Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis

We have investigated the origin of genes, the genetic code, proteins and life using six indices (hydropathy, α-helix, β-sheet and β-turn formabilities, acidic amino acid content and basic amino acid content) necessary for appropriate three-dimensional structure formation of globular proteins. From the analysis of microbial genes, we have concluded that newly-born genes are products of nonstop frames (NSF) on antisense strands of microbial GC-rich genes [GC-NSF(a)] and from SNS repeating sequences [(SNS)_n] similar to the GC-NSF(a) (S and N mean G or C and either of four bases, respectively). We have also proposed that the universal genetic code used by most organisms on the earth presently could be derived from a GNC-SNS primitive genetic code. We have further presented the [GADV]-protein world hypothesis of the origin of life as well as a hypothesis of protein production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions termed as GNC-, SNS and GC-NSF(a)-0th order structures of proteins. The [GADV]-protein world hypothesis is primarily derived from the GNC-primitive genetic code hypothesis. It is also expected that basic properties of extant genes and proteins could be revealed by considerations based on the scenario with four stages This review is a modified English version of the paper, which was written in Japanese and published inViva Origino 2001 29 66–85.     

Biochemical analysis of a DNA replication origin in the archaeon Aeropyrum pernix

We have characterised the interaction of the Aeropyrum pernix origin recognition complex proteins (ORC1 and ORC2) with DNA using DNase I footprinting. Each protein binds upstream of its respective gene. However, ORC1 protein alone interacts more tightly with an additional region containing multiple origin recognition box (ORB) sites that we show to be a replication origin. At this origin, there are four ORB elements disposed either side of an A+T-rich region. An ORC1 protein dimer binds at each of these ORB sites. Once all four ORB sites have bound ORC1 protein, there is a transition to a higher-order assembly with a defined alteration in topology and superhelicity. Furthermore, after this transition, the A+T-rich region becomes sensitive to digestion by DNase I and P1 nuclease, revealing that the transition promotes distortion of the DNA in this region, presumably as a prelude to loading of MCM helicase.     

Identification and functional analysis of a human homologue of the monkey replication origin ors8

We previously isolated from African green monkey (CV-1) cells a replication origin, ors8, that is active at the onset of S-phase. Here, its homologous sequence (hors8, accession number: DQ230978) was amplified from human cells, using the monkey-ors8-specific primers. Sequence alignment between the monkey and the human fragment revealed a 92% identity. Nascent DNA abundance analysis, involving quantification by real-time PCR, indicated that hors8 is an active replication origin, as the abundance of nascent DNA from a genomic region containing it was 97-fold higher relative to a non-origin region in the same locus. Furthermore, the data showed that the hors8 fragment is capable of supporting the episomal replication of its plasmid, when cloned into pBlueScript (pBS), as assayed by the DpnI resistance assay after transfection of HeLa cells. A quantitative chromatin immunoprecipitation (ChIP) assay, using antibodies against Ku, Orc2, and Cdc6, showed that these DNA replication initiator proteins were associated in vivo with the human ors8 (hors8). Finally, nascent DNA abundance experiments from human cells synchronized at different phases of the cell cycle revealed that hors8 is a late-firing origin of DNA replication, having the highest activity 8 h after release from late G(1).     

The origin of protein bodies in developing soybean cotyledons: a proposal

Summary The biogenesis of protein bodies is examined in cotyledons of soybean (Glycine max, Merr) at the time when reserve protein is beginning to accumulate in the cotyledons. Reserve protein is deposited in the central vacuoles of parenchyma cells and new protein bodies arise from the central vacuole by pinching-off small masses of reserve protein surrounded by a portion of the tonoplast.Supported by a grant to MJC from the National Science Foundation (Metabolic Biology) and a grant (to BYY) from the National Research Council of Canada.On leave from the Department of Biology, University of New Brunswick, N.B., Canada.     

