Biomedical subjects

Terry T Takahashi

Publications and source records attributed to Terry T Takahashi.

15 recordsLinked to original sources

PubMed2006

Combined auditory and visual stimuli facilitate head saccades in the barn owl (Tyto alba).

The barn owl naturally responds to an auditory or visual stimulus in its environment with a quick head turn toward the source. We measured these head saccades evoked by auditory, visual, and simultaneous, co-localized audiovisual stimuli to quantify multisensory interactions in the barn owl. Stimulus levels ranged from near to well above saccadic threshold. In accordance with previous human psychophysical findings, the owl's saccade reaction times (SRTs) and errors to unisensory stimuli were inversely related to stimulus strength. Auditory saccades characteristically had shorter reaction times but were less accurate than visual saccades. Audiovisual trials, over a large range of tested stimulus combinations, had auditory-like SRTs and visual-like errors, suggesting that barn owls are able to use both auditory and visual cues to produce saccades with the shortest possible SRT and greatest accuracy. These results support a model of sensory integration in which the faster modality initiates the saccade and the slower modality remains available to refine saccade trajectory.

Acoustic Stimulation↗

PubMed2006

Sound localization by barn owls in a simulated echoic environment.

We examined the accuracy and precision with which the barn owl (Tyto alba) turns its head toward sound sources under conditions that evoke the precedence effect (PE) in humans. Stimuli consisted of 25-ms noise bursts emitted from two sources, separated horizontally by 40 degrees, and temporally by 3-50 ms. At delays from 3 to 10 ms, head turns were always directed at the leading source, and were nearly as accurate and precise as turns toward single sources, indicating that the leading source dominates perception. This lead dominance is particularly remarkable, first, because on some trials, the lagging source was significantly higher in amplitude than the lead, arising from the directionality of the owl's ears, and second, because the temporal overlap of the two sounds can degrade the binaural cues with which the owl localizes sounds. With increasing delays, the influence of the lagging source became apparent as the head saccades became increasingly biased toward the lagging source. Furthermore, on some of the trials at delays > or = 20 ms, the owl turned its head, first, in the direction of one source, and then the other, suggesting that it was able to resolve two separately localizable sources. At all delays <50 ms, response latencies were longer for paired sources than for single sources. With the possible exception of response latency, these findings demonstrate that the owl exhibits precedence phenomena in sound localization similar to those in humans and cats, and provide a basis for comparison with neurophysiological data.

Acoustic Stimulation↗

PubMed2005

Localization and identification of concurrent sounds in the owl's auditory space map.

In nature, sounds from multiple sources sum at the eardrums, generating complex cues for sound localization and identification. In this clutter, the auditory system must determine "what is where." We examined this process in the auditory space map of the barn owl's (Tyto alba) inferior colliculus using two spatially separated sources simultaneously emitting uncorrelated noise bursts, which were uniquely identified by different frequencies of sinusoidal amplitude modulation. Spatial response profiles of isolated neurons were constructed by testing the source-pair centered at various locations in virtual auditory space. The neurons responded whenever a source was placed within the receptive field, generating two clearly segregated foci of activity at appropriate loci. The spike trains were locked strongly to the amplitude modulation of the source within the receptive field, whereas the other source had minimal influence. Two sources amplitude modulated at the same rate were resolved successfully, suggesting that source separation is based on differences of fine structure. The spike rate and synchrony were stronger for whichever source had the stronger average binaural level. A computational model showed that neuronal activity was primarily proportional to the degree of matching between the momentary binaural cues and the preferred values of the neuron. The model showed that individual neurons respond to and synchronize with sources in their receptive field if there are frequencies having an average binaural-level advantage over a second source. Frequencies with interaural phase differences that are shared by both sources may also evoke activity, which may be synchronized with the amplitude modulations from either source.

Acoustic Stimulation↗

PubMed2005

A general route for post-translational cyclization of mRNA display libraries.

Cyclic peptides are attractive scaffolds for the design of conformationally constrained molecular therapeutics. Previously, biological display libraries could only be cyclized via disulfide bonds, which are labile and can be reduced in an intracellular environment. In this paper, we construct high diversity, covalently cyclized mRNA display libraries (>1013 sequences) and analyze the cyclization reaction using MALDI-TOF MS and unnatural amino acid incorporation. Our route allows the extent of cyclization to be evaluated quantitatively and is broadly applicable to a variety of cyclization chemistries.

