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PubMed2002

Thoroughly sampling sequence space: large-scale protein design of structural ensembles.

Modeling the inherent flexibility of the protein backbone as part of computational protein design is necessary to capture the behavior of real proteins and is a prerequisite for the accurate exploration of protein sequence space. We present the results of a broad exploration of sequence space, with backbone flexibility, through a novel approach: large-scale protein design to structural ensembles. A distributed computing architecture has allowed us to generate hundreds of thousands of diverse sequences for a set of 253 naturally occurring proteins, allowing exciting insights into the nature of protein sequence space. Designing to a structural ensemble produces a much greater diversity of sequences than previous studies have reported, and homology searches using profiles derived from the designed sequences against the Protein Data Bank show that the relevance and quality of the sequences is not diminished. The designed sequences have greater overall diversity than corresponding natural sequence alignments, and no direct correlations are seen between the diversity of natural sequence alignments and the diversity of the corresponding designed sequences. For structures in the same fold, the sequence entropies of the designed sequences cluster together tightly. This tight clustering of sequence entropies within a fold and the separation of sequence entropy distributions for different folds suggest that the diversity of designed sequences is primarily determined by a structure's overall fold, and that the designability principle postulated from studies of simple models holds in real proteins. This has important implications for experimental protein design and engineering, as well as providing insight into protein evolution.

Amino Acid Sequence↗

PubMed2006

Methionine oxidation of monomeric lambda repressor: the denatured state ensemble under nondenaturing conditions.

Although poorly understood, the properties of the denatured state ensemble are critical to the thermodynamics and the kinetics of protein folding. The most relevant conformations to cellular protein folding are the ones populated under physiological conditions. To avoid the problem of low expression that is seen with unstable variants, we used methionine oxidation to destabilize monomeric lambda repressor and predominantly populate the denatured state under nondenaturing buffer conditions. The denatured ensemble populated under these conditions comprises conformations that are compact. Analytical ultracentrifugation sedimentation velocity experiments indicate a small increase in Stokes radius over that of the native state. A significant degree of alpha-helical structure in these conformations is detected by far-UV circular dichroism, and some tertiary interactions are suggested by near-UV circular dichroism. The characteristics of the denatured state populated by methionine oxidation in nondenaturing buffer are very different from those found in chemical denaturant.

Circular Dichroism↗

PubMed2006

Native state energetics of the Src SH2 domain: evidence for a partially structured state in the denatured ensemble.

We have defined the free-energy profile of the Src SH2 domain using a variety of biophysical techniques. Equilibrium and kinetic experiments monitored by tryptophan fluorescence show that Src SH2 is quite stable and folds rapidly by a two-state mechanism, without populating any intermediates. Native state hydrogen-deuterium exchange confirms this two-state behavior; we detect no cooperative partially unfolded forms in equilibrium with the native conformation under any conditions. Interestingly, the apparent stability of the protein from hydrogen exchange is 2 kcal/mol greater than the stability determined by both equilibrium and kinetic studies followed by fluorescence. Native-state proteolysis demonstrates that this "super protection" does not result from a deviation from the linear extrapolation model used to fit the fluorescence data. Instead, it likely arises from a notable compaction in the unfolded state under native conditions, resulting in an ensemble of conformations with substantial solvent exposure of side chains and flexible regions sensitive to proteolysis, but backbone amides that exchange with solvent approximately 30-fold slower than would be expected for a random coil. The apparently simple behavior of Src SH2 in traditional unfolding studies masks the significant complexity present in the denatured-state ensemble.

Animals↗

PubMed2006

FOXP3 ensembles in T-cell regulation.

Our recent studies have identified dynamic protein ensembles containing forkhead box protein 3 (FOXP3) that provide insight into the molecular complexity of suppressor T-cell activities, and it is our goal to determine how these ensembles regulate FOXP3's transcriptional activity in vivo. In this review, we summarize our current understanding of how FOXP3 expression is induced and how FOXP3 functions in vivo as a transcriptional regulator by assembling a multisubunit complex involved in histone modification as well as chromatin remodeling.

Animals↗

PubMed1990

Clinical evaluation of an ensemble-averaging impedance cardiograph for monitoring stroke volume during spontaneous breathing.

Simultaneous determination of stroke volume (SV) with an ensemble-averaging impedance cardiograph (AIGG) and the thermodilution technique (TD) was compared in 10 patients scheduled for major vascular surgery. A small, successive increase in SV was achieved by a step-wise infusion of dextran-70 and elevation of the patient's legs. The patients were allowed to breathe normally during the measurement procedures. There was no difference between the ability of AICG and TD to monitor changes in SV and the correlation coefficient for the measurement of changes in SV by the two methods was 0.88. There was no difference between the reproducibility of AICG- (4.6 ml) and TD- (9.2 ml) determined SV or between the coefficient of variation for AICG (4.8%) and TD (9.9%). The mean difference between AICG- and TD-determined SV at the different measurement points (range 1.3-4.2 ml) was well within acceptable limits. In conclusion, the ensemble-averaging impedance cardiograph described in this study was found to be reliable for monitoring changes in SV during uninterrupted, spontaneous breathing.

Aged↗

PubMed2005

Frontal and parietal cortical ensembles predict single-trial muscle activity during reaching movements in primates.

Previously we have shown that the kinematic parameters of reaching movements can be extracted from the activity of cortical ensembles. Here we used cortical ensemble activity to predict electromyographic (EMG) signals of four arm muscles in New World monkeys. The overall shape of the EMG envelope was predicted, as well as trial-to-trial variations in the amplitude and timing of bursts of muscle activity. Predictions of EMG patterns exhibited during reaching movements could be obtained not only from primary motor cortex, but also from dorsal premotor, primary somatosensory and posterior parietal cortices. These results suggest that these areas represent signals correlated to EMGs of arm muscles in a distributed manner, and that the larger the population sampled, the more reliable the predictions. We propose that, in the future, recordings from multiple cortical areas and the extraction of muscle patterns from these recordings will help to restore limb mobility in paralysed patients.

Algorithms↗

PubMed1996

Movement illusions evoked by ensemble cutaneous input from the dorsum of the human hand.

1. In this study we tested the hypothesis that ensemble activity in human cutaneous sensory afferents evoked by the stretching of skin over and around the finger joints contributes to the conscious perception of movement of the fingers. 2. In nineteen normal adults, ensembles of cutaneous afferents were activated either by electrical stimulation, delivered through an array of electrodes on the dorsum of the hand and fingers, or by mechanical stretching of the skin over and around the joints. The stretching was applied through an array of threads stuck to the skin, in such a way as to avoid or minimize moving the underlying joints and to avoid applying pressure to underlying tendons and ligaments. Perceived movements were mimicked by voluntary movements of the fingers of the contralateral hand. 3. By way of comparison, kinaesthetic illusions were also evoked by activation of muscle receptors by vibration. 4. Illusions of movement were elicited with each type of stimulus. Electrical stimulation of skin afferents caused clear illusory movements in six out of seventeen subjects (35%), and borderline movement illusions in three out of the same seventeen subjects (total 9/17, 53%). Various other localized skin sensations were also reported. Skin stretch evoked movement illusions in eleven out of nineteen of subjects (58%). In all subjects who received both cutaneous stimuli, twelve out of seventeen (71%) reported some movement sensations with one or other of the stimulation techniques. Vibration tended to be the most reliable stimulus modality, eliciting illusory movements in fourteen out of sixteen subjects (88%). 5. Although the skin stretching technique did cause minute movements of nearby joints in several cases, these were monitored and shown in separate control experiments to be below perceptual threshold, and so the movement illusions could be safely attributed to the cutaneous afferent input evoked by skin stretch. 6. The results support the hypothesis that input from skin stretched during finger movement contributes to the conscious perception of the movement. Vibration-evoked muscle afferent input tended to be more reliable than the skin input in producing kinaesthetic illusions, though comparisons of the relative efficacy of the three techniques must be made with caution.

Adolescent↗

PubMed2004

Distinct ensemble codes in hippocampal areas CA3 and CA1.

The hippocampus has differentiated into an extensively connected recurrent stage (CA3) followed by a feed-forward stage (CA1). We examined the function of this structural differentiation by determining how cell ensembles in rat CA3 and CA1 generate representations of rooms with common spatial elements. In CA3, distinct subsets of pyramidal cells were activated in each room, regardless of the similarity of the testing enclosure. In CA1, the activated populations overlapped, and the overlap increased in similar enclosures. After exposure to a novel room, ensemble activity developed slower in CA3 than CA1, suggesting that the representations emerged independently.

Action Potentials↗

PubMed2005

Creating order from random fluctuations in small spin ensembles.

We demonstrate the ability to create spin order by using a magnetic resonance force microscope to harness the naturally occurring statistical fluctuations in small ensembles of electron spins. In one method, we hyperpolarized the spin system by selectively capturing the transient spin order created by the statistical fluctuations. In a second method, we took a more active approach and rectified the spin fluctuations by applying real-time feedback to the entire spin ensemble. The created spin order can be stored in the laboratory frame for a period on the order of the longitudinal relaxation time of 30 seconds and then read out.

Journal Article↗

PubMed1995

Sensorimotor encoding by synchronous neural ensemble activity at multiple levels of the somatosensory system.

Neural ensemble processing of sensorimotor information during behavior was investigated by simultaneously recording up to 48 single neurons at multiple relays of the rat trigeminal somatosensory system. Cortical, thalamic, and brainstem neurons exhibited widespread 7- to 12-hertz synchronous oscillations, which began during attentive immobility and reliably predicted the imminent onset of rhythmic whisker twitching. Each oscillatory cycle began as a traveling wave of neural activity in the cortex that then spread to the thalamus. Just before the onset of rhythmic whisker twitching, the oscillations spread to the spinal trigeminal brainstem complex. Thereafter, the oscillations at all levels were synchronous with whisker protraction. Neural structures manifesting these rhythms also exhibited distributed spatiotemporal patterns of neuronal ensemble activity in response to tactile stimulation. Thus, multilevel synchronous activity in this system may encode not only sensory information but also the onset and temporal domain of tactile exploratory movements.

Animals↗

PubMed2004

Theory of single-molecule spectroscopy: beyond the ensemble average.

Single-molecule spectroscopy (SMS) is a powerful experimental technique used to investigate a wide range of physical, chemical, and biophysical phenomena. The merit of SMS is that it does not require ensemble averaging, which is found in standard spectroscopic techniques. Thus SMS yields insight into complex fluctuation phenomena that cannot be observed using standard ensemble techniques. We investigate theoretical aspects of SMS, emphasizing (a) dynamical fluctuations (e.g., spectral diffusion, photon-counting statistics, antibunching, quantum jumps, triplet blinking, and nonergodic blinking) and (b) single-molecule fluctuations in disordered systems, specifically distribution of line shapes of single molecules in low-temperature glasses. Special emphasis is given to single-molecule systems that reveal surprising connections to Levy statistics (i.e., blinking of quantum dots and single molecules in glasses). We compare theory with experiment and mention open problems. Our work demonstrates that the theory of SMS is a complementary field of research for describing optical spectroscopy in the condensed phase.

Journal Article↗

PubMed2001

Impact of pulsatility on the ensemble orderliness (approximate entropy) of neurohormone secretion.

Regular patterns of neurohormone secretion are driven by underlying pulsatile and subordinate (feedback sensitive) dynamics. Measures of time-series orderliness, e.g., the approximate entropy (ApEn) statistic (Pincus SM. Proc Natl Acad Sci 88: 2297-2301, 1991), vividly discriminate pathological and physiological patterns of hormone release. To investigate how specific pulsatility features impact regularity estimates, we have examined the sensitivity of the ApEn metric to systematic variations in the frequency, amplitude, and half-life of simulated neurohormone pulse trains (Veldhuis JD, Carlson ML, and Johnson ML. Proc Natl Acad Sci 84: 7686-7690, 1987) and compared the impact of a high vs. low baseline luteinizing hormone (LH) pattern regularity state mimicking the normal female luteal phase and the young male, respectively. Shortening the interpulse interval length elevated ApEn in both pulsatility models, thereby signifying greater ensemble series irregularity. The frequency sensitivity of ApEn was robust to several complementary renditions of ApEn and to variations in experimental uncertainty, basal (nonpulsatile) LH secretion, and secretory burst amplitude. ApEn rose with increasing hormone half-life, especially in the face of low baseline variability emulated by midluteal LH secretion profiles. High variability of secretory burst amplitude, pulse duration, or interpeak intervals increased ApEn in the more orderly femalelike construct; in the highly irregular malelike LH pulse model, these variability changes had little effect on ApEn. In summary, the ensemble regularity statistic, ApEn, quantifies unequal pattern orderliness in neurohormone pulse trains with minimal dependence on mean pulse amplitude, interpulse baseline, or (subthreshold) sample uncertainty. Thus ApEn monitors changing secretory event frequency and interpulse variability with sensitivity to starting pattern regularity, providing a mechanistic linkage between model evolution and statistical change.

Female↗

PubMed2006

Fast modulation of prefrontal cortex activity by basal forebrain noncholinergic neuronal ensembles.

Traditionally, most basal forebrain (BF) functions have been attributed to its cholinergic neurons. However, the majority of cortical-projecting BF neurons are noncholinergic and their in vivo functions remain unclear. We investigated how BF modulates cortical dynamics by simultaneously recording </=50 BF single neurons along with local field potentials (LFPs) from the prefrontal cortex (PFCx) in different wake-sleep states of adult rats. Using stereotypical spike time correlations, we identified a large (roughly 70%) subset of BF neurons, which we named BF tonic neurons (BFTNs). BFTNs fired tonically at 2-8 Hz without significantly changing their average firing rate across wake-sleep states. As such, these cannot be classified as cholinergic neurons. BFTNs substantially increased the spiking variability during waking and rapid-eye-movement sleep, by exhibiting frequent spike bursts with <50-ms interspike interval. Spike bursts among BFTNs were highly correlated, leading to transient population synchronization events of BFTN ensembles that lasted on average 160 ms. Most importantly, BFTN synchronization occurred preferentially just before the troughs of PFCx LFP oscillations, which reflect increased cortical activity. Furthermore, BFTN synchronization was accompanied by transient increases in prefrontal cortex gamma oscillations. These results suggest that synchronization of BFTN ensembles, which are likely to be formed by cortical-projecting GABAergic neurons from the BF, could be primarily responsible for fast cortical modulations to provide transient amplification of cortical activity.

Animals↗

PubMed2002

The KOX zinc finger genes: genome wide mapping of 368 ZNF PAC clones with zinc finger gene clusters predominantly in 23 chromosomal loci are confirmed by human sequences annotated in EnsEMBL.

The chromosome locations of 368 human Kruppel-type zinc finger (ZNF) PAC clones were physically mapped by FISH to human chromosomes in support of recent efforts of assigning KOX cDNAs (KOX1-KOX32) to zinc finger gene clusters. Recent mapping results were validated and confirmed by sequence comparisons to zinc finger gene sequences automatically annotated in EnsEMBL. In toto, 799 Kruppel-type zinc finger genes have been annotated in EnsEMBL of which 290 genes are found to encode KRAB domains. Sequence homologies of the zinc finger domains were used to establish phylogenic trees of KOX zinc finger genes as well as of all KRAB containing human zinc finger and KOX genes documenting the evolution of KRAB zinc finger genes late in primate evolution. A list of 368 assigned ZNF PAC clones is available under http://www.pzr.uni-rostock.de/supplements.

Base Sequence↗

PubMed2004

Dynamic analyses of information encoding in neural ensembles.

Neural spike train decoding algorithms and techniques to compute Shannon mutual information are important methods for analyzing how neural systems represent biological signals. Decoding algorithms are also one of several strategies being used to design controls for brain-machine interfaces. Developing optimal strategies to design decoding algorithms and compute mutual information are therefore important problems in computational neuroscience. We present a general recursive filter decoding algorithm based on a point process model of individual neuron spiking activity and a linear stochastic state-space model of the biological signal. We derive from the algorithm new instantaneous estimates of the entropy, entropy rate, and the mutual information between the signal and the ensemble spiking activity. We assess the accuracy of the algorithm by computing, along with the decoding error, the true coverage probability of the approximate 0.95 confidence regions for the individual signal estimates. We illustrate the new algorithm by reanalyzing the position and ensemble neural spiking activity of CA1 hippocampal neurons from two rats foraging in an open circular environment. We compare the performance of this algorithm with a linear filter constructed by the widely used reverse correlation method. The median decoding error for Animal 1 (2) during 10 minutes of open foraging was 5.9 (5.5) cm, the median entropy was 6.9 (7.0) bits, the median information was 9.4 (9.4) bits, and the true coverage probability for 0.95 confidence regions was 0.67 (0.75) using 34 (32) neurons. These findings improve significantly on our previous results and suggest an integrated approach to dynamically reading neural codes, measuring their properties, and quantifying the accuracy with which encoded information is extracted.

Action Potentials↗

PubMed1999

Boosted mixture of experts: an ensemble learning scheme.

We present a new supervised learning procedure for ensemble machines, in which outputs of predictors, trained on different distributions, are combined by a dynamic classifier combination model. This procedure may be viewed as either a version of mixture of experts (Jacobs, Jordan, Nowlan, & Hintnon, 1991), applied to classification, or a variant of the boosting algorithm (Schapire, 1990). As a variant of the mixture of experts, it can be made appropriate for general classification and regression problems by initializing the partition of the data set to different experts in a boostlike manner. If viewed as a variant of the boosting algorithm, its main gain is the use of a dynamic combination model for the outputs of the networks. Results are demonstrated on a synthetic example and a digit recognition task from the NIST database and compared with classifical ensemble approaches.

Algorithms↗

PubMed2004

Scattering phase function measurements on single particles and on particle ensembles.

We present measurements of the light-scattering phase function of selected carbon and ash particles in the geometric-optics regime in which the particle diameter is much larger than the wavelength of the light source. Measurements were performed on both single particles and particle ensembles. This was accomplished with two separate methodologies: an electrodynamic levitator for single-particle measurements and a particle feeder for the ensemble measurements. For each methodology, two irradiation sources were utilized: an argon-ion laser (lambda = 496 nm) and a xenon lamp. Results of the normalized phase functions are presented.

Journal Article↗

PubMed2005

Stable ensemble performance with single-neuron variability during reaching movements in primates.

Significant variability in firing properties of individual neurons was observed while two monkeys, chronically implanted with multielectrode arrays in frontal and parietal cortical areas, performed a continuous arm movement task. Although the degree of correlation between the firing of single neurons and movement parameters was nonstationary, stable predictions of arm movements could be obtained from the activity of neuronal ensembles. This result adds support to the idea that movement parameters are redundantly encoded in the motor cortex, such that brain networks can achieve the same behavioral goals through different patterns and relative contribution of individual neuron activity. This has important implications for neural prosthetics, suggesting that accurate operation of a brain-machine interface requires recording from large neuronal ensembles to minimize the effect of variability and ensuring stable performance over long periods of time.

Action Potentials↗