Multicopy and stochastic transformation of multipartite pure states

International Nuclear Information System (INIS)

Chen Lin; Hayashi, Masahito

2011-01-01

Characterizing the transformation and classification of multipartite entangled states is a basic problem in quantum information. We study the problem under the two most common environments, local operations and classical communications (LOCC), stochastic LOCC and two more general environments, multicopy LOCC (MCLOCC), and multicopy SLOCC (MCSLOCC). We show that two transformable multipartite states under LOCC or SLOCC are also transformable under MCLOCC and MCSLOCC. What is more, these two environments are equivalent in the sense that two transformable states under MCLOCC are also transformable under MCSLOCC, and vice versa. Based on these environments we classify the multipartite pure states into a few inequivalent sets and orbits, between which we build the partial order to decide their transformation. In particular, we investigate the structure of SLOCC-equivalent states in terms of tensor rank, which is known as the generalized Schmidt rank. Given the tensor rank, we show that Greenberger-Horne-Zeilinger states can be used to generate all states with a smaller or equivalent tensor rank under SLOCC, and all reduced separable states with a cardinality smaller than or equivalent to the tensor rank under LOCC. Using these concepts, we extended the concept of the ''maximally entangled state'' in the multipartite system.

Social participation of children age 8-12 with SLI.

Science.gov (United States)

Sylvestre, Audette; Brisson, Jacinthe; Lepage, Céline; Nadeau, Line; Deaudelin, Isabelle

2016-01-01

Two objectives are being pursued: (1) to describe the level of social participation of children aged 8-12 presenting a specific language impairment (SLI) and (2) to identify personal and family factors associated with their level of social participation. This cross-sectional study was conducted among 29 children with SLI and one of their parents. Parental stress and family adversity were measured as risk factors. The measure of life habits (LIFE-H) adapted to children aged 5-3 was used to measure social participation. The assumption that social participation of these children is impaired in relation to the communication dimension was generally confirmed. The statements referring to the "communication in the community" and "written communication" are those for which the results are weaker. "Communication at home" is made easier albeit with some difficulties, while "telecommunication" is totally preserved. A high level of parental stress is also confirmed, affecting the willingness of parents to support their child's autonomy. The achievement of a normal lifestyle of children with SLI is upset in many spheres of life. Methods of intervention must better reflect the needs and realities experienced by these children in their various living environments, in order to optimize social participation, and consequently, to improve their well-being and that of their families. The need to develop strategies to develop children's independence and to reduce parental stress must be recognized and all stakeholders need to be engaged in the resolution of this challenge. The realization of life habits of SLI children is compromised at various levels, especially in the domain related to "communication in the community" and "written communication". Speech-language pathologists must consider providing ongoing support throughout the primary years of these children and during adolescence, to promote and facilitate the continued realization of life habits of SLI persons. Providing ongoing

Oral Narratives in Monolingual and Bilingual Preschoolers with SLI

Science.gov (United States)

Rezzonico, Stefano; Chen, Xi; Cleave, Patricia L.; Greenberg, Janice; Hipfner-Boucher, Kathleen; Johnson, Carla J.; Milburn, Trelani; Pelletier, Janette; Weitzman, Elaine; Girolametto, Luigi

2015-01-01

Background: The body of literature on narratives of bilingual children with and without specific language impairment (SLI) is growing. However, little is known about the narrative abilities of bilingual preschool children with SLI and their patterns of growth. Aims: To determine the similarities and differences in narrative abilities between…

Benefits of Repeated Book Readings in Children with SLI

Science.gov (United States)

Rohlfing, Katharina J.; Ceurremans, Josefa; Horst, Jessica S.

2018-01-01

In this pilot study, we ask whether repeated storybook reading is also beneficial for word learning in children diagnosed with specific language impairment (SLI). We compared 3-year-old German learning children diagnosed with SLI to typically developing children matched on age and socioeconomic status (SES). One week later, children with SLI…

Narrative comprehension and production in children with SLI: An eye movement study

Science.gov (United States)

ANDREU, LLORENÇ; SANZ-TORRENT, MONICA; OLMOS, JOAN GUÀRDIA; MACWHINNEY, BRIAN

2014-01-01

This study investigates narrative comprehension and production in children with specific language impairment (SLI). Twelve children with SLI (mean age 5; 8 years) and 12 typically developing children (mean age 5; 6 years) participated in an eye-tracking experiment designed to investigate online narrative comprehension and production in Catalan- and Spanish-speaking children with SLI. The comprehension task involved the recording of eye movements during the visual exploration of successive scenes in a story, while listening to the associated narrative. With regard to production, the children were asked to retell the story, while once again looking at the scenes, as their eye movements were monitored. During narrative production, children with SLI look at the most semantically relevant areas of the scenes fewer times than their age-matched controls, but no differences were found in narrative comprehension. Moreover, the analyses of speech productions revealed that children with SLI retained less information and made more semantic and syntactic errors during retelling. Implications for theories that characterize SLI are discussed. PMID:21453036

Executive function behaviours in children with specific language impairment (SLI)

NARCIS (Netherlands)

Cuperus, J.M.; Vugs, B.A.M.; Scheper, A.R.; Hendriks, M.P.H.

2014-01-01

Background: There is growing evidence that linguistic and non-linguistic factors may contribute to the problems associated with specific language impairment (SLI). One factor that has been implicated is executive functioning (EF). Most studies investigating EF in children with SLI use performance

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms.

Science.gov (United States)

Li, Zhen; Defoort, Jonas; Tasdighian, Setareh; Maere, Steven; Van de Peer, Yves; De Smet, Riet

2016-02-01

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. © 2016 American Society of Plant Biologists. All rights reserved.

Executive function training in children with SLI: A pilot study

NARCIS (Netherlands)

Vugs, B.A.M.; Knoors, H.E.T.; Cuperus, J.M.; Hendriks, M.P.H.; Verhoeven, L.T.W.

2017-01-01

The aim of this study was to evaluate the effectiveness of a computer-based executive function (EF) training in children with specific language impairment (SLI). Ten children with SLI, ages 8 to 12 years, completed a 25-session training of visuospatial working memory, inhibition and cognitive

Comparing SLI and dyslexia: developmental language profiles and reading outcomes

NARCIS (Netherlands)

Wijnen, F.N.K.; de Bree, E.H.; van Alphen, P.M.; de Jong, Jan; van der Leij, A.

2015-01-01

In light of the striking overlap in symptoms, it has been proposed that SLI and dyslexia reflect the same underlying disorder, differing only in severity. An alternative view is that SLI and dyslexia overlap (only) partially, sharing some risk factors, and differing on various others. We will

Comparing SLI and dyslexia: Developmental language profiles and reading outcomes

NARCIS (Netherlands)

Wijnen, F.; de Bree, E.; van Alphen, P.M.; de Jong, J.; van der Leij, A.; Stavrakaki, S.

2015-01-01

In light of the striking overlap in symptoms, it has been proposed that SLI and dyslexia reflect the same underlying disorder, differing only in severity. An alternative view is that SLI and dyslexia overlap (only) partially, sharing some risk factors, and differing on various others. We will

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms[OPEN

Science.gov (United States)

Li, Zhen; Van de Peer, Yves; De Smet, Riet

2016-01-01

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of “gene duplicability” is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. PMID:26744215

Interactions between working memory and language in young children with specific language impairment (SLI).

Science.gov (United States)

Vugs, Brigitte; Knoors, Harry; Cuperus, Juliane; Hendriks, Marc; Verhoeven, Ludo

2016-01-01

The underlying structure of working memory (WM) in young children with and without specific language impairment (SLI) was examined. The associations between the components of WM and the language abilities of young children with SLI were then analyzed. The Automated Working Memory Assessment and four linguistic tasks were administered to 58 children with SLI and 58 children without SLI, aged 4-5 years. The WM of the children was best represented by a model with four separate but interacting components of verbal storage, visuospatial storage, verbal central executive (CE), and visuospatial CE. The associations between the four components of WM did not differ significantly for the two groups of children. However, the individual components of WM showed varying associations with the language abilities of the children with SLI. The verbal CE component of WM was moderately to strongly associated with all the language abilities in children with SLI: receptive vocabulary, expressive vocabulary, verbal comprehension, and syntactic development. These results show verbal CE to be involved in a wide range of linguistic skills; the limited ability of young children with SLI to simultaneously store and process verbal information may constrain their acquisition of linguistic skills. Attention should thus be paid to the language problems of children with SLI, but also to the WM impairments that can contribute to their language problems.

Toward epigenetic and gene regulation models of specific language impairment: looking for links among growth, genes, and impairments

Directory of Open Access Journals (Sweden)

Rice Mabel L

2012-11-01

Full Text Available Abstract Children with specific language impairment (SLI are thought to have an inherited form of language impairment that spares other developmental domains. SLI shows strong heritability and recent linkage and association studies have replicated results for candidate genes. Regulatory regions of the genes may be involved. Behavioral growth models of language development of children with SLI reveal that the onset of language is delayed, and the growth trajectories of children with SLI parallel those of younger children without SLI. The rate of language acquisition decelerates in the pre-adolescent period, resulting in immature language levels for the children with SLI that persist into adolescence and beyond. Recent genetic and epigenetic discoveries and models relevant to language impairment are reviewed. T cell regulation of onset, acceleration, and deceleration signaling are described as potential conceptual parallels to the growth timing elements of language acquisition and impairment. A growth signaling disruption (GSD hypothesis is proposed for SLI, which posits that faulty timing mechanisms at the cellular level, intrinsic to neurocortical functioning essential for language onset and growth regulation, are at the core of the growth outcomes of SLI. The GSD highlights the need to document and account for growth patterns over childhood and suggests needed directions for future investigation.

Self-esteem, shyness, and sociability in adolescents with specific language impairment (SLI).

Science.gov (United States)

Wadman, Ruth; Durkin, Kevin; Conti-Ramsden, Gina

2008-08-01

To determine if lower global self-esteem, shyness, and low sociability are outcomes associated with SLI in adolescence. Possible concurrent predictive relationships and gender differences were also examined. Fifty-four adolescents with SLI, aged between 16 and 17 years, were compared with a group of 54 adolescents with typical language abilities on the Rosenberg Self-Esteem scale (Rosenberg, 1965) and the Cheek and Buss Shyness and Sociability scales (Cheek & Buss, 1981). The SLI group had significantly lower global self-esteem scores than the group with typical language abilities. The adolescents with SLI were more shy than their peers, but the groups did not differ in their sociability ratings. Regression analysis found that language ability was not concurrently predictive of self-esteem but shyness was. Mediation analysis suggested that shyness could be a partial but significant mediator in the relationship between language ability and global self-esteem. Older adolescents with SLI are at risk of lower global self-esteem and experience shyness, although they want to interact socially. The relationship between language ability and self-esteem at this point in adolescence is complex, with shyness potentially playing an important mediating role.

Can Children with SLI Detect Cognitive Conflict? Behavioral and Electrophysiological Evidence

Science.gov (United States)

Epstein, Baila; Shafer, Valerie L.; Melara, Robert D.; Schwartz, Richard G.

2014-01-01

Purpose: This study examined whether children with specific language impairment (SLI) are deficient in detecting cognitive conflict between competing response tendencies in a GO/No-GO task. Method: Twelve children with SLI (ages 10--12), 22 children with typical language development matched group-wise on age (TLD-A), and 16 younger children with…

Sentence Imitation as a Marker of SLI in Czech: Disproportionate Impairment of Verbs and Clitics

Science.gov (United States)

Smolík, Filip; Vávru, Petra

2014-01-01

Purpose: The authors examined sentence imitation as a potential clinical marker of specific language impairment (SLI) in Czech and its use to identify grammatical markers of SLI. Method: Children with SLI and the age-and language-matched control groups (total N = 57) were presented with a sentence imitation task, a receptive vocabulary task, and…

Verb inflection in Monolingual Dutch and Sequential Bilingual Turkish-Dutch Children with and without SLI

Science.gov (United States)

Blom, Elma; De Jong, Jan; Orgassa, Antje; Baker, Anne; Weerman, Fred

2013-01-01

Both children with specific language impairment (SLI) and children who acquire a second language (L2) make errors with verb inflection. This overlap between SLI and L2 raises the question if verb inflection can discriminate between L2 children with and without SLI. In this study we addressed this question for Dutch. The secondary goal of the study…

Self-Esteem, Shyness, and Sociability in Adolescents with Specific Language Impairment (SLI)

Science.gov (United States)

Wadman, Ruth; Durkin, Kevin; Conti-Ramsden, Gina

2008-01-01

Purpose: To determine if lower global self-esteem, shyness, and low sociability are outcomes associated with SLI in adolescence. Possible concurrent predictive relationships and gender differences were also examined. Method: Fifty-four adolescents with SLI, aged between 16 and 17 years, were compared with a group of 54 adolescents with typical…

Analogical mapping across modalities in children with specific language impairment (SLI).

Science.gov (United States)

Leroy, Sandrine; Maillart, Christelle; Parisse, Christophe

2014-09-01

Analogical mapping is a domain-general cognitive process found in language development, and more particularly in the abstraction of construction schemas. Analogical mapping is considered as the general cognitive process which consists in the alignment of two or several sequences in order to detect their common relational structure and generalize it to new items. The current study investigated analogical mapping across modalities in children with specific language impairment (SLI). Nineteen children with SLI and their age-matched peers were administered two tasks: a linguistic analogical reasoning task (composed of syllables) and a similar non-linguistic analogical reasoning task (composed of pictures). In the two tasks, the items presented were divided into two groups: items with perceptual cues and items without perceptual cues. Children had to complete a sequence sharing the same relational structure as previously presented sequences. Results showed an expected group effect with poorer performance for children with SLI compared to children with typical language development (TLD). Results corroborate hypotheses suggesting that children with SLI have difficulties with analogical mapping, which may hinder the abstraction of construction schemas. Interestingly, whereas no interaction effect between group and modality (linguistic vs. non-linguistic) was revealed, a triple interaction Group*Modality*Perceptual support was observed. In the non-linguistic task, the performance of children with SLI was the same for items with and without perceptual clues, but in the linguistic task they performed more poorly for items without perceptual cues compared to items with perceptual cues. The results and limits of the study are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Generation of Nanobodies against SlyD and development of tools to eliminate this bacterial contaminant from recombinant proteins.

Science.gov (United States)

Hu, Yaozhong; Romão, Ema; Vertommen, Didier; Vincke, Cécile; Morales-Yánez, Francisco; Gutiérrez, Carlos; Liu, Changxiao; Muyldermans, Serge

2017-09-01

The gene for a protein domain, derived from a tumor marker, fused to His tag codons and under control of a T7 promotor was expressed in E. coli strain BL21 (DE3). The recombinant protein was purified from cell lysates through immobilized metal affinity chromatography and size-exclusion chromatography. A contaminating bacterial protein was consistently co-purified, even using stringent washing solutions containing 50 or 100 mM imidazole. Immunization of a dromedary with this contaminated protein preparation, and the subsequent generation and panning of the immune Nanobody library yielded several Nanobodies of which 2/3 were directed against the bacterial contaminant, reflecting the immunodominance of this protein to steer the dromedary immune response. Affinity adsorption of this contaminant using one of our specific Nanobodies followed by mass spectrometry identified the bacterial contaminant as FKBP-type peptidyl-prolyl cis-trans isomerase (SlyD) from E. coli. This SlyD protein contains in its C-terminal region 14 histidines in a stretch of 31 amino acids, which explains its co-purification on Ni-NTA resin. This protein is most likely present to varying extents in all recombinant protein preparations after immobilized metal affinity chromatography. Using our SlyD-specific Nb 5 we generated an immune-complex that could be removed either by immunocapturing or by size exclusion chromatography. Both methods allow us to prepare a recombinant protein sample where the SlyD contaminant was quantitatively eliminated. Copyright © 2017 Elsevier Inc. All rights reserved.

SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Emily Olorin

2015-08-01

Full Text Available Short linear motifs (SLiMs are small protein sequence patterns that mediate a large number of critical protein-protein interactions, involved in processes such as complex formation, signal transduction, localisation and stabilisation. SLiMs show rapid evolutionary dynamics and are frequently the targets of molecular mimicry by pathogens. Identifying enriched sequence patterns due to convergent evolution in non-homologous proteins has proven to be a successful strategy for computational SLiM prediction. Tools of the SLiMSuite package use this strategy, using a statistical model to identify SLiM enrichment based on the evolutionary relationships, amino acid composition and predicted disorder of the input proteins. The quality of input data is critical for successful SLiM prediction. Cytoscape provides a user-friendly, interactive environment to explore interaction networks and select proteins based on common features, such as shared interaction partners. SLiMScape embeds tools of the SLiMSuite package for de novo SLiM discovery (SLiMFinder and QSLiMFinder and identifying occurrences/enrichment of known SLiMs (SLiMProb within this interactive framework. SLiMScape makes it easier to (1 generate high quality hypothesis-driven datasets for these tools, and (2 visualise predicted SLiM occurrences within the context of the network. To generate new predictions, users can select nodes from a protein network or provide a set of Uniprot identifiers. SLiMProb also requires additional query motif input. Jobs are then run remotely on the SLiMSuite server (http://rest.slimsuite.unsw.edu.au for subsequent retrieval and visualisation. SLiMScape can also be used to retrieve and visualise results from jobs run directly on the server. SLiMScape and SLiMSuite are open source and freely available via GitHub under GNU licenses.

Self-regulatory speech during planning and problem-solving in children with SLI and their typically developing peers.

Science.gov (United States)

Abdul Aziz, Safiyyah; Fletcher, Janet; Bayliss, Donna M

2017-05-01

Past research with children with specific language impairment (SLI) has shown them to have poorer planning and problem-solving ability, and delayed self-regulatory speech (SRS) relative to their typically developing (TD) peers. However, the studies are few in number and are restricted in terms of the number and age range of participants, which limits our understanding of the nature and extent of any delays. Moreover, no study has examined the performance of a significant subset of children with SLI, those who have hyperactive and inattentive behaviours. This cross-sectional study aimed to compare the performance of young children with SLI (aged 4-7 years) with that of their TD peers on a planning and problem-solving task and to examine the use of SRS while performing the task. Within each language group, the performance of children with and without hyperactive and inattentive behaviours was further examined. Children with SLI (n = 91) and TD children (n = 81), with and without hyperactive and inattentive behaviours across the three earliest school years (Kindergarten, Preprimary and Year 1) were video-taped while they completed the Tower of London (TOL), a planning and problem-solving task. Their recorded speech was coded and analysed to look at differences in SRS and its relation to TOL performance across the groups. Children with SLI scored lower on the TOL than TD children. Additionally, children with hyperactive and inattentive behaviours performed worse than those without hyperactive and inattentive behaviours, but only in the SLI group. This suggests that children with SLI with hyperactive and inattentive behaviours experience a double deficit. Children with SLI produced less inaudible muttering than TD children, and showed no reduction in social speech across the first three years of school. Finally, for children with SLI, a higher percentage performed better on the TOL when they used SRS than when they did not. The results point towards a significant delay

Metacognitive Strategies: A Foundation for Early Word Spelling and Reading in Kindergartners with SLI

Science.gov (United States)

Schiff, Rachel; Nuri Ben-Shushan, Yohi; Ben-Artzi, Elisheva

2017-01-01

This study assessed the effect of metacognitive instruction on the spelling and word reading of Hebrew-speaking children with specific language impairment (SLI). Participants were 67 kindergarteners with SLI in a supported learning context. Children were classified into three spelling instruction groups: (a) metalinguistic instruction (ML), (b) ML…

Self-esteem, shyness, and sociability in adolescents with specific language impairment (SLI).

OpenAIRE

Wadman, R.; Durkin, K.; Conti-Ramsden, G.

2008-01-01

Purpose: To determine if lower global self-esteem, shyness, and low sociability are outcomes associated with SLI in adolescence. Possible concurrent predictive relationships and gender differences were also examined. Method: Fifty-four adolescents with SLI, aged between 16 and 17 years, were compared with a group of 54 adolescents with typical language abilities on the Rosenberg Self-Esteem scale (Rosenberg, 1965) and the Cheek and Buss Shyness and Sociability scales (Cheek & Buss, 1981)....

KONTRIBUSI MODAL SOSIAL DALAM PENGEMBANGAN OTOMASI PERPUSTAKAAN: STUDI KASUS KOMUNITAS SLiMS (SENAYAN LIBRARY MANAGEMENT SYSTEM YOGYAKARTA

Directory of Open Access Journals (Sweden)

Yanuar Yoga Prasetyawan

2016-11-01

Full Text Available Today the implementation of information technology in libraries has become a basic need to organize the information, not least in Indonesia. Lack of economic capital (fund and intellectual capital (human resources that have IT educational background cause many library in Indonesia can not be able to buy or self develop the information technology. However SLiMS attend like a panacea, which capable of treating and eliminating the limitations of most libraries in Indonesia. SLiMS is an open source software for the Library Management that can be downloaded and implemented for free. In addition Slims rarely have the power owned by a software (information systems that is a SLiMS User Community. In Indonesia, SLiMS User Community has mushrooming in various regions across Indonesia, one of them in Yogyakarta. Growth and development of SLiMS User Community in Yogyakarta is a manifestation of social capital for the library with lack of information technology implementation. The purpose of this study is to reveal the values and norms are upheld by the Yogyakarta SLiMS User Community that foster social capital which drives community activities as an agent who eliminate the lack of economic capital and intellectual capital that suffered by many libraries in Indonesia. The method used is qualitative method with phenomenological approach. The results showed that the values and norms are upheld together by the Yogyakarta SLiMS User Community is becoming a agent of change of the library conditions in Indonesia, to contribute the automation development in Indonesia. That value and norms are expressed through the sinau bareng. Through sinau bareng, they were learning together to implement SLiMS. Sinau bareng was held each month by a Yogyakarta SLiMS User Community. it became the antidote the lack of libraries. So it will bring justice for all types of libraries to have the right to fulfi ll their basic needs of implementing information technology as library

Correlation between PFGE Groups and mrp/epf/sly Genotypes of Human Streptococcus suis Serotype 2 in Northern Thailand.

Science.gov (United States)

Tharavichitkul, Prasit; Wongsawan, Kanreuthai; Takenami, Naoki; Pruksakorn, Sumalee; Fongcom, Achara; Gottschalk, Marcelo; Khanthawa, Banyong; Supajatura, Volaluk; Takai, Shinji

2014-01-01

Streptococcus suis infection is a severe zoonotic disease commonly found in Northern Thailand where people often consume raw pork and/or pig's blood. The most frequent clinical presentations are meningitis, sepsis, and endocarditis with higher rate of mortality and hearing loss sequelae. To clarify the correlation between pulsed-field gel electrophoresis (PFGE) groups and mrp/epf/sly genotypes of S. suis serotype 2, 62 patient and 4 healthy pig isolates from Northern Thailand were studied. By PFGE analysis, at 66% homology, most human isolates (69.4%) and 1 pig isolate were in group A, whereas 14.5% of human isolates and 3 out of 4 pig isolates were in group D. According to mrp/epf/sly genotypes, 80.6% of human isolates were identified in mrp (+) epf (-) sly (-) and only 12.9% were in mrp (-) epf (-) sly (+) genotypes; in contrast, 1 and 3 pig isolates were detected in these two genotypes, respectively. Interestingly, all isolates of S. suis serotype 2 classified in PFGE groups A, B, and E were set in mrp (+) epf (-) sly (-) genotypes. These data show a close correlation between PFGE groups and mrp/epf/sly genotypes of human S. suis serotype 2.

Multi-copy entanglement purification with practical spontaneous parametric down conversion sources

International Nuclear Information System (INIS)

Zhang Shuai-Shuai; Shu Qi; Sheng Yu-Bo; Zhou Lan

2017-01-01

Entanglement purification is to distill the high quality entanglement from the low quality entanglement with local operations and classical communications. It is one of the key technologies in long-distance quantum communication. We discuss an entanglement purification protocol (EPP) with spontaneous parametric down conversion (SPDC) sources, in contrast to previous EPP with multi-copy mixed states, which requires ideal entanglement sources. We show that the SPDC source is not an obstacle for purification, but can benefit the fidelity of the purified mixed state. This EPP works for linear optics and is feasible in current experiment technology. (paper)

Early preschool processing abilities predict subsequent reading outcomes in bilingual Spanish-Catalan children with Specific Language Impairment (SLI).

Science.gov (United States)

Aguilar-Mediavilla, Eva; Buil-Legaz, Lucía; Pérez-Castelló, Josep A; Rigo-Carratalà, Eduard; Adrover-Roig, Daniel

2014-01-01

Children with Specific Language Impairment (SLI) have severe language difficulties without showing hearing impairments, cognitive deficits, neurological damage or socio-emotional deprivation. However, previous studies have shown that children with SLI show some cognitive and literacy problems. Our study analyses the relationship between preschool cognitive and linguistic abilities and the later development of reading abilities in Spanish-Catalan bilingual children with SLI. The sample consisted of 17 bilingual Spanish-Catalan children with SLI and 17 age-matched controls. We tested eight distinct processes related to phonological, attention, and language processing at the age of 6 years and reading at 8 years of age. Results show that bilingual Spanish-Catalan children with SLI show significantly lower scores, as compared to typically developing peers, in phonological awareness, phonological memory, and rapid automatized naming (RAN), together with a lower outcome in tasks measuring sentence repetition and verbal fluency. Regarding attentional processes, bilingual Spanish-Catalan children with SLI obtained lower scores in auditory attention, but not in visual attention. At the age of 8 years Spanish-Catalan children with SLI had lower scores than their age-matched controls in total reading score, letter identification (decoding), and in semantic task (comprehension). Regression analyses identified both phonological awareness and verbal fluency at the age of 6 years to be the best predictors of subsequent reading performance at the age of 8 years. Our data suggest that language acquisition problems and difficulties in reading acquisition in bilingual children with SLI might be related to the close interdependence between a limitation in cognitive processing and a deficit at the linguistic level. After reading this article, readers will be able to: identify their understanding of the relation between language difficulties and reading outcomes; explain how processing

Substitution rates in the X- and Y-linked genes of the plants, Silene latifolia and S. dioica.

Science.gov (United States)

Filatov, Dmitry A; Charlesworth, Deborah

2002-06-01

Theory predicts that selection should be less effective in the nonrecombining genes of Y-chromosomes, relative to the situation for genes on the other chromosomes, and this should lead to the accumulation of deleterious nonsynonymous substitutions. In addition, synonymous substitution rates may differ between X- and Y-linked genes because of the male-driven evolution effect and also because of actual differences in per-replication mutation rates between the sex chromosomes. Here, we report the first study of synonymous and nonsynonymous substitution rates on plant sex chromosomes. We sequenced two pairs of sex-linked genes, SlX1-SlY1 and SlX4-SlY4, from dioecious Silene latifolia and S. dioica, and their non-sex-linked homologues from nondioecious S. vulgaris and Lychnis flos-jovis, respectively. The rate of nonsynonymous substitutions in the SlY4 gene is significantly higher than that in the SlX4 gene. Silent substitution rates are also significantly higher in both Y-linked genes, compared with their X-linked homologues. The higher nonsynonymous substitution rate in the SlY4 gene is therefore likely to be caused by a mutation rate difference between the sex chromosomes. The difference in silent substitution rates between the SlX4 and SlY4 genes is too great to be explained solely by a higher per-generation mutation rate in males than females. It is thus probably caused by a difference in per-replication mutation rates between the sex chromosomes. This suggests that the local mutation rate can change in a relatively short evolutionary time.

Influence of Phonology on Morpho-Syntax in Romance Languages in Children with Specific Language Impairment (SLI)

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Aguilar-Mediavilla, Eva; Sanz-Torrent, Monica; Serra-Raventos, Miquel

2007-01-01

Background: The profiles of children with Specific Language Impairment (SLI) differ greatly according to the language they speak. The Surface Hypothesis attempts to explain these differences through the theory that children with SLI will incorrectly produce elements in their language with low phonological weights or that are produced in a…

Children with a History of SLI Show Reduced Sensitivity to Audiovisual Temporal Asynchrony: An ERP Study

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Kaganovich, Natalya; Schumaker, Jennifer; Leonard, Laurence B.; Gustafson, Dana; Macias, Danielle

2014-01-01

Purpose: The authors examined whether school-age children with a history of specific language impairment (H-SLI), their peers with typical development (TD), and adults differ in sensitivity to audiovisual temporal asynchrony and whether such difference stems from the sensory encoding of audiovisual information. Method: Fifteen H-SLI children, 15…

The Surgeons' Leadership Inventory (SLI): a taxonomy and rating system for surgeons' intraoperative leadership skills.

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Henrickson Parker, Sarah; Flin, Rhona; McKinley, Aileen; Yule, Steven

2013-06-01

Surgeons must demonstrate leadership to optimize performance and maximize patient safety in the operating room, but no behavior rating tool is available to measure leadership. Ten focus groups with members of the operating room team discussed surgeons' intraoperative leadership. Surgeons' leadership behaviors were extracted and used to finalize the Surgeons' Leadership Inventory (SLI), which was checked by surgeons (n = 6) for accuracy and face validity. The SLI was used to code video recordings (n = 5) of operations to test reliability. Eight elements of surgeons' leadership were included in the SLI: (1) maintaining standards, (2) managing resources, (3) making decisions, (4) directing, (5) training, (6) supporting others, (7) communicating, and (8) coping with pressure. Interrater reliability to code videos of surgeons' behaviors while operating using this tool was acceptable (κ = .70). The SLI is empirically grounded in focus group data and both the leadership and surgical literature. The interrater reliability of the system was acceptable. The inventory could be used for rating surgeons' leadership in the operating room for research or as a basis for postoperative feedback on performance. Copyright © 2013 Elsevier Inc. All rights reserved.

Emotional health in adolescents with and without a history of specific language impairment (SLI)

OpenAIRE

Conti-Ramsden, G.; Botting, N.

2008-01-01

Objective:  This study examined the emotional health of adolescents with and without specific language impairment (SLI).\\ud \\ud Method:  One hundred and thirty-nine adolescents with a history of SLI (15;10 years) and a peer group of 124 adolescents with normal language development (NLD) (15;11 years) participated, who were in their final year of compulsory schooling. The risk of emotional difficulties was assessed using the Moods and Feelings Questionnaire (MFQ) and the Child Manifest Anxiety...

Story grammar elements and causal relations in the narratives of Russian-Hebrew bilingual children with SLI and typical language development.

Science.gov (United States)

Fichman, Sveta; Altman, Carmit; Voloskovich, Anna; Armon-Lotem, Sharon; Walters, Joel

2017-09-01

While there is general agreement regarding poor performance of children with Specific Language Impairment (SLI) on microstructure measures of narrative production, findings on macrostructure are inconsistent. The present study analyzed narrative abilities of Russian-Hebrew bilingual preschool children with and without SLI, with a particular focus on story grammar (SG) elements and causal relations, in order to identify macrostructure features which distinguish bilingual children with SLI from those with typical development. Narratives were collected from 35 typically developing bilinguals (BiTD) and 14 bilinguals with SLI (BiSLI) in both Russian/L1 and Hebrew/L2 using a retelling procedure (LITMUS-Multilingual Assessment Instrument for Narratives) (Gagarina, Klop, Kunnari, Tantele, Välimaa, Balčiūnienė, Bohnacker, & Walters, 2012). Each story contained three episodes, and each episode introduced a different protagonist with explicitly stated Goals (G), Attempts (A) and Outcomes (O). Causal relations assessed included Enabling, Physical, Motivational, and Psychological relations, following Trabasso & Nickels (1992). Each Goal-Attempt-Outcome (GAO) episode was examined for the use of SG elements and causal relations. Group differences emerged for both aspects of macrostructure. For causal relations, narratives of BiSLI children contained fewer Enabling and Physical relations, and differed qualitatively from those of BiTD children. For SG elements, BiSLI children referred to fewer SG elements than BiTD children in the first episode, but performed like BiTD children in the second and the third episodes. Story grammar elements in specific episodes along with Enabling and Physical causal relations distinguish the narratives of children with BiSLI from those with BiTD, which stresses the importance of examining wider array of macrostructure features in narratives. Copyright © 2017 Elsevier Inc. All rights reserved.

