THE NOTATION OF BIRD-SONG:A REVIEW AND A RECOMMENDATION

The reasons for a systematic form of notation of bird-song are discussed. Though the sound spectrograph will remain the primary tool in any study of bird-vocalization, there is still a need for a simple, comprehensive notation for the bird-watcher. This will act as a supplement to the bird-song recordings now available. After a survey of various attempts at bird-notation, from syllabic notation to the sophisticated graph-methods suggested by Stadler & Schmitt, A. A. Saunders and Gladys Page-Wood, recommendations for a comprehensive notation are made, illustrated by notated examples of song-phrases from the Nightingale.     

A new method in applying power spectral statistics to examine cardio-respiratory interactions in fish

Power spectral analysis (PSA) provides a powerful tool for determining frequency oscillations in time signals, and it is accepted that mammals can show distinct components in the heart rate (fH) spectrum that are synchronous with ventilatory frequency (fV). Using similar signal processing techniques, these fundamental components at fV are not apparent in the spectrum calculated from fish fH. Here we compare conventional PSA on the R-R interval tachogram generated from ECG traces recorded in rats and fish, with PSA on the raw ECG waveform. The rat R-R tachogram showed a defined sigmoidal component, whereas the fish R-R tachogram was a more chaotic waveform. In agreement with the literature, PSA of these respective waveforms produced a component at the same frequency as ventilation in the rat, but of lower frequency than ventilation for the fish. Applying PSA to the rat ECG produced a spectrum with a fundamental component of similar frequency to that observed in the R-R tachogram spectrum, indicating that the latter adequately contained heart rate variability (HRV) oscillations. However, PSA of the ECG in fish contrasted with that from the R-R tachogram, with components observed in the latter spectrum being absent from the former. This suggests that the frequency components determined by PSA on the fish R-R tachogram were not true components, but were aliased (or folded-back) from higher up in the spectrum. Using established aliasing equations, recalculation of these peaks showed that their true frequency was similar to that of the ventilatory frequency for individual fish. The extent of cardio-respiratory interaction, resulting in fV < f(H/2) in rats but fV > f(H/2) in fish, is suggested to be the origin of the differences observed.     

蝉的变音调复合声和发声机制的分析

蛙鸣蝉(Meimuna opalifera (Walk).ab.punctata Kato)的自然鸣声为“ji…guái”的重复单变调复合声.“ji”为主音频约4800Hz的准单音;“guái”的波形和主音频呈明显的演变,优势主频约2100Hz和2800Hz的变音调声.鸟鸣蝉(Meimuna opalifera (Walk)var.formosana Kato)的自然鸣声由重复的“jiū…ruǎ”和“jiū…gū…”合成的双变调复合声.“jiū”为基频和主频分别约625Hz和2100—2300Hz的准单音;“ruǎ”的波形和主音频呈明显的演变,基音和优势主频分别约575—625Hz和1550—1750Hz的变音调声.“gū”为优势主频约625Hz的准单音.变音调复合声不仅与腹部运动有关,而主要取决于发声肌的收缩特性和发声膜肋结构的振动特性.     

The individual tyrosines of proteins: their spectra may or may not differ from those in water or other solvents

The overall derivative spectrum of a protein is the sum of the individual derivative spectra just as the overall ultraviolet spectrum of a protein is the sum of its component parts. The RNase and DNA binding protein Sso7d has two tyrosines and one tryptophan. We used two mutant forms of the protein to show that the individual aromatics contribute derivative spectra that can be explained on the basis of their environments. We used mutant forms of iso-1-cytochrome c to estimate the contributions of the single tryptophan and three of the five tyrosines to the overall derivative spectrum. The tryptophan spectrum is not exceptional. The comparable tyrosine spectra are more complex. The derivative spectrum of individual tyrosines does not correspond to that expected on the basis of concentration. This is a reflection of two factors: (1) the extent to which mutations are sensed distally through the introduction and compression of packing defects; and (2) the extent to which electronic transitions of tyrosine are influenced by nearby atoms. This influence could take the form of tyrosine residing in an area where the dielectric coefficient is not uniform; it could also result from tyrosine bumping into neighboring atoms with lower frequency than it does in solution.     

