Hydrogel Models with Stiffness Gradients for Interrogating Pancreatic Cancer Cell Fate
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Development of Microfluidic Devices to Study Algal Chemotaxis and Long-Term Growth Dynamics" (2016)
Louisiana State University LSU Digital Commons LSU Master's Theses Graduate School 2016 Development of Microfluidic evD ices to Study Algal Chemotaxis and Long-Term Growth Dynamics Benjamin Seth Roberts Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_theses Part of the Chemical Engineering Commons Recommended Citation Roberts, Benjamin Seth, "Development of Microfluidic Devices to Study Algal Chemotaxis and Long-Term Growth Dynamics" (2016). LSU Master's Theses. 4496. https://digitalcommons.lsu.edu/gradschool_theses/4496 This Thesis is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Master's Theses by an authorized graduate school editor of LSU Digital Commons. For more information, please contact [email protected]. DEVELOPMENT OF MICROFLUIDIC DEVICES TO STUDY ALGAL CHEMOTAXIS AND LONG-TERM GROWTH DYNAMICS A Thesis Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Master of Science in The Cain Department of Chemical Engineering by Benjamin S. Roberts B.S., Mississippi State University, 2014 December 2016 TABLE OF CONTENTS ABSTRACT ................................................................................................................................... iii CHAPTER 1. INTRODUCTION ....................................................................................................1 -
Boards' Fodder
boards’ fodder Cosmeceuticals Contributed by Elisabeth Hurliman, MD, PhD; Jennifer Hayes, MD; Hilary Reich MD; and Sarah Schram, MD. INGREDIENT FUNCTION MECHANISM ASSOCIATIONS/SIDE EFFECTS Vitamin A/ Antioxidant (reduces free Affects gene transcription Comedolysis epidermal thickening, dermal Derivatives (retinal, radicals, lowers concentration differentiation and growth of regeneration, pigment lightening retinol, retinoic of matrix metalloproteinases cells in the skin acid, provitamin reduces collagen degradation) Side effects: Irritation, erythema, desquamation A, asthaxanthin, Normalizes follicular Elisabeth Hurliman, lutein) epithelial differentiation and keratinization MD, PhD, is a PGY-4 dermatology resident Vitamin C (L Secondary endogenous Ascorbic acid: necessary L-ascorbic acid + alpha-tocopherol (vitamin E)= ascorbic acid, antioxidant in skin cofactor for prolylhydroxylase UVA and UVB protection at University of tetrahexyldecyl and lysyl hydroxylase Minnesota department ascorbate) Lightens pigment Zinc, resveratrol, L-ergothioneine and tyrosine add of dermatology. (affects melanogenesis) L-ascorbic acid: scavenges to vitamin C bioavailability free oxygen radicals, Protects Vitamin E from oxidation stimulates collagen synthesis Improves skin texture and hydration May interrupt melanogenesis by interacting with copper ions Vitamin E/ Primary endogenous antioxidant Prevents lipid peroxidation; Alpha tocopherol is the most physiologically Tocopherols, in skin scavenges free oxygen active isomer Jennifer Hayes, MD, Tocotrienols -
Morphological Study of Cell Protrusions During Redirected Migration in Human Fibroblast Cells
MORPHOLOGICAL STUDY OF CELL PROTRUSIONS DURING REDIRECTED MIGRATION IN HUMAN FIBROBLAST CELLS Congyingzi Zhang A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2013 Committee: Dr. Carol Heckman, Advisor Dr. Roudabeh Jamasbi Dr. Peter Gorsevski ii ABSTRACT Carol A. Heckman, Advisor From the perspective of cell motility mechanisms, migration patterns arise from two opposing sources which can be viewed as forces. One, called intrinsic, maintains the cell persistence. The extrinsic arises from signals (repulsive or attractive) exerted by an external stimulus. The extrinsic force is stronger than the intrinsic, since it can overcome the intrinsic force and cause the cell to change direction. The current studies were designed to determine whether these forces were associated with different protrusions. I