Boundaries that demarcate structural and functional domains of chromatin

Understanding of how the eukaryotic genome is packaged into chromatin and what the functional consequences of this organization are has begun to emerge recently. The concept of ‘chromatin domains’ — the topologically independent structural unit — is the basis of higher order chromatin organization. The idea that this structural unit may also coincide with the functional unit, offers a useful framework in dissecting the structure-function relationship. Boundaries that define these domains have been identified and several assays have been developed to test themin vivo. We have used genetic means to identify and analyse such boundary elements in the bithorax complex ofDrosophila melanogaster. In this review we discuss chromatin domain boundaries identified in several systems using different means. Although there is no significant sequence conservation among various chromatin domain boundaries, these elements show functional conservation across the species. Finally, we discuss mechanistic aspects of how chromatin domain boundaries may function in organizing and regulating eukaryotic genome.     

Structure and Function of the Hair Cell Ribbon Synapse

Faithful information transfer at the hair cell afferent synapse requires synaptic transmission to be both reliable and temporally precise. The release of neurotransmitter must exhibit both rapid on and off kinetics to accurately follow acoustic stimuli with a periodicity of 1 ms or less. To ensure such remarkable temporal fidelity, the cochlear hair cell afferent synapse undoubtedly relies on unique cellular and molecular specializations. While the electron microscopy hallmark of the hair cell afferent synapse — the electron-dense synaptic ribbon or synaptic body — has been recognized for decades, dissection of the synapse’s molecular make-up has only just begun. Recent cell physiology studies have added important insights into the synaptic mechanisms underlying fidelity and reliability of sound coding. The presence of the synaptic ribbon links afferent synapses of cochlear and vestibular hair cells to photoreceptors and bipolar neurons of the retina. This review focuses on major advances in understanding the hair cell afferent synapse molecular anatomy and function that have been achieved during the past years.     

Structural changes in the vacuole and cytoskeleton are key to development of the two cytoplasmic domains supporting single-cell C<Subscript>4</Subscript> photosynthesis in <Emphasis Type="Italic">Bienertia sinuspersici</Emphasis>

Bienertia sinuspersici Akhani has an unusual mechanism of C₄ photosynthesis which occurs within individual chlorenchyma cells. To perform C₄, the mature cells have two cytoplasmic compartments consisting of a central (CCC) and a peripheral (PCC) domain containing dimorphic chloroplasts which are interconnected by cytoplasmic channels. Based on leaf development studies, young chlorenchyma cells have not developed the two cytoplasmic compartments and dimorphic chloroplasts. Fluorescent dyes which are targeted to membranes or to specific organelles were used to follow changes in cell structure and organelle distribution during formation of C₄-type chlorenchyma. Chlorenchyma cell development was divided into four stages: 1—the nucleus and chloroplasts occupy much of the cytoplasmic space and only small vacuoles are formed; 2—development of larger vacuoles, formation of a pre-CCC with some scattered chloroplasts; 3—the vacuole expands, cells have directional growth; 4—mature stage, cells have become elongated, with a distinctive CCC and PCC joined by interconnecting cytoplasmic channels. By staining vacuoles with a fluorescent dye and constructing 3D images of chloroplasts, and by microinjecting a fluorescence dye into the vacuole of living cells, it was demonstrated that the mature cell has only one vacuole, which is traversed by cytoplasmic channels connecting the CCC with the PCC. Immunofluorescent studies on isolated chlorenchyma cells treated with cytoskeleton disrupting drugs suspended in different levels of osmoticum showed that both microtubules and actin filaments are important in maintaining the cytoplasmic domains. With prolonged exposure of plants to dim light, the cytoskeleton undergoes changes and there is a dramatic shift of the CCC from the center toward the distal end of the cell.     

Pourquoi deux sexes?

This paper is a concrete approach to the problem of the number of the sexes. We try to imagine—on the example of three sexes—the mechanisms which would have to accompany a reproduction with several sexes. We have limited our study to the monohybridism, dihybridism and determinism of the sex.      

