Quantum biology at the cellular level—Elements of the research program

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) – a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the ‘basis-dependent’ nature of these concepts. We introduce the notion of ‘formal superposition’ and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular ‘decision-making’ and adaptation. We stress that the interpretation of the notion of ‘formal superposition’ should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., ‘Basis-Dependent Selection’, BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the ‘evolvability mechanism’ loophole are also discussed.     

Correspondences between classifications and between classes of entities in molecular genetics

Certain correspondences appear between the classifications and between the classes of various entities at molecular genetic level: types of fundamental correspondences between classifications and between classes of normal entities, on the one hand, and of mutant entities on the other hand; ranks of correspondences between classifications and between classes of entities. The concept of universality of the genetic code was reformulated on the basis of the above correspondences.     

Ecological Mechanisms of Evolution by Natural Selection: Causal Processes Generating Density-and-frequency Dependent Fitness

The current theory of natural selection explains that adaptive evolution occurs because genotypes with greater survival or reproductive tendencies, due to their particular biological properties, tend to increase in frequency over the lesser ones in a common environment; therefore, the former will eventually replace the latter. In nature, such a selection process most often occurs in a local population which is nested in a community involving local ecological dynamics which are not clearly articulated in the explanatory scheme of the theory. This paper seeks to explicate such an ecological process giving rise to the volution of a local population with a particular focus on dynamic effects of an increase in the number of invasive, new types on the fate of old ones. Arguments using the ecological-mechanistic model, representing negative interactions among alternative types of organisms, suggest major ecological mechanisms by which the new replace the old; a selective increase in the number of one type leads to a decrease in the equilibrial abundance of a limiting resource, an increase in the density of conspecifics, and/or an increase in the density of predators, which would in turn lower theper capitareproductive rate, or raise the morality rate of another and make it extinct. Thus, replacement due to selection is associated with such dynamic shifts in equilibria occurring in a local community. The analysis of three (a resource, a prey and a predator) and four species (those plus a top predator) models suggests that evolutionary processes cannot be predicted without reference to the web structure of the community, that some fitness components causing a selective increase in a particular type can have, in some cases, nothing to do with factors causing selective decreases in alternatives, and that evolution of some traits can occur without resource competition.     

A taxonomic revision of a Hypnea charoides-valentiae complex (Rhodophyta, Gigartinales) in Japan, with a description of Hypnea flexicaulis sp. nov.

Morphology of a Hypnea charoides‐valentiae complex (Rhodophyta, Gigartinales) in Japan is investigated on the basis of field‐collected and cultured plants. We can recognize two species, Hypnea charoides Lamouroux and H. flexicaulis Yamagishi et Masuda, sp. nov., which are distinguished by: (i) conspicuous percurrent main axes growing straight in the former versus less conspicuous percurrent main axes growing flexuosely in the latter; (ii) narrow branching angles (less than 90°) in the former versus wide branching angles (up to 150°) in the latter; (iii) the presence of branches and branchlets showing abrupt adaxial bending in the former versus those showing pronounced abaxial bending, some growing into hooked branchlets in the latter; and (iv) the absence (in the former) or presence (in the latter) of antler‐like branches. Nucleotide sequences of the plastid‐encoded large subunit of the ribulose‐1,5‐bisphosphate carboxylase/oxygenase gene (rbcL) support the differentiation of these two entities: the pairwise distance between them was 83 b.p. (6.2%).     

Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

Interaction of the monoaminergic and opioidergic brain systems in the course of nociceptive and antinociceptive reactions in cats

