Stationary cell size distributions and mean protein chain length distributions of Archaea,Bacteria and Eukaryotes described with an increment model in terms of irreversible thermodynamics

In terms of an increment model irreversible thermodynamics allows to formulate general relations of stationary cell size distributions observed in growing colonies. The treatment is based on the following key postulates: i) The growth dynamics covers a broad spectrum of fast and slow processes. ii) Slow processes are considered to install structural patterns that operate in short periods as temporary stationary states of reference in the sense of irreversible thermodynamics. iii) Distortion during growth is balanced out via the many fast processes until an optimized stationary state is achieved. The relation deduced identifies the numerous different stationary patterns as equivalents, predicting that they should fall on one master curve. Stationary cell size distributions of different cell types, like Hyperphilic archaea, E. coli (Prokaryotes) and S. cerevisiae (Eukaryotes), altogether taken from the literature, are in fact consistently described. As demanded by the model they agree together with the same master curve. Considering the “protein factories” as subsystems of cells the mean protein chain length distributions deduced from completely sequenced genomes should be optimized. In fact, the mean course can be described with analogous relations as used above. Moreover, the master curve fits well to the patterns of different species of Archaea, Bacteria and Eukaryotes. General consequences are discussed.     

Density induced transition in a school of fish

Collective behaviour has been studied in various fields of science. As an example, we may consider the patterns observed in living systems, whose aggregates form organized groups such as flocks of birds, herds of mammals and schools of fish. These aggregates may be formed as a consequence of an external stimulus or due to the local interaction among nearby specimens. As an example of the latter case one may think about a school of fish, where each individual bases its behaviour on its perception of the position and velocity of its nearest neighbours. As a result of these interactions, global collective behaviour may emerge, originating and maintaining the cohesion of the aggregate. In this work, we model the collective movement of a school of fish using an agent-based model which follows biologically motivated behavioural rules previously proposed. The distributions of nearest neighbour distance and relative orientations between neighbouring fishes are measured and the results are found to be in good agreement with previous experimental measurements.     

扑翼尾迹中细丝的柔性对气动效能的影响

柔性对生物的运动起着至关重要的作用,例如鸟类的飞行和鱼类的游动.对柔性的研究有利于深刻地认识一些动物的运动机制和制造高效推进的仿生机器.文章在侧向自由弹性细丝的模型基础上,对不同柔性细丝的气动效能进行了研究.数值模拟结果表明,在Kárman涡街中,细丝的阻力系数随着其柔性减小而减小,细丝尾端的振幅随着其柔性减小而增大.结果还表明,在一定范围的Reynolds数下,减小细丝柔性,细丝由在涡核之间穿梭摆动运动模式变成在涡街外侧摆动运动模式,其尾涡的对称性也发生了明显的变化.      

Tissue-specific δ13C in ancient and modern tropical seabirds and flying fish in the Xisha Islands,South China Sea

We analyzed ¹³C characteristics in samples of bird bones, feathers, eggshell carbonate and membrane from modern specimens of red-footed booby (Sula sula) as well as fish muscle, scales, and bones from its predominant food source, flying fish (Exocoetus volitans), and muscle from its secondary food source squid (Loligo chinensis), as well as in ancient sub-fossil samples of seabird and flying fish at the Xisha Islands, South China Sea. δ¹³C is tissue-specific in both seabirds and flying fish due to the variance in turn-over among the tissues and differences in the type and content of amino acids across a diverse range of tissues. The δ¹³C discrimination factors also differed significantly among the various tissues between tropical seabirds and their prey. A Suess effect, caused by fossil fuel combustion and the emission of carbon with fewer ¹³C isotopes, was observed in the bird and fish tissue from ancient to modern time. Our study provides a multiple variability index for δ¹³C in organisms along a food chain, and verifies that tissue-specific ¹³C analysis is essential to identify diet and species and thus is a valuable tool for research on tropical seabird ecology.     

Personality from a cognitive-biological perspective

The term “personality” is used to describe a distinctive and relatively stable set of mental traits that aim to explain the organism's behavior. The concept of personality that emerged in human psychology has been also applied to the study of non-human organisms from birds to horses. In this paper, I critically review the concept of personality from an interdisciplinary perspective, and point to some ideas that may be used for developing a cognitive-biological theory of personality. Integrating theories and research findings from various fields such as cognitive ethnology, clinical psychology, and neuroscience, I argue that the common denominator of various personality theories are neural systems of threat/trust management and their emotional, cognitive, and behavioral dimensions. In this context, personality may be also conceived as a meta-heuristics both human and non-human organisms apply to model and predict the behavior of others. The paper concludes by suggesting a minimal computational model of personality that may guide future research.     

