Coevolution of compositional protocells and their environment

The coevolution of environment and living organisms is well known in nature. Here, it is suggested that similar processes can take place before the onset of life, where protocellular entities, rather than full-fledged living systems, coevolve along with their surroundings. Specifically, it is suggested that the chemical composition of the environment may have governed the chemical repertoire generated within molecular assemblies, compositional protocells, while compounds generated within these protocells altered the chemical composition of the environment. We present an extension of the graded autocatalysis replication domain (GARD) model--the environment exchange polymer GARD (EE-GARD) model. In the new model, molecules, which are formed in a protocellular assembly, may be exported to the environment that surrounds the protocell. Computer simulations of the model using an infinite-sized environment showed that EE-GARD assemblies may assume several distinct quasi-stationary compositions (composomes), similar to the observations in previous variants of the GARD model. A statistical analysis suggested that the repertoire of composomes manifested by the assemblies is independent of time. In simulations with a finite environment, this was not the case. Composomes, which were frequent in the early stages of the simulation disappeared, while others emerged. The change in the frequencies of composomes was found to be correlated with changes induced on the environment by the assembly. The EE-GARD model is the first GARD model to portray a possible time evolution of the composomes repertoire.     

Sugar amino acids in designing new molecules

Emulating the basic principles followed by Nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks and using them to create ‘nature-like’ and yet unnatural organic molecules. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to Nature’s molecular arsenal. This article describes some of our works on various sugar amino acids and many other related building blocks, like furan amino acids, pyrrole amino acids etc. used in wide-ranging peptidomimetic studies. Published in 2005.Based on the invited lecture presented at the XVII International Symposium on Glycoconjugates held in January 12–16, 2003 at Bangalore, India.     

Matrix interferences in the analysis of benzene in urine

The analysis of benzene in urine of the general population or of exposed workers can be performed with different methods using the ‘purge and trap’ or ‘solid-phase microextraction’ techniques in combination with gas chromatographic analysis and photoionisation or mass spectrometric detection. The published results, however, are deeply conflicting. Differences in sample preparation by different research groups and our own preliminary observations prompted us to investigate pre-analytical and analytical factors potentially capable of modifying the urinary benzene quantification results. Benzene concentrations were measured in 20 urine samples in relation to different conditioning conditions (at 24, 40 and 80°C) and at basic or acid pH. Urinary protein concentrations were measured in the same samples. Urine heating at 80°C yields benzene concentrations on average five times higher than at 24°C. On acidification of urine, the benzene released increases up to 28-fold in comparison to that obtained at uncorrected ‘physiological’ pH. Despite a widely scattered data distribution, a statistically significant linear correlation was found between ‘heat-released’ and ‘acid-labile’ benzene values. There was no correlation between total urinary proteins present in ‘physiological’ concentrations (between 12 and 110 mg/l) and the different kinds of benzene in urine. Our results could perhaps be explained if it is supposed that part of the benzene in urine is absorbed onto sediment, or bound to specific proteins, or derived from parent molecules and is released with pH modification or heat administration. Our observations may also help to explain why the urinary benzene concentrations reported by different investigators vary considerably even when environmental levels are comparable.     

An approximate likelihood for genetic data under a model with recombination and population splitting

We describe a new approximate likelihood for population genetic data under a model in which a single ancestral population has split into two daughter populations. The approximate likelihood is based on the ‘Product of Approximate Conditionals’ likelihood and ‘copying model’ of Li and Stephens [Li, N., Stephens, M., 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165 (4), 2213–2233]. The approach developed here may be used for efficient approximate likelihood-based analyses of unlinked data. However our copying model also considers the effects of recombination. Hence, a more important application is to loosely-linked haplotype data, for which efficient statistical models explicitly featuring non-equilibrium population structure have so far been unavailable. Thus, in addition to the information in allele frequency differences about the timing of the population split, the method can also extract information from the lengths of haplotypes shared between the populations. There are a number of challenges posed by extracting such information, which makes parameter estimation difficult. We discuss how the approach could be extended to identify haplotypes introduced by migrants.     

