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At least 127 records · Page 7Linked to original sources

Identification of novel beta-mannan- and beta-glucan-binding modules: evidence for a superfamily of carbohydrate-binding modules.

Many glycoside hydrolases, which degrade long-chain carbohydrate polymers, possess distinct catalytic modules and non-catalytic carbohydrate-binding modules (CBMs). On the basis of conserved protein secondary structure, we describe here the identification and experimental characterization of novel type of mannanase-associated mannan-binding module and also characterization of two CBM family 4 laminarinase-associated beta-glucan-binding modules. These modules are predicted to belong to a superfamily of CBMs which include families 4, 16, 17, 22 and a proposed new family, family 27.

Amino Acid Sequence↗

A proximal tissue-specific module and a distal negative regulatory module control apolipoprotein(a) gene transcription.

The apo(a) [apolipoprotein(a)] gene is responsible for variations in plasma lipoprotein(a), high levels of which are a risk factor for atherosclerosis and myocardial infarction. The apo(a) promoter stimulates the expression of reporter genes in HepG2 cells, but not in HeLa cells. In the present study, we demonstrate that the 1.4 kb apo(a) promoter comprises two composite regulatory regions: a distal negative regulatory module (positions -1432 to -716) and a proximal tissue-specific module (-716 to -616). The distal negative regulatory module contains two strong negative regulatory regions [polymorphic PNR (pentanucleotide repeat region) and NREbeta (negative regulatory element beta)], which sandwich the postive regulatory region PREbeta (positive regulatory element beta). The PNR was shown to bind to transcription factors in a tissue-specific manner, whereas the ubiquitous transcription factors hepatocyte nuclear factor 3alpha and GATA binding protein 4 bound to NREbeta to repress gene transcription. The proximal tissue-specific module contains two regulatory elements: an activating region (PREalpha) that activates transcription in HepG2 cells, and NREalpha, which is responsible for repressing the apo(a) gene in HeLa cells. NREalpha binds to a HeLa-specific repressor. These multiple regulatory elements might work co-operatively to finely regulate apo(a) gene expression. Although the tissue-specific module is required for apo(a) gene activation and repression in a tissue-specific manner, the combinatorial interplay of the distal and proximal regulators might define the complex pathway(s) of apo(a) gene regulation.

Apolipoproteins A↗

Absolute thresholds for frequency-modulated signals: effects of rate, pattern, and percentage of modulation.

Absolute monaural thresholds for continuous unmodulated and frequency-modulated signals were determined for five normal-hearing subjects using the method of adjustment. Three carrier signals (250, 1000, and 4000 HZ) were modulated at rates of 2 and 20 times per sec using frequency deviations of +/- 5, 10, and 20%, and both ramp and sinusoidal modulation. Thresholds measured at the slower modulation rate were 5 to 10 dB lower than those measured for unmodulated signals at the two higher test frequencies. Suggestions are presented as to how the clinician may minimize the possible discrepancy between modulated and unmodulated signals using currently available warble-tone equipment.

Adult↗

Comparing contrast-modulated and luminance-modulated masking: effects of spatial frequency and phase.

The masking of a sinusoidal test grating by contrast-modulated (CM) gratings could, in principle, be attributable to the presence of a distortion product, injected into the stimulus during some nonlinear transformation at an early level of visual processing (e.g. Nachmias, 1989 Vision Research 29 137-142). If so, CM gratings and luminance-modulated (LM) gratings of similar effective contrast and spatial frequency should mask the detection of sinusoids in a similar fashion. We compared the effects of masking by 1 cycle deg-1 CM gratings [both simple beats (8 + 9 cycles deg-1) and amplitude-modulated gratings (8 + 9 + 10 cycles deg-1)], with those of masking by 1 cycle deg-1 LM gratings of low contrast. We found that: (i) CM and low-contrast LM grating masks yielded similar spatial-frequency tuning functions around the modulation frequency of 1 cycle deg-1; (ii) low-contrast LM gratings masked the detection of test sinusoids in a highly phase-dependent fashion, while masking by CM gratings did not vary systematically with relative spatial phase. The results suggest that masking produced by CM gratings cannot simply be explained by the presence of a distortion product at the beat or modulation frequency.

