Biochemical Unity Revisited: Microbial Central Carbon Metabolism Holds
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Recombination and the Evolution of Mutational Robustness
ARTICLE IN PRESS Journal of Theoretical Biology 241 (2006) 707–715 www.elsevier.com/locate/yjtbi Recombination and the evolution of mutational robustness Andy Gardnera,b,c,Ã, Alex T. Kalinkaa aInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK bDepartment of Mathematics & Statistics, Queen’s University, Kingston, Ont., Canada K7L 3N6 cDepartment of Biology, Queen’s University, Kingston, Ont., Canada K7L 3N6 Received 25 July 2005; received in revised form 8 December 2005; accepted 5 January 2006 Available online 20 February 2006 Abstract Mutational robustness is the degree to which a phenotype, such as fitness, is resistant to mutational perturbations. Since most of these perturbations will tend to reduce fitness, robustness provides an immediate benefit for the mutated individual. However, robust systems decay due to the accumulation of deleterious mutations that would otherwise have been cleared by selection. This decay has received very little theoretical attention. At equilibrium, a population or asexual lineage is expected to have a mutation load that is invariant with respect to the selection coefficient of deleterious alleles, so the benefit of robustness (at the level of the population or asexual lineage) is temporary. However, previous work has shown that robustness can be favoured when robustness loci segregate independently of the mutating loci they act upon. We examine a simple two-locus model that allows for intermediate rates of recombination and inbreeding to show that increasing the effective recombination rate allows for the evolution of greater mutational robustness. r 2006 Elsevier Ltd. All rights reserved. Keywords: Canalization; Epistasis; Linkage disequilibrium; Multilocus methodology; Mutation–selection balance 1. -
Antigen-Receptor Degeneracy and Immunological Paradigms Irun R
Molecular Immunology 40 (2004) 993–996 Antigen-receptor degeneracy and immunological paradigms Irun R. Cohen a,∗, Uri Hershberg b, Sorin Solomon c a The Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100 Israel b Interdisciplinary Center for Neuronal Computation, The Hebrew University of Jerusalem, Jerusalem, Israel c The Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel Abstract This paper discusses some consequences of the discovery that antigen receptors are degenerate: Immune specificity, in contrast to the tenets of the clonal selection paradigm, must be generated by the immune response down-stream of initial antigen recognition; and specificity is a property of a collective of cells and not of single clones. © 2003 Elsevier Ltd. All rights reserved. Keywords: T cells; T-cell receptor; Inflammation; Specificity; Degeneracy; Clonal selection; Cognitive paradigm 1. Degeneracy problems characterized by extreme poly-clonality; in fact, most nat- ural T-cell responses are oligo-clonal (Douek et al., 2003). Degeneracy, in the present discourse, refers to the capac- So, there must be a mechanism or mechanisms that operate ity of any single antigen receptor to bind and respond to to restrict poly-clonality in wild-type adaptive immune sys- (recognize) many different ligands. The Oxford English Dic- tems. The inherent potential for extreme poly-clonality, in tionary (Second Edition, 1989) defines the primary meaning practice, may be tempered by clonal competition. Compe- of degeneracy as: tition among clones for access, energy or space will most likely reward the fast and the avid. Since the best clones Having lost the qualities proper to the race or kind; having should win, clonal competition does not threaten the logic declined from a higher to a lower type; hence, declined of the clonal selection theory (CST) of adaptive immunity. -
Multiple Receptor Tyrosine Kinases Are Expressed in Adult Rat Retinal Ganglion Cells As Revealed by Single-Cell Degenerate Primer Polymerase Chain Reaction
Upsala Journal of Medical Sciences. 2010; 115: 65–80 ORIGINAL ARTICLE Multiple receptor tyrosine kinases are expressed in adult rat retinal ganglion cells as revealed by single-cell degenerate primer polymerase chain reaction NICLAS LINDQVIST1, ULRIKA LÖNNGREN1, MARTA AGUDO2,3, ULLA NÄPÄNKANGAS1, MANUEL VIDAL-SANZ2 & FINN HALLBÖÖK1 1Department of Neuroscience, Unit for Developmental Neuroscience, Biomedical Center, Uppsala University, 75123 Uppsala, Sweden, 2Departamento de Oftalmología, Facultad de Medicina, Universidad de Murcia, Murcia, Spain, and 3Fundación para la Formación e Investigación Sanitaria de la Región de Murcia, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain Abstract Background. To achieve a better understanding of the repertoire of receptor tyrosine kinases (RTKs) in adult retinal ganglion cells (RGCs) we performed polymerase chain reaction (PCR), using degenerate primers directed towards conserved sequences in the tyrosine kinase domain, on cDNA from isolated single RGCs univocally identified by retrograde tracing from the superior colliculi. Results. All the PCR-amplified fragments of the expected sizes were sequenced, and 25% of them contained a tyrosine kinase domain. These were: Axl, Csf-1R, Eph A4, Pdgfrb, Ptk7, Ret, Ros, Sky, TrkB, TrkC, Vegfr-2, and Vegfr-3. Non-RTK sequences were Jak1 and 2. Retinal expression of Axl, Csf-1R, Pdgfrb, Ret, Sky, TrkB, TrkC, Vegfr-2, and Vegfr-3, as well as Jak1 and 2, was confirmed by PCR on total retina cDNA. Immunodetection of Csf-1R, Pdgfra/b, Ret, Sky, TrkB, and Vegfr-2 on retrogradely traced retinas demonstrated that they were expressed by RGCs. Co-localization of Vegfr-2 and Csf-1R, of Vegfr-2 and TrkB, and of Csf-1R and Ret in retrogradely labelled RGCs was shown. -
