Biomedical subjects

E R Lewis

Publications and source records attributed to E R Lewis.

At least 19 recordsLinked to original sources

PubMed2000

Enzyme-induced strain/distortion in the ground-state ES complex in beta-lactamase catalysis revealed by FTIR.

Class A beta-lactamases hydrolyze penicillins and other beta-lactams via an acyl-enzyme catalytic mechanism. Ser70 is the active site nucleophile. By constructing the S70A mutant, which is unable to form the acyl-enzyme intermediate, it was possible to make stable ES complexes with various substrates. The stability of such Michaelis complexes permitted acquisition of their infrared spectra. Comparison of the beta-lactam carbonyl stretch frequency (nu(CO)) in the free and enzyme-bound substrate revealed an average decrease of 13 cm(-)(1), indicating substantial strain/distortion of the lactam carbonyl when bound in the ES complex. Interestingly, regardless of the frequency of the C=O stretch in the free substrate, when complexed to Bacillus licheniformis beta-lactamase, the frequency was always 1755 +/- 2 cm(-)(1). This suggests the active site environment induces a similar conformation of the beta-lactam in all substrates when bound to the enzyme. Using deuterium substitution, it was shown that the "oxyanion hole", which involves hydrogen bonding to two backbone amides, is the major source of the enzyme-induced strain/distortion. The very weak catalytic activity of the S70A beta-lactamase suggests enzyme-facilitated hydrolysis due to substrate distortion on binding to the enzyme. Thus the binding of the substrate in the active site induces substantial strain and distortion that contribute significantly to the overall rate enhancement in beta-lactamase catalysis.

Bacillus↗

PubMed1999

Predicting the temporal responses of non-phase-locking bullfrog auditory units to complex acoustic waveforms.

Axons from the basilar papilla of the American bullfrog (Rana catesbeiana) do not phase lock to stimuli within an octave of their best frequencies. Nevertheless, they show consistent temporal patterns of instantaneous spike rate (as reflected in peristimulus time histograms) in response to repeated stimuli in that frequency range. We show that the second-order Wiener kernels for these axons, derived from the cross-correlation of continuous (non-repeating), broad-band noise stimulus with the spike train produced in response to that stimulus, can predict with considerable precision the temporal pattern of instantaneous spike rate in response to a novel, complex acoustic waveform (a repeated, 100-ms segment of noise, band-limited to cover the single octaves above and below best frequency). Furthermore, we show that most of this predictive power is retained when the second-order Wiener kernel is reduced to the highest-ranking pair of singular vectors derived from singular-value decomposition, that the retained pair of vectors corresponds to a single auditory filter followed by an envelope-detection process, and that the auditory filter itself predicts the characteristic frequency (CF) of the axon and the shape of the frequency-threshold tuning curve in the vicinity of CF.

Acoustic Stimulation↗

PubMed1999

Localization by interaural time difference (ITD): effects of interaural frequency mismatch.

A commonly accepted physiological model for lateralization of low-frequency sounds by interaural time delay (ITD) stipulates that binaural comparison neurons receive input from frequency-matched channels from each ear. Here, the effects of hypothetical interaural frequency mismatches on this model are reported. For this study, the cat's auditory system peripheral to the binaural comparison neurons was represented by a neurophysiologically derived model, and binaural comparison neurons were represented by cross-correlators. The results of the study indicate that, for binaural comparison neurons receiving input from one cochlear channel from each ear, interaural CF mismatches may serve to either augment or diminish the effective difference in ipsilateral and contralateral axonal time delays from the periphery to the binaural comparison neuron. The magnitude of this increase or decrease in the effective time delay difference can be up to 400 microseconds for CF mismatches of 0.2 octaves or less for binaural neurons with CFs between 250 Hz and 2.5 kHz. For binaural comparison neurons with nominal CFs near 500 Hz, the 25-microsecond effective time delay difference caused by a 0.012-octave CF mismatch is equal to the ITD previously shown to be behaviorally sufficient for the cat to lateralize a low-frequency sound source.

Animals↗

PubMed1998

A comparison of the linear tuning properties of two classes of axons in the bullfrog lagena.

