Biomedical subjects

T T Takahashi

Publications and source records attributed to T T Takahashi.

At least 19 recordsLinked to original sources

PubMed2003

The synthesis and use of the owl's auditory space map.

The barn owl ( Tyto alba) is capable of capturing prey by passive hearing alone, guided by a topographic map of auditory space in the external nucleus of its inferior colliculus. The neurons of this auditory space map have discrete spatial receptive fields that result from the computation of interaural differences in the level (ILD) and time-of-arrival (ITD) of sounds. Below we review the synthesis of the spatial receptive fields from the frequency-specific ITDs and ILDs to which the neurons are tuned, concentrating on recent studies exploiting virtual auditory space techniques to analyze the contribution of ILD. We then compared the owl's spatial discrimination, assessed behaviorally, with that of its space map neurons. Spatial discrimination was assessed using a novel paradigm involving the pupillary dilation response (PDR), and neuronal acuity was assessed by measuring the changes in firing rate resulting from changes in source location, scaled to the variance. This signal-detection-based approach revealed that the change in the position of the neural image on this map best explains the spatial discrimination measured using the PDR. We compare this result to recent studies in mammalian systems.

Animals↗

PubMed2001

Large libraries reveal diverse solutions to an RNA recognition problem.

RNA loops that adopt a characteristic GNRA "tetraloop" fold are common in natural RNAs. Here, we have used in vitro selection by means of mRNA-peptide fusions to select peptides that bind an example of this RNA loop motif. Starting with the RNA recognition domain from the lambda N protein, we have constructed libraries containing 150, 1,600, and 9 trillion different peptide sequences as mRNA-peptide fusions and isolated those capable of high-affinity RNA binding. These selections have resulted in more than 80 different peptides that bind the same RNA loop. The highest affinity peptides exhibit low nanomolar dissociation constants as well as the ability to discriminate RNA hairpins differing by a single loop nucleotide. Thus, our work demonstrates that numerous, chemically distinct solutions exist for a particular RNA recognition problem.

Amino Acid Sequence↗

PubMed2001

Selection of RNA-binding peptides using mRNA-peptide fusions.

We have been working to apply in vitro selection to isolate novel RNA-binding peptides. To do this, we use mRNA-protein fusions, peptides covalently attached to their own mRNA. Here, we report selection protocols developed using the arginine-rich domain of bacteriophage lambda-N protein and its binding target, the boxB RNA. Systematic investigation of possible paths for a selection round has allowed us to design a reliable and efficient protocol to enrich RNA-binding peptides from nonfunctional members of a complex mixture. The protocols we have developed should greatly facilitate the isolation of new molecules using the fusion system.

DNA, Complementary↗

PubMed2000

Engineered metal binding sites on green fluorescence protein.

The ability to assay a variety of metals by noninvasive methods has applications in both biomedical and environmental research. Green fluorescent protein (GFP) is a protein isolated from coelenterates that exhibits spontaneous fluorescence. GFP does not require any exogenous cofactors for fluorescence, and can be easily appended to other proteins at the DNA level, producing a fluorescence-labeled target protein in vivo. Metals in close proximity to chromophores are known to quench fluorescence in a distance-dependent fashion. Potential metal binding sites on the surface of GFP have been identified and mutant proteins have been designed, created, and characterized. These metal-binding mutants of GFP exhibit fluorescence quenching at lower transition metal ion concentrations than those of the wild-type protein. These GFP mutants represent a new class of protein-based metal sensors.

Binding Sites↗

PubMed2000

Pupillary dilation response as an indicator of auditory discrimination in the barn owl.

The pupil of an awake, untrained, head-restrained barn owl was found to dilate in response to sounds with a latency of about 25 ms. The magnitude of the dilation scaled with signal-to-noise ratio. The dilation response habituated when a sound was repeated, but recovered when stimulus frequency or location was changed. The magnitude of the recovered response was related to the degree to which habituating and novel stimuli differed and was therefore exploited to measure frequency and spatial discrimination. Frequency discrimination was examined by habituating the response to a reference tone at 3 kHz or 6 kHz and determining the minimum change in frequency required to induce recovery. We observed frequency discrimination of 125 Hz at 3 kHz and 250 Hz at 6 kHz--values comparable to those reported by others using an operant task. Spatial discrimination was assessed by habituating the response to a stimulus from one location and determining the minimum horizontal speaker separation required for recovery. This yielded the first measure of the minimum audible angle in the barn owl: 3 degrees for broadband noise and 4.5 degrees for narrowband noise. The acoustically evoked pupillary dilation is thus a promising indicator of auditory discrimination requiring neither training nor aversive stimuli.