A Dicarboxylate/4-Hydroxybutyrate Autotrophic Carbon Assimilation Cycle in the Hyperthermophilic Archaeum Ignicoccus Hospitalis
A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis Harald Huber*†, Martin Gallenberger*, Ulrike Jahn*, Eva Eylert‡, Ivan A. Berg§, Daniel Kockelkorn§, Wolfgang Eisenreich‡, and Georg Fuchs§ *Lehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany; ‡Lehrstuhl fu¨r Biochemie, Department Chemie, Technische Universita¨t Mu¨ nchen, Lichtenbergstrasse 4, D-85748 Garching, Germany; and §Lehrstuhl fu¨r Mikrobiologie, Universita¨t Freiburg, Scha¨nzlestrasse 1, D-79104 Freiburg, Germany Edited by Dieter So¨ll, Yale University, New Haven, CT, and approved April 1, 2008 (received for review February 1, 2008) Ignicoccus hospitalis is an anaerobic, autotrophic, hyperthermophilic starting from acetyl-CoA (4). On the basis of these data, pyruvate Archaeum that serves as a host for the symbiotic/parasitic Archaeum synthase and phosphoenolpyruvate (PEP) carboxylase were pos- Nanoarchaeum equitans. It uses a yet unsolved autotrophic CO2 tulated as CO2 fixing enzymes, with PEP carboxylase serving as the fixation pathway that starts from acetyl-CoA (CoA), which is reduc- only enzyme used for oxaloacetate synthesis. In addition, the tively carboxylated to pyruvate. Pyruvate is converted to phosphoe- operation of an incomplete ‘‘horseshoe-type’’ citric acid cycle, in nol-pyruvate (PEP), from which glucogenesis as well as oxaloacetate which 2-oxoglutarate oxidation does not take place, was demon- formation branch off. Here, we present the complete metabolic cycle strated. Enzyme and labeling data indicated a conventional glu- by which the primary CO2 acceptor molecule acetyl-CoA is regener- coneogenesis, but with some enzymes unrelated to those of the ated. Oxaloacetate is reduced to succinyl-CoA by an incomplete classical pathway. -
Degeneracy in Hippocampal Physiology and Plasticity
bioRxiv preprint doi: https://doi.org/10.1101/203943; this version posted July 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Degeneracy in hippocampal physiology and plasticity * Rahul Kumar Rathour and Rishikesh Narayanan Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. * Corresponding Author Rishikesh Narayanan, Ph.D. Molecular Biophysics Unit Indian Institute of Science Bangalore 560 012, India. e-mail: [email protected] Phone: +91-80-22933372 Fax: +91-80-23600535 Abbreviated title: Degeneracy in the hippocampus Keywords: hippocampus; degeneracy; learning; memory; encoding; homeostasis; plasticity; physiology; causality; reductionism; holism; structure-function relationships; variability; compensation; intrinsic excitability 1 bioRxiv preprint doi: https://doi.org/10.1101/203943; this version posted July 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT Degeneracy, defined as the ability of structurally disparate elements to perform analogous function, has largely been assessed from the perspective of maintaining robustness of physiology or plasticity. How does the framework of degeneracy assimilate into an encoding system where the ability to change is an essential ingredient for storing new incoming information? Could degeneracy maintain the balance between the apparently contradictory goals of the need to change for encoding and the need to resist change towards maintaining homeostasis? In this review, we explore these fundamental questions with the mammalian hippocampus as an example encoding system. We systematically catalog lines of evidence, spanning multiple scales of analysis, that demonstrate the expression of degeneracy in hippocampal physiology and plasticity. -
Recreating Ancient Metabolic Pathways Before Enzymes Kamila B
