Models on prebiotic polymer competition: A deterministic approach

Two simple models are proposed and analysed, in which it is shown that the formation of a new polymer, resulting from an “error” in the template action mechanism of production of an old polymer, may compromise the stability of the initial system under specific conditions, in the context of prebiotic evolution. Autocatalysis is shown to be a “selective advantage”, enabling the “mutant” to dominate in concentration and even replace the initial polymer. The addition of a third molecule playing the role of a catalyst causes hysteresis effects.     

Modeling of the actomyosin ATPase activity

In the rapid “quench” kientics of myosin, the “initial phosphate burst” is the excess inorganic phosphate that is produced during the early time-course of ATP hydrolysis by myosin subfragment-1 (S-1) or HMM. In general, the existence of a Pi burst implies a rapid (i.e., generally an order of magnitude faster than the steady-state hydrolysis rate) lysis of the phospho-anhydride bond within the ATP molecule, followed by one or more slower steps that are rate limiting for the process. Thus, the presence of a Pi burst can provide an important clue to the mechanism of the reaction. However, in the case of actomyosin, this clue as long been the subject of controversy and misunderstanding. To measure the (initial) Pi burst, myosin S-1 (or HMM) is rapidly mixed with ATP and then the mixture is acid quenched after a specific time period. The medium produced contains free Pi generated from hydrolysis of the ATP. The quantitative measure of the phosphate generated in this way has always been significantly greater than that expected by steady-state “release” of Pi alone, and it is that very difference between this measured Pi after the quench and that amount of Pi expected to be released by steady-state considerations in that same time period that has been referred to as the “initial Pi burst”. Recent investigations of the kinetics of Pi release have used an entirely new method that directly measures the release of Pi from the enzyme-product complex. These studies have made reference to the properties of the “initial Pi burst” in the presence of actin, as well as to a new kinetic entity: the “burst of Pi release”, and have been often vague concerning the true nature of the initial Pi burst, as well as the properties of Pi release as predicted by the current models of the actin activation of the myosin ATPase activity. The purpose of the current article is to correct this oversight, to discuss the “burst” in some detail, and to display the kinetics predicted by the current models for the actin activation of myosin. Furthermore, predictions for the kinetics of the new “burst of Pi release” are discussed in terms of its ability to discriminate between the two current competing models for actin activation of the myosin ATPase activity.     

Growth and reproduction in higher plants I. Theoretical analysis by mathematical models

To analyse the whole life of higher plants, an attempt was made to describe their growth and reproduction by mathematical models based on the elements determining matter production and economy of the matter. A plant body was regarded as a compound system of two parts; “productive part” and “reproductive part”. A parameter (reproductive index) was introduced to connect these two parts, and a set of the mathematical models describing the quantitative growth of these two parts were established. Two basic patterns of reproduction in higher plants were distinguished into “D-reproduction” and “I-reproduction”. The state of matter production of the mother plant determined an initial size of the daughter plant in theD-reproduction, while, in theI-reproduction, it did not determine the initial size of the daughter, but determined the number of propagules. The model of each reproduction pattern was also constructed. A formula determining the initial size of a plant in a given generation was constructed as the model of theD-reproduction. The model for theI-reproduction described the number of propagules produced in a given generation. Some aspects of the plant life, e.g. the optimum reproductive index, the switch-over time from the vegetative to the reproductive growth phase, the seed number, types of expansive reproduction, were theoretically analysed and discussed under these mathematical models.     

Effect of individual peculiarities of emotional sphere on formation of preference of ethanol in female and male Wistar rats

Individual characteristics of animal behavior can serve a prognostic parameter of predisposition to use of alcohol. The goal of the work was to study dynamics of formation of preference of alcohol at early stages in the process of forced alcoholization in male and female rats as well as the accompanying changes in behavior parameters. For 3 months, the rats were submitted to the forced alcoholization with 10% ethanol. Each week the rats were tested in the “two-glass trial.” Individual peculiarities of all animals were evaluated prior to, after 6 weeks, and after the end of the experiment with aid of the “open field test” and “Suok-test.” Results showed that the male rats demonstrating by the end of the experiment the significantly higher level of the alcohol preference, demonstrated at the initial stages of the forced alcoholization the significantly lower preference as compared with the remaining ones. These rats also showed before alcoholization the lower levels of the motor and exploratory activities as compared with control. On the contrary, the individuals that by the end of the experiment did not differ from control by the level of the alcohol preference demonstrated prior to alcoholization in the “Suok-test” the higher anxiety level. In females there was observed a positive correlation of a decrease of the anxiety level in the process of alcoholization with a rise of ethanol consumption. Thus, in male rats, the prognostic parameter predicting formation of the abuse can serve the degree of alcohol preference at the initial stages.     