Minimal model systems for β-sheet secondary structure in proteins

Use of model systems to explore the forces that control β sheet formation was stymied for many years by the perception that small increments of β sheet necessarily aggregate. Recently, however, a number of short peptides (9–16 residues in length) that fold into two-stranded antiparallel β sheets (‘β hairpins’) have been reported; several short peptides (20–24 residues in length) that fold into three-stranded antiparallel β sheets have also been described. These model systems are beginning to provide fundamental insights into the origins of β sheet conformational stability.     

Stimulation of afferent vagal endings in the intrapulmonary airways by prostaglandin endoperoxide analogues

Two cyclic ether (CE) analogues of the prostaglandin endoperoxide PGH₂, CE I and CE II, have been found to exert powerful stimulant effects on lung ‘irritant’ receptors and bronchial C-fiber endings after intravascular or aerosol administration in open-chest dogs under Dial-pentobarbital anesthesia. ‘Irritant’ receptors responded to a dose as small as 0.1 μg/kg CE II, injected into the right atrium. CE II was twice as effective as CE I and 10–20 times more potent than PGF_2α. As an aerosol, it exceeded histamine in potency by more than 800 times. ‘Irritant’ receptor stimulation was always associated with decrease in lung compliance and increase in lung resistance. Isoproterenol which reduced the latter effects also diminished the response of ‘irritant’ receptors. Left atrial injection of GE_S had only weak and delayed effects. CE-induced ‘irritant’ receptor firing declined or ceased during ventilatory arrest in expiration and following hyperinflation of the lungs. In contrast to ‘irritant’ receptors, C-fibers responded more effectively and more rapidly, and in the absence of mechanical changes, when the drugs were injected into the left atrium as compared to right atrial injection. These findings suggest that CE-induced ‘irritant’ receptor stimulation is secondary to changes in lung mechanics, whereas C-fiber stimulation is a direct effect upon the nerve ending.     

Invasion of a Top Predator into an Epipelagic Ecosystem can bring a Paradoxical Top-Down Trophic Control

We apply mathematical modeling to explore different scenarios of invasion of a top predator (carnivorous zooplankton or planktivorous fish) into an epipelagic plankton ecosystem. We use a ‘minimal’ model of three nonlinear ordinary differential equations (nutrient–phytoplankton–herbivores) with the top predator density as a time-dependent parameter. The ecosystem shows different types of response, which can be described in terms of top-down trophic control. Our investigation indicates that under certain conditions the plankton ecosystem model demonstrates a surprising kind of response: in a wide range of realistic ecosystem parameters the invasion of the top predator leads to a prominent increase in the average density of zooplankton and to a resulting decrease of phytoplankton density. This phenomenon is opposite to the ‘typical’ top–down control when the carnivore pressure decreases zooplankton density which, in turn, increases phytoplankton biomass. We call the revealed type of top-down control ‘paradoxical’. Examples of such a response in natural aquatic ecosystems were reported earlier but no clear explanation has been provided hitherto. In this paper, we analyze possible mechanisms of ‘paradoxical top–down control’ and show that it can occur in eutrophic epipelagic ecosystems subject to high rate of cross-pycnocline exchange.     

Autophagic degradation in rat liver after vinblastine treatment

Mechanisms of autophagic proteolysis in the liver have been studied using vinblastine. Vinblastine stimulated degradation by induced autophagy in a dose-related fashion [1, 2]. Insulin partially inhibits the increased rate of degradation and the formation of autophagosomes as well as the lysosomal fragility induced by vinblastine. Insulin has little effect, however, on basal, non-induced degradation rates. Vinblastine-induced autophagy enhances the degradation of both ‘old’ and ‘newly’ synthesized proteins and is therefore in that sense a random process. The administration of high doses of colchicine also augments proteolysis. This effect is attributed to increase in autophagy. The very nascent vinblastine-induced autophagosomes appear to lack hydrolytic enzymes and acquire them only after fusion with lysosomes. The autophagolysosomal population induced by vinblastine is heterogeneous with respect to shape, size, content and density. Isolated secondary lysosomes (‘residual bodies’) lacking morphologically recognizable sequestered membranes (degradable substrate) show no release of degradation products. Autophagosomes fuse with secretory vesicles originating from the Golgi apparatus.     