Short-lived non-coding transcripts (SLiTs): Clues to regulatory long non-coding RNA.

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Tani, Hidenori

2017-03-22

Whole transcriptome analyses have revealed a large number of novel long non-coding RNAs (lncRNAs). Although the importance of lncRNAs has been documented in previous reports, the biological and physiological functions of lncRNAs remain largely unknown. The role of lncRNAs seems an elusive problem. Here, I propose a clue to the identification of regulatory lncRNAs. The key point is RNA half-life. RNAs with a long half-life (t 1/2 > 4 h) contain a significant proportion of ncRNAs, as well as mRNAs involved in housekeeping functions, whereas RNAs with a short half-life (t 1/2 regulatory ncRNAs and regulatory mRNAs. This novel class of ncRNAs with a short half-life can be categorized as Short-Lived non-coding Transcripts (SLiTs). I consider that SLiTs are likely to be rich in functionally uncharacterized regulatory RNAs. This review describes recent progress in research into SLiTs.

Penerapan Peminjaman Mandiri Berbasis SLiMS Versi Desktop: Studi Kasus di Perpustakaan STAIN Kediri

Directory of Open Access Journals (Sweden)

Muhamad Hamim

2016-07-01

Full Text Available Abstrak; Layanan peminjaman mandiri adalah layanan peminjaman yang dilakukan sendiri oleh pemustaka. Peminjaman mandiri merupakan antarmuka peminjaman koleksi perpustakaan yang terkoneksi dengan database perpustakaan berbasis SLiMS sebagai pusat datanya. Tujuan layanan mandiri adalah untuk mengefektifkan layanan peminjaman di Perpustakaan STAIN Kediri yang memiliki petugas terbatas. Sebelumnya, transaksi peminjaman dilakukan oleh seorang petugas saja. Sering terjadi antrian panjang terutama ketika perpustakaan menjelang tutup atau istirahat. Sehingga diperlukan alternatif pelaksanaan transaksi peminjaman yang lebih efektif dan efisien. Layanan mandiri dikembangkan dengan menggunakan bahasa pemrograman lazarus freepascal dan mengambil data dari aplikasi senayan. Proses peminjaman dilakukan dengan melakukan verifikasi user akun pemustaka, verifikasi koleksi dan verifikasi peminjaman di database SLiMS. Abstract; Selfservice loan isa loan services conducted by the member of library themselves. Self services loan is interface loan transaction that connected to SLiMS Library database server. The purpose is to get more efectivelly loan services at Library of STAIN Kediri because of the lack of staffs. Before hand, Loan services was controlled by one operator. Long waiting line happens almost everyday asspecially at the approach of closing library or break time. however, it needed to develop the loan services that is more effective and eficient. Self sevices loan is developed by using Lazarus free Pascal software and the data is connected to senayan database. Self services loan processed is initiated from the verification of user account, verification of bibliography data and verification of loan data in the SLiMS database.

Adolescents with a history of specific language impairment (SLI): strengths and difficulties in social, emotional and behavioral functioning.

Science.gov (United States)

Conti-Ramsden, Gina; Mok, Pearl L H; Pickles, Andrew; Durkin, Kevin

2013-11-01

Adolescents with specific language impairment (SLI) are at a greater risk of emotional and behavioral problems compared to their typically developing (TD) peers, but little is known about their self-perceived strengths and difficulties. In this study, the self-reported social, emotional and behavioral functioning of 139 adolescents with a history of SLI and 124 TD individuals at age 16 was examined. The self-report version of the Strengths and Difficulties Questionnaire (SDQ) was used to assess their prosocial behavior and levels of peer, emotional and behavioral difficulties. Associations of these areas of functioning with gender, verbal and non-verbal skills were also investigated. Adolescents with a history of SLI were more likely than their TD peers to report higher levels of peer problems, emotional symptoms, hyperactivity and conduct problems. The majority of adolescents in both groups (87% SLI and 96% TD), however, reported prosocial behavior within the typical range. Difficulty with peer relations was the strongest differentiator between the groups, with the odds of reporting borderline or abnormally high levels of peer problems being 12 times higher for individuals with a history of SLI. Adolescents with poorer receptive language skills were also more likely to report higher levels of emotional and behavioral difficulties. The findings of this study identify likely traits that may lead to referral to services. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Transcriptional mechanisms associated with seed dormancy and dormancy loss in the gibberellin-insensitive sly1-2 mutant of Arabidopsis thaliana

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While widespread transcriptome changes have been previously observed with seed dormancy loss, this study specifically characterized transcriptional changes associated with the increased seed dormancy and dormancy loss of the gibberellin (GA) hormone-insensitive sleepy1-2 (sly1-2) mutant. The SLY1 g...

System Life Cycle Evaluation(SM) (SLiCE): harmonizing water treatment systems with implementers' needs.

Science.gov (United States)

Goodman, Joseph; Caravati, Kevin; Foote, Andrew; Nelson, Molly; Woods, Emily

2013-06-01

One of the methods proposed to improve access to clean drinking water is the mobile packaged water treatment system (MPWTS). The lack of published system performance comparisons combined with the diversity of technology available and intended operating conditions make it difficult for stakeholders to choose the system best suited for their application. MPWTS are often deployed in emergency situations, making selection of the appropriate system crucial to avoiding wasted resources and loss of life. Measurable critical-to-quality characteristics (CTQs) and a system selection tool for MPWTS were developed by utilizing relevant literature, including field studies, and implementing and comparing seven different MPWTS. The proposed System Life Cycle Evaluation (SLiCE) method uses these CTQs to evaluate the diversity in system performance and harmonize relevant performance with stakeholder preference via a selection tool. Agencies and field workers can use SLiCE results to inform and drive decision-making. The evaluation and selection tool also serves as a catalyst for communicating system performance, common design flaws, and stakeholder needs to system manufacturers. The SLiCE framework can be adopted into other emerging system technologies to communicate system performance over the life cycle of use.

Correlation between PFGE Groups and mrp/epf/sly Genotypes of Human Streptococcus suis Serotype 2 in Northern Thailand

Directory of Open Access Journals (Sweden)

Prasit Tharavichitkul

2014-01-01

Full Text Available Streptococcus suis infection is a severe zoonotic disease commonly found in Northern Thailand where people often consume raw pork and/or pig’s blood. The most frequent clinical presentations are meningitis, sepsis, and endocarditis with higher rate of mortality and hearing loss sequelae. To clarify the correlation between pulsed-field gel electrophoresis (PFGE groups and mrp/epf/sly genotypes of S. suis serotype 2, 62 patient and 4 healthy pig isolates from Northern Thailand were studied. By PFGE analysis, at 66% homology, most human isolates (69.4% and 1 pig isolate were in group A, whereas 14.5% of human isolates and 3 out of 4 pig isolates were in group D. According to mrp/epf/sly genotypes, 80.6% of human isolates were identified in mrp+epf−sly− and only 12.9% were in mrp−epf−sly+ genotypes; in contrast, 1 and 3 pig isolates were detected in these two genotypes, respectively. Interestingly, all isolates of S. suis serotype 2 classified in PFGE groups A, B, and E were set in mrp+epf−sly− genotypes. These data show a close correlation between PFGE groups and mrp/epf/sly genotypes of human S. suis serotype 2.

Core subjects at the end of primary school: identifying and explaining relative strengths of children with specific language impairment (SLI)

Science.gov (United States)

Durkin, Kevin; Mok, Pearl L H; Conti-Ramsden, Gina

2015-01-01

Background In general, children with specific language impairment (SLI) tend to fall behind their typically developing (TD) peers in educational attainment. Less is known about how children with SLI fare in particular areas of the curriculum and what predicts their levels of performance. Aims To compare the distributions of performance of children with SLI in three core school subjects (English, Mathematics and Science); to test the possibility that performance would vary across the core subjects; and to examine the extent to which language impairment predicts performance. Methods & Procedures This study was conducted in England and reports historical data on educational attainments. Teacher assessment and test scores of 176 eleven-year-old children with SLI were examined in the three core subjects and compared with known national norms. Possible predictors of performance were measured, including language ability at ages 7 and 11, educational placement type, and performance IQ. Outcomes & Results Children with SLI, compared with national norms, were found to be at a disadvantage in core school subjects. Nevertheless, some children attained the levels expected of TD peers. Performance was poorest in English; relative strengths were indicated in Science and, to a lesser extent, in Mathematics. Language skills were significant predictors of performance in all three core subjects. PIQ was the strongest predictor for Mathematics. For Science, both early language skills at 7 years and PIQ made significant contributions. Conclusions & Implications Language impacts on the school performance of children with SLI, but differentially across subjects. English for these children is the most challenging of the core subjects, reflecting the high levels of language demand it incurs. Science is an area of relative strength and mathematics appears to be intermediate, arguably because some tasks in these subjects can be performed with less reliance on verbal processing. Many children

Core subjects at the end of primary school: identifying and explaining relative strengths of children with specific language impairment (SLI).

Science.gov (United States)

Durkin, Kevin; Mok, Pearl L H; Conti-Ramsden, Gina

2015-01-01

In general, children with specific language impairment (SLI) tend to fall behind their typically developing (TD) peers in educational attainment. Less is known about how children with SLI fare in particular areas of the curriculum and what predicts their levels of performance. To compare the distributions of performance of children with SLI in three core school subjects (English, Mathematics and Science); to test the possibility that performance would vary across the core subjects; and to examine the extent to which language impairment predicts performance. This study was conducted in England and reports historical data on educational attainments. Teacher assessment and test scores of 176 eleven-year-old children with SLI were examined in the three core subjects and compared with known national norms. Possible predictors of performance were measured, including language ability at ages 7 and 11, educational placement type, and performance IQ. Children with SLI, compared with national norms, were found to be at a disadvantage in core school subjects. Nevertheless, some children attained the levels expected of TD peers. Performance was poorest in English; relative strengths were indicated in Science and, to a lesser extent, in Mathematics. Language skills were significant predictors of performance in all three core subjects. PIQ was the strongest predictor for Mathematics. For Science, both early language skills at 7 years and PIQ made significant contributions. Language impacts on the school performance of children with SLI, but differentially across subjects. English for these children is the most challenging of the core subjects, reflecting the high levels of language demand it incurs. Science is an area of relative strength and mathematics appears to be intermediate, arguably because some tasks in these subjects can be performed with less reliance on verbal processing. Many children with SLI do have the potential to reach or exceed educational targets that are set

The Role of Phonological Working Memory in Children with SLI

Science.gov (United States)

Torrens, Vicenç; Yagüe, Esther

2018-01-01

This article studies three measures of phonological working memory as tools to identify SLI children: word repetition, nonce word repetition, and digit memory. We propose that a deficit in the phonological loop causes a delay in the acquisition of lexicon, morphosyntax, and discourse. In this research we try to find out whether the scores in these…

Multi-copy entanglement purification with practical spontaneous parametric down conversion sources

Science.gov (United States)

Zhang, Shuai-Shuai; Shu, Qi; Zhou, Lan; Sheng, Yu-Bo

2017-06-01

Entanglement purification is to distill the high quality entanglement from the low quality entanglement with local operations and classical communications. It is one of the key technologies in long-distance quantum communication. We discuss an entanglement purification protocol (EPP) with spontaneous parametric down conversion (SPDC) sources, in contrast to previous EPP with multi-copy mixed states, which requires ideal entanglement sources. We show that the SPDC source is not an obstacle for purification, but can benefit the fidelity of the purified mixed state. This EPP works for linear optics and is feasible in current experiment technology. Project supported by the National Natural Science Foundation of China (Grant Nos. 11474168 and 61401222), the Natural Science Foundation of Jiangsu Province, China (Grant No. BK20151502), the Qing Lan Project in Jiangsu Province, China, and a Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions, China.

Theory of mind in SLI revisited: links with syntax, comparisons with ASD.

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Durrleman, Stephanie; Burnel, Morgane; Reboul, Anne

2017-11-01

According to the linguistic determinism approach, knowledge of sentential complements such as: John says that the earth is flat plays a crucial role in theory of mind (ToM) development by providing a means to represent explicitly people's mental attitudes and beliefs. This approach predicts that mastery of complements determines successful belief reasoning across explicit ToM tasks, even low-verbal ones, and across populations. (1) To investigate the link between a low-verbal ToM-task and complements in Specific Language Impairment (SLI), (2) To determine whether this population shows similar ToM performance to that of children with Autism Spectrum Disorder (ASD) or those with Typical Development (TD) once these groups are matched on competency for complements, (3) To explore whether complements conveying a falsehood without jeopardizing the veracity of the entire sentence, such as complements of verbs of communication, are more crucial for belief attribution than complements which do not have this property, namely complements of verbs of perception, (?John sees that the earth is flat). Children with SLI (n = 20), with ASD (n = 34) and TD (n = 30) completed sentence-picture-matching tasks assessing complementation with communication and perception verbs, as well as a picture-sequencing task assessing ToM. Children were furthermore evaluated for general grammatical and lexical abilities and non-verbal IQ. Results reveal that competency on complements relates to ToM performance with a low-verbal task in SLI, and that SLI, ASD and TD groups of equivalent performance on complements also perform similarly for ToM. Results further suggest that complements with an independent truth-value are the only ones to show a significant relation to ToM performance after teasing out the impact of non-verbal reasoning. This study suggests that clinical groups of different aetiologies as well as TD children perform comparably for ToM once they have similar complementation skills

Diagnostic accuracy of repetition tasks for the identification of specific language impairment (SLI) in bilingual children: evidence from Russian and Hebrew.

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Armon-Lotem, Sharon; Meir, Natalia

2016-11-01

Previous research demonstrates that repetition tasks are valuable tools for diagnosing specific language impairment (SLI) in monolingual children in English and a variety of other languages, with non-word repetition (NWR) and sentence repetition (SRep) yielding high levels of sensitivity and specificity. Yet, only a few studies have addressed the diagnostic accuracy of repetition tasks in bilingual children, and most available research focuses on English-Spanish sequential bilinguals. To evaluate the efficacy of three repetition tasks (forward digit span (FWD), NWR and SRep) in order to distinguish mono- and bilingual children with and without SLI in Russian and Hebrew. A total of 230 mono- and bilingual children aged 5;5-6;8 participated in the study: 144 bilingual Russian-Hebrew-speaking children (27 with SLI); and 52 monolingual Hebrew-speaking children (14 with SLI) and 34 monolingual Russian-speaking children (14 with SLI). Parallel repetition tasks were designed in both Russian and Hebrew. Bilingual children were tested in both languages. The findings confirmed that NWR and SRep are valuable tools in distinguishing monolingual children with and without SLI in Russian and Hebrew, while the results for FWD were mixed. Yet, testing of bilingual children with the same tools using monolingual cut-off points resulted in inadequate diagnostic accuracy. We demonstrate, however, that the use of bilingual cut-off points yielded acceptable levels of diagnostic accuracy. The combination of SRep tasks in L1/Russian and L2/Hebrew yielded the highest overall accuracy (i.e., 94%), but even SRep alone in L2/Hebrew showed excellent levels of sensitivity (i.e., 100%) and specificity (i.e., 89%), reaching 91% of total diagnostic accuracy. The results are very promising for identifying SLI in bilingual children and for showing that testing in the majority language with bilingual cut-off points can provide an accurate classification. © 2016 Royal College of Speech and Language

Auditory short-term memory trace formation for nonspeech and speech in SLI and dyslexia as indexed by the N100 and mismatch negativity electrophysiological responses.

