An enzyme family reunion — similarities,differences and eccentricities in actions on <Emphasis Type="Italic">α</Emphasis>-glucans

α-Glucans in general, including starch, glycogen and their derived oligosaccharides are processed by a host of more or less closely related enzymes that represent wide diversity in structure, mechanism, specificity and biological role. Sophisticated three-dimensional structures continue to emerge hand-in-hand with the gaining of novel insight in modes of action. We are witnessing the “test of time” blending with remaining questions and new relationships for these enzymes. Information from both within and outside of ALAMY_3 Symposium will provide examples on what the family contains and outline some future directions. In 2007 a quantum leap crowned the structural biology by the glucansucrase crystal structure. This initiates the disclosure of the mystery on the organisation of the multidomain structure and the “robotics mechanism” of this group of enzymes. The central issue on architecture and domain interplay in multidomain enzymes is also relevant in connection with the recent focus on carbohydrate-binding domains as well as on surface binding sites and their long underrated potential. Other questions include, how different or similar are glycoside hydrolase families 13 and 31 and is the lid finally lifted off the disguise of the starch lyase, also belonging to family 31? Is family 57 holding back secret specificities? Will the different families be sporting new “eccentric” functions, are there new families out there, and why are crystal structures of “simple” enzymes still missing? Indeed new understanding and discovery of biological roles continuously emphasize value of the collections of enzyme models, sequences, and evolutionary trees which will also be enabling advancement in design for useful and novel applications.     

Quantum information teleportation through biological wires,gravitational micro-bio-holes and holographic micro-bio-systems: A hypothesis

Biological systems like cells, bacteria, chloroplasts and other micro-organisms could exchange quantum particles like electrons, photons and gravitational waves and have large distant information teleportation. This is because that their DNAs and membranes are formed from quantum particles like electrons and protons and by their motions, some currents and waves are emerged. These waves have the main role in information teleportation. There are different methods which could be used for quantum information teleportation in biological system. Some of these mechanisms are: 1. Microbes, micro-bubbles and some other biological molecules like to form some biological lines specially near the cellular gates. Also, some biological lines may be formed between two cells. These biological lines could play the role of wires which transmit information from a place to another one. For example, some signatures of this quantum information teleportation could be seen in biological lines which are emerged near the plant cell walls or gates or close to chloroplasts. Chloroplasts shoot some spinors which maybe confined within the micro-bubbles or absorb by microbes. These bubbles and microbes may join to each other and form some biological lines which may be strengthen from a plant cell to another. These biological lines could be seen near the plant cell walls or on a metal which connects two parts of a leaf. 2. Some another signatures of “quantum photon exchange or quantum information teleportation” could be seen between microbes under the objective lenses and macro-objects on the eye lenses of a light microscope. It seems that as microscope make big images from microbes for us, produce small pictures of macro-objects for microbes such as they could diagnose them and interact with them. This property could be used in controlling microbes. 3. Another way for controlling microbes is using of virtual shapes which are induced by a special light source. For example, using a multi-gonal lamp, one can induce multi-gonal shape within the micro-bubbles. Also, this special lamp could force microbes and micro-bubbles to build multi-gonal colonies on a metal-glass slide. Maybe, by using this property, one can build a light source with the shape of anti-microbial matter and induce anti-microbial property within micro-bubbles. 4. Another main way for quantum teleportation is using of gravitational holes which may be emerged by increasing concentration of microbes and heavy cells in some points. These holes absorb microbes and micro-bubbles and conduct them to the heavy cells. Usually, there are some white holes near these dark holes which as a proposal, one can assume that these white holes are another end of gravitational holes and emit photons which are entered from dark end. 5. And finally, a very main mechanism for quantum information teleportation with microbes and controlling them is using of a holography and inducing virtual microbes and biological molecules in biological systems. For example, by a combinations of two lights with different colors under a light microscope in a dark room, one may induce some non-virtual microbes in biological systems such as each microbe interacts with a virtual microbe. This is because that light waves take photos of microbes, collide with lenses of microscopes and return to the slide and form virtual microbes or biological molecules. This technique could be used in curing diseases. Although, results of our experiments show the correctness of these mechanisms and theories, however, for the moment, we propose them only as a proposal and hypothesis and hope that other scientists do similar experiments. Also, some of our experiments may be at preliminary stages; however they could be used as a hypothesis, proposal and guidance.     