Instability helps virtual flies to mate

In this paper we perform a bifurcation analysis for a discrete time dynamical system, describing the behavior of a virtual fly, developed by Böddeker and Egelhaaf (2003). Like real blowflies, the virtual counterparts exhibit a dichotomous behavior: they catch small targets but follow big objects at a constant distance. We consider this model for targets on linear and on circular trajectories. Then we transform the system into a ‘‘frozen’’ form, such that the position of the target is fixed. It turns out that the loss of stability of a fixed point in the frozen system due to a Neimark-Sacker bifurcation, explains the dichotomous behavior of the virtual fly.     

Electrostimulated fusion and fission of bilayer lipid membranes

The interaction and fusion of black lipid membranes have been studied. Two planar bilayers were simultaneously inflated towards each other; when they made contact, spontaneous formation of a ‘trilaminar structure’ (one bilayer bounded by two bilayers along the perimeter) was observed. Application of a discrete voltage pulse gave rise to the formation of a cylindrical membrane, that is, to the fusion of two bilayers. It is shown that fusion results from electrical breakdown in the contact region of the ‘trilaminar structure’.     

Patterns of Patchy Spread in Deterministic and Stochastic Models of Biological Invasion and Biological Control

A few spatiotemporal models of population dynamics are considered in relation to biological invasion and biological control. The patterns of spread in one and two spatial dimensions are studied by means of extensive numerical simulations. We show that, in the case that population multiplication is damped by the strong Allee effect (when the population growth rate becomes negative for small population density), in a certain parameter range the spread can take place not via the intuitively expected circular expanding population front but via motion and interaction of separate patches. Alternatively, the patchy spread can take place in a system without Allee effect as a result of strong environmental noise. We then show that the phenomenon of deterministic patchy invasion takes place ‘at the edge of extinction’ so that a small change of controlling parameters either brings the species to extinction or restores the travelling population fronts. Moreover, we show that the regime of patchy invasion in two spatial dimensions actually takes place when the species go extinct in the corresponding 1-D system.     

A second cell-binding domain on fibronectin (RGDS-independent) for neurite extension of human neuroblastoma cells

Human neuroblastoma cells (Platt and La-N1) have previously been shown to adhere and extend neurites on tissue-culture substrata coated with a 120K chymotryptic cell-binding fragment (CBF) of plasma fibronectin (pFN), a fragment which lacks heparan sulfate- and collagen-binding activities, and to adhere to—but not extend neurites on—substrata coated with the heparan sulfate (HS)-binding protein, platelet factor-4 (PF4) ([3.]). The mechanisms of these processes on CBF, on the intact pFN molecule, or on heparin-binding fragments of pFN have been tested using a heptapeptide (peptide A) containing the Arg---Gly---Asp---Ser (RGDS) sequence which recognizes a specific ‘receptor’ on the surface of a variety of cells or a control peptide with a single amino acid substitution. Adherence and neurite extension were completely inhibited on the 120K CBF by peptide A but not by control peptide; these results indicate that the RGDS-dependent ‘receptor’ is solely responsible for adhesive responses to the 120K CBF-containing region of the pFN molecule. When peptide A was added to cells on CBF which had already formed neuntes to test reversibility, retraction of all neurite processes was induced by 1 h and cells eventually detached. In contrast, on intact pFN, peptide A had very limited effects on either initial adherence or neurite extension, revealing a second ‘cell-binding’ domain on the fibronectin molecule outside of the 120K region competent for neurite differentiation; addition of peptide A at later times to pFN-adherent, neurite-containing cells could induce only a small subset of neurites to retract, thus supporting evidence for the presence of this second domain. A second ‘cell-binding’ domain was further confirmed by quantitation of neurite outgrowth on these substrata and by analyses of cells on substrata coated with mixtures of CBF/PF4. When substrata coated with chymotrypsin-liberated HBF were tested in a similar fashion, adherence was rapid but neurite outgrowth required much longer times and was completely sensitive to RGDS peptides; supplementation of cells with the complex ganglioside GT1b could not induce RGDS-resistant neurites on heparin-binding fragments (HBF). These latter results indicate that neurite extension on HBF is a consequence of a low concentration of RGDS-dependent activity in HBF (but not to HS-binding activity as characterized by Tobey et al. [3]) and that the second ‘cell-binding’ domain is sensitive to chymotrypsin digestion of pFN during the liberation of HBF. Possible candidate molecules for this second activity as well as its preliminary location in the pFN molecule are discussed and evidence, is provided in ref. [37] ([37.]) for the potential role for one class of molecules as a ‘receptor’. These neural tumor cells therefore have multiple and alternative mechanisms of adherence and differentiation on fibronectin matrices.     