N. V. Timofeev-Resovski? and the development of molecular radiobiology of eukaryote gene]

The nature and mechanisms of formation of spectrum and frequency of gene mutations induced by ionizing radiation of different quality have been the two key interdependent problems in radiation mutagenesis (at the gene level) of higher eukaryotes. The history of both problems, that were first given consideration by N.W.Timofeeff-Ressovsky, a known Russian radiobiologist and evolutionist, has been followed up. The author emphasizes some characteristic features of methodology of those works and shows that negative consequences for the development of the theory of radiation mutagenesis of higher eucaryotes are unavoidable if the study on the problems is carried out with the use of different approaches and test-systems. The joining up of both methods used by N.W.Timofeeff-Ressovsky in various time periods and for different purposes (analysis of the spectrum and frequency of mutations of individual genes, on the one hand, and modification analysis of the processes that lead to these mutations, on the other) and the use of current molecular and genetic methods signifies a qualitatively new stage in studying the above-mentioned problems and the onset of a new scientific orientation, that is, molecular radiobiology of an eukaryote gene.     

Population dynamics of sperm and pollen killers

Summary A model of segregation distortion is assumed in which the action of the distorter when heterozygous is to render dysfunctional those gametes that carry its allele. Two gamete killers when homozygous are assumed to distort each other. Individuals that carry the gamete killer suffer a reduction in the number of functional gametes they produce, but this deleterious effect is counterbalanced by the segregation ratio advantage of the distorter. The dynamics of such a system are analyzed in terms of a generalized fecundity function, which is defined as a function which assigns to any individual his relative fecundity in terms of the fraction of functional gametes he produces. Three general classes of fecundity functions are considered: (a) proportionality, in which the relative fecundity of an individual is proportional to the fraction of functional gametes he produces, (b) compensation, in which the relative fecundity of an individual is always greater than the fraction of functional gametes he produces, and (c) mass action, in which the relative fecundity of an individual is less than or greater than the fraction of functional gametes he produces according to whether the fraction of functional gametes is less than or greater than some threshold. In case (a) all gamete killers are always at neutral equilibria and gene frequency changes at the locus are governed by random drift. In case (b) all gamete killers will be fixed if the fecundity function is such that its second derivative is negative, whenever its argument is greater than one-half. And in case (c) some gamete killers will converge to stable equilibria, others will be fixed. If a gamete killer is homozygous lethal it will almost always converge to a stable equilibrium.This work was made possible by grant number GB-18786 from the National Science Foundation.     

The effect of the membrane compression wave on the light scattering spectrum from a protein monomer-dimer equilibrium

The membrane compression wave on the Rayleigh-Brillouin spectrum of a solution of protein in a monomer-timer equilibrium has been calculated. When the frequency of the longitudinal wave is slow compared to the monomer-dimer exchange frequency the compaction wave produces an asymmetry in the spectrum. The asymmetry is small and may be undetectable in the experimental spectra. If the frequency of the compression wave is high compared to the exchange rate then new bands will appear in the experimental spectra. The amplitude and shift of these peaks are related to the amplitude and frequency of the longitudinal wave, respectively. The bands due to the compression wave in this limit should be detectable in the experimental spectrum. Fitting of the experimental spectrum to the form calculated below will yield valuable information about the membrane compression wave.     

Method for measuring sensitivity to periodic spectral energy modulations in human

The distribution of spectral energy of a visual stimulus can be subject to Fourier analysis. In this perspective, we have built a device which produces periodic variations in energy (square waves) over the visible spectrum (400-700 nm), and where the amplitude, phase and frequency of the stimuli can be independently controlled. From the non-modulated spectrum, supplying a white spot, for a given frequency and phase, there is a minimal amplitude modulation (contrast threshold) for which the spot becomes chromatic. As an illustrative example we present here a curve of optimal sensitivity values (inverse of contrast) as a function of frequency (from 0.5 to 3.6 cycles/300 nm) for a normal subject.     

鸣禽发声学习记忆与即刻早期基因

鸣禽受到声音信号的刺激或自身表现出发声行为时,脑内即刻早期基因(immediate early gene,IEG)能迅速被激活而表达.其中zenk、c-fos和c-jun表达的脑区及水平与鸟在鸣唱时神经元的活动区域及活动程度相一致,暗示IEG在鸣禽发声学习记忆中起重要作用.     