The uniqueness of biological self-organization: challenging the Darwinian paradigm

Here we discuss the challenge posed by self-organization to the Darwinian conception of evolution. As we point out, natural selection can only be the major creative agency in evolution if all or most of the adaptive complexity manifest in living organisms is built up over many generations by the cumulative selection of naturally occurring small, random mutations or variants, i.e., additive, incremental steps over an extended period of time. Biological self-organization—witnessed classically in the folding of a protein, or in the formation of the cell membrane—is a fundamentally different means of generating complexity. We agree that self-organizing systems may be fine-tuned by selection and that self-organization may be therefore considered a complementary mechanism to natural selection as a causal agency in the evolution of life. But we argue that if self-organization proves to be a common mechanism for the generation of adaptive order from the molecular to the organismic level, then this will greatly undermine the Darwinian claim that natural selection is the major creative agency in evolution. We also point out that although complex self-organizing systems are easy to create in the electronic realm of cellular automata, to date translating in silico simulations into real material structures that self-organize into complex forms from local interactions between their constituents has not proved easy. This suggests that self-organizing systems analogous to those utilized by biological systems are at least rare and may indeed represent, as pre-Darwinists believed, a unique ascending hierarchy of natural forms. Such a unique adaptive hierarchy would pose another major challenge to the current Darwinian view of evolution, as it would mean the basic forms of life are necessary features of the order of nature and that the major pathways of evolution are determined by physical law, or more specifically by the self-organizing properties of biomatter, rather than natural selection.     

Numerical investigation of the physical model of a high-power electromagnetic wave in a magnetically insulated transmission line

An efficient numerical code for simulating the propagation of a high-power electromagnetic pulse in a vacuum transmission line is required to study the physical phenomena occurring in such a line, to analyze the operation of present-day megavolt generators at an ∼10-TW power level, and to design such new devices. The main physical theoretical principles are presented, and the stability of flows in the near-threshold region at the boundary of the regime of magnetic self-insulation is investigated based on one-dimensional telegraph equations with electron losses. Numerical (difference) methods—specifically, a method of characteristics and a finite-difference scheme—are described and their properties and effectiveness are compared by analyzing the high-frequency modes.     

A comparison of approaches for modelling the occurrence of marine animals

Approaches for modelling the distribution of animals in relation to their environment can be divided into two basic types, those which use records of absence as well as records of presence and those which use only presence records. For terrestrial species, presence–absence approaches have been found to produce models with greater predictive ability than presence-only approaches. This study compared the predictive ability of both approaches for a marine animal, the harbour porpoise (Phoceoena phocoena). Using data on the occurrence of harbour porpoises in the Sea of Hebrides, Scotland, the predictive abilities of one presence–absence approach (generalised linear modelling—GLM) and three presence-only approaches (Principal component analysis—PCA, ecological niche factor analysis—ENFA and genetic algorithm for rule-set prediction—GARP) were compared. When the predictive ability of the models was assessed using receiver operating characteristic (ROC) plots, the presence–absence approach (GLM) was found to have the greatest predictive ability. However, all approaches were found to produce models that predicted occurrence significantly better than a random model and the GLM model did not perform significantly better than ENFA and GARP. The PCA had a significantly lower predictive ability than GLM but not the other approaches. In addition, all models predicted a similar spatial distribution. Therefore, while models constructed using presence–absence approaches are likely to provide the best understanding of species distribution within a surveyed area, presence-only models can perform almost as well. However, careful consideration of the potential limitations and biases in the data, especially with regards to representativeness, is needed if the results of presence-only models are to be used for conservation and/or management purposes. Guest editor: V. D. Valavanis Essential Habitat Mapping in the Mediterranean     

The Intelligent Egg, and How It Got That Way: from Genes to Genius in a Few Easy Lessons

A seed has no flowers or leaves, and an egg no fingers or lungs. Yet plants and animals not only have these things but they resemble their parents in detail throughout their bodies. Something is inherited, but what is it? Life is based on the activities of cells. An organism has large numbers of them—a human has trillions! Cells live as separate units, which enables them each to do its own thing within its particular organ, but to be an organism they must work together. A cell can only detect its immediate local environment, but that includes various kinds of signals or information from nearby or far away within the body—or even from the external environment. It is by being local but responding globally in this way that an egg becomes an organism, an organism manages its way through life, and organisms make up species and ecosystems that interact with each other. The evolution of these abilities has produced the glorious array of living forms that populate the world. In these ways, an egg may have no thoughts but is a highly intelligent being.     

