normally restricted to tight junctions, is sufficient to alter apical membrane identity through its interactions with phosphatidylinositol 3-kinase (PI3K) and the Rac1 guanine nucleotide exchange factor Tiam1. We further show that PI3K activity is required upstream of Rac1, and that simultaneously targeting PI3K and Tiam1 to the apical membrane has a synergistic effect on membrane remodeling. Thus, Par3 coordinates the action of PI3K and Tiam1 to define membrane identity, revealing a signaling mechanism that can be exploited by human mucosal pathogens.

The formation of distinct subdomains of the cell surface is crucial for multicellular organism development. The most striking example of this is apical-basal polarization. What is much less appreciated is that underpinning an asymmetric cell surface is an equally dramatic intracellular endosome rearrangement. Here, we review the interplay between classical cell polarity proteins and membrane trafficking pathways, and discuss how this marriage gives rise to cell polarization. We focus on those mechanisms that regulate apical polarization, as this is providing a number of insights into how membrane traffic and polarity are regulated at the tissue level.

The embedding of finite metrics in $\ell_1$ has become a fundamental tool for both combinatorial optimization and large-scale data analysis. One important application is to network flow problems in which there is close relation between max-flow min-cut theorems and the minimal distortion embeddings of metrics into $\ell_1$. Here we show that this theory can be generalized considerably to encompass Steiner tree packing problems in both graphs and hypergraphs. Instead of the theory of $\ell_1$ metrics and minimal distortion embeddings, the parallel is the theory of diversities recently introduced by Bryant and Tupper, and the corresponding theory of $\ell_1$ diversities and embeddings which we develop here., Comment: 19 pages, no figures. This version: further small corrections

Simulations often involve the use of model parameters which are unknown or uncertain. For this reason, simulation experiments are often repeated for multiple combinations of parameter values, often iterating through parameter values lying on a fixed grid. However, the use of a discrete grid places limits on the dimension of the parameter space and creates the potential to miss important parameter combinations which fall in the gaps between grid points. Here we draw parallels with strategies for numerical integration and describe a Markov chain Monte-Carlo strategy for exploring parameter values. We illustrate the approach using examples from phylogenetics, archaeology, and epidemiology., Comment: 29 pages incl. supplementary information. 4 figures, 2 supp. figures, 2 supp. tables

We derive exact formulae for the allele frequency spectrum under the coalescent with mutation, conditioned on allele counts at some fixed time in the past. We consider unlinked biallelic markers mutating according to a finite sites, or infinite sites, model. This work extends the coalescent theory of unlinked biallelic markers, enabling fast computations of allele frequency spectra in multiple populations. Our results have applications to demographic inference, species tree inference, and the analysis of genetic variation in closely related species more generally.

The asymmetric polarization of cells allows specialized functions to be performed at discrete subcellular locales. Spatiotemporal coordination of polarization between groups of cells allowed the evolution of metazoa. For instance, coordinated apical-basal polarization of epithelial and endothelial cells allows transport of nutrients and metabolites across cell barriers and tissue microenvironments. The defining feature of such tissues is the presence of a central, interconnected luminal network. Although tubular networks are present in seemingly different organ systems, such as the kidney, lung, and blood vessels, common underlying principles govern their formation. Recent studies using in vivo and in vitro models of lumen formation have shed new light on the molecular networks regulating this fundamental process. We here discuss progress in understanding common design principles underpinning de novo lumen formation and expansion.

Growing evidence is pointing to the importance of multicellular bacterial structures in the interaction of pathogenic bacteria with their host. Transition from planktonic to host cell-associated multi- cellular structures is an essential infection step that has not been described for the opportunistic human pathogen Pseudomonas aeruginosa. In this study we show that P. aeruginosa interacts with the surface of epithelial cells mainly forming aggregates. Dynamics of aggregate formation typically follow a sigmoidal curve. First, a single bacterium attaches at cell–cell junctions. This is followed by rapid recruitment of free-swimming bacteria and association of bacterial cells result- ing in the formation of an aggregate on the order of minutes. Aggregates are associated with phosphatidylinositol 3,4,5-trisphosphate (PIP3)- enriched host cell membrane protrusions. We further show that aggregates can be rapidly inter- nalized into epithelial cells. Lyn, a member of the Src family tyrosine kinases previously implicated in P. aeruginosa infection, mediates both PIP3- enriched protrusion formation and aggregate internalization. Our results establish the first framework of principles that define P. aeruginosa transition to multicellular structures during inter- action with host cells. Agencia Nacional de Investigación e Innovación (ANII) Fogarty International Center, National Institutes of Health (NIH)

This paper demonstrates the influence of the trailing end of the piston, or inboard, pad on the propensity of a brake to generate audible squeal. The unique technique was employed to measure the dynamic centre of pressure at the pad/disc interface during a normal braking operation. This novel technique uses an embedded pressure sensitive film within the pad. The paper also presents the co-planar analysis of the pad/caliper contact regions and its influence on the position of the disk/pad “Centre of Pressure” (CoP). The analysis shows how the trailing end of the piston pad influences the position of the CoP and goes on to explain why the centre moves as the pad abutment vibrates against the abutment. The paper includes additional work with a 12 piston opposed caliper where the initial CoP may be varied both along the pad and radially. Results show a very definite movement of the centre of pressure as the brake pressure is increased.