Origins of Life and Evolution of Biospheres最新文献

{"title":"Introduction to Origins of Biological Homochirality.","authors":"Axel Brandenburg, David Hochberg","doi":"10.1007/s11084-022-09629-4","DOIUrl":"https://doi.org/10.1007/s11084-022-09629-4","url":null,"abstract":"","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"52 1-3","pages":"1-2"},"PeriodicalIF":2.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9169486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spontaneous Emergence of Transient Chirality in Closed, Reversible Frank-like Deterministic Models","authors":"T. Buhse, J. Micheau","doi":"10.1007/s11084-022-09621-y","DOIUrl":"https://doi.org/10.1007/s11084-022-09621-y","url":null,"abstract":"","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"13 1","pages":"1-18"},"PeriodicalIF":2.0,"publicationDate":"2022-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77719296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Self-Assembly as a Trigger of Life Origin and Development","authors":"D. Zlenko, A. M. Zanin, S. Stovbun","doi":"10.1007/s11084-022-09620-z","DOIUrl":"https://doi.org/10.1007/s11084-022-09620-z","url":null,"abstract":"","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"77 ","pages":"105-111"},"PeriodicalIF":2.0,"publicationDate":"2022-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72544902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gaia as Solaris: An Alternative Default Evolutionary Trajectory","authors":"S. Janković, Ana Katić, M. 'Cirkovi'c","doi":"10.1007/s11084-022-09619-6","DOIUrl":"https://doi.org/10.1007/s11084-022-09619-6","url":null,"abstract":"","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"6 1","pages":"129-147"},"PeriodicalIF":2.0,"publicationDate":"2022-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76671432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational Study of the Stability of Natural Amino Acid isomers.","authors":"Stefano Crespi,&nbsp;Dhanalakshmi Vadivel,&nbsp;Alfredo Bellisario,&nbsp;Daniele Dondi","doi":"10.1007/s11084-021-09615-2","DOIUrl":"https://doi.org/10.1007/s11084-021-09615-2","url":null,"abstract":"<p><p>The secular debate on the origin of life on our planet represents one of the open challenges for the scientific community. In this endeavour, chemistry has a pivotal role in disclosing novel scenarios that allow us to understand how the formation of simple organic molecules would be possible in the early primitive geological ages of Earth. Amino acids play a crucial role in biological processes. They are known to be formed in experiments simulating primitive conditions and were found in meteoric samples retrieved throughout the years. Understanding their formation is a key step for prebiotic chemistry. Following this reasoning, we performed a computational investigation over 100'000 structural isomers of natural amino acids. The results we have found suggest that natural amino acids are among the most thermodynamically stable structures and, therefore, one of the most probable ones to be synthesised among their possible isomers.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"51 4","pages":"287-298"},"PeriodicalIF":2.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39593312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ribozyme Mutagenic Evolution: Mechanisms of Survival.","authors":"Carolina Diaz Arenas,&nbsp;Aleksandra Ardaševa,&nbsp;Jonathan Miller,&nbsp;Alexander S Mikheyev,&nbsp;Yohei Yokobayashi","doi":"10.1007/s11084-021-09617-0","DOIUrl":"https://doi.org/10.1007/s11084-021-09617-0","url":null,"abstract":"<p><p>Primeval populations replicating at high error rates required a mechanism to overcome the accumulation of mutations and information deterioration. Known strategies to overcome mutation pressures include RNA processivity, epistasis, selection, and quasispecies. We investigated the mechanism by which small molecular ribozyme populations can survive under high error rates by propagating several lineages under different mutagen concentrations. We found that every population that evolved without mutagen went extinct, while those subjected to mutagenic evolution survived. To understand how they survived, we characterized the evolved genotypic diversity, the formation of genotype-genotype interaction networks, the fitness of the most common mutants for each enzymatic step, and changes in population size along the course of evolution. We found that the elevated mutation rate was necessary for the populations to survive in the novel environment, in which all the steps of the metabolism worked to promote the survival of even less catalytically efficient ligases. Besides, an increase in population size and the mutational coupling of genotypes in close-knit networks, which helped maintain or recover lost genotypes making their disappearance transient, prevented Muller's ratchet and extinction.