Javier Díaz

Molecular Evolution, Mutation Size and Gene Pleiotropy: A Geometric Reexamination

The influence of phenotypic effects of genetic mutations on molecular evolution is not well understood. Neutral and nearly neutral theories of molecular evolution predict a negative relationship between the evolutionary rate of proteins and their functional importance; nevertheless empirical studies seeking relationships between evolutionary rate and the phenotypic role of proteins have not produced conclusive results. In particular, previous studies have not found the expected negative correlation between evolutionary rate and gene pleiotropy. Here, we studied the effect of gene pleiotropy and the phenotypic size of mutations on the evolutionary rate of genes in a geometrical model, in which gene pleiotropy was characterized by n molecular phenotypes that affect organismal fitness. For a nearly neutral process, we found a negative relationship between evolutionary rate and mutation size but pleiotropy did not affect the evolutionary rate. Further, for a selection model, where most of the substitutions were fixed by natural selection in a randomly fluctuating environment, we also found a negative relationship between evolutionary rate and mutation size, but interestingly, gene pleiotropy increased the evolutionary rate as \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\sqrt{n}\) \end{document}. These findings may explain part of the disagreement between empirical data and traditional expectations.

Amplitude Modulation Patterns of Local Field Potentials Reveal Asynchronous Neuronal Populations

Neural oscillations, which appear in several areas of the nervous system and cover a wide frequency range, are a prominent issue in current neuroscience. Extracellularly recorded oscillations are generally thought to be a manifestation of a neural population with synchronized electrical activity resulting from coupling mechanisms. The vertebrate olfactory neuroepithelium exhibits β-band oscillations, termed peripheral waves (PWs), in their population response to odor stimulation. Here, we examine PWs in the channel catfish and propose that their properties could be explained as the superposition of asynchronous oscillators. Our model shows that the intriguing random pattern of amplitude-modulated PWs could be explained by Rayleigh fading, an interference phenomenon well known in physics and recognizable using statistical methods and signal analysis. We are proposing a mathematical fingerprint to characterize neural signals generated by the addition of random phase oscillators. Our interpretation of PWs as arising from asynchronous oscillators could be generalized to other neuronal populations, because it suggests that neural oscillations, detected in local field potential recordings within a narrow frequency band, do not necessarily originate from synchronization events.

NO activates the olfactory cyclic nucleotide-gated conductance independent from cGMP in isolated rat olfactory receptor neurons

Nitric oxide (NO) is a putative neuronal messenger in the olfactory epithelium. We analysed the electrical responses of rat olfactory receptor neurones to NO stimulation in the whole-cell patch clamp mode and found that NO activates the cyclic nucleotide-gated conductance, independent from cyclic GMP. As NO may also open calcium-dependent potassium channels and raise cyclic GMP levels, it appears to act as a complex modulator of olfactory receptor neuron physiology in vivo.

Validation of a clinical-radiographic score to assess the probability of pulmonary tuberculosis in suspect patients with negative sputum smears.

Background Clinical suspects of pulmonary tuberculosis in which the sputum smears are negative for acid fast bacilli represent a diagnostic challenge in resource constrained settings. Our objective was to validate an existing clinical-radiographic score that assessed the probability of smear-negative pulmonary tuberculosis (SNPT) in high incidence settings in Peru. Methodology/Principal Findings We included in two referral hospitals in Lima patients with clinical suspicion of pulmonary tuberculosis and two or more negative sputum smears. Using a published but not externally validated score, patients were classified as having low, intermediate or high probability of pulmonary tuberculosis. The reference standard for the diagnosis of tuberculosis was a positive sputum culture in at least one of 2 liquid (MGIT or Middlebrook 7H9) and 1 solid (Ogawa) media. Prevalence of tuberculosis was calculated in each of the three probability groups. 684 patients were included. 184 (27.8%) had a diagnosis of pulmonary tuberculosis. The score did not perform well in patients with a previous history of pulmonary tuberculosis. In patients without, the prevalence of tuberculosis was 5.1%, 31.7% and 72% in the low, intermediate and high probability group respectively. The area under de ROC curve was 0.76 (95% CI 0.72–0.80) and scores ≥6 had a positive LR of 10.9. Conclusions/Significance In smear negative suspects without previous history of tuberculosis, the clinical-radiographic score can be used as a tool to assess the probability of pulmonary tuberculosis and to guide the decision to initiate or defer treatment or to requesting additional tests.