Relating side-chain mobility in proteins to rotameric transitions: Insights from molecular dynamics simulations and NMR

The dynamic aspect of proteins is fundamental to understanding protein stability and function. One of the goals of NMR studies of side-chain dynamics in proteins is to relate spin relaxation rates to discrete conformational states and the timescales of interconversion between those states. Reported here is a physical analysis of side-chain dynamics that occur on a timescale commensurate with monitoring by ²H spin relaxation within methyl groups. Motivated by observations made from tens-of-nanoseconds long MD simulations on the small protein eglin c in explicit solvent, we propose a simple molecular mechanics-based model for the motions of side-chain methyl groups. By using a Boltzmann distribution within rotamers, and by considering the transitions between different rotamer states, the model semi-quantitatively correlates the population of rotamer states with ‘model-free’ order parameters typically fitted from NMR relaxation experiments. Two easy-to-use, analytical expressions are given for converting S²_axis’ values (order parameter for C–CH₃ bond) into side-chain rotamer populations. These predict that S²_axis’ values below 0.8 result from population of more than one rotameric state. The relations are shown to predict rotameric sampling with reasonable accuracy on the ps–ns timescale for eglin c and are validated for longer timescales on ubiquitin, for which side-chain residual dipolar coupling (RDC) data have been collected.     

The expansion of information in ecological systems: Emergence as a quantifiable state

Although the term ‘emergence’ has received wide attention in the literature, most of this attention has been focused on epistemological discussions about the nature of what might be considered emergent behavior in self-organizing systems. For the concept of emergence to have any great utility for biologists, it must (1) be perceptible as a physical, quantitative property rather than just a philosophical one; (2) have a quantitative definition applicable to all levels of biological organization; and (3) be an essential component of biological system performance or evolution. Using an independent, cellular population model (running in the StarLogo system), we have developed a mutual information calculation to measure the information expansion when considering the interactions between a population of herbivores and an environment in comparison to the interactions between the individual herbivores and that environment. In self-organizing biological systems, the collective action of massively parallel units generates a greater potential complexity in the information processing capacity of the ‘whole’ system relative to the ‘individual’ parts, and as such, there is a demonstrable increase in mutual information content. From this perspective, we consider emergence to exist as a simple information expansion that is a default behavior of any system with multiple, component parts governed by a simple, probabilistic rule set. It is not a first principle of self-organizing biological systems, but rather a collective behavior that can be quantitatively described in practical terms for experimental biologists. With a quantitative formulation, the concept of emergence may become a useful information statistic in assessing the structure of biological systems.     

