1,721,036 research outputs found
The emergence of life. From chemical origins to synthetic biology
No full textPreface page xi Acknowledgments xiii List of books on the origin of life xiv 1 Conceptual framework of research on the origin of life on Earth 1 Introduction 1 Determinism and contingency in the origin of life 4 Only one start or many? 10 The anthropic principle, SETI, and the creationists 12 Questions for the reader 16 2 Approaches to the definitions of life 17 Introduction 17 A historical framework 19 The visit of the Green Man 23 Main operational approaches to the origin of life 26 I. The prebiotic RNA world 27 II. The compartmentalistic approach 29 III. The prebiotic metabolism approach 31 Concluding remarks 36 Questions for the reader 37 3 Selection in prebiotic chemistry: why this . . . and not that? 38 Introduction 38 From Oparin to Miller and beyond 40 Other sources of organic molecules 46 Millers α-amino acids: why do they form? 50 Some notes on homochirality 52 Concluding remarks 56 Questions for the reader 58 4 The bottle neck: macromolecular sequences 59 Introduction 59 Proteins and nucleic acids are copolymers 60 The quest for macromolecular sequences 62 What about polynucleotides? 65 A grain of sand in the Sahara 68 The never-born proteins 70 A model for the aetiology of macromolecular sequences and a testable one 72 Homochirality in chains 76 Chain chirality and chain growth 78 Concluding remarks 82 Questions for the reader 84 5 Self-organization 85 Introduction 85 Self-organization of simpler molecular systems 87 Self-organization and autocatalysis 91 Polymerization 93 Self-organization and kinetic control 95 Self-organization and breaking of symmetry 97 Complex biological systems 100 Self-organization and finality 105 Out-of-equilibrium self-organization 106 Concluding remarks 109 Questions for the reader 111 6 The notion of emergence 112 Introduction 112 A few simple examples 114 Emergence and reductionism 116 Deducibility and predictability 117 Downward causation 119 Emergence and non-linearity 120 Life as an emergent property 123 Concluding remarks 125 Questions for the reader 128 7 Self-replication and self-reproduction 129 Introduction 129 Self-replication and non-linearity 129 Myths and realities of self-replication 132 Self-replicating, enzyme-free chemical systems 133 One more step towards complexity 141 Self-reproducing micelles and vesicles 143 Concluding remarks 153 Questions for the reader 154 8 Autopoiesis: the logic of cellular life 155 Introduction 155 Historical background 156 Basic autopoiesis 157 Criteria of autopoiesis 159 What autopoiesis does not include 160 Chemical autopoiesis 162 Autopoiesis and cognition 164 Cognition and enaction 167 Necessary and sufficient? 169 One glance further up: from autopoiesis to the cognitive domain 172 Social autopoiesis 175 Autopoiesis and the chemoton: a comparison of the views of Ganti with those of Maturana and Varela 177 Concluding remarks 179 Questions for the reader 181 9 Compartments 182 Introduction 182 Surfactant aggregates 182 Aqueous micelles 187 Compartmentation in reverse micelles 189 Cubic phases 1
Novel Properties of DDAB: Matrix Effect and Interaction with Oleate.
No full textWe report an investigation on the interaction of the positively charged surfactant DDAB (didodecyldimethylammoniumbromide) with preformed vesicles from POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine).Addition of 1.9 mM DDAB to preformed POPC vesicles of different concentrations results in mixed vesicles,owing to the avid uptake of DDAB by POPC. This leads to the so-called matrix effect: when preformedPOPC liposomes with a narrow size distribution are present in the aqueous solution, there is a fast formationprocess of mixed vesicles and the final size distribution closely resembles that of the preformed POPCliposomes. The final mixed vesicle system is stable in size and size distribution. The effect is independent ofthe initial size of the POPC vesicles and requires low relative concentrations of POPC with respect to DDAB(up to 1:4). Aside this, we report about the time stability of DDAB vesicles as a function of the aqueousbuffer ionic strength and we investigate the interaction between negatively charged surfactant oleate andDDAB. The formation of mixed vesicles is observed, whose size distribution is strongly dependent on themixing ratio of the two surfactants. Interestingly, the mixing of DDAB and oleate vesicles for values ofDDAB molar fraction close to 0.4 leads to a very narrowly distributed vesicular species centered around 100nm
Cell-free Protein Synthesis through Solubilisate Exchange in Water/Oil Emulsion Compartments.
