Onset and phoneme awareness and its relationship to letter knowledge in German-speaking preschool children

This is the authors' post-print version of an article published in Folia Phoniatrica et Logopaedica© 2014. The definitive version is available at http://dx.doi.org/10.1159/000368228Objectives: The aim was to explore whether word initial onset awareness is acquired before phoneme awareness and whether onset complexity influences performance on identification tasks. In addition, the relationship between onset and phoneme awareness and letter knowledge was investigated. Method: In this study 22 monolingual German-speaking preschool children aged 5;00 – 5;11 were tested. Onset, phoneme identification, and letter knowledge tasks were administered. The children were presented with pictures of word pairs. Both words in each pair shared a single consonant onset, a two consonant onset cluster or the first consonant of a consonant cluster. The children were asked to pronounce the shared sound(s). Additionally, they were asked to name all 26 upper-case letters. Results: Onset awareness tasks were significantly easier to complete than phoneme awareness tasks. However, no influence of onset complexity on onset awareness performance was found. Moreover, letter knowledge correlated with all phonological awareness tasks. Conclusions: The results corroborate that phoneme awareness develops already at preschool age irrespective of explicit literacy tuition. Nevertheless, letter knowledge is closely related and should be linked to onset/phoneme awareness tasks

De novo assembly of the zucchini genome reveals a whole‐genome duplication associated with the origin of the Cucurbita genus

The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus

Development of a tablet application for the screening of receptive vocabulary skills in multilingual children: A pilot study

For professionals working with multi-lingual children, detecting language deficits in a child’s home language can present a challenge. This is largely due to the scarcity of standardised assessments in many children’s home languages and missing normative data on multilingual language acquisition. A common approach is to translate existing English language vocabulary measures into other languages. However, this approach does not take into account the cultural and linguistic differences between languages. This pilot study explored whether English and home language receptive vocabulary skills can be objectively and reliably screened using a tablet application. Preliminary data on mono- and multilingual vocabulary skills was collected from 139 children aged 6-7 years. A tablet application was designed to assess children’s receptive vocabulary in both English, and an additional eight languages using a four choice picture paradigm. Linguistically controlled and pre-recorded target items are presented orally via the tablet in each language and responses are made via the touchscreen and automatically scored. The English version of the test was administered to 67 mono- and 72 multilingual children, while 38 multilingual children also completed the test in their home language. Test criteria measures, including reliability and concurrent validity showed satisfactory results. These findings suggest that the tablet application could be a useful tool for professionals to screen receptive vocabulary skills in mono- and multilingual children. Limitations of the first version of the RVS and future steps are discussed

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

Despite almost 40 years of molecular genetics research in Escherichia coli a major fraction of its Transcription Start Sites (TSSs) are still unknown, limiting therefore our understanding of the regulatory circuits that control gene expression in this model organism. RegulonDB (http://regulondb.ccg.unam.mx/) is aimed at integrating the genetic regulatory network of E. coli K12 as an entirely bioinformatic project up till now. In this work, we extended its aims by generating experimental data at a genome scale on TSSs, promoters and regulatory regions. We implemented a modified 5′ RACE protocol and an unbiased High Throughput Pyrosequencing Strategy (HTPS) that allowed us to map more than 1700 TSSs with high precision. From this collection, about 230 corresponded to previously reported TSSs, which helped us to benchmark both our methodologies and the accuracy of the previous mapping experiments. The other ca 1500 TSSs mapped belong to about 1000 different genes, many of them with no assigned function. We identified promoter sequences and type of σ factors that control the expression of about 80% of these genes. As expected, the housekeeping σ70 was the most common type of promoter, followed by σ38. The majority of the putative TSSs were located between 20 to 40 nucleotides from the translational start site. Putative regulatory binding sites for transcription factors were detected upstream of many TSSs. For a few transcripts, riboswitches and small RNAs were found. Several genes also had additional TSSs within the coding region. Unexpectedly, the HTPS experiments revealed extensive antisense transcription, probably for regulatory functions. The new information in RegulonDB, now with more than 2400 experimentally determined TSSs, strengthens the accuracy of promoter prediction, operon structure, and regulatory networks and provides valuable new information that will facilitate the understanding from a global perspective the complex and intricate regulatory network that operates in E. coli

Repeated domestication of melon (Cucumis melo) in Africa and Asia and a new close relative from India

[EN] Premise of the Study Methods The domestication history of melon is still unclear. An African or Asian origin has been suggested, but its closest wild relative was recently revealed to be an Australian species. The complicated taxonomic history of melon has resulted in additional confusion, with a high number of misidentified germplasm collections currently used by breeders and in genomics research. Using seven DNA regions sequenced for 90% of the genus and the major cultivar groups, we sort out described names and infer evolutionary origins and domestication centers. Key Results Conclusions We found that modern melon cultivars go back to two lineages, which diverged ca. 2 million years ago. One is restricted to Asia (Cucumis melo subsp. melo), and the second, here described as C. melo subsp. meloides, is restricted to Africa. The Asian lineage has given rise to the widely commercialized cultivar groups and their market types, while the African lineage gave rise to cultivars still grown in the Sudanian region. We show that C. trigonus, an overlooked perennial and drought-tolerant species from India is among the closest living relatives of C. melo. Melon was domesticated at least twice: in Africa and Asia. The African lineage and the Indian C. trigonus are exciting new resources for breeding of melons tolerant to climate change.Endl, J.; Achigan-Dako, E.; Pandey, A.; Monforte Gilabert, AJ.; Picó Sirvent, MB.; Schaefer, H. (2018). Repeated domestication of melon (Cucumis melo) in Africa and Asia and a new close relative from India. American Journal of Botany. 105(10):1662-1671. https://doi.org/10.1002/ajb2.1172S166216711051