Contrast Sensitivity↗

Coactivator/corepressor ratios modulate PR-mediated transcription by the selective receptor modulator RU486.

Selective receptor modulators, such as the antiprogestin RU486, are known to exhibit partial agonist activities in a cell-type-dependent manner. Employing an in vitro chromatin transcription system that recapitulates progesterone receptor (PR)-mediated transcription in vivo, we have investigated the molecular basis by which the antiprogestin RU486 regulates transcription in a cell-type-specific manner. We have compared the effects of RU486 on PR-dependent transcription in vitro using T47D and HeLa cell nuclear extracts. RU486 exhibits a differential ability to activate transcription within these two cell types. The differential effect on transcription correlates with different ratios of endogenous coactivators/corepressors in these cells. Unlike agonist-bound PR that interacts only with coactivators such as steroid receptor coactivator-1 (SRC-1), RU486-bound PR binds to both coactivator SRC-1 and corepressor silencing mediator for retinoid and thyroid hormone receptor (SMRT) in vitro. Both SRC-1 and SMRT have the capacity to modulate RU486-dependent activity. Moreover, a change in the relative levels of SRC-1 and SMRT contained in our chromatin transcription system modulates agonist/antagonist effects of RU486 on transcription by PR. Our data indicate that the ability of RU486 to activate transcription is modulated by the ratio of coactivators to corepressors and substantiate the important roles of coregulators in the regulation of steroid receptor mediated transactivation in response to selective receptor modulators.

Gonanes↗

X4 modules represent a new family of carbohydrate-binding modules that display novel properties.

The hydrolysis of the plant cell wall by microbial glycoside hydrolases and esterases is the primary mechanism by which stored organic carbon is utilized in the biosphere, and thus these enzymes are of considerable biological and industrial importance. Plant cell wall-degrading enzymes in general display a modular architecture comprising catalytic and non-catalytic modules. The X4 modules in glycoside hydrolases represent a large family of non-catalytic modules whose function is unknown. Here we show that the X4 modules from a Cellvibrio japonicus mannanase (Man5C) and arabinofuranosidase (Abf62A) bind to polysaccharides, and thus these proteins comprise a new family of carbohydrate-binding modules (CBMs), designated CBM35. The Man5C-CBM35 binds to galactomannan, insoluble amorphous mannan, glucomannan, and manno-oligosaccharides but does not interact with crystalline mannan, cellulose, cello-oligosaccharides, or other polysaccharides derived from the plant cell wall. Man5C-CBM35 also potentiates mannanase activity against insoluble amorphous mannan. Abf62A-CBM35 interacts with unsubstituted oat-spelt xylan but not substituted forms of the hemicellulose or xylo-oligosaccharides, and requires calcium for binding. This is in sharp contrast to other xylan-binding CBMs, which interact in a calcium-independent manner with both xylo-oligosaccharides and decorated xylans.

Amino Acid Sequence↗

Amplitude modulation following responses in awake and sleeping humans--a comparison for 40 Hz and 80 Hz modulation frequency.

There have been several studies, which suggest that the amplitude of amplitude modulation following responses (AMFR) is correlated to the state of vigilance, similar to the 40 Hz event-related potentials. The aim of the present study was to compare the dependency of the AMFR-amplitude from the state of sleep for 40 Hz and 80 Hz modulation frequency. Eight normal hearing adults were investigated during natural and drug-induced sleep. The stimuli used were sinusoidally amplitude-modulated tones of 1 kHz carried frequency and 40 or 80 Hz modulation frequency at 60 dB nH stimulation level. For 40 Hz modulation frequency an increase of EEG-activity in the Delta-and Theta-band during periods of sleep correlates significantly with a decreased AMFR-amplitude whereas for 80 Hz no significant relation between stage of sleep and AMFR-amplitude could be found. The results suggest that in audiological use of 40 Hz-AMFR the state of vigilance should be monitored and stabilized at a high level.