Individual identity coding depends on call type in the South Polar skua Catharacta maccormicki

In colonial birds, acoustic communication is essential for mate recognition. The South Polar skua (Catharacta maccormicki) lives in loose colonies and is highly territorial for feeding and breeding. We studied the potential of individual identity coding in the three main calls of the South Polar skua repertoire: the courtship, the contact and the alarm calls. We investigated parameters in both temporal and frequencial domains, i.e. amplitude modulation, frequency modulation and power spectrum density. For each parameter, the intra- and inter-individual variabilities were calculated. The ratio between these values represents the potential of individuality coding (PIC) of the considered feature. Low values of PICs for amplitude and frequency modulations show that both parameters may not be used for individual recognition. In contrast, high values of PIC for the power spectrum density indicate that the energy distribution among the frequency spectrum is likely to be an individual marker. PIC also varies according to the call type. Both courtship and contact calls have a higher potentiality of individual identity coding than the alarm call. The two former calls may allow individual recognition whereas the latter may not, and this last result can be extrapolated to many other species.     

Potential of 13C and 15N labeling for studying protein-protein interactions using Fourier transform infrared spectroscopy.

In this study, we examine the interaction between two bacterial proteins, namely HPr and IIAmtl of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system, using FTIR spectroscopy. In an interaction involving a 1:1 molar ratio of these two proteins, when they are unlabeled, the overlap of absorbance of the amide I band arising from the peptide group vibrations of the two proteins is such that it is not possible to determine the contribution which each protein makes to the absorbance. Uniform 15N labeling has little effect on the frequency of the amide I band although there is a significant shift of the amide II band. However, we show that uniform (90%) 13C labeling produces a large shift of bands associated with the carbonyl moiety, especially the amide I band. This opens up windows in different regions of the infrared spectrum. Thus, when the same mixture of the two bacterial proteins is made where one of the proteins is uniformly 13C-labeled (in our case HPr), the amide I maxima of this protein shifts by approximately 45 cm-1 toward lower frequency and reveals the previously overlapped amide I band of the unlabeled IIAmtl. This application of 13C labeling shows the potential of studying protein-protein interactions using FTIR spectroscopy. With thoughtful selection of systems and labeling strategies, numerous studies with proteins should be possible. These could include, among others, enzyme-substrate and protein-ligand interactions.     

SIGNAL™/RTSD™ SOUND ANALYSIS SYSTEM

ABSTRACT

The prevalence of complex acoustic structures in mammalian vocalisations can make it difficult to quantify frequency characteristics. We describe two methods developed for the frequency analysis of a complex swift fox Vulpes velox vocalisation, the barking sequence: (1) autocorrelation function analysis and (2) instantaneous frequency analysis. The autocorrelation function analysis results in an energy density spectrum of the signal's averaged amplitude and frequency information. This analysis was used for locating possible formant structures and quantifying the energy distribution of single barks in the barking sequence. The instantaneous frequency analysis is applied to individual continuous frequency bands and generates frequency contours with a resolution of a couple of Hertz. It was used to quantify frequency modulation and calculate average frequencies of harmonic bands in individual barks and to estimate fundamental frequencies. This second method of analysis had to be evaluated with spectrographic analysis to gauge its reliability for each band analysed. The algorithms used should make both of these methods applicable to other complex vocalisations.     

Amplitude modulation is a major marker of individual signature in lamb bleats

The source-filter theory of vocal production supports the idea that acoustic signatures are preferentially coded by the fundamental frequency (source-induced variability) and the distribution of energy among the frequency spectrum (filter-induced variability). By investigating the acoustic parameters supporting individuality in lamb bleats, a vocalization which mediates recognition by ewes, here we show that amplitude modulation – an acoustic feature largely independent of the shape of the acoustic tract – can also be an important cue defining an individual vocal signature. Female sheep (Ovis aries) show an acoustic preference for their own lamb. Although playback experiments have shown that this preference is established soon after birth and relies on a unique vocal signature contained in the bleats of the lamb, the physical parameters that encode this individual identity remained poorly identified. We recorded 152 bleats from 13 fifteen-day-old lambs and analyzed their acoustic structure with four complementary statistical methods (ANOVA, potential for individual identity coding PIC, entropy calculation 2^Hs, discriminant function analysis DFA). Although there were slight differences in the acoustic parameters identified by the four methods, it remains that the individual signature relies on both the temporal and frequency domains. The coding of the identity is thus multi-parametric and integrates modulation of amplitude and energy parameters. Specifically, the contribution of the amplitude modulation is important, together with the fundamental frequency F ₀ and the distribution of energy in the frequency spectrum.     