Nociceptive responses were evoked in cats by electrical transcutaneous stimulation of the forepaw or electrical stimulation of respective brain structures; these responses could be modulated (intensified or suppressed) by combined electrical stimulation of different brain structures or by neurochemical influences upon these structures. Intensification of nociceptive responses was observed after stimulation of the noradrenergic orP-ergic systems localized in the ventral zone of the central gray (vl SGC) and the structures monosynaptically connected with the latter: the posterior and lateral hypothalamic nuclei (Hp andHl) and preoptic region (RPO). Similar effects were induced by suppression of the serotoninergic system concentrated within the dorsolateral central gray (dl SGC), dorsal raphe nucleus (Rd), and closely related structures: the ventromedial, dorsomedial, and paraventricular hypothalamic nuclei (Hvm, Hdm, andHpv), septum (Sep), basolateral amygdalar nucleus (Am bl), fields 3–4 of the hippocampus (CA3–4), and cingular cortex (GC). Suppression of the serotoninergic system resulted in a decrease in the levels of functioning of the met-enkephalin- and β-endorphinergic systems and facilitation of theP-ergic system. Moderation of nociceptive responses, i.e., an analgesic effect, was observed after either stimulation of the serotonin-, met-enkephalin-, and β-endorphinergic systems localized in thedl SGC, Rd, Hvm, Hdm, Sep, Am bl, CA3–4, andGC, or suppression of the noradrenergic system. The latter influence resulted in inhibition of theP-ergic system and a rise in the functional activity of the met-enkephalin- and β-endorphinergic systems. The composition of two antagonistic brain systems, nociceptive and antinociceptive, is considered. The antinociceptive system includes serotonin-, met-enkephalin-, and β-endorphinergic elements. Leu-enkephalin is a nonspecific activator of the met-enkephalin-, β-endorphin-, andP-ergic systems. The nociceptive system consists of thevl SGC, Hp, Hl, andRPO, while the antinociceptive system includes thedl SGC, Rd, Hvm, Hdm, Hpv, Sep, Am dl, CA3–4, andGC.     

Allozyme variation in the annual weed species complexPolygonum aviculare (Polygonaceae) in relation to ploidy level and colonizing ability

Variation at six polymorphic enzymatic loci was studied in 50 populations of the selfing annualPolygonum aviculare from Belgium. The results show that theP. aviculare complex has an allopolyploid origin and comprises two main genetic entities, viz.P. aviculare subsp.depressum (2n = 4x = 40), restricted to urban sites subject to trampling stress, andP. aviculare subsp.aviculare (2n = 4x = 40, 2n = 6x = 60), with a wider ecological amplitude. The latter had a higher genetic diversity and a higher frequency of fixed heterozygosity than the former. WithinP. aviculare subsp.aviculare, genetic diversity and ecological amplitude correlated positively with ploidy level. Additionally, stronger genetic differentiation among and lower variation within populations was found in urban areas than in cultivated fields.     

Entity grammar systems: A grammatical tool for studying the hierarchal structures of biological systems

The hierarchal structures of biological systems are the typical complex hierarchal dynamical structures in the physical world, the effective investigations on which could not be performed with the existing formal grammar systems. To meet the needs of the investigation on these kinds of systems, especially the emerging field of system biology, a grammatical tool was proposed in the present article. Because the grammatical toolmainly deals with the systems composed of structured entities, they are called entity grammar systems (EGSs). The structure of entities in EGSs have the general form of the objects in the physical world, which means EGSs could be used as a tool to study the complex system composed of many objects with different structures, just like the biological systems. The article contains the formal definition of EGSs and the hierarchy of EGSs, which is congruent with the Chomsky hierarchy. The relationship between EGSs and array grammar systems, graph grammar systems, tree grammar systems, multi-set grammar systems are discussed to show the generative power of EGSs. At the end of the present article, the steps to define new grammar systems with the form of EGS are provided and the possible applicable fields of EGSs are discussed.     