Various vertebrate inner-ear end organs appear to have switched their sensory function between equilibrium sensing and acoustic sensing over the courses of various lines of evolution. It is possible that all that is required to make this transition is to provide an end organ with access to the appropriate stimulus mode and frequency range. If, as we believe, however, the adaptive advantage of an acoustic sensory system lies in its ability to sort the total acoustic input into components that correspond to individual acoustic sources, and the adaptive advantage of an equilibrium sensory system lies in its ability to compute the total orientation and motion of the head without regard to the individual sources contributing to that orientation and motion, then it is easy to argue that the differences between acoustic and equilibrium sensors should be more profound than simply access to the appropriate stimuli. Effective signal-sorting requires high resolution in both time and frequency; to achieve this resolution, a peripheral tuning structure must be one of high dynamic order (i.e., constructed from multiple independent energy storage elements). If the peripheral tuning structure simply converts head acceleration to head displacement, velocity, or jerk (i.e., provides one or two steps of integration or differentiation with respect to time, where one energy storage element per step is required), then high dynamic order is inappropriate. Because the bullfrog lagena possesses both acoustic and equilibrium sensitive regions, it is especially suited for comparing these two sensor types and addressing the question of dynamic order of tuning. In this paper we report observations of the linear tuning properties of bullfrog lagenar primary afferent nerve fibers obtained by stimulating the lagena with random, dorsoventral micromotion over the frequency range from 10 Hz to 1.0 kHz. Tuning curves obtained by reverse correlation analysis and discrete Fourier transformation were used to estimate the dynamic order of each fiber's associated peripheral tuning structure. We found two classes of lagenar afferent axons--those with lowpass amplitude tuning characteristics (44 units) and those with bandpass amplitude tuning characteristics (73 units). Lowpass units were found to originate at the equilibrium region of the macula, and they exhibited low dynamic order--summed low- and high-frequency slopes (absolute values) ranged from 10 dB/decade to 64 dB/decade, implying dynamic orders of less than one to three (the modal value was equal to one). Bandpass units were found to originate at the acoustic region of the macula, and they exhibited higher dynamic order than lowpass units--summed low- and high-frequency slopes (absolute values) ranged from 53 dB/decade to 185 dB/decade, implying dynamic orders of three to nine (the modal value was equal to five). It appears that while lagenar equilibrium and acoustic sensors both possess access to signals in the acoustic frequency range, lagenar acoustic sensors are tuned by means of peripheral structures with markedly greater dynamic order and consequently markedly greater physical complexity. These results suggest that steep-sloped (high-dynamic-order) tuning properties reflect special adaptations in acoustic sensors not found in equilibrium sensors, and that any evolutionary transition between the two sensor types must have involved profound structural changes.

Acoustic Maculae↗

PubMed1997

A point mutation leads to altered product specificity in beta-lactamase catalysis.

beta-Lactamases are the primary cause of beta-lactam antibiotic resistance in many pathogenic organisms. The beta-lactamase catalytic mechanism has been shown to involve a covalent acyl-enzyme. Examination of the structure of the class A beta-lactamase from Bacillus licheniformis suggested that replacement of Asn-170 by leucine would disrupt the deacylation reaction by displacing the hydrolytic water molecule. When N170L beta-lactamase was reacted with penicillins, a novel product was formed. We postulate that with leucine at position 170 the acyl-enzyme undergoes deacylation by an intramolecular rearrangement (rather than hydrolysis) to form a thiazolidine-oxazolinone as the initial product. The oxazolinone subsequently undergoes rapid breakdown leading to the formation of N-phenylacetylglycine and N-formylpenicillamine. This appears to be the first reported case where a point mutation leads to a change in enzyme mechanism resulting in a substantially altered product, effectively changing the product specificity of beta-lactamase into that of D-Ala-D-Ala-carboxypeptidase interacting with benzylpenicillin.

Asparagine↗

PubMed1997

Seismic communication between the burrows of kangaroo rats, Dipodomys spectabilis.

Banner-tailed kangaroo rats, Dipodomys spectabilis, footdrum to produce substrate-borne and airborne acoustic energy. Previous studies show that they communicate territorial ownership via airborne footdrumming signals. The research reported here used simulated footdrum patterns generated by an artificial 'thumper' to address the question of whether kangaroo rats communicate through seismic components of these acoustic signals. With microphones suspended in sealed burrows, we found that airborne sounds were attenuated by approximately 40 dB as they passed through the burrow wall into the burrow chamber. The substrate-borne vibrations from the thumper yielded sound approximately 40 dB greater in peak amplitude than the attenuated airborne sound. Thus, 99.9% of the peak power of the thumper was transmitted directly through the substrate into the burrow. The rats in sealed burrows timed their responses to playbacks of footdrums from the thumper and a loudspeaker so they did not initiate a drumming sequence during either the seismic or airborne signals. When these signals were masked by loud noise, the rats continued to drum to the seismic signal but drummed randomly during the airborne playback. These results suggest that the sealed burrow provides a quiet place in which D. spectabilis can listen for substrate-borne communications from conspecifics.

