Hypothesized origin of microbial life in a prebiotic gel and the transition to a living biofilm and microbial mats

This article hypothesizes that the origin of the first microbial cell(s) occurred as a series of increasing levels of organization within a prebiotic gel attached to a mineral surface, which made the transition to a biofilm composed of the first cell(s) capable of growth and division. A gel microenvironment attached to a surface for the origin of life, and subsequent living cells offers numerous advantages. These include acting as a water and nutrient trap on a surface, physical protection as well as protection from UV radiation. The prebiotic gel and the living biofilm contained the necessary water, does not impede diffusion of molecules including gases, provides a structured gel microscopic location for biochemical interactions and polymerisation reactions, where the necessary molecules for life need to be present and not limiting. The composition of the first gel environment may have been an oily-water mixture (or the interface between an oily-water mixture) of microscopic dimensions, but large enough for the organization of the first cell(s). The living biofilm then made the evolutionary transition to a microbial mat.     

Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses

During packaging in positive-sense single-stranded RNA (+ssRNA) viruses, coat proteins (CPs) interact directly with multiple regions in genomic RNA (gRNA), but the underlying physicochemical principles remain unclear. Here we analyze the high-resolution cryo-EM structure of bacteriophage MS2 and show that the gRNA/CP binding sites, including the known packaging signal, overlap significantly with regions where gRNA nucleobase-density profiles match the corresponding CP nucleobase-affinity profiles. Moreover, we show that the MS2 packaging signal corresponds to the global minimum in gRNA/CP interaction energy in the unstructured state as derived using a linearly additive model and knowledge-based nucleobase/amino-acid affinities. Motivated by this, we predict gRNA/CP interaction sites for a comprehensive set of 1082 +ssRNA viruses. We validate our predictions by comparing them with site-resolved information on gRNA/CP interactions derived in SELEX and CLIP experiments for 10 different viruses. Finally, we show that in experimentally studied systems CPs frequently interact with autologous coding regions in gRNA, in agreement with both predicted interaction energies and a recent proposal that proteins in general tend to interact with own mRNAs, if unstructured. Our results define a self-consistent framework for understanding packaging in +ssRNA viruses and implicate interactions between unstructured gRNA and CPs in the process.     

A model for the prebiotic synthesis of peptides which throws light on the origin of the genetic code and the observed chirality of life

A model is proposed which indicates that peptides could have been synthesized on RNA templates. L-amino acids are selectively trapped and orientated in clefts in an apparently stable RNA structure attached to a solid phase. Each cleft is bounded by three bases which correspond to the codon for that amino acid. Rotation during a dehydration phase orientates the amino acids so that peptide bond formation can occur by condensation. Rehydration releases the formed peptides.     

Diatom life cycles and ecology in the Cretaceous

The earliest known diatom fossils with well‐preserved siliceous frustules are from Lower Cretaceous neritic marine deposits in Antarctica. In this study, we analyzed the cell wall structure to establish whether their cell and life cycles were similar to modern forms. At least two filamentous species (Basilicostephanus ornatus and Archepyrgus melosiroides) had girdle band structures that functioned during cell division in a similar way to present day Aulacoseira species. Also, size analyses of cell diameter indicated that the cyclic process of size decline and size restoration used to time modern diatom life cycles was present in five species from the Lower Cretaceous (B. ornatus, A. melosiroides, Gladius antiquus, Ancylopyrgus reticulatus, Kreagra forfex) as well as two species from Upper Cretaceous deposits (Trinacria anissimowii and Eunotogramma fueloepi) from the Southwest Pacific. The results indicate that the “Diatom Sex Clock” was present from an early evolutionary stage. Other ecological adaptations included changes in mantle height and coiling. Overall, the results suggest that at least some of the species in these early assemblages are on a direct ancestral line to modern forms.     

Inadequacy of prebiotic synthesis as origin of proteinous amino acids

Summary The production of some nonproteinous, and lack of production of other proteinous, amino acids in model prebiotic synthesis, along with the instability of glutamine and asparagine, suggest that not all of the 20 presentday proteinous amino acids gained entry into proteins directly from the primordial soup. Instead, a process of active co-evolution of the genetic code and its constituent amino acids would have to precede the final selection of these proteinous amino acids.     

Macromolecules and the origin of life

From our knonwledge of present day organisms, it is hard to imagine a living assembly, even at its most primitive stage, without macromolecules.In order to look for the macromolecules which possibly participated in the assembly of the primitive organisms, the reaction and formation of polymers in HCN under irradiation of ultraviolet ray of 184.9 nm. was studied.As a example of a simple way of producing an assembly of macromolecules, the mechanism of coacervation was studied by using gelatin as the material.     

Chance and the origin of life

Random chemical reactions in the Earth's primitive hydrosphere could have generated no more than 200 bits of information, whereas the first Darwinian organism must have encoded about a million bits, and therefore could not have arisen by chance. This information gap is bridged by separating reproduction from organism, and postulating a reproductive chemical community that would generate information by proto-Darwinian evolution. The information content of the initial community could have been as low as 160 bits, and its evolution might have led to the first Darwinian cell.     