Epstein-Barr virus-associated lymphoproliferative disorders

Epstein-Barr virus (EBV) is a ubiquitous member of the herpesvirus family that is associated with a variety of lymphomas and lymphoproliferative diseases. It encodes a multitude of genes that drive proliferation or confer resistance to cell death. Among these are two key viral proteins which mimic the effects of the activated cellular signaling proteins. EBV-associated lymphomas include Burkitt's lymphoma; natural killer (NK)/T-cell lymphoma, lymphoma and lymphoproliferative diseases in immunocompromized populations, and Hodgkin's lymphoma. The character of the viral association differs among these entities with some consistently associated with EBV in all populations and all parts of the world, and others associated with the virus only in particular circumstances. An example of the former is nasal NK/T-cell lymphoma, while an example of the latter is Burkitt's lymphoma. The pattern of viral gene expression also varies among tumor types with different viral genes playing key roles in different tumors and conferring sensitivity to immune surveillance. Thus some of the post-transplant lymphoproliferative diseases are exquisitely sensitive to CD8 T-cell immunosurveillance, while other tumors such as Burkitt's lymphoma may be nearly impervious to such surveillance. Knowledge of the EBV association is not only important for understanding the pathogenesis of these tumors, but is increasingly important for diagnosis, monitoring and treatment.     

Should Bacteriophages Be Classified As Parasites Or Predators?

Bacteriophages are viruses infecting bacteria and propagating in bacterial cells. They were discovered over 100 years ago, and for decades they played crucial roles as models in genetics and molecular biology and as tools in genetic engineering and biotechnology. Now we also recognize their huge role in natural environment and their importance in human health and disease. Despite our understanding of bacteriophage mechanisms of development, these viruses are described as parasites or predators in the literature. From the biological point of view, there are fundamental differences between parasites and predators. Therefore, in this article, I asked whether bacteriophages should be classified as former or latter biological entities. Analysis of the literature and biological definitions led me to conclude that bacteriophages are parasites rather than predators and should be classified and described as such. If even more precise ecological classification is needed, bacteriophages can perhaps be included in the group of parasitoids. It might be the most appropriate formal classification of these viruses, especially if strictly virulent phages are considered, contrary to phages which lysogenize host cells and those which develop according to the permanent infection mode (or chronic cycle, like filamentous phages) revealing features of classical parasites.     

Nitrate reductases inEscherichia coli

Escherichia coli expresses two different membrane-bound respiratory nitrate reductases, nitrate reductase A (NRA) and nitrate reductase Z (NRZ). In this review, we compare the genetic control, biochemical properties and regulation of these two closely related enzyme systems. The two enzymes are encoded by distinct operons located within two different loci on theE. coli chromosome. ThenarGHJI operon, encoding nitrate reductaseA, is located in thechlC locus at 27 minutes, along with several functionally related genes:narK, encoding a nitrate/nitrite antiporter, and thenarXL operon, encoding a nitrate-activated, two component regulatory system. ThenarZYWV operon, encoding nitrate reductase Z, is located in thechlZ locus located at 32.5 minutes, a region which includes anarK homologue,narU, but no apparent homologue to thenarXL operon. The two membrane-bound enzymes have similar structures and biochemical properties and are capable of reducing nitrate using normal physiological substrates. The homology of the amino acid sequences of the peptides encoded by the two operons is extremely high but the intergenic regions share no related sequences. The expression of both thenarGHJI operon and thenarK gene are positively regulated by two transacting factors Fnr and NarL-Phosphate, activated respectively by anaerobiosis and nitrate, while thenarZYWV operon and thenarU gene are constitutively expressed. Nitrate reductase A, which accounts for 98% of the nitrate reductase activity when fully induced, is clearly the major respiratory nitrate reductase inE. coli while the physiological role of the constitutively expressed nitrate reductase Z remains to be defined.Abbreviations NR nitrate reductase On leave from Department of Biochemistry and Molecular Biology, The University of Texas Medical school at Houston, Houston, Texas, 77225, USA     

桥粒相关蛋白Pinin的生物学功能及其在肿瘤发生中的作用

桥粒不但参与上皮和心肌细胞的连接,增强细胞承受机械应力时的黏附作用,还能调控细胞行为和组织形态发生改变时的信号传导通路过程.桥粒相关蛋白Pinin(PNN)自发现以来,其位置和功能就备受争议.现有结果表明,PNN包含与细胞膜上桥粒共定位的桥粒型PNN和位于细胞核中的核型PNN两种,前者参与上皮细胞的黏附,后者与m RNA的选择性剪接功能有关.新近研究发现,PNN与肿瘤发生密切相关,然而其作用及其分子机制却不相同.本文对PNN的结构、功能及其与肿瘤发生的关系作一综述.     

