On the Stabilizing Role of Stage Structure in Piscene Consumer–Resource Interactions

A stage-structured consumer–resource model is investigated using plausible biological parameter estimates. The model, developed from patterns in energy allocation across fish life-history strategies, explicitly considers the effects of delays in maturation on juvenile growth and mortality. It is found that stage structure in the consumer fish population tends to locally stabilize consumer–resource dynamics for realistic parameters. Additionally, it is shown that stage structure bounds nonequilibrium behavior relative to the case without stage structure. Finally, it is shown that the increased stability and bounding of solutions has the seemingly paradoxical consequence of promoting nonequilibrium dynamics when even small amounts of noise are added to the system.     

Is bioconvection enhancing bacterial growth in quiescent environments?

Bioconvection is an intriguing pattern-forming phenomenon driven by the swimming activity of various aquatic microorganisms. It is generally assumed that bioconvection has a positive effect on the entire microbial population by carrying oxygen into deep layers of non-aerated suspensions. In order to examine the presence of such a biological benefit, we analysed the correlation between bioconvective pattern formation and population growth of several Bacillus subtilis and Bacillus licheniformis strains under non-aerated conditions. Bioconvection is a robust phenomenon, we observed its development in numerous cultures of various strains and growth phases. Nevertheless, evaluation of the data has not revealed detectable positive effects on population growth, questioning the potential biological relevance of bioconvection in natural habitats.     

Bose–Einstein condensates form in heuristics learned by ciliates deciding to signal ‘social’ commitments

Fringe quantum biology theories often adopt the concept of Bose–Einstein condensation when explaining how consciousness, emotion, perception, learning, and reasoning emerge from operations of intact animal nervous systems and other computational media. However, controversial empirical evidence and mathematical formalism concerning decoherence rates of bioprocesses keep these frameworks from satisfactorily accounting for the physical nature of cognitive-like events. This study, inspired by the discovery that preferential attachment rules computed by complex technological networks obey Bose–Einstein statistics, is the first rigorous attempt to examine whether analogues of Bose–Einstein condensation precipitate learned decision making in live biological systems as bioenergetics optimization predicts. By exploiting the ciliate Spirostomum ambiguum's capacity to learn and store behavioral strategies advertising mating availability into heuristics of topologically invariant computational networks, three distinct phases of strategy use were found to map onto statistical distributions described by Bose–Einstein, Fermi–Dirac, and classical Maxwell–Boltzmann behavior. Ciliates that sensitized or habituated signaling patterns to emit brief periods of either deceptive ‘harder-to-get’ or altruistic ‘easier-to-get’ serial escape reactions began testing condensed on initially perceived fittest ‘courting’ solutions. When these ciliates switched from their first strategy choices, Bose–Einstein condensation of strategy use abruptly dissipated into a Maxwell–Boltzmann computational phase no longer dominated by a single fittest strategy. Recursive trial-and-error strategy searches annealed strategy use back into a condensed phase consistent with performance optimization. ‘Social’ decisions performed by ciliates showing no nonassociative learning were largely governed by Fermi–Dirac statistics, resulting in degenerate distributions of strategy choices. These findings corroborate previous work demonstrating ciliates with improving expertise search grouped ‘courting’ assurances at quantum efficiencies and verify efficient processing by primitive ‘social’ intelligences involves network forms of Bose–Einstein condensation coupled to preceding thermodynamic-sensitive computational phases.     

Force spectroscopy studies on protein–ligand interactions: A single protein mechanics perspective

Protein–ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein–ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein–ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein–ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings.     

Imaging of jasmonic acid binding sites in tissue

Hormones regulate the mechanism of plant growth and development, senescence, and plants’ adaptation to the environment; studies of the molecular mechanisms of plant hormone action are necessary for the understanding of these complex phenomena. However, there is no measurable signal for the hormone signal transduction process. We synthesized and applied a quantum dot-based fluorescent probe for the labeling of jasmonic acid (JA) binding sites in plants. This labeling probe was obtained by coupling mercaptoethylamine-modified CdTe quantum dots with JA using N-hydroxysuccinimide (NHS) as a coupling agent. The probe, CdTe–JA, was characterized by transmission electron microscopy, dynamic light scattering, and fluorescent spectrum and applied in labeling JA binding sites in tissue sections of mung bean seedlings and Arabidopsis thaliana root tips. Laser scanning confocal microscopy (LSCM) revealed that the probe selectively labeled JA receptor. The competition assays demonstrated that the CdTe–JA probe retained the original bioactivity of JA. An LSCM three-dimensional reconstruction experiment demonstrated excellent photostability of the probe.     