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"51 4","pages":"321-339"},"PeriodicalIF":2.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39793637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Effect of Goethites on the Polymerization of Glycine and Alanine Under Prebiotic Chemistry Conditions.","authors":"João Paulo T Baú,&nbsp;Cristine E A Carneiro,&nbsp;Antônio Carlos S da Costa,&nbsp;Daniel F Valezi,&nbsp;Eduardo di Mauro,&nbsp;Eduardo Pilau,&nbsp;Dimas A M Zaia","doi":"10.1007/s11084-021-09618-z","DOIUrl":"https://doi.org/10.1007/s11084-021-09618-z","url":null,"abstract":"<p><p>After pre concentration of monomers, polymerization is the second most important step for molecular evolution. The formation of peptides is an important issue for prebiotic chemistry and consequently for the origin of life. In this work, goethite was synthesized by two different routes, named goethite-I and goethite-II. Although both samples are goethite, Far-FT-IR spectroscopy and EPR spectroscopy showed differences between them, and these differences had an effect on the polymerization of glycine and alanine. For the amino acid polymerization, three protocols were used, that resembled prebiotic Earth conditions: a) amino acid plus goethite were mixed and heated at 90 °C for 10 days in solid state, b) a wet impregnation of the amino acid in the goethite, with subsequent heating at 90 °C for 10 days in solid state, and c) 10 wet/dry cycles each one for 24 h at 90 °C. Experiments with glycine plus goethite-II, using protocols B and C, produced only Gly-Gly. In addition, for the C protocol the amount of Gly-Gly synthesized was 3 times higher than the amount of Ala-Ala. Goethite-I presented a decrease in the EPR signal, when it was submitted to the protocols with and without amino acids. It is probable the decrease in the intensity of the EPR signal was due to a decrease in the imperfections of the mineral. For all protocols the mixture of alanine plus goethite-I or goethite-II produced c(Ala-Ala). However, for wet/dry cycles, protocol C presented higher yields (p < 0.05). In addition, Ala-Ala was produced using protocols A and C. The c(Ala-Ala) formation fitted a zero-order kinetic equation model. The surface areas of goethite-I and goethite-II were 35 m² g^-1 and 37 m² g^-1, respectively. Thermal analysis indicated that the mineral changes the thermal behavior of the amino acids. The main reactions for the thermal decomposition of glycine were deamination and dehydration and for alanine was deamination.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"51 4","pages":"299-320"},"PeriodicalIF":2.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39962188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Codon Usage in the Minimal Natural Cell.","authors":"Piotr H Pawłowski","doi":"10.1007/s11084-021-09616-1","DOIUrl":"https://doi.org/10.1007/s11084-021-09616-1","url":null,"abstract":"<p><p>A statistical analysis of the variation in contents with the size of the current known smallest genomes, N. deltocephalinicola, C. ruddii, N. equitans, and M. genitalium, enabled the indication of a minimal set of codons capable of naturally building a modern-type free-living unicellular organism in an early stage of evolution. Using a linear regression model, the potential codon distribution in the minimal natural cell was predicted and compared to the composition of the smallest synthetic, JCVI-Syn3.0. The distribution of the molecular weight of potentially coded amino acids was also calculated. The main differences in the features of the minimal natural cell and H. Sapiens genome were analyzed. In this regard, the content percentage of respective amino acids and their polarization charge properties were reported and compared. The fractions of occurring nucleotides were calculated, too. Then, the estimated numbers of codons in a minimal natural cell were related to the expected numbers for random distribution. Shown increase, or decrease in the contents, relative to the calculated random filling was related to the evolutionary preferences, varying with the subsequent eras of the evolution of genetic code.