Science.gov (United States)

Tuomainen, Outi T

2015-04-15

This study investigates nonspeech and speech processing in specific language impairment (SLI) and dyslexia. We used a passive mismatch negativity (MMN) task to tap automatic brain responses and an active behavioural task to tap attended discrimination of nonspeech and speech sounds. Using the roving standard MMN paradigm, we varied the number of standards ('few' vs. 'many') to investigate the effect of sound repetition on N100 and MMN responses. The results revealed that the SLI group needed more repetitions than dyslexics and controls to create a strong enough sensory trace to elicit MMN. In contrast, in the behavioural task, we observed good discrimination of speech and nonspeech in all groups. The findings indicate that auditory processing deficits in SLI and dyslexia are dissociable and that memory trace formation may be implicated in SLI.

Gene copy number reduction in the azoospermia factor c (AZFc) region and its effect on total motile sperm count

NARCIS (Netherlands)

Noordam, Michiel J.; Westerveld, G. Henrike; Hovingh, Suzanne E.; van Daalen, Saskia K. M.; Korver, Cindy M.; van der Veen, Fulco; van Pelt, Ans M. M.; Repping, Sjoerd

2011-01-01

The azoospermia factor c (AZFc) region harbors multi-copy genes that are expressed in the testis. Deletions of the AZFc region lead to reduced copy numbers of these genes. Four (partial) AZFc deletions have been described of which the b2/b4 and gr/gr deletions affect semen quality. In most studies,

Can you spell dyslexia without SLI? Comparing the cognitive profiles of dyslexia and specific language impairment and their roles in learning.

Science.gov (United States)

Alloway, Tracy Packiam; Tewolde, Furtuna; Skipper, Dakota; Hijar, David

2017-06-01

The aim of the present study is to explore whether those with Specific Language Impairment (SLI) and dyslexia display distinct or overlapping cognitive profiles with respect to learning outcomes. In particular, we were interested in two key cognitive skills associated with academic performance - working memory and IQ. We recruited three groups of children - those with SLI, those with dyslexia, and a control group. All children were given standardized tests of working memory, IQ (vocabulary and matrix), spelling, and math. The pattern of results suggests that both children with dyslexia and SLI are characterized with poorer verbal working memory and IQ compared to controls, but preserved nonverbal cognitive skills. It appears that that these two disorder groups cannot be distinguished by the severity of their cognitive deficits. However, there was a differential pattern with respect to learning outcomes, where the children with dyslexia rely more on visual skills in spelling, while those with SLI use their relative strengths in vocabulary. These findings can have important implications for how intervention is tailored in the classroom, as disorder-specific support could yield important gains in learning. Copyright © 2017. Published by Elsevier Ltd.

COBRA System Engineering Processes to Achieve SLI Strategic Goals

Science.gov (United States)

Ballard, Richard O.

2003-01-01

The COBRA Prototype Main Engine Development Project was an endeavor conducted as a joint venture between Pratt & Whitney and Aerojet to conduct risk reduction in LOX/LH2 main engine technology for the NASA Space Launch Initiative (SLI). During the seventeen months of the project (April 2001 to September 2002), approximately seventy reviews were conducted, beginning with the Engine Systems Requirements Review (SRR) and ending with the Engine Systems Interim Design Review (IDR). This paper discusses some of the system engineering practices used to support the reviews and the overall engine development effort.

Development of morphosyntactic accuracy and grammatical complexity in Dutch school-age children with SLI

NARCIS (Netherlands)

Zwitserlood, R.L.M.; Weerdenburg, M.W.C. van; Verhoeven, L.T.W.; Wijnen, F.N.K.

2015-01-01

Purpose: The purpose of this study was to identify the development of morphosyntactic accuracy and grammatical complexity in Dutch school-age children with specific language impairment (SLI). Method: Morphosyntactic accuracy, the use of dummy auxiliaries, and complex syntax were assessed using a

Development of morphosyntactic accuracy and grammatical complexity in dutch school-age children with SLI

NARCIS (Netherlands)

Zwitserlood, Rob; van Weerdenburg, Marjolijn; Verhoeven, Ludo; Wijnen, Frank

2015-01-01

Purpose: The purpose of this study was to identify the development of morphosyntactic accuracy and grammatical complexity in Dutch school-age children with specific language impairment (SLI). Method: Morphosyntactic accuracy, the use of dummy auxiliaries, and complex syntax were assessed using a

The role of candidate-gene CNTNAP2 in childhood apraxia of speech and specific language impairment.

Science.gov (United States)

Centanni, T M; Sanmann, J N; Green, J R; Iuzzini-Seigel, J; Bartlett, C; Sanger, W G; Hogan, T P

2015-10-01

Childhood apraxia of speech (CAS) is a debilitating pediatric speech disorder characterized by varying symptom profiles, comorbid deficits, and limited response to intervention. Specific Language Impairment (SLI) is an inherited pediatric language disorder characterized by delayed and/or disordered oral language skills including impaired semantics, syntax, and discourse. To date, the genes associated with CAS and SLI are not fully characterized. In the current study, we evaluated behavioral and genetic profiles of seven children with CAS and eight children with SLI, while ensuring all children were free of comorbid impairments. Deletions within CNTNAP2 were found in two children with CAS but not in any of the children with SLI. These children exhibited average to high performance on language and word reading assessments in spite of poor articulation scores. These findings suggest that genetic variation within CNTNAP2 may be related to speech production deficits. © 2015 Wiley Periodicals, Inc.

Transcription of the var genes from a freshly-obtained field isolate of Plasmodium falciparum shows more variable switching patterns than long laboratory-adapted isolates.

Science.gov (United States)

Ye, Run; Zhang, Dongmei; Chen, Biaobang; Zhu, Yongqiang; Zhang, Yilong; Wang, Shengyue; Pan, Weiqing

2015-02-07

Antigenic variation in Plasmodium falciparum involves switching among multicopy var gene family and is responsible for immune evasion and the maintenance of chronic infections. Current understanding of var gene expression and switching patterns comes from experiments conducted on long laboratory-adapted strains, with little known about their wild counterparts. Genome sequencing was used to obtain 50 var genes from a parasite isolated from the China-Myanmar border. Four clones with different dominant var genes were cultured in vitro in replicates for 50 generations. Transcription of the individual var gene was detected by real-time PCR and then the switching process was analysed. The expression of multicopy var genes is mutually exclusive in clones of a wild P. falciparum isolate. The activation of distinct primary dominant var genes leads to different and favoured switching patterns in the four clones. The on/off rates of individual var genes are variable and the choice of subsequent dominant var genes are random, which results in the different switching patterns among replicates of each clonal wild P. falciparum isolate with near identical initial transcription profiles. This study suggests that the switching patterns of var genes are abundant, which consist of both conserved and random parts.

'Sly grog' and 'homebrew': a qualitative examination of illicit alcohol and some of its impacts on Indigenous communities with alcohol restrictions in regional and remote Queensland (Australia).

Science.gov (United States)

Fitts, Michelle S; Robertson, Jan; Towle, Simon; Doran, Chris M; McDermott, Robyn; Miller, Adrian; Margolis, Stephen; Ypinazar, Valmae; Clough, Alan R

2017-08-01

Indigenous communities in Queensland (Australia) have been subject to Alcohol Management Plans since 2002/03, with significant penalties for breaching restrictions. 'Sly grog' and 'homebrew' provide access to alcohol despite restrictions. This paper describes how this alcohol is made available and the risks and impacts involved. In affected towns and communities across a large area of rural and remote Queensland, interviews and focus groups documented experiences and views of 255 long-standing community members and service providers. Using an inductive framework, transcribed interviews were analysed to identify supply mechanisms, community and service provider responses and impacts experienced. 'Homebrew' was reportedly manufactured in just a few localities, in locally-specific forms bringing locally-specific harms. However, 'sly grog' sourced from licensed premises located long distances from communities, is a widespread concern across the region. 'Sly grog' sellers circumvent retailers' takeaway liquor license conditions, stockpile alcohol outside restricted areas, send hoax messages to divert enforcement and take extraordinary risks to avoid apprehension. Police face significant challenges to enforce restrictions. On-selling of 'sly grog' appears more common in remote communities with total prohibition. Despite different motives for involvement in an illicit trade 'sly grog' consumers and sellers receive similar penalties. There is a need for: (a) a more sophisticated regional approach to managing takeaway alcohol sales from licensed suppliers, (b) targeted penalties for 'sly grog' sellers that reflect its significant community impact, (c) strategies to reduce the demand for alcohol and (d) research to assess the effects of these strategies in reducing harms.

Results form 2+1 flavours of SLiNC fermions

International Nuclear Information System (INIS)

Bietenholz, W.; Cundy, N.

2009-10-01

QCD results are presented for a 2+1 flavour fermion clover action (which we call the SLiNC action). A method of tuning the quark masses to their physical values is discussed. In this method the singlet quark mass is kept fixed, which solves the problem of different renormalisations (for singlet and non-singlet quark masses) occuring for non-chirally invariant lattice fermions. This procedure enables a wide range of quark masses to be probed, including the case with a heavy up-down quark mass and light strange quark mass. Preliminary results show the correct splittings for the baryon (octet and) decuplet spectrum. (orig.)

Fabricating 40 µm-thin silicon solar cells with different orientations by using SLiM-cut method

Science.gov (United States)

Wang, Teng-Yu; Chen, Chien-Hsun; Shiao, Jui-Chung; Chen, Sung-Yu; Du, Chen-Hsun

2017-10-01

Thin silicon foils with different crystal orientations were fabricated using the stress induced lift-off (SLiM-cut) method. The thickness of the silicon foils was approximately 40 µm. The ≤ft foil had a smoother surface than the ≤ft foil. With surface passivation, the minority carrier lifetimes of the ≤ft and ≤ft silicon foil were 1.0 µs and 1.6 µs, respectively. In this study, 4 cm2-thin silicon solar cells with heterojunction structures were fabricated. The energy conversion efficiencies were determined to be 10.74% and 14.74% for the ≤ft and ≤ft solar cells, respectively. The surface quality of the silicon foils was determined to affect the solar cell character. This study demonstrated that fabricating the solar cell by using silicon foil obtained from the SLiM-cut method is feasible.

Enablers and challenges of post-16 education and employment outcomes: the perspectives of young adults with a history of SLI.

Science.gov (United States)

Carroll, Catherine; Dockrell, Julie

2012-01-01

Research studies have begun to investigate the post-16 outcomes for young adults with a specific language impairment (SLI). As yet only tentative conclusions can be drawn with respect to academic and employment outcomes and the factors that are associated with more positive outcomes. Evidence for these findings has relied predominantly on associations between various language, academic and psychosocial assessments. Little attention has been paid to the perspective of the young person. To investigate from the perspective of a group of young people with a history of SLI the factors they believed have enabled and presented a challenge to their post-16 education and employment outcomes and experiences. Nineteen (four female, 15 male) young people aged from 19 to 23 years (average age 21 years), who had all attended the same residential special school for pupils with SLI, were interviewed face to face to explore their views as to what had enabled and limited their transition experiences to date. The data were analysed using thematic analysis. The majority of the young people saw themselves as key agents of change and very active participants in steering their own transition since leaving school. They acknowledged the important role played by their parents and families and how factors such as SLI had affected their transition experiences. The study supports evidence from research with different groups of young people with special educational needs (SEN) and disabilities of the importance of school and post-16 curriculums which develop agency on behalf of the young person. © 2012 Royal College of Speech and Language Therapists.

Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations

DEFF Research Database (Denmark)

Lucotte, Elise A; Skov, Laurits; Jensen, Jacob Malte

2018-01-01

we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing...... related Y haplogroups, that diversified less than 50,000 years ago. Moreover, X and Y-linked ampliconic genes seem to have a faster amplification dynamic than autosomal multicopy genes. Looking at expression data from another study, we also find that XY-linked ampliconic genes with extensive copy number...

Bacillus caldolyticus prs gene encoding phosphoribosyldiphosphate synthase

DEFF Research Database (Denmark)

Krath, Britta N.; Hove-Jensen, Bjarne

1996-01-01

The prs gene, encoding phosphoribosyl-diphosphate (PRPP) synthase, as well as the flanking DNA sequences were cloned and sequenced from the Gram-positive thermophile, Bacillus caldolyticus. Comparison with the homologous sequences from the mesophile, Bacillus subtilis, revealed a gene (gca......D) encoding N-acetylglucosamine-l-phosphate uridyltransferase upstream of prs, and a gene homologous to ctc downstream of prs. cDNA synthesis with a B. caldolyticus gcaD-prs-ctc-specified mRNA as template, followed by amplification utilising the polymerase chain reaction indicated that the three genes are co......-transcribed. Comparison of amino acid sequences revealed a high similarity among PRPP synthases across a wide phylogenetic range. An E. coli strain harbouring the B. caldolyticus prs gene in a multicopy plasmid produced PRPP synthase activity 33-fold over the activity of a haploid B. caldolyticus strain. B. caldolyticus...

The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design.

Science.gov (United States)

Schubert, Christian R; Stultz, Collin M

2009-08-01

Fragment-based ligand design approaches, such as the multi-copy simultaneous search (MCSS) methodology, have proven to be useful tools in the search for novel therapeutic compounds that bind pre-specified targets of known structure. MCSS offers a variety of advantages over more traditional high-throughput screening methods, and has been applied successfully to challenging targets. The methodology is quite general and can be used to construct functionality maps for proteins, DNA, and RNA. In this review, we describe the main aspects of the MCSS method and outline the general use of the methodology as a fundamental tool to guide the design of de novo lead compounds. We focus our discussion on the evaluation of MCSS results and the incorporation of protein flexibility into the methodology. In addition, we demonstrate on several specific examples how the information arising from the MCSS functionality maps has been successfully used to predict ligand binding to protein targets and RNA.

Rapid Integration of Multi-copy Transgenes Using Optogenetic Mutagenesis in Caenorhabditis elegans

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Kentaro Noma

2018-06-01

Full Text Available Stably transmitted transgenes are indispensable for labeling cellular components and manipulating cellular functions. In Caenorhabditis elegans, transgenes are generally generated as inheritable multi-copy extrachromosomal arrays, which can be stabilized in the genome through a mutagenesis-mediated integration process. Standard methods to integrate extrachromosomal arrays primarily use protocols involving ultraviolet light plus trimethylpsoralen or gamma- or X-ray irradiation, which are laborious and time-consuming. Here, we describe a one-step integration method, following germline-mutagenesis induced by mini Singlet Oxygen Generator (miniSOG. Upon blue light treatment, miniSOG tagged to histone (Histone-miniSOG generates reactive oxygen species (ROS and induces heritable mutations, including DNA double-stranded breaks. We demonstrate that we can bypass the need to first establish extrachromosomal transgenic lines by coupling microinjection of desired plasmids with blue light illumination on Histone-miniSOG worms to obtain integrants in the F3 progeny. We consistently obtained more than one integrant from 12 injected animals in two weeks. This optogenetic approach significantly reduces the amount of time and labor for transgene integration. Moreover, it enables to generate stably expressed transgenes that cause toxicity in animal growth.

Duration of Auditory Sensory Memory in Parents of Children with SLI: A Mismatch Negativity Study

Science.gov (United States)

Barry, Johanna G.; Hardiman, Mervyn J.; Line, Elizabeth; White, Katherine B.; Yasin, Ifat; Bishop, Dorothy V. M.