Stochastic models for an enzyme reaction in an open linear system

A stochastic model is developed for an enzyme reaction in an open linear system. The proposed model assumes that the open system maintains the concentration of substrate and inhibitor at constant levels and that the product molecules are removed from the system by a first order reaction. Stochastic models for several enzyme reactions occurring in this open system are shown to correspond to special cases of theGI/M/∞ queue. Takács’ (1958) results for this queueing system are used to obtain the stochastic properties of the enzyme systems. A specific model we studied assumed completely competitive inhibition in an open system. The stationary distribution for the number of product molecules in the system is obtained. The enzyme reaction which incorporated the “intermediate chain hypothesis” can also be investigated by the queueing theory approach. It is shown that for this open system, if the model which incorporated the intermediate chain hypothesis has the same deterministic properties as the Michaelis-Menten model, then the latter has greater stochastic variation than the former. Research supported by the NIH Training Grant No. GM 1237-05 awarded to the Department of Statistics, The Johns Hopkins University. This paper in whole or in part may be reproduced for any purpose of the United States Government.     

C-banding patterns in the AustralianBulbine (Liliaceae): The perennial group,B. bulbosa s. lato

C-banding studies support earlier evidence thatB. bulbosa, as a previously circumscribed, is heterogeneous, consisting of three distinct entities: (1) theB. bulbosa complex (B. bulbosa s. str.) at 4x (2n = 24), 8x (2n = 48) and 12x (2n = 72) ploidy levels, (2) the rock lily and (3) the Kroombit population (both 2n = 46). Each of these three main groups has a distinctive banding profile, though centromeric and telomeric dot bands, variably expressed, are common to all. In theB. bulbosa complex, substantial heterochromatin development, apart from bands associated with the NORs on chromosomes 1 L, 2 S and 3 L, occurs only at the terminal regions of the short arms of the large and middlesized acrocentric chromosomes, with considerable polymorphic and polytypic variation in the number and size of the heterochromatic blocks, especially at the 4x level. Queensland 8xB. bulbosa populations differ in having terminal heterochromatin, probably associated with NORs, on 11 S and 12 S, and in having some strong interstitial bands. The differences appear to correlate with attributes relating to flower morphology, and may have systematic significance. The karyotypes of rock lily and Kroombit are somewhat similar but the former has a characteristic C-band profile with multiple interstitial bands on chromosomes 1–5 and 7–9, whereas the latter has only one interstitial band on chromosome 9.First contribution of a series on cytoevolution in the AustralianBulbine. Two introductory papers in Austral. J. Bot.34 (2)     

Comparative ultrastructure of adhesive systems in the turbellaria

Summary Glandular adhesive organs and other structures by which turbellarians attach themselves temporarily to surfaces have been studied by electron microscopy. Adhesive organs in representatives of the turbellarian orders Haplopharyngida, Macrostomida, Polycladida, Rhabdocoela, Proseriata, and Tricladida are composed of three cell types: two gland cell types and a modified epidermal cell type through which the necks of the glands project. One of the gland types is characterized by its dense membrane-bound, 0.2–0.7Μm diameter, secretion granules and is called here theviscid gland on the basis of evidence that it secretes the adhesive substance by which the organs attach to surfaces. The other gland type is characterized by smaller (0.1Μm), less-dense, membrane-bound secretion granules and is called thereleasing gland on the basis of evidence that it secretes a substance by which adhering organs are released from surfaces. The modified epidermal cell is called theanchor cell; it has a well-developed cell web and bears microvilli with fibrous cores surrounding the tips of the gland necks in a collar-like fashion. Adhesive organs that have the two gland types, viscid and releasing glands, are referred to here asduo-gland adhesive organs. Other turbellarians, including orders Nemertodermatida, Acoela, and Lecithoepitheliata, have adhesive glands or other adhesive structures with a morphology unlike that of duo-gland adhesive organs. Ultrastructural characters of the adhesive organs show that the Macrostomida and Haplopharyngida are related, and that the Polycladida, Rhabdocoela, Proseriata, and Tricladida are related, and that these two groups of orders share a common ancestor. The Nemertodermatida, Acoela, and Lecithoepitheliata, with morphologically different adhesive systems, are apparently derived separately from these orders.     