Acoustic Stimulation↗

PubMed2000

Head-related transfer functions of the Rhesus monkey.

Head-related transfer functions (HRTFs) are direction-specific acoustic filters formed by the head, the pinnae and the ear canals. They can be used to assess acoustical cues available for sound localization and to construct virtual auditory environments. We measured the HRTFs of three anesthetized Rhesus monkeys (Macaca mulatta) from 591 locations in the frontal hemisphere ranging from -90 degrees (left) to 90 degrees (right) in azimuth and -60 degrees (down) to 90 degrees (up) in elevation for frequencies between 0.5 and 15 kHz. Acoustic validation of the HRTFs shows good agreement between free field and virtual sound sources. Monaural spectra exhibit deep notches at frequencies above 9 kHz, providing putative cues for elevation discrimination. Interaural level differences (ILDs) and interaural time differences (ITDs) generally vary monotonically with azimuth between 0.5 and 8 kHz, suggesting that these two cues can be used to discriminate azimuthal position. Comparison with published subsets of HRTFs from squirrel monkeys (Saimiri sciureus) shows good agreement. Comparison with published human HRTFs from the frontal hemisphere demonstrates overall similarity in the patterns of ILD and ITD, suggesting that the Rhesus monkey is a good acoustic model for these two sound localization cues in humans. Finally, the measured ITDs in the horizontal plane agree well between -40 degrees and 40 degrees in azimuth with those calculated from a spherical head model with a radius of 52 mm, one-half the interaural distance of the monkey.

Animals↗

PubMed2000

Representation of temporal features of complex sounds by the discharge patterns of neurons in the owl's inferior colliculus.

The spiking pattern evoked in cells of the owl's inferior colliculus by repeated presentation of the same broadband noise was found to be highly reproducible and synchronized with the temporal features of the noise stimulus. The pattern remained largely unchanged when the stimulus was presented from spatial loci that evoke similar average firing rates. To better understand this patterning, we computed the pre-event stimulus ensemble (PESE)-the average of the stimuli that preceded each spike. Computing the PESE by averaging the pressure waveforms produced a noisy, featureless trace, suggesting that the patterning was not synchronized to a particular waveform in the fine structure. By contrast, computing the PESE by averaging the stimulus envelope revealed an average envelope waveform, the "PESE envelope," typically having a peak preceded by a trough. Increasing the overall stimulus level produced PESE envelopes with higher amplitudes, suggesting a decrease in the jitter of the cell's response. The effect of carrier frequency on the PESE envelope was investigated by obtaining a cell's response to broadband noise and either estimating the PESE envelope for each spectral band or by computing a spectrogram of the stimulus prior to each spike. Either method yielded the cell's PESE spectrogram, a plot of the average amplitude of each carrier-frequency component at various pre-spike times. PESE spectrograms revealed surfaces with peaks and troughs at certain frequencies and pre-spike times. These features are collectively called the spectrotemporal receptive field (STRF). The shape of the STRF showed that in many cases, the carrier frequency can affect the PESE envelope. The modulation transfer function (MTF), which describes a cell's ability to respond to time-varying amplitudes, was estimated with sinusoidally amplitude-modulated (SAM) noises. Comparison of the PESE envelope with the MTF in the time and frequency domains showed that the two were closely matched, suggesting that a cell's response to SAM stimuli is largely predictable from its response to a noise-modulated carrier. The STRF is considered to be a model of the linear component of a system's response to dynamic stimuli. Using the STRF, we estimated the degree to which we could predict a cell's response to an arbitrary broadband noise by comparing the convolution of the STRF and the envelope of the noise with the cell's post-stimulus time histogram to the same noise. The STRF explained 18-46% of the variance of a cell's response to broadband noise.

Acoustic Stimulation↗

PubMed1998

Head-related transfer functions of the barn owl: measurement and neural responses.

Sounds arriving at the eardrum are filtered by the external ear and associated structures in a frequency and direction specific manner. When convolved with the appropriate filters and presented to human listeners through headphones, broadband noises can be precisely localized to the corresponding position outside of the head (reviewed in Blauert, 1997). Such a 'virtual auditory space' can be a potentially powerful tool for neurophysiological and behavioral work in other species as well. We are developing a virtual auditory space for the barn owl, Tyto alba, a highly successful auditory predator that has become a well-established model for hearing research. We recorded catalogues of head-related transfer functions (HRTFs) from the frontal hemisphere of 12 barn owls and compared virtual and free sound fields acoustically and by their evoked neuronal responses. The inner ca. 1 cm of the ear canal was found to contribute little to the directionality of the HRTFs. HRTFs were recorded by inserting probetube microphones to within about 1 or 2 mm of the eardrum. We recorded HRTFs at frequencies between 2 and 11 kHz, which includes the frequencies most useful to the owl for sound localization (3-9 kHz; Konishi, 1973). Spectra of virtual sounds were within +/- 1 dB of amplitude and +/- 10 degrees of phase of the spectra of free field sounds measured near to the eardrum. The spatial pattern of responses obtained from neurons in the inferior colliculus were almost indistinguishable in response to virtual and to free field stimulation.

