The Hippo Pathway Component Wwc2 Is a Key Regulator of Embryonic Development and Angiogenesis in Mice Anke Hermann1,Guangmingwu2, Pavel I
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Request for Contract Update
DocuSign Envelope ID: 0E48A6C9-4184-4355-B75C-D9F791DFB905 Request for Contract Update Pursuant to the terms of contract number________________R142201 for _________________________ Office Furniture and Installation Contractor must notify and receive approval from Region 4 ESC when there is an update in the contract. No request will be officially approved without the prior authorization of Region 4 ESC. Region 4 ESC reserves the right to accept or reject any request. Allsteel Inc. hereby provides notice of the following update on (Contractor) this date April 17, 2019 . Instructions: Contractor must check all that may apply and shall provide supporting documentation. Requests received without supporting documentation will be returned. This form is not intended for use if there is a material change in operations, such as assignment, bankruptcy, change of ownership, merger, etc. Material changes must be submitted on a “Notice of Material Change to Vendor Contract” form. Authorized Distributors/Dealers Price Update Addition Supporting Documentation Deletion Supporting Documentation Discontinued Products/Services X Products/Services Supporting Documentation X New Addition Update Only X Supporting Documentation Other States/Territories Supporting Documentation Supporting Documentation Notes: Contractor may include other notes regarding the contract update here: (attach another page if necessary). Attached is Allsteel's request to add the following new product lines: Park, Recharge, and Townhall Collection along with the respective price -
PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
The Geometry of Nim Arxiv:1109.6712V1 [Math.CO] 30
The Geometry of Nim Kevin Gibbons Abstract We relate the Sierpinski triangle and the game of Nim. We begin by defining both a new high-dimensional analog of the Sierpinski triangle and a natural geometric interpretation of the losing positions in Nim, and then, in a new result, show that these are equivalent in each finite dimension. 0 Introduction The Sierpinski triangle (fig. 1) is one of the most recognizable figures in mathematics, and with good reason. It appears in everything from Pascal's Triangle to Conway's Game of Life. In fact, it has already been seen to be connected with the game of Nim, albeit in a very different manner than the one presented here [3]. A number of analogs have been discovered, such as the Menger sponge (fig. 2) and a three-dimensional version called a tetrix. We present, in the first section, a generalization in higher dimensions differing from the more typical simplex generalization. Rather, we define a discrete Sierpinski demihypercube, which in three dimensions coincides with the simplex generalization. In the second section, we briefly review Nim and the theory behind optimal play. As in all impartial games (games in which the possible moves depend only on the state of the game, and not on which of the two players is moving), all possible positions can be divided into two classes - those in which the next player to move can force a win, called N-positions, and those in which regardless of what the next player does the other player can force a win, called P -positions. -
Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
Notes Has Not Been Formally Reviewed by the Lecturer
6.896 Topics in Algorithmic Game Theory February 22, 2010 Lecture 6 Lecturer: Constantinos Daskalakis Scribe: Jason Biddle, Debmalya Panigrahi NOTE: The content of these notes has not been formally reviewed by the lecturer. It is recommended that they are read critically. In our last lecture, we proved Nash's Theorem using Broweur's Fixed Point Theorem. We also showed Brouwer's Theorem via Sperner's Lemma in 2-d using a limiting argument to go from the discrete combinatorial problem to the topological one. In this lecture, we present a multidimensional generalization of the proof from last time. Our proof differs from those typically found in the literature. In particular, we will insist that each step of the proof be constructive. Using constructive arguments, we shall be able to pin down the complexity-theoretic nature of the proof and make the steps algorithmic in subsequent lectures. In the first part of our lecture, we present a framework for the multidimensional generalization of Sperner's Lemma. A Canonical Triangulation of the Hypercube • A Legal Coloring Rule • In the second part, we formally state Sperner's Lemma in n dimensions and prove it using the following constructive steps: Colored Envelope Construction • Definition of the Walk • Identification of the Starting Simplex • Direction of the Walk • 1 Framework Recall that in the 2-dimensional case we had a square which was divided into triangles. We had also defined a legal coloring scheme for the triangle vertices lying on the boundary of the square. Now let us extend those concepts to higher dimensions. 1.1 Canonical Triangulation of the Hypercube We begin by introducing the n-simplex as the n-dimensional analog of the triangle in 2 dimensions as shown in Figure 1. -