Acoustic Stimulation↗

PubMed1997

Multi-unit recording from regenerated bullfrog eighth nerve using implantable silicon-substrate microelectrodes.

Multi-microelectrode silicon devices were developed for extracellular recording from multiple axons in regenerated eighth cranial nerves of American bullfrogs. Each includes a photolithographically defined array of holes and adjacent metal microelectrodes. A device is implanted within a transected eighth nerve; regenerating fibers grow through the holes en route to the brainstem. Multiple spike trains were recorded from two animals at up to 21 weeks after implantation. Single units were tracked for over 8 h. Some responded to sound with tuning typical of fibers innervating the amphibian and basilar papillae. Units of vestibular origin also were recorded. Action potentials were 30-140 microV P-P amid noise of 5 10 microV RMS, an adequate signal-to-noise ratio for spike detection and sorting. Histology confirmed that bundles of myelinated fibers grew through holes near electrodes that recorded activity. The implantation success rate was low, due to surgical morbidity, device extrusion, and lack of nerve regeneration through some devices. Future designs will address these issues and incorporate transistor amplifiers on devices to increase signal-to-noise ratios. The potential of implanted silicon devices to simultaneously record from many axons offers an opportunity for multicellular studies of auditor, vestibular and seismic signal processing in the vertebrate inner ear.

Acoustic Stimulation↗

PubMed1997

The use of seismic signals by fossorial southern African mammals: a neuroethological gold mine.

Behavioral adaptations exhibited by two African fossorial mammals for the reception of vibrational signals are discussed. The Namib Desert golden mole (Eremitalpa granti namibensis) is a functionally blind, nocturnal insectivore in the family Chrysochloridae that surface forages nightly in the Namib desert. Both geophone and microphone recordings in the substrate suggest that the golden mole is able to detect termite colonies and other prey items solely using seismic cues. This animal exhibits a hypertrophied malleus, an adaptation favoring detection of low-frequency signals. In a field study of the Cape mole-rat (Georychus capensis), a subterranean rodent in the family Bathyergidae, both seismic and auditory signals were tested for their propagation characteristics. This solitary animal is entirely fossorial and apparently communicates with its conspecifics by drumming its hind legs on the burrow floor. Auditory signals attenuate rapidly in the substrate, whereas vibratory signals generated in one burrow are easily detectable in neighboring burrows. The sensitivity to substrate vibrations in two orders of burrowing mammals suggests that this sense is likely to be widespread within this taxon and may serve as a neuroethological model for understanding the evolution of vibrational communication. Neuroethological implications of these findings are discussed.

Animal Communication↗

PubMed1995

Network thermodynamics revisited.

Modeling provides a bridge between the natural sciences (physics, chemistry, biology, and the like) and the axiomatic sciences (mathematics and statistics). Inductively-derived descriptive models map observations of physical processes into mathematical descriptions that can be treated as axioms (e.g., the various laws of physics). A synthetic model combines descriptive models of several physical processes with a structural model (representing the interactions of those processes) for the purpose of deducing or predicting the consequences of interactions. When applied together with elementary thermodynamic principles, circuit theory provides an excellent framework for synthetic modeling.

Electronics↗

PubMed1995

Temperature-dependence of saccular nerve fiber response in the North American bullfrog.

A clinical microwave device was used to heat the head and ear of the North American bullfrog in order to observe the temperature dependence of tuning in the sacculus, an organ known to possess the capability of electrical resonance in its hair cells. In tuning curves derived from reverse correlation analysis with noise stimuli, the temperature dependencies of the frequencies of tuning peaks and notches typically exhibited Q10s less than 1.1; whereas the frequencies of electrical resonances are expected to have Q10s of the order of 1.7. Therefore we conclude that electrical resonances are not significantly involved in tuning in the bullfrog sacculus.

Acoustic Stimulation↗

PubMed1995

Nonlinear effects of noise on phase-locked cochlear-nerve responses to sinusoidal stimuli.

