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Xuejing Lu,1,2 William Forde Thompson,3,4 Libo Zhang,1,2 Li Hu1,2 1CAS Key Laboratory of Mental Health, Institute of Psychology, Beijing, People’s Republic of China; 2Department of Psychology, University of Chinese Academy of Sciences, Beijing, People’s Republic of China; 3Department of Psychology, Macquarie University, Sydney, New South Wales, Australia; 4ARC Centre of Excellence in Cognition and Its Disorders, Sydney, New South Wales, AustraliaCorrespondence: Li HuCAS Key Laboratory of Mental Health, Institute of Psychology, Beijing 100101, People’s Republic of ChinaTel +86 18084053555Fax +86-10-84249369Email huli@psych.ac.cnBackground: Music is sometimes used as an adjunct to pain management. However, there is limited understanding of by what means music modulates pain perception and how the brain responds to nociceptive inputs while listening to music, because clinical practice typically involves the coexistence of multiple therapeutic interventions. To address this challenge, laboratory studies with experimental and control conditions are needed.Methods: In the present investigation, we delivered nociceptive laser stimuli on 30 participants under three conditions – participants were sitting in silence, listening to their preferred music, or listening to white noise. Differences among conditions were quantified by self-reports of pain intensity and unpleasantness, and brain activity sampled by electroencephalography (EEG).Results: Compared with the noise and silence conditions, participants in the music condition reported lower ratings on pain unpleasantness, as reflected by reduced brain oscillations immediately prior to the nociceptive laser stimulus at frequencies of 4–15 Hz in EEG. In addition, participants showed smaller P2 amplitudes in laser-evoked potentials (LEPs) when they were listening to music or white noise in comparison to sitting in silence. These findings suggest that a general modulation effect of sounds on pain, with a specific reduction of pain unpleasantness induced by the positive emotional impact.Conclusion: Music may serve as a real-time regulator to modulate pain unpleasantness. Results are discussed in view of current understandings of music-induced analgesia.Keywords: preferred music, pain, analgesic effect, emotional modulation, EEG, brain oscillations

Background: Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing., Results: To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds., Conclusions: Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.

Individuals with congenital amusia usually exhibit impairments in melodic contour processing when asked to compare pairs of melodies that may or may not be identical to one another. However, it is unclear whether the impairment observed in contour processing is caused by an impairment of pitch discrimination, or is a consequence of poor pitch memory. To help resolve this ambiguity, we designed a novel Self-paced Audio-visual Contour Task (SACT) that evaluates sensitivity to contour while placing minimal burden on memory. In this task, participants control the pace of an auditory contour that is simultaneously accompanied by a visual contour, and they are asked to judge whether the two contours are congruent or incongruent. In Experiment 1, melodic contours varying in pitch were presented with a series of dots that varied in spatial height. Amusics exhibited reduced sensitivity to audio-visual congruency in comparison to control participants. To exclude the possibility that the impairment arises from a general deficit in cross-modal mapping, Experiment 2 examined sensitivity to cross-modal mapping for two other auditory dimensions: timbral brightness and loudness. Amusics and controls were significantly more sensitive to large than small contour changes, and to changes in loudness than changes in timbre. However, there were no group differences in cross-modal mapping, suggesting that individuals with congenital amusia can comprehend spatial representations of acoustic information. Taken together, the findings indicate that pitch contour processing in congenital amusia remains impaired even when pitch memory is relatively unburdened.

