17 Cell Differentiation and Gene Expression Investigation a N D M O D E L I N G • 1–2 C L a S S S E S S I O N S
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Introduction to the Cell Cell History Cell Structures and Functions
Introduction to the cell cell history cell structures and functions CK-12 Foundation December 16, 2009 CK-12 Foundation is a non-profit organization with a mission to reduce the cost of textbook materials for the K-12 market both in the U.S. and worldwide. Using an open-content, web-based collaborative model termed the “FlexBook,” CK-12 intends to pioneer the generation and distribution of high quality educational content that will serve both as core text as well as provide an adaptive environment for learning. Copyright ©2009 CK-12 Foundation This work is licensed under the Creative Commons Attribution-Share Alike 3.0 United States License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/us/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA. Contents 1 Cell structure and function dec 16 5 1.1 Lesson 3.1: Introduction to Cells .................................. 5 3 www.ck12.org www.ck12.org 4 Chapter 1 Cell structure and function dec 16 1.1 Lesson 3.1: Introduction to Cells Lesson Objectives • Identify the scientists that first observed cells. • Outline the importance of microscopes in the discovery of cells. • Summarize what the cell theory proposes. • Identify the limitations on cell size. • Identify the four parts common to all cells. • Compare prokaryotic and eukaryotic cells. Introduction Knowing the make up of cells and how cells work is necessary to all of the biological sciences. Learning about the similarities and differences between cell types is particularly important to the fields of cell biology and molecular biology. -
Cell Growth-Regulated Expression of Mammalian MCM5 and MCM6 Genes Mediated by the Transcription Factor E2F
Oncogene (1999) 18, 2299 ± 2309 ã 1999 Stockton Press All rights reserved 0950 ± 9232/99 $12.00 http://www.stockton-press.co.uk/onc Cell growth-regulated expression of mammalian MCM5 and MCM6 genes mediated by the transcription factor E2F Kiyoshi Ohtani1, Ritsuko Iwanaga1, Masataka Nakamura*,1, Masa-aki Ikeda2, Norikazu Yabuta3, Hiromichi Tsuruga3 and Hiroshi Nojima3 1Human Gene Sciences Center, Tokyo Medical and Dental University, Tokyo 113-8510, Japan 2Department of Developmental Biology, Graduate School of Dentistry, Tokyo Medical and Dental University, Tokyo 113-8549, Japan; 3Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan Initiation of DNA replication requires the function of family (MCM2-7) that have been identi®ed in yeast, MCM gene products, which participate in ensuring that Xenopus, and human. Mcm proteins seem to regulate DNA replication occurs only once in the cell cycle. the initiation at the replication origin where the loading Expression of all mammalian genes of the MCM family of the proteins onto the origin recognition complex is induced by growth stimulation, unlike yeast, and the (ORC) is regulated by Cdc6 and cyclin-dependent mRNA levels peak at G1/S boundary. In this study, we kinases (Donovan et al., 1997; Tanaka et al., 1997). examined the transcriptional activities of isolated human However, the mechanism(s) by which Mcm proteins MCM gene promoters. Human MCM5 and MCM6 control the initiation of DNA replication remains promoters with mutation in the E2F sites failed in unclear. promoter regulation following serum stimulation and Xenopus Mcm proteins seem to be able to access exogenous E2F expression. -
Zinc Fingers and a Green Thumb: Manipulating Gene Expression in Plants Segal, Stege and Barbas 165
163 Zinc fingers and a green thumb: manipulating gene expression in plants David J Segaly, Justin T Stegez and Carlos F Barbas IIIç Artificial transcription factors can be rapidly constructed A variety of techniques have been developed to manip- from predefined zinc-finger modules to regulate virtually any ulate gene expression in plants. Increased expression of gene. Stable, heritable up- and downregulation of endogenous genes is most commonly achieved through endogenous genes has been demonstrated in transgenic transgene overexpression [1]. The introduction of tissue- plants. These advances promise new approaches for creating specific and inducible promoters has improved the utility functional knockouts and conditional overexpression, and of this approach, and efficient and robust plant transforma- for other gene discovery and manipulation applications in tion techniques have made the construction of transgenes plants. a relatively routine task. However, variable expression and co-suppression of transgenes often complicate this process. Addresses Furthermore, transgenes cannot accommodate alternative ÃThe Skaggs