Cyclization↗

PubMed2005

The N-end rule pathway as a nitric oxide sensor controlling the levels of multiple regulators.

The conjugation of arginine to proteins is a part of the N-end rule pathway of protein degradation. Three amino (N)-terminal residues--aspartate, glutamate and cysteine--are arginylated by ATE1-encoded arginyl-transferases. Here we report that oxidation of N-terminal cysteine is essential for its arginylation. The in vivo oxidation of N-terminal cysteine, before its arginylation, is shown to require nitric oxide. We reconstituted this process in vitro as well. The levels of regulatory proteins bearing N-terminal cysteine, such as RGS4, RGS5 and RGS16, are greatly increased in mouse ATE1-/- embryos, which lack arginylation. Stabilization of these proteins, the first physiological substrates of mammalian N-end rule pathway, may underlie cardiovascular defects in ATE1-/- embryos. Our findings identify the N-end rule pathway as a new nitric oxide sensor that functions through its ability to destroy specific regulatory proteins bearing N-terminal cysteine, at rates controlled by nitric oxide and apparently by oxygen as well.

Aminoacyltransferases↗

PubMed2005

Learned modification of the nictitating membrane reflex by auditory stimuli in the barn owl.

The barn owl, Tyto alba, extends its nictitating membrane (NM) in response to an air puff to the cornea or a mild para-orbital electrodermal shock. The NM extension habituated rapidly if the stimulus was repeated. Habituation was prevented by pairing the aversive stimulus with a sound. The sound stimulus did not, by itself, induce an NM extension. Repeated pairing of sound with the aversive stimulus caused the subjects to modify the duration of their NM extension, increasing the duration when exposed to longer aversive stimuli and decreasing in response to shorter stimuli. No transference of the response was seen from the aversive stimulus to the sound. The learned change in duration of the NM extension resisted extinction. This modification of the NM extension reflex resembles previous descriptions of primer-produced facilitation.

Acoustic Stimulation↗

PubMed2004

A neuronal correlate of the precedence effect is associated with spatial selectivity in the barn owl's auditory midbrain.

Sound localization in echoic conditions depends on a precedence effect (PE), in which the first arriving sound dominates the perceived location of later reflections. Previous studies have demonstrated neurophysiological correlates of the PE in several species, but the underlying mechanisms remain unknown. The present study documents responses of space-specific neurons in the barn owl's inferior colliculus (IC) to stimuli simulating direct sounds and reflections that overlap in time at the listener's ears. Responses to 100-ms noises with lead-lag delays from 1 to 100 ms were recorded from neurons in the space-mapped subdivisions of IC in anesthetized owls (N2O/isofluorane). Responses to a target located at a unit's best location were usually suppressed by a masker located outside the excitatory portion of the spatial receptive field. The least spatially selective units exhibited temporally symmetric effects, in that the amount of suppression was the same whether the masker led or lagged. Such effects mirror the alteration of localization cues caused by acoustic superposition of leading and lagging sounds. In more spatially selective units, the suppression was often temporally asymmetric, being more pronounced when the masker led. The masker often evoked small changes in spatial tuning that were not related to the magnitude of suppressive effects. The association of temporally asymmetric suppression with spatial selectivity suggests that this property emerges within IC, and not at earlier stages of auditory processing. Asymmetric suppression reduces the ability of highly spatially selective neurons to encode the location of lagging sounds, providing a possible basis for the PE.

Acoustic Stimulation↗

PubMed2003

Differential modes of recognition in N peptide-boxB complexes.