激光诱导击穿光谱对污染鱼体内重金属元素分布与含量的分析

环境污染可造成生物体的中毒、病变及死亡。生物体各组织对污染物质的吸收、积累情况是不同的。生物体各组织对污染物质重金属元素的吸收是生物医学中的一项重要研究。采用激光诱导击穿光谱(LIBS)方法对受污染的鱼体各组织进行了重金属元素定量分析。实验中得到了一组探测鱼类组织元素成份的LIBS最佳条件,拟合了Pb和Ba元素的定标曲线并通过外标法测定了重金属含量。实验结果表明,鱼体中肝脏及口腮等部位有重金属积累,而在鱼肉中重金属含量极低。所提出的方法可用于生物体受污染影响的评估研究, 在生物医学领域有重要推广价值。     

Fish host-cestode parasite stable isotope enrichment patterns in marine, estuarine and freshwater fishes from Northern Canada

Cestode parasites from freshwater (threespine stickleback, Gasterosteus aculeatus), estuarine (brook charr, Salvelinus fontinalis) and marine (Greenland cod, Gadus ogac) fish from northern Quebec, Canada, were used to investigate the hypotheses that cestode parasites are (13)C and (15)N enriched relative to host food sources, but (15)N depleted with respect to host muscle tissue as a result of differential enrichment during the assimilation of common nutrient sources. Cestode parasites and fish were generally similarly enriched in (13)C with respect to common food sources and, in the case of Greenland cod, cestode parasites were (13)C enriched relative to host tissue. Cestode parasites were also generally (15)N enriched with respect to mean host dietary signatures, but depleted with respect to host muscle tissue. In the case of Greenland cod cestode parasites, no significant (15)N enrichment relative to host dietary signature was observed. Cestode parasites appear generally to experience smaller (15)N enrichment than hosts as a result of trophic transfer of common dietary sources. Differential (15)N enrichment patterns in parasites and fish may be attributed to differences in parasite and host metabolism, particularly the anaerobic and aerobic natures of their respective metabolisms. Results imply that isotope enrichment paradigms developed for the study of aquatic foodwebs cannot be routinely applied to quantitatively assess the role of parasites in aquatic foodwebs and that reference to host muscle tissue measures will not allow accurate characterization of parasite foodweb position. Appropriate reference to assimilated food sources is required to accurately estimate parasite isotopic enrichment patterns and to determine parasite trophic position relative to the host.     

Phase separation driven by density-dependent movement: A novel mechanism for ecological patterns

Many ecosystems develop strikingly regular spatial patterns because of small-scale interactions between organisms, a process generally referred to as spatial self-organization. Self-organized spatial patterns are important determinants of the functioning of ecosystems, promoting the growth and survival of the involved organisms, and affecting the capacity of the organisms to cope with changing environmental conditions. The predominant explanation for self-organized pattern formation is spatial heterogeneity in establishment, growth and mortality, resulting from the self-organization processes. A number of recent studies, however, have revealed that movement of organisms can be an important driving process creating extensive spatial patterning in many ecosystems. Here, we review studies that detail movement-based pattern formation in contrasting ecological settings. Our review highlights that a common principle, where movement of organisms is density-dependent, explains observed spatial regular patterns in all of these studies. This principle, well known to physics as the Cahn–Hilliard principle of phase separation, has so-far remained unrecognized as a general mechanism for self-organized complexity in ecology. Using the examples presented in this paper, we explain how this movement principle can be discerned in ecological settings, and clarify how to test this mechanism experimentally. Our study highlights that animal movement, both in isolation and in unison with other processes, is an important mechanism for regular pattern formation in ecosystems.     

Minimal mechanisms for school formation in self-propelled particles

In the context of social organisms, a school refers to a cohesive group of organisms that share a common speed and direction of motion, as well as a common axis of body alignment or polarization. Schools are also noted for the relatively fixed nearest-neighbour distances between individuals. The rules of interaction that lead to the formation and maintenance of a school structure have been explored experimentally, analytically, and by simulation. Interest in biological examples, and non-biological “self-propelled particles” such as robots, vehicles, or autonomous agents leads to the question of what are the simplest possible sets of rules that can assure the formation and the stability of the “perfect school”: an aggregate in which the nearest-neighbour distances and speeds are identical.Here we explore mechanisms that lead to a perfect school structure in one and two dimensions. We consider distance-detection as well as velocity-detection between the interacting pairs of self-propelled particles. We construct interaction forces and formulate schooling equations. In the simplest cases, these equations have analytic solutions. In many cases, the stability of the perfect school can be explored. We then investigate how these structures form and evolve over time from various initial configurations using simulations. We study the relationship between the assumed interaction forces and the school patterns that emerge. While true biological schools are far from perfect, the insights gained from this investigation can help to understand some properties of real schools, and to suggest the appropriate properties of artificial schools where coordinated motion is desired.     