Musical imagery is a relatively unexplored area, partly because of deficiencies in existing experimental paradigms, which are often difficult, unreliable, or do not provide objective measures of performance. Here we describe a novel protocol, the Pitch Imagery Arrow Task (PIAT), which induces and trains pitch imagery in both musicians and non-musicians. Given a tonal context and an initial pitch sequence, arrows are displayed to elicit a scale-step sequence of imagined pitches, and participants indicate whether the final imagined tone matches an audible probe. It is a staircase design that accommodates individual differences in musical experience and imagery ability. This new protocol was used to investigate the roles that musical expertise, self-reported auditory vividness and mental control play in imagery performance. Performance on the task was significantly better for participants who employed a musical imagery strategy compared to participants who used an alternative cognitive strategy and positively correlated with scores on the Control subscale from the Bucknell Auditory Imagery Scale (BAIS). Multiple regression analysis revealed that Imagery performance accuracy was best predicted by a combination of strategy use and scores on the Vividness subscale of BAIS. These results confirm that competent performance on the PIAT requires active musical imagery and is very difficult to achieve using alternative cognitive strategies. Auditory vividness and mental control were more important than musical experience in the ability to perform manipulation of pitch imagery.

Congenital amusia is a neuro-developmental disorder of pitch perception that causes severe problems with music processing but only subtle difficulties in speech processing. This study investigated speech processing in a group of Mandarin speakers with congenital amusia. Thirteen Mandarin amusics and thirteen matched controls participated in a set of tone and intonation perception tasks and two pitch threshold tasks. Compared with controls, amusics showed impaired performance on word discrimination in natural speech and their gliding tone analogs. They also performed worse than controls on discriminating gliding tone sequences derived from statements and questions, and showed elevated thresholds for pitch change detection and pitch direction discrimination. However, they performed as well as controls on word identification, and on statement-question identification and discrimination in natural speech. Overall, tasks that involved multiple acoustic cues to communicative meaning were not impacted by amusia. Only when the tasks relied mainly on pitch sensitivity did amusics show impaired performance compared to controls. These findings help explain why amusia only affects speech processing in subtle ways. Further studies on a larger sample of Mandarin amusics and on amusics of other language backgrounds are needed to consolidate these results.

The Sulfur gene of tobacco is nuclearly encoded. A Su allele at this locus acts as a dominant semilethal mutation and causes reduced accumulation of chlorophyll, resulting in a yellow color in the plant. An engineered transposon tagging system, based upon the maize element Ac/Ds, was used to mutate the gene. High frequency of transposon excision from the Su locus produced variegated sectors. Plants regenerated from the variegated sector exhibited a similar variegated phenotype. Genetic analyses showed that the variegation was always associated with the transposase construct and the transposon was linked to the Su locus. Sequences surrounding the transposon were isolated, and five revertant sectors possessed typical direct repeats following Ds excisions. These genetic and molecular data are consistent with the tagging of the Su allele by the transposon.

All but one of the PstI restriction fragments from mung bean, pea, and spinach chloroplast DNAs have been stably cloned into pBR322. Large fragments (15-54 kb) were cloned at low efficiencies which decreased with increasing fragment length. However, plasmids containing fragments above 25-30 kb were too unstable to be useful. In particular, pBR322 derivatives containing the largest mung bean and spinach fragments (34 kb and 54 kb, respectively) are extremely unstable and rapidly delete parts of the plasmid sequence. The PstI fragments of mung bean chloroplast DNA which cover the 34-kb PstI fragment have been cloned into pACYC177. After a search of several thousand recombinants we were unable to recover a clone containing a 12.2-kb pea chloroplast PstI fragment and suggest that some property of its sequence may be inimical to the cloning process. The identity of the cloned fragments to native chloroplast DNA restriction fragments is demonstrated by restriction analysis and the ability to construct detailed restriction maps of the mung bean and pea chloroplast genomes.

The higher proportion of repeated DNA sequences in the garden pea (Pisum sativum) than in the mung bean (Vigna radiata), as well as other differences between these legume genomes, are consistent with a higher rate of sequence amplification in the former. This hypothesis leads to a prediction that repeated sequence families in Pisum are mostly heterogeneous, as defined by Bendich and Anderson (1977), while Vigna families are homogeneous. An assay developed by these authors to distinguish between the two types of families, by comparison of reassociation rates at different temperatures, was utilized. The results for Vigna defied the predictions of the assay for either homogeneous or heterogeneous model. Evaluation of the kinetic data in light of the great diversity of repeated family copy numbers in both genomes enabled an interpretation of the results as consistent with heterogeneous families in Pisum and homogeneous families in Vigna. These tentative conclusions were supported by the results of a thermal denaturation (melting) assay described in the accompanying paper.