An initial attempt to map carbonate buildups using Ground-Penetrating Radar: An example from the Upper Jurassic of SW-Germany

Summary Although carbonate buildups host important hydrocarbon reservoirs and industrial minerals, relatively little is known about their three-dimensional architecture. Ground-penetrating radar (GPR, “Georadar”) studies provide the opportunity to reconstruct both their internal anatomy and external geometry. This short paper reports an initial attempt to map some Upper Jurassic sponge/algal buildups in the Upper Jurassic of SW-Germany using georadar. Several distinct radar facies types can be distinguished and calibrated to lithofacies in adjacent quarry outcrops. Mapping of the radar facies types reveals the potential to reconstruct the distribution of “buildup” versus other facies. Moreover, it highlights the need of obtaining more closely spaced radar lines in order to arrive at a high-resolution image.     

Proliferation of the hyperthermophilic archaeon Pyrobaculum islandicum by cell fission

Pyrobaculum islandicum is a hyperthermophilic archaeon. P. islandicum cells have been suggested to multiply by constriction, budding and branching, as no septa were observed in cells by phase-contrast light microscopy. In this study, we observed the cells using transmission electron microscopy, scanning electron microscopy, and light microscopy with dark-field image analyses, and we report binary fission via septum formation to be the main mode of P. islandicum’s proliferation. “Long cells” reported previously were found to comprise several cylindrical cells that align in tandem.     

The status and phylogenetic relationships of “Zanclodon”arenaceus: the earliest known phytosaur?

“Zanclodon”arenaceus has been suggested to represent the oldest reliably dated phytosaur. The type and only specimen, a mandibular fragment of an archosaur from the Schilfsandstein (Carnian; Late Triassic) of Southwest Germany, is described in detail for the first time. “Z.”arenaceus is characterized by a great elongation of the mandible and symphysis, and labiolingually flattened, serrated teeth, a combination that is so far unique among Triassic archosaurs. The previous assignment to the enigmatic reptilian genusZanclodon is unsubstantiated. “Z.”arenaceus shares with Phytosauria both these mandibular characters, but differs in numerous other characters, including most of the autapomorphic mandibular and dental features of Phytosauria. Thus, “Z.”arenaceus is not a phytosaur as currently defined. A cladistic analysis identified “Z.”arenaceus as the sister-taxon of Phytosauria, but because of the limited data available and numerous homoplasies that occur among mandibular characters of archosaurs a closer relationship with other archosaur taxa is a reasonable alternative. It seems unjustified to redefine Phytosauria, or to propose a more inclusive taxon to include “Z.”arenaceus, and therefore the species is assessed as Archosauriaincertae sedis.     

Subchondral bone microarchitecture and failure mechanism under compression: A finite element study

Subchondral bone (SCB) microdamage is commonly observed in traumatic joint injuries and has been strongly associated with post-traumatic osteoarthritis (PTOA). Knowledge of the three-dimensional stress and strain distribution within the SCB tissue helps to understand the mechanism of SCB failure, and may lead to an improved understanding of mechanisms of PTOA initiation, prevention and treatment. In this study, we used high-resolution micro-computed tomography (µCT)-based finite element (FE) modelling of cartilage-bone to evaluate the failure mechanism and the locations of SCB tissue at high-risk of initial failure under compression. The µCT images of five cartilage-bone specimens with an average SCB thickness of 1.23 ± 0.20 mm were used to develop five µCT-based FE models. The FE models were analysed under axial compressions of approximately 30 MPa applied to the cartilage surface while the bone edges were constrained. Strain and stress-based failure criteria were then applied to evaluate the failure mechanism of the SCB tissue under excessive compression through articular cartilage. µCT-based FE models predicted two locations in the SCB at high-risk of initial failure: (1) the interface of the calcified-uncalcified cartilage due to excessive tension, and (2) the trabecular bone beneath the subchondral plate due to excessive compression. µCT-based FE models of cartilage-bone enabled us to quantify the distribution of the applied compression which was transferred through the articular cartilage to its underlying SCB, and to investigate the mechanism and the mode of SCB tissue failure. Ultimately, the results will help to understand the mechanism of injury formation in relation to PTOA.     