studied human fibroblast cells that collide with a haptotactic boundary between an adhesive substrate (germanium) and a non- adhesive substrate (plastic) in a chemokinesis system. The morphologies of cells migrating on the two substrates reflected the cells’ preference for the adhesive substrate. I measured the prevalence of various protrusions during the process of cells turning away from the boundary and reorienting their direction of travel. Classes that corresponded to protrusive features were identified by extracting latent factors from a number of primary, geometric variables, and included factor 4 (filopodia), factor 5 (cell mass displacement), and factor 7 (nascent neurites). The data showed that as cells moved further and further from the boundary, they had progressively lower values of factor 5. The correlation coefficient between the values is -0.4924. -
Negative Durotaxis: Cell Movement Toward Softer Environments
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.27.357178; this version posted October 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Negative durotaxis: cell movement toward softer environments Aleksi Isomursu1,*, Keun-Young Park2,*, Jay Hou3,*, Bo Cheng4,5,*, Ghaidan Shamsan3, Benjamin Fuller3, Jesse Kasim3, M. Mohsen Mahmoodi2, Tian Jian Lu6,7, Guy M. Genin4,5,8, Feng Xu4,5, Min Lin4,5,#, Mark Distefano2,#, Johanna Ivaska1,9,#, and David J. Odde3,# 1Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland 2Department of Chemistry, University of Minnesota, Minneapolis 55455, MN, USA 3Department of Biomedical Engineering, University of Minnesota, Minneapolis 55455, MN, USA 4The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China 5Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, P.R. China 6State Key Laboratory of Mechanics and Control of Mechanical Structures, Nanjing University of Aeronautics and Astronautics, NanjinG 210016, P.R. China 7MOE Key Laboratory of Multifunctional Materials and Structures, Xi’an JiaotonG University, Xi’an 710049, P.R. China 8NSF Science and TechnoloGy Center for EnGineerinG MechanobioloGy, WashinGton University in St. Louis, St. Louis 63130, MO, USA 9Department of Biochemistry, University of Turku, 20520 Turku, Finland *Equal contribution #Corresponding authors Email: [email protected] (D.J.O.); [email protected] (J.I.); [email protected] (M.D.); [email protected] (M.L.) Abstract: Durotaxis – the ability of cells to sense and migrate along stiffness gradients – is important for embryonic development and has been implicated in pathologies including fibrosis and cancer. -
Enzymatic Encoding Methods for Efficient Synthesis Of
(19) TZZ__T (11) EP 1 957 644 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 15/10 (2006.01) C12Q 1/68 (2006.01) 01.12.2010 Bulletin 2010/48 C40B 40/06 (2006.01) C40B 50/06 (2006.01) (21) Application number: 06818144.5 (86) International application number: PCT/DK2006/000685 (22) Date of filing: 01.12.2006 (87) International publication number: WO 2007/062664 (07.06.2007 Gazette 2007/23) (54) ENZYMATIC ENCODING METHODS FOR EFFICIENT SYNTHESIS OF LARGE LIBRARIES ENZYMVERMITTELNDE KODIERUNGSMETHODEN FÜR EINE EFFIZIENTE SYNTHESE VON GROSSEN BIBLIOTHEKEN PROCEDES DE CODAGE ENZYMATIQUE DESTINES A LA SYNTHESE EFFICACE DE BIBLIOTHEQUES IMPORTANTES (84) Designated Contracting States: • GOLDBECH, Anne AT BE BG CH CY CZ DE DK EE ES FI FR GB GR DK-2200 Copenhagen N (DK) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • DE LEON, Daen SK TR DK-2300 Copenhagen S (DK) Designated Extension States: • KALDOR, Ditte Kievsmose AL BA HR MK RS DK-2880 Bagsvaerd (DK) • SLØK, Frank Abilgaard (30) Priority: 01.12.2005 DK 200501704 DK-3450 Allerød (DK) 02.12.2005 US 741490 P • HUSEMOEN, Birgitte Nystrup DK-2500 Valby (DK) (43) Date of publication of application: • DOLBERG, Johannes 20.08.2008 Bulletin 2008/34 DK-1674 Copenhagen V (DK) • JENSEN, Kim Birkebæk (73) Proprietor: Nuevolution A/S DK-2610 Rødovre (DK) 2100 Copenhagen 0 (DK) • PETERSEN, Lene DK-2100 Copenhagen Ø (DK) (72) Inventors: • NØRREGAARD-MADSEN, Mads • FRANCH, Thomas DK-3460 Birkerød (DK) DK-3070 Snekkersten (DK) • GODSKESEN, -