Variation in 30 chloroplast DNAs, representing 22 wild and cultivated accessions in the genus Pisum, was analyzed by comparing fragment patterns produced by 16 restriction endonucleases. Three types of mutations were detected. First, an inversion of between 2.2 kilobase pairs (kb) and 5.2 kb distinguished a population of P. humile from all other Pisum accessions examined. Second, deletions and insertions of between 50 and 1200 base pairs produced small restriction fragment length variations in four regions of the 120-kb chloroplast genome. Two of these regions-one of which is located within the sequence that is inverted in P. humile-showed a high degree of size polymorphism, to the extent that size differences were detected between individuals from the same accession. Finally, a total of only 11 restriction site mutations were detected among the 165 restriction sites sampled in the 30 DNAs. Based on these results and previous data, we conclude that the chloroplast genome is evolving very slowly relative to nuclear and mitochondrial DNAs. The Pisum chloroplast DNA restriction site mutations define two major lineages: One includes all tested accessions of P. fulvum, which is known to be cytogenetically quite distinct from all other Pisum taxa. The second includes 12 of 13 cultivated lines of the garden pea (P. sativum) and a wild population of P. humile from northern Israel. These observations strongly reinforce an earlier conclusion that the cultivated pea was domesticated primarily from northern populations of P. humile. A 13th P. sativum cultivar has a chloroplast genome that is significantly different from those of the aforementioned lines and somewhat more similar to those of P. elatius and southern populations of P. humile. This observation indicates that secondary hybridization may have occurred during the domestication of the garden pea.

Phylogenetic relationships of Osmunda cinnamomea, O. claytoniana, and O. regalis were explored by means of DNA sequence comparisons. Hydroxyapatite thermal elution profiles of self-reassociated repetitive DNA fragments were very similar, indicating the absence of gross differences in the amount of recent amplification or addition of repetitive DNA in any of these three genomes. Interspecific DNA sequence comparisons showed, in contrast to our earlier interpretation, that repeated DNA sequences of O. claytoniana are nearly equally diverged from those of O. cinnamomea and O. regalis. Differences between repetitive sequences of the three species can be interpreted as reflecting amplification events which occurred subsequent to speciation. The data obtained suggest that the three Osmunda species most likely arose more or less simultaneously from a common ancestor. These findings were verified in experiments with tracer DNA preparations enriched for single copy sequences. On the basis of the hydridization data presented here and of the fossil record, the rate of single copy sequence divergence in the ferns is comparable to that in the primates, although slower than that observed in other animal taxa. From this first evaluation of rates of DNA evolution in plants it would seem that the rates for plants and animals are roughly comparable. The evidence suggests that species divergence is accompanied by further reiteration of preexisting repeat sequences. The rate of addition of repetitive sequences probably is slower in ferns than in angiosperms. This difference might be attributable to the much larger effective generation time in ferns.

An assay based on derivative analysis of thermal denaturation (melting) behavior of reassociated DNA was developed in an attempt to characterize the sequence relationships in repeated DNA families according to the homogeneous or heterogeneous models of Bendich and Anderson (1977). The validity of the technique was confirmed by the use of deaminated Escherichia coli DNA models for repetitive families. The melting data for DNA reassociated at two different temperatures provided strong evidence that Pisum sativum repeated families are mostly heterogeneous, while homogeneous families predominate in Vigna radiata. These findings, together with other differences between the two genomes, suggest that the rate of sequence amplification has been higher in the evolutionary history of Pisum DNA. A general trend seems to exist for high amplification rates in large, highly repetitive plant genomes such as Pisum and lower rates in smaller plant genomes such as Vigna, as well as in the generally smaller, less repetitive genomes of most animal species.