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"51 3","pages":"215-230"},"PeriodicalIF":2.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39555370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Does Stochasticity Favour Complexity in a Prebiotic Peptide-Micelle System?","authors":"Rowena Ball,&nbsp;John Brindley","doi":"10.1007/s11084-021-09614-3","DOIUrl":"https://doi.org/10.1007/s11084-021-09614-3","url":null,"abstract":"<p><p>A primordial environment that hosted complex pre- or proto-biochemical activity would have been subject to random fluctuations. A relevant question is then: What might be the optimum variance of such fluctuations, such that net progress could be made towards a living system? Since lipid-based membrane encapsulation was undoubtedly a key step in chemical evolution, we used a peptide-micelle system in simulated experiments where simple micelles and peptide-stabilized micelles compete for the same amphiphilic lipid substrate. As cyclic thermal driver and energy source we used a thermochemical redox oscillator, to which the micelle reactions are coupled thermally through the activation energies. The long-time series averages taken for increasing values of the fluctuation variance show two distinct minima for simple micelles, but are smoothly increasing for complex micelles. This result suggests that the fluctuation variance is an important parameter in developing and perpetuating complexity. We hypothesize that such an environment may be self-selecting for a complex, evolving chemical system to outcompete simple or parasitic molecular structures.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"51 3","pages":"259-271"},"PeriodicalIF":2.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39399452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plausible Emergence and Self Assembly of a Primitive Phospholipid from Reduced Phosphorus on the Primordial Earth.","authors":"Michael O Gaylor, Pere Miro, Bess Vlaisavljevich, Ashen Anuradha Suduweli Kondage, Laura M Barge, Arthur Omran, Patrick Videau, Vaille A Swenson, Lucas J Leinen, Nathaniel W Fitch, Krista L Cole, Chris Stone, Samuel M Drummond, Kayli Rageth, Lillian R Dewitt, Sarah González Henao, Vytis Karanauskus","doi":"10.1007/s11084-021-09613-4","DOIUrl":"10.1007/s11084-021-09613-4","url":null,"abstract":"<p><p>How life arose on the primitive Earth is one of the biggest questions in science. Biomolecular emergence scenarios have proliferated in the literature but accounting for the ubiquity of oxidized (+ 5) phosphate (PO₄^3-) in extant biochemistries has been challenging due to the dearth of phosphate and molecular oxygen on the primordial Earth. A compelling body of work suggests that exogenous schreibersite ((Fe,Ni)₃P) was delivered to Earth via meteorite impacts during the Heavy Bombardment (ca. 4.1-3.8 Gya) and there converted to reduced P oxyanions (e.g., phosphite (HPO₃^2-) and hypophosphite (H₂PO₂^-)) and phosphonates. Inspired by this idea, we review the relevant literature to deduce a plausible reduced phospholipid analog of modern phosphatidylcholines that could have emerged in a primordial hydrothermal setting. A shallow alkaline lacustrine basin underlain by active hydrothermal fissures and meteoritic schreibersite-, clay-, and metal-enriched sediments is envisioned. The water column is laden with known and putative primordial hydrothermal reagents. Small system dimensions and thermal- and UV-driven evaporation further concentrate chemical precursors. We hypothesize that a reduced phospholipid arises from Fischer-Tropsch-type (FTT) production of a C8 alkanoic acid, which condenses with an organophosphinate (derived from schreibersite corrosion to hypophosphite with subsequent methylation/oxidation), to yield a reduced protophospholipid. This then condenses with an α-amino nitrile (derived from Strecker-type reactions) to form the polar head. Preliminary modeling results indicate that reduced phospholipids do not aggregate rapidly; however, single layer micelles are stable up to aggregates with approximately 100 molecules.</p>","PeriodicalId":19614,"journal":{"name":"Origins of Life and Evolution of Biospheres","volume":"51 3","pages":"185-213"},"PeriodicalIF":1.9,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39198521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}