Molecular Systematics of Middle American Cichlid Fishes and the Evolution of Trophic-Types in ‘Cichlasoma(Amphilophus)’ and ‘C.(Thorichthys)’

The majority of Middle American cichlids are placed in the informal assemblage ‘Cichlasoma.’ The group is divided into eight sections which appear to be based primarily on trophic morphology. Although several members of ‘Cichlasoma’ have been used in ecomorphological, behavioral, and biogeographic studies, no phylogenetic hypotheses for the group exist. In an attempt to develop a better understanding of the phylogenetic relationships of ‘cichlasomine’ cichlids, we examined the evolution of the trophic specialization, substratum-sifting, in two sections, ‘Cichlasoma(Thorichthys)’ and ‘C.(Amphilophus),’ to determine whether the trait reflects common ancestry. We sequenced the complete mitochondrial cytochromebgene for 19 cichlids representing six sections of ‘Cichlasoma,’ and representatives of other Neotropical Cichlidae. Additional cichlid, and noncichlid outgroup sequences were included for a total of 22 taxa. The molecular phylogeny supports the recognition of the section ‘C.(Thoricthys)’ as a natural group, and we place those cichlids in the genusThorichthys.The phylogeny also depicts ‘C.(Amphilophus)’ as paraphyletic, with substratum-sifters and generalized predators forming separate nonsister clades. We recommend that the substratum-sifting clade of the section ‘C.(Amphilophus)’ be placed in the resurrected genusAstatheros.The generalized predator clade of ‘C.(Amphilophus)’ contains only two species, ‘C. (A.) citrinellum’ and ‘C. (A.) labiatum,’ which we place in the genusAmphilophus.The phylogenetic hypotheses generated indicate that the substratum-sifting generaThorichthysandAmphilophusdo not share a common ancestor. Reconstruction of the evolution of substratum-sifting is equivocal, requiring either the independent evolution of the trait on two separate occasions or its presence in a more inclusive clade and subsequent loss in nonsubstratum sifting species.     

Vicariance and dispersal form a ring distribution in nightsnakes around the Gulf of California

Plate tectonics can have profound effects on organismal distribution and is often the driving force in speciation. Through geologic processes, the Baja California Peninsula depicts two faunal patterns: one through southern vicariance with Cape separation, and the other through dispersal onto the northern peninsula, referred to as a ‘dual-peninsular effect.’ Here we apply a hierarchical sampling strategy that combines population-level sequence data (800 bp, nad4 region) with complete mt-genome data (aligned 15,549 bp) and 5 nuclear protein encoding loci (3315 bp), to test whether both patterns have occurred in one group of nightsnakes (Hypsiglena). The geologic formation of the peninsula is thought to have occurred in three stages: (1) Cape separation from mainland Mexico; (2) the northern peninsula separated, forming the northern Gulf of California; and (3) the peninsula was united through volcanic activity, while moving northward causing collision with southern California. However, the timing of events is debated. We explore phylogenetic relationships and estimate dates of divergence for nightsnakes using our hierarchical sampling strategy. Our data support both ‘southern-vicariance’ and ‘northern-dispersal’ have occurred in nightsnakes, forming a ring distribution around the Gulf of California. Two divergent forms are sympatric on the southern half of the peninsula with no indication of hybridization. Nightsnakes represent the first group to depict the ‘dual-peninsular effect’ with extensive overlap on the Baja California Peninsula.     

Mutations and Lethality in Simulated Prebiotic Networks

The Graded Autocatalysis Replication Domain (GARD) model describes an origin of life scenario which involves non-covalent compositional assemblies, made of monomeric mutually catalytic molecules. GARD constitutes an alternative to informational biopolymers as a mechanism of primordial inheritance. In the present work, we examined the effect of mutations, one of the most fundamental mechanisms for evolution, in the context of the networks of mutual interaction within GARD prebiotic assemblies. We performed a systematic analysis analogous to single and double gene deletions within GARD. While most deletions have only a small effect on both growth rate and molecular composition of the assemblies, ~10% of the deletions caused lethality, or sometimes showed enhanced fitness. Analysis of 14 different network properties on 2,000 different GARD networks indicated that lethality usually takes place when the deleted node has a high molecular count, or when it is a catalyst for such node. A correlation was also found between lethality and node degree centrality, similar to what is seen in real biological networks. Addressing double knockout mutations, our results demonstrate the occurrence of both synthetic lethality and extragenic suppression within GARD networks, and convey an attempt to correlate synthetic lethality to network node-pair properties. The analyses presented help establish GARD as a workable alternative prebiotic scenario, suggesting that life may have begun with large molecular networks of low fidelity, that later underwent evolutionary compaction and fidelity augmentation.     