Spatially encoded strategies in the execution of biomolecular-oriented 3D NMR experiments

Three-dimensional nuclear magnetic resonance (3D NMR) provides one of the foremost analytical tools available for the elucidation of biomolecular structure, function and dynamics. Executing a 3D NMR experiment generally involves scanning a series of time-domain signals S(t ₃), as a function of two time variables (t ₁, t ₂) which need to undergo parametric incrementations throughout independent experiments. Recent years have witnessed extensive efforts towards the acceleration of this kind of experiments. Among the different approaches that have been proposed counts an “ultrafast” scheme, which distinguishes itself from other propositions by enabling—at least in principle—the acquisition of the complete multidimensional NMR data set within a single transient. 2D protein NMR implementations of this single-scan method have been demonstrated, yet its potential for 3D acquisitions has only been exemplified on model organic compounds. This publication discusses a number of strategies that could make these spatial encoding protocols compatible with 3D biomolecular NMR applications. These include a merging of 2D ultrafast NMR principles with temporal 2D encoding schemes, which can yield 3D HNCO spectra from peptides and proteins within ≈100 s timescales. New processing issues that facilitate the collection of 3D NMR spectra by relying fully on spatial encoding principles are also assessed, and shown capable of delivering HNCO spectra within 1 s timescales. Limitations and prospects of these various schemes are briefly addressed.     

Cosmic gourds: Cucurbit and Crescentia effigy pottery of coastal Ecuador

This paper treats the identification of modeled images of cucurbits —gourds and squash—in the ceramics of the Late Formative Era (or Chorrera culture) of coastal Ecuador (ca. 900 B.C. to 100 A.D.). These images provide good evidence for the sophisticated cultivation of cucurbits by the native peoples of the coast of South America from very early time periods in Ecuador. Their importance in the iconography of Late Formative cultures certainly demonstrates that the domestication of fruits with both hard and soft rinds must have been well established by the time ceramic production had begun. Depictions of combinations of animals with cucurbit-shaped bodies in the mortuary ceramics of the Late Formative period also demonstrate that cucurbits were an essential part of life (and death) on the coast of Ecuador.     

Assessment of higher insect taxa as bioindicators for different logging-disturbance regimes in lowland tropical rain forest in Sabah, Malaysia

One of the serious environmental problems since the 1980s has been the conflict between the high rate of deforestation and maintenance of healthy ecosystem services and biological values in tropical forests. There is an urgent demand for setting up an appropriate environmental assessment to keep healthy ecosystem functions and biodiversity along with sustainable forest use based on ecology. In this study, we tried to assess logging-disturbance effects on the abundances of several flying insect groups (higher-taxon approach) in lowland tropical rain forest (Deramakot Forest Reserve, Sabah, Malaysia), while considering seasonal changes and vertical forest stratification. The season was the most important factor affecting the abundances of all the insect groups. Effects of logging disturbance were prominent in the understorey but obscure in the canopy. Changes in physical conditions caused by logging—possibly an increased evaporation due to solar radiation—may have decreased the abundance of desiccation-sensitive insects, especially in the understorey. There are also two probable reasons for the difference between events in the understorey and those in the canopy: (1) noise effects of various physical, environmental factors may have obscured insect responses to logging disturbance in the canopy; (2) higher spatio-temporal variation in quality and quantity of living food resources—such as leaves, flowers and fruits—provided in the canopy may have affected the abundance of their consumer insects independently of logging disturbance. Thus, this study suggests that the abundance of some insect groups at higher-taxon level, especially in the understorey, can be used as bioindicators for assessing effects of logging disturbance on the forest ecosystem.     

Cytochrome <Emphasis Type="Italic">c</Emphasis> signalosome in mitochondria

Cytochrome c delicately tilts the balance between cell life (respiration) and cell death (apoptosis). Whereas cell life is governed by transient electron transfer interactions of cytochrome c inside the mitochondria, the cytoplasmic adducts of cytochrome c that lead to cell death are amazingly stable. Interestingly, the contacts of cytochrome c with its counterparts shift from the area surrounding the heme crevice for the redox complexes to the opposite molecule side when the electron flow is not necessary. The cytochrome c signalosome shows a higher level of regulation by post-translational modifications—nitration and phosphorylation—of the hemeprotein. Understanding protein interfaces, as well as protein modifications, would puzzle the mitochondrial cytochrome c-controlled pathways out and enable the design of novel drugs to silence the action of pro-survival and pro-apoptotic partners of cytochrome c.     