Rescuing Robert Brown—The Origins of Angio-Ovuly in Seed Cones of Conifers

Robert Brown (1827) recognized the distinction between the two major classes of seed plants on the basis, respectively, of exposed ovules, which receive pollen directly, and enclosed ovules, which do not, at the time of pollination. The two groups, unfortunately, became known as “Gymnosperms” and “Angiosperms”, a distinction not made by Brown. The names are, at best, useful only as identifying labels. As is established here, gymno-ovuly and angio-ovuly would have been better words and should serve as the most consistent distinguishing character among groups of seed plants. Although conifers can hardly be claimed to be members of any lineage that led to the Angiosperms, the gymno-ovulate method of reproduction must have occurred in the direct ancestors of flowering plants. Interpolating development and functional evidence serves to resurrect Robert Brown’s important but neglected observation and correct misstatements implied in generally accepted systematic terminology. The result of this approach is to discover that the conifers in their reproductive diversity show some trends indicative of those characters that define the flowering plants. Although non-homologous these character manifestations provide useful models which can lead to a better understanding of the origin of “Angiosperms” from “Gymnosperms.” In the complex and extended process of reproductive development in both major groups regular transpositions occur, depending on whether “gymno-”and “angio-”are applied to ovules or seeds. Gymno-ovuly and angio-spermy are the most common conditions in conifers but result in intrinsically opposed processes of pollen reception and subsequent seed protection, which are resolved by successive changes in seed-cone structure. The modern conifers illustrate considerable diversity of ovulate and seed cone structure in relation to several biological functions, including traits that anticipate the angio-ovulate condition, in cone inception, ovule enclosure, pollen and embryo development and seed dispersal. From the paleobotanical record we do have a good grasp of the structural changes in the progressive modification of the coniferous seed cone in conifers, starting with the antecedent Carboniferous Cordaitales. These changes have involved the progressive condensation of a lax, branched strobilus and end with the highly condensed uniovulate “cone” as in many Podocarpus species in which the equivalent of a bitegmic ovule exists. The progressive changes can be perceived typologically among existing conifers but need to be understood as the result of biological processes that suggest increased reproductive efficiency, and can be added to our present quite robust understanding of conifer phylogeny.     

The Last Month of Szent-Györgyi in Groningen

Albert (von) Szent-Györgyi started his studies on biological oxidation processes – which also resulted in the discovery of vitamin C, for which he received the Nobel Price in 1937 – in the Laboratory of Physiology of the University in Groningen in 1922–1926. These studies were later continued in Cambridge (UK) and Szeged (Hungary). When he had already received the invitation as well as the financial means to come and work in Cambridge, he still did experiments in Groningen to find out whether the adrenal extract, isolated by him and later found to be a major source of vitamin C, contained the hormone essential for the survival of cats whose adrenals were removed. He was rather upset by the negative results of this experiment, judging by the recollections of a former student of his. This history constitutes an interesting example of the difference between serendipitous discovery and planned invention.     

GM plants as sources of im/possibility: a developmental systems view of stabilization

This paper generates a heuristic understanding of the stabilization dynamic of genetically modified plants. This heuristic, the paper argues, can provide a fruitful platform for studying the political dimensions embedded in GM plants. Focusing on stabilization is important, because outside laboratories a plant can have an intermediating role only as a cultivar; as something which has integrated into biological processes and human practices. The actual stabilizing entity is not just an object, but a dynamic analogous to what is called a developmental system. The empowering or suppressing consequences of GM plants depend significantly on the qualities of this spatio-temporal order stabilizing; on the “possibility space” it opens up. Moreover, stabilization connects and makes things possible, but it does not do so automatically, predictably – or for everyone. Centralized control may support stability, but it may also increase vulnerability by reducing local possibility space.     

Quantum Requirements of Photosynthetic Electron Transport In Sitka Spruce from Different Light Environments

Quantum requirements of photosynthetic electron transport have been measured in shoots of Picea sitchensis (Bong.) Carr. (Sitka spruce) from different levels in a forest canopy and in shoots from plants grown in contrasting light environments in controlled environment chambers. Neutral density filters were used to obtain very low photon flux densities. The light absorbed by the chloroplast suspensions was calculated from measurements of the transmittance of the suspensions. The shoots from the top of the forest canopy (“sun” shoots) had lower quantum requirements for photosystems I and II than the shoots from the bottom of the forest canopy (“shade” shoots). High light grown plants and “sun” shoots had higher rates of electron transport at light saturation than low light grown plants and “shade” shoots. Thus a higher potential for electron transport was found to exist in “sun” shoots than in “shade” shoots at both high and low photon flux densities.     

Was heißt “lebendig”?

“Life” means “being alive” of special entities, which we call “organisms”. From a physical point of view, living entities are open systems, which exchange matter as well as energy with their surroundings. Against disruptive influences permanently present, they maintain actively and autonomously a steady state far from the thermodynamic equilibrium. This dynamic state of living beings represents a functional order, an internal “organization”. That means that the involved processes one and all must be correlated in such a way that they in sum prevent the breakdown of the living state. Organization implies functionality, which in turn requires structural relationships, and structures require information for their specification. Information in turn presupposes a source, which is constituted in living systems by the nucleic acids. Organisms are unique in having a capacity to use information, which is stored in the nucleic acid and yields the basis for their specific internal organization in its perpetuation: Living beings, and only they, show a self‐maintained organization.     