N proteins from bacteriophages lambda, P22, and phi21 modulate transcription elongation by binding nascent "boxB" mRNA hairpins. This RNA recognition is mediated by N-terminal arginine-rich peptide sequences capable of interacting with their cognate boxB RNA targets. Here, we have analyzed the affinity and specificity of the peptide-RNA interactions that modulate this transcriptional switch. To do this, we constructed a series of peptides based on the wild-type lambda, P22, and phi21 N protein binding domains ranging from 11 to 22 residues and analyzed their interactions with the leftward and rightward boxB RNA hairpin targets for all three phage. Binding constant (K(d)) values were determined using RNA hairpins labeled with 2-aminopurine (2AP) and monitoring the fluorescence change as peptide was added. K(d)'s demonstrate that lambda and P22 N peptides bind to their cognate boxB targets with high specificity and show equal affinities for their leftward and rightward hairpins. Surprisingly, phi21 shows very little specificity for its cognate targets. Lambda and P22 N peptides exhibit differential modes of recognition with specificity conferred by their amino- and carboxy-terminal modules, respectively. We have generated a reciprocal matrix of substituted peptides to examine the contributions of individual residues to specificity. Amino acid coupling analysis supports a binding model where the Arg8 residue of lambda peptide acts as a conformational hot spot, anchoring the induced loop fold of its boxB hairpin target.

Amino Acid Sequence↗

PubMed2003

Context and conformation dictate function of a transcription antitermination switch.

In bacteriophage l, transcription elongation is regulated by the N protein, which binds a nascent mRNA hairpin (termed boxB) and enables RNA polymerase to read through distal terminators. We have examined the structure, energetics and in vivo function of a number of N-boxB complexes derived from in vitro protein selection. Trp18 fully stacks on the RNA loop in the wild-type structure, and can become partially or completely unstacked when the sequence context is changed three or four residues away, resulting in a recognition interface in which the best binding residues depend on the sequence context. Notably, in vivo antitermination activity correlates with the presence of a stacked aromatic residue at position 18, but not with N-boxB binding affinity. Our work demonstrates that RNA polymerase responds to subtle conformational changes in cis-acting regulatory complexes and that approximation of components is not sufficient to generate a fully functional transcription switch.

Bacterial Proteins↗

PubMed2003

Prediction of auditory spatial acuity from neural images on the owl's auditory space map.

The owl can discriminate changes in the location of sound sources as small as 3 degrees and can aim its head to within 2 degrees of a source. A typical neuron in its midbrain space map has a spatial receptive field that spans 40 degrees--a width that is many times the behavioural threshold. Here we have quantitatively examined the relationship between neuronal activity and perceptual acuity in the auditory space map in the barn owl midbrain. By analysing changes in firing rate resulting from small changes of stimulus azimuth, we show that most neurons can reliably signal changes in source location that are smaller than the behavioural threshold. Each source is represented in the space map by a focus of activity in a population of neurons. Displacement of the source causes the pattern of activity in this population to change. We show that this change predicts the owl's ability to detect a change in source location.

Acoustic Stimulation↗

PubMed2003

Frequency-specific interaural level difference tuning predicts spatial response patterns of space-specific neurons in the barn owl inferior colliculus.

Space-specific neurons in the barn owl's inferior colliculus have spatial receptive fields (RFs) because of sensitivity to interaural time difference and frequency-specific interaural level difference (ILD). These neurons are assumed to be tuned to the frequency-specific ILDs occurring at their spatial RFs, but attempts to assess this tuning with traditional narrowband stimuli have had limited success. Indeed, tuning assessed in this manner, when processed via a linear model of spectral integration, typically explains only approximately half the variance in spatial response patterns. Here we report our findings that frequency-specific ILD tuning of space-specific neurons, when assessed from responses to broadband stimuli, predicted nearly 75% of the variance in spatial responses, using a linear model of spectral integration (p < 0.0001; n = 97 neurons). Furthermore, when we tested neurons using only those frequencies we found to be spatially relevant, we saw that their responses were similar to those elicited by broadband stimuli. When we used frequencies not identified as spatially relevant, such similarity was lacking. Furthermore, spectral components that elicited high firing rates when presented as narrowband stimuli were found in several cases to be irrelevant for or detrimental to the definition of spatial RFs. Thus, neurons achieved sharp spatial tuning by selecting for ILDs of a subset of spectral components in noise, some of which were not identified using narrowband stimuli.

Acoustic Stimulation↗

PubMed2003

mRNA display: ligand discovery, interaction analysis and beyond.