2008-01-01

In a previous behavioral study, we showed that parents of children with SLI had a subclinical deficit in phonological short-term memory. Here, we tested the hypothesis that they also have a deficit in nonverbal auditory sensory memory. We measured auditory sensory memory using a paradigm involving an electrophysiological component called the…

Comparing Multilingual Children with SLI to Their Bilectal Peers: Evidence from Object and Action Picture Naming

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Kambanaros, Maria; Grohmann, Kleanthes K.; Michaelides, Michalis; Theodorou, Elena

2013-01-01

Against the background of the increasing number of multilingual children with atypical language development around the world, this study reports research results on grammatical word class processing involving children with specific language impairment (SLI). The study investigates lexical retrieval of verbs (through picture-naming actions) and…

Three gene expression vector sets for concurrently expressing multiple genes in Saccharomyces cerevisiae.

Science.gov (United States)

Ishii, Jun; Kondo, Takashi; Makino, Harumi; Ogura, Akira; Matsuda, Fumio; Kondo, Akihiko

2014-05-01

Yeast has the potential to be used in bulk-scale fermentative production of fuels and chemicals due to its tolerance for low pH and robustness for autolysis. However, expression of multiple external genes in one host yeast strain is considerably labor-intensive due to the lack of polycistronic transcription. To promote the metabolic engineering of yeast, we generated systematic and convenient genetic engineering tools to express multiple genes in Saccharomyces cerevisiae. We constructed a series of multi-copy and integration vector sets for concurrently expressing two or three genes in S. cerevisiae by embedding three classical promoters. The comparative expression capabilities of the constructed vectors were monitored with green fluorescent protein, and the concurrent expression of genes was monitored with three different fluorescent proteins. Our multiple gene expression tool will be helpful to the advanced construction of genetically engineered yeast strains in a variety of research fields other than metabolic engineering. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

DNA probe labeling with digoxigenin-dUTP and its application in gene diagnosis

International Nuclear Information System (INIS)

Liu Guoyang

1992-01-01

DNA probe labeling by the randomly primed incorporation of digoxigenin-dUTP is reported. The sensitivity of color reaction and hybridization were 32 fg and 200 fg, respectively, and both were specific for the target. Single-copy and multi-copy gene fragments among 2 μg human genomic DNA were detected by β IVS II, Fr 3-42 and 3'HVR labeled with digoxigenin-dUTP. The results were consistent with a radioactive control assay. This method has been successfully used in the gene diagnosis of adult polycystic kidney disease

Communication and Social Deficits in Relatives of Individuals with SLI and Relatives of Individuals with ASD

Science.gov (United States)

Pickles, Andrew; St Clair, Michelle C.; Conti-Ramsden, Gina

2013-01-01

We investigate two aspects of the autism triad, communication and social difficulties, in relatives of specific language impairment (SLI) probands (with and without additional autistic symptomatology) as compared to relatives of autism spectrum disorder (ASD) and Down's syndrome (DS) probands. Findings involving 726 first degree relatives of 85…

Do children with SLI use verbs to predict arguments and adjuncts: evidence from eye movements during listening.

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Llorenç eAndreu

2016-01-01

Full Text Available Different psycholinguistic theories have suggested the importance of verb semantics in rapidly anticipating upcoming information during real-time sentence comprehension. To date, no study has examined if children use verbs to predict arguments and adjuncts in sentence comprehension using children with specific language impairment (SLI.Twenty-five children with SLI (aged 5 years and 3 months to 8 years and 2 months, twenty-five age-matched controls (aged 5 years and 3 months to 8 years and 2 months, twenty-five MLU-w controls (aged 3 years and 3 months to 7 years and 1 month, and 31 adults took part in the study. The eye movements of participants were monitored while they heard twenty-four sentences, such as El hombre lee con atención un cuento en la cama (translation: The man carefully reads a storybook in bed, in the presence of four depicted objects, one of which was the target (storybook, another, the competitor (bed, and another two, distracters (wardrobe and grape. The proportion of looks revealed that, when the meaning of the verb was retrieved, the upcoming argument and adjunct referents were rapidly anticipated. However, the proportion of looks at the theme, source/goal and instrument referents were significantly higher than the looks at the locatives. This pattern was found in adults as well as children with and without language impairment. The present results suggest that, in terms of sentence comprehension, the ability to understand verb information is not severely impaired in children with SLI.

Characterization of the ovine ribosomal protein SA gene and its pseudogenes

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Van Zeveren Alex

2010-03-01

Full Text Available Abstract Background The ribosomal protein SA (RPSA, previously named 37-kDa laminin receptor precursor/67-kDa laminin receptor (LRP/LR is a multifunctional protein that plays a role in a number of pathological processes, such as cancer and prion diseases. In all investigated species, RPSA is a member of a multicopy gene family consisting of one full length functional gene and several pseudogenes. Therefore, for studies on RPSA related pathways/pathologies, it is important to characterize the whole family and to address the possible function of the other RPSA family members. The present work aims at deciphering the RPSA family in sheep. Results In addition to the full length functional ovine RPSA gene, 11 other members of this multicopy gene family, all processed pseudogenes, were identified. Comparison between the RPSA transcript and these pseudogenes shows a large variety in sequence identities ranging from 99% to 74%. Only one of the 11 pseudogenes, i.e. RPSAP7, shares the same open reading frame (ORF of 295 amino acids with the RPSA gene, differing in only one amino acid. All members of the RPSA family were annotated by comparative mapping and fluorescence in situ hybridization (FISH localization. Transcription was investigated in the cerebrum, cerebellum, spleen, muscle, lymph node, duodenum and blood, and transcripts were detected for 6 of the 11 pseudogenes in some of these tissues. Conclusions In the present work we have characterized the ovine RPSA family. Our results have revealed the existence of 11 ovine RPSA pseudogenes and provide new data on their structure and sequence. Such information will facilitate molecular studies of the functional RPSA gene taking into account the existence of these pseudogenes in the design of experiments. It remains to be investigated if the transcribed members are functional as regulatory non-coding RNA or as functional proteins.

Article choice in children with High Functioning Autism (HFA) and in children with Specific Language Impairment (SLI).

NARCIS (Netherlands)

Schaeffer, J.; van Witteloostuijn, M.; de Haan, D.

2014-01-01

This study reports on the choice between a definite and an indefinite article by children with High Functioning Autism (HFA) and children with Specific Language Impairment (SLI). We carried out an elicited production task with 16 Dutch-speaking non-grammatically impaired children with HFA aged 6-13,

Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens

Energy Technology Data Exchange (ETDEWEB)

Elfenbein, Johanna R.; Knodler, Leigh A.; Nakayasu, Ernesto S.; Ansong, Charles; Brewer, Heather M.; Bogomolnaya, Lydia; Adams, L. Garry; McClelland, Michael; Adkins, Joshua N.; Andrews-Polymenis, Helene L.; Fang, Ferric C.

2015-09-14

Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking its retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.

Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

Science.gov (United States)

Bickhart, Derek M.; Xu, Lingyang; Hutchison, Jana L.; Cole, John B.; Null, Daniel J.; Schroeder, Steven G.; Song, Jiuzhou; Garcia, Jose Fernando; Sonstegard, Tad S.; Van Tassell, Curtis P.; Schnabel, Robert D.; Taylor, Jeremy F.; Lewin, Harris A.; Liu, George E.

2016-01-01

The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future. PMID:27085184

Cross-Linguistic Transfer Effects after Phonologically Based Cognate Therapy in a Case of Multilingual Specific Language Impairment (SLI)

Science.gov (United States)

Kambanaros, Maria; Michaelides, Michalis; Grohmann, Kleanthes K.

2017-01-01

Background: Clinicians globally recognize as exceptionally challenging the development of effective intervention practices for bi- or multilingual children with specific language impairment (SLI). Therapy in both or all of an impaired child's languages is rarely possible. An alternative is to develop treatment protocols that facilitate the…

A new polymorphic and multicopy MHC gene family related to nonmammalian class I

Energy Technology Data Exchange (ETDEWEB)

Leelayuwat, C.; Degli-Esposti, M.A.; Abraham, L.J. [Univ. of Western Australia, Perth (Australia); Townend, D.C. [Sir Charles Gairdner Hospital, Perth (Australia); Dawkins, R.L. [Royal Perth Hospital, Perth (Australia)]|[Univ. of Western Australia, Perth (Australia)]|[Sir Charles Gairdner Hospital, Perth (Australia)

1994-12-31

The authors have used genomic analysis to characterize a region of the central major histocompatibility complex (MHC) spanning {approximately} 300 kilobases (kb) between TNF and HLA-B. This region has been suggested to carry genetic factors relevant to the development of autoimmune diseases such as myasthenia gravis (MG) and insulin dependent diabetes mellitus (IDDM). Genomic sequence was analyzed for coding potential, using two neural network programs, GRAIL and GeneParser. A genomic probe, JAB, containing putative coding sequences (PERB11) located 60 kb centromeric of HLA-B, was used for northern analysis of human tissues. Multiple transcripts were detected. Southern analysis of genomic DNA and overlapping YAC clones, covering the region from BAT1 to HLA-F, indicated that there are at least five copies of PERB11, four of which are located within this region of the MHC. The partial cDNA sequence of PERB11 was obtained from poly-A RNA derived from skeletal muscle. The putative amino acid sequence of PERB11 shares {approximately} 30% identity to MHC class I molecules from various species, including reptiles, chickens, and frogs, as well as to other MHC class I-like molecules, such as the IgG FcR of the mouse and rat and the human Zn-{alpha}2-glycoprotein. From direct comparison of amino acid sequences, it is concluded that PERB11 is a distinct molecule more closely related to nonmammalian than known mammalian MHC class I molecules. Genomic sequence analysis of PERB11 from five MHC ancestral haplotypes (AH) indicated that the gene is polymorphic at both DNA and protein level. The results suggest that the authors have identified a novel polymorphic gene family with multiple copies within the MHC. 48 refs., 10 figs., 2 tabs.

Phosphoribosylpyrophosphate synthetase of Escherichia coli. Properties of the purified enzyme and primary structure of the prs gene

DEFF Research Database (Denmark)

Hove-Jensen, Bjarne; Harlow, Kenneth W.; King, Cheryl J.

1986-01-01

of ADP. The nucleotide sequence of the E. coli prs gene has been determined and the coding segment established. The deduced amino acid sequence of P-Rib-PP synthetase contained 314 amino acid residues and the molecular weight was calculated as 34,060. The initiation site of transcription was determined......Phosphoribosylpyrophosphate (P-Rib-PP) synthetase of Escherichia coli has been purified to near homogeneity from a strain harboring the prs gene, encoding P-Rib-PP synthetase, on a multicopy plasmid. Analysis of the enzyme showed that it required inorganic phosphate for activity and for stability...

Children's grammatical categories of verb and noun: a comparative look at children with specific language impairment (SLI) and normal language (NL).

Science.gov (United States)

Skipp, Amy; Windfuhr, Kirsten L; Conti-Ramsden, Gina

2002-01-01

The study investigated the development of grammatical categories (noun and verb) in young language learners. Twenty-eight children with specific language impairment (SLI) with a mean language age of 35 months and 28 children with normal language (NL) with a mean language age of 34 months were exposed to four novel verbs and four novel nouns during 10 experimental child-directed play sessions. The lexical items were modelled with four experimentally controlled argument structures. Both groups of children showed little productivity with syntactic marking of arguments in the novel verb conditions. Thus, both groups of children mostly followed the surface structure of the model presented to them, regardless of the argument they were trying to express. Therefore, there was little evidence of verb-general processes. In contrast, both groups used nouns in semantic roles that had not been modelled for them. Importantly, however, children with SLI still appeared to be more input dependent than NL children. This suggests that children with NL were working with a robust noun schema, whereas children with SLI were not. Taken together, the findings suggest that neither group of children had a grammatical category of verb, but demonstrated a general knowledge of the grammatical category of noun. These findings are discussed in relation to current theories of normal and impaired language development.

Multiple genes encode the major surface glycoprotein of Pneumocystis carinii

DEFF Research Database (Denmark)

Kovacs, J A; Powell, F; Edman, J C

1993-01-01

hydrophobic region at the carboxyl terminus. The presence of multiple related msg genes encoding the major surface glycoprotein of P. carinii suggests that antigenic variation is a possible mechanism for evading host defenses. Further characterization of this family of genes should allow the development......The major surface antigen of Pneumocystis carinii, a life-threatening opportunistic pathogen in human immunodeficiency virus-infected patients, is an abundant glycoprotein that functions in host-organism interactions. A monoclonal antibody to this antigen is protective in animals, and thus...... blot studies using chromosomal or restricted DNA, the major surface glycoproteins are the products of a multicopy family of genes. The predicted protein has an M(r) of approximately 123,000, is relatively rich in cysteine residues (5.5%) that are very strongly conserved, and contains a well conserved...

Cognitive neuropsychological and regional cerebral blood flow study of a Japanese-English bilingual girl with specific language impairment (SLI).

Science.gov (United States)

Uno, Akira; Wydell, Taeko N; Kato, Motoichiro; Itoh, Kanae; Yoshino, Fumihiro

2009-02-01

We report here on an investigation into the possible factors which might have contributed to language impairment (LI) in EM, a 14-year-old Japanese-English bilingual girl. EM was born in the UK to Japanese parents with no other siblings, and used English to communicate with all other people except for her parents. A delay in her English language development was identified at primary school in the UK, which was attributed to her bilingualism. The deficiency in her English language skills persisted into her adolescence despite more than adequate educational opportunities (including additional language support). At the start of her secondary education, language ability/literacy attainment tests were conducted in both English and Japanese, and the results suggested specific language impairment (SLI) in both languages. Further, her brain Single Photon Emission Computed Tomography (SPECT) revealed significantly lower Regional Cerebral Blood Flow(rCBF) in the left temporo-parietal area, which is also similar to the area of dysfunction often found among Japanese individuals with SLI.

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Science.gov (United States)

Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

2015-01-01

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Directory of Open Access Journals (Sweden)

Nathan D. Olson

2015-03-01

Full Text Available This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1 identity of biologically conserved position, (2 ratio of 16S rRNA gene copies featuring identified variants, and (3 the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

Short-lived long non-coding RNAs as surrogate indicators for chemical exposure and LINC00152 and MALAT1 modulate their neighboring genes.

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Hidenori Tani

Full Text Available Whole transcriptome analyses have revealed a large number of novel long non-coding RNAs (lncRNAs. Although accumulating evidence demonstrates that lncRNAs play important roles in regulating gene expression, the detailed mechanisms of action of most lncRNAs remain unclear. We previously reported that a novel class of lncRNAs with a short half-life (t1/2 < 4 h in HeLa cells, termed short-lived non-coding transcripts (SLiTs, are closely associated with physiological and pathological functions. In this study, we focused on 26 SLiTs and nuclear-enriched abundant lncRNA, MALAT1(t1/2 of 7.6 h in HeLa cells in neural stem cells (NSCs derived from human induced pluripotent stem cells, and identified four SLiTs (TUG1, GAS5, FAM222-AS1, and SNHG15 that were affected by the following typical chemical stresses (oxidative stress, heavy metal stress and protein synthesis stress. We also found the expression levels of LINC00152 (t1/2 of 2.1 h in NSCs, MALAT1 (t1/2 of 1.8 h in NSCs, and their neighboring genes were elevated proportionally to the chemical doses. Moreover, we confirmed that the overexpression of LINC00152 or MALAT1 upregulated the expressions of their neighboring genes even in the absence of chemical stress. These results reveal that LINC00152 and MALAT1 modulate their neighboring genes, and thus provide a deeper understanding of the functions of lncRNAs.