Adult↗

Random and systematic beam modulator errors in dynamic intensity modulated radiotherapy.

This paper reports on the dosimetric effects of random and systematic modulator errors in delivery of dynamic intensity modulated beams. A sliding-widow type delivery that utilizes a combination of multileaf collimators (MLCs) and backup diaphragms was examined. Gaussian functions with standard deviations ranging from 0.5 to 1.5 mm were used to simulate random positioning errors. A clinical example involving a clival meningioma was chosen with optic chiasm and brain stem as limiting critical structures in the vicinity of the tumour. Dose calculations for different modulator fluctuations were performed, and a quantitative analysis was carried out based on cumulative and differential dose volume histograms for the gross target volume and surrounding critical structures. The study indicated that random modulator errors have a strong tendency to reduce minimum target dose and homogeneity. Furthermore, it was shown that random perturbation of both MLCs and backup diaphragms in the order of sigma = 1 mm can lead to 5% errors in prescribed dose. In comparison, when MLCs or backup diaphragms alone was perturbed, the system was more robust and modulator errors of at least sigma = 1.5 mm were required to cause dose discrepancies greater than 5%. For systematic perturbation, even errors in the order of +/- 0.5 mm were shown to result in significant dosimetric deviations.

Brain Neoplasms↗

Purification of modulator-deficient myosin light-chain kinase by modulator protein-Sepharose affinity chromatography.

Modulator-deficient myosin light-chain kinase from rabbit skeletal muscle was purified by modulator protein-Sepharose 4B affinity chromatography. The purified protein showed a single band (MW 80,000) on polyacrylamide gel electrophoresis in sodium dodecyl sulfate, and it exists as a monomer in the native state as determined by gel filtration. The modulator-deficient myosin light-chain kinase (MW 80,000), modulator protein (MW 16,500) and Ca2+ were essential for the kinase activity. The half-maximal activity of the kinase in the presence of excess modulator protein with 10 mM MgCl2 was at pCa 5.1, where full activity of actomyosin-ATPase is observed in the presence of the troponin--tropomyosin system. Assuming a rapid equilibrium between myosin light-chain kinase and two substrates, ATP and g2 light-chain, Km values for ATP and g2 light chain were evaluated as 0.28 mM and 0.024 mM, respectively. Vm/e was 5.7 s-1.

Adenosine Triphosphatases↗

Rapid Modulation of Spinach Leaf Nitrate Reductase by Photosynthesis : II. In Vitro Modulation by ATP and AMP.

Assimilatory nitrate reductase activity (NRA) in crude spinach leaf (Spinacia oleracea) extracts undergoes rapid changes following fluctuations in photosynthesis brought about by changes in external CO(2) or by water stress (WM Kaiser, E Brendle-Behnisch [1991] Plant Physiol 96:363-367). A modulation of NRA sharing several characteristics (stability, response to Mg(2+) or Ca(2+), kinetic constants) with the in vivo modulation was obtained in vitro by preincubating desalted leaf extracts with physiological concentrations of Mg(2+) and ATP (deactivating) or AMP (activating). When nitrate reductase (NR) was inactivated in vivo by illuminating leaves at the CO(2) compensation point, it could be reactivated in vitro by incubating leaf extracts with AMP. For the in vitro inactivation, ATP could be replaced by GTP or UTP. Nonhydrolyzable ATP analogs (beta, gamma-imido ATP, beta, gamma-methyl-ATP) had no effect on NR, whereas gamma-S-ATP caused an irreversible inactivation. This suggests that NR modulation involves ATP hydrolysis. In contrast to NR in crude leaf extracts, partially purified NR did not respond to ATP or AMP. ATP and AMP levels in whole leaf extracts changed in the way predicted by the modulation of NRA when leaves were transferred from photosynthesizing (low ATP/AMP) to photorespiratory (high ATP/AMP) conditions. Adenine nucleotide levels in leaves could be effectively manipulated by feeding mannose through the leaf petiole. NRA followed these changes as expected from the in vitro results. This suggests that cytosolic ATP/AMP levels are indeed the central link between NRA in the cytosol and photosynthesis in the chloroplast. Phosphorylation/dephosphorylation of NR or of NR-regulating protein factors is discussed as a mechanism for a reversible modulation of NR by ATP and AMP.