Recreating ancient metabolic pathways before enzymes Kamila B. Muchowska, Elodie Chevallot-Beroux, Joseph Moran To cite this version: Kamila B. Muchowska, Elodie Chevallot-Beroux, Joseph Moran. Recreating ancient metabolic path- ways before enzymes. Bioorganic and Medicinal Chemistry, Elsevier, 2019, 27 (12), pp.2292-2297. 10.1016/j.bmc.2019.03.012. hal-02516541 HAL Id: hal-02516541 https://hal.archives-ouvertes.fr/hal-02516541 Submitted on 23 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Graphical Abstract To create your abstract, type over the instructions in the template box below. Fonts or abstract dimensions should not be changed or altered. Recreating ancient metabolic pathways Leave this area blank for abstract info. before enzymes Kamila B. Muchowskaa* , Elodie Chevallot-Berouxa, and Joseph Morana* University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France Bioorganic & Medicinal Chemistry journal homepage: www.elsevier.com Recreating ancient metabolic pathways before enzymes Kamila B. Muchowska,a* Elodie Chevallot-Beroux,a and Joseph Morana* a University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France. ARTICLE INFO ABSTRACT Article history: The biochemistry of all living organisms uses complex, enzyme-catalyzed metabolic reaction Received networks. -
An Interdisciplinary Perspective on Artificial Immune Systems
Evol. Intel. (2008) 1:5–26 DOI 10.1007/s12065-007-0004-2 REVIEW ARTICLE An interdisciplinary perspective on artificial immune systems J. Timmis Æ P. Andrews Æ N. Owens Æ E. Clark Received: 7 September 2007 / Accepted: 11 October 2007 / Published online: 10 January 2008 Ó Springer-Verlag 2008 Abstract This review paper attempts to position the area 1 Introduction of Artificial Immune Systems (AIS) in a broader context of interdisciplinary research. We review AIS based on an Artificial Immune Systems (AIS) is a diverse area of established conceptual framework that encapsulates math- research that attempts to bridge the divide between ematical and computational modelling of immunology, immunology and engineering and are developed through abstraction and then development of engineered systems. the application of techniques such as mathematical and We argue that AIS are much more than engineered systems computational modelling of immunology, abstraction from inspired by the immune system and that there is a great those models into algorithm (and system) design and deal for both immunology and engineering to learn from implementation in the context of engineering. Over recent each other through working in an interdisciplinary manner. years there have been a number of review papers written on AIS with the first being [25] followed by a series of others Keywords Artificial immune systems Á that either review AIS in general, for example, [29, 30, 43, Immunological modelling Á Mathematical modelling Á 68, 103], or more specific aspects of AIS such as data Computational modelling Á mining [107], network security [71], applications of AIS Applications of artificial immune systems Á [58], theoretical aspects [103] and modelling in AIS [39]. -
Degeneracy and Genetic Assimilation in RNA Evolution Reza Rezazadegan1* and Christian Reidys1,2
Rezazadegan and Reidys BMC Bioinformatics (2018) 19:543 https://doi.org/10.1186/s12859-018-2497-3 RESEARCH ARTICLE Open Access Degeneracy and genetic assimilation in RNA evolution Reza Rezazadegan1* and Christian Reidys1,2 Abstract Background: The neutral theory of Motoo Kimura stipulates that evolution is mostly driven by neutral mutations. However adaptive pressure eventually leads to changes in phenotype that involve non-neutral mutations. The relation between neutrality and adaptation has been studied in the context of RNA before and here we further study transitional mutations in the context of degenerate (plastic) RNA sequences and genetic assimilation. We propose quasineutral mutations, i.e. mutations which preserve an element of the phenotype set, as minimal mutations and study their properties. We also propose a general probabilistic interpretation of genetic assimilation and specialize it to the Boltzmann ensemble of RNA sequences. Results: We show that degenerate sequences i.e. sequences with more than one structure at the MFE level have the highest evolvability among all sequences and are central to evolutionary innovation. Degenerate sequences also tend to cluster together in the sequence space. The selective pressure in an evolutionary simulation causes the population to move towards regions with more degenerate sequences, i.e. regions at the intersection of different neutral networks, and this causes the number of such sequences to increase well beyond the average percentage of degenerate sequences in the sequence space. We also observe that evolution by quasineutral mutations tends to conserve the number of base pairs in structures and thereby maintains structural integrity even in the presence of pressure to the contrary. -
Tyrosine Kinases