Clinical implications of early differential diagnostic between Language Delay (LD and Specific Language Impairment (SLI [mplicaciones clínicas del diagnóstico diferencial temprano entre Retraso de Lenguaje (RL y Trastorno Específico del Lenguaje (TEL

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Víctor Acosta Rodríguez

2012-03-01

Full Text Available The aim of this paper is to analyze the differences between Language Delay (LD and Specific Language Impairment (SLI concepts from a clinical point of view. The selected sample consisted of 6 LD and 6 SLI individuals, who were chosen with standarized tools and qualitative tasks. LD children had not any treatment, meanwhile SLI children underwent an intervention program which pursued two aims: on one hand, to improve the development of linguistic comprehension and production and on the other hand, to encourage the progress of basic skills for literacy, focusing on narrative development and phonological processing. The contents of the program have been sequenced in increasing order of cognitive complexity. The U of Mann-Whitney was used to check the similarities and differences of the children´ linguistic development according to their diagnosis. Results show important differences between both groups. A positive progress of LD children stand outs, although they didn´t undergo an intervention program. Meanwhile, just the opposite happens with SLI children. These data make us think that there is not an obligatory sequence from LD to SLI children. Therefore, we regard them as different categories.

Phosphoribosylpyrophosphate synthetase of Escherichia coli. Properties of the purified enzyme and primary structure of the prs gene

DEFF Research Database (Denmark)

Hove-Jensen, Bjarne; Harlow, Kenneth W.; King, Cheryl J.

1986-01-01

Phosphoribosylpyrophosphate (P-Rib-PP) synthetase of Escherichia coli has been purified to near homogeneity from a strain harboring the prs gene, encoding P-Rib-PP synthetase, on a multicopy plasmid. Analysis of the enzyme showed that it required inorganic phosphate for activity and for stability...... the UAA translation stop codon, within a Thy-rich region following an inverted repeat sequence, indicative of an rho-independent transcription terminator....

The association between expressive grammar intervention and social and emergent literacy outcomes for preschoolers with SLI.

Science.gov (United States)

Washington, Karla N

2013-02-01

To determine whether (a) expressive grammar intervention facilitated social and emergent literacy outcomes better than no intervention and (b) expressive grammar gains and/or initial expressive grammar level predicted social and emergent literacy outcomes. This investigation was a follow-up to a recently published study exploring the impact of grammatical language intervention on expressive grammar outcomes for preschoolers with specific language impairment (SLI). Twenty-two 3- to 5-year-old preschoolers received ten 20-minute intervention sessions addressing primary deficits in grammatical morphology. Participants' social and emergent literacy skills were not targeted. Twelve children awaiting intervention, chosen from the same selection pool as intervention participants, served as controls. Blind assessments of social and emergent literacy outcomes were completed at preintervention, immediately postintervention, and 3 months postintervention. Only intervention participants experienced significant gains in social and emergent literacy outcomes and maintained these gains for 3 months postintervention. Expressive grammar gains was the only single significant predictor of these outcomes. Expressive grammar intervention was associated with broad impacts on social and emergent literacy outcomes that were maintained beyond the intervention period. Gains in expressive grammar predicted these outcomes. Social and emergent literacy skills were positively affected for preschoolers with SLI during a grammatical language intervention program.

Kikker, waar ben jij? - Wat de Frog Story ons kan vertellen over grammaticale en lexicale vaardigheden in SLI en tweetaligheid.

NARCIS (Netherlands)

A. Orgassa; Maaske Treurniet

2012-01-01

Many bilingual children have an acquisition delay in their L2, which is easily mistaken for SLI. With the aim to, on the one hand, tackle this 'disentangling problem' and, on the other hand, create adequate expectations regarding bilingual "normal" development, we compared Dutch lexical and

Phosphoribosylpyrophosphate synthetase of Bacillus subtilis. Cloning, characterization and chromosomal mapping of the prs gene

DEFF Research Database (Denmark)

Nilsson, Dan; Hove-Jensen, Bjarne

1987-01-01

The gene (prs) encoding phosphoribosylpyrophosphate (PRPP) synthetase has been cloned from a library of Bacillus subtilis DNA by complementation of an Escherichia coli prs mutation. Flanking DNA sequences were pruned away by restriction endonuclease and exonuclease BAL 31 digestions, resulting...... in a DNA fragment of approx. 1.8 kb complementing the E. coli prs mutation. Minicell experiments revealed that this DNA fragment coded for a polypeptide, shown to be the PRPP synthetase subunit, with an Mr of approx. 40,000. B. subtilis strains harbouring the prs gene in a multicopy plasmid contained up...... to nine-fold increased PRPP synthetase activity. The prs gene was cloned in an integration vector and the resulting hybrid plasmid inserted into the B. subtilis chromosome by homologous recombination. The integration site was mapped by transduction and the gene order established as purA-guaA-prs-cysA....

Exploring the outcomes of a novel computer-assisted treatment program targeting expressive-grammar deficits in preschoolers with SLI.

Science.gov (United States)

Washington, Karla N; Warr-Leeper, Genese; Thomas-Stonell, Nancy

2011-01-01

The impact of a newly designed computer-assisted treatment (C-AT) program, My Sentence Builder, for the remediation of expressive-grammar deficits in children with specific language impairment (SLI) was explored. This program was specifically designed with features to directly address expressive-grammar difficulties, thought to be associated with hypothesized deficits in verbal working memory (VWM). Thirty-four preschoolers with deficits in expressive-grammar morphology participated. Using the randomization procedure of consecutive sampling, participants were recruited. Twenty-two participants were consecutively assigned to one of two treatment groups, C-AT or non C-AT (nC-AT). The nC-AT utilized conventional language stimulation procedures containing features which have been traditionally used to address expressive-grammar deficits. A group of equivalent children awaiting treatment and chosen from the same sample of children as the treatment participants served as a control group. Blind assessments of outcomes were completed pre-, post-, and 3-months post-treatment in a formal and informal context. C-AT and nC-AT participants significantly outperformed controls pre-to-post to 3-months post-treatment in both assessment contexts. No significant differences in treatment gains were found between C-AT and nC-AT. Results suggested that treatments designed to directly address expressive-grammar deficits were better than no treatment for preschool SLI. Further, use of a C-AT program may be another feasible treatment method for this disorder population. As a result of this activity, the reader will recognize that: (1) expressive-grammar treatment is better than no treatment for immediate and continued language growth, (2) use of a C-AT program containing specific features designed to directly address expressive-grammar deficits is another viable, but not necessarily a better treatment option for the remediation of expressive-grammar deficits in preschool children with SLI

Grammatical and pragmatic properties of the DP in children with Specific Language Impairment (SLI) and in children with High Functioning Autism (HFA)

NARCIS (Netherlands)

Creemers, A.; Schaeffer, J.C.; Köhnlein, B.; Audring, J.

2015-01-01

This study investigates whether grammar and pragmatics are separate linguistic components or not, and whether children with SLI and children with HFA have overlapping or distinct linguistic profiles. We examine two DP-related phenomena: the mass-count distinction (grammatical) and the choice for a

Language and Social Factors in the Use of Cell Phone Technology by Adolescents with and without Specific Language Impairment (SLI)

Science.gov (United States)

Conti-Ramsden, Gina; Durkin, Kevin; Simkin, Zoe

2010-01-01

Purpose: This study aimed to compare cell phone use (both oral and text-based) by adolescents with and without specific language impairment (SLI) and examine the extent to which language and social factors affect frequency of use. Method: Both interview and diary methods were used to compare oral and text-based communication using cell phones by…

Effect of Sentence Length and Complexity on Working Memory Performance in Hungarian Children with Specific Language Impairment (SLI): A Cross-Linguistic Comparison

Science.gov (United States)

Marton, Klara; Schwartz, Richard G.; Farkas, Lajos; Katsnelson, Valeriya

2006-01-01

Background: English-speaking children with specific language impairment (SLI) perform more poorly than their typically developing peers in verbal working memory tasks where processing and storage are simultaneously required. Hungarian is a language with a relatively free word order and a rich agglutinative morphology. Aims: To examine the effect…

Commentary: Increased Risk of Later Emotional and Behavioural Problems in Children with SLI -- Reflections on Yew and O'Kearney (2013)

Science.gov (United States)

Conti-Ramsden, Gina

2013-01-01

Children with Specific Language Impairment (SLI) find it effortful to learn to talk and these difficulties can be persistent. Given the importance of language to human behaviour, it is not surprising to find that language difficulties are a risk factor for associated difficulties in other aspects of children's development. This article asks…

Production of a heterologous proteinase A by Saccharomyces kluyveri

DEFF Research Database (Denmark)

Møller, Kasper; Tidemand, L.D.; Winther, J.R.

2001-01-01

In order to evaluate the potential of Saccharomyces kluyveri for heterologous protein production, S. kluyveri Y159 was transformed with a S. cerevisiae-based multi-copy plasmid containing the S. cerevisiae PEP4 gene, which encodes proteinase A, under the control of its native promoter. As a refer......In order to evaluate the potential of Saccharomyces kluyveri for heterologous protein production, S. kluyveri Y159 was transformed with a S. cerevisiae-based multi-copy plasmid containing the S. cerevisiae PEP4 gene, which encodes proteinase A, under the control of its native promoter...

Three genes for mitochondrial proteins suppress null-mutations in both Afg3 and Rca1 when over-expressed.

Science.gov (United States)

Rep, M; Nooy, J; Guélin, E; Grivell, L A

1996-08-01

The AFG3 gene of Saccharomyces cerevisiae encodes a mitochondrial inner membrane protein with ATP-dependent protease activity. To gain more insight into the function of this protein, multi-copy suppressors of an afg3-null mutation were isolated. Three genes were found that restored partial growth on non-fermentable carbon sources, all of which affect the biogenesis of respiratory competent mitochondria: PIM1(LON) encodes a matrix-localized ATP-dependent protease involved in the turnover of matrix proteins; OXA1(PET1402) encodes a putative mitochondrial inner membrane protein involved in the biogenesis of the respiratory chain; and MBA1 encodes a mitochondrial protein required for optimal respiratory growth. All three genes also suppressed a null mutation in a related gene, RCA1, as well as in the combination of afg3- and rca1-null.

Functional identification of an Arabidopsis snf4 ortholog by screening for heterologous multicopy suppressors of snf4 deficiency in yeast

DEFF Research Database (Denmark)

Kleinow, T.; Bhalerao, R.; Breuer, F.

2000-01-01

Yeast Snf4 is a prototype of activating gamma-subunits of conserved Snf1/AMPK-related protein kinases (SnRKs) controlling glucose and stress signaling in eukaryotes. The catalytic subunits of Arabidopsis SnRKs, AKIN10 and AKIN11, interact with Snf4 and suppress the snf1 and snf4 mutations in yeast....... By expression of an Arabidopsis cDNA library in yeast, heterologous multicopy snf4 suppressors were isolated. In addition to AKIN10 and AKIN11, the deficiency of yeast snf4 mutant to grown on non-fermentable carbon source was suppressed by Arabidopsis Myb30, CAAT-binding factor Hap3b, casein kinase I, zinc......-finger factors AZF2 and ZAT10, as well as orthologs of hexose/UDP-hexose transporters, calmodulin, SMC1-cohesin and Snf4. Here we describe the characterization of AtSNF4, a functional Arabidopsis Snf4 ortholog, that interacts with yeast Snf1 and specifically binds to the C-terminal regulatory domain...

Transcriptional analysis of the multicopy hao gene coding for hydroxylamine oxidoreductase in Nitrosomonas sp. strain ENI-11.

Science.gov (United States)

Hirota, Ryuichi; Kuroda, Akio; Ikeda, Tsukasa; Takiguchi, Noboru; Ohtake, Hisao; Kato, Junichi

2006-08-01

The nitrifying bacterium Nitrosomonas sp. strain ENI-11 has three copies of the gene encoding hydroxylamine oxidoreductase (hao(1), hao(2), and hao(3)) on its genome. Broad-host-range reporter plasmids containing transcriptional fusion genes between hao copies and lacZ were constructed to analyze the expression of each hydroxylamine oxidoreductase gene (hao) copy individually and quantitatively. beta-Galactosidase assays of ENI-11 harboring reporter plasmids revealed that all hao copies were transcribed in the wild-type strain. Promoter analysis of hao copies revealed that transcription of hao(3) was highest among the hao copies. Expression levels of hao(1) and hao(2) were 40% and 62% of that of hao(3) respectively. Transcription of hao(1) was negatively regulated, whereas a portion of hao(3) transcription was read through transcription from the rpsT promoter. When energy-depleted cells were incubated in the growth medium, only hao(3) expression increased. This result suggests that it is hao(3) that is responsible for recovery from energy-depleted conditions in Nitrosomonas sp. strain ENI-11.

Evolution of blue-flowered species of genus Linum based on high-throughput sequencing of ribosomal RNA genes.

Science.gov (United States)

Bolsheva, Nadezhda L; Melnikova, Nataliya V; Kirov, Ilya V; Speranskaya, Anna S; Krinitsina, Anastasia A; Dmitriev, Alexey A; Belenikin, Maxim S; Krasnov, George S; Lakunina, Valentina A; Snezhkina, Anastasiya V; Rozhmina, Tatiana A; Samatadze, Tatiana E; Yurkevich, Olga Yu; Zoshchuk, Svyatoslav A; Amosova, Аlexandra V; Kudryavtseva, Anna V; Muravenko, Olga V

2017-12-28

The species relationships within the genus Linum have already been studied several times by means of different molecular and phylogenetic approaches. Nevertheless, a number of ambiguities in phylogeny of Linum still remain unresolved. In particular, the species relationships within the sections Stellerolinum and Dasylinum need further clarification. Also, the question of independence of the species of the section Adenolinum still remains unanswered. Moreover, the relationships of L. narbonense and other species of the section Linum require further clarification. Additionally, the origin of tetraploid species of the section Linum (2n = 30) including the cultivated species L. usitatissimum has not been explored. The present study examines the phylogeny of blue-flowered species of Linum by comparisons of 5S rRNA gene sequences as well as ITS1 and ITS2 sequences of 35S rRNA genes. High-throughput sequencing has been used for analysis of multicopy rRNA gene families. In addition to the molecular phylogenetic analysis, the number and chromosomal localization of 5S and 35S rDNA sites has been determined by FISH. Our findings confirm that L. stelleroides forms a basal branch from the clade of blue-flowered flaxes which is independent of the branch formed by species of the sect. Dasylinum. The current molecular phylogenetic approaches, the cytogenetic analysis as well as different genomic DNA fingerprinting methods applied previously did not discriminate certain species within the sect. Adenolinum. The allotetraploid cultivated species L. usitatissimum and its wild ancestor L. angustifolium (2n = 30) could originate either as the result of hybridization of two diploid species (2n = 16) related to the modern L. gandiflorum and L. decumbens, or hybridization of a diploid species (2n = 16) and a diploid ancestor of modern L. narbonense (2n = 14). High-throughput sequencing of multicopy rRNA gene families allowed us to make several adjustments to the

Ssb1 chaperone is a [PSI+] prion-curing factor.

Science.gov (United States)

Chacinska, A; Szczesniak, B; Kochneva-Pervukhova, N V; Kushnirov, V V; Ter-Avanesyan, M D; Boguta, M

2001-04-01

Yeast SUP7' or SUP11 nonsense suppressors have no phenotypic expression in strains deficient in the isopentenylation of A37 in tRNA. Here we show that such strains spontaneously produce cells with a nonsense suppressor phenotype which is related to the cytoplasmically inherited determinant and manifests all the key features of the [PSI+] prion. A screen of a multicopy yeast genomic library for genes that inactivate the [PSI+]-related suppressor phenotype resulted in the isolation of the SSB1 gene. Moreover, we demonstrate that multicopy plasmid encoding the Ssb1 chaperone cures cells of the [PSI+] prion.

Speech Perception and Phonological Short-Term Memory Capacity in Language Impairment: Preliminary Evidence from Adolescents with Specific Language Impairment (SLI) and Autism Spectrum Disorders (ASD)

Science.gov (United States)

Loucas, Tom; Riches, Nick Greatorex; Charman, Tony; Pickles, Andrew; Simonoff, Emily; Chandler, Susie; Baird, Gillian

2010-01-01

Background: The cognitive bases of language impairment in specific language impairment (SLI) and autism spectrum disorders (ASD) were investigated in a novel non-word comparison task which manipulated phonological short-term memory (PSTM) and speech perception, both implicated in poor non-word repetition. Aims: This study aimed to investigate the…

Design and methods in a survey of living conditions in the Arctic - the SLiCA study.