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

Background: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding.Results: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions.Conclusion: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties. © 2011 Blanca et al; licensee BioMed Central Ltd.Blanca Postigo, JM.; Cañizares Sales, J.; Roig Montaner, MC.; Ziarsolo Areitioaurtena, P.; Nuez Viñals, F.; Picó Sirvent, MB. (2011). Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics. 12:104-117. doi:10.1186/1471-2164-12-104S1041171

Patterns in German /ʃC/-cluster acquisition

This study reports on the developmental patterns of /ʃC/ clusters in 145 normally developing monolingual German-speaking children between 2;00 and 2;11. All children completed a picture naming task to allow a systematic qualitative analysis of the production patterns. Children’s reductions of target /ʃC/clusters are examined and are evaluated with respect to two models, ‘factorial typology’ and ‘headedness’, to account for them. The results reveal expected patterns of C2 retention for ‘/ʃ/+[−continuant]’ (e.g. ‘/ʃ/+stop’ and ‘/ʃ/+nasal’) targets, and a rather indeterminate pattern for /ʃl/ and /ʃʁ/. The results for /ʃv/, a clear-cut preference of C2 retention, were rather unexpected, as the C2 is a [+continuant]. The explanation offered for the retention of /v/ is related to a place constraint. The study also examines the data from children who reached an advanced stage of cluster formation with differential targets. More specifically, in several children, one target, /ʃv/, is found to have stayed behind in the reduction phase while all others have advanced to the ‘cluster stage’. Neither the type nor the token frequencies seem satisfactory in accounting for the specific behaviour of /ʃv/. The explanation offered for the uniqueness of this target may be its non-abidence to the Sonority Sequencing Principle (SSP) because of its flat sonority and the Obligatory Contour Principle (OCP) [continuant], because of the unchanging ‘continuance’ which is demanded by the OCP. Theoretical and clinical implications are discussed

Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

Genetic influences on psychiatric disorders transcend diagnostic boundaries, suggesting substantial pleiotropy of contributing loci. However, the nature and mechanisms of these pleiotropic effects remain unclear. We performed analyses of 232,964 cases and 494,162 controls from genome-wide studies of anorexia nervosa, attention-deficit/hyper-activity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, and Tourette syndrome. Genetic correlation analyses revealed a meaningful structure within the eight disorders, identifying three groups of inter-related disorders. Meta-analysis across these eight disorders detected 109 loci associated with at least two psychiatric disorders, including 23 loci with pleiotropic effects on four or more disorders and 11 loci with antagonistic effects on multiple disorders. The pleiotropic loci are located within genes that show heightened expression in the brain throughout the lifespan, beginning prenatally in the second trimester, and play prominent roles in neurodevelopmental processes. These findings have important implications for psychiatric nosology, drug development, and risk prediction.Peer reviewe

Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Background Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. Methods We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors. Results Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged. Conclusions Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.Peer reviewe

First international descriptive and interventional survey for cholesterol and non-cholesterol sterol determination by gas- and liquid- chromatography–Urgent need for harmonisation of analytical methods

Serum concentrations of lathosterol, the plant sterols campesterol and sitosterol and the cholesterol metabolite 5α-cholestanol are widely used as surrogate markers of cholesterol synthesis and absorption, respectively. Increasing numbers of laboratories utilize a broad spectrum of well-established and recently developed methods for the determination of cholesterol and non-cholesterol sterols (NCS). In order to evaluate the quality of these measurements and to identify possible sources of analytical errors our group initiated the first international survey for cholesterol and NCS. The cholesterol and NCS survey was structured as a two-part survey which took place in the years 2013 and 2014. The first survey part was designed as descriptive, providing information about the variation of reported results from different laboratories. A set of two lyophilized pooled sera (A and B) was sent to twenty laboratories specialized in chromatographic lipid analysis. The different sterols were quantified either by gas chromatography-flame ionization detection, gas chromatography- or liquid chromatography-mass selective detection. The participants were requested to determine cholesterol and NCS concentrations in the provided samples as part of their normal laboratory routine. The second part was designed as interventional survey. Twenty-two laboratories agreed to participate and received again two different lyophilized pooled sera (C and D). In contrast to the first international survey, each participant received standard stock solutions with defined concentrations of cholesterol and NCS. The participants were requested to use diluted calibration solutions from the provided standard stock solutions for quantification of cholesterol and NCS. In both surveys, each laboratory used its own internal standard (5α-cholestane, epicoprostanol or deuterium labelled sterols). Main outcome of the survey was, that unacceptably high interlaboratory variations for cholesterol and NCS concentrations are reported, even when the individual laboratories used the same calibration material. We discuss different sources of errors and recommend all laboratories analysing cholesterol and NCS to participate in regular quality control programs