Molecular Biology of Bacteria and Its Relevance for P Systems

We recall several elements of molecular biology of bacteria, also discussing their (possible) relevance for the membrane computing area.

[1]  Stefan E. Szedlacsek,et al.  Time-Dependent or Steady-State Control of Metabolic Systems? , 2000 .

[2]  C. Jacq,et al.  Transcriptomes, transcription activators and microarrays , 2001, FEBS letters.

[3]  Rudolf Freund,et al.  Membrane Systems with Symport/Antiport Rules: Universality Results , 2002, WMC-CdeA.

[4]  Roberto R Kampfner,et al.  Digital and biological computing in organizations. , 2002, Bio Systems.

[5]  F. Bruggeman,et al.  Macromolecular Intelligence in Microorganisms , 2000, Biological chemistry.

[6]  B. Bassler.  How bacteria talk to each other: regulation of gene expression by quorum sensing. , 1999, Current opinion in microbiology.

[7]  M. Kleerebezem,et al.  Hierarchical control versus autoregulation of carbohydrate utilization in bacteria. , 2001, Journal of molecular microbiology and biotechnology.

[8]  Olaf Wolkenhauer,et al.  Mathematical modelling in the post-genome era: understanding genome expression and regulation--a system theoretic approach. , 2002, Bio Systems.

[9]  J. Costerton,et al.  The involvement of cell-to-cell signals in the development of a bacterial biofilm. , 1998, Science.

[10]  Hidde de Jong,et al.  Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..

[11]  W. Hillen,et al.  Carbon catabolite repression in bacteria. , 1999, Current opinion in microbiology.

[12]  C. Anthony.  Bacterial energy transduction , 1988 .

[13]  K R Hess,et al.  Microarrays: handling the deluge of data and extracting reliable information. , 2001, Trends in biotechnology.

[14]  K. Hughes,et al.  Regulation of flagellar assembly. , 2002, Current opinion in microbiology.

[15]  Pedro C Marijuán,et al.  Bionformation: untangling the networks of life. , 2002, Bio Systems.

[16]  J E Bailey,et al.  Mathematical Modeling and Analysis in Biochemical Engineering: Past Accomplishments and Future Opportunities , 1998, Biotechnology progress.

[17]  Y. Gerchman,et al.  Na(+)/H(+) antiporters. , 2001, Biochimica et biophysica acta.

[18]  M Conrad,et al.  Information processing in molecular systems. , 1972, Currents in modern biology.

[19]  M. Springer,et al.  Post-transcriptional control by global regulators of gene expression in bacteria. , 2000, Current opinion in microbiology.

[20]  Hendrik Jan Hoogeboom,et al.  Simulating Counter Automata by P Systems with Symport/Antiport , 2002, WMC-CdeA.

[21]  Gheorghe Paun,et al.  Membrane Computing , 2002, Natural Computing Series.

[22]  Grzegorz Rozenberg,et al.  Membrane Computing , 2003, Lecture Notes in Computer Science.

[23]  N. Goodman.  Biological data becomes computer literate: new advances in bioinformatics. , 2002, Current opinion in biotechnology.

[24]  Andrei Paun,et al.  ReMembrane Systems with Coupled Transport: Universality and Normal Forms , 2002, Fundam. Informaticae.

[25]  Spengler Sj.  Techview: computers and biology. Bioinformatics in the information age. , 2000 .

[26]  Pierluigi Frisco,et al.  Towards a Hierarchy of Conformons-P Systems , 2002, WMC-CdeA.

[27]  G Stephanopoulos,et al.  Metabolic engineering as an integrating platform for strain development. , 2001, Current opinion in microbiology.

[28]  Gheorghe Paun,et al.  P systems with energy accounting , 2001, Int. J. Comput. Math..

[29]  M. Saier.  Genome archeology leading to the characterization and classification of transport proteins. , 1999, Current opinion in microbiology.

[30]  R. Blumenthal,et al.  Mapping regulatory networks in microbial cells. , 1999, Trends in microbiology.

[31]  S. Singer,et al.  The Fluid Mosaic Model of the Structure of Cell Membranes , 1972, Science.

[32]  Andrei Paun,et al.  Further Remarks on P Systems with Symport Rules , 2001, Sci. Ann. Cuza Univ..

[33]  H. Jung,et al.  Towards the molecular mechanism of Na(+)/solute symport in prokaryotes. , 2001, Biochimica et biophysica acta.

[34]  D. Ramkrishna,et al.  Mathematical models of metabolic pathways. , 1999, Current opinion in biotechnology.

[35]  G Păun,et al.  From cells to computers: computing with membranes (P systems). , 2001, Bio Systems.

[36]  I. Booth,et al.  Protection of Escherichia coli cells against extreme turgor by activation of MscS and MscL mechanosensitive channels: identification of genes required for MscS activity , 1999, The EMBO journal.

[37]  Rudolf Freund,et al.  GP Systems with Forbidding Context , 2002, Fundam. Informaticae.

[38]  T. Gaasterland,et al.  Whole-genome analysis: annotations and updates. , 2001, Current opinion in structural biology.

[39]  J R Yates,et al.  Analysis of the microbial proteome. , 2000, Current opinion in microbiology.

[40]  I. Booth,et al.  Rapid inactivation of the Escherichia coli Kdp K+ uptake system by high potassium concentrations , 2000, Molecular microbiology.

[41]  D Thieffry,et al.  Qualitative analysis of gene networks. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[42]  Sylvia J. Spengler,et al.  Bioinformatics in the Information Age , 2000, Science.

[43]  J. Vervoort,et al.  19F NMR metabolomics for the elucidation of microbial degradation pathways of fluorophenols , 2001, Journal of Industrial Microbiology and Biotechnology.

[44]  Gheorghe Paun.  P Systems with Active Membranes: Attacking NP-Complete Problems , 2001, J. Autom. Lang. Comb..

[45]  Pierluigi Frisco,et al.  Towards a Hierarchy of Info-Energy P Systems , 2002 .

[46]  S J Singer,et al.  The molecular organization of membranes. , 1974, Annual review of biochemistry.

[47]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[48]  Neil L. Kelleher,et al.  Informatics and multiplexing of intact protein identification in bacteria and the archaea , 2001, Nature Biotechnology.

[49]  P. James,et al.  Of genomes and proteomes. , 1997, Biochemical and biophysical research communications.

[50]  D. Bray.  Protein molecules as computational elements in living cells , 1995, Nature.

[51]  Reinhold Brückner,et al.  Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. , 2002, FEMS microbiology letters.

[52]  Ioan I. Ardelean,et al.  The Relevance of Cell Membranes for P Systems. General Aspects , 2002, Fundam. Informaticae.

[53]  Christos A. Ouzounis.  Bioinformatics and the theoretical foundations of molecular biology , 2002, Bioinform..

[54]  G. Stormo,et al.  Mining genome databases to identify and understand new gene regulatory systems. , 2002, Current opinion in microbiology.

[55]  G. Thomas,et al.  The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea. , 2001, FEMS microbiology reviews.

[56]  Taishin Yasunobu Nishida.  Simulations of Photosynthesis by a K-Subset Transforming System with Membrane , 2002, Fundam. Informaticae.

[57]  A. Arkin,et al.  Simulation of prokaryotic genetic circuits. , 1998, Annual review of biophysics and biomolecular structure.

[58]  D. Kell,et al.  A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations , 2001, Nature Biotechnology.

[59]  Tommy J Phelps,et al.  Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. , 2002, Current opinion in biotechnology.

[60]  Rudolf Freund,et al.  Energy-Controlled P Systems , 2002, WMC-CdeA.