A physical (electromagnetic) model of differentiation. 1. Basic considerations

There are a number of biological phenomena and events that cannot yet be adequately described, such as cell growth and differentiation, which may be controlled by physical factors. Fr?hlich (1980) has discussed the principles of dissipative structures as applied to electromagnetic interactions in relation to basic couplings in biological systems. Recently, increasing evidence of photon storage and ultraweak photon emission from living systems, particularly from DNA, has suggested the concept of an electromagnetic model of differentiation, based on the known quantum optical properties of nucleic acids. This model has the advantage over all ideas so far published, that it is (1) simple; (2) universally applicable to events in living matter, because it is consistent with both the quantum mechanical and the thermodynamic properties on the one hand, and the known biological and biochemical data and phenomena at the other hand; (3) it not only describes the phenomena and events in terms of pure mathematical parameters, but it can also explain them; and (4) it escapes the difficulty of finding basic control mechanisms, which themselves do not need a regulator, ad infinitum.     

Evolutionary classification of toxin mediated interactions in microorganisms

A trade-off between the parameters of Lotka–Volterra systems is used to give verifications of relations between intrinsic growth rate and limiting capacity and the stability type of the resulting dynamical system. The well known rock–paper–scissors game serves as a template for toxin mediated interactions, which is best represented by the bacteriocin producing Escherichia coli bacteria. There, we have three strains of the same species. The producer produces a toxin lethal to the sensitive, while the resistant is able to protect itself from that toxin. Due to the fact that there are costs for production and for resistance, a dynamics similar to the rock–paper–scissors game results. By using an adaptive dynamics approach for competitive Lotka–Volterra systems and assuming an inverse relation (trade-off) between intrinsic growth rate (IGR) and limiting capacity (LC) we obtain evolutionary and convergence stable relations between the IGR’s and the LC’s. Furthermore this evolutionary process leads to a phase topology of the population dynamics with a globally stable interior fixed point by leaving the interaction parameters constant. While the inverse trade-off stabilizes coexistence and does not allow branching, toxicity itself can promote diversification. The results are discussed in view of several biological examples indicating that the above results are structurally valid.     

Fluorescence lifetime imaging microscopy in the medical sciences

The steady improvement in the imaging of cellular processes in living tissue over the last 10–15 years through the use of various fluorophores including organic dyes, fluorescent proteins and quantum dots, has made observing biological events common practice. Advances in imaging and recording technology have made it possible to exploit a fluorophore's fluorescence lifetime. The fluorescence lifetime is an intrinsic parameter that is unique for each fluorophore, and that is highly sensitive to its immediate environment and/or the photophysical coupling to other fluorophores by the phenomenon Förster resonance energy transfer (FRET). The fluorescence lifetime has become an important tool in the construction of optical bioassays for various cellular activities and reactions. The measurement of the fluorescence lifetime is possible in two formats; time domain or frequency domain, each with their own advantages. Fluorescence lifetime imaging applications have now progressed to a state where, besides their utility in cell biological research, they can be employed as clinical diagnostic tools. This review highlights the multitude of fluorophores, techniques and clinical applications that make use of fluorescence lifetime imaging microscopy (FLIM).     

Forming and maintaining a heat engine for quantum biology

Chemical reactions upholding biological functions and structures are the process of measurement taking place among the participating chemical reactants. Chemical reactions occurring in thermal environments are either endothermic or exothermic. In particular, exothermic reactions that can live with temperature gradients of exogenous origin could potentially be competent enough to synthesize a robust quantum as a heat engine. Molecular organizations leading to the origin of the phenomenon of life might have been associated with the emergence of a quantum coherence embodied in a robust heat engine feeding on quantum decoherence. Evolutionary maintenance of a robust quantum heat engine, once appeared, can further be empowered by the build-up of temperature gradients of endogenous origin. Biology enriches the repertoire of quantum mechanics so as to include a robust heat engine as a legitimate member of a quantum in addition to the already established member of a quantum including an atom, molecule, and macromolecule.     

A challenge for miRNA: multiple isomiRs in miRNAomics

Accumulating evidence suggests that a single microRNA (miRNA) locus can generate a series of sequences during miRNA maturation process. These multiple sequences, called miRNA variants, or isomiRs, have different lengths and different 5′ and 3′ ends. Some of these isomiRs are detected as varied nucleotides and 3′ additional non-template nucleotides. As physiological miRNA isoforms, they have drawn attention for possible regulatory biological roles. The present work mainly reviews miRNA/isomiR biogenesis, isomiR expression patterns, and functional and evolutionary implications, especially between isomiRs from homologous and clustered miRNA loci. The phenomenon of multiple isomiRs and their biological roles indicates that analysis performed at the miRNA and isomiR levels should be included in miRNA studies. This may enrich and complicate miRNA biogenesis and coding–non-coding RNA regulatory networks.     