Dissection of the Role of VIMP in Endoplasmic Reticulum-Associated
www.nature.com/scientificreports OPEN Dissection of the Role of VIMP in Endoplasmic Reticulum-Associated Degradation of CFTRΔF508 Received: 10 November 2017 Xia Hou1,2, Hongguang Wei1, Carthic Rajagopalan1, Hong Jiang1, Qingtian Wu2, Accepted: 6 March 2018 Khalequz Zaman3, Youming Xie4 & Fei Sun1 Published: xx xx xxxx Endoplasmic reticulum (ER)-associated protein degradation (ERAD) is an important quality control mechanism that eliminates misfolded proteins from the ER. The Derlin-1/VCP/VIMP protein complex plays an essential role in ERAD. Although the roles of Derlin-1 and VCP are relatively clear, the functional activity of VIMP in ERAD remains to be understood. Here we investigate the role of VIMP in the degradation of CFTRΔF508, a cystic fbrosis transmembrane conductance regulator (CFTR) mutant known to be a substrate of ERAD. Overexpression of VIMP markedly enhances the degradation of CFTRΔF508, whereas knockdown of VIMP increases its half-life. We demonstrate that VIMP is associated with CFTRΔF508 and the RNF5 E3 ubiquitin ligase (also known as RMA1). Thus, VIMP not only forms a complex with Derlin-1 and VCP, but may also participate in recruiting substrates and E3 ubiquitin ligases. We further show that blocking CFTRΔF508 degradation by knockdown of VIMP substantially augments the efect of VX809, a drug that allows a fraction of CFTRΔF508 to fold properly and mobilize from ER to cell surface for normal functioning. This study provides insight into the role of VIMP in ERAD and presents a potential target for the treatment of cystic fbrosis patients carrying the CFTRΔF508 mutation. Elimination of misfolded endoplasmic reticulum (ER) proteins by the ER-associated protein degradation (ERAD) pathway is an important physiological adaptation to ER stress1,2. -
Interval Vector Polytopes
Interval Vector Polytopes By Gabriel Dorfsman-Hopkins SENIOR HONORS THESIS ROSA C. ORELLANA, ADVISOR DEPARTMENT OF MATHEMATICS DARTMOUTH COLLEGE JUNE, 2013 Contents Abstract iv 1 Introduction 1 2 Preliminaries 4 2.1 Convex Polytopes . 4 2.2 Lattice Polytopes . 8 2.2.1 Ehrhart Theory . 10 2.3 Faces, Face Lattices and the Dual . 12 2.3.1 Faces of a Polytope . 12 2.3.2 The Face Lattice of a Polytope . 15 2.3.3 Duality . 18 2.4 Basic Graph Theory . 22 3IntervalVectorPolytopes 23 3.1 The Complete Interval Vector Polytope . 25 3.2 TheFixedIntervalVectorPolytope . 30 3.2.1 FlowDimensionGraphs . 31 4TheIntervalPyramid 38 ii 4.1 f-vector of the Interval Pyramid . 40 4.2 Volume of the Interval Pyramid . 45 4.3 Duality of the Interval Pyramid . 50 5 Open Questions 57 5.1 Generalized Interval Pyramid . 58 Bibliography 60 iii Abstract An interval vector is a 0, 1 -vector where all the ones appear consecutively. An { } interval vector polytope is the convex hull of a set of interval vectors in Rn.Westudy several classes of interval vector polytopes which exhibit interesting combinatorial- geometric properties. In particular, we study a class whose volumes are equal to the catalan numbers, another class whose legs always form a lattice basis for their affine space, and a third whose face numbers are given by the pascal 3-triangle. iv Chapter 1 Introduction An interval vector is a 0, 1 -vector in Rn such that the ones (if any) occur consecu- { } tively. These vectors can nicely and discretely model scheduling problems where they represent the length of an uninterrupted activity, and so understanding the combi- natorics of these vectors is useful in optimizing scheduling problems of continuous activities of certain lengths. -
Dysfunctional Mechanotransduction Through the YAP/TAZ/Hippo Pathway As a Feature of Chronic Disease
