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Origins of linewidth in 1H magic-angle spinning NMR.

A detailed study of the factors determining the linewidth (and hence resolution) in 1H solid-state magic-angle spinning NMR is described. Although it has been known from the early days of magic-angle spinning (MAS) that resolution of spectra from abundant nuclear spins, such as 1H, increases approximately linearly with increasing sample rotation rate, the difficulty of describing the dynamics of extended networks of coupled spins has made it difficult to predict a priori the resolution expected for a given sample. Using recently developed, highly efficient methods of numerical simulation, together with experimental measurements on a variety of test systems, we propose a comprehensive picture of 1H resolution under MAS. The "homogeneous" component of the linewidth is shown to depend primarily on the ratio between an effective local coupling strength and the spin rate, modified by geometrical factors which loosely correspond to the "dimensionality" of the coupling network. The remaining "inhomogeneous" component of the natural linewidth is confirmed to have the same properties as in dilute-spin NMR. Variations in the NMR frequency due to chemical shift effects are shown to have minimal impact on 1H resolution. The implications of these results for solid-state NMR experiments involving 1H and other abundant-spin nuclei are discussed.

Journal Article↗

Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations.

Stochastic effects in biomolecular systems have now been recognized as a major physiologically and evolutionarily important factor in the development and function of many living organisms. Nevertheless, they are often thought of as providing only moderate refinements to the behaviors otherwise predicted by the classical deterministic system description. In this work we show by using both analytical and numerical investigation that at least in one ubiquitous class of (bio)chemical-reaction mechanisms, enzymatic futile cycles, the external noise may induce a bistable oscillatory (dynamic switching) behavior that is both quantitatively and qualitatively different from what is predicted or possible deterministically. We further demonstrate that the noise required to produce these distinct properties can itself be caused by a set of auxiliary chemical reactions, making it feasible for biological systems of sufficient complexity to generate such behavior internally. This new stochastic dynamics then serves to confer additional functional modalities on the enzymatic futile cycle mechanism that include stochastic amplification and signaling, the characteristics of which could be controlled by both the type and parameters of the driving noise. Hence, such noise-induced phenomena may, among other roles, potentially offer a novel type of control mechanism in pathways that contain these cycles and the like units. In particular, observations of endogenous or externally driven noise-induced dynamics in regulatory networks may thus provide additional insight into their topology, structure, and kinetics.

Enzyme Stability↗

A transdisciplinary focus on drug abuse prevention: an introduction.

This article introduces the scope of the Special Issue. A variety of scientific disciplines are brought together to establish theoretical integration of the arenas of drug use, misuse, "abuse," and drug misuse prevention. Transdisciplinary scientific collaboration (TDSC) is utilized as a process of integration. Introductory comments regarding the strengths and limitations of TDSC are presented. Then, the relevance of genetics to substance misuse and substance misuse prevention is presented. Next, the relevance of cognition for prevention is discussed. Specifically, neurologically plausible distinctions in cognition and implicit cognition and their relevance for prevention are discussed. At a relatively molar social-level of analysis, social network theory, systems dynamic models, geographic information systems models, cultural psychology, and political science approaches to drug misuse and its prevention are introduced. The uses of both quantitative and qualitative statistical approaches to prevention are mentioned next. Finally, targeted prevention, bridging the efficacy-effectiveness gap, and a statement on overcoming disbalance round out the Special Issue. The bridges created will serve to propel drug misuse "prevention science" forward in the years to come. Advances in understanding etiological issues, translation to programs, and ecological fit of programming are desired results.

Cognition↗

Phosphorylation on carboxyl terminus domains of neurofilament proteins in retinal ganglion cell neurons in vivo: influences on regional neurofilament accumulation, interneurofilament spacing, and axon caliber.