Spatial symmetries in vestibular projections to the uvula-nodulus

The discharge of secondary vestibular neurons relays the activity of the vestibular endorgans, occasioned by movements in three-dimensional physical space. At a slightly higher level of analysis, the discharge of each secondary vestibular neuron participates in a multifiber projection or pathway from primary afferents via the secondary neurons to another neuronal population. The logical organization of this projection determines whether characteristics of physical space are retained or lost. The logical structure of physical space is standardly expressed in terms of the mathematics of group theory. The logical organization of a projection can be compared to that of physical space by evaluating its symmetry group. The direct projection from the semicircular canal nerves via the vestibular nuclei to neck motor neurons has a full three-dimensional symmetry group, allowing it to maintain a three-dimensional coordinate frame. However, a projection may embed only a subgroup of the symmetry group of physical space, which incompletely mirrors the properties of physical space. The major visual and vestibular projections in the rabbit via the inferior olive to the uvula-nodulus carry three degrees of freedom—rotations about one vertical and two horizontal axes—but do not have full three dimensional symmetry. Instead, the vestibulo-olivo-nodular projection has symmetries corresponding to a product of two-dimensional vestibular and one-dimensional optokinetic spaces. This combination of projection symmetries provides the foundation for distinguishing horizontal from vertical rotations within a three dimensional space. In this study, we evaluate the symmetry group given by the physiological organization of the vestibulo-olivo-nodular projection. Although it acts on the same sets of elements and mirrors the rotations that occur in physical space, the physiological transformation group is distinct from the spatial group. We identify symmetries as products of physiological and spatial transformations. The symmetry group shapes the information the projection conveys to the uvula-nodulus; this shaping may depend on a physiological choice of generators, in the same way that function depends on the physiological choice of coordinates. We discuss the implications of the symmetry group for uvula-nodulus function, evolution, and functions of the vestibular system in general.     

Key transitions during the evolution of animal phototransduction: novelty, "tree-thinking," co-option, and co-duplication

Biologists are amazed by the intricacy and complexity of biologicalinteractions between molecules, cells, organisms, and ecosystems.Yet underlying all this biodiversity is a universal common ancestry.How does evolution proceed from common starting points to generatethe riotous biodiversity we see today? This "novelty problem"—understandinghow novelty and common ancestry relate—has become of criticalimportance, especially since the realization that genes anddevelopmental processes are often conserved across vast phylogeneticdistances. In particular, two processes have emerged as theprimary generators of diversity in organismal form: duplicationplus divergence and co-option. In this article, we first illustratehow phylogenetic methodology and "tree-thinking" can be usedto distinguish duplication plus divergence from co-option. Second,we review two case studies in photoreceptor evolution—onesuggesting a role for duplication plus divergence, the otherexemplifying how co-option can shape evolutionary change. Finally,we discuss how our tree-thinking approach differs from othertreatments of the origin of novelty that utilized a "linear-thinking"approach in which evolution is viewed as a linear and gradualprogression, often from simple to complex phenotype, drivenby natural selection.     

Valuing Lives and Allocating Resources: A Defense of the Modified Youngest First Principle of Scarce Resource Distribution

In this paper, I argue that the ‘modified youngest first’ principle provides a morally appropriate criterion for making decisions regarding the distribution of scarce medical resources, and that it is morally preferable to the simple ‘youngest first’ principle. Based on the complete lives system's goal of maximizing complete lives rather than individual life episodes, I argue that essential to the value we see in complete lives is the first person value attributed by the experiencer of that life. For a life to be ‘complete’ or ‘incomplete,’ the subject of that life must be able to understand the concept of a complete life, to have started goals and projects, and to know what it would be for that life to be complete. As the very young are not able to do this, it can reasonably be said that their characteristically human lives have not yet begun, giving those accepting a complete lives approach good reason to accept the modified youngest first principle over a simple ‘youngest first’ approach.     