Symbiosis and the origin of life

The paper uses chemical kinetic arguments and illustrations by computer modelling to discuss the origin and evolution of life. Complex self-reproducing chemical systems cannot arise spontaneously, whereas simple auto-catalytic systems can, especially in an irradiated aqueous medium. Self-reproducing chemical particles of any complexity, in an appropriate environment, have a self-regulating property which permits long-term survival. However, loss of materials from the environment can lead to continuing decay which is circumvented by physical union between different kinds of self-reproducing particles. The increasing complexity produced by such unions (symbioses) is irreversible so that the chemical system evolves. It is suggested that evolution by successive symbioses brough about the change from simple, spontaneously arising, auto-catalytic particles to complex prokaryotic cells.     

Chance and the origin of life

Random chemical reactions in the Earth's primitive hydrosphere could have generated no more than 200 bits of information, whereas the first Darwinian organism must have encoded about a million bits, and therefore could not have arisen by chance. This information gap is bridged by separating reproduction from organism, and postulating a reproductive chemical community that would generate information by proto-Darwinian evolution. The information content of the initial comunity could have been as low as 160 bits, and its evolution might have led to the first Darwinian cell.     

Clay and the origin of life

Research concerning the possible role of clay in chemical evolution is reviewed. The probable importance of clays in the origin of life is assessed.     

On the origin of life

On the basis of the recently proposed new fundamental equation of mathematical biophysics, a suggestion is made for a theory of the formation of a primitive cell from nonliving material. The discussion includes a suggestion for a quantitative formulation of the degree of biological organization. It is shown that according to the fundamental equation of mathematical biophysics, organization of the nonliving material may spontaneously increase under certain conditions, leading to a formation of a primitive organism. This process however, is a very slow one, requiring time intervals of several years or even decades. This may account for the failure in observing or artificially producing spontaneous generation.     

Chromatographic separation as selection process for prebiotic evolution and the origin of the genetic code

A model for the evolution of a translation apparatus has been suggested where oligonucleotides in a hairpin conformation act as primordial adapters. Specifically activated amino acids are assumed to be attached to these hairpin molecules. For the specific activation, a chromatographic separation of, e.g. ala and CMP from gly and GMP can be accomplished on silica (e.g. of volcanic origin) with aqueous salt solutions. Other adsorbents like clays (kaolin, bentonite, montmorillonite), different silicates (florisil, magnesium trisilicate, calcium silicate, talc), hydroxyapatite, barium sulfate, calcium carbonate, calcium fluoride and titanoxide have been examined as model systems for the separation of nucleotides, nucleosides and amino acids on mineral surfaces. The possible role of chromatographic separation of amino acids for the formation of proteinoids, composed of selected amino acids, is also considered.     

After the origin of life

Acta Biotheoretica - As to the primary morphogenesis which occurred after the origin of life, two conditions are considered. The above conditions are satisfied by the morphogenetic polarity....     

区域生态学的国际起源和研究热点

20世纪80年代以来,区域生态学迅速发展,成为生态学领域重要的分支学科。本文综述了区域生态学的国际起源、发展脉络,以及主要研究热点,对比了国内外区域生态学研究的区别以及对国内区域生态学发展的启示。分析表明,在国际上,区域生态学的研究热点主要集中在生物多样性保护、区域气候变化影响、生态系统服务、城市生态学、区域生态修复和可持续发展等方面。由于国情以及学科发展进度不同,国内外区域生态学研究在关注问题、研究思路和研究手段上存在区别。国内区域生态学受学科起步较晚、相关数据的质、量和利用率较低及对方法和模型研究尚浅的影响,未来研究要在深度利用遥感数据的基础上,加强学科理论和方法的学习,重点关注气候变化影响生态过程的机理、生态模型优化、全国生态系统服务评估与定价、区域生态安全以及区域可持续发展规划。     

The predatory ecology of Deinonychus and the origin of flapping in birds

Most non-avian theropod dinosaurs are characterized by fearsome serrated teeth and sharp recurved claws. Interpretation of theropod predatory ecology is typically based on functional morphological analysis of these and other physical features. The notorious hypertrophied 'killing claw' on pedal digit (D) II of the maniraptoran theropod Deinonychus (Paraves: Dromaeosauridae) is hypothesized to have been a predatory adaptation for slashing or climbing, leading to the suggestion that Deinonychus and other dromaeosaurids were cursorial predators specialized for actively attacking and killing prey several times larger than themselves. However, this hypothesis is problematic as extant animals that possess similarly hypertrophied claws do not use them to slash or climb up prey. Here we offer an alternative interpretation: that the hypertrophied D-II claw of dromaeosaurids was functionally analogous to the enlarged talon also found on D-II of extant Accipitridae (hawks and eagles; one family of the birds commonly known as "raptors"). Here, the talon is used to maintain grip on prey of subequal body size to the predator, while the victim is pinned down by the body weight of the raptor and dismembered by the beak. The foot of Deinonychus exhibits morphology consistent with a grasping function, supportive of the prey immobilisation behavior model. Opposite morphological trends within Deinonychosauria (Dromaeosauridae + Troodontidae) are indicative of ecological separation. Placed in context of avian evolution, the grasping foot of Deinonychus and other terrestrial predatory paravians is hypothesized to have been an exaptation for the grasping foot of arboreal perching birds. Here we also describe "stability flapping", a novel behaviour executed for positioning and stability during the initial stages of prey immobilisation, which may have been pivotal to the evolution of the flapping stroke. These findings overhaul our perception of predatory dinosaurs and highlight the role of exaptation in the evolution of novel structures and behaviours.