Science.gov (United States)

Eliassen, Bent-Martin; Melhus, Marita; Kruse, Jack; Poppel, Birger; Broderstad, Ann Ragnhild

2012-03-19

The main objective of this study is to describe the methods and design of the survey of living conditions in the Arctic (SLiCA), relevant participation rates and the distribution of participants, as applicable to the survey data in Alaska, Greenland and Norway. This article briefly addresses possible selection bias in the data and also the ways to tackle it in future studies. Population-based cross-sectional survey. Indigenous individuals aged 16 years and older, living in Greenland, Alaska and in traditional settlement areas in Norway, were invited to participate. Random sampling methods were applied in Alaska and Greenland, while non-probability sampling methods were applied in Norway. Data were collected in 3 periods: in Alaska, from January 2002 to February 2003; in Greenland, from December 2003 to August 2006; and in Norway, in 2003 and from June 2006 to June 2008. The principal method in SLiCA was standardised face-to-face interviews using a questionnaire. A total of 663, 1,197 and 445 individuals were interviewed in Alaska, Greenland and Norway, respectively. Very high overall participation rates of 83% were obtained in Greenland and Alaska, while a more conventional rate of 57% was achieved in Norway. A predominance of female respondents was obtained in Alaska. Overall, the Sami cohort is older than the cohorts from Greenland and Alaska. Preliminary assessments suggest that selection bias in the Sami sample is plausible but not a major threat. Few or no threats to validity are detected in the data from Alaska and Greenland. Despite different sampling and recruitment methods, and sociocultural differences, a unique database has been generated, which shall be used to explore relationships between health and other living conditions variables.

Nucleotide sequence of the Escherichia coli pyrE gene and of the DNA in front of the protein-coding region

DEFF Research Database (Denmark)

Poulsen, Peter; Jensen, Kaj Frank; Valentin-Hansen, Poul

1983-01-01

leader segment in front of the protein-coding region. This leader contains a structure with features characteristic for a (translated?) rho-independent transcriptional terminator, which is preceded by a cluster of uridylate residues. This indicates that the frequency of pyrE transcription is regulated......Orotate phosphoribosyltransferase (EC 2.4.2.10) was purified to electrophoretic homogeneity from a strain of Escherichia coli containing the pyrE gene cloned on a multicopy plasmid. The relative molecular masses (Mr) of the native enzyme and its subunit were estimated by means of gel filtration...

Mechanisms of mtDNA segregation and mitochondrial signalling in cells with the pathogenic A3243G mutation

NARCIS (Netherlands)

Jahangir Tafrechi, Roshan Sakineh

2008-01-01

Using newly developed single cell A3243G mutation load assays a novel mechanism of mtDNA segregation was identified in which the multi-copy mtDNA nucleoid takes a central position. Furthermore, likely due to low level changes in gene expression, no genes or gene sets could be identified with gene

Involvement of Multiple Gene-Silencing Pathways in a Paramutation-like Phenomenon in Arabidopsis

Directory of Open Access Journals (Sweden)

Zhimin Zheng

2015-05-01

Full Text Available Paramutation is an epigenetic phenomenon that has been observed in a number of multicellular organisms. The epigenetically silenced state of paramutated alleles is not only meiotically stable but also “infectious” to active homologous alleles. The molecular mechanism of paramutation remains unclear, but components involved in RNA-directed DNA methylation (RdDM are required. Here, we report a multi-copy pRD29A-LUC transgene in Arabidopsis thaliana that behaves like a paramutation locus. The silent state of LUC is induced by mutations in the DNA glycosylase gene ROS1. The silent alleles of LUC are not only meiotically stable but also able to transform active LUC alleles into silent ones, in the absence of ros1 mutations. Maintaining silencing at the LUC gene requires action of multiple pathways besides RdDM. Our study identified specific factors that are involved in the paramutation-like phenomenon and established a model system for the study of paramutation in Arabidopsis.

Cloned Bacillus subtilis alkaline protease (aprA) gene showing high level of keratinolytic activity.

Science.gov (United States)

Zaghloul, T I

1998-01-01

The Bacillus subtilis alkaline protease(aprA) gene was previously cloned on a pUBHO-derivative plasmid. High levels of expression and gene stability were demonstrated when B. subtilis cells were grown on the laboratory medium 2XSG. B. subtilis cells harboring the multicopy aprA gene were grown on basal medium, supplemented with 1 % chicken feather as a source of energy, carbon, and nitrogen. Proteolytic and keratinolytic activities were monitored throughout the cultivation time. A high level of keratinolytic activity was obtained, and this indicates that alkaline protease is acting as a keratinase. Furthermore, considerable amounts of soluble proteins and free amino acids were obtained as a result of the enzymatic hydrolysis of feather. Biodegradation of feather waste using these cells represents an alternative way to improve the nutritional value of feather, since feather waste is currently utilized on a limited basis as a dietary protein supplement for animal feedstuffs. Moreover, the release of free amino acids from feather and the secreted keratinase enzyme would promote industries based on feather waste.

SLiM : an improved soil moisture balance method to simulate runoff and potential groundwater recharge processes using spatio-temporal weather and catchment characteristics

OpenAIRE

Wang, Lei; Barkwith, Andrew; Jackson, Christopher; Ellis, Michael

2012-01-01

The numerical modelling of runoff and groundwater recharge plays an important role in water resource management. The methodologies developed for these simulations should represent the key physical processes, and be applicable in a wide variety of climates for routine simulations using readily available field information. This paper describes the development of a Soil and Landuse based rainfall-runoff and recharge Model (SLiM) based on Rushton’s method – a single soil layer groundwater recharg...

Rapid duplication and loss of nbs-encoding genes in eurosids II

International Nuclear Information System (INIS)

Si, W.; Gu, L.; Yang, S.; Zhang, X.; Memon, S.

2015-01-01

Eurosids basically evolved from the core Eudicots Rosids. The Rosids consist of two large assemblages, Eurosids I (Fabids) and Eurosids II (Malvids), which belong to the largest group of Angiosperms, comprising of >40,000 and ∼ 15,000 species, respectively. Although the evolutionary patterns of the largest class of disease resistance genes consisting of a nucleotide binding site (NBS) and leucine-rich repeats (LRRs) have been studied in many species, systemic research of NBS-encoding genes has not been performed in different orders of Eurosids II. Here, five Eurosids II species, Gossypium raimondii, Theobroma cacao, Carica papaya, Citrus clementina, and Arabidopsis thaliana, distributing in three orders, were used to gain insights into the evolutionary patterns of the NBS-encoding genes. Our data showed that frequent copy number variations of NBS-encoding genes were found among these species. Phylogenetic tree analysis and the numbers of the NBS-encoding genes in the common ancestor of these species showed that species-specific NBS clades, including multi-copy and single copy numbers are dominant among these genes. However, not a single clade was found with only five copies, which come from all of the five species, respectively, suggesting rapid turn-over with birth and death of the NBS-encoding genes among Eurosids II species. In addition, a strong positive correlation was observed between the Toll/interleukin receptor (TIR)) type NBS-encoding genes and species-specific genes, indicating rapid gene loss and duplication. Whereas, non- TIR type NBS-encoding genes in these five species showed two distinct evolutionary patterns. (author)

Antisense long noncoding RNAs regulate var gene activation in the malaria parasite Plasmodium falciparum.

Science.gov (United States)

Amit-Avraham, Inbar; Pozner, Guy; Eshar, Shiri; Fastman, Yair; Kolevzon, Netanel; Yavin, Eylon; Dzikowski, Ron

2015-03-03

The virulence of Plasmodium falciparum, the causative agent of the deadliest form of human malaria, is attributed to its ability to evade human immunity through antigenic variation. These parasites alternate between expression of variable antigens, encoded by members of a multicopy gene family named var. Immune evasion through antigenic variation depends on tight regulation of var gene expression, ensuring that only a single var gene is expressed at a time while the rest of the family is maintained transcriptionally silent. Understanding how a single gene is chosen for activation is critical for understanding mutually exclusive expression but remains a mystery. Here, we show that antisense long noncoding RNAs (lncRNAs) initiating from var introns are associated with the single active var gene at the time in the cell cycle when the single var upstream promoter is active. We demonstrate that these antisense transcripts are incorporated into chromatin, and that expression of these antisense lncRNAs in trans triggers activation of a silent var gene in a sequence- and dose-dependent manner. On the other hand, interference with these lncRNAs using complement peptide nucleic acid molecules down-regulated the active var gene, erased the epigenetic memory, and induced expression switching. Altogether, our data provide evidence that these antisense lncRNAs play a key role in regulating var gene activation and mutually exclusive expression.

Characterization of a novel cation transporter ATPase gene (ATP13A4) interrupted by 3q25-q29 inversion in an individual with language delay.

Science.gov (United States)

Kwasnicka-Crawford, Dorota A; Carson, Andrew R; Roberts, Wendy; Summers, Anne M; Rehnström, Karola; Järvelä, Irma; Scherer, Stephen W

2005-08-01

Specific language impairment (SLI) is defined as failure to acquire normal language skills despite adequate intelligence and environmental stimulation. Although SLI disorders are often heritable, the genetic basis is likely to involve a number of risk factors. This study describes a 7-year-old girl carrying an inherited paracentric inversion of the long arm of chromosome 3 [46XX, inv(3)(q25.32-q29)] having clinically defined expressive and receptive language delay. Fluorescence in situ hybridization (FISH) with locus-specific bacterial artificial chromosome clones (BACs) as probes was used to characterize the inverted chromosome 3. The proximal and distal inversion breakpoint was found to reside between markers D3S3692/D3S1553 and D3S3590/D3S2305, respectively. ATP13A4, a novel gene coding for a cation-transporting P-type ATPase, was found to be disrupted by the distal breakpoint. The ATP13A4 gene was shown to comprise a 3591-bp transcript encompassing 30 exons spanning 152 kb of the genomic DNA. This study discusses the characterization of ATP13A4 and its possible involvement in speech-language disorder.

Large proteoglycan complexes and disturbed collagen architecture in the corneal extracellular matrix of mucopolysaccharidosis type VII (Sly syndrome).

Science.gov (United States)

Young, Robert D; Liskova, Petra; Pinali, Christian; Palka, Barbara P; Palos, Michalis; Jirsova, Katerina; Hrdlickova, Enkela; Tesarova, Marketa; Elleder, Milan; Zeman, Jiri; Meek, Keith M; Knupp, Carlo; Quantock, Andrew J

2011-08-24

Deficiencies in enzymes involved in proteoglycan (PG) turnover underlie a number of rare mucopolysaccharidoses (MPS), investigations of which can considerably aid understanding of the roles of PGs in corneal matrix biology. Here, the authors analyze novel pathologic changes in MPS VII (Sly syndrome) to determine the nature of PG-collagen associations in stromal ultrastructure. Transmission electron microscopy and electron tomography were used to investigate PG-collagen architectures and interactions in a cornea obtained at keratoplasty from a 22-year-old man with MPS VII, which was caused by a compound heterozygous mutation in the GUSB gene. Transmission electron microscopy showed atypical morphology of the epithelial basement membrane and Bowman's layer in MPS VII. Keratocytes were packed with cytoplasmic vacuoles containing abnormal glycosaminoglycan (GAG) material, and collagen fibrils were thinner than in normal cornea and varied considerably throughout anterior (14-32 nm), mid (13-42 nm), and posterior (17-39 nm) regions of the MPS VII stroma. PGs viewed in three dimensions were striking in appearance in that they were significantly larger than PGs in normal cornea and formed highly extended linkages with multiple collagen fibrils. Cellular changes in the MPS VII cornea resemble those in other MPS. However, the wide range of collagen fibril diameters throughout the stroma and the extensive matrix presence of supranormal-sized PG structures appear to be unique features of this disorder. The findings suggest that the accumulation of stromal chondroitin-, dermatan-, and heparan-sulfate glycosaminoglycans in the absence of β-glucuronidase-mediated degradation can modulate collagen fibrillogenesis.

Single nucleotide polymorphism analysis of ubiquitin extension protein genes (ubq) of gossypium arboreum and gossypium herbaceum in comparison with arabidopsis thaliana

International Nuclear Information System (INIS)

Shaheen, T.; Zafar, Y.; Rahman, M.

2014-01-01

Single nucleotide polymorphism analysis is an expedient way to study polymorphisms at genomic level. In the present study we have explored Ubiquitin extension protein gene of G. arboreum (A2) and G. herbaceum (A1) of cotton which is a multiple copy gene. We have found SNPs at 16 positions in 200 bp region within A genome of cotton indicating frequency of SNPs 1/13 bp. Both sequences from cotton have shown maximum similarity with UBQ5 and UBQ6 of Arabidopsis thaliana. Sequence obtained from G. arboreum has shown SNPs at 28 positions in comparison with each UBQ5 and UBQ6 of Arabidopsis thaliana while sequence obtained from G. herbaceum has shown SNPs at 31 positions in comparison with each UBQ5 and UBQ6 of Arabidopsis thaliana. In conclusion although during pace of evolution ubiquitin extension protein genes of both A genome species have got some mutations from nature but still most of their sequence is similar. Single nucleotide polymorphism study can prove a vital tool to identify gene type in case of Multicopy genes. (author)

Detection of denitrification genes by in situ rolling circle amplification - fluorescence in situ hybridization (in situ RCA-FISH) to link metabolic potential with identity inside bacterial cells

DEFF Research Database (Denmark)

Hoshino, Tatsuhiko; Schramm, Andreas

2010-01-01

target site. Finally, the RCA product inside the cells was detected by standard fluorescence in situ hybridization (FISH). The optimized protocol showed high specificity and signal-to-noise ratio but low detection frequency (up to 15% for single-copy genes and up to 43% for the multi-copy 16S rRNA gene...... as Candidatus Accumulibacter phosphatis by combining in situ RCA-FISH with 16S rRNA-targeted FISH. While not suitable for quantification because of its low detection frequency, in situ RCA-FISH will allow to link metabolic potential with 16S rRNA (gene)-based identification of single microbial cells.......). Nevertheless, multiple genes (nirS and nosZ; nirS and the 16S rRNA gene) could be detected simultaneously in P. stutzeri. Environmental application of in situ RCA-FISH was demonstrated on activated sludge by the differential detection of two types of nirS-defined denitrifiers; one of them was identified...

A study of the role of the FOXP2 and CNTNAP2 genes in persistent developmental stuttering.

Science.gov (United States)

Han, Tae-Un; Park, John; Domingues, Carlos F; Moretti-Ferreira, Danilo; Paris, Emily; Sainz, Eduardo; Gutierrez, Joanne; Drayna, Dennis

2014-09-01

A number of speech disorders including stuttering have been shown to have important genetic contributions, as indicated by high heritability estimates from twin and other studies. We studied the potential contribution to stuttering from variants in the FOXP2 gene, which have previously been associated with developmental verbal dyspraxia, and from variants in the CNTNAP2 gene, which have been associated with specific language impairment (SLI). DNA sequence analysis of these two genes in a group of 602 unrelated cases, all with familial persistent developmental stuttering, revealed no excess of potentially deleterious coding sequence variants in the cases compared to a matched group of 487 well characterized neurologically normal controls. This was compared to the distribution of variants in the GNPTAB, GNPTG, and NAGPA genes which have previously been associated with persistent stuttering. Using an expanded subject data set, we again found that NAGPA showed significantly different mutation frequencies in North Americans of European descent (p=0.0091) and a significant difference existed in the mutation frequency of GNPTAB in Brazilians (p=0.00050). No significant differences in mutation frequency in the FOXP2 and CNTNAP2 genes were observed between cases and controls. To examine the pattern of expression of these five genes in the human brain, real time quantitative reverse transcription PCR was performed on RNA purified from 27 different human brain regions. The expression patterns of FOXP2 and CNTNAP2 were generally different from those of GNPTAB, GNPTG and NAPGA in terms of relatively lower expression in the cerebellum. This study provides an improved estimate of the contribution of mutations in GNPTAB, GNPTG and NAGPA to persistent stuttering, and suggests that variants in FOXP2 and CNTNAP2 are not involved in the genesis of familial persistent stuttering. This, together with the different brain expression patterns of GNPTAB, GNPTG, and NAGPA compared to that of

Mutational analysis of the multicopy hao gene coding for hydroxylamine oxidoreductase in Nitrosomonas sp. strain ENI-11.