The production of copper,zinc and molybdenum deficiencies in crop plants grown in sand culture with special reference to some effects of water supply and seed reserves

Summary (1) A method is described for the production of acute deficiencies of copper, zinc or molybdenum in large scale sand cultures in which an adequate and satisfactory supply of water was obtained by treating rain water with ion-exchange resins. Results compared favourably with the use of glass distilled water.(2) Visual symptoms of copper, zinc and molybdenum deficiencies in large seeded leguminous crops, and in other species are summarised.(3) Seed reserves played an important part in the incidence of copper and molybdenum deficiencies and to a lesser extent of zinc deficiency in pea, runner bean, dwarf bean and broad bean.(4) The deficient seed was obtained by harvesting seed from plants grown in the respective deficiency sand cultures, and was compared with seed obtained similarly from complete nutrient sand cultures or commercially from field-grown plants.(5) Seed reserves of molybdenum were usually sufficient for a complete generation but reserves of copper and zinc were not adequate for the whole copper or zinc requirements of the plants.(6) Analytical data showed a marked decrease in the copper or molybdenum content of deficient seed, and a less striking decrease in zinc.(7) Foliage of deficient plants showed decreased content of copper and molybdenum and often of zinc compared with plants given the complete nutrient treatment, but use of deficient seed only decreased yields without further appreciably decreasing the mineral content of the foliage.     

Slow modulation of synaptic transmission by brain-derived neurotrophic factor leads to the central sensitization associated with neuropathic pain

Chronic constriction injury (CCI) of the rat sciatic nerve increases the dorsal horn excitability. This “central sensitization” leads to behavioral manifestations analogous to those related to human neuropathic pain. We found, using whole-cell recording from acutely isolated spinal cord slices, that 7-to 10-day-long CCI increases excitatory synaptic drive to putative excitatory “delay”-firing neurons in the substantia gelatinosa but attenuates that to putative inhibitory “tonic”-firing neurons. A defined-medium organotypic culture (DMOTC) system was used to investigate the long-term actions of brain-derived neurotrophic factor (BDNF) as a possible instigator of these changes. When all five neuronal types found in the substantia gelatinosa were considered, BDNF and CCI produced similar patterns, or “footprints,” of changes across the whole population. This pattern was not seen with another putative “pain mediator,” interleukin 1β. Thus, BDNF decreased synaptic drive to “tonic” neurons and increased synaptic drive to “delay” neurons. Actions of BDNF on “delay” neurons were presynaptic and involved increased mEPSC frequency and amplitude without changes in the function of postsynaptic AMPA receptors. By contrast, BDNF exerted both pre-and post-synaptic actions on “ tonic” cells to reduce the mEPSC frequency and amplitude. These differential actions of BDNF on excitatory and inhibitory neurons contributed to a global increase in the dorsal horn network excitability as assessed by the amplitude of depolarization-induced increases in the intracellular [Ca²⁺]. Experiments with the BDNF-binding protein TrkB-d5 provided additional evidence for BDNF as a harbinger of neuropathic pain. Thus, the cellular processes altered by BDNF likely contribute to “central sensitization” and hence to the onset of neuropathic pain. Neirofiziologiya/Neurophysiology, Vol. 39, Nos. 4/5, pp. 315–326, July–October, 2007.     

Characterization of the thermal tolerances of forest ants of New England

Characterization of thermal tolerances of ants, which are both abundant and important in most terrestrial ecosystems, is needed since thermal constraints can inform how a species may respond to local climatic change. Here we identified the thermal tolerances of 16 common ant species of the Northeastern United States and determined relationships between body size, desiccation, and thermal tolerance among species. We hypothesized that maximum heat tolerances of these species would differ and be related to body size and capacity to resist desiccation. We identified four distinct groups of species belonging to one of three subfamilies, Dolichoderinae, Formicinae, or Myrmicinae, with different maximum thermal tolerances. Group “a” had a mean thermal tolerance of approximately 43°C (±1°C), group “b” had a mean thermal tolerance of 40°C (±1°C), group “c” had a mean thermal tolerance of 38°C (±0°C), and group “d” had a mean thermal tolerance of 36°C (±0°C). Groups “a” and “d” consisted of a single species (in the subfamilies Myrmicinae and Formicinae, respectively), while groups “b” and “c” were a mix of species in the subfamilies Myrmicinae, Formicinae, and Dolichoderinae. In the subfamily Formicinae, thermal tolerance increased with body size and critical water content, a metric of desiccation tolerance. In contrast, in the subfamily Myrmicinae, higher thermal tolerance was correlated with intermediate body size and lower critical water content. These findings suggest that the two dominant subfamilies in Northeastern deciduous forests have different relationships between body size, capacity to tolerate desiccation, and thermal tolerances across species. This variation in thermal tolerance suggests that climatic change may impact species differently.     