cells Review Dysfunctional Mechanotransduction through the YAP/TAZ/Hippo Pathway as a Feature of Chronic Disease 1, 2, 2,3, 4 Mathias Cobbaut y, Simge Karagil y, Lucrezia Bruno y, Maria Del Carmen Diaz de la Loza , Francesca E Mackenzie 3, Michael Stolinski 2 and Ahmed Elbediwy 2,* 1 Protein Phosphorylation Lab, Francis Crick Institute, London NW1 1AT, UK; [email protected] 2 Department of Biomolecular Sciences, Kingston University, Kingston-upon-Thames KT1 2EE, UK; [email protected] (S.K.); [email protected] (L.B.); [email protected] (M.S.) 3 Department of Chemical and Pharmaceutical Sciences, Kingston University, Kingston-upon-Thames KT1 2EE, UK; [email protected] 4 Epithelial Biology Lab, Francis Crick Institute, London NW1 1AT, UK; [email protected] * Correspondence: [email protected] These authors contribute equally to this work. y Received: 30 November 2019; Accepted: 4 January 2020; Published: 8 January 2020 Abstract: In order to ascertain their external environment, cells and tissues have the capability to sense and process a variety of stresses, including stretching and compression forces. These mechanical forces, as experienced by cells and tissues, are then converted into biochemical signals within the cell, leading to a number of cellular mechanisms being activated, including proliferation, differentiation and migration. If the conversion of mechanical cues into biochemical signals is perturbed in any way, then this can be potentially implicated in chronic disease development and processes such as neurological disorders, cancer and obesity. This review will focus on how the interplay between mechanotransduction, cellular structure, metabolism and signalling cascades led by the Hippo-YAP/TAZ axis can lead to a number of chronic diseases and suggest how we can target various pathways in order to design therapeutic targets for these debilitating diseases and conditions. -
Systematic Identification of Recognition Motifs for the Hub Protein
Published Online: 2 July, 2019 | Supp Info: http://doi.org/10.26508/lsa.201900366 Downloaded from life-science-alliance.org on 25 September, 2021 Research Article Systematic identification of recognition motifs for the hub protein LC8 Nathan Jespersen1 , Aidan Estelle1, Nathan Waugh1 , Norman E Davey2, Cecilia Blikstad3 , York-Christoph Ammon4, Anna Akhmanova4, Ylva Ivarsson3, David A Hendrix1,5, Elisar Barbar1 Hub proteins participate in cellular regulation by dynamic binding of extensively studied, including the dynein intermediate chain (IC) multiple proteins within interaction networks. The hub protein LC8 (Makokha et al, 2002; Benison et al, 2006; Nyarko & Barbar, 2011) and reversibly interacts with more than 100 partners through a flexible the transcription factor ASCIZ (Jurado et al, 2012; Zaytseva et al, 2014; pocket at its dimer interface. To explore the diversity of the LC8 Clark et al, 2018). In addition, expression patterns show that LC8 is partner pool, we screened for LC8 binding partners using a proteomic highly expressed across a wide variety of cell types (Petryszak et al, phage display library composed of peptides from the human pro- 2016) and is broadly distributed within individual cells (Chen et al, teome, which had no bias toward a known LC8 motif. Of the identified 2009; Wang et al, 2016). hits, we validated binding of 29 peptides using isothermal titration LC8 is an 89–amino acid homodimeric protein first identified as a calorimetry.Ofthe29peptides,19were entirely novel, and all had the subunit of the dynein motor complex. Colocalization and binding canonical TQT motif anchor. A striking observation is that numerous studies with dynein led to a common perception that LC8 functions peptides containing the TQT anchor do not bind LC8, indicating that as a dynein “cargo adaptor” to facilitate transport of dynein cargo residues outside of the anchor facilitate LC8 interactions. -
Specificity Landscapes Unmask Submaximal Binding Site Preferences of Transcription Factors
Specificity landscapes unmask submaximal binding site preferences of transcription factors Devesh Bhimsariaa,b,1, José A. Rodríguez-Martíneza,2, Junkun Panc, Daniel Rostonc, Elif Nihal Korkmazc, Qiang Cuic,3, Parameswaran Ramanathanb, and Aseem Z. Ansaria,d,4 aDepartment of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706; bDepartment of Electrical and Computer Engineering, University of Wisconsin–Madison, Madison, WI 53706; cDepartment of Chemistry, University of Wisconsin–Madison, Madison, WI 53706; and dThe Genome Center of Wisconsin, University of Wisconsin–Madison, Madison, WI 53706 Edited by Michael Levine, Princeton University, Princeton, NJ, and approved September 24, 2018 (received for review July 13, 2018) We have developed Differential Specificity and Energy Landscape Here, we report the development of Differential Specificity (DiSEL) analysis to comprehensively compare DNA–protein inter- and Energy Landscapes (DiSEL) to compare experimental actomes (DPIs) obtained by high-throughput experimental plat- platforms, computational methods, and interactomes of TFs, forms and cutting