Information processing mechanisms in microtubules at physiological temperature: Model predictions for experimental tests

Both direct and indirect experimental evidence has shown signaling, communication and conductivity in microtubules (MTs). Theoretical models have predicted that MTs can be potentially used for both classical and quantum information processing although controversies arose in regard to physiological temperature effects on these capabilities. In this paper, MTs have been studied using well-established principles of classical statistical physics as applied to information processing, information storage and signal propagation. To investigate the existence of information processing in MTs we used cellular automata (CA) models with neighbor rules based on the electrostatic properties of the molecular structure of tubulin, and both synchronous and asynchronous updating methods. We obtained a phase diagram of possible dynamic behaviors in MTs that depend on the values of characteristic physical parameters that can be experimentally verified.     

Biological complexity,quantum coherent states and the problem of efficient transmission of information inside a cell

The intracellular channel of information transmission was analyzed from the point of view of complexity. The most important steps in the transfer of information within a cell are the folding, transport and recognition of proteins. It was shown that the large number of conformational degrees of freedom that proteins possess can paradoxically lead to an information channel with an exponentially small capacity. To resolve this paradox, a model, which assumes a quantum collective behavior of biologically important molecules, was proposed. Experiments to test the quantum nature of the intracellular transfer of information were also proposed.     

A critical assessment of different measures of the information carried by correlated neuronal firing

Information theoretic measures have been proposed as a quantitative framework to clarify the role of correlated neuronal activity in the brain. In this paper we review some recent methods that allow precise assessments of the role of correlation in stimulus coding and decoding by the nervous system. We present new results that make explicit links between types of encoding and decoding mechanisms based on correlations. We illustrate the concepts by showing that the spike trains of pairs of neurons in rat somatosensory cortex can be decoded almost perfectly without including knowledge of correlation in the read-out model, although in this neural system correlations between spike times contribute appreciably to stimulus encoding.     

Structure of microtubules: A study of freeze-etched and negatively stained microtubules from the ovaries of Notonecta

Summary Insect ovaries of the telotrophic type contain large numbers of microtubules within the tubes which connect an anterior trophic region to each oocyte within the ovariole. We have examined these microtubules using the freeze-etch technique and found that our observations correspond in many ways with the image of microtubules which have been subjected to chemical fixation. Obliquely fractured microtubules show sub-filaments within their walls, while both obliquely and longitudinally fractured microtubules display a periodicity of approximately 4 nm along many of the sub-filaments. In transverse fracture, a clear zone can be seen around individual microtubules and this confirms that the clear zones which are often seen around transverse sections of microtubules, are real features and not artefacts of fixation.The electron beam evaporation source equipment, used for shadowing the freeze-etched specimens, was obtained on a grant from the S.R.C. The AEI EM 802 electron microscope was purchased with M.R.C. Grant No. 971/55/B.     

A critical assessment of standard processing methods for the preparation of palynological samples

Standard processing techniques for the isolation of organic walled dinoflagellate cysts from geological samples are examined, with particular attention to the size and type of sieve mesh used. Variations within the ‘standard’ processing techniques used by different laboratories are identified, and an assessment of the retention capacities of meshes of different sizes and different materials is carried out. Some dinoflagellate cysts and large numbers of Lycopodium spores, used for the calculations of absolute abundance data, were found to pass through 20 μm meshes. This is due to a combination of factors including: the diagonal aperture diameter of a 20 μm mesh measuring over 28 μm; the three-dimensional properties of different mesh weaves (nylon and polyester); and the non-spherical shape of the particles. Experiments demonstrate that the maximum mesh size that should be used in palynological processing is 15 μm. Nylon mesh is more practical to use than polyester as processing time is reduced, but nylon is degraded by contact with acid solutions. Meshes with apertures < 15 μm may be used, though this may be impractical for large samples containing significant quantities of fine siliciclastic or organic material.     

A review on the cognitive function of information structure during language comprehension

During communication, information structure can be used to highlight the most relevant piece of information, so that sufficient amount of attention can be allocated to the most important information. This paper aims to review the cognitive function of information structure during language comprehension from a neurocognitve perspective. First, we gave a brief introduction to the concept of information structure that has been studied mostly in linguistic field. Then we introduced recent studies on information structure using electrophysiological and neuroimaging techniques. After that, we discussed the relationship between attention and language processing more generally. Finally, we discussed potential directions for future studies.     

