A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL.

The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates. The process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. We find that RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation, a conclusion which is supported by analysis of RNase H1-deficient patient cells. A second nuclease is therefore required to remove the last ribonucleotides and we demonstrate that Flap endonuclease 1 (FEN1) can execute this function in vitro. Removal of RNA primers at OriL thus depends on a two-nuclease model, which in addition to RNase H1 requires FEN1 or a FEN1-like activity. These findings define the role of RNase H1 at OriL and help to explain the pathogenic consequences of disease causing mutations in RNase H1

The effect of L1 orthography on non-native vowel perception

Previous research has shown that orthography influences the learning and processing of spoken non-native words. In this paper, we examine the effect of L1 orthography on non-native sound perception. In Experiment 1, 204 Spanish learners of Dutch and a control group of 20 native speakers of Dutch were asked to classify Dutch vowel tokens by choosing from auditorily presented options, in one task, and from the orthographic representations of Dutch vowels, in a second task. The results show that vowel categorization varied across tasks: the most difficult vowels in the purely auditory task were the easiest in the orthographic task and, conversely, vowels with a relatively high success rate in the purely auditory task were poorly classified in the orthographic task. The results of Experiment 2 with 22 monolingual Peruvian Spanish listeners replicated the main results of Experiment 1 and confirmed the existence of orthographic effects. Together, the two experiments show that when listening to auditory stimuli only, native speakers of Spanish have great difficulty classifying certain Dutch vowels, regardless of the amount of experience they may have with the Dutch language. Importantly, the pairing of auditory stimuli with orthographic labels can help or hinder Spanish listeners' sound categorization, depending on the specific sound contrast

Evidence for immature perception in adolescents:Adults process reduced speech better and faster than 16-year olds

Previous work suggests that adolescents are still refining acoustic-phonetic cue use in clear-speech perception. This study shows adolescents’ immature perception of reduced speech, in which speech sounds are naturally deleted and merged within and across words. German adults and 16-year-olds listened to either German reduced or unreduced (few or full cues) part- and full phrases (without and with context) in a phrase-intelligibility task. As expected, adolescents had lower scores when adequate perception required flexible acoustic-phonetic cue use most, i.e., when hearing reduced speech without context. Participants also listened to reduced and unreduced words and pseudowords (no context) in a lexical decision task. Here, 16-year-olds had poorer and slower responses than adults overall and particularly when hearing pseudowords. Explanations for the age effects are discussed. We conclude that experience continues to refine linguistic representations, at least until adulthood

Observed effects of "distributional learning" may not relate to the number of peaks. A test of "dispersion" as a confounding factor

Distributional learning of speech sounds is learning from simply being exposed to frequency distributions of speech sounds in one’s surroundings. In laboratory settings, the mechanism has been reported to be discernible already after a few minutes of exposure, in both infants and adults. These “effects of distributional training” have traditionally been attributed to the difference in the number of peaks between the experimental distribution (two peaks) and the control distribution (one or zero peaks). However, none of the earlier studies fully excluded a possibly confounding effect of the dispersion in the distributions. Additionally, some studies with a non-speech control condition did not control for a possible difference between processing speech and non-speech. The current study presents an experiment that corrects both imperfections. Spanish listeners were exposed to either a bimodal distribution encompassing the Dutch contrast /ɑ/∼/a/ or a unimodal distribution with the same dispersion. Before and after training, their accuracy of categorization of [ɑ]- and [a]-tokens was measured. A traditionally calculated p-value showed no significant difference in categorization improvement between bimodally and unimodally trained participants. Because of this null result, a Bayesian method was used to assess the odds in favor of the null hypothesis. Four different Bayes factors, each calculated on a different belief in the truth value of previously found effect sizes, indicated the absence of a difference between bimodally and unimodally trained participants. The implication is that “effects of distributional training” observed in the lab are not induced by the number of peaks in the distributions.13 page(s

What do listeners learn from exposure to a vowel distribution? An analysis of listening strategies in distributional learning