Shoot dynamics and architecture of saplings in Fagus crenata across its geographical range

 Relationships between leaf or shoot size, number, and arrangement in response to light were investigated to test the hypothesis that these characteristics are linked. In order to test this hypothesis, the divergence in allometry and shoot dynamics in saplings of Japanese beech (Fagus crenata) obtained from four populations and having different leaf sizes were examined in a nursery under both full sun and shade conditions. Trees with different leaf sizes also showed large differences in canopy structure, particularly when shade-grown saplings were compared. The final leaf mass distributions of the large-leaf populations were conical or “bottom - heavy”, while those of the small-leaf populations were planar or “top - heavy”. The slope of the allometric relations between leaf mass and shoot and branch mass in small-leaved populations were steeper than those in large-leaf populations. The four populations were classified into two growth types: populations producing a few large leaf and shoot modules corresponded to “stem growth type”, and those producing many small leaf and shoot modules corresponded to “leaf growth type”. These kinds of intra-specific variation in architecture and growth of F. crenata trees may influence the structure and dynamics of forests in accordance with differences in competitive ability or sensitivity to disturbances such as windstorm. Received: 18 March 1997 / Accepted: 21 October 1997     

“Force-Talk” in Evolutionary Explanation: Metaphors and Misconceptions

The notion of “pressure” as an evolutionary “force” that “causes” evolution is a pervasive linguistic feature of biology textbooks, journal articles, and student explanatory discourse. We investigated the consequences of using a textbook and curriculum that incorporate so-called force-talk. We examined the frequency with which biology majors spontaneously used notions of evolutionary “pressures” in their explanations, students’ definitions and explanations of what they meant when they used pressures, and the structure of explanatory models that incorporated evolutionary pressures and forces. We found that 12–20 percent of undergraduates spontaneously used “pressures” and/or “forces” as explanatory factors but significantly more often in trait gain scenarios than in trait loss scenarios. The majority of explanations using “force-talk” were characterized by faulty evolutionary reasoning. We discuss the conceptual similarity between faulty notions of evolutionary pressures and linguists’ force-dynamic models of everyday reasoning and ultimately question the appropriateness of force-talk in evolution education.     

Noise transmission during the dynamic pattern formation in fly embryos

Background: Developmental patterning is highly reproducible and accurate at the single-cell level during fly embryogenesis despite the gene expression noise and external perturbations such as the variation of the embryo length, temperature and genes. To reveal the underlying mechanism, it is very important to characterize the noise transmission during the dynamic pattern formation. Two hypotheses have been proposed. The “channel” scenario requires a highly reproducible input and an accurate interpretation by downstream genes. In contrast, the “filter” scenario proposes a noisy input and a noise filter via the cross-regulation of the downstream network. It has been under great debates which scenario the fly embryogenesis follows. Results: The first 3-h developmental patterning of fly embryos is orchestrated by a hierarchical segmentation gene network, which rewires upon the maternal to zygotic transition. Starting from the highly reproducible maternal gradients, the positional information is refined to the single-cell precision through the highly dynamical evolved zygotic gene expression profiles. Thus the fly embryo development might strictly fit into neither the originally proposed “filter” nor “channel” scenario. The controversy that which scenario the fly embryogenesis follows could be further clarified by combining quantitative measurements and modeling. Conclusions: Fly embryos have become one of the perfect model systems for quantitative systems biology studies. The underlying mechanism discovered from fly embryogenesis will deepen our understanding of the noise control of the gene network, facilitate searching for more efficient and safer methods for cell programming and reprogramming, and have the great potential for tissue engineering and regenerative medicine.     