A critical assessment of the h-index

Editor's suggested further reading in BioEssays: Can we do better than existing author citation metrics? Abstract and Counting citations in texts rather than reference lists to improve the accuracy of assessing scientific contribution Abstract     

Nuclear cytoplasmic domains,microtubules and organelles in microsporocytes of the slipper orchid Cypripedium californicum A. Gray dividing by simultaneous cytokinesis

Microsporocytes of the slipper orchidCypripedium californicum A. Gray divide simultaneously after second meiosis. The organization and apportionment of the cytoplasm throughout meiosis are functions of nuclear-based radial microtubule systems (RMSs) that define domains of cytoplasm - a single sporocyte domain before meiosis, dyad domains within the undivided cytoplasm after first meiosis, and four spore domains after second meiosis. Organelles migrate to the interface of dyad domains in the undivided cytoplasm after first meiotic division, and second meiotic division takes place simultaneously on both sides of the equatorial organelle band. Microtubules emanating from the telophase II nuclei interact to form columnar arrrays that interconnect all four nuclei, non-sister as well as sister. Cell plates are initiated in these columns of microtubules and expand centrifugally along the interface of opposing RMSs, coalescing in the center of the sporocyte and joining with the original sporocyte wall at the periphery to form the tetrad of microspores. Organelles are distributed into the spore domains in conjunction with RMSs. These data, demonstrating that cytokinesis in microsporogenesis can occur in the absence of both components of the typical cytokinetic apparatus (the preprophase band of microtubules which predicts the division site and the phragmoplast which controls cell-plate deposition), suggest that plant nuclei have an inherent ability to establish a domain of cytoplasm via radial microtubule systems and to regulate wall deposition independently of the more complex cytokinetic apparatus of vegetative cells.     

Using reflexive behaviors of the medicinal leech to study information processing

The interneuronal network that produces local bending in the leech is distributed, in the sense that most of the interneurons involved are activated in all forms of local bending, even those in which their outputs would produce inappropriate movements. Such networks have been found to control a number of different behaviors in a variety of animals. This article reviews three issues: the physiological and modeling observations that led to the conclusion that local bending in leeches is controlled by a distributed system; what distributed processing means for this and other behaviors; and why the leech interneuronal network may have evolved to be distributed in the first place. © 1995 John Wiley & Sons, Inc.     

Adaptability and the integration of computer-based information processing into the dynamics of organizations

The structure of a system influences its adaptability. An important result of adaptability theory is that subsystem independence increases adaptability [Conrad, M., 1983. Adaptability. Plenum Press, New York]. Adaptability is essential in systems that face an uncertain environment such as biological systems and organizations. Modern organizations are the product of human design. And so it is their structure and the effect that it has on their adaptability. In this paper we explore the potential effects of computer-based information processing on the adaptability of organizations. The integration of computer-based processes into the dynamics of the functions they support and the effect it has on subsystem independence are especially relevant to our analysis.     

Simplifying the assessment of human breast cancer by mapping a micro‐scale heterogeneity index in optical coherence elastography

Surgical treatment of breast cancer aims to identify and remove all malignant tissue. Intraoperative assessment of tumor margins is, however, not exact; thus, re‐excision is frequently needed, or excess normal tissue is removed. Imaging methods applicable intraoperatively could help to reduce re‐excision rates whilst minimizing removal of excess healthy tissue. Optical coherence elastography (OCE) has been proposed for use in breast‐conserving surgery; however, intraoperative interpretation of complex OCE images may prove challenging. Observations of breast cancer on multiple length scales, by OCE, ultrasound elastography, and atomic force microscopy, have shown an increase in the mechanical heterogeneity of malignant breast tumors compared to normal breast tissue. In this study, a micro‐scale mechanical heterogeneity index is introduced and used to form heterogeneity maps from OCE scans of 10 ex vivo human breast tissue samples. Through comparison of OCE, optical coherence tomography images, and corresponding histology, malignant tissue is shown to possess a higher heterogeneity index than benign tissue. The heterogeneity map simplifies the contrast between tumor and normal stroma in breast tissue, facilitating the rapid identification of possible areas of malignancy, which is an important step towards intraoperative margin assessment using OCE.