This study first confirms the previous finding that Spanish learners improve their perception of a difficult Dutch vowel contrast through listening to a frequency distribution of the vowels involved in the contrast, a technique also known as distributional training. Secondly, it is demonstrated that learners' initial use of acoustic cues influences their performance after distributional training. To that end, types of unique listening strategies, i.e., specific ways of using acoustic cues in vowel perception, are identified using latent class regression models. The results before training show a split between "low performers", who did not use the two most important cues to the Dutch vowel contrast, namely the first and second vowel formants, and "high performers", who did. Distributional training diversified the strategies and influenced the two types of listeners differently. Crucially, not only did it bootstrap the use of cues present in the training stimuli but also the use of an untrained cue, namely vowel duration. We discuss the implications of our findings for the general field of distributional learning, and compare our listening strategies to the developmental stages that have been proposed for the acquisition of second-language vowels in Spanish learners

Distributional training of speech sounds can be done with continuous distributions

In previous research on distributional training of non-native speech sounds, distributions were always discontinuous: typically, each of only eight different stimuli was repeated multiple times. The current study examines distributional training with continuous distributions, in which all presented tokens are acoustically different. Adult Spanish learners of Dutch were trained on either a discontinuous or a continuous bimodal distribution of the Dutch vowel contrast /ɑ/-/aː/. Both groups improved their perception of the contrast; this shows that continuous training works equally well as discontinuous training. Using the more natural continuous distributions is therefore recommended for future distributional learning experiments

The Effect of L1 Orthography on Non-native Vowel Perception

Previous research has shown that orthography influences the learning and processing of spoken non-native words. In this paper, we examine the effect of L1 orthography on non-native sound perception. In Experiment 1, 204 Spanish learners of Dutch and a control group of 20 native speakers of Dutch were asked to classify Dutch vowel tokens by choosing from auditorily presented options, in one task, and from the orthographic representations of Dutch vowels, in a second task. The results show that vowel categorization varied across tasks: the most difficult vowels in the purely auditory task were the easiest in the orthographic task and, conversely, vowels with a relatively high success rate in the purely auditory task were poorly classified in the orthographic task. The results of Experiment 2 with 22 monolingual Peruvian Spanish listeners replicated the main results of Experiment 1 and confirmed the existence of orthographic effects. Together, the two experiments show that when listening to auditory stimuli only, native speakers of Spanish have great difficulty classifying certain Dutch vowels, regardless of the amount of experience they may have with the Dutch language. Importantly, the pairing of auditory stimuli with orthographic labels can help or hinder Spanish listeners’ sound categorization, depending on the specific sound contrast

Distributional learning in adults and infants

<p><strong>1. The experiment<br></strong>The experiment is described in detail in the following publication:<br>Wanrooij, Boersma & Van Zuijen (under review; details will follow soon).<br><br><strong>2. The dataset<br></strong>This dataset consists of EEG-recordings (39 files in BDF-format) and a table (4 files = the same table in four formats: PDF, TXT, CSV and XLSX).<br><br><strong>2.1. The EEG recordings<br></strong>The 39 files with EEG recordings are the files for the adults (= 1 file per participant).<br>The files for the infants can be found here: http://dx.doi.org/10.6084/m9.figshare.1157812.<br><br>Each of the 39 files is a recording of an adult participant’s EEG during a discrimination test after distributional vowel training. In the discrimination test, the mismatch response (MMR) was measured in an oddball paradigm.<br><br>The files were recorded with a Biosemi Active Two system (Biosemi Instrumentation BV, Amsterdam, The Netherlands), and downsampled from 8 kHz to 512 Hz (with Biosemi Decimator 86).<br><br><strong>2.2. The table<br></strong>The table presents the following data per adult and infant participant: the identification number (ID), the age group (infant or adult), the experimental condition as specified by the Distribution Type (unimodal or bimodal) and the Standard Stimulus ([ε] or [æ]), and the results of our measurements as represented in the mean amplitude of the mismatch response (in microvolt).<br>The ID corresponds to the name of the BDF-files.</p

The interaction between Age Group and Distribution Type.

<p>Age group: infant, left vs. adult, right. Distribution Type: unimodal, grey vs. bimodal, black.</p

A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL.

The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates. The process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. We find that RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation, a conclusion which is supported by analysis of RNase H1-deficient patient cells. A second nuclease is therefore required to remove the last ribonucleotides and we demonstrate that Flap endonuclease 1 (FEN1) can execute this function in vitro. Removal of RNA primers at OriL thus depends on a two-nuclease model, which in addition to RNase H1 requires FEN1 or a FEN1-like activity. These findings define the role of RNase H1 at OriL and help to explain the pathogenic consequences of disease causing mutations in RNase H1