Acoustic Stimulation↗

PubMed1997

Global air-sea flux of CO2: an estimate based on measurements of sea-air pCO2 difference.

Approximately 250,000 measurements made for the pCO2 difference between surface water and the marine atmosphere, DeltapCO2, have been assembled for the global oceans. Observations made in the equatorial Pacific during El Nino events have been excluded from the data set. These observations are mapped on the global 4 degrees x 5 degrees grid for a single virtual calendar year (chosen arbitrarily to be 1990) representing a non-El Nino year. Monthly global distributions of DeltapCO2 have been constructed using an interpolation method based on a lateral advection-diffusion transport equation. The net flux of CO2 across the sea surface has been computed using DeltapCO2 distributions and CO2 gas transfer coefficients across sea surface. The annual net uptake flux of CO2 by the global oceans thus estimated ranges from 0.60 to 1.34 Gt-Cyr-1 depending on different formulations used for wind speed dependence on the gas transfer coefficient. These estimates are subject to an error of up to 75% resulting from the numerical interpolation method used to estimate the distribution of DeltapCO2 over the global oceans. Temperate and polar oceans of the both hemispheres are the major sinks for atmospheric CO2, whereas the equatorial oceans are the major sources for CO2. The Atlantic Ocean is the most important CO2 sink, providing about 60% of the global ocean uptake, while the Pacific Ocean is neutral because of its equatorial source flux being balanced by the sink flux of the temperate oceans. The Indian and Southern Oceans take up about 20% each.

Journal Article↗

PubMed1996

Binaural cross-correlation predicts the responses of neurons in the owl's auditory space map under conditions simulating summing localization.

Summing localization describes the perceptions of human listeners to two identical sounds from different locations presented with delays of 0-1 msec. Usually a single source is perceived to be located between the two actual source locations, biased toward the earlier source. We studied neuronal responses within the space map of the barn owl to sounds presented with this same paradigm. The owl's primary cue for localization along the azimuth, interaural time difference (ITD), is based on a cross-correlation-like treatment of the signals arriving at each ear. The output of this cross-correlation is displayed as neural activity across the auditory space map in the external nucleus of the owl's inferior colliculus. Because the ear input signals reflect the physical summing of the signals generated by each speaker, we first recorded the sounds at each ear and computed their cross-correlations at various interstimulus delays. The resulting binaural cross-correlation surface strongly resembles the pattern of activity across the space map inferred from recordings of single space-specific neurons. Four peaks are observed in the cross-correlation surface for any nonzero delay. One peak occurs at the correlation delay equal to the ITD of each speaker. Two additional peaks reflect "phantom sources" occurring at correlation delays that match the signal of the left speaker in one ear with the signal of the right speaker in the other ear. At zero delay, the two phantom peaks coincide. The surface features are complicated further by the interactions of the various correlation peaks.

Animals↗

PubMed1996

Responses to simulated echoes by neurons in the barn owl's auditory space map.

The natural acoustical environment contains many reflective surfaces that give rise to echoes, complicating the task of sound localization and identification. The barn owl (Tyto alba), as a nocturnal predator, relies heavily on its auditory system for tracking and capturing prey in this highly echoic environment. The external nucleus of the owl's inferior colliculus (ICx) contains a retina-like map of space composed of "space-specific" auditory neurons that have spatially limited receptive fields. We recorded extracellularly from individual space-specific neurons in an attempt to understand the pattern of activity across the ICx in response to a brief direct sound and a simulated echo. Space-specific neurons responded strongly to the direct sound, but their response to a simulated echo was suppressed, typically, if the echo arrived within 5 ms or less of the direct sound. Thus we expect there to be little or no representation within the ICx of echoes arriving within such short delays. Behavioral tests using the owl's natural tendency to turn their head toward a sound source suggested that owls, like their space-specific neurons, similarly localize only the first of two brief sounds. Naive, untrained owls were presented with a pair of sounds in rapid succession from two horizontally-separated speakers. With interstimulus delays of less than 10 ms, the owl consistently turned its head toward the leading speaker. Longer delays elicited head turns to either speaker with approximately equal frequency and in some cases to both speakers sequentially.