Structural Properties of Additive Nano/Microcellular Automata

A detailed structural analysis of 2D patterns generated by one‐dimensional M‐state additive cellular automata (ACA), where M is a prime (p) to a non‐negative power (t), is performed by using the transition matrix (TM), the barycentric fixed‐mass (BFM) method, and the small‐angle scattering (SAS) technique. The BFM method shows that, for M‐state ACA, the subsets of particular states are multifractals. The fractal dimensions of ACA of a given transition rule are shown to be equal at constant p and arbitrary t, and there is a prime p at which the fractal dimensions of different ACA are equal. The SAS technique is shown to be able to differentiate between patterns of such ACA. In addition, SAS can also provide complementary information about the overall size, number of elements, and number of rows generated by ACA. In the case of monofractals, SAS can recover also the scaling factor, which is shown to be, for the ‐state ACA, the inverse of p. The above findings on the 2‐ and 3‐state Rule 90 and Rule 150 are illustrated as idealized models with possible applications toward assembly of nanoparticles into programmable patterns or in modeling biological systems such as fibroblast aggregation, the growth of bacterial colonies, neuronal maps, and virus spreading.     

Evolution of groups with a hierarchical structure

The universal occurrence of a hierarchical structure and its dynamic behavior in various types of group, living or abstract, are discussed. Here the word “group” refers not only to tangible aggregation but also to invisible aggregation of social psychological and of geopolitical meaning. The evolution of these groups is simulated using a model of agents distributed on the lattices of cellular grids. It is assumed that agents, fearing isolation, interact asymmetrically with each other with regard to exchange of “power”. As an indicator of hierarchy, the Gini coefficient is introduced. Example calculations are made for the aggregation, fusion and fission of animal groups, and for the appearance of a powerful empire and the rise and fall of supremacy. It is shown that such abstract objects evolve with time in accordance with the universal rules of groups common to birds and fish.     

Physics of transport and traffic phenomena in biology: from molecular motors and cells to organisms

Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukaryotic cells, sometimes encounter traffic jam that manifests as a disease of the organism. Similarly, traffic jam of collagenase MMP-1, which moves on the collagen fibrils of the extracellular matrix of vertebrates, has also been observed in recent experiments. Novel efforts have been made to utilize some uni-cellular organisms as “micro-transporters”. Traffic-like movements of social insects like ants and termites on trails are, perhaps, more familiar in our everyday life. Experimental, theoretical and computational investigations in the last few years have led to a deeper understanding of the generic or common physical principles involved in these phenomena. In this review we critically examine the current status of our understanding, expose the limitations of the existing methods, mention open challenging questions and speculate on the possible future directions of research in this interdisciplinary area where physics meets not only chemistry and biology but also (nano-)technology.     

Effects of fish farm loading on sea grass Posidonia oceanica at Vrgada Island (Central Adriatic): a nitrogen stable isotope study

Analyses of nitrogen stable isotopes in the marine sea grass Posidonia oceanica were used to investigate the influence of fish farming on the coastal ecosystem of Vrgada Island in the Murter Sea, Central Adriatic. The results show a statistically significant ¹⁵N enrichment (up to 4.7‰ at p?<?0.005) in P. oceanica leaf and shoot tissues from fish cage sites with respect to the unaffected offshore reference site of Lumbarda Reef Flat (Kornati Islands). Heavy nitrogen enrichment was also detected in other benthic organisms analysed during this study and is attributed to the absorption and assimilation of ¹⁵N-enriched fish farm derived nitrogen waste.     

Structural modification of swai-fish (Pangasius hypophthalmus)-based emulsions containing non-meat protein additives by ultra-high pressure and thermal treatments

Swai-fish emulsions containing fermented soybeans (thua nao and rice-koji miso) were pressurized at 600?MPa for 20 min or heated at 72°C for 30 min. The fish batters were blended with soy protein isolate (SPI) or whey protein concentrate (WPC) to stabilize the emulsions. The processed fish emulsions were then subjected to physical, chemical and microbiological examinations. The results of gel strength and water-holding potential showed that SPI addition yielded higher impact on these properties than WPC addition, which was also confirmed by the interactions between SPI and native fish proteins depicted by electrophoregrams. The frequency profiles suggested that the heated gels had a greater storage and loss moduli than pressurized gels, while pressurized WPC set-gel displayed larger loss tangent (the predominance of viscous moiety) than those pressurized SPI set-gel. High bacteria and spore counts of B. subtilis (residual of the thua nao) were observed in both pressurized and heated fish-based emulsions.     