In vitro peptide and protein selection using mRNA display enables the discovery and directed evolution of new molecules from combinatorial libraries. These selected molecules can serve as tools to control and understand biological processes, enhance our understanding of molecular interactions and potentially treat disease in therapeutic applications. In mRNA display, mRNA molecules are covalently attached to the peptide or protein they encode. These mRNA-protein fusions enable in vitro selection of peptide and protein libraries of >10(13) different sequences. mRNA display has been used to discover novel peptide and protein ligands for RNA, small molecules and proteins, as well as to define cellular interaction partners of proteins and drugs. In addition, several unique applications are possible with mRNA display, including self-assembling protein chips and library construction with unnatural amino acids and chemically modified peptides.

Adenosine Triphosphate↗

PubMed2003

Auditory spatial discrimination by barn owls in simulated echoic conditions.

In humans, directional hearing in reverberant conditions is characterized by a "precedence effect," whereby directional information conveyed by leading sounds dominates perceived location, and listeners are relatively insensitive to directional information conveyed by lagging sounds. Behavioral studies provide evidence of precedence phenomena in a wide range of species. The present study employs a discrimination paradigm, based on habituation and recovery of the pupillary dilation response, to provide quantitative measures of precedence phenomena in the barn owl. As in humans, the owl's ability to discriminate changes in the location of lagging sources is impaired relative to that for single sources. Spatial discrimination of lead sources is also impaired, but to a lesser extent than discrimination of lagging sources. Results of a control experiment indicate that sensitivity to monaural cues cannot account for discrimination of lag source location. Thus, impairment of discrimination ability in the two-source conditions most likely reflects a reduction in sensitivity to binaural directional information. These results demonstrate a similarity of precedence effect phenomena in barn owls and humans, and provide a basis for quantitative comparison with neuronal data from the same species.

Animals↗

PubMed2002

Designed arginine-rich RNA-binding peptides with picomolar affinity.

Arginine-rich peptide motifs (ARMs) capable of binding unique RNA structures play critical roles in transcription, translation, RNA trafficking, and RNA packaging. Bacteriophage ARMs necessary for transcription antitermination bind to distinct boxB RNA hairpin sequences with a characteristic induced alpha-helical structure. Characterization of ARMs from lambdoid phages reveals that the dissociation constant of the P22 bacteriophage model-antitermination complex (P22(N21)-P22boxB) is 200 +/- 56 pM in free solution at physiologic concentrations of monovalent cation, significantly stronger than previously determined by gel mobility shift and polyacrylamide gel coelectophoresis, and 2 orders of magnitude stronger than the tightest known native ARM-RNA interaction at physiological salt. Here, we use a reciprocal design approach to enhance the binding affinity of two separate alpha-helical ARM-RNA interactions; one derived from the native lambda phage antitermination complex and a second isolated using mRNA display selection experiments targeting boxB RNA.

Arginine↗

PubMed2002

From spectrum to space: the contribution of level difference cues to spatial receptive fields in the barn owl inferior colliculus.

Space-specific neurons in the owl's inferior colliculus have spatial receptive fields (RFs) computed from interaural time (ITD) and level (ILD) differences. Because of the shape of the owl's head, these cues vary with frequency in a manner specific for each location. We sought to determine the contribution of ILD to spatial selectivity. We measured the normal spatial receptive fields of space-specific neurons using virtual sound sources (i.e., noises filtered to simulate external sound sources, presented using headphones). The virtual-source filters were then altered so that ITD was fixed while frequency-specific ILDs varied according to location in the usual manner. The resulting "ILD-alone" RF typically revealed a horizontal band of excitation that included the normal RF. Above and below, the neurons were inhibited. Interestingly, the maxima of ILD-alone RFs were generally outside the normal RF, suggesting that space-specific neurons are not optimally tuned to the ILD spectrum occurring at the normal RF location. Congruously, frequency-specific ILD tuning, assessed with tones, better matched the ILDs at the peak of the ILD-alone RF than those at the peak of the normal RF. The firing evoked from the normal RF may thus reflect the balance of excitatory and inhibitory inputs needed to appropriately restrict the receptive field. Frequency-specific ILD tuning curves were combined with measured head-filtering characteristics to predict responses to the frequency-specific ILDs at each location. The predicted ILD-alone RFs, which are based on a simple sum of frequency-specific inputs, accounted for 56% of the variance in our measured ILD-alone RFs.

Acoustic Stimulation↗