Skip to main content
SpringerLink
Log in
Book cover

Bioinformatics and Genome Analysis pp 221–243Cite as

Bioinformatics, Cellular Flows, and Calculation

  • Conference paper

  • 307 Accesses

Part of the book series: Ernst Schering Research Foundation Workshop ((SCHERING FOUND,volume 38))

Abstract

The elucidation of the sequence of entire genomes has enriched science in more than one way. It has delivered the primary sequence of many new genes, the functions of which need to be verified or discovered. Also, it has increased our insight into the homology between organisms. The fact that the sequence was one of complete genomes has a number of extra ramifications. One is that we now have, in one sense, complete catalogues of what constitutes “life,” or at least of what seems necessary to encode life. Various perceptions exist regarding the diversity of life on earth. From a superficial point of view, life seems to be highly diverse, ranging from minute bacteria to highly social animals. From a biochemical point of view, however, life is surprisingly uniform, with many biochemical conversions being common to most organisms, both at the level of the chemical reaction routes and with respect to the catalytic mechanisms. Proteins in distinct organisms are surprisingly homologous, reflecting considerable hysteresis in biological evolution; solutions of catalytic problems are only found once and then further copied. Appreciable similarities occur in the development and anatomy of different organisms.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Bakker BM, Westerhoff HV, Opperdoes FR, Michels PA (2000) Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Mol Biochem Parasitol 106: 1–10

    Article  PubMed  CAS  Google Scholar 

  • Bruggeman FJ, van Heeswijk WC, Boogerd FC, Westerhoff HV (2000) Macromolecular intelligence in microorganisms. Biol Chem 381: 965–972

    Article  PubMed  CAS  Google Scholar 

  • Dam) S, Hynne F, De Monte S, d’Ovido F, Sorensen PG, Westerhoff HV (2001) Synchronization of glycolytic oscillations in a yeast cell population. Faraday Discuss 120: 261–276

    Google Scholar 

  • Getz WM (1991) A unified approach to multispecies modeling. Natural Resource Management 5: 393–421

    Google Scholar 

  • Getz WM (1993) Metaphysiological and evolutionary dynamics of populations exploiting constant and interactive resources: r-K selection revisited. Evolutionary Ecology 7: 287–305

    Article  Google Scholar 

  • Giersch C (1991) Sensitivity analysis of ecosystems: an analytical treatment. Ecological Modelling 53: 131–146

    Article  Google Scholar 

  • Higashi M, Nakajima H (1995) Indirect effects in ecological interaction networks I. The chain rule approach. Mathematical Biosciences 130:99–128 Hofmeyr J-HS, Westerhoff HV (2001) Building the cellular puzzle. J Theor Biol 202: 261–285

    Google Scholar 

  • Hofmeyr J-HS, Cornish-Bowden A, Rohwer JM (1993) Taking enzyme kinetics out of control; putting control into regulation. Eur J Biochem 212: 833–837

    Article  PubMed  CAS  Google Scholar 

  • Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, Smith HO, Venter JC (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286: 2165–2169

    Article  PubMed  CAS  Google Scholar 

  • Jensen PR, Van Der Weijden CC, Jensen LB, Westerhoff HV, Snoep JL (1999) Extensive regulation compromises the extent to which DNA gyrase controls DNA supercoiling and growth rate of Escherichia coli. Eur J Biochem 266: 865–877

    Article  PubMed  CAS  Google Scholar 

  • Juretic D, Westerhoff HV (1987) Variation of efficiency with free-energy dissipation in models of biological energy transduction. Biophys Chem 28: 21–34

    Article  PubMed  CAS  Google Scholar 

  • Kahn D, Westerhoff HV (1991) Control theory of regulatory cascades. J Theor Biol 153: 255–285

    Article  PubMed  CAS  Google Scholar 

  • Kamp F, Astumian RD, Westerhoff HV (1988) Coupling of vectorial proton flow to a biochemical reaction by local electric interactions. Proc Nail Acad Sci USA 85: 3792–3796

    Article  CAS  Google Scholar 

  • Kholodenko BN, Hoek JB, Westerhoff HV (2000) Why cytoplasmic signalling proteins should be recruited to cell membranes. Trends Cell Biol 10: 173–178

    Article  PubMed  CAS  Google Scholar 

  • Lawrence PA (1992) The making of a fly. Blackwell Scientific Publications, Oxford

    Google Scholar 

  • Lafontaine DL, Tollervey D (2001) The function and synthesis of ribosomes. Nat Rev Mol Cell Biol 2: 514–520

    Article  PubMed  CAS  Google Scholar 

  • Marinissen MJ, Gutkind JS (2001) G-protein-coupled receptors and signaling networks: emerging paradigms. Trends Pharmacol Sci 22: 368–376