The Nearly Neutral and Selection Theories of Molecular Evolution Under the Fisher Geometrical Framework: Substitution Rate, Population Size, and Complexity

The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population’s phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model in which evolutionary rate does not depend on population size, but is critically dependent on the complexity of organisms and mutation size. For SR as well as VR we found that key parameters of molecular evolution are linked by biological factors, and we showed that they cannot be fixed independently by arbitrary criteria, as has usually been assumed in previous molecular evolutionary models.

Temporal Organization of the Sleep-Wake Cycle under Food Entrainment in the Rat.

STUDY OBJECTIVES To analyze the temporal organization of the sleep-wake cycle under food entrainment in the rat. METHODS Eighteen male Sprague-Dawley rats were chronically implanted for polysomnographic recording. During the baseline (BL) protocol, rats were recorded under a 12:12 light-dark (LD) schedule in individual isolation chambers with food and water ad libitum. Food entrainment was performed by means of a 4-h food restriction (FR) protocol starting at photic zeitgeber time 5. Eight animals underwent a 3-h phase advance of the FR protocol (A-FR). We compared the mean curves and acrophases of wakefulness, NREM sleep, and REM sleep under photic and food entrainment and after a phase advance in scheduled food delivery. We further evaluated the dynamics of REM sleep homeostasis and the NREM sleep EEG delta wave profile. RESULTS A prominent food-anticipatory arousal interval was observed after nine or more days of FR, characterized by increased wakefulness and suppression of REM sleep propensity and dampening of NREM sleep EEG delta activity. REM sleep exhibited a robust nocturnal phase preference under FR that was not explained by a nocturnal REM sleep rebound. The mean curve of sleep-wake states and NREM sleep EEG delta activity remained phase-locked to the timing of meals during the A-FR protocol. CONCLUSIONS Our results support the hypothesis that under food entrainment, the sleep-wake cycle is coupled to a food-entrainable oscillator (FEO). Our findings suggest an unexpected interaction between FEO output and NREM sleep EEG delta activity generators.

On-line analysis of biosignals for the automation of total and specific sleep deprivation in the rat

A computer-based system that automates sleep studies, including sleep deprivation paradigms, is described. The system allows for total or REM-specific sleep deprivation and is based on a reliable, fast-responding, on-line state detection algorithm linked to a dependable intervention device. Behavioral state detection is achieved by dimension reduction of short-term EEG power spectrum. Interventions are made by serial outputs to servomotors that move a cage with different patterns and variable intensity. The system can adapt itself to individual characteristics and to changes in recording conditions. Customized protocols can be designed by defining the states or stages to be deprived, including scheduling temporal patterns. A detailed analysis of the relevant signals during and after deprivation is readily available. Data is presented from two experimental designs in rats. One consisted of specific REM-sleep short-term deprivation and the other of 10-hour total sleep deprivation. An outline of conceptual and practical considerations involved in the automation of laboratory set-ups oriented to biosignal analysis is provided. Careful monitoring of sleep EEG variables during sleep deprivation suggests peculiarities of brain functioning in that condition. A corollary is that sleep deprivation should not be considered to be merely a forced prolonged wakefulness.

Envelope analysis of the airflow signal to improve polysomnographic assessment of sleep disordered breathing.

STUDY OBJECTIVES Given the detailed respiratory waveform signal provided by the nasal cannula in polysomnographic (PSG) studies, to quantify sleep breathing disturbances by extracting a continuous variable based on the coefficient of variation of the envelope of that signal. DESIGN Application of an algorithm for envelope analysis to standard nasal cannula signal from actual polysomnographic studies. SETTING PSG recordings from a sleep disorders center were analyzed by an algorithm developed on the Igor scientific data analysis software. PATIENTS OR PARTICIPANTS Recordings representative of different degrees of sleep disordered breathing (SDB) severity or illustrative of the covariation between breathing and particularly relevant factors and variables. INTERVENTIONS The method calculated the coefficient of variation of the envelope for each 30-second epoch. The normalized version of that coefficient was defined as the respiratory disturbance variable (RDV). The method outcome was the all-night set of RDV values represented as a time series. MEASUREMENTS AND RESULTS RDV quantitatively reflected departure from normal sinusoidal breathing at each epoch, providing an intensity scale for disordered breathing. RDV dynamics configured itself in recognizable patterns for the airflow limitation (e.g., in UARS) and the apnea/hypopnea regimes. RDV reliably highlighted clinically meaningful associations with staging, body position, oximetry, or CPAP titration. CONCLUSIONS Respiratory disturbance variable can assess sleep breathing disturbances as a gradual phenomenon while providing a comprehensible and detailed representation of its dynamics. It may thus improve clinical diagnosis and provide a revealing descriptive tool for mechanistic sleep disordered breathing modeling. Respiratory disturbance variable may contribute to attaining simplified screening methodologies, novel diagnostic criteria, and insightful research tools.