It is well known that, in a cochlear afferent axon with background spike activity, a sinusoidal stimulus (tone) of sufficiently low frequency will produce periodic modulation of the instantaneous spike rate, the alternating half cycles of which comprise excursions above and below the mean background spike rate. It also is known that if the amplitude of the stimulus is sufficiently small, the instantaneous spike rate follows very nearly a sinusoidal trajectory through these positive and negative excursions. For such cases, we define the AC responsiveness of a primary auditory afferent axon to be the amplitude of sinusoidal modulation of the instantaneous spike rate divided by the amplitude of the tone producing that modulation. In the experiments described in this paper, changes in AC responsiveness were followed during and after sudden changes in the background noise level. When the amplitude of the tone was sufficiently small relative to that of the noise, we found that the AC responsiveness can be strongly dependent on the time elapsed since the last change in noise level, while being nearly independent of the amplitude of the tone itself. Under those circumstances, after transitions between noise levels 20 dB apart, we observed changes in AC responsiveness that consistently followed time courses similar to those of the short-term mean (background) spike rate (approximating the adapting response to the noise alone), unfolding over several milliseconds or tens of milliseconds. At the time of the transition between noise levels, there was another change in AC responsiveness, which appeared to be instantaneous; as the noise level increased, the AC responsiveness immediately increased with it. This seemingly paradoxical effect and the similarity of the time courses of AC responsiveness and short-term mean spike rate both are consistent with a simple, descriptive model of spike generation involving the shifting of threshold along a bell curve.

Acoustic Stimulation↗

PubMed1994

Site-directed mutagenesis of glutamate-166 in beta-lactamase leads to a branched path mechanism.

Glutamate-166 of the Bacillus licheniformis beta-lactamase was specifically mutated to aspartate and cysteine in order to probe the function of this residue in catalysis. In both cases, a large decrease in activity (kcat/Km was 3.5 x 10(-5) smaller for E166C and 1 x 10(-3) smaller for E166D than for the wild-type) was observed, although the kinetics for the two mutants were very different. The pH-rate profiles for E166D and E166C reflected the ionization characteristics of the new residue at site 166. This result indicates that the ionization of Glu-166 is responsible for the acidic limb of the kcat/Km-pH profiles, and suggests that the function of Glu-166 is that of a general base catalyst. The kinetics of the E166C mutant were investigated in detail. An initial burst was observed, whose amplitude was stoichiometric with the enzyme concentration, suggesting rate-limiting deacylation of the acyl-enzyme intermediate. However, further study revealed that in the presence of 0.5 M sodium sulfate, which stabilizes the native conformational state, the magnitude of the burst corresponded to 2 equiv of enzyme. This observation, in conjunction with the limited effect of the mutation on Km, indicated that the mutation resulted in a change in the kinetic mechanism from the linear, acyl-enzyme pathway to one with a branch leading to an inactive form of the acyl-enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)

Acylation↗

PubMed1994

Dynamic changes in tuning in the gerbil cochlea.

Afferent axons of the gerbil cochlear nerve were studied with reverse correlation analyses carried out with movable time windows and with noise that was modulated with a 10-Hz trapezoidal envelope that switched the noise amplitude between two levels, 20 dB apart. At the time of switching, the attributes of the axonal tuning curves derived in this manner switched very rapidly (e.g., within 10 ms) from those characteristic of lower-level stimuli to those characteristic of higher-level stimuli and vice versa. As previous investigators have shown, the attributes of tuning curves at higher levels include broader bandwidth and an accentuated low-frequency hump. Characteristic frequencies (CFs) of gerbil axons used in this study ranged from approximately 500 Hz to approximately 5 kHz. Over this range, the low-frequency hump was most pronounced in our studies for units with higher CFs, each of which showed a sharp high-frequency peak and a distinctly separate, broad low-frequency hump (reminiscent of the tip and tail of a conventional frequency-threshold tuning curve). The amplitude of the peak relative to that of the hump, and the breadth of the peak, both changed rapidly and reversibly following sudden change of noise level. Observation of such rapid changes of tuning would be difficult to achieve with conventional frequency-threshold tuning curves, derived from tonal stimuli.

Acoustic Stimulation↗

PubMed1994

Silicon-substrate microelectrode arrays for parallel recording of neural activity in peripheral and cranial nerves.

A new process for the fabrication of regeneration microelectrode arrays for peripheral and cranial nerve applications is presented. This type of array is implanted between the severed ends of nerves, the axons of which regenerate through via holes in the silicon and are thereafter held fixed with respect to the microelectrodes. The process described is designed for compatibility with industry-standard CMOS or BiCMOS processes (it does not involve high-temperature process steps nor heavily-doped etch-stop layers), and provides a thin membrane for the via holes, surrounded by a thick silicon supporting rim. Many basic questions remain regarding the optimum via hole and microelectrode geometries in terms of both biological and electrical performance of the implants, and therefore passive versions were fabricated as tools for addressing these issues in on-going work. Versions of the devices were implanted in the rat peroneal nerve and in the frog auditory nerve. In both cases, regeneration was verified histologically and it was observed that the regenerated nerves had reorganized into microfascicles containing both myelinated and unmyelinated axons and corresponding to the grid pattern of the via holes. These microelectrode arrays were shown to allow the recording of action potential signals in both the peripheral and cranial nerve setting, from several microelectrodes in parallel.