Tracing origins and migration of wildlife using stable isotopes: a review

To understand the ecology of migratory animals it is important to link geographic regions used by individuals including breeding, wintering, and intermediate stopover sites. Previous conventional approaches used to track animal movements have relied on extrinsic markers and typically the subsequent recovery of individuals. This approach has generally been inappropriate for most small, or non-game animals. The use of intrinsic markers such as fatty acid profiles, molecular DNA analyses, and the measurement of naturally occurring stable isotopes in animal tissues offer alternative approaches. This paper reviews the use of stable isotope analyses (primarily δ¹³C, δ¹⁵N, δ³⁴S, δD, δ⁸⁷Sr) to trace nutritional origin and migration in animals. This approach relies on the fact that foodweb isotopic signatures are reflected in the tissues of organisms and that such signatures can vary spatially based on a variety of biogeochemical processes. Organisms moving between isotopically distinct foodwebs can carry with them information on the location of previous feeding. Such an approach has been used to track animal use of inshore versus offshore, marine versus freshwater, terrestrial C₃ versus marine, terrestrial mesic versus xeric, and C₃ versus C₄ or Crassulacean acid metabolism foodwebs. More recently, the use of stable hydrogen isotope analyses (δD) to link organisms to broad geographic origin in North America is based on large-scale isotopic contours of growing-season average δD values in precipitation. This technique, especially when combined with the assay of other stable isotopes, will be extremely useful in helping to track migration and movement of a wide range of animals from insects to birds and mammals. Future research to refine our understanding of natural and anthropogenic-induced isotopic gradients in nature, and to explore the use of stable isotopes of other elements, is recommended. Received: 1 July 1998 / Accepted: 9 December 1998     

Predation between prokaryotes and the origin of eukaryotes

Accumulating data suggest that the eukaryotic cell originated from a merger of two prokaryotes, an archaeal host and a bacterial endosymbiont. However, since prokaryotes are unable to perform phagocytosis, the means by which the endosymbiont entered its host is an enigma. We suggest that a predatory or parasitic interaction between prokaryotes provides a reasonable explanation for this conundrum. According to the model presented here, the host in this interaction was an anaerobic archaeon with a periplasm‐like space. The predator was a small (facultative) aerobic α‐proteobacterium, which penetrated and replicated within the host periplasm, and later became the mitochondria. Plausible conditions under which this interaction took place and circumstances that may have led to the contemporary complex eukaryotic cell are discussed.     

Dissociation in a Polymerization Model of Homochirality

A fully self-contained model of homochirality is presented that contains the effects of both polymerization and dissociation. The dissociation fragments are assumed to replenish the substrate from which new monomers can grow and undergo new polymerization. The mean length of isotactic polymers is found to grow slowly with the normalized total number of corresponding building blocks. Alternatively, if one assumes that the dissociation fragments themselves can polymerize further, then this corresponds to a strong source of short polymers, and an unrealistically short average length of only 3. By contrast, without dissociation, isotactic polymers becomes infinitely long.     

Aspects of the history and evolution of Alpine lakes in Austria

The age of lake basins, the onset of meromictic conditions and some consequences of eutrophication and reoligotrophication of Austrian Alpine lakes are presented. The obviously conflicting view of archeologists about lake levels during the period of lake dwellings is brought forward and some data about the effects of fish stocking are discussed.     

Kinetic Origin of Heredity in a Replicating System with a Catalytic Network

The origin of heredity is studied as a recursive state in a replicatingprotocell consisting of many molecule species in mutually catalyzingreaction networks. Protocells divide when the number of molecules, increasing due to replication, exceeds a certain threshold. We study how the chemicals in a catalytic network can form recursive production states in the presence of errors in the replication process. Depending on the balance between the total number of molecules in a cell and the number of molecule species, we have found three phases; a phase without a recursive production state, a phase with itinerancy over a few recursive states, and a phase with fixedrecursive production states. Heredity is realized in the latter two phaseswhere molecule species that are population-wise in the minority are preserved and control the phenotype of the cell. It is shown that evolvability is realized in the itinerancy phase, where a change in the number of minority molecules controls a change of the chemical state.     