The Sleep–Wake Cycle in the Nicotinic Alpha-9 Acetylcholine Receptor Subunit Knock-Out Mice

There is a neural matrix controlling the sleep–wake cycle (SWC) embedded within high ranking integrative mechanisms in the central nervous system. Nicotinic alpha-9 acetylcholine receptor subunit (alpha-9 nAChR) participate in physiological processes occurring in sensory, endocrine and immune systems. There is a relationship between the SWC architecture, body homeostasis and sensory afferents so that disruption of afferent signaling is expected to affect the temporal organization of sleep and wake states. The analysis of the SWC of 9 nAChR knock-out animals may help to reveal the contribution of alpha-9 nAChR to sleep chronobiological determinants. Here we explore the polysomnogram in chronically implanted alpha-9 nAChR knock-out (KO) and wild-type (WT) individuals of the hybrid CBA/Sv129 mouse strain. Records were obtained in isolation chambers under a stable 12:12 light:dark cycle (LD). To unmask the 24-h modulation of the SWC a skeleton photoperiod (SP) protocol was performed. Under LD the daily quota (in %) of wakefulness (W), NREM sleep and REM sleep obtained in KO and WT animals were 45, 48 and 7, and 46, 46 and 8 respectively. Both groups exhibit nocturnal phase preference of W as well as diurnal and unimodal phase preference of NREM and REM sleep. The acrophase mean angles of KO vs. WT genotypes were not different (Zeitgeber Time: 6.5 vs. 14.9 for W, 4.3 vs. 2.8 for NREM sleep and 5.3 vs. 3.4 for REM sleep, respectively). Transference to SP do not affect daily state quotas, phase preferences and acrophases among genotypes. Unmasking phenomena of the SWC such as wake increment during the rest phase under SP was evident only among WT mice suggesting the involvement of retinal structures containing alpha-9 nAChR in masking processes. Furthermore, KO animals exhibit longer NREM and REM sleep episodes that is independent of illumination conditions. Consolidated diurnal NREM sleep contributed to obtain higher values of NREM sleep delta-EEG activity among KO mice during rest phase. In conclusion, circadian and sleep homeostatic aspects of the SWC are operative among alpha-9 nAChR KO animals. We propose that alpha-9 nAChR participate in retinal signaling processes responsible of the positive masking of sleep by light.

Envelope analysis links oscillatory and arrhythmic EEG activities to two types of neuronal synchronization

&NA; Traditionally, EEG is understood as originating from the synchronous activation of neuronal populations that generate rhythmic oscillations in specific frequency bands. Recently, new neuronal dynamics regimes have been identified (e.g. neuronal avalanches) characterized by irregular or arrhythmic activity. In addition, it is starting to be acknowledged that broadband properties of EEG spectrum (following a Symbol law) are tightly linked to brain function. Nevertheless, there is still no theoretical framework accommodating the coexistence of these two EEG phenomenologies: rhythmic/narrowband and arrhythmic/broadband. To address this problem, we present a new framework for EEG analysis based on the relation between the Gaussianity and the envelope of a given signal. EEG Gaussianity is a relevant assessment because if EEG emerges from the superposition of uncorrelated sources, it should exhibit properties of a Gaussian process, otherwise, as in the case of neural synchronization, deviations from Gaussianity should be observed. We use analytical results demonstrating that the coefficient of variation of the envelope (CVE) of Gaussian noise (or any of its filtered sub‐bands) is the constant Symbol, thus enabling CVE to be a useful metric to assess EEG Gaussianity. Furthermore, a new and highly informative analysis space (envelope characterization space) is generated by combining the CVE and the envelope average amplitude. We use this space to analyze rat EEG recordings during sleep‐wake cycles. Our results show that delta, theta and sigma bands approach Gaussianity at the lowest EEG amplitudes while exhibiting significant deviations at high EEG amplitudes. Deviations to low‐CVE appeared prominently during REM sleep, associated with theta rhythm, a regime consistent with the dynamics shown by the synchronization of weakly coupled oscillators. On the other hand, deviations to high‐CVE, appearing mostly during NREM sleep associated with EEG phasic activity and high‐amplitude Gaussian waves, can be interpreted as the arrhythmic superposition of transient neural synchronization events. These two different manifestations of neural synchrony (low‐CVE/high‐CVE) explain the well‐known spectral differences between REM and NREM sleep, while also illuminating the origin of the EEG Symbol spectrum. Symbol. No caption available. Symbol. No caption available. Graphical abstract Figure. No caption available.