Journal Article↗

Intensity modulation delivery techniques: "step & shoot" MLC auto-sequence versus the use of a modulator.

Two intensity modulation radiotherapy (IMRT) delivery systems, the "step & shoot" multileaf collimator (MLC) auto-sequence and the use of an intensity modulator, are compared with emphasis on the dose optimization quality and the treatment irradiation time. The intensity modulation (IM) was created by a dose gradient optimization algorithm which maximizes the target dose uniformity while maintaining dose to critical structures below a set tolerance defined by the user in terms of either a single dose value or a dose volume histogram curve for each critical structure. Two clinical cases were studied with and without dose optimization: a three-field sinus treatment and a six-field nasopharyngeal treatment. The optimization goal of the latter case included the sparing of several nearby normal structures in addition to the target dose uniformity. In both cases, the target dose uniformity initially improved quickly as the IM level increased to 5, then started to approach saturation when the MLC technique was used. In the absence of the both space and intensity discreteness intrinsic to the MLC technique, the modulator technique produced greater tumor dose uniformity and normal structure sparing. The latter showed no systematic improvement with increasing IM level using the MLC technique. For the sinus tumor treatment of 2 Gy the treatment irradiation time of the modulator technique is no more than that of the conventional treatment. For the MLC technique the irradiation time increased rapidly from 4.4 min to 12.4 min as the IM level increased from 2 to 10. Both clinical cases suggested that an IM level of 5 offered a good compromise between the dose optimization quality and treatment irradiation time. We showed that a realistic photon source model is necessary for dose computation accuracy in the MLC-IM treatments.

Algorithms↗

Discrimination of interaural phase differences in the envelopes of sinusoidally amplitude-modulated 4-kHz tones as a function of modulation depth.

Psychometric functions were measured for the discrimination of the interaural phase difference (IPD) of the envelope of a sinusoidally amplitude-modulated (SAM) 4-kHz pure tone for modulation frequencies of 128 and 300 Hz and modulation depths (m) of 0.2, 0.6, 0.9, and 1.0. Contrary to recent modeling assumptions, it was found that a constant change in normalized interaural envelope correlation, with or without additional model stages to simulate peripheral auditory processing, did not produce a constant level of performance. Rather, in some cases, performance could range from chance to near perfect across modulation depths for a given change in normalized interaural envelope correlation. This was also true for the maximum change in normalized interaural envelope correlation computed across the cross-correlation functions for the stimuli to be discriminated. The change in the interaural time difference (ITD) computed from the IPD accounted for discriminability across modulation depths better than the change in normalized interaural envelope correlation, although ITD could not account for all the data, particularly those for lower values of m.

Acoustic Stimulation↗

Masking by modulated and unmodulated noise: effects of bandwidth, modulation rate, signal frequency, and masker level.