Action Potentials↗

PubMed1992

Seismic signal transmission between burrows of the Cape mole-rat, Georychus capensis.

Both seismic and auditory signals were tested for their propagation characteristics in a field study of the Cape mole-rat (Georychus capensis), a subterranean rodent in the family Bathyergidae. This solitary animal is entirely fossorial and apparently communicates with its conspecifics by alternately drumming its hind legs on the burrow floor. Signal production in this species is sexually dimorphic, and mate attraction is likely mediated primarily by seismic signalling between individuals in neighboring burrows. Measurements within, and at various distances away from, natural burrows suggest that seismic signals propagate at least an order of magnitude better than auditory signals. Moreover, using a mechanical thumper which could be triggered from a tape recording of the mole-rat's seismic signals, we established that the vertically-polarized surface wave (Rayleigh wave) propagates with less attenuation than either of the two horizontally-polarized waves. Thus, we tentatively hypothesize that Rayleigh waves subserve intraspecific communication in this species.

Acoustic Stimulation↗

PubMed1992

Diversity of form in the amphibian papilla of Puerto Rican frogs.

In modern frogs, the amphibian papilla exhibits a caudal extension whose shape, relative length, and proportion of hair cells vary markedly from species to species. Tuning in the caudal extension is organized tonotopically and evidently involves the tectorium. In terms of the proportion of amphibian-papillar hair cells in the caudal extension, we report more diversity among 8 species of a single genus (Eleutherodactylus) on a single island (Puerto Rico) than has been found so far among all of the (more than 50) other modern anurans examined for this feature from around the world. These 8 Puerto Rican species have overlapping habitat and conspicuous diversity in the male advertisement call. For 7 of the 8 species, we report that the call has transient spectral components in the frequency range of the amphibian papilla, and that the proportion of caudal extension hair cells and the frequency distribution of those components are correlated. Thus one might conclude that the selective pressures that led to diversity of calls among the 8 species also led to diversity in form of the amphibian papilla.

Acoustic Stimulation↗

PubMed1992

One-tone suppression in the cochlear nerve of the gerbil.

One-tone rate suppression has been reported several times for auditory nerve fibers of mammalian and non-mammalian vertebrates. Because its properties are very similar to those of two-tone rate suppression, the possibility exists that one-tone rate suppression is the result of an interaction within the inner ear of the suppressing tonal stimulus and some ongoing extraneous acoustic stimulus. For this reason, reports of one-tone rate suppression often elicit suspicions that the investigators were not sufficiently careful in controlling leaks in their acoustic barriers or in the electrical pathways to their acoustic drivers. Recent reports of one-tone rate suppression in pigeon basilar-papillar fibers and goldfish saccular fibers were accompanied by descriptions of measures taken to avoid such leaks. In this paper, we describe one-tone rate suppression in a mammal, the Mongolian gerbil; and we demonstrate that the background spike activity being suppressed is not driven by either external sounds coming from outside the acoustic isolation test chamber or by non-stimulus electrical inputs to the acoustic driver. The suppressed background spike activity evidently arises from sources within the animal. These sources may be non-acoustic, associated with spontaneous pre- or post-synaptic ion-channel activity; or they may be acoustic sources--internal sound or vibration generators.

Acoustic Stimulation↗

PubMed1992

Modulation of cochlear nerve spike rate by cardiac activity in the gerbil.

Among primary auditory axons with characteristic frequencies (CFs) below 2500 Hz, a substantial subpopulation was found in which spike activity was driven by cardiac events. The presence of cardiac-driven activity was inferred from cycle histograms triggered on the peak of the electrocardiogram (ECG). This driven activity was either like a simple onset response (often followed by a reduction of spike activity to below background level), or as a longer lasting series of peaks and troughs. In two axons with high CFs (7 kHz and 12.5 kHz), cardiac-driven suppression was observed. Recordings made by a probe microphone revealed the presence of heart-related sound in the external ear canal. The onset of that sound coincided with the onset of cardiac-driven spike activity (and suppression).

Action Potentials↗