Mutant IDH, (R)-2-Hydroxyglutarate, and Cancer
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer Julie-Aurore Losman1 and William G. Kaelin Jr.1,2,3 1Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA; 2Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Mutations in metabolic enzymes, including isocitrate whether altered cellular metabolism is a cause of cancer dehydrogenase 1 (IDH1) and IDH2, in cancer strongly or merely an adaptive response of cancer cells in the face implicate altered metabolism in tumorigenesis. IDH1 of accelerated cell proliferation is still a topic of some and IDH2 catalyze the interconversion of isocitrate and debate. 2-oxoglutarate (2OG). 2OG is a TCA cycle intermediate The recent identification of cancer-associated muta- and an essential cofactor for many enzymes, including tions in three metabolic enzymes suggests that altered JmjC domain-containing histone demethylases, TET cellular metabolism can indeed be a cause of some 5-methylcytosine hydroxylases, and EglN prolyl-4-hydrox- cancers (Pollard et al. 2003; King et al. 2006; Raimundo ylases. Cancer-associated IDH mutations alter the enzymes et al. 2011). Two of these enzymes, fumarate hydratase such that they reduce 2OG to the structurally similar (FH) and succinate dehydrogenase (SDH), are bone fide metabolite (R)-2-hydroxyglutarate [(R)-2HG]. Here we tumor suppressors, and loss-of-function mutations in FH review what is known about the molecular mechanisms and SDH have been identified in various cancers, in- of transformation by mutant IDH and discuss their im- cluding renal cell carcinomas and paragangliomas. -
Page Numbers in Bold Indicate Main Discus- Sion of Topic. Page Numbers
168397_P489-520.qxd7.0:34 Index 6-2-04 26p 2010.4.5 10:03 AM Page 489 source of, 109, 109f pairing with thymine, 396f, 397, 398f in tricarboxylic acid cycle, 109–111, 109f Adenine arabinoside (vidarabine, araA), 409 Acetyl CoA-ACP acetyltransferase, 184 Adenine phosphoribosyltransferase (APRT), Index Acetyl CoA carboxylase, 183, 185f, 190 296, 296f in absorptive/fed state, 324 Adenosine deaminase (ADA), 299 allosteric activation of, 183–184, 184f deficiency of, 298, 300f, 301–302 allosteric inactivation of, 183, 184f gene therapy for, 485, 486f dephosphorylation of, 184 Adenosine diphosphate (ADP) in fasting, 330 in ATP synthesis, 73, 77–78, 78f Page numbers in bold indicate main discus- hormonal regulation of, 184, 184f isocitrate dehydrogenase activation by, sion of topic. Page numbers followed by f long-term regulation of, 184 112 denote figures. “See” cross-references direct phosphorylation of, 183–184 transport of, to inner mitochondrial short-term regulation of, 183–184, 184f membrane, 79 the reader to the synonymous term. “See Acetyl CoA carboxylase-2 (ACC2), 191 in tricarboxylic acid cycle regulation, 114, also” cross-references direct the reader to N4-Acetylcytosine, 292f 114f related topics. [Note: Positional and configura- N-Acetyl-D-glucosamine, 142 in urea cycle, 255–256 N-Acetylgalactosamine (GalNAc), 160, 168 ribosylation, 95 tional designations in chemical names (for N-Acetylglucosamindase deficiency, 164f Adenosine monophosphate (AMP; also called example, “3-“, “α”, “N-“, “D-“) are ignored in N-Acetylglucosamine (GlcNAc), -
Bimodal Rheotactic Behavior Reflects Flagellar Beat Asymmetry in Human Sperm Cells