Spatial detection of outlier loci with Moran eigenvector maps

The spatial signature of microevolutionary processes structuring genetic variation may play an important role in the detection of loci under selection. However, the spatial location of samples has not yet been used to quantify this. Here, we present a new two‐step method of spatial outlier detection at the individual and deme levels using the power spectrum of Moran eigenvector maps (MEM). The MEM power spectrum quantifies how the variation in a variable, such as the frequency of an allele at a SNP locus, is distributed across a range of spatial scales defined by MEM spatial eigenvectors. The first step (Moran spectral outlier detection: MSOD) uses genetic and spatial information to identify outlier loci by their unusual power spectrum. The second step uses Moran spectral randomization (MSR) to test the association between outlier loci and environmental predictors, accounting for spatial autocorrelation. Using simulated data from two published papers, we tested this two‐step method in different scenarios of landscape configuration, selection strength, dispersal capacity and sampling design. Under scenarios that included spatial structure, MSOD alone was sufficient to detect outlier loci at the individual and deme levels without the need for incorporating environmental predictors. Follow‐up with MSR generally reduced (already low) false‐positive rates, though in some cases led to a reduction in power. The results were surprisingly robust to differences in sample size and sampling design. Our method represents a new tool for detecting potential loci under selection with individual‐based and population‐based sampling by leveraging spatial information that has hitherto been neglected.     

A comprehensive computational model of animal biosonar signal processing

Computational models of animal biosonar seek to identify critical aspects of echo processing responsible for the superior, real-time performance of echolocating bats and dolphins in target tracking and clutter rejection. The Spectrogram Correlation and Transformation (SCAT) model replicates aspects of biosonar imaging in both species by processing wideband biosonar sounds and echoes with auditory mechanisms identified from experiments with bats. The model acquires broadband biosonar broadcasts and echoes, represents them as time-frequency spectrograms using parallel bandpass filters, translates the filtered signals into ten parallel amplitude threshold levels, and then operates on the resulting time-of-occurrence values at each frequency to estimate overall echo range delay. It uses the structure of the echo spectrum by depicting it as a series of local frequency nulls arranged regularly along the frequency axis of the spectrograms after dechirping them relative to the broadcast. Computations take place entirely on the timing of threshold-crossing events for each echo relative to threshold-events for the broadcast. Threshold-crossing times take into account amplitude-latency trading, a physiological feature absent from conventional digital signal processing. Amplitude-latency trading transposes the profile of amplitudes across frequencies into a profile of time-registrations across frequencies. Target shape is extracted from the spacing of the object’s individual acoustic reflecting points, or glints, using the mutual interference pattern of peaks and nulls in the echo spectrum. These are merged with the overall range-delay estimate to produce a delay-based reconstruction of the object’s distance as well as its glints. Clutter echoes indiscriminately activate multiple parts in the null-detecting system, which then produces the equivalent glint-delay spacings in images, thus blurring the overall echo-delay estimates by adding spurious glint delays to the image. Blurring acts as an anticorrelation process that rejects clutter intrusion into perceptions.     

Mother Vocal Recognition in Antarctic Fur Seal Arctocephalus gazella Pups: A Two-Step Process

In otariids, mother’s recognition by pups is essential to their survival since females nurse exclusively their own young and can be very aggressive towards non-kin. Antarctic fur seal, Arctocephalus gazella, come ashore to breed and form dense colonies. During the 4-month lactation period, females alternate foraging trips at sea with suckling period ashore. On each return to the colony, females and pups first use vocalizations to find each other among several hundred conspecifics and olfaction is used as a final check. Such vocal identification has to be highly efficient. In this present study, we investigated the components of the individual vocal signature used by pups to identify their mothers by performing playback experiments on pups with synthetic signals. We thus tested the efficiency of this individual vocal signature by performing propagation tests and by testing pups at different playback distances. Pups use both amplitude and frequency modulations to identify their mother’s voice, as well as the energy spectrum. Propagation tests showed that frequency modulations propagated reliably up to 64m, whereas amplitude modulations and spectral content greatly were highly degraded for distances over 8m. Playback on pups at different distances suggested that the individual identification is a two-step process: at long range, pups identified first the frequency modulation pattern of their mother’s calls, and other components of the vocal signature at closer range. The individual vocal recognition system developed by Antarctic fur seals is well adapted to face the main constraint of finding kin in a crowd.     