Institute for Chemical Biology and the Department of splicing, which may be important for the appropriate Molecular Biology, The Scripps Research Institute, La Jolla, function of some transgenes [2]. California 92037, USA yDepartment of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, USA Reducing or eliminating the expression of a gene in plants zDiversa Corporation, San Diego, California 92121, USA is not as simple as overexpressing a gene. Gene disruption §The Scripps Research Institute, BCC-550, North Torrey Pines Road, by homologous recombination, tDNA insertions and che- La Jolla, California 92037, USA mical mutagenesis has been used successfully, but these e-mail: [email protected] Correspondence: Carlos F Barbas III approaches are inefficient and time-consuming technolo- gies. -
Creating a Census of Human Cells
XO FILES SCIENCE eXtraordinary Opportunity PHILANTHROPY ALLIANCE Creating a Census of Human Cells For the first time, new techniques make possible a systematic description of the myriad types of cells in the human body that underlie both health and disease. Aviv Regev Imagine you had a way to cure cancer that involved taking a molecule from a tumor and engineering the body’s immune cells to recognize and kill any cell with that molecule. But before you could apply this approach, you would need to be sure that no healthy cell also expressed that molecule. Given the 20 trillion cells in a human body, how would you do that? This is not a hypothetical example, but was one recently posed to our laboratory. More fundamentally, without a map of different cell types and where they are found within the body, how could you systematically study changes in the map associated with different diseases, or High resolution images of retinal tissue from the human eye, showing ganglion cells (in green). The circular cell body is attached to thin dendrites on which nerve synapses form—in different understand where genes associated with tissue layers depending on the cell type and function. Credit: Lab of Joshua Sanes, Harvard. disease are active in our body or analyze the regulatory mechanisms that govern the production of different cell types, or genetic profile of an individual cell— proteins they use and that information sort out how different cell types combine identifying which genes are turned synthesized with the location into an to form specific tissues? on, actively making proteins. -
Robustness and Timing of Cellular Differentiation Through Population-Based Symmetry Breaking
AR TI CLE Robustness AND TIMING OF CELLULAR DIFFERENTIATION THROUGH population-based SYMMETRY BREAKING Angel StanoeV1 | Christian Schröter1 | Aneta KOSESKA1∗ 1Department OF Systemic Cell Biology, Max Planck Institute OF Molecular PhYSIOLOGY, Although COORDINATED BEHAVIOR OF MULTICELLULAR ORGANISMS Dortmund, GermanY RELIES ON INTERCELLULAR communication, THE DYNAMICAL mech- Correspondence ANISM THAT UNDERLIES SYMMETRY BREAKING IN HOMOGENEOUS Email: populations, THEREBY GIVING RISE TO HETEROGENEOUS CELL TYPES ∗[email protected] REMAINS UNCLEAR. In CONTRAST TO THE PREVALENT cell-intrinsic VIEW OF DIFFERENTIATION WHERE MULTISTABILITY ON THE SINGLE CELL LEVEL IS A NECESSARY pre-requisite, WE PROPOSE THAT het- EROGENEOUS CELLULAR IDENTITIES EMERGE AND ARE MAINTAINED COOPERATIVELY ON A POPULATION LEVel. Identifying A GENERIC SYMMETRY BREAKING mechanism, WE DEMONSTRATE THAT ROBUST PROPORTIONS BETWEEN DIFFERENTIATED CELL TYPES ARE INTRINSIC FEATURES OF THIS INHOMOGENEOUS STEADY STATE solution. Crit- ICAL ORGANIZATION IN THE VICINITY OF THE SYMMETRY BREAKING BIFURCATION ON THE OTHER hand, SUGGESTS THAT TIMING OF cel- LULAR DIFFERENTIATION EMERGES FOR GROWING POPULATIONS IN A self-organized MANNER. Setting A CLEAR DISTINCTION BETWEEN pre-eXISTING ASYMMETRIES AND SYMMETRY BREAKING EVents, WE THUS DEMONSTRATE THAT EMERGENT SYMMETRY breaking, IN CONJUNCTION WITH ORGANIZATION NEAR CRITICALITY NECESSARILY LEADS TO ROBUSTNESS AND ACCURACY DURING DEVelopment. KEYWORDS SYMMETRY breaking; differentiation; INHOMOGENEOUS STEADY STATE Abbreviations: -
A Concise Review on the Classification and Nomenclature of Stem Cells Kök Hücrelerinin S›N›Fland›R›Lmas› Ve Isimlendirilmesine Iliflkin K›Sa Bir Derleme