     

Binding of the GABA(A) receptor-associated protein (GABARAP) to microtubules and microfilaments suggests involvement of the cytoskeleton in GABARAPGABA(A) receptor interaction

GABA(A) receptor-associated protein (GABARAP) was isolated on the basis of its interaction with the gamma2 subunit of GABA(A) receptors. It has sequence similarity to light chain 3 (LC3) of microtubule-associated proteins 1A and 1B. This suggests that GABARAP may link GABA(A) receptors to the cytoskeleton. GABARAP associates with tubulin in vitro. However, little is known about the mechanism for the interaction, and it is not clear whether the interaction occurs in vivo. Here, we report that GABARAP interacts directly with both tubulin and microtubules in a salt-sensitive manner, indicating the association is mediated by ionic interactions. GABARAP coimmunoprecipitates with tubulin and associates with both microtubules and microfilaments in intact cells. The cellular distribution is altered by treatment with taxol, nocodazole, and cytochalasin D. The tubulin binding domain was located at the N terminus of GABARAP by using synthetic peptides and deletion constructs and is marked by a specific arrangement of basic amino acids. The interaction between GABARAP and actin might be mediated by other proteins. These results demonstrate the GABARAP interacts with the cytoskeleton both in vitro and in cells and suggest a role of GABARAP in the interaction between GABA(A) receptors and the cytoskeleton. Such interactions are presumably needed for receptor trafficking, anchoring, and/or synaptic clustering. The structural arrangement of the basic amino acids present in the tubulin binding domain of GABARAP may aid in recognition of the potential of tubulin binding activity in other known proteins.     

A critical assessment of the utility of protein-free splicing systems

U2 and U6 snRNAs form part of the catalytic spliceosome and represent strong candidates for components of its active site. Over the past decade it has become clear that these snRNAs are capable of catalyzing several different chemical reactions, leading to the widespread conclusion that the spliceosome is a ribozyme. Here, we discuss the advances in both protein-free and fully spliceosomal systems that would be required to conclude that the reactions observed to be catalyzed by protein-free snRNAs are related to splicing and question the reliability of snRNA-only systems as tools for mechanistic splicing research.     

A critical assessment of the impact of mixing on dilution refolding

Refolding often presents a bottleneck in the generation of recombinant protein expressed as inclusion bodies. Few studies have looked at the effect of physical factors on the yield from refolding steps. Refold reactors typically operate in fed-batch mode with a slow injection rate. This paper characterizes mixing in a novel reactor, and seeks to relate the conditions of mixing to native lysozyme yields after refolding. A novel twin-impeller system incorporating a mini-paddle impeller located in the vicinity of the injection point was used to increase the local levels of energy dissipation experienced by the injected material, and to improve refolding yields. Mixing only affected yields during and immediately after denatured protein addition. Analysis of lysozyme refolding yield, under a variety of conditions, revealed that dispersive mixing affected the yield. The beneficial effect of the mini-paddle impeller in providing a source of localized energy dissipation was limited to conditions where the bulk impeller intensity was low. The effects appeared to become more significant when injection times were longer, because of increased exposure of the injected material to the energy dissipation of the mini-impeller. The results suggest that for fed-batch protein refolding systems, where mixing has been shown to be a critical factor, the local energy dissipation experienced in the vicinity of the injection point is critical to the refolding yields.     

Quantum-like model of processing of information in the brain based on classical electromagnetic field

We propose a model of quantum-like (QL) processing of mental information. This model is based on quantum information theory. However, in contrast to models of "quantum physical brain" reducing mental activity (at least at the highest level) to quantum physical phenomena in the brain, our model matches well with the basic neuronal paradigm of the cognitive science. QL information processing is based (surprisingly) on classical electromagnetic signals induced by joint activity of neurons. This novel approach to quantum information is based on representation of quantum mechanics as a version of classical signal theory which was recently elaborated by the author. The brain uses the QL representation (QLR) for working with abstract concepts; concrete images are described by classical information theory. Two processes, classical and QL, are performed parallely. Moreover, information is actively transmitted from one representation to another. A QL concept given in our model by a density operator can generate a variety of concrete images given by temporal realizations of the corresponding (Gaussian) random signal. This signal has the covariance operator coinciding with the density operator encoding the abstract concept under consideration. The presence of various temporal scales in the brain plays the crucial role in creation of QLR in the brain. Moreover, in our model electromagnetic noise produced by neurons is a source of superstrong QL correlations between processes in different spatial domains in the brain; the binding problem is solved on the QL level, but with the aid of the classical background fluctuations.     