The high molecular weight subunits of neurofilaments, NF-H and NF-M, have distinctively long carboxyl-terminal domains that become highly phosphorylated after newly formed neurofilaments enter the axon. We have investigated the functions of this process in normal, unperturbed retinal ganglion cell neurons of mature mice. Using in vivo pulse labeling with [35S]methionine or [32P]orthophosphate and immunocytochemistry with monoclonal antibodies to phosphorylation-dependent neurofilament epitopes, we showed that NF-H and NF-M subunits of transported neurofilaments begin to attain a mature state of phosphorylation within a discrete, very proximal region along optic axons starting 150 microns from the eye. Ultrastructural morphometry of 1,700-2,500 optic axons at each of seven levels proximal or distal to this transition zone demonstrated a threefold expansion of axon caliber at the 150-microns level, which then remained constant distally. The numbers of neurofilaments nearly doubled between the 100- and 150-microns level and further increased a total of threefold by the 1,200-microns level. Microtubule numbers rose only 30-35%. The minimum spacing between neurofilaments also nearly doubled and the average spacing increased from 30 nm to 55 nm. These results show that carboxyl-terminal phosphorylation expands axon caliber by initiating the local accumulation of neurofilaments within axons as well as by increasing the obligatory lateral spacing between neurofilaments. Myelination, which also began at the 150-microns level, may be an important influence on these events because no local neurofilament accumulation or caliber expansion occurred along unmyelinated optic axons. These findings provide evidence that carboxyl-terminal phosphorylation triggers the radial extension of neurofilament sidearms and is a key regulatory influence on neurofilament transport and on the local formation of a stationary but dynamic axonal cytoskeletal network.

Actin Cytoskeleton↗

In situ localization of mitochondrial DNA replication in intact mammalian cells.

Nearly all of the known activities required for mitochondrial DNA (mtDNA) replication and expression are nuclear-encoded gene products, necessitating communication between these two physically distinct intracellular compartments. A significant amount of both general and specific biochemical information about mtDNA replication in mammalian cells has been known for almost two decades. Early studies achieved selective incorporation of the thymidine analog 5-Bromo-2-deoxy-Uridine (BrdU) into mtDNA of thymidine kinase-deficient (TK[-]) cells. We have revisited this approach from a cellular perspective to determine whether there exist spatiotemporal constraints on mtDNA replication. Laser-scanning confocal microscopy was used to selectively detect mtDNA synthesis in situ in cultured mammalian cells using an immunocytochemical double-labeling approach to visualize the incorporation of BrdU into mtDNA of dye-labeled mitochondria. In situ detection of BrdU-incorporated mtDNA was feasible after a minimum of 1-2 h treatment with BrdU, consistent with previous biochemical studies that determined the time required for completion of a round of mtDNA replication. Interestingly, the pattern of BrdU incorporation into the mtDNA of cultured mammalian cells consistently radiated outward from a perinuclear position, suggesting that mtDNA replication first occurs in the vicinity of nuclear-provided materials. Newly replicated mtDNA then appears to rapidly distribute throughout the dynamic cellular mitochondrial network.

Animals↗

Architecture of metaphase chromosomes and chromosome scaffolds.

We have developed procedures for depositing intact mitotic chromosomes and isolated residual scaffolds on electron microscope grids at controlled and reproducible levels of compaction. The chromosomes were isolated using a recently developed aqueous method. Our study has addressed two different aspects of chromosome structure. First, we present a method for improved visualization of radial chromatin loops in undisrupted mitotic chromosomes. Second, we have visualized a nonhistone protein residual scaffold isolated from nuclease-digested chromosomes under conditions of low salt protein extraction. These scaffolds, which have an extremely simple protein composition, are the size of chromosomes, are fibrous in nature, and are found to retain differentiated regions that appear to derive from the kinetochores and the chromatid axis. When our standard preparation conditions were used, the scaffold appearance was found to be very reproducible. If the ionic conditions were varied, however, the scaffold appearance underwent dramatic changes. In the presence of millimolar concentrations of Mg++ or high concentrations of NaCl, the fibrous scaffold protein network was observed to undergo a lateral aggregation or assembly into a coarse meshlike structure. The alteration of scaffold structure was apparently reversible. This observation is consistent with a model in which the scaffolding network plays a dynamic role in chromosome condensation at mitosis.

Chromatin↗

The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins.

Dynamic molecular interaction networks underlie biological phenomena. Among the many genes which are involved, p53 plays a central role in networks controlling cellular life and death. It not only operates as a tumor suppressor, but also helps regulate hundreds of genes in response to various types of stress. To accomplish these functions as a guardian of the genome, p53 interacts extensively with both nucleic acids and proteins. This paper examines the physical interfaces of the p53 protein with cellular proteins. Previously, in the analysis of the structures of protein-protein complexes, we have observed that amino acids Trp, Met and Phe are important for protein-protein interactions in general. Here we show that these residues are critical for the many functions of p53. Several clusters of the Trp/Met/Phe residues are involved in the p53 protein-protein interactions. Phe19/Trp23 in the TA1 region extensively binds to the transcriptional factors and the MDM2 protein. Trp53/Phe54 in the TA2 region is crucial for transactivation and DNA replication. Met243 in the core domain interacts with 53BP1, 53BP2 and Rad 51 proteins. Met384/Phe385 in the C-terminal region interacts with the S100B protein and the Bromodomain of the CBP protein. Thus, these residues may assist in elucidating the p53 interactions when structural data are not available.