No full textThis work is aimed at finding conditions under which syntheticcompartments used as cell models can fuse with each other andallow reagents contained in the different compartments to react.This goal seems to be best achieved by the use of water in oilemulsions (w/o) with dimensions in the range of 30±60 mm. Inparticular, cell-free EGFP (enhanced green fluorescent protein)synthesis takes place in Tween 80/Span 80 w/o emulsions, andthe extent of the reaction can be monitored directly by fluorescence.The medium is mineral oil, containing 0.5% v/v aqueous solution. Different premixing configurations of the components(plasmid, amino acids, E. Coli extract) are used and compared.The in vitro synthesis of EGFP in emulsion droplets proceeds for1 h, and the yield is 7.5 ngmL1 protein. EGFP synthesis in aqueoussolution takes place for at least 5 h. The yield is 10.5 ngmL1protein after 1 h and 15.8 ng/mL protein after 5 h. The resultswith the w/o emulsions show that solubilisate exchange takesplace among the different water droplets, but it is not possible todemonstrate clearly that a true fusion takes place
Spontaneous onset of homochirality in oligopeptide chains generated in the polymerization of N-carboxyanhydride amino acids in water.
No full textThis article is concerned with the spontaneous onset of homochiral oligopeptide sequences.We will show that the polymerization of hydrophobic NCA (N-carboxyanhydride = cyclicanhydride)-amino acid racemates (i.e. tryptophane, leucine and isoleucine) in aqueous solution yieldsoligopeptides that are characterized by a high degree of homochiral sequences. Furthermore we willshow that quartz enhances efficiently the mole fraction of oligopeptides with homochiral sequence byselectively adsorbing the more stereoregular oligopeptides from an aqueous solution of oligo-D,Lleucine.We find in particular that the mole fraction of the adsorbed homochiral 7mers is 17 timeslarger than the mole fraction calculated for a theoretical, random process. Experimentally the stereoisomerdistribution for each oligomer length can be determined by the use of enantio-labeling andLC-MS (Liquid Chromatography-Mass Spectrometry). Furthermore, if we start the polymerizationwith an enantiomeric excess (e.e.) of 20% of L-leucine (L-amino acid : D-amino acid = 6 : 4, molarratio) we observe a chiral amplification in the enantiomeric homochiral oligopeptides. We think thatsuch processes are relevant to the chemical evolution of single handedness
Semi-synthetic minimal cells: origin and recent developments
No full textThe notion of minimal cells refers to cellular structures that contain the minimal and sufficient complexity to still be defined as living, or at least capable to display the most important features of biological cells. Here we briefly describe the laboratory construction of minimal cells, a project within the broader field of synthetic biology. In particular we discuss the advancements in the preparation of semi-synthetic cells based on the encapsulation of biochemicals inside liposomes, illustrating from the one hand the origin of this research and the most recent developments; and from the other the difficulties and limits of the approach. The role of physicochemical understandings is greatly emphasized
Self-reproduction of micelles, reverse micelles and vesicles. Compartments disclose a general transformation pattern
No full textThe discovery of self-reproduction of micelles and vesicles about 15 years ago opened anew page in the field of the supramolecular chemistry of surfactant aggregation phenomena, both for the importance of dynamic aspects of complexity of these systems and for its biological meaning. In fact, the self-reproduction of vesicles has suggested that the growth and the population increase of structures resembling the cells may take place solely because of physical and chemical forces. An increasing number of reports demonstrate that reverse micelles, micelles, sub-micrometric as well as giant vesicles readily undergo self-reproduction, generating new particles from a suitable precursor.The process follows an autocatalytic pattern, namely, the progressive increase in particlenumber is a nonlinear time course.In this chapter, we will review the most significant studies on the self-reproduction ofdifferent compartments, by following a combined historical and classifying approach thatspans from the pioneering work on reverse micelles, to the case of normal (aqueous)micelles, to the studies on vesicles, giant vesicles, and water-in-oil emulsion droplets.Similarities and differences in reactive patterns are highlighted, indicating at the sametime the unanswered questions. Some of the theoretical models, which have beenproposed in the literature to interpret or model self-reproduction of micelles and vesicles,will be illustrated. We will also discuss whether and to what extent such processescomply with the theory of autopoiesis—from which they have been in fact generated,from the historical as well as strategic viewpoint.Finally, we will also shortly discuss the relevance of the self-reproduction of vesicles foremerging avenues of research, in particular for the field of minimal cells, meant as thecompartments having the minimal and sufficient complexity to be defined as living
Approaches to semi-synthetic minimal cells: a review.