The threshold for a sinusoidal signal masked by a band of noise is often times lower when the masking noise is modulated than when it is unmodulated. The difference in masked thresholds is referred to as the modulated-unmodulated difference, or MUD. These present experiments examined the effects of masker bandwidth, masker rate, and masker level on the MUD at several different signal frequencies. The MUD generally increased with increasing masker bandwidth; for masker bandwidths wider than a critical band (or an equivalent rectangular bandwidth-ERB), the results may be influenced by across-channel processes underlying comodulation masking release. The MUD for an ERB masker (MUDERB) was influenced less by masker rate than was the MUD for a broadband (BB) masker (MUDBB). The MUDERB and especially the MUDBB increased significantly with increasing masker level when the modulated masker was modulated at a depth (m) of 1.0, but not when it was modulated at a depth of 0.75. These results have significant implications for extending the MUD paradigm to hearing-impaired subjects. Finally, the MUDERB and the MUDBB increased with increasing signal frequency. This effect for the ERB masker is largely (if not completely) due to the wider absolute bandwidths at higher frequencies. The effect with the BB masker may be influenced by differences in the magnitude of suppression across frequency.

Adult↗

The modulated-unmodulated difference: effects of signal frequency and masker modulation depth.

The masked threshold for a signal is often times lower when the masker is modulated than when it is unmodulated. The difference in masked thresholds is referred to as the modulated-unmodulated difference, or MUD. The purpose of the present study was to follow up on the results of a previous study [Bacon et al., J. Acoust. Soc. Am. 101, 1600-1610 (1997)] which showed that the MUD is larger for high than for low signal frequencies, both when the masker is no wider than a critical band (and the processing is solely within channel) and when it is broadband (and the processing may be both within and across channel). The present results indicate that the effects of signal frequency primarily exist only when the modulated masker is modulated at a depth greater than about 0.75, and that at these large depths, thresholds in the presence of the modulated masker are governed largely by forward masking. By far, the effect of signal frequency is larger with the broadband masker than with the critical-band masker, suggesting that there may be an across-channel process whose contribution is greater at high than at low signal frequencies. It is argued here that this across-channel process may be related to psychophysical suppression.

Adult↗

The effect of modulation rate on the detection of frequency modulation and mistuning of complex tones.

Experiment 1 measured frequency modulation detection thresholds (FMTs) for harmonic complex tones as a function of modulation rate. Six complexes were used, with fundamental frequencies (F0s) of either 88 or 250 Hz, bandpass filtered into a LOW (125-625 Hz), MID (1375-1875 Hz) or HIGH (3900-5400 Hz) frequency region. The FMTs were about an order of magnitude greater for the three complexes whose harmonics were unresolved by the peripheral auditory system (F0 = 88 Hz in the MID region and both F0s in the HIGH region) than for the other three complexes, which contained some resolved harmonics. Thresholds increased with increases in FM rate above 2 Hz for all conditions. The increase was larger when the F0 was 88 Hz than when it was 250 Hz, and was also larger in the LOW than in the MID and HIGH regions. Experiment 2 measured thresholds for detecting mistuning produced by modulating the F0s of two simultaneously presented complexes out of phase by 180 degrees. The size of the resulting mistuning oscillates at a rate equal to the rate of FM applied to the two carriers. At low FM rates, thresholds were lowest when the harmonics were either resolved for both complexes or unresolved for both complexes, and highest when resolvability differed across complexes. For pairs of complexes with resolved harmonics, mistuning thresholds increased dramatically as the FM rate was increased above 2-5 Hz, in a way which could not be accounted for by the effect of modulation rate on the FMTs for the individual complexes. A third experiment, in which listeners detected constant ("static") mistuning between pairs of frequency-modulated complexes, provided evidence that this deterioration was due the harmonics in one of the two "resolved" complexes becoming unresolved at high FM rates, when analyzed over some finite time window. It is concluded that the detection of time-varying mistuning between groups of harmonics is limited by factors that are not apparent in FM detection data.

Adult↗

An analysis of quasi-frequency-modulated noise and random-sideband noise as comparisons for amplitude-modulated noise.