Biophysics↗

Inferring a system model of subcellular topoisomerase II beta localization dynamics.

Measuring the mobility of proteins in living cells has become critical to many studies in cell biology and forms the basis for discussion on sub-cellular dynamics. Increasingly localization networks are being put together into compartment models to represent the exchange of molecules, represented mathematically as ordinary differential equations (ODE). The set-up is based on published literature, the "knowledge" of the investigator and 3D visualization of the data. Here we demonstrate this method on the example of a simple distribution model of the molecule Topoisomerase II beta (Topo II beta), nuclear protein that modifies DNA topology. It is found in high concentration in the nucleolus and diffuse in the nucleoplasm, demonstrating a non-membranous inhomogeneity in its distribution. We expand on the simple model by adding additional components to fit fluorescence recovery after photobleaching (FRAP) experiments for protein (GFP) labeled Topo II beta to measure its mobility. This model is then validated by comparing it with alternative scenarios and shown to have predictive power.

Animals↗

Executive functions and their disorders.

The term executive function defines complex cognitive processing requiring the co-ordination of several subprocesses to achieve a particular goal. Neuropsychological evidence suggests that executive processing is intimately connected with the intact function of the frontal cortices. Executive dysfunction has been associated with a range of disorders, and is generally attributed to structural or functional frontal pathology. Neuroimaging, with PET and fMRI, has confirmed the relationship; however, attempts to link specific aspects of executive functioning to discrete prefrontal foci have been inconclusive. Instead, the emerging view suggests that executive function is mediated by dynamic and flexible networks, that can be characterised using functional integration and effective connectivity analyses. This view is compatible with the clinical presentation of executive dysfunction associated with a range of pathologies, and also with evidence that recovery of executive function can occur after traumatic brain injury, perhaps due to functional reorganisation within executive networks.

Brain Injuries↗

The 'functional connection' of neurones in relation to behavioural states in rats.

In order to investigate whether dynamics of neuronal networks change during differing behavioural states, the 'functional connection' between neurones in the rat vibrissal sensorimotor system during two different behavioural states (active vs passive whiskering) were revealed using time-dependent scatter diagrams. The functional connection between neurones in the vibrissal motor (MCx) and sensory (SCx) cortices and the superior colliculus (SC) changed depending on the behavioural state. In the rat vibrissal system, the pattern of correlated activities among neurones in the MCx, SCx and SC may play an important role in determining behaviour.

Animals↗

Human gamma-band activity: a window to cognitive processing.

This review highlights recent developments in research on human cortical oscillations in the gamma-band range (30-100 Hz). Electroencephalography has demonstrated a role of these signals for cognitive functions including visual perception, attention, learning and memory. During auditory processing, magnetoencephalogram has identified oscillatory activity in higher frequency ranges and with a more discrete localization than electroencephalogram. Gamma-band activity increases have been observed in the putative auditory dorsal and ventral processing streams during the processing of auditory spatial and pattern information, respectively. Additional gamma-band activity has been found over the frontal cortex during top-down tasks. Oscillatory activity in the gamma range may serve to assess the temporal dynamics of cortical networks and their interactions.

Biological Clocks↗

Who mixes with whom? A method to determine the contact patterns of adults that may lead to the spread of airborne infections.

Although mixing patterns are thought to be important determinants of the spread of airborne infectious diseases, to our knowledge, there have been no attempts to directly quantify them for humans. We report on a preliminary study to identify such mixing patterns. A sample of 92 adults were asked to detail the individuals with whom they had conversed over the period of one, randomly assigned, day. Sixty-five (71%) completed the questionnaire, providing their age, the age of their contacts and the social context in which the contacts took place. The data were analysed using multilevel modelling. The study identified, and allowed the quantification of, contact patterns within this sample that may be of epidemiological significance. For example, the degree of assortativeness of mixing with respect to age was dependent not only on the age of participants but the number of contacts made. Estimates of the relative magnitude of contact rates between different social settings were made, with implications for outbreak potential. Simple questionnaire modifications are suggested which would yield information on the structure and dynamics of social networks and the intensity of contacts. Surveys of this nature may enable the quantification of who acquires infection from whom and from where.