No full textFollowing is a synthetic review on the minimal living cell, defined as an artificial or a semi-artificial cellhaving the minimal and sufficient number of componentsto be considered alive. We describe concepts and experimentsbased on these constructions, and we point out thatan operational definition of minimal cell does not define asingle species, but rather a broad family of interrelated celllike structures. The relevance of these researches, considering that the minimal cell should also correspond to the early simple cell in the origin of life and early evolution, is also explained. In addition, we present detailed data in relation to minimal genome, with observations cited by several authors who agree on setting the theoretical fullfledged minimal genome to a figure between 200 and 300 genes. However, further theoretical assumptions may significantly reduce this number (i.e. by eliminating ribosomal proteins and by limiting DNA and RNA polymerases to only a few, less specific molecular species). Generally, the experimental approach to minimal cells consists in utilizing liposomes as cell models and in filling them with genes/ enzymes corresponding to minimal cellular functions. To date, a few research groups have successfully induced the expression of single proteins, such as the green fluorescence protein, inside liposomes. Here, different approaches are described and compared. Present constructs are still rather far from the minimal cell, and experimental as well as theoretical difficulties opposing further reduction of complexity are discussed. While most of these minimal cell constructions may represent relatively poor imitations of amodern full-fledged cell, further studies will begin precisely from these constructs. In conclusion, we give a brief outline of the next possible steps on the road map to the minimal cell
From the minimal genome to the minimal cell: theoretical and experimental investigations.
No full textIt is known that even the simplest living cells existing on the Earth have several hundredgenes, with hundreds of expressed proteins that catalyse simultaneously hundreds ofreactions within the same tiny compartment the cell representing a maize of anenormous and fascinating complexity. On the other hand, if we think to early cells orprotocells (those that played a key role in the origin of life), it is conceivable that theycould display some living properties with a minor number of biochemicalcomponents. In particular, the present huge complexity is most likely resulted frombillions of years of evolution, that developed a series of defence and securitymechanisms, redundancies, metabolic loops and highly sophisticated regulatoryprocesses.These considerations elicit the question, whether such a complexity is reallyessential for life, or whether instead cellular life might be possible with a much smallernumber of components. In this chapter we describe the basis of the concepts ofminimal genome and of the minimal cell.The question of the minimal genome and minimal cell has been considered sincemany years, and one should in particular recall the work of Morowitz (1967), who,based on the enzymatic components of primary metabolism, estimated that the size of aminimal cell should be about one-tenth smaller than Mycoplasma genitalium.Significant earlier insights into the field are those by Jay and Gilbert (1987) as well asby Woese (1983) and Dyson (1982). More recently, the reviews by Deamer andcoworkers (Pohorille and Deamer, 2002) and Luisis group (Luisi 2002, Oberholzer andLuisi, 2002) have sharpened the question and brought it in the perspective of modernmolecular tools. In fact, the last years have seen a significant revival of interest in thefield of the minimal cell, as witnessed for example by two international meetings held in2004 on the subject (Szathmáry, 2005). A more detailed version of a review on theminimal cell is in press elsewhere (Luisi et al., 2005)
HIGH THROUGHPUT PROTEIN STRUCTURE PREDICTION IN A GRID ENVIRONMENT
No full textThe number of known natural protein sequences, though quite large, is infinitely small as compared to the number of proteins theoretically possible with the twenty natural amino acids. Thus, there exists a huge number of protein sequences which have never been observed in nature, the so called “never born proteins”. The study of the structural and functional properties of "never born proteins" represents a way to improve our knowledge on the fundamental properties that make existing protein sequences so unique. Furthermore it is of great interest to understand if the extant proteins are only the result of contingency or else the result of a selection process based on the peculiar physico-chemical properties of their protein sequence. Protein structure prediction tools combined with the use of large computing resources allow to tackle this problem. In fact, the study of never born proteins requires the generation of a large library of protein sequences not present in nature and the prediction of their three-dimensional structure. This is not trivial when facing 105-107 protein sequences. Indeed, on a single CPU it would require years to predict the structure of such a large library of protein sequences. On the other hand, this is an embarassingly parallel problem in which the same computation (i.e. the prediction of the three-dimensional structure of a protein sequence) must be repeated several times (i.e. on a large number of protein sequences). The use of grid infrastructures makes feasible to approach this problem in an acceptable time frame. In this paper we describe the set up of a simulation environment within the EUChinaGRID infrastructure that allows user friendly exploitation of grid resources for large-scale protein structure prediction
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