Abiogenic synthesis of prebiotic matter for the Earth’s biosphere as a stage of self-organization on an astrophysical and paleontological time scale

Existing data suggest that an early circumstellar preplanetary disk was the most likely location for primary abiogenic synthesis of prebiotic organic matter from simple molecules along with the “RNA world” and the origin of life. This paper discusses the stages of self-organization that have resulted in the Earth’s modern biosphere, and the relationships between astrophysical and paleontological events in evolution.     

Polycyclic Aromatic Hydrocarbons (PAHs) in Soil and Sediment from Industrial,Residential, and Agricultural Areas in Central South Africa: An Initial Assessment

Polycyclic aromatic hydrocarbons (PAHs) are of global concern due to their ubiquitous presence, toxicity, and carcinogenicity. No data on PAHs in soils from South Africa have been published, even though it has the largest economy and industrial base in Africa. During this initial assessment, the levels of PAHs were determined in soils and sediments collected from central South Africa, specifically targeting industrial, residential, and agricultural areas. Analysis was performed by gas chromatography/mass spectrometry (GC/MS). The total concentration of PAHs (Σt-PAH) ranged between 44 and 39,000 ng/g, dw and the concentration of carcinogenic PAHs (Σc-PAH) ranged between 19 and 19,000 ng/g, dw. Pyrogenic processes were the most likely sources, with minimal petrogenic contributions. PAH levels were in the same range as levels reported from other countries, and the majority of the sites did not exceed Canadian environmental quality guidelines. Based on assumptions for dermal contact and ingestion of PAH-contaminated soil, we provisionally calculated only a small increase in cancer risk, but additional PAH inhalation could add considerably to this risk. Our data indicates a need for more analysis in industrial and residential areas, and should include air.     

质体样细胞器APICOPLAST起源的分子证据评述

顶复合器门的原生动物（Apicomplexan protozoa）含有一个高度退化的质体样（plastid-like）细胞器,定名为apicoplast。Apicoplast的进化起源是一个长期激烈争论的问题,尽管使用了多种分子技术,但尚未取得一致的结论,以致成为质体起源研究的典型案例。文章评述了apicoplast起源研究的分子证据,分析了新的分子证据的可能来源,为进一步研究提供线索。     

The evolution of multicellularity in animals as a shift in biological autonomy

The hypothesis is advanced that major evolutionary innovations are characterized by an increase of organismal autonomy in the sense of an emancipation from the environment. After a brief overview of the literature on this concept, increasing autonomy is defined as the evolutionary shift in the individual system-environment relationship, so that the direct influences of the environment are gradually reduced and a stabilization of self-referential, intrinsic functions within the system is generated. This is described as relative autonomy because numerous interconnections with the environment and dependencies upon it are retained. Elements of an increasing autonomy are spatial separations, an increase in homeostatic functions, internalizations and an increase in physiological and behavioral flexibility. These elements are described by taking the transition from single cells to metazoans as a case study. The principle of increasing autonomy is of central relevance for understanding this transition. The hypothesis does not contradict the principle of adaptation, but rather contributes to a further understanding of its elements as it supplies aspects for a reconsideration of the relationship between the outside and the inside, between organism and environment.     

Self-Organization and Evolutionin a Simulated Cross Catalyzed Network

Motivated by an alternative to the concept of a prebiotic soup inthe form of interacting crystal growth close to hot vents, we investigatea model system in which the growth rate of a particular entity is modified (enhanced or reduced) by other entities present, thus forming aweb of cross catalysis. Initially random interactions are imposed, butthe entities compete for a common source, and some entities may thusvanish in the competition. New entities, or mutations (error copies),with randomly selected interactions to the web are then introduced,and the concentrations of the entities are followed as solutions to stiffordinary differential equations. Entities with positive growth maycreate new related entities with slightly randomly modified interactions to the web. Extinctions, wild-type survival and replacement,and self-organization to sustain periodic external variations, are studied. It is shown that even systems with mostly cross-inhibition and noinitial autocatalysis may eventually create highly stable self-organizedsystems. We find that an already established cross catalyzed systemoften wins over a selfreplicating invader (or mutant).     