Acoustic Stimulation↗

PubMed1995

An anatomical substrate for the inhibitory gradient in the VLVp of the owl.

The interaural difference in the level of sounds is an important cue for the localization of the sound's source. In the barn owl, a keen auditory predator, this binaural cue is first computed in the nucleus ventralis lemnisci laterale, pars posterior (VLVp), a cell group found within the fibers of the lateral lemniscus. Its neurons are excited by inputs from the contralateral ear and inhibited by inputs to the ipsilateral ear and are therefore sensitive indicators of interaural level difference. The excitation arrives by a direct input from the contralateral nucleus angularis, a cochlear nucleus, and the inhibition is mediated by a commissural projection that interconnects the VLVps of the two sides. The dorsally located neurons in the VLVp are more heavily inhibited than those found more ventrally, thus giving rise to a gradient of inhibition. This inhibitory gradient plays a central role in recent models of VLVp function. We present evidence based on standard anterograde tracing methods that this gradient of inhibition is mediated by a dorsoventral gradient in the density of synaptic inputs from the contralateral VLVp, the source of inhibition. Specifically, injection of tracers into one VLVp, regardless of the position of the injection within the nucleus, produced a vertically oriented field of label that was densest along the dorsal margin of the contralateral VLVp and became sparser a more ventral levels. Furthermore, we found that injections into the medial and lateral aspects of the nucleus produced this dorsoventrally graded field of label along the medial and lateral aspects of the contralateral VLVp, respectively. Finally, we confirmed an earlier observation suggesting that the anterior and posterior aspects of one VLVp project to the anterior and posterior aspects of the contralateral nucleus, respectively.

Animals↗

PubMed1994

Immunohistochemical localization of thyrotropin-releasing hormone in the brain of chinook salmon (Oncorhynchus tshawytscha).

This report describes the distribution of thyrotropin-releasing hormone (TRH) immunoreactivity in the brain of juvenile chinook salmon. TRH-positive cell bodies are observed in the preoptic region of the diencephalon, in the supracommissural nucleus of the ventral telencephalon, and in the internal cellular layer of the olfactory bulb. Immunoreactive fibers occur in the olfactory bulb, the dorsal and ventral telencephalon and were particularly extensive in hypothalamic regions. TRH-positive fibers also are observed in the optic tectum, posterior pituitary and the brainstem. The cell bodies in the preoptic area reside in the magnocellular preoptic nucleus. The position of these cell bodies along with the location of fibers in the hypothalamus and pituitary is consistent with the role of TRH as a hypothalamic releasing hormone. TRH-positive cell bodies also occur in the supracommissural nucleus of the ventral telencephalon and in the internal cellular layer of the olfactory bulb. The cell bodies in the olfactory bulb may account for some of the fibers in the telencephalon, as there are TRH fibers in the olfactory tracts. The presence of TRH-positive fibers with bouton-like swellings raise the possibility that the TRH peptide may act as a central neurotransmitter of neuromodulator. The results of this study suggest that TRH functions as a modulator of the pituitary activity in salmonids and that TRH is used as a transmitter or modulator in the olfactory system. The presence of TRH-positive somata in the olfactory bulb and ventral telencephalon provides new insights into the comparative anatomy of the salmon telencephalon.

Animals↗

PubMed1994

Representation of multiple sound sources in the owl's auditory space map.

The barn owl's inferior colliculus contains a retina-like map of space on which a sound generates a focus of activity whose position corresponds to the location of the sound source. When there is more than one source of sound, the sound waves sum and may generate spurious binaural cues that degrade the auditory image. We investigated the signal conditions under which neurons in the owl's auditory space map are able to resolve two simultaneously active sound sources. We recorded from space map neurons responding to sounds from a pair of speakers separated in azimuth by 45 degrees and mounted on a rotatable arm. Stimuli consisted of a sum of sinusoids or pseudorandom noise bursts emitted simultaneously and at equal overall levels. The characteristics of the sounds in each speaker were varied, and the neuron's response was plotted as a function of the speaker pair's position. When the speakers emitted different sets of summed sinusoids, the cells responded to each speaker separately; that is, the cells were able to resolve two separate targets. However, when the speakers emitted identical summed sinusoids generating binaural cues that were identical to those of a single phantom source between the two speakers, the neurons responded when the speakers were on either side of their receptive fields. By manipulating the amplitude at which each speaker emitted the various frequencies, we could control the position, number, and size of the phantom sources detected by the cell. The cells also resolved two separate sources when they emitted noise bursts that were statistically independent or temporally reversed versions of one another. Since the overall spectra of such waveforms are identical, we suggest that the space map relies on differences between noise bursts that exist over brief time spans.

