Literature DB >> 20018695

A feeling for the numbers in biology.

Rob Phillips1, Ron Milo.   

Abstract

Although the quantitative description of biological systems has been going on for centuries, recent advances in the measurement of phenomena ranging from metabolism to gene expression to signal transduction have resulted in a new emphasis on biological numeracy. This article describes the confluence of two different approaches to biological numbers. First, an impressive array of quantitative measurements make it possible to develop intuition about biological numbers ranging from how many gigatons of atmospheric carbon are fixed every year in the process of photosynthesis to the number of membrane transporters needed to provide sugars to rapidly dividing Escherichia coli cells. As a result of the vast array of such quantitative data, the BioNumbers web site has recently been developed as a repository for biology by the numbers. Second, a complementary and powerful tradition of numerical estimates familiar from the physical sciences and canonized in the so-called "Fermi problems" calls for efforts to estimate key biological quantities on the basis of a few foundational facts and simple ideas from physics and chemistry. In this article, we describe these two approaches and illustrate their synergism in several particularly appealing case studies. These case studies reveal the impact that an emphasis on numbers can have on important biological questions.

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Year:  2009        PMID: 20018695      PMCID: PMC2799844          DOI: 10.1073/pnas.0907732106

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  26 in total

1.  Receptor sensitivity in bacterial chemotaxis.

Authors:  Victor Sourjik; Howard C Berg
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-11       Impact factor: 11.205

2.  Genetic Effects of Ultraviolet Radiation in Maize. IV. Comparison of Monochromatic Radiations.

Authors:  L J Stadler; F M Uber
Journal:  Genetics       Date:  1942-01       Impact factor: 4.562

Review 3.  Can improvement in photosynthesis increase crop yields?

Authors:  Stephen P Long; Xin-Guang Zhu; Shawna L Naidu; Donald R Ort
Journal:  Plant Cell Environ       Date:  2006-03       Impact factor: 7.228

4.  STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES : INDUCTION OF TRANSFORMATION BY A DESOXYRIBONUCLEIC ACID FRACTION ISOLATED FROM PNEUMOCOCCUS TYPE III.

Authors:  O T Avery; C M Macleod; M McCarty
Journal:  J Exp Med       Date:  1944-02-01       Impact factor: 14.307

5.  Kinetic proofreading in T-cell receptor signal transduction.

Authors:  T W McKeithan
Journal:  Proc Natl Acad Sci U S A       Date:  1995-05-23       Impact factor: 11.205

6.  A theoretical study on the amount of ATP required for synthesis of microbial cell material.

Authors:  A H Stouthamer
Journal:  Antonie Van Leeuwenhoek       Date:  1973       Impact factor: 2.271

7.  Global analysis of protein expression in yeast.

Authors:  Sina Ghaemmaghami; Won-Ki Huh; Kiowa Bower; Russell W Howson; Archana Belle; Noah Dephoure; Erin K O'Shea; Jonathan S Weissman
Journal:  Nature       Date:  2003-10-16       Impact factor: 49.962

8.  The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography.

Authors:  Cristina V Iancu; H Jane Ding; Dylan M Morris; D Prabha Dias; Arlene D Gonzales; Anthony Martino; Grant J Jensen
Journal:  J Mol Biol       Date:  2007-06-29       Impact factor: 5.469

9.  A continuous culture study of an ATPase-negative mutant of Escherichia coli.

Authors:  A H Stouthamer; C W Bettenhaussen
Journal:  Arch Microbiol       Date:  1977-06-20       Impact factor: 2.552

10.  Quantifying and mapping the human appropriation of net primary production in earth's terrestrial ecosystems.

Authors:  Helmut Haberl; K Heinz Erb; Fridolin Krausmann; Veronika Gaube; Alberte Bondeau; Christoph Plutzar; Simone Gingrich; Wolfgang Lucht; Marina Fischer-Kowalski
Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-06       Impact factor: 11.205

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  37 in total

1.  Architecture-dependent robustness and bistability in a class of genetic circuits.

Authors:  Jiajun Zhang; Zhanjiang Yuan; Han-Xiong Li; Tianshou Zhou
Journal:  Biophys J       Date:  2010-08-09       Impact factor: 4.033

Review 2.  Carboxylases in natural and synthetic microbial pathways.

Authors:  Tobias J Erb
Journal:  Appl Environ Microbiol       Date:  2011-10-14       Impact factor: 4.792

3.  Quantification of behavior.

Authors:  Alan Leshner; Donald W Pfaff
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-13       Impact factor: 11.205

4.  Metallobiology: zinc differently.

Authors:  Kyle P Carter; Amy E Palmer
Journal:  Nat Chem       Date:  2015-02       Impact factor: 24.427

5.  Generic metric to quantify quorum sensing activation dynamics.

Authors:  Anand Pai; Jaydeep K Srimani; Yu Tanouchi; Lingchong You
Journal:  ACS Synth Biol       Date:  2013-09-23       Impact factor: 5.110

Review 6.  A short history of RubisCO: the rise and fall (?) of Nature's predominant CO2 fixing enzyme.

Authors:  Tobias J Erb; Jan Zarzycki
Journal:  Curr Opin Biotechnol       Date:  2017-08-29       Impact factor: 9.740

7.  Bacterial growth laws reflect the evolutionary importance of energy efficiency.

Authors:  Arijit Maitra; Ken A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-29       Impact factor: 11.205

Review 8.  Transcription by the numbers redux: experiments and calculations that surprise.

Authors:  Hernan G Garcia; Alvaro Sanchez; Thomas Kuhlman; Jane Kondev; Rob Phillips
Journal:  Trends Cell Biol       Date:  2010-12       Impact factor: 20.808

9.  How to build a course in mathematical-biological modeling: content and processes for knowledge and skill.

Authors:  Anne-Marie Hoskinson
Journal:  CBE Life Sci Educ       Date:  2010       Impact factor: 3.325

Review 10.  Cell wall-related bionumbers and bioestimates of Saccharomyces cerevisiae and Candida albicans.

Authors:  Frans M Klis; Chris G de Koster; Stanley Brul
Journal:  Eukaryot Cell       Date:  2013-11-15
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