Dynamics of additional food provided predator–prey system with mutually interfering predators

Use of additional/alternative food source to predators is one of the widely recognised practices in the field of biological control. Both theoretical and experimental works point out that quality and quantity of additional food play a vital role in the controllability of the pest. Theoretical studies carried out previously in this direction indicate that incorporating mutual interference between predators can stabilise the system. Experimental evidence also point out that mutual interference between predators can affect the outcome of the biological control programs. In this article dynamics of additional food provided predator–prey system in the presence of mutual interference between predators has been studied. The mutual interference between predators is modelled using Beddington–DeAngelis type functional response. The system analysis highlights the role of mutual interference on the success of biological control programs when predators are provided with additional food. The model results indicate the possibility of stable coexistence of predators with low prey population levels. This is in contrast to classical predator–prey models wherein this stable co-existence at low prey population levels is not possible. This study classifies the characteristics of biological control agents and additional food (of suitable quality and quantity), permitting the eco-managers to enhance the success rate of biological control programs.     

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.     

Highly specific quantification of microRNA by coupling probe–rolling circle amplification and Förster resonance energy transfer

MicroRNA (miRNA) plays vital roles in various biological processes. In general, sensitivity and specificity are the major parameters for the quantification of miRNA. In this study, padlock probe–rolling circle amplification and Förster resonance energy transfer (pRCA–FRET) were coupled for specific and quantitative detection of miRNA. pRCA–FRET showed superior specificity to differentiate single-base mismatch and excellent sensitivity with a detection limit of 103 aM. The current method has the potential to quantify low amounts of miRNA in the same family for studies on their biological functions.     

N-acetylglucosamine kinase, HXK1 contributes to white–opaque morphological transition in Candida albicans

Morphological transition (yeast-hyphal and white–opaque) is an important biological process in the life cycle of pathogenic yeast, Candida albicans and is a major determinant of virulence. Earlier reports show that the amino sugar, N-acetylglucosamine (GlcNAc) induces white to opaque switching in this pathogen. We report here a new contributor to this switching phenomenon, namely N-acetylglucosamine kinase or HXK1, the first enzyme of the GlcNAc catabolic cascade. Microarray profile analysis of wild type vs. hxk1 mutant cells grown under switching inducing condition showed upregulation of opaque specific and cell wall specific genes along genes involved in the oxidative metabolism. Further, our qRT-PCR and immunoblot analysis revealed that the expression levels of Wor1, a master regulator of the white–opaque switching phenomenon remained unaltered during this HXK1 mediated transition. Thus the derepression of opaque specific gene expression observed in hxk1 mutant could be uncoupled to the expression of WOR1. Moreover, this regulation via HXK1 is independent of Ras1, a major regulator of morphogenetic transition and probably independent of MTL locus too. These results extend our understanding of multifarious roles of metabolic enzymes like Hxk1 and suggest an adaptive mechanism during host–pathogen interactions.     

Yeast proteomics and protein microarrays

Our understanding of biological processes as well as human diseases has improved greatly thanks to studies on model organisms such as yeast. The power of scientific approaches with yeast lies in its relatively simple genome, its facile classical and molecular genetics, as well as the evolutionary conservation of many basic biological mechanisms. However, even in this simple model organism, systems biology studies, especially proteomic studies had been an intimidating task. During the past decade, powerful high-throughput technologies in proteomic research have been developed for yeast including protein microarray technology. The protein microarray technology allows the interrogation of protein–protein, protein–DNA, protein–small molecule interaction networks as well as post-translational modification networks in a large-scale, high-throughput manner. With this technology, many groundbreaking findings have been established in studies with the budding yeast Saccharomyces cerevisiae, most of which could have been unachievable with traditional approaches. Discovery of these networks has profound impact on explicating biological processes with a proteomic point of view, which may lead to a better understanding of normal biological phenomena as well as various human diseases.     

Potential allelopatic effects of stilbenoids and flavonoids from leaves of Carex distachya Desf.

The potential allelopathic effects of 14 stilbenoids and five flavonoids, isolated from leaves of Carex distachya Desf., were evaluated on the seed germination and seedling growth of three coexisting Mediterranean species (Dactylis hispanica, Petrorhagia velutina, and Phleum subulatum). The structures of the metabolites have been elucidated on the basis of their spectroscopic features (1D and 2D NMR experiments and EI–MS and ESI–MS data). The bioassays showed species-specific effects of the metabolites from C. distachya, specially on the plant growth (root and shoot elongation) which resulted significantly stimulated or inhibited at 10⁻⁴ M concentration. The effects on root elongation is generally greater than the shoot growth at all the tested concentrations (10⁻⁴–10⁻⁸ M). Cluster of biological data showed interesting relationships between the chemical structures of the compounds and their biological effects.