KEVANM SHOKAT MINIREVIEW Tyrosine kinases: modular signaling enzymes with tunable specificities Cytoplasmic tyrosine kinases are composed of modular domains; one (SHl) has catalytic activity, the other two (SH2 and SH3) do not. Kinase specificity is largely determined by the binding preferences of the SH2 domain. Attaching the SHl domain to a new SH2 domain, via protein-protein association or mutation, can thus dramatically change kinase function. Chemistry & Biology August 1995, 2:509-514 Protein kinases are one of the largest protein families identified, This is a result of the overlapping substrate identified to date; over 45 new members are identified specificities of many tyrosine kinases, which makes it each year. It is estimated that up to 4 % of vertebrate pro- difficult to dissect the individual signaling pathways by teins are protein kinases [l].The protein kinases are cate- scanning for unique target motifs [2]. gorized by their specificity for serineithreonine, tyrosine, or histidine residues. Protein tyrosine kinases account for The apparent promiscuity of individual tyrosine kinases roughly half of all kinases. They occur as membrane- is a result of their unique structural organization. bound receptors or cytoplasmic proteins and are involved Enzyme specificity is typically programmed by one in a wide variety of cellular functions, including cytokine binding site, which recognizes the substrate and also con- responses, antigen-dependent immune responses, cellular tains exquisitely oriented active-site functional groups transformation by RNA viruses, oncogenesis, regulation that help to lower the energy of the transition state for of the cell cycle, and modification of cell morphology the conversion of specific substrates to products.Tyrosine (Fig. -
A Survey of Carbon Fixation Pathways Through a Quantitative Lens
Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed. -
A Numerical Representation and Classification of Codons To
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.02.971036; this version posted March 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A Numerical Representation and Classication of Codons to Investigate Codon Alternation Patterns during Genetic Mutations on Disease Pathogenesis Antara Senguptaa, Pabitra Pal Choudhuryd, Subhadip Chakrabortyb,e, Swarup Royc,∗∗, Jayanta Kumar Dasd,∗, Ditipriya Mallicke, Siddhartha S Janae aDepartment of Master of Computer Applications, MCKV Institute of Engineering, Liluah, India bDepartment of Botany, Nabadwip Vidyasagar College, Nabadwip, India cDepartment of Computer Applications,Sikkim University, Gangtok, Sikkim, India dApplied Statistical Unit, Indian Statistical Institute, Kolkata, India eSchool of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, India 1. Introduction Genes are the functional units of heredity [4]. It is mainly responsible for the structural and functional changes and for the variation in organisms which could be good or bad. DNA (Deoxyribose Nucleic Acid) sequences build the genes of organisms which in turn encode for particular protein us- ing codon. Any uctuation in this sequence (codons), for example, mishaps during DNA transcription, might lead to a change in the genetic code which alter the protein synthesis. This change is called mutation. Mutation diers from Single Nucleotide Polymorphism(SNP) in many ways [23]. For instance, occurrence of mutation in a population should be less than 1% whereas SNP occurs with greater than 1%. Mutation always occurs in diseased group whereas SNP is occurs in both diseased and control population. Mutation is responsible for some disease phenotype but SNP may or may not be as- sociated with disease phenotype. -
The Immune System in Pieces: Computational Lessons from Degeneracy in the Immune System (Special Session: Foundations of Artificial Immune Systems) M
Proceedings of the 2007 IEEE Symposium on Foundations of Computational Intelligence (FOCI 2007) The Immune System in Pieces: Computational Lessons from Degeneracy in the Immune System (Special session: Foundations of Artificial Immune Systems) M. Mendao∗, J. Timmis∗†, P. S. Andrews∗ and M. Davies‡ ∗Department of Computer Science, University of York, Heslington, York, UK Email: [email protected] †Department of Electronics, University of York, Heslington, York, UK ‡Jenner Institute, University of Oxford. UK Abstract— The concept of degeneracy in biology, including the of the immune response. The next stage is to develop a high- immune system, is well accepted and has been demonstrated to level algorithm that is derived from the model. Independently, be present at many different levels. We explore this concept from recent work by Bersini [7] has highlighted the benefits of a computational point of view and demonstrate how we can use computational models of degeneracy to aid the development of adopting object orientated methodologies in the use of mod- more biologically plausible Artificial Immune Systems (AIS). The elling biological systems. In our work, we have made use of outcome of these models has lead us to perform an analysis of the the Unified Modelling language (UML), not only to represent receptor dynamics in the model and we discuss the computational our agent model, but also to aid the development of a high- implications of a “degenerate” repertoire. Through the use of level algorithm that we have derived from the model. It should the Unified Modelling language (UML) we have abstracted a high level immune inspire algorithm that will be used as part of be noted that the model we have developed and the high-level a larger project to develop an immune inspired bioinformatics algorithm that we have derived is only the first step towards the system.