Information processing for the organization of chemotactic behavior ofPhysarum polycephalum studied by micro-thermography

Summary The spatial and temporal pattern of oscillating temperatures on the cell surface of a plasmodial strand ofPhysarum polycephalum was measured with a sensitive thermal image camera. The longitudinal tension of the strand was studied simultaneously. In the absence of chemical stimulation, the phases of the temperature oscillation observed at various portions of the strand were entrained with almost coincidental phase. The temperature and tension oscillation were synchronized, although the phase difference between them was occasionally changed. With local chemical stimulation, the phase of the temperature oscillation advanced in the portion to which the plasmodium would be induced to migrate. The phases between temperature and tension oscillations then became constant. The mechanism by which the plasmodium processes local information of chemical stimulus to global information for the migration is discussed.     

A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling

Recently, a series of closely related theoretical constructs termed the "topomer search model" (TSM) has been proposed for the folding mechanism of small, single-domain proteins. A basic assumption of the proposed scenarios is that the rate-limiting step in folding is an essentially unbiased, diffusive search for a conformational state called the native topomer defined by an overall native-like topological pattern. Successes in correlating TSM-predicted folding rates with that of real proteins have been interpreted as experimental support for the model. To better delineate the physics entailed, key TSM concepts are examined here using extensive Langevin dynamics simulations of continuum C(alpha) chain models. The theoretical native topomers of four experimentally well-studied two-state proteins are characterized. Consistent with the TSM perspective, we found that the sizes of the native topomers increase with experimental folding rate. However, a careful determination of the corresponding probabilities that the native topomers are populated during a random search fails to reproduce the previously predicted folding rates. Instead, our results indicate that an unbiased TSM search for the native topomer amounts to a Levinthal-like process that would take an impossibly long average time to complete. Furthermore, intraprotein contacts in all four native topomers considered exhibit no apparent correlation with the experimental phi-values determined from the folding kinetics of these proteins. Thus, the present findings suggest that certain basic, generic yet essential energetic features in protein folding are not accounted for by TSM scenarios to date.     

A guide to the processing and standardization of global palaeoecological data for large-scale syntheses using fossil pollen

Aim

Palaeoecological data are crucial for comprehending large-scale biodiversity patterns and the natural and anthropogenic drivers that influence them over time. Over the last decade, the availability of open-access research databases of palaeoecological proxies has substantially increased. These databases open the door to research questions needing advanced numerical analyses and modelling based on big-data compilations. However, compiling and analysing palaeoecological data pose unique challenges that require a guide for producing standardized and reproducible compilations.

Innovation

We present a step-by-step guide of how to process fossil pollen data into a standardized dataset compilation ready for macroecological and palaeoecological analyses. We describe successive criteria that will enhance the quality of the compilations. Though these criteria are project and research question-dependent, we discuss the most important assumptions that should be considered and adjusted accordingly. Our guide is accompanied by an R-workflow—called FOSSILPOL—and corresponding R-package—called R-Fossilpol—that provide a detailed protocol ready for interdisciplinary users. We illustrate the workflow by sourcing and processing Scandinavian fossil pollen datasets and show the reproducibility of continental-scale data processing.

Main Conclusions

The study of biodiversity and macroecological patterns through time and space requires large-scale syntheses of palaeoecological datasets. The data preparation for such syntheses must be transparent and reproducible. With our FOSSILPOL workflow and R-package, we provide a protocol for optimal handling of large compilations of fossil pollen datasets and workflow reproducibility. Our workflow is also relevant for the compilation and synthesis of other palaeoecological proxies and as such offers a guide for synthetic and cross-disciplinary analyses with macroecological, biogeographical and palaeoecological perspectives. However, we emphasize that expertise and informed decisions based on palaeoecological knowledge remain crucial for high-quality data syntheses and should be strongly embedded in studies that rely on the increasing amount of open-access palaeoecological data.     

A neural circuit model of emotional learning using two pathways with different granularity and speed of information processing

We propose a neural circuit model of emotional learning using two pathways with different granularity and speed of information processing. In order to derive a precise time process, we utilized a spiking model neuron proposed by Izhikevich and spike-timing-dependent synaptic plasticity (STDP) of both excitatory and inhibitory synapses. We conducted computer simulations to evaluate the proposed model. We demonstrate some aspects of emotional learning from the perspective of the time process. The agreement of the results with the previous behavioral experiments suggests that the structure and learning process of the proposed model are appropriate.