Cryptic phenology in plants: Case studies,implications, and recommendations

Plant phenology—the timing of cyclic or recurrent biological events in plants—offers insight into the ecology, evolution, and seasonality of plant‐mediated ecosystem processes. Traditionally studied phenologies are readily apparent, such as flowering events, germination timing, and season‐initiating budbreak. However, a broad range of phenologies that are fundamental to the ecology and evolution of plants, and to global biogeochemical cycles and climate change predictions, have been neglected because they are “cryptic”—that is, hidden from view (e.g., root production) or difficult to distinguish and interpret based on common measurements at typical scales of examination (e.g., leaf turnover in evergreen forests). We illustrate how capturing cryptic phenology can advance scientific understanding with two case studies: wood phenology in a deciduous forest of the northeastern USA and leaf phenology in tropical evergreen forests of Amazonia. Drawing on these case studies and other literature, we argue that conceptualizing and characterizing cryptic plant phenology is needed for understanding and accurate prediction at many scales from organisms to ecosystems. We recommend avenues of empirical and modeling research to accelerate discovery of cryptic phenological patterns, to understand their causes and consequences, and to represent these processes in terrestrial biosphere models.     

Singlet oxygen production by biological systems

Singlet oxygen (1 delta g) is a highly reactive, short-lived intermediate which readily oxidizes a variety of biological molecules. The biochemical production of singlet oxygen has been proposed to contribute to the destructive effects seen in a number of biological processes. Several model biochemical systems have been shown to produce singlet oxygen. These systems include the peroxidase-catalyzed oxidations of halide ions, the peroxidase-catalyzed oxidations of indole-3-acetic acid, the lipoxygenase-catalyzed oxidation of unsaturated long chain fatty acids and the bleomycin-catalyzed decomposition of hydroperoxides. Results from these model systems should not be uncritically extrapolated to living systems. Recently, however, an intact cell, the human eosinophil, was shown to generate detectable amounts of singlet oxygen. This result suggests that singlet oxygen may be shown to be a significant biochemical intermediate in a few biological processes.     

Can we make sense of subjective experience in metabolically situated cognitive processes?

In “Mind, matter and metabolism,” Godfrey-Smith’s objective is to “develop a picture” in which, first, the basis of living activity in physical processes “makes sense,” second, the basis of proto-cognitive activity in living activity “makes sense” and third, “the basis of subjective experience in metabolically situated cognitive processes also makes sense.” show that he fails to attain all three of these objectives, largely owing to the nature and modularization of metabolism.     

Protein Structures and Neutral Theory of Evolution

Abstract

The neutral theory of evolution is extended to the origin of protein molecules. Arguments are presented which suggest that the amino acid sequences of many globular proteins mainly represent “memorized” random sequences while biological evolution reduces to the “editing” these random sequences. Physical requirements for a functional globular protein are formulated and it is shown that many of these requirements do not involve strategical selection of amino acid sequences during biological evolution but are inherent also for typical random sequences. In particular, it is shown that random sequences of polar and unpolar amino acid residues can form α-helices and β-strands with lengths and arrangement along the chain similar to those in real globular proteins. These α- and β-regions in random sequences can form three-dimensional folding patterns also similar to those in real proteins. The arguments are presented suggesting that even the tight packing of side groups inside protein core do not require very strong biological selection of amino acid sequences either. Thus many structural features of real proteins can exist also in random sequences and the biological selection is needed mainly for the creation of active sites of proteins and for their stability under physiological conditions.     

Small zebrafish in a big chemical pond

The number of possible small organic molecules of different structure is virtually limitless. One of the main goals of chemical biologists is to identify, from this “chemical space”, entities that affect biological processes or systems in a specific manner. This can lead to a better understanding of the regulation and components of various biological machineries, as well as provide insights into efficacious therapeutic targets and drug candidates. However, the challenges confronting chemical biologists are multiple. How do we efficiently identify compounds that possess desirable activities without unwanted off‐target effects? Once a candidate compound has been found, how do we determine its mode of action? In this Prospects piece, we call attention to recent studies using embryonic and larval zebrafish to illustrate the breadth and depth of questions in chemical biology that may be addressed using this model, and hope that they can serve as catalysts for future investigational ideas. J. Cell. Biochem. 113: 2208–2216, 2012. © 2012 Wiley Periodicals, Inc.     