Multiple relational equilibria: Polymorphism,metamorphosis and other possibly similar phenomena

In a preceding paper (Rashevsky, 1969. “Outline of a Unified Approach to Physics, Biology and Sociology.”Bulletin of Mathematical Biophysics,31, 159–198) certain isomorphisms between biological and social systems on the one hand and physical systems on the other were studied. The notion or relational forces, of which ordinary physical forces are a particular case, was introduced. In the present paper an attempt is made to establish analogies between stable equilibria in physical systems, equilibria due to physical forces, and stable equilibria in biological and social systems which are due to purely relational forces. The notion of relational forces causing multiple equilibria similar to multiple equilibria in some physical systems is studied, and it is outlined how this notion may possibly help the understanding of such phenomena as polymorphism, metamorphosis and the existence of rudimentary organs or rudimentary functions.     

Different origins of fragile exines within theAnnonaceae

Besides tectate and columellate, 3-layered exine types, in theAnnonaceae, one also finds very fragile, thin exine types. Their single exine layer corresponds either to a former tectum (including infratectal layer) or a former basal layer. The interpretation of the different origin of the remaining layers is based on their different structure and position within the intine. The fact that reduced exine types are obviously not always homologous should be regarded in systematic interpretations.     

The latent trichophytosis of human clothing,II. Some data relating to Trichophyton pratense

Summary The author refers to the results of his investigations carried out with theT. pratense in 1940. He could continue these experiments only in the year 1965. This time he came to the conclusion that three fungi species:T. terrestre Durie &Frey,T. pratense andT. gypseum var.asteroides belong together. He could observe that the cultures of these fungi develop well on some kinds of textile materials. Relying upon these findings he applied the TO-KA-VA method in an inverted way to demonstrate the fungi which had settled on the textiles with the dust of soil. By means of this method he observed thatT. pratense had indeed occurred on some cloths. By further investigation he proved the identity ofT. terrestre Durie &Frey withT. pratense andT. gypseum var.asteroides and demonstrated, that this latter fungus might be the degenerative derivate of the former ones. Finally, he gave as his opinion that the settlement of theT. gypseum var.asteroides is also likely to occur on human clothing; however, far more rarely than that of other kinds of fungi.     

Grinnellian and Eltonian niches and geographic distributions of species

In the recent past, availability of large data sets of species presences has increased by orders of magnitude. This, together with developments in geographical information systems and statistical methods, has enabled scientists to calculate, for thousands of species, the environmental conditions of their distributional areas. The profiles thus obtained are obviously related to niche concepts in the Grinnell tradition, and separated from those in Elton's tradition. I argue that it is useful to define Grinnellian and Eltonian niches on the basis of the types of variables used to calculate them, the natural spatial scale at which they can be measured, and the dispersal of the individuals over the environment. I use set theory notation and analogies derived from population ecology theory to obtain formal definitions of areas of distribution and several types of niches. This brings clarity to several practical and fundamental questions in macroecology and biogeography.     

Genetics of mosquitoes

Beginning in the mid-1950s, much progress has been made in studying various aspects of the genetics of mosquitoes, particularly involving several species of three principal genera,Aedes, Culex andAnopheles, that transmit important human diseases. Here I discuss selected areas of research involving formal genetics; genome structure, organization and evolution at the interspecific and intraspecific level; and evolutionary genetics of theAedes scutellaris group. Information and insights gained from in-depth analyses of these areas, particularly transmission genetics, cytogenetics and genetics of chromosomal rearrangements, and of mutagen-induced sexual sterility, have proved invaluable for the development of the theory and evaluation of feasibility of genetic control of natural populations. As a result, mosquitoes represent some of the best studied taxa at various levels of genetic organization. Recent developments in molecular genetics offer exciting possibilities for extension of these concepts.