From the salt marsh to the ID-card: Bacteriorhodopsin as a functional material in nanobiotechnology

Bacteriorhodopsin (BR) is an evolutionary highly optimized photochromic retinal protein, which is found in extremely halophilic bacteria, e.g., in salt marshes. We demonstrated that starting from the wildtype as a blueprint by means of gene technology and biotechnology a versatile material for optical information recording can be developed. BR is structurally related to the visual pigment rhodopsin. It is the key molecule in the halobacterial photosynthetic system — an alternative to the chlorophyll-dependent photosynthesis. Its biological function ist that of a light-driven proton pump. In the halobacterial cell — which are found e.g. in salt marshes — it converts light energy into chemical energy, i.e. a proton gradient over the cell membrane, which finally supplies ATP to the cell. The photochromic properties of BR are very attractive compared to those of known organic photochromic compounds, in particular as far as longevity under exposure to oxygen and light is concerned. This is one of the reasons why we try to utilized this evolutionary optimized biomaterial for technical applications in particular in optical data storage and processing. As the biological function of BR is optimized for energy conversion, the physical properties of BR need to be tuned to turn this molecule into a material which matches the requirements of optical applications in data storage and processing. Gene technology is a powerful tool for the controlled modification of physical properties of a biomolecule like BR. In technical applications water needs to be omitted. However, the function of biomaterials strictly depends on the presence of water. Membrane proteins are much less dependent on the presence of water which makes them good candidates for technical applications. We showed that BR can be processed into dry polymeric films where its function is preserved. In a field test where ID-cards comprising BR-based inks as security elements it has been demonstrated that biomaterials may be integrated in active form as functional components into conventional technical applications. Conventional nanomaterials supply properties to a product, biomaterials supply functions.     

Evolutionary view of waste-management behavior using volatile chemical cues in social spider mites

Spider mites of the genus Stigmaeopsis (Acari: Tetranychidae) construct and live gregariously inside woven nests on the leaf surface of host plants. This genus shows waste-management behavior—they defecate at particular sites—but the rules for management differ between species. The utilization of chemical cues for waste management is known in two species, Stigmaeopsis miscanthi inhabiting Miscanthus sinensis and S. longus inhabiting Sasa senanensis, but not in any others. In this study, we first investigated the origin of the chemical compounds to understand how the behavior evolved, and then investigated the responses of each species to chemical compounds from different sources. The results show that the chemical compounds are commonly contained in the feces of several Stigmaeopsis species, as well as in their host plant juices, suggesting this behavior evolved using the chemical compounds originally contained in their feces. Our results also show that the chemical compounds used by S. miscanthi and S. longus are subtly different and involve host plant differences, and that S. miscanthi could respond to both compounds, but S. longus could not. Considering this in terms of their phylogenetic relationship, it is expected that these two species may have evolved from a common ancestor living on Sasa senanensis.     

What Capabilities for the Animal?

In this essay, I defend a bi-constructivist approach to ethology—a constructivist ethology assuming that each animal adopts constructivist strategies. I put it in opposition to what I call a realist-Cartesian approach, which is currently the dominant approach to ethology and comparative psychology. The starting point of the bi-constructivist approach can be formulated as a shift from the classical Aristotelian question “What is an animal?” to the Spinozean question, which is much less classical but which seems to me to be much stronger: “What are the capacities of the animal?”. Is it possible to conceptualize an ethology which insists on interpretation and therefore on invention, innovation and creativity, rather than on causality, the monotony of behavioural routines, and/or genetic or environmental determination? Such an ethology would be based not on the fiction of an absent observer but on fully recognizing the necessity of an observer, who is effectively present in order to get an observation. A pluralistic ethology does not dissociate itself from the marginal epistemologies of practitioners like animal trainers, hunters, stockbreeders etc., or, moreover, non-western experts. An ethology of this kind is not clamped within the boundaries of purely academic epistemology, obsessed by demarcation lines between the human and the animal. My work on the bi-constructivist approach represents a contribution towards the elaboration of an authentically biosemiotic ethology, one which is significantly different from the mechanical ethology of today.     

Determination of pulmonary mean transit time and cardiac output using a one-dimensional model

In this work, we show that a one-dimensional model of the blood flow across the lungs can reproduce the evolution of a bolus versus the time. Solving the differential equation governing the bolus concentration in the framework of this model, we determine the solution which fulfills Gaussian initial boundary conditions. An effective parameter related to the ratio of a diffusion coefficient to the square of the mean speed of the flow is defined. The determination of its numerical values following a semi-empirical approach enables us to know accurately the mean transit time and the cardiac output. The results have been compared to other methods, and were found in good agreement. Such an approach could be of interest in all studies where the knowledge of flow—including micro-circulation—is needed.