    Article  PubMed  CAS  Google Scholar 

  • Mitchell P (1979) The Ninth Sir Hans Krebs Lecture. Compartmentation and communication in living systems. Ligand conduction: a general catalytic principle in chemical, osmotic and chemiosmotic reaction systems. Eur J Biochem 95: 1–20

    Article  PubMed  CAS  Google Scholar 

  • Prigogine I, Nicolis G (1971) Biological order, structure and instabilities. Q Rev Biophys 4: 107–148

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez R, Chinea G, Lopez N, Pons T, Vriend G (1998) Homology modeling, model and software evaluation: three related resources. Bioinformatics 14: 523–528

    Article  PubMed  CAS  Google Scholar 

  • Schopf JW (2000) Solution to Darwin’s dilemma: discovery of the missing Precambrian record of life. Proc Natl Acad Sci USA 97: 6947–6953

    Article  PubMed  CAS  Google Scholar 

  • Schulze E-D (1995) Flux control at the ecosystem level. TREE 10: 40–43

    PubMed  CAS  Google Scholar 

  • Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273–3297

    PubMed  CAS  Google Scholar 

  • Ter Kuile BH (1997) Adaptation of metabolic enzyme activities of Trypanosoma brucei promastigotes to growth rate and carbon regimen. J Bacteriol 179: 4699–4705

    PubMed  Google Scholar 

  • Ter Kuile BH, Westerhoff HV (2001) Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett 500: 169–171

    Article  PubMed  Google Scholar 

  • Teusink B, Walsh MC, van Dam K, Westerhoff HV (1998) The danger of metabolic pathways with turbo design. Trends Biochem Sci 23: 162–169

    Article  PubMed  CAS  Google Scholar 

  • Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Darn K, Westerhoff HV, Snoep JL (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267: 5313–5329

    Article  PubMed  CAS  Google Scholar 

  • van Heeswijk WC, Hoving S, Molenaar D, Stegeman B, Kahn D, Westerhoff HV. (1996) An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli. Mol Microbiol 21: 133–146

    Article  PubMed  Google Scholar 

  • van Heeswijk WC, Wen D, Clancy P, Jaggi R, 011is DL, Westerhoff HV, Vasudevan SG (2000) The Escherichia coli signal transducers PII (G1nB) and GlnK form heterotrimers in vivo: fine tuning the nitrogen signal cascade. Proc Natl Acad Sci USA 97: 3942–3947

    Article  PubMed  Google Scholar 

  • Venter JC, Adams MD, Myers EW, Li PW, Mural RI, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine M, Roberts RI, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yon C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barn-stead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X (2001) The sequence of the human genome. Science 291: 1304–1351

    Google Scholar 

  • Wallace DC, Morowitz HJ (1973) Genome size and evolution. Chromosoma 40: 121–126

    Article  PubMed  CAS  Google Scholar 

  • Westerhoff HV (2001) The silicon cell, not dead but live! Metab Eng 3: 207–210

    Article  PubMed  CAS  Google Scholar 

  • Westerhoff HV, Van Dam K (1987) Thermodynamics and control of biological free-energy transduction. Elsevier, Amsterdam

    Google Scholar 

  • Westerhoff HV, Koster JG, Van Workum M, Rudd KE (1995) On the control of gene expression. In: Cornish-Bowden A, Cardenas ML (eds) Control of metabolic processes. Plenum Press, New York, pp 399–412

    Google Scholar 

  • Wijker JE, Jensen PR, Snoep JL, Gomes AV, Guiral M, Jongsma APM (1995) Energy, control and DNA structure in the living cell. Biophys Chem 55: 153–165

    Article  PubMed  CAS  Google Scholar 

Download references

Authors
  1. H. V. Westerhoff
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. W. M. Getz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. H. W. van Verseveld
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J.-H S. Hofmeyr
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. L. Snoep
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institute for Bioinformatics, GSF-Forschungszentrum für Umwelt, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany

    H.-W. Mewes

  2. Genomics/Bioinformatics, Schering AG, Müllerstrasse 178, 13342, Berlin, Germany

    H. Seidel  & B. Weiss  & 

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Westerhoff, H.V., Getz, W.M., van Verseveld, H.W., Hofmeyr, JH.S., Snoep, J.L. (2002). Bioinformatics, Cellular Flows, and Calculation. In: Mewes, HW., Seidel, H., Weiss, B. (eds) Bioinformatics and Genome Analysis. Ernst Schering Research Foundation Workshop, vol 38. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-04747-7_11

Download citation

  • DOI: https://doi.org/10.1007/978-3-662-04747-7_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-04749-1

  • Online ISBN: 978-3-662-04747-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation