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Domain structure and functional activity of the recombinant human fibrinogen gamma-module (gamma148-411).

Human fibrinogen gamma-module comprising residues gamma148-411 was expressed in Escherichia coli and refolded in vitro. Differential scanning calorimetry revealed that in addition to the two previously identified independently folded thermolabile domains, one in each half of the module, the gamma-module also contains one or two thermostable domains that melt above 65 degrees C. To localize the latter, an NH2-terminal 6-kDa fragment was prepared by limited proteolysis of the recombinant gamma-module. It melted at high temperature, indicating that this portion is folded into a compact structure that represents a thermostable domain, also identified in the proteolytic fibrinogen fragment D1 which contains the natural gamma-module. Thus the NH2-terminal half of the gamma-module forms two domains, a thermostable one and a thermolabile one, leaving the rest of the module to be responsible for the formation of the other one or two domains. The thermal stability of some domains was lower in the recombinant gamma-module than in its natural counterpart in D1, reflecting most probably the loss of interactions with neighboring domains; however, the major functional sites were essentially preserved. The module bound Ca2+ and was stabilized by it against denaturation and proteolysis. It inhibited fibrin polymerization and was efficiently cross-linked by factor XIIIa. The gamma-module supported adhesion of platelets via their GP IIbIIIa (alpha(IIb)beta3) receptor in the same manner as D1 fragment. It also supported the adhesion of alpha(M)beta2- (Mac-1-) transfected cells and in the fluid phase was more effective than D1 as an inhibitor of that adhesion, suggesting that the Mac-1 binding site is better exposed.

Calorimetry, Differential Scanning↗

Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast.

Molecular networks in cells are organized into functional modules, where genes in the same module interact densely with each other and participate in the same biological process. Thus, identification of modules from molecular networks is an important step toward a better understanding of how cells function through the molecular networks. Here, we propose a simple, automatic method, called MC(2), to identify functional modules by enumerating and merging cliques in the protein-interaction data from large-scale experiments. Application of MC(2) to the S. cerevisiae protein-interaction data produces 84 modules, whose sizes range from 4 to 69 genes. The majority of the discovered modules are significantly enriched with a highly specific process term (at least 4 levels below root) and a specific cellular component in Gene Ontology (GO) tree. The average fraction of genes with the most enriched GO term for all modules is 82% for specific biological processes and 78% for specific cellular components. In addition, the predicted modules are enriched with coexpressed proteins. These modules are found to be useful for annotating unknown genes and uncovering novel functions of known genes. MC(2) is efficient, and takes only about 5 min to identify modules from the current yeast gene interaction network with a typical PC (Intel Xeon 2.5 GHz CPU and 512 MB memory). The CPU time of MC(2) is affordable (12 h) even when the number of interactions is increased by a factor of 10. MC(2) and its results are publicly available on http://theory.med.buffalo.edu/MC2.

Algorithms↗

Pectate lyase 10A from Pseudomonas cellulosa is a modular enzyme containing a family 2a carbohydrate-binding module.

Pectate lyase 10A (Pel10A) enzyme from Pseudomonas cellulosa is composed of 649 residues and has a molecular mass of 68.5 kDa. Sequence analysis revealed that Pel10A contained a signal peptide and two serine-rich linker sequences that separate three modules. Sequence similarity was seen between the 9.2 kDa N-terminal module of Pel10A and family 2a carbohydrate-binding modules (CBMs). This N-terminal module of Pel10A was shown to encode an independently functional module with affinity to crystalline cellulose. A high sequence identity of 66% was seen between the 14.2 kDa central module of Pel10A and the functionally uncharacterized central modules of the xylan-degrading enzymes endoxylanase 10B, arabinofuranosidase 62C and esterase 1D, also from P. cellulosa. The 35.8 kDa C-terminal module of Pel10A was shown to have 30 and 36% identities with the family 10 pectate lyases from Azospirillum irakense and an alkaliphilic strain of Bacillus sp. strain KSM-P15, respectively. This His-tagged C-terminal module of the Pel10A was shown to encode an independent catalytic module (Pel10Acm). Pel10Acm was shown to cleave pectate and pectin in an endo-fashion and to have optimal activity at pH 10 and in the presence of 2 mM Ca2+. Highest enzyme activity was detected at 62 degrees C. Pel10Acm was shown to be most active against pectate (i.e. polygalacturonic acid) with progressively less activity against 31, 67 and 89% esterified citrus pectins. These data suggest that Pel10A has a preference for sequences of non-esterified galacturonic acid residues. Significantly, Pel10A and the P. cellulosa rhamnogalacturonan lyase 11A, in the accompanying article [McKie, Vincken, Voragen, van den Broek, Stimson and Gilbert (2001) Biochem. J. 355, 167-177], are the first CBM-containing pectinases described to date.

Amino Acid Sequence↗

Masking of tone bursts by modulated noise in normal, noise-masked normal, and hearing-impaired listeners.

Threshold of 4.6-ms tone bursts was measured in quiet and in the presence of a 100% sinusoidally amplitude-modulated speech-shaped noise. For the modulated-noise conditions, the onset of the tone burst coincided either with the maximum or the minimum modulator amplitude. The difference in these two masked thresholds provided an indication of the psychoacoustic modulation depth, or the modulation depth preserved within the auditory system. Modulation frequencies spanning the modulation spectrum of speech (2.5 to 20 Hz) were examined. Tone bursts were 500, 1400, and 4000 Hz. Subjects included normal listeners, normal listeners with a hearing loss simulated by high-pass noise, and hearing-impaired listeners having high-frequency sensorineural hearing loss. Normal listeners revealed a psychoacoustic modulation depth of 30-40 dB for the lowest modulation frequencies which decreased to about 15 dB at 20 Hz. The psychoacoustic modulation depth was decreased in the normal listeners with simulated hearing loss and in the hearing-impaired listeners. There was general agreement in the data, however, for the latter two groups of listeners suggesting that the normal listeners with hearing loss simulated by an additional masking noise provided a good representation of the performance of hearing-impaired listeners on this task.

Adult↗

The dynamics of spatiotemporal modulations.

The modulational instability of traveling waves is often thought to be a crucial point in the mechanism of transition to space-time disorder and turbulence. The aim of this paper is to study the effect of spatiotemporal modulations on some dynamics u(0)(x,t), which may occur as an instability process when a control parameter varies, for instance. We analyze the properties of the modulated dynamics of the form g(1)(x)g(2)(t)u(0)(x,t) compared to those of the reference dynamics u(0)(x,t), using operator theory. We show that, if the reference dynamics is invariant under some space-time symmetry in the sense of Ref. [J. Nonlinear Sci. 2, 183 (1992)], the modulation has the effect of either deforming this symmetry or breaking it, depending on whether the corresponding operator remains unitary or not. We also demonstrate that the smallest Euclidean space containing the modulated dynamics has a dimension smaller than or equal to the smallest Euclidean space containing u(0)(x,t). The previous results are then applied to the case of modulated uniformly traveling waves. While the spatiotemporal translation invariance of the wave never persists in the presence of a modulation, the existence of a spatiotemporal symmetry depends on the resonance of the Fourier sidebands due to the modulation. In case of nonresonance, a spatiotemporal symmetry exists and is explicitly determined. In this situation, the modulated wave and the carrier wave have the same spectrum (up to a normalization factor), the same entropy, and the spatial (resp., temporal) two-point correlation is deformed only by the spatial (resp., temporal) modulation. (c) 1995 American Institute of Physics.

Journal Article↗

A strategy to retrieve the whole set of protein modules in microbial proteomes.

Protein homology is often limited to long structural segments that we have previously called modules. We describe here a suite of programs used to catalog the whole set of modules present in microbial proteomes. First, the Darwin AllAll program detects homologous segments using thresholds for evolutionary distance and alignment length, and another program classifies these modules. After assembling these homologous modules in families, we further group families which are related by a chain of neighboring unrelated homologous modules. With the automatic analysis of these groups of families sharing homologous modules in independent multimodular proteins, one can split into their component parts many fused modules and/or deduce by logic more distant modules. All detected and inferred modules are reassembled in refined families. These two last steps are made by a unique program. Eventually, the soundness of the data obtained by this experimental approach is checked using independent tests. To illustrate this modular approach, we compared four proteobacterial proteomes (Campylobacter jejuni, Escherichia coli, Haemophilus influenzae, and Helicobacter pylori). It appears that this method might retrieve from present-day proteins many of the modules which can help to trace back ancient events of gene duplication and/or fusion.

Bacterial Proteins↗

Feedback control of electrically stimulated muscle using simultaneous pulse width and stimulus period modulation.

This paper considers the closed-loop control of electrically stimulated muscle using simultaneous pulse width and frequency modulation. Previous work has experimentally demonstrated good feedback regulation of muscle force using fixed parameter and an adaptive controller modulating pulse width. In this work, it is shown how the addition of pulse frequency modulation to pulse width modulation can improve controller performance. This combination controller has been developed for both single muscle activation and for costimulation of antagonists. This is accomplished using a single command input. In single muscle operation, the combination of pulse width and stimulus pulse frequency modulation results in better control of transient responses than with pulse width modulation alone; the total number of stimulus pulses is increased, however, when compared with pulse width-only modulation at the muscle fusion frequency. In the case of costimulation, the controller modulates the pulse stimulus periods of the antagonists in a reciprocal manner, to ensure stable and fast responses. That is, the frequency of stimulation of the antagonist is increased when that of the agonist is decreased. This results in better control performance with generally fewer stimulus pulses than those generated by costimulation using only pulse width modulation. This feedback controller was evaluated in animal experiments. Step responses with rapid rise times but without overshoot were obtained by the combined modulation. Good steady-state and transient performance were obtained over a wide range of static lengths and commands, under different loading conditions and in different animals. This controller is a promising potential component of neural prostheses to restore functional movement in paralyzed individuals.

Animals↗

Calcium-binding properties of the third and fourth epidermal-growth-factor-like modules in vitamin-K-dependent protein S.

Protein S is a plasma glycoprotein requiring vitamin K for normal biosynthesis and functioning as a cofactor of activated protein C, a regulator of blood coagulation. Protein S contains four modules that are similar to the epidermal growth factor (EGF) precursor. Qualitative Ca2+-binding experiments have indicated that the EGF-module region of bovine protein S harbors high-affinity Ca2+-binding sites. We have chemically synthesized the third and fourth EGF modules from human protein S, which both have the sequence motif associated with Ca2+-binding and Asp/Asn beta-hydroxylation. Both modules were folded to a native conformation, as judged by immunochemical experiments and NMR spectroscopy. Ca2+ binding to the modules was monitored with 1H-NMR spectroscopy. At physiological pH and 0.15 M NaCl, each module was found to have a single Ca2+-binding site with low affinity, i.e. Kd values of 6.1 mM for the third and 8.6 mM for the fourth EGF module. At low salt conditions the Ca2+ affinities are 5.2 mM and 0.6 mM, respectively. This Ca2+ affinity is similar to that of the isolated N-terminal EGF module from coagulation factors IX and X. The very high affinity Ca2+ binding to the EGF-module region of protein S thus appears to be due to the influence of neighboring modules.

Amino Acid Sequence↗

Activation of a PTX-insensitive G protein is involved in histamine-induced recombinant M-channel modulation.

The M-type potassium current (I(M)) plays a dominant role in regulating membrane excitability and is modulated by many neurotransmitters. However, except in the case of bradykinin, the signal transduction pathways involved in M-channel modulation have not been fully elucidated. The channels underlying I(M) are produced by the coassembly of KCNQ2 and KCNQ3 channel subunits and can be expressed in heterologous systems where they can be modulated by several neurotransmitter receptors including histamine H(1) receptors. In HEK293T cells, histamine acting via transiently expressed H(1)R produced a strong inhibition of recombinant M-channels but had no overt effects on the voltage dependence or voltage range of I(M) activation. In addition, the modulation of I(M) by histamine was not voltage sensitive, whereas channel gating, particularly deactivation, was accelerated by histamine. Non-hydrolysable guanine nucleotide analogues (GDP-beta-S and GTP-gamma-S) and pertussis toxin (PTX) treatment demonstrated the involvement of a PTX-insensitive G protein in the signal transduction pathway mediating histamine-induced I(M) modulation. Abrogation of the histamine-induced modulation of I(M) by expression of a C-terminal construct of phospholipase C (PLC-beta1-ct), which buffers activated Galpha(q/11) subunits, implicates this G protein alpha subunit in the modulatory pathway. On the other hand, abrogation of the histamine-induced modulation of I(M) by expression of two constructs which buffer free betagamma subunits, transducin (Galphat) and a C-terminal construct of a G protein receptor kinase (MAS-GRK2-ct), implicates betagamma dimers in the modulatory pathway. These findings demonstrate that histamine modulates recombinant M-channels in HEK293T cells via a PTX-insensitive G protein, probably Galpha(q/11), in a similar manner to a number of other G protein-coupled receptors. However, histamine-induced I(M) modulation in HEK293T cells is novel in that betagamma subunits in addition to Galpha(q/11) subunits appear to be involved in the modulation of KCNQ2/3 channel currents.

Buffers↗

Quantitative analysis of cardiovascular modulation in respiratory neural activity.

We propose the 'delta(2)-statistic' for assessing the magnitude and statistical significance of arterial pulse-modulated activity of single neurones and present the results of applying this tool to medullary respiratory-modulated units. This analytical tool is a modification of the eta(2)-statistic and, consequently, based on the analysis of variance. The eta(2)-statistic reflects the consistency of respiratory-modulated activity on a cycle-by-cycle basis. However, directly applying this test to activity during the cardiac cycle proved ineffective because subjects-by-treatments matrices did not contain enough 'information'. We increased information by dividing the cardiac cycle into fewer bins, excluding cycles without activity and summing activity over multiple cycles. The analysed neuronal activity was an existing data set examining the neural control of respiration and cough. Neurones were recorded in the nuclei of the solitary tracts, and in the rostral and caudal ventral respiratory groups of decerebrate, neuromuscularly blocked, ventilated cats (n= 19). Two hundred of 246 spike trains were respiratory modulated; of these 53% were inspiratory (I), 36.5% expiratory (E), 6% IE phase spanning and 4.5% EI phase spanning and responsive to airway stimulation. Nearly half (n= 96/200) of the respiratory-modulated units were significantly pulse modulated and 13 were highly modulated with delta(2) values exceeding 0.3. In 10 of these highly modulated units, eta(2) values were greater than 0.3 and all 13 had, at least, a portion of their activity during expiration. We conclude that cardiorespiratory interaction is reciprocal; in addition to respiratory-modulated activity in a subset of neuronal activity patterns controlling the cardiovascular system, pulse-modulated activity exists in a subset of neuronal activity patterns controlling the respiratory system. Thus, cardio-ventilatory coupling apparent in respiratory motor output is evident and, perhaps, derived from the neural substrate driving that output.

Action Potentials↗

Dose reduction in CT by anatomically adapted tube current modulation. I. Simulation studies.

Tube current modulation governed by x-ray attenuation during CT (computed tomography) acquisition can lead to noise reduction which in turn can be used to achieve patient dose reduction without loss in image quality. The potential of this technique was investigated in simulation studies calculating both noise amplitude levels and noise distribution in CT images. The dependence of noise on the inodulation function, amplitude of modulation, shape and size of the object, and possible phase shift between attenuation and modulation function were examined. Both sinusoidal and attenuation-based control functions were used to modulate tube current. Noise reduction was calculated for both ideal systems and for real systems with limited modulation amplitude. Dose reductions up to 50% can be achieved depending on the phantom geometry and tube current modulation function. Attenuation-based tube current modulation yields substantially higher reduction than fixed-shape modulation functions. Optimal results are obtained when the current is modulated as a function of the square root of attenuation. A modulation amplitude of at least 90% should be available to exploit the potential of these techniques.

Air Pollutants, Radioactive↗

Information theory analysis of patterns of modulation in the advertisement call of the male bullfrog, Rana catesbeiana.

Male bullfrogs often amplitude modulate the envelopes of the individual notes (croaks) in their multinote advertisement calls. These amplitude modulations change the envelope of the note from smooth and unmodulated to one with varying numbers of modulations. A Markov analysis shows the pattern of change in the envelope to be highly ordered, but not completely so (semi-Markovian). Three simple rules govern the presence or absence of modulations in individual notes. These rules are (1) all calls begin with an unmodulated note; (2) the first note to be modulated will contain only one modulation; and (3) when a change in modulation occurs from one note to the next, it does so with an increase or a decrease of one modulation only. The addition of modulations is correlated with an increase in note duration. Physiologically, the presence of modulations might increase the precision of temporal coding of note periodicities in the central auditory system.

Animals↗

Comodulation masking release using SAM tonal complex maskers: effects of modulation depth and signal position.

The purpose of this investigation was to examine two stimulus parameters that were reasoned to be of importance to comodulation masking release (CMR). The first was the degree of fluctuation, or depth of modulation, in the masker bands, and the second was the temporal position of the signal with respect to the modulations of the masker. The investigation began by demonstrating the efficacy of sinusoidally amplitude-modulated (SAM) tonal complex maskers in eliciting CMR. "Nine-band" maskers, 650 ms in duration, were constructed by adding together nine SAM tones spaced at 100-Hz intervals from 300 to 1100 Hz. The rate of modulation for each SAM tone was 10 Hz, and the depth of modulation was 100%. Using such maskers, it was shown that when the on-frequency SAM tone had a modulation depth of 100%, the threshold for a 250-ms, 700-Hz tone improved monotonically as the modulation depths of the flanking SAM tones increased from 0% to 100%. When the on-frequency SAM tone had a modulation depth of 63%, some listeners performed optimally when the flanking SAM tones also exhibited a modulation depth of 63%, whereas others performed best when the flankers had modulation depths of 100%. With regard to signal position, a typical CMR effect was observed when the signal, consisting of a train of three 50-ms, 700-Hz tone bursts, was placed in the dips of the on-frequency masker. However, when the signal was placed at the peaks of the envelope, an increase in masking was observed for a comodulated masker.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

Segregation of concurrent sounds. I: Effects of frequency modulation coherence.

Frequency modulation coherence was investigated as a possible cue for the perceptual segregation of concurrent sound sources. Synthesized chords of 2-s duration and comprising six permutations of three sung vowels (/a/, /i/, /o/) at three fundamental frequencies (130.8, 174.6, and 233.1 Hz) were constructed. In one condition, no vowels were modulated, and, in a second, all three were modulated coherently such that the ratio relations among all frequency components were maintained. In a third group of conditions, one vowel was modulated, while the other two remained steady. In a fourth group, one vowel was modulated independently of the two other vowels, which were modulated coherently with one another. Subjects were asked to judge the perceived prominence of each of the three vowels in each chord. Judged prominence increased significantly when the target vowel was modulated compared to when it was not, with the greatest increase being found for higher fundamental frequencies. The increase in prominence with modulation was unaffected by whether the target was modulated coherently or not with nontarget vowels. The modulation and pitch position of nontarget vowels had no effect on target vowel prominence. These results are discussed in terms of possible concurrent auditory grouping principles.

Acoustic Stimulation↗

Some effects of auditory grouping factors on modulation detection interference (MDI).

The ability to detect the existence of amplitude modulation at a target frequency is reduced when amplitude modulation exists at a flanking frequency. This effect has been termed modulation detection interference (MDI) [Yost and Sheft, J. Acoust. Soc. Am. 85, 848-857 (1989)]. One explanation for MDI holds that the masking and target frequencies are grouped together by the auditory system such that it is difficult to analyze the modulation at each frequency separately. The present study investigated conditions where the asynchrony of temporal gating of the target and flanking frequencies was manipulated in order to make the frequencies more or less likely to be grouped together by the auditory system and perceived as originating from a single putative source. A second experimental manipulation attempted to perceptually segregate the masking and target frequencies on the basis of harmonicity or spectral proximity. The results of the experiments indicated that manipulations that were intended to enhance the segregation of the masking and target frequencies reduced the magnitude of MDI effects. This generally supported an interpretation that MDI is related in some way to auditory grouping. A final experiment was performed in which the subject had to detect the presence of amplitude modulation, but also had to identify which of two frequency components carried the modulation. Subjects were often poor in discriminating which of two frequencies was amplitude modulated, even when the modulation itself was clearly audible. It was concluded that part of the MDI effect might be due to the poor ability of the auditory system to associate modulation with the carrier of the modulation.(ABSTRACT TRUNCATED AT 250 WORDS)

Acoustics↗

Amplitude modulation rate discrimination with sinusoidal carriers.

Discrimination of the change in rate of sinusoidal amplitude modulation was investigated for sinusoidal carriers. The just-noticeable change in the modulation rate was measured as a function of (1) carrier frequency (fc = 500, 1000, 2000, or 4000 Hz), (2) initial modulation rate (fm = 10, 20, 40, 80, 160, or 320 Hz), and (3) stimulus duration (T = 62, 125, 250, 500, 1000, or 2000 ms). For modulation rates less than 320 Hz, the thresholds for a change in modulation rate were not affected by changing the carrier frequency. When fm = 320 Hz, the threshold for changes in the modulation rate ordered in the same way as the threshold for changes in the frequency of a pure tone, suggesting that the primary cue for discriminating a change in modulation rate was the frequency of either sideband. As stimulus duration increased to a certain T (critical duration), the thresholds decreased by more than a factor of 2. Above that duration, the thresholds for changes in modulation rate decreased only slightly or remained constant. The critical duration corresponded to about five cycles of modulation, at least for the slower modulation rates.

Adult↗

Amplitude-modulation detection at low- and high-audio frequencies.

Estimates of temporal acuity under comparable conditions at low- and high-audio frequencies are rare. The present study used the amplitude-modulation detection paradigm to estimate temporal acuity over a range of audio frequencies from 800 to 12,800 Hz. Amplitude-modulation detection was measured as a function of modulation frequency for bandlimited noise carriers, and the resulting temporal modulation-transfer functions were used to characterize temporal acuity. The most important result from the two experiments reported is that systematic manipulations of carrier upper-cutoff frequency produced estimates of temporal acuity that did not vary from 800 to 12,800 Hz. When the modulated noise bands were filtered after modulation to control for potential spectral cues, the low-pass cutoff of the modulation-transfer function varied with the carrier bandwidth. However, when the standard stimulus was a quasifrequency-modulated (QFM) noise and the signal was an unfiltered, amplitude-modulated noise, the low-pass cutoff of the modulation-transfer function was independent of carrier bandwidth. These results are consistent with a growing body of evidence demonstrating that auditory temporal acuity is constant throughout most of the audible frequency range.

Adult↗

A high-precision magnetoencephalographic study of human auditory steady-state responses to amplitude-modulated tones.

The cerebral magnetic field of the auditory steady-state response (SSR) to sinusoidal amplitude-modulated (SAM) tones was recorded in healthy humans. The waveforms of underlying cortical source activity were calculated at multiples of the modulation frequency using the method of source space projection, which improved the signal-to-noise ratio (SNR) by a factor of 2 to 4. Since the complex amplitudes of the cortical source activity were independent of the sensor position in relation to the subject's head, a comparison of the results across experimental sessions was possible. The effect of modulation frequency on the amplitude and phase of the SSR was investigated at 30 different values between 10 and 98 Hz. At modulation frequencies between 10 and 20 Hz the SNR of harmonics near 40 Hz were predominant over the fundamental SSR. Above 30 Hz the SSR showed an almost sinusoidal waveform with an amplitude maximum at 40 Hz. The amplitude decreased with increasing modulation frequency but was significantly different from the magnetoencephalographic (MEG) background activity up to 98 Hz. Phase response at the fundamental and first harmonic decreased monotonically with increasing modulation frequency. The group delay (apparent latency) showed peaks of 72 ms at 20 Hz, 48 ms at 40 Hz, and 26 ms at 80 Hz. The effects of stimulus intensity, modulation depth, and carrier frequency on amplitude and phase of the SSR were also investigated. The SSR amplitude decreased linearly when stimulus intensity or the modulation depth were decreased in logarithmic steps. SSR amplitude decreased by a factor of 3 when carrier frequency increased from 250 to 4000 Hz. From the phase characteristics, time delays were found in the range of 0 to 6 ms for stimulus intensity, modulation depth, and carrier frequency, which were maximal at low frequencies, low intensities, or maximal modulation depth.

Adult↗