Source-sink landscape theory and its ecological significance

Exploring the relationships between landscape pattern and ecological processes is the key topic of landscape ecology, for which, a large number of indices as well as landscape pattern analysis model were developed. However, one problem faced by landscape ecologists is that it is hard to link the landscape indices with a specific ecological process. Linking landscape pattern and ecological processes has become a challenge for landscape ecologists. “Source” and “sink” are common concepts used in air pollution research, by which the movement direction and pattern of different pollutants in air can be clearly identified. In fact, for any ecological process, the research can be considered as a balance between the source and the sink in space. Thus, the concepts of “source” and “sink” could be implemented to the research of landscape pattern and ecological processes. In this paper, a theory of sourcesink landscape was proposed, which include: (1) In the research of landscape pattern and ecological process, all landscape types can be divided into two groups, “source” landscape and “sink” landscape. “Source” landscape contributes positively to the ecological process, while “sink” landscape is unhelpful to the ecological process. (2) Both landscapes are recognized with regard to the specific ecological process. “Source” landscape in a target ecological process may change into a “sink” landscape as in another ecological process. Therefore, the ecological process should be determined before “source” or “sink” landscape were defined. (3) The key point to distinguish “source” landscape from “sink” landscape is to quantify the effect of landscape on ecological process. The positive effect is made by “source” landscape, and the negative effect by “sink” landscape. (4) For the same ecological process, the contribution of “source” landscapes may vary, and it is the same to the “sink” landscapes. It is required to determine the weight of each landscape type on ecological processes. (5) The sourcesink principle can be applied to non-point source pollution control, biologic diversity protection, urban heat island effect mitigation, etc. However, the landscape evaluation models need to be calibrated respectively, because different ecological processes correspond with different source-sink landscapes and evaluation models for the different study areas. This theory is helpful to further study landscape pattern and ecological process, and offers a basis for new landscape index design. __________ Translated from Acta Ecologica Sinica, 2006, 26(5): 1444–1449 [译自: 生态学报]     

“L” forms of Staphylococci; Their reversibility; Changes in the sensitivity pattern after several intermediary passages in the “L” phase

Summary Strains of Staphylococci originally resistant to chloramphenicol, tetracycline and erythromycin, or made resistantin vitro to tyrothricin and streptomycin, were transformed into the “L” form and subcultured in this phase for more than twenty passages. The “L” colonies of the entire series could be reversed to bacterial forms. From all theisolated staphylococci strains the phage pattern was found to be maintained; slight changes in the number of active phages and the degree of activity are deemed to be insignificant. New types were never found. The strains made resistant to tyrothricin and streptomycin remained insensitive, those, however, that were originally resistant to chloramphenicol, tetracycline and erythromycin, became sensitive after a number of passages in the “L” phase. This loss of resistance—the only significant change from the original strains—is thought not to be due to mutation.

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Résumé Des souches de Staphylocoques sensibles à la pénicilline, mais naturellement résistantes au chloramphénicol, à la tétracycline et à l'érythromycine, aussi bien que des souches rendues insensibles à la tyrothricine ou à la streptomycine, étaient transformées en phase “L”. Dans cette phase plus de vingt subcultures étaient faites; les colonies “L” de chaque passage pouvaient être reversées en phase bacillaire. Toutes les souches récupérées avaient conservé le type bactériophagique des souches d'origine; l'augmentation du nombre des phages actifs et le changement du degré de leur activité ne peuvent être considérés signifiants. Nous n'avons jamais trouvé de nouveaux types. Les souches résistantes à la streptomycine et à la tyrothricine restaient insensibles; celles au contraire, qui étaient naturellement résistantes a la tétracycline, à l'érythromycine ou au chloramphénicol devenaient sensibles après peu de subcultures en phase “L”. Cette perte de résistance est considérée être d'origine non-mutationelle. L'existence d'un cycle “L” des Staphylocoques s'est averée ainsi.

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Working with grants of the foundation “De Drie Lichten” and the “Stichting ter Bevordering van Medisch-Wetenschappelijk Onderzoek”.     

Dynamic analysis,with feedback characterization,of hybrid human musculoskeletal frameworks by the linegraph-flowgraph procedure

The dynamic response of human musculo-skeletal framework is treated by (i) idealization of the musculo-skeletal framework as hybrid structural networks possessing feedback characteristics and then (ii) employing linegraph-flowgraph procedures for the feedback characterization of the hybrid structural networks. Topological procedures are used in which a “tree” of a network furnishes the skeleton upon which the “linkage” (muscle representing) members provide interaction. Feedback characterization (representing the sensitivity of the skeletal members to the tensile forces) is defined, between the internal “linkage” and “tree” members, by means of the flowgraph. Mikusinski operational calculus is used to facilitate representation of inertia effects by dynamic feedback characterization, with inclusion of initial conditions.