Animals↗

PubMed1992

Commissural connections mediate inhibition for the computation of interaural level difference in the barn owl.

In the barn owl (Tyto alba), the posterior nucleus of the ventral lateral lemniscus (VLVp) is the first site of binaural convergence in the pathway that processes interaural level difference (ILD), an important sound-localization cue. The neurons of VLVp are sensitive to ILD because of an excitatory input from the contralateral ear and an inhibitory input from the ipsilateral ear. A previously described projection from the contralateral cochlear nucleus, can account for the excitation. The present study addresses the source of the inhibitory input. We demonstrate with standard axonal transport methods that the left and right VLVps are interconnected via fibers of the commissure of Probst. We further show that the anesthetization of one VLVp renders ineffective the inhibition that is normally evoked by stimulation of the ipsilateral ear. Thus, one cochlear nucleus (driven by the ipsilateral ear) appears to provide inhibition to the ipsilateral VLVp by exciting commissurally-projecting inhibitory neurons in the contralateral VLVp.

Animals↗

PubMed1992

Simulated motion enhances neuronal selectivity for a sound localization cue in background noise.

In nature, sound sources move and signals are accompanied by background noise. Noting that motion helps the perception of visual stimuli, we tested whether motion similarly facilitates the detection of acoustic targets, at the neuronal level. Auditory neurons in the central nucleus of the barn owl's inferior colliculus (ICc), due to their selectivity for interaural phase difference (delta phi), are sharply tuned to the azimuth of sound sources and are arrayed to form a topographic map of delta phi. While recording from single ICc neurons, we presented tones that simulated either moving or stationary sound sources with and without background noise. We found that the tuning of cells in the ICc for delta phi was sharper for stimuli that simulated motion than for those that simulated stationary targets. The neurons signaled the presence of a tone obscured by noise better if the tone moved than if the tone remained stationary. The resistance to noise observed with moving stimuli could not be reproduced with the temporal modulation of the stimulus amplitude, suggesting that a change of position over time was required.

Acoustic Stimulation↗

PubMed1989

Role of commissural projections in the representation of bilateral auditory space in the barn owl's inferior colliculus.

The central nucleus of the barn owl's inferior colliculus (ICc) contains a representation of both the ipsilateral and contralateral auditory hemifields. The representation of ipsilateral space is found in the "core" of the ICc, a subdivision defined by the terminal field of nucleus laminaris, the avian analogue of the medial superior olivary nucleus. The representation of contralateral space is found in the lateral portion of the "shell" of the ICc. The shell surrounds the core and is defined by the terminal field of the nucleus angularis, one of the cochlear nuclei. The representation of ipsilateral space in the core of the ICc may be accounted for by the crossed projection from the nucleus laminaris because most of the nucleus laminaris is devoted to a representation of contralateral space. We present evidence to suggest that the representation of contralateral space is due to a commissural projection from the core of one side to the lateral shell of the opposite side. Injection of horseradish peroxidase (HRP) into the lateral portion of the ICc shell produced retrogradely labeled somata in the core of the opposite side. Injection of tritiated proline into the core produced anterograde label confined to the lateral shell, thus confirming the observations made with HRP. Thus, for example, the left ICc core, which contains predominantly a representation of the left hemifield, innervates the right lateral shell, endowing it with a representation of the left, or contralateral hemifield. The representation of contralateral space in the lateral shell is ultimately conveyed to the external nucleus of the inferior colliculus where it contributes the horizontal axis to a two-dimensional map of space.

Acoustic Stimulation↗

PubMed1989

Construction of an auditory space map.

The computation of ITD begins with preservation of the phase angle of spectral components by eighth-nerve fibers and by cells of the nucleus magnocellularis. At the level of the nucleus laminaris, the difference in phase angle of corresponding spectral components in the left and right ears is extracted. At the next level, the central nucleus, neurons are consolidated into tonotopic ensembles in which preferred delta phi and frequency covary, so that only a single ITD coactivates all constituent neurons. Neurons of such ensembles project convergently on space-specific neurons, endowing the space-specific neuron with a selectivity for ITD and, therefore, a selectivity for azimuth. Ensembles representing ITDs corresponding to ipsilateral and contralateral auditory hemi-fields are found in the core and lateral shell of the central nucleus, respectively. The lateral shell receives its representation of the contralateral hemi-field from the opposite central nucleus core. The central nucleus core is innervated by the contralateral nucleus laminaris, which contains a representation of contralateral space. The projection from the lateral shell to the ipsilateral external nucleus forms a map of contralateral space in the external nucleus.

Animals↗