Morphology and diversity of the forcipules in Strigamia centipedes (Chilopoda,Geophilomorpha)

The morphology of the venomous limbs (forcipules) of 13 species of Strigamia and of six other geophilomorphs was studied with light microscopy, scanning electron microscopy, and, for a subsample, with confocal laser scanning microscopy. In all Strigamia species a well-distinct denticle is present invariantly on the inner side of the terminal article (tarsungulum), in sub-basal position, just proximal to a faint transverse sulcus and a cuticular introflexion that corresponds to the insertion point of a tendon. Strigamia species differ mainly in size and shape of the denticle and thickness of the distal part of the tarsungulum, suggesting some functional diversity in piercing and handling prey. Anatomical evidence supports the hypothesis that the tarsungulum corresponds to two ancestral articles and a denticle at the basis of the tarsungulum originated multiple times within geophilomorphs, however in different positions corresponding to either the ancestral sub-terminal article (in Strigamia, other Geophiloidea and some Schendylidae) or the ancestral terminal article (in the himantariid Thracophilus).     

Reproductive efficiency of captive Chinese- and Indian-origin rhesus macaque (Macaca mulatta) females

Reproductive and survival records (n=2,913) from 313 Chinese-origin and 365 Indian-derived rhesus macaques at the Tulane National Primate Research Center (TNPRC) spanning three generations were studied. Least-squares analysis of variance procedures were used to compare reproductive and infant survival traits while proportional hazards regression procedures were used to study female age at death, number of infants born per female, and time from last birth to death. Chinese females were older at first parturition than Indian females because they were older when placed with males, but the two subspecies had similar first postpartum birth interval (1st PPBI) and lifetime postpartum birth interval (LPPBI). Females that gave birth to stillborn infants had shorter first postpartum birth intervals (1st PPBI) than females giving birth to live infants. Postpartum birth intervals decreased in females from age 3 to 12 but then increased again with advancing age. Chinese infants had a greater survival rate than Indian infants at 30 days, 6 months, and 1 year of age. Five hundred and forty-three females (80.01%) had uncensored, or true records for age at death, number of infants born per female, and time from the birth until death whereas 135 females (19.91%) had censored records for these traits. Low- and high-uncensored observations for age at death were 3 and 26 years for Chinese, and 3 and 23 years for Indian females. Uncensored number of infants born per female ranged from 1 to 15 for Chinese females and 1 to 18 for Indian females. Each of these traits was significantly influenced by the origin×generation interaction in the proportional hazards regression analyses, indicating that probabilities associated with age at death, number of infants born per female, and time from last birth to death for Chinese and Indian females did not rank the same across generations.     

Trace and rare earth elements in monofloral and multifloral honeys from Northwestern Italy; A first attempt of characterization by a multi-elemental profile

BackgroundMetals are a minor constituent in honey, but they have been suggested to be a potential tool to characterize honeys according to their botanical or geographical origin.MethodsA total of 40 metals were analyzed by Inductively Coupled Plasma-Mass Spectrometry in monofloral and multifloral honeys from Northwestern Italy. PCA and ANOVA were used to discriminate honeys according to the various floral types.ResultsThe highest levels of trace elements and rare earth elements (REEs) were found in chestnut honey, while the lowest concentrations were recorded in acacia and rhododendron honeys. Rubidium and aluminum were the most represented nonessential elements, while manganese, iron, zinc and copper had the highest values of the essential elements. Potentially toxic elements arsenic, cadmium and lead were close to or below the limit of quantification.ConclusionsThe present study showed significant differences in metal concentrations according to honey floral type, reflecting the strong influence of botanical origin on the chemical composition of this particular food.