Bimodal rheotactic behavior reflects flagellar beat asymmetry in human sperm cells Anton Bukatina,b,1, Igor Kukhtevichb,c,1, Norbert Stoopd,1, Jörn Dunkeld,2, and Vasily Kantslere aSt. Petersburg Academic University, St. Petersburg 194021, Russia; bInstitute for Analytical Instrumentation of the Russian Academy of Sciences, St. Petersburg 198095, Russia; cITMO University, St. Petersburg 197101, Russia; dDepartment of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307; and eDepartment of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom Edited by Charles S. Peskin, New York University, New York, NY, and approved November 9, 2015 (received for review July 30, 2015) Rheotaxis, the directed response to fluid velocity gradients, has whether this effect is of mechanical (20) or hydrodynamic (21, been shown to facilitate stable upstream swimming of mamma- 22) origin. Experiments (23) show that the alga’s reorientation lian sperm cells along solid surfaces, suggesting a robust physical dynamics can lead to localization in shear flow (24, 25), with mechanism for long-distance navigation during fertilization. How- potentially profound implications in marine ecology. In contrast ever, the dynamics by which a human sperm orients itself relative to taxis in multiflagellate organisms (2, 5, 18, 26, 27), the navi- to an ambient flow is poorly understood. Here, we combine micro- gation strategies of uniflagellate cells are less well understood. fluidic experiments with mathematical modeling and 3D flagellar beat For instance, it was discovered only recently that uniflagellate reconstruction to quantify the response of individual sperm cells in marine bacteria, such as Vibrio alginolyticus and Pseudoalteromonas time-varying flow fields. Single-cell tracking reveals two kinematically haloplanktis, use a buckling instability in their lone flagellum to distinct swimming states that entail opposite turning behaviors under change their swimming direction (28). -
Meta-Analyses of Expression Profiling Data in the Postmortem
META-ANALYSES OF EXPRESSION PROFILING DATA IN THE POSTMORTEM HUMAN BRAIN by Meeta Mistry B.Sc., McMaster University, 2005 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2012 © Meeta Mistry, 2012 Abstract Schizophrenia is a severe psychiatric illness for which the precise etiology remains unknown. Studies using postmortem human brain have become increasingly important in schizophrenia research, providing an opportunity to directly investigate the diseased brain tissue. Gene expression profiling technologies have been used by a number of groups to explore the postmortem human brain and seek genes which show changes in expression correlated with schizophrenia. While this has been a valuable means of generating hypotheses, there is a general lack of consensus in the findings across studies. Expression profiling of postmortem human brain tissue is difficult due to the effect of various factors that can confound the data. The first aim of this thesis was to use control postmortem human cortex for identification of expression changes associated with several factors, specifically: age, sex, brain pH and postmortem interval. I conducted a meta-analysis across the control arm of eleven microarray datasets (representing over 400 subjects), and identified a signature of genes associated with each factor. These genes provide critical information towards the identification of problematic genes when investigating postmortem human brain in schizophrenia and other neuropsychiatric illnesses. The second aim of this thesis was to evaluate gene expression patterns in the prefrontal cortex associated with schizophrenia by exploring two methods of analysis: differential expression and coexpression. -
A Hybrid Computational Model for Collective Cell Durotaxis
Biomechanics and Modeling in Mechanobiology https://doi.org/10.1007/s10237-018-1010-2 ORIGINAL PAPER A hybrid computational model for collective cell durotaxis Jorge Escribano1 · Raimon Sunyer2,5 · María Teresa Sánchez3 · Xavier Trepat2,4,5,6 · Pere Roca-Cusachs2,4 · José Manuel García-Aznar1 Received: 13 September 2017 / Accepted: 17 February 2018 © Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Collective cell migration is regulated by a complex set of mechanical interactions and cellular mechanisms. Collective migration emerges from mechanisms occurring at single cell level, involving processes like contraction, polymerization and depolymerization, of cell–cell interactions and of cell–substrate adhesion. Here, we present a computational framework which simulates the dynamics of this emergent