edge computational methods. While high-affinity especially those factors that bind identical consensus motifs. Our DNA binding sites are identified by most methods, DiSEL uncovered results reveal that (i) most high-throughput experimental plat- nuanced sequence preferences displayed by homologous transcription forms reliably identify high-affinity motifs but yield less reliable factors. Pairwise analysis of 726 DPIs uncovered homolog-specific dif- information on submaximal sites; (ii) with few exceptions, com- ferences at moderate- to low-affinity binding sites (submaximal sites). putational methods model DPIs with a focus on high-affinity DiSEL analysis of variants of 41 transcription factors revealed that sites; (iii) submaximal sites improve the annotation of biologi- many disease-causing mutations result in allele-specific changes in cally relevant binding sites across genomes; (iv) among members binding site preferences. -
Increased ACTL6A Occupancy Within Mswi/SNF Chromatin Remodelers
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.22.435873; this version posted March 22, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Increased ACTL6A Occupancy Within mSWI/SNF Chromatin Remodelers Drives Human Squamous Cell Carcinoma Chiung-Ying Chang1,2,7, Zohar Shipony3,7, Ann Kuo1,2, Kyle M. Loh4,5, William J. Greenleaf3,6, Gerald R. Crabtree1,2,5* 1Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA. 2Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA. 3Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA. 4Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA. 5Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA. 6Department of Applied Physics, Stanford University, Stanford, California 94305, USA. 7These authors contributed equally. *Corresponding author: Gerald R. Crabtree, [email protected] Summary Mammalian SWI/SNF (BAF) chromatin remodelers play dosage-sensitive roles in many human malignancies and neurologic disorders. The gene encoding the BAF subunit, ACTL6A, is amplified at an early stage in the development of squamous cell carcinomas (SCCs), but its oncogenic role remains unclear. Here we demonstrate that ACTL6A overexpression leads to its stoichiometric assembly into BAF complexes and drives its interaction and engagement with specific regulatory regions in the genome. In normal epithelial cells, ACTL6A was sub-stoichiometric to other BAF subunits. However, increased ACTL6A levels by ectopic expression or in SCC cells led to near-saturation of ACTL6A within BAF complexes. -
Sequential Evolutionary Operations of Trigonometric Simplex Designs For
SEQUENTIAL EVOLUTIONARY OPERATIONS OF TRIGONOMETRIC SIMPLEX DESIGNS FOR HIGH-DIMENSIONAL UNCONSTRAINED OPTIMIZATION APPLICATIONS Hassan Musafer Under the Supervision of Dr. Ausif Mahmood DISSERTATION SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIRMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOHPY IN COMPUTER SCIENCE AND ENGINEERING THE SCHOOL OF ENGINEERING UNIVERSITY OF BRIDGEPORT CONNECTICUT May, 2020 SEQUENTIAL EVOLUTIONARY OPERATIONS OF TRIGONOMETRIC SIMPLEX DESIGNS FOR HIGH-DIMENSIONAL UNCONSTRAINED OPTIMIZATION APPLICATIONS c Copyright by Hassan Musafer 2020 iii SEQUENTIAL EVOLUTIONARY OPERATIONS OF TRIGONOMETRIC SIMPLEX DESIGNS FOR HIGH-DIMENSIONAL UNCONSTRAINED OPTIMIZATION APPLICATIONS ABSTRACT This dissertation proposes a novel mathematical model for the Amoeba or the Nelder- Mead simplex optimization (NM) algorithm. The proposed Hassan NM (HNM) algorithm allows components of the reflected vertex to adapt to different operations, by breaking down the complex structure of the simplex into multiple triangular simplexes that work sequentially to optimize the individual components of mathematical functions. When the next formed simplex is characterized by different operations, it gives the simplex similar reflections to that of the NM algorithm, but with rotation through an angle determined by the collection of nonisometric features. As a consequence, the generating sequence of triangular simplexes is guaranteed that not only they have different shapes, but also they have different directions, to search the complex landscape of mathematical problems and to perform better performance than the traditional hyperplanes simplex. To test reliability, efficiency, and robustness, the proposed algorithm is examined on three areas of large- scale optimization categories: systems of nonlinear equations, nonlinear least squares, and unconstrained minimization. The experimental results confirmed that the new algorithm delivered better performance than the traditional NM algorithm, represented by a famous Matlab function, known as "fminsearch".