Oxidative stress,antioxidant activity and Fe(III)-chelate reductase activity of five <Emphasis Type="Italic">Prunus</Emphasis> rootstocks explants in response to Fe deficiency

The aim of this work was to investigate whether Fe reduction and antioxidant mechanisms were expressed differently in five Prunus rootstocks (‘Peach seedling,’ ‘Barrier,’ ‘Cadaman,’ ‘Saint Julien 655/2’ and ‘GF-677’). These rootstocks differ in their tolerance to Fe deficiency when grown in the absence of Fe (−Fe) or in presence of bicarbonate (supplied as 5 or 10 mM NaHCO₃). Fe deficiency conditions, especially bicarbonate, were shown to decrease Fe and total chlorophyll (CHL) concentration. In the (−Fe)-treated roots of all rootstocks and in the 5 mM NaHCO₃-treated ones of the tolerant ‘GF-677’ the Fe(III)-chelate reductase (FCR) activity was stimulated. On the contrary, apart from the ‘GF-677,’ FCR activity was greatly inhibited by the 10 mM NaHCO₃. From the results obtained with decapitated rootstocks, it is not entirely clear whether or not the presence of shoot apex was a prerequisite to induce FCR function in all rootstocks tested. In the leaves of rootstocks exposed to the (−Fe) treatment, superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities were enhanced whereas the levels of the non-enzymatic antioxidants (FRAP values) were increased in the Fe-deprived leaves, irrespective of the rootstock. Except for ‘Peach seedling,’ foliar SOD activity was stimulated by the presence of NaHCO₃. Furthermore, POD activity was increased in the ‘Saint Julien 655/2’ and ‘GF-677,’ but was depressed in the ‘Barrier’ rootstocks exposed to 10 mM NaHCO₃. As a result of 10 mM NaHCO₃, the expression of a Cu/Zn-SOD and a POD isoform was diminished in the leaves of ‘Peach seedling’ and ‘Barrier,’ respectively. By contrast, an additional isoform of both POD and Mn–SOD were expressed in the leaves of ‘GF-677’ exposed to 10 mM NaHCO₃ suggesting that the tolerance of rootstocks to Fe deficiency is associated with induction of an antioxidant defense mechanism. Although CAT activity was increased in the 5 mM NaHCO₃-treated leaves of ‘GF-677,’ specifically the 10 mM NaHCO₃ treatment resulted in a decrease of CAT activity and an accumulation of H₂O₂, indicating that bicarbonate-induced Fe deficiency may cause more severe oxidative stress in the rootstocks, than the absence of Fe. A general link between Fe deficiency-induced oxidative stress and Fe reduction-sensing mechanism is also discussed.     

Cobalt(II) ion as a promoter of hydroxyl radical and possible ‘crypto-hydroxyl’ radical formation under physiological conditions. Differential effects of hydroxyl radical scavengers

Co(II) ions react with hydrogen peroxide under physiological conditions to form a ‘reactive species’ that can hydroxylate aromatic compounds (phenol and salicylate) and degrade deoxyribose to thiobarbituric-acid-reactive material. Catalase decreases the formation of this species but superoxide dismutase or low concentrations of ascorbic acid have little effect. EDTA, present in excess over the Co(II), can accelerate deoxyribose degradation and aromatic hydroxylation. In the presence of EDTA, deoxyribose degradation by the reactive species is inhibited competitively by scavengers of the hydroxyl radical (OH), their effectiveness being related to their second-order rate constants for reaction with OH. In the absence of EDTA the scavengers inhibit only at much higher concentrations and their order of effectiveness is changed. It is suggested that, in the presence of EDTA, hydroxyl radical is formed ‘in free solution’ and attacks deoxyribose or an aromatic molecule. In the absence of EDTA, OH radical is formed in a ‘site-specific’ manner and is difficult to intercept by OH scavengers. The relationship of these results to the proposed ‘crypto OH’ radical is discussed.