Review 57 A concise review on the classification and nomenclature of stem cells Kök hücrelerinin s›n›fland›r›lmas› ve isimlendirilmesine iliflkin k›sa bir derleme Alp Can Ankara University Medical School, Department of Histology and Embryology, Ankara, Turkey Abstract Stem cell biology and regenerative medicine is a relatively young field. However, in recent years there has been a tremen- dous interest in stem cells possibly due to their therapeutic potential in disease states. As a classical definition, a stem cell is an undifferentiated cell that can produce daughter cells that can either remain a stem cell in a process called self-renew- al, or commit to a specific cell type via the initiation of a differentiation pathway leading to the production of mature progeny cells. Despite this acknowledged definition, the classification of stem cells has been a perplexing notion that may often raise misconception even among stem cell biologists. Therefore, the aim of this brief review is to give a conceptual approach to classifying the stem cells beginning from the early morula stage totipotent embryonic stem cells to the unipotent tissue-resident adult stem cells, also called tissue-specific stem cells. (Turk J Hematol 2008; 25: 57-9) Key words: Stem cells, embryonic stem cells, tissue-specific stem cells, classification, progeny. Özet Kök hücresi biyolojisi ve onar›msal t›p görece yeni alanlard›r. Buna karfl›n, son y›llarda çeflitli hastal›klarda tedavi amac›yla kullan›labilme potansiyelleri nedeniyle kök hücrelerine ola¤anüstü bir ilgi art›fl› vard›r. Klasik tan›m›yla kök hücresi, kendini yenileme ad› verilen mekanizmayla farkl›laflmadan kendini ço¤altan veya bir dizi farkl›laflma aflamas›ndan geçerek olgun hücrelere dönüflebilen hücrelerdir. -
Chapter 12 Gene Expression and Regulation
PYF12 3/21/05 8:04 PM Page 191 Chapter 12 Gene expression and regulation Bacterial genomes usually contain several thousand different genes. Some of the gene products are required by the cell under all growth conditions and are called house- keeping genes. These include the genes that encode such proteins as DNA poly- merase, RNA polymerase, and DNA gyrase. Many other gene products are required under specific growth conditions. These include enzymes that synthesize amino acids, break down specific sugars, or respond to a specific environmental condition such as DNA damage. Housekeeping genes must be expressed at some level all of the time. Frequently, as the cell grows faster, more of the housekeeping gene products are needed. Even under very slow growth, some of each housekeeping gene product is made. The gene prod- ucts required for specific growth conditions are not needed all of the time. These genes are frequently expressed at extremely low levels, or not expressed at all when they are not needed and yet made when they are needed. This chapter will examine gene regulation or how bacteria regulate the expression of their genes so that the genes that are being expressed meet the needs of the cell for a specific growth condition. Gene regulation can occur at three possible places in the production of an active gene product. First, the transcription of the gene can be regulated. This is known as transcriptional regulation. When the gene is transcribed and how much it is transcribed influences the amount of gene product that is made. Second, if the gene encodes a protein, it can be regulated at the translational level. -
Gene Expression: Layers of Gene Regulation
RESEARCH HIGHLIGHTS GENE EXPRESSION methylation. Spearman’s rank cor- relation between methylation levels Layers of gene regulation (within 50 kb on either side of the transcription start site) and alterna- A new study investigates genetic and expression and DNA methylation lev- tive splicing levels show that, for epigenetic influences on genome els often overlap functional elements. many of the genes tested, there is a regulation and alternative splicing, Across cell types, expression quantita- significant association. Of note, many and highlights the tissue specificity of tive trait loci (eQTLs) are enriched in of the associations between DNA some of these interactions. DNase I-hypersensitive sites, whereas methylation and alternative splicing In a previous study, the researchers methylation QTLs (mQTLs) are are cell type-specific, illustrating examined the relationship between enriched in enhancers and insulators. another layer of cellular variability. genetic variation, DNA methyation Their statistical analyses show that, A complex relationship between and gene expression using samples generally, genetic variation has a more DNA methylation and gene expres- from the GenCord cohort that were consistent effect on gene expres- sion is beginning to emerge. This derived from umbilical cords of 204 sion across cell types, although the study further defines the roles of newborn children. They genotyped strength of the effect can be variable. genomic and epigenomic variation 2.5 million single-nucleotide poly- However, the effects of epigenetic in determining cellular phenotypes, morphisms (SNPs), assayed the meth- variation on gene expression are more and the mechanisms by which these ylation levels of 482,421 CpG sites tissue-specific. Methylation sites effects might occur. -
How Are Protein Products Made from a Gene?