Experiments were performed to determine under what conditions quasi-frequency-modulated (QFM) noise and random-sideband noise are suitable comparisons for AM noise in measuring a temporal modulation transfer function (TMTF). Thresholds were measured for discrimination of QFM from random-sideband noise and AM from QFM noise as a function of sideband separation. In the first experiment, the upper spectral edge of the noise stimuli was at 2400 Hz and the bandwidth was 1600 Hz. For sideband separations up to 256 Hz, at threshold sideband levels for discriminating AM from QFM noise, QFM was indiscriminable from random-sideband noise. For the largest sideband separation used (512 Hz), listeners may have used within-stimulus envelope correlation in the QFM noise to discriminate it from the random-sideband noise. Results when stimulus bandwidth was varied suggest that listeners were able to use this cue when the carrier was wider than a critical band, and the sideband separation approached the carrier bandwidth. Within-stimulus envelope correlation was also present in AM noise, and thus QFM noise was a suitable comparison because it made this cue unusable and forced listeners to use across-stimulus envelope differences. When the carrier bandwidth was less than a critical band or was wideband, QFM noise and random-sideband noise were equally suitable comparisons for AM noise. When discrimination thresholds for QFM and random-sideband noise were converted to modulation depth and modulation frequency, they were nearly identical to those for discrimination of AM from QFM noise, suggesting that listeners were using amplitude modulation cues in both cases.

Adult↗

Neuromuscular modulation in Aplysia. II. Modulation of the neuromuscular transform in behavior.

In this work we use mathematical modeling and complementary experiments to study the dynamics of modulation in the accessory radula closer (ARC) neuromuscular system of Aplysia. Here we join a dynamic model of the modulation from the preceding paper to a model of the basal neuromuscular transform (NMT). The resulting complete model of the NMT allows us to predict, test, and analyze the actual modulated contraction shapes in different types of feeding behavior, through entire quasi-realistic meals. The model reproduces a variety of published and new experimental observations. We find that components of the modulatory network act in interdependency and mutual complementarity, one or another playing a key role depending on the behavior and its past history. The history is remembered by slow dynamical components whose persistence prepares the system for future behavior of the same kind. The persistence becomes counterproductive, however, when the behavior suddenly changes. Superposition of fast dynamical components alleviates the problem under most, but not all, circumstances. In the quasi-realistic meals, the modulation improves functional performance on average, but degrades it after certain behavioral switches, when the model predicts sharp contraction transients. These are indeed seen in the real muscle. We propose that the real system does not switch the underlying motor neuron firing patterns abruptly, but relaxes them gradually, matching the relaxation of the peripheral modulatory state, through such behavioral transitions. We model food-induced arousal, a known phenomenon of this kind. The peripheral dynamics of the modulated NMT thus constrain the motor commands of the CNS.

Animals↗

The RsbRST stress module in bacteria: a signalling system that may interact with different output modules.

In the Gram-positive bacterium Bacillus subtilis, the activity of the alternative sigma factor sigma(B) is triggered upon exposure of the bacteria to environmental stress conditions or to nutrient limitation. sigma(B) activity is controlled by protein-phosphorylation-dependent interactions of anti-sigma with anti-anti-sigma factors. Under stress conditions, the phosphatase RsbU triggers release of sigma(B) and thus induces the expression of stress genes. RsbU activity is controlled by three proteins, RsbR, RsbS and RsbT which form a supramolecular complex called the stressosome. Here we review the occurrence of the genes encoding the stressosome proteins (called the RsbRST module) in a wide variety of bacteria. While this module is linked to the gene encoding sigma(B) and its direct regulators in B. subtilis and its close relatives, genes encoding two-component regulatory systems and more complex phosphorelays are clustered with the RsbRST module in bacteria as diverse as cyanobacteria, bacteroidetes, proteobacteria, and deinococci. The conservation of the RsbRST module and its clustering with different types of regulatory systems suggest that the stressosome proteins form a signal sensing and transduction unit that relays information to very different output modules.

Bacillus subtilis↗