behavior conditioned by substrates with stiffness gradients. The computational model reproduces the cell’s ability to move toward the stiffer part of the substrate, process known as durotaxis. It combines the continuous formulation of truss elements and a particle-based approach to simulate the dynamics of cell–matrix adhesions and cell–cell interactions. Using this hybrid approach, researchers can quickly create a quantitative model to understand the regulatory role of different mechanical conditions on the dynamics of collective cell migration. Our model shows that durotaxis occurs due to the ability of cells to deform the substrate more in the part of lower stiffness than in the stiffer part. This effect explains why cell collective movement is more effective than single cell movement in stiffness gradient conditions. In addition, we numerically evaluate how gradient stiffness properties, cell monolayer size and force transmission between cells and extracellular matrix are crucial in regulating durotaxis. -
Engineering 3D Systems with Tunable Mechanical Properties to Mimic the Tumor Microenvironment Shalini Raj Unnikandam Veettil Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2018 Engineering 3D systems with tunable mechanical properties to mimic the tumor microenvironment Shalini Raj Unnikandam Veettil Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Chemical Engineering Commons Recommended Citation Unnikandam Veettil, Shalini Raj, "Engineering 3D systems with tunable mechanical properties to mimic the tumor microenvironment" (2018). Graduate Theses and Dissertations. 17339. https://lib.dr.iastate.edu/etd/17339 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Engineering 3D systems with tunable mechanical properties to mimic the tumor microenvironment by Shalini Raj Unnikandam Veettil A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Chemical Engineering Program of Study Committee: Ian C Schneider, Major Professor Kaitlin Bratlie Michael Bartlett The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2018 Copyright © Shalini Raj Unnikandam Veettil, 2018. All rights reserved. ii DEDICATION This thesis is dedicated to my family and friends who have been a great source of support. -
Hypoxia-Inducible Factors and RAB22A Mediate Formation of Microvesicles That Stimulate Breast Cancer Invasion and Metastasis
Hypoxia-inducible factors and RAB22A mediate formation of microvesicles that stimulate breast cancer invasion and metastasis Ting Wanga,b, Daniele M. Gilkesb,c, Naoharu Takanob,c, Lisha Xiangb,c, Weibo Luob,d, Corey J. Bishope, Pallavi Chaturvedib,c, Jordan J. Greene, and Gregg L. Semenzab,c,d,f,g,h,i,1 aDepartment of Hematology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; and bVascular Program, Institute for Cell Engineering, cMcKusick-Nathans Institute of Genetic Medicine, and Departments of dBiological Chemistry, eBiomedical Engineering, fOncology, gPediatrics, hMedicine, and iRadiation Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 Contributed by Gregg L. Semenza, May 30, 2014 (sent for review May 2, 2014) Extracellular vesicles such as exosomes and microvesicles (MVs) melanoma cells into the peripheral blood of mice induced are shed by cancer cells, are detected in the plasma of cancer prometastatic behavior of bone marrow cells, and the small patients, and promote cancer progression, but the molecular mech- GTPase RAB27A was required for exosome biogenesis in mel- anisms regulating their production are not well understood. Intra- anoma cells (10). In HeLa cells, RAB27A and RAB27B were tumoral hypoxia is common in advanced breast cancers and each required for exosome biogenesis, based on different loss-of- is associated with an increased risk of metastasis and patient function phenotypes (11). RAB27A loss of function in 4T1 breast mortality that is mediated in part by the activation of hypoxia- cancer cells inhibited both primary tumor growth and lung me- inducible factors (HIFs). In this paper, we report that exposure of tastasis (12).