Epifluorescence and light microscopy evidencing structural and functional polymorphism of ribosomal DNA in fish (Teleostei: Astyanax fasciatus)

New karyotypic data are presented for the Astyanax fasciatus species complex from four different locations on the Upper Tibagi River in the state of Paraná, Brazil. Chromosome markers were analyzed using conventional (Ag-NOR) and molecular (FISH with 18S biotinylated probes) methods. Two cytotypes were found in cell counts with diploid number 2n = 48 chromosomes and 2n = 50 chromosomes, previously denominated Cytotype A and B, respectively. Two specific patterns of Ag-NORs markers (ribosomal gene activity) were found, with intra-population and inter-population variations. Cytotype A exhibited two to three chromosomes with NOR sites in the metaphases analyzed. In Cytotype B specimens, up to three markers were found, demonstrating greater intra-population and inter-population variation. All individuals with only one chromosome pair with NORs were located in the telomeric region of the short arm of Chromosome 5. This characteristic was interpreted as ancestral for the species. Another identified pattern revealed a site in the telomeric region probably in the long arm of Chromosome 4 and another submetacentric chromosome with bitelomeric marks exclusively in specimens with 2n = 50 chromosomes. In the FISH analysis (ribosomal gene structure), five to seven markers were identified in Cytotype A and three to seven markers were identified in Cytotype B. Structural chromosome events and/or transposable elements are required to explain the ribosomal gene location diversity in these organisms. The results of the present study corroborate the hypothesis that the A. fasciatus of the Upper Tibagi River region constitute a species complex.     

Polyenic pigments from the Brazilian octocoral Phyllogorgia dilatata Esper, 1806 characterized by Raman spectroscopy

Phyllogorgia dilatata is a Brazilian endemic gorgonian with a natural color ranging from white to pale yellow. An unusual violet pigmentation has been observed in colonies with tissue damage and skeleton anomalies. In order to investigate the chemical composition of these pigments, we have used in situ Raman spectroscopy to characterize the white/cream and violet tissues as well as sclerites, a skeletal component consisting of calcite, from both samples. Violet/purple pigmentation surrounding tissue necrosis is characterized as purpling, in response to fungus infection and allelopathic interactions. The spectroscopic analysis of the white‐cream tissues, designated as healthy, has revealed the presence of the carotenoid peridinin, typical of the endosymbiont that harbors this species; however, peridinin was not observed in the colorless sclerites analysis, presenting bands exclusively of calcite. In contrast, the violet coloration of damaged tissue has also been observed in the sclerites. Both showed Raman bands corresponding to unmethylated polyunsaturated aldehyde, besides calcite bands. This is the first report of purpling in a Brazilian octocoral, identified as a derivative of the biochromes named psittacofulvins, which have been reported as exclusive in parrots. Copyright © 2011 John Wiley & Sons, Ltd.     

The colour of domestication and the designer chicken

Colour is an important feature of most living organisms. In the wild, colour has great significance affecting the survival and reproductive success of the species. The environmental constraints which lead to the specific colours of birds and animals are very strong and individuals of novel colours tend not to survive. Under domestication, mankind has transformed all the species involved which have thus been freed from environmental pressures to a large extent. Early colour variants were mostly selected for utility reasons or religious practices. In more recent centuries colour varieties have been created purely for ornament and pleasure, fashion playing a surprisingly large part in their development. A bewildering array of colours and patterns can now be found in all our commensal species, especially the Domestic Fowl (Gallus gallus domesticus).     

The principle that generates dissimilar patterns inside aggregates of organisms

Pattern formation and self-organization are phenomena that occur across the board, in animate and inanimate systems. In this paper, we rely on the constructal law to explain the generation of patterns (shapes, structures) in aggregates of organisms-pedestrian crowds and stony corals. In pedestrian crowds a variety of patterns are often observed, from ‘chaotic’ appearances to spontaneous organization in lanes of uniform walking direction. Stony corals and other organisms also present intraspecific variability in shape. We show that flow systems develop in time patterns which provide easier access to the nutrients and space, within a set of constraints imposed by each situation. Flow systems have the freedom to morph their shape in search for architectures that allows them to have greater access to the space that they inhabit. We identify the mechanisms allowing pedestrians to evolve in space and time. We also show that stony corals may develop branched or spherical shapes, depending on which shape performs best in response to the environmental conditions. The constructal law allows systems with complex internal flows to be described and understood for a unified view.     

Power and beam-width dependence of a BaTiO3: Ce self-pumped phase conjugator

Power and beam-width dependences of the performance of self-pumped phase conjugators using a BaTiO₃: Ce crystal have been investigated. The incident beam was permitted to enter the crystal by thea-face or the +c-face. In both cases, the phase-conjugate reflectivity was observed to vary with the power and beam width of the incident beam. In the former case, two different optical beam patterns in the crystal can be observed under different conditions. Qualitative explanations are given to some of the results observed.