Adult↗

Viscoelastic properties of semiflexible filamentous bacteriophage fd.

The cytoskeletal protein filament F-actin has been treated in a number of recent studies as a model physical system for semiflexible filaments. In this work, we studied the viscoelastic properties of entangled solutions of the filamentous bacteriophage fd as an alternative to F-actin with similar physical parameters. We present both microrheometric and macrorheometric measurements of the viscoelastic storage and loss moduli, G'(f ) and G"(f ), respectively, in a frequency range 0.01<f<4 Hz, for fd solutions in the concentration range 5<c<15 mg/ml. The onset of a narrow and slanted plateaulike region of G'(f ) is located at around 2 Hz. The variation of the plateau modulus with concentration obeys a power law G(')(N) approximately c(1.4+/-0.3), similar to that found for entangled solutions of F-actin. In the low-frequency regime, the frequency dependence of the viscoelastic moduli can be described by power laws G'(f ) approximately f(0.9-1.2) and G"(f ) approximately f(0.7-0.9), which deviate significantly from the simple theoretical predictions of G'(f ) approximately f(2) and G"(f ) approximately f(1). The latter behavior cannot yet be understood within the framework of current theories of semiflexible filament networks. For the dynamic viscosity at the low shear rate limit, a concentration dependence of eta(0) approximately c(2.6) was found. Finally, a linear scaling of the terminal relaxation time with concentration, tau(d) approximately c, was observed.

Actin Cytoskeleton↗

Random coupling of chaotic maps leads to spatiotemporal synchronization.

We investigate the spatiotemporal dynamics of a network of coupled chaotic maps, with varying degrees of randomness in coupling connections. While strictly nearest neighbor coupling never allows spatiotemporal synchronization in our system, randomly rewiring some of those connections stabilizes entire networks at x*, where x* is the strongly unstable fixed point solution of the local chaotic map. In fact, the smallest degree of randomness in spatial connections opens up a window of stability for the synchronized fixed point in coupling parameter space. Further, the coupling epsilon(bifr) at which the onset of spatiotemporal synchronization occurs, scales with the fraction of rewired sites p as a power law, for 0.1<p<1. We also show that the regularizing effect of random connections can be understood from stability analysis of the probabilistic evolution equation for the system, and approximate analytical expressions for the range and epsilon(bifr) are obtained.

Journal Article↗

Networking the seceder model: Group formation in social and economic systems.

The seceder model illustrates how the desire to be different from the average can lead to formation of groups in a population. We turn the original, agent based, seceder model into a model of network evolution. We find that the structural characteristics of our model closely match empirical social networks. Statistics for the dynamics of group formation are also given. Extensions of the model to networks of companies are also discussed.

Journal Article↗

Neural mechanism for a cognitive timer.

To examine a possible biological mechanism for a cognitive timer, the stochastic dynamics of a network of neurons possessing two stable states ("on" and "off" states) is studied. The fraction of on neurons existing at t = 0 remains large for an extended interval, and then abruptly falls. The distribution of the lengths of the interval is scale invariant in the following sense: The ratio (k root of (mu(k))/m, with m and mu(k) being the mean and the kth central moment, respectively, is invariant under scale transformations of m and mu(k). In the special case k = 2, this gives Weber's law, a hallmark of cognitive timing.

Animals↗

Induced oscillations in the alpha band: functional meaning.

The phenomena of event-related desynchronization (ERD) and synchronization (ERS) reflect the dynamics of neural networks and can be observed on different scalp locations at the same moment of time. Whereas on one cortical area a focal 10-Hz ERD can be found, other areas can display a 10-Hz ERS. This phenomenon is called focal ERD/surround ERS and is interpreted as a correlate of an activated cortical area (ERD) and simultaneously deactivated or inhibited other areas. The induced oscillations (ERS) are dominant in the 10- to 13-Hz band and very likely mediated by thalamic gating.

Alpha Rhythm↗

How to make an egg: transcriptional regulation in oocytes.

The oocyte is a highly differentiated cell. It makes organelles specialized to its unique functions and progresses through a series of developmental stages to acquire a fertilization competent phenotype. This review will integrate the biology of the oocyte with what is known about oocyte-specific gene regulation and transcription factors involved in oocyte development. We propose that oogenesis is reliant on a dynamic gene regulatory network that includes oocyte-specific transcriptional regulators.

Animals↗