Sodium—A Functional Plant Nutrient

Plant scientists usually classify plant mineral nutrients based on the concept of “essentiality” defined by Arnon and Stout as those elements necessary to complete the life cycle of a plant. Certain other elements such as Na have a ubiquitous presence in soils and waters and are widely taken up and utilized by plants, but are not considered as plant nutrients because they do not meet the strict definition of “essentiality.” Sodium has a very specific function in the concentration of carbon dioxide in a limited number of C₄ plants and thus is essential to these plants, but this in itself is insufficient to generalize that Na is essential for higher plants. The unique set of roles that Na can play in plant metabolism suggests that the basic concept of what comprises a plant nutrient should be reexamined. We contend that the class of plant mineral nutrients should be comprised not only of those elements necessary for completing the life cycle, but also those elements which promote maximal biomass yield and/or which reduce the requirement (critical level) of an essential element. We suggest that nutrients functioning in this latter manner should be termed “functional nutrients.” Thus plant mineral nutrients would be comprised of two major groups, “essential nutrients” and “functional nutrients.” We present an array of evidence and arguments to support the classification of Na as a “functional nutrient,” including its requirement for maximal biomass growth for many plants and its demonstrated ability to replace K in a number of ways, such as being an osmoticium for cell enlargement and as an accompanying cation for long-distance transport. Although in this paper we have only attempted to make the case for Na being a “functional nutrient,” other elements such as Si and Se may also confirm to the proposed category of “functional nutrients.”     

Phénoménologie de la subjectivité : Tatossian et la clinique psychiatrique

The human sciences are now celebrating the return of the Subject. However, as a form of resistance to science, the issue of subjectivity justifies a methodological resort to a phenomenological posture. This posture consists in “seeing” and “showing” the experience of foundations. In Arthur Tatossian’s distinction between Subject and subjectivity, the Subject carries out the synthesis of forms in which the subjectivity expresses and alienates itself. These forms include: the Self, the consciousness, the inner mind, etc. Subjectivity is what makes the Subject possible. Subjectivity is time, space, the body and the Other, and is shaped by time into a living present, by space into a common place, by the body into flesh, and by the Other as alterity. In psychiatric disorders, the patient fails to be a Subject. Whoever he or she is, a Self without subjectivity, as with a melancholic or a maniac, or subjectivity without Self, as with a schizophrenic, the issue of human identity arises. The central problem of the human condition, which is at the heart of psychiatric disorders, is the challenge of being a Self while retaining a degree of subjectivity. This in turn merges with another central problem: that of freedom. Subjectivity is the other face of freedom because it is the power to create meaning.     

Press discourses on Roma in the UK,Finland and Hungary

ABSTRACT

This article analyses the political and media discourses on Roma in Hungary, Finland and the UK, in relation to the local Roma in these countries as well as those who migrated from Central and Eastern Europe countries following the fall of communism. The authors have analysed left of centre and right of centre major newspapers in these three countries, focusing on specific case studies which were the foci of public debates during the last two decades. We also examined a common case study in 2013 (“blond Maria”) that was discussed throughout Europe. In each news paper, the constructions of Roma, local and migrant, and the changes to related discourses over the period were studied. In conclusion, we examine the multi-layered processes of social and political borderings in Europe which dominate discourses on Roma, “indigenous” and migrant, and the extent to which they constitute a coherent “European” construction of “the Roma”.     

Rethinking genes

The gene is the central construct of twentieth-century biology and evolution. It is a construct because, like “culture” in anthropology, “gene” is widely used and is central to the discipline's discourse, but eludes rigorous definition. Although the gene is acknowledged as a material entity, its membership criteria are unclear and its boundaries are fuzzy—indeed, more than one can occupy the same space at the same time. The purpose of this essay is to bring to light recent refinements in our conception of the gene and their implications for its use in biological anthropology.     

The Biological Applications of Two Aggregation‐Induced Emission Luminogens

Fluorescence imaging, as a commonly used scientific tool, is widely applied in various biomedical and material structures through visualization technology. Highly selective and sensitive luminescent biological probes, as well as those with good water solubility, are urgently needed for biomedical research. In contrast to the traditional aggregation‐caused quenching of fluorescence, in the unique phenomenon of aggregation‐induced emission (AIE), the individual luminogens have extremely weak or no emissivity because they each have free intramolecular motion; however, when they form aggregates, these components immediately “light up”. Since the discovery of “turn‐on” mechanism, researchers have been studying and applying AIE in a variety of fields to develop more sensitive, selective, and efficient strategies for the AIE dyes. There are numerous advantages to the use of AIE‐based methods, including low background interference, strong contrast, high performance in intracellular imaging, and the ability for long‐term monitoring in vivo. In this review, two typical examples of AIEgens, TPE‐Cy and TPE‐Ph‐In, are described, including their structure properties and applications. Recent progress in the biological applications is mainly focused on. Undoubtedly, in the near future, an increasing number of encouraging and practical ideas will promote the development of more AIEgens for broad use in biomedical applications.