How are protein products made from a gene? Copyright 2016 by the Rector and Visitors of the University of Virginia How are protein products made from a gene? Step 1: Deoxyribonucleic acid (DNA) is stored within the compartment of the cell called the nucleus. Nucleus DNA is a sequence made up of building blocks called nucleotides (more information can be found DNA in “What is some basic information about DNA?”). RNA When a gene is expressed, the DNA opens up and is transcribed into RNA; this step is called transcription. Cytoplasm Copyright 2016 by the Rector and Visitors of the University of Virginia How are protein products made from a gene? Step 2: Nucleus Ribonucleic acid (RNA) is created from transcribing DNA. DNA The RNA is exported from the nucleus into RNA the large compartment of the cell called the cytoplasm. A structure called the ribosome will read the RNA sequence; this step is called translation. protein ribosome In this step, an amino acid sequence will be Cytoplasm generated. There are 20 amino acids used to make proteins (more details about DNA, RNA and amino acids can be found in “What is some basic information about DNA?”, “What is transcription?” and “What is translation?”). Copyright 2016 by the Rector and Visitors of the University of Virginia How are protein products made from a gene? Nucleus Step 3: Once the amino acid sequence is DNA generated, the molecule will fold into a three-dimensional (3-D) RNA structure. The protein may go through other processing, but essentially is ready protein to perform its function. -
Cell Life Cycle and Reproduction the Cell Cycle (Cell-Division Cycle), Is a Series of Events That Take Place in a Cell Leading to Its Division and Duplication
Cell Life Cycle and Reproduction The cell cycle (cell-division cycle), is a series of events that take place in a cell leading to its division and duplication. The main phases of the cell cycle are interphase, nuclear division, and cytokinesis. Cell division produces two daughter cells. In cells without a nucleus (prokaryotic), the cell cycle occurs via binary fission. Interphase Gap1(G1)- Cells increase in size. The G1checkpointcontrol mechanism ensures that everything is ready for DNA synthesis. Synthesis(S)- DNA replication occurs during this phase. DNA Replication The process in which DNA makes a duplicate copy of itself. Semiconservative Replication The process in which the DNA molecule uncoils and separates into two strands. Each original strand becomes a template on which a new strand is constructed, resulting in two DNA molecules identical to the original DNA molecule. Gap 2(G2)- The cell continues to grow. The G2checkpointcontrol mechanism ensures that everything is ready to enter the M (mitosis) phase and divide. Mitotic(M) refers to the division of the nucleus. Cell growth stops at this stage and cellular energy is focused on the orderly division into daughter cells. A checkpoint in the middle of mitosis (Metaphase Checkpoint) ensures that the cell is ready to complete cell division. The final event is cytokinesis, in which the cytoplasm divides and the single parent cell splits into two daughter cells. Reproduction Cellular reproduction is a process by which cells duplicate their contents and then divide to yield multiple cells with similar, if not duplicate, contents. Mitosis Mitosis- nuclear division resulting in the production of two somatic cells having the same genetic complement (genetically identical) as the original cell. -
Deciphering Genetic Determinants of Cell Growth by Single-Cell RNA Sequencing Deregulated Growth Is a Hallmark of Human Diseases
Deciphering genetic determinants of cell growth by single-cell RNA sequencing Deregulated growth is a hallmark of human diseases such as cancer. A wide range of therapeutic approaches target proliferating cells effectively through inhibition of pathways related to growth and division. However, cells can often escape arrest due to the genetic and phenotypic heterogeneity present in cancer cell populations leading to relapse of the disease. Likewise, heterogeneity in gene expression makes treatment of persistent microbial infections an important challenge for human health. Identifying genetic and non-genetic features that can drive individual cells to overcome growth inhibition is therefore required to understand disease progression and resistance. Recent experimental protocols made it possible to characterise the transcriptomes and genotypes of single cells simultaneously. These opened the door to investigate the dynamics and heterogeneity of gene expression in population of cells with variable genotypes. These methods are technically challenging, generate large amounts of complex data, and require the development of state-of-the-art computational methods for their analysis. Yet, when coupled with mathematical modelling of cell physiology, these single cells approaches have an unprecedented potential to unravel complex genetic and gene expression programmes that underlie growth dynamics of cell populations. This project aims at: i) understanding the genetic basis of cell growth under conditions were gene expression or proliferation are compromised by associating high fitness genotypes to transcriptome signatures in single cells, ii) develop computational tools to integrate single-cell and population level genotyping and gene expression data, iii) improve selected aspect of the laboratory single-cell RNA-seq protocol to improve data quality. -
How Genes Work
Help Me Understand Genetics How Genes Work Reprinted from MedlinePlus Genetics U.S. National Library of Medicine National Institutes of Health Department of Health & Human Services Table of Contents 1 What are proteins and what do they do? 1 2 How do genes direct the production of proteins? 5 3 Can genes be turned on and off in cells? 7 4 What is epigenetics? 8 5 How do cells divide? 10 6 How do genes control the growth and division of cells? 12 7 How do geneticists indicate the location of a gene? 16 Reprinted from MedlinePlus Genetics (https://medlineplus.gov/genetics/) i How Genes Work 1 What are proteins and what do they do? Proteins are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of thebody’s tissues and organs. Proteins are made up of hundreds or thousands of smaller units called amino acids, which are attached to one another in long chains. There are 20 different types of amino acids that can be combined to make a protein. The sequence of amino acids determineseach protein’s unique 3-dimensional structure and its specific function. Aminoacids are coded by combinations of three DNA building blocks (nucleotides), determined by the sequence of genes. Proteins can be described according to their large range of functions in the body, listed inalphabetical order: Antibody. Antibodies bind to specific foreign particles, such as viruses and bacteria, to help protect the body. Example: Immunoglobulin G (IgG) (Figure 1) Enzyme.