A common PEX1 frameshift mutation in patients with disorders of peroxisome biogenesis correlates with the severe Zellweger syndrome phenotype

Peroxisome biogenesis disorders are a heterogeneous group of human neurodegenerative diseases caused by peroxisomal metabolic dysfunction. At the molecular level, these disorders arise from mutations in PEX genes that encode proteins required for the import of proteins into the peroxisomal lumen. The Zellweger syndrome spectrum of diseases is a major sub-set of these disorders and represents a clinical continuum from Zellweger syndrome (the most severe) through neonatal adrenoleukodystrophy to infantile Refsum disease. The PEX1 gene, which encodes a cytoplasmic AAA ATPase, is the responsible gene in more than half of the Zellweger syndrome spectrum patients, and mutations in PEX1 can account for the full spectrum of phenotypes seen in these patients. In these studies, we have undertaken mutation analysis of PEX1 in skin fibroblast cell lines from Australasian Zellweger syndrome spectrum patients. A previously reported common PEX1 mutation that gives rise to a G843D substitution and correlates with the less severe disease phenotypes has been found to be present at high frequency in our patient cohort. We also report a novel PEX1 mutation that occurs at high frequency in Zellweger syndrome spectrum patients. This mutation produces a frameshift in exon 13, a change that leads to the premature truncation of the PEX1 protein. A Zellweger syndrome patient who was homozygous for this mutation and who survived for less than two months from birth had undetectable levels of PEX1 mRNA. This new common mutation therefore correlates with a severe disease phenotype. We have adopted procedures for the detection of this mutation for successful prenatal diagnosis. Electronic Publication     

Restriction endonuclease BglI as a tool for in vitro reconstruction and recombination of plasmid and bacteriophage genomes

The restriction endonuclease BglI produces different individual fragment ends from different cut sites. This property has allowed us to reconstruct efficiently several commonly used plasmid and bacteriophage genomes and a number of recombinant plasmids containing up to seven BglI restriction sites from their constituent BglI fragments. It is demonstrated that in vitro reconstitution from BglI fragments can be used to create, in a simple way, recombinant DNA molecules by recombining in vitro BglI fragments from different mutated or otherwise related genomes. Further applications of the method are discussed.     

The Yule Approximation for the Site Frequency Spectrum after a Selective Sweep

In the area of evolutionary theory, a key question is which portions of the genome of a species are targets of natural selection. Genetic hitchhiking is a theoretical concept that has helped to identify various such targets in natural populations. In the presence of recombination, a severe reduction in sequence diversity is expected around a strongly beneficial allele. The site frequency spectrum is an important tool in genome scans for selection and is composed of the numbers , where is the number of single nucleotide polymorphisms (SNPs) present in from individuals. Previous work has shown that both the number of low- and high-frequency variants are elevated relative to neutral evolution when a strongly beneficial allele fixes. Here, we follow a recent investigation of genetic hitchhiking using a marked Yule process to obtain an analytical prediction of the site frequency spectrum in a panmictic population at the time of fixation of a highly beneficial mutation. We combine standard results from the neutral case with the effects of a selective sweep. As simulations show, the resulting formula produces predictions that are more accurate than previous approaches for the whole frequency spectrum. In particular, the formula correctly predicts the elevation of low- and high-frequency variants and is significantly more accurate than previously derived formulas for intermediate frequency variants.     

The perception of fricative peaks and noise bands

Recent work on the identification and perception of fricatives has focussed on the use by listeners of spectral moments derived from the whole spectrum and there appears to be no work in the literature on the use of prominent spectral peaks. In this study, we map the response of a single listener to narrow bands of noise that "mimic" the spectral peaks of English voiceless fricatives. The stimuli are based on the critical-band rate scale (Zwicker and Fastl, 1990) which divides the audible frequency range up to 15,500 Hz into 24 abutting critical bands. The results suggest that listeners have knowledge that enables them to connect a narrow-band spectral peak with a particular fricative consonant. We demonstrate that such knowledge, particularly in conjunction with a normalization metric that takes account of an individual speaker's vocal tract characteristics (F0 of the vowel following the fricative), could be used to good effect, particularly in noisy conditions which impair the use of the whole spectrum.