Science.gov (United States)

Yamagata, A; Hirota, R; Kato, J; Kuroda, A; Ikeda, T; Takiguchi, N; Ohtake, H

2000-08-01

The ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11 contains three copies of the hao gene (hao1, hao2, and hao3) coding for hydroxylamine oxidoreductase (HAO). Three single mutants (hao1::kan, hao2::kan, or hao3::kan) had 68 to 75% of the wild-type growth rate and 58 to 89% of the wild-type HAO activity when grown under the same conditions. A double mutant (hao1::kan and hao3::amp) also had 68% of the wild-type growth and 37% of the wild-type HAO activity.

Functional expression in Lactobacillus plantarum of xylP encoding the isoprimeverose transporter of Lactobacillus pentosus

NARCIS (Netherlands)

Chaillou, S.; Postma, P.W.; Pouwels, P.H.

1998-01-01

The xylP gene of Lactobacillus pentosus, the first gene of the xylPQR operon, was recently found to be involved in isoprimeverose metabolism. By expression of xylP on a multicopy plasmid in Lactobacillus plantarum 80, a strain which lacks active isoprimeverose and D-xylose transport activities, it

Improvement of fermentation ability under baking-associated stress conditions by altering the POG1 gene expression in baker's yeast.

Science.gov (United States)

Sasano, Yu; Haitani, Yutaka; Hashida, Keisuke; Oshiro, Satoshi; Shima, Jun; Takagi, Hiroshi

2013-08-01

During the bread-making process, yeast cells are exposed to many types of baking-associated stress. There is thus a demand within the baking industry for yeast strains with high fermentation abilities under these stress conditions. The POG1 gene, encoding a putative transcription factor involved in cell cycle regulation, is a multicopy suppressor of the yeast Saccharomyces cerevisiae E3 ubiquitin ligase Rsp5 mutant. The pog1 mutant is sensitive to various stresses. Our results suggested that the POG1 gene is involved in stress tolerance in yeast cells. In this study, we showed that overexpression of the POG1 gene in baker's yeast conferred increased fermentation ability in high-sucrose-containing dough, which is used for sweet dough baking. Furthermore, deletion of the POG1 gene drastically increased the fermentation ability in bread dough after freeze-thaw stress, which would be a useful characteristic for frozen dough baking. Thus, the engineering of yeast strains to control the POG1 gene expression level would be a novel method for molecular breeding of baker's yeast. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterization of the ptr5+ gene involved in nuclear mRNA export in fission yeast

International Nuclear Information System (INIS)

Watanabe, Nobuyoshi; Ikeda, Terumasa; Mizuki, Fumitaka; Tani, Tokio

2012-01-01

Highlights: ► We cloned the ptr5 + gene involved in nuclear mRNA export in fission yeast. ► The ptr5 + gene was found to encode nucleoporin 85 (Nup85). ► Seh1p and Mlo3p are multi-copy suppressors for the ptr5 mutation. ► Ptr5p/Nup85p functions in nuclear mRNA export through the mRNA export factor Rae1p. ► Ptr5p/Nup85p interacts genetically with pre-mRNA splicing factors. -- Abstract: To analyze the mechanisms of mRNA export from the nucleus to the cytoplasm, we have isolated eleven mutants, ptr [poly(A) + RNA transport] 1 to 11, which accumulate poly(A) + RNA in the nucleus at a nonpermissive temperature in Schizosaccharomyces pombe. Of those, the ptr5–1 mutant shows dots- or a ring-like accumulation of poly(A) + RNA at the nuclear periphery after shifting to the nonpermissive temperature. We cloned the ptr5 + gene and found that it encodes a component of the nuclear pore complex (NPC), nucleoporin 85 (Nup85). The ptr5–1 mutant shows no defects in protein transport, suggesting the specific involvement of Ptr5p/Nup85p in nuclear mRNA export in S. pombe. We identified Seh1p, a nucleoporin interacting with Nup85p, an mRNA-binding protein Mlo3p, and Sac3p, a component of the TREX-2 complex involved in coupling of nuclear mRNA export with transcription, as multi-copy suppressors for the ptr5–1 mutation. In addition, we found that the ptr5–1 mutation is synthetically lethal with a mutation of the mRNA export factor Rae1p, and that the double mutant exaggerates defective nuclear mRNA export, suggesting that Ptr5p/Nup85p is involved in nuclear mRNA export through Rae1p. Interestingly, the ptr5–1 mutation also showed synthetic effects with several prp pre-mRNA splicing mutations, suggesting a functional linkage between the NPCs and the splicing apparatus in the yeast nucleus.

Fluoride exposure changed the structure and the expressions of Y chromosome related genes in testes of mice.

Science.gov (United States)

Cao, Jinling; Chen, Yan; Chen, Jianjie; Yan, Hanghang; Li, Meiyan; Wang, Jundong

2016-10-01

It is known that during spermatogenesis, pluripotent germ cells differentiate to become efficient delivery vehicles to the oocyte of paternal DNA, and the process is easily damaged by external poison. In this study, the effects of fluoride on the body weight, fluoride content in femur, testosterone levels in serum and testis, sperm quality, and the expressions of Y chromosome microdeletion genes and protein levels were examined in testes of Kunming male mice treated with different concentrations of 0, 25, 50, 100 mg/L of NaF in drinking water for 11 weeks, respectively. The results showed that compared with the control group, fluoride contents in three treatment groups were significantly increased and the structure of testes was seriously injured. The testosterone contents and the sperm count were decreased. Sperm malformation ratio was distinctly elevated. The expressions of Sly and HSF2 mRNA were markedly reduced in 100 mg/L NaF group and Ssty2 mRNA expression was dramatically decreased in 50 and 100 mg/L NaF groups. Meanwhile, the protein levels of Ssty2 and Sly were significantly reduced in 50 and 100 mg/L NaF groups and HSF2 protein levels were significantly decreased in 100 mg/L NaF group. These studies indicated that fluoride had toxic effects on male reproductive system by reducing the testosterone and sperm count, and increasing the sperm malformation ratio, supported by the damage of testicular structure, as a consequence of depressed HSF2 level, which resulted in the down-regulation of Ssty2 and Sly mRNA and protein. Copyright © 2016 Elsevier Ltd. All rights reserved.

Sporozoite Route of Infection Influences In Vitro var Gene Transcription of Plasmodium falciparum Parasites From Controlled Human Infections.

Science.gov (United States)

Dimonte, Sandra; Bruske, Ellen I; Hass, Johanna; Supan, Christian; Salazar, Carmen L; Held, Jana; Tschan, Serena; Esen, Meral; Flötenmeyer, Matthias; Koch, Iris; Berger, Jürgen; Bachmann, Anna; Sim, Betty K L; Hoffman, Stephen L; Kremsner, Peter G; Mordmüller, Benjamin; Frank, Matthias

2016-09-15

Antigenic variation in Plasmodium falciparum is mediated by the multicopy var gene family. Each parasite possesses about 60 var genes, and switching between active var loci results in antigenic variation. In the current study, the effect of mosquito and host passage on in vitro var gene transcription was investigated. Thirty malaria-naive individuals were inoculated by intradermal or intravenous injection with cryopreserved, isogenic NF54 P. falciparum sporozoites (PfSPZ) generated from 1 premosquito culture. Microscopic parasitemia developed in 22 individuals, and 21 in vitro cultures were established. The var gene transcript levels were determined in early and late postpatient cultures and in the premosquito culture. At the early time point, all cultures preferentially transcribed 8 subtelomeric var genes. Intradermal infections had higher var gene transcript levels than intravenous infections and a significantly longer intrahost replication time (P = .03). At the late time point, 9 subtelomeric and 8 central var genes were transcribed at the same levels in almost all cultures. Premosquito and late postpatient cultures transcribed the same subtelomeric and central var genes, except for var2csa  The duration of intrahost replication influences in vitro var gene transcript patterns. Differences between premosquito and postpatient cultures decrease with prolonged in vitro growth. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Characterization of the ptr5{sup +} gene involved in nuclear mRNA export in fission yeast

Energy Technology Data Exchange (ETDEWEB)

Watanabe, Nobuyoshi; Ikeda, Terumasa; Mizuki, Fumitaka [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto 860-8555 (Japan); Tani, Tokio, E-mail: ttani@sci.kumamoto-u.ac.jp [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto 860-8555 (Japan)

2012-02-03

Highlights: Black-Right-Pointing-Pointer We cloned the ptr5{sup +} gene involved in nuclear mRNA export in fission yeast. Black-Right-Pointing-Pointer The ptr5{sup +} gene was found to encode nucleoporin 85 (Nup85). Black-Right-Pointing-Pointer Seh1p and Mlo3p are multi-copy suppressors for the ptr5 mutation. Black-Right-Pointing-Pointer Ptr5p/Nup85p functions in nuclear mRNA export through the mRNA export factor Rae1p. Black-Right-Pointing-Pointer Ptr5p/Nup85p interacts genetically with pre-mRNA splicing factors. -- Abstract: To analyze the mechanisms of mRNA export from the nucleus to the cytoplasm, we have isolated eleven mutants, ptr [poly(A){sup +} RNA transport] 1 to 11, which accumulate poly(A){sup +} RNA in the nucleus at a nonpermissive temperature in Schizosaccharomyces pombe. Of those, the ptr5-1 mutant shows dots- or a ring-like accumulation of poly(A){sup +} RNA at the nuclear periphery after shifting to the nonpermissive temperature. We cloned the ptr5{sup +} gene and found that it encodes a component of the nuclear pore complex (NPC), nucleoporin 85 (Nup85). The ptr5-1 mutant shows no defects in protein transport, suggesting the specific involvement of Ptr5p/Nup85p in nuclear mRNA export in S. pombe. We identified Seh1p, a nucleoporin interacting with Nup85p, an mRNA-binding protein Mlo3p, and Sac3p, a component of the TREX-2 complex involved in coupling of nuclear mRNA export with transcription, as multi-copy suppressors for the ptr5-1 mutation. In addition, we found that the ptr5-1 mutation is synthetically lethal with a mutation of the mRNA export factor Rae1p, and that the double mutant exaggerates defective nuclear mRNA export, suggesting that Ptr5p/Nup85p is involved in nuclear mRNA export through Rae1p. Interestingly, the ptr5-1 mutation also showed synthetic effects with several prp pre-mRNA splicing mutations, suggesting a functional linkage between the NPCs and the splicing apparatus in the yeast nucleus.

Mapping of a Leishmania major gene/locus that confers pentamidine resistance by deletion and insertion of transposable element

Directory of Open Access Journals (Sweden)

Coelho Adriano C.

2004-01-01

Full Text Available Pentamidine (PEN is an alternative compound to treat antimony-resistant leishmaniasis patients, which cellular target remains unclear. One approach to the identification of prospective targets is to identify genes able to mediate PEN resistance following overexpression. Starting from a genomic library of transfected parasites bearing a multicopy episomal cosmid vector containing wild-type Leishmania major DNA, we isolated one locus capable to render PEN resistance to wild type cells after DNA transfection. In order to map this Leishmania locus, cosmid insert was deleted by two successive sets of partial digestion with restriction enzymes, followed by transfection into wild type cells, overexpression, induction and functional tests in the presence of PEN. To determine the Leishmania gene related to PEN resistance, nucleotide sequencing experiments were done through insertion of the transposon Mariner element of Drosophila melanogaster (mosK into the deleted insert to work as primer island. Using general molecular techniques, we described here this method that permits a quickly identification of a functional gene facilitating nucleotide sequence experiments from large DNA fragments. Followed experiments revealed the presence of a P-Glycoprotein gene in this locus which role in Leishmania metabolism has now been analyzed.

Identification of Tunisian Leishmania spp. by PCR amplification of cysteine proteinase B (cpb) genes and phylogenetic analysis.

Science.gov (United States)

Chaouch, Melek; Fathallah-Mili, Akila; Driss, Mehdi; Lahmadi, Ramzi; Ayari, Chiraz; Guizani, Ikram; Ben Said, Moncef; Benabderrazak, Souha

2013-03-01

Discrimination of the Old World Leishmania parasites is important for diagnosis and epidemiological studies of leishmaniasis. We have developed PCR assays that allow the discrimination between Leishmania major, Leishmania tropica and Leishmania infantum Tunisian species. The identification was performed by a simple PCR targeting cysteine protease B (cpb) gene copies. These PCR can be a routine molecular biology tools for discrimination of Leishmania spp. from different geographical origins and different clinical forms. Our assays can be an informative source for cpb gene studying concerning drug, diagnostics and vaccine research. The PCR products of the cpb gene and the N-acetylglucosamine-1-phosphate transferase (nagt) Leishmania gene were sequenced and aligned. Phylogenetic trees of Leishmania based cpb and nagt sequences are close in topology and present the classic distribution of Leishmania in the Old World. The phylogenetic analysis has enabled the characterization and identification of different strains, using both multicopy (cpb) and single copy (nagt) genes. Indeed, the cpb phylogenetic analysis allowed us to identify the Tunisian Leishmania killicki species, and a group which gathers the least evolved isolates of the Leishmania donovani complex, that was originated from East Africa. This clustering confirms the African origin for the visceralizing species of the L. donovani complex. Copyright © 2012 Elsevier B.V. All rights reserved.

Judgments of omitted BE and DO in questions as extended finiteness clinical markers of specific language impairment (SLI) to 15 years: a study of growth and asymptote.

Science.gov (United States)

Rice, Mabel L; Hoffman, Lesa; Wexler, Ken

2009-12-01

Clinical grammar markers are needed for children with SLI older than 8 years. This study followed children who were previously studied on sentences with omitted finiteness to determine if affected children continue to perform at low levels and to examine possible predictors of low performance. This is the first longitudinal report of grammaticality judgments of questions. Three groups of children participated: 20 SLI, 20 age controls, and 18 language-matched controls, followed from ages 6-15 years. An experimental grammaticality judgment task was administered with BE copula/auxiliary and DO auxiliary in wh- and yes/no questions for 9 times of measurement. Predictors were indices of vocabulary, nonverbal intelligence, and maternal education. Growth curve analyses show that the affected group performed below the younger controls at each time of measurement, for each variable. Growth analyses show linear and quadratic effects for both groups across variables, with the exception of BE acquisition, which was flat for both groups. The control children reached ceiling levels; the affected children reached a lower asymptote. The results suggest an ongoing maturational lag in finiteness marking for affected children with promise as a clinical marker for language impairment in school-aged and adolescent children and probably adults as well.

Core-shell Li2S@Li3PS4 nanoparticles incorporated into graphene aerogel for lithium-sulfur batteries with low potential barrier and overpotential

Science.gov (United States)

Jiao, Zheng; Chen, Lu; Si, Jian; Xu, Chuxiong; Jiang, Yong; Zhu, Ying; Yang, Yaqing; Zhao, Bing

2017-06-01

Lithium sulfide as a promising cathode material not only have a high theoretical specific capacity, but also can be paired with Li-free anode material to avoid potential safety issues. However, how to prepare high electrochemical performance material is still challenge. Herein, we present a facile way to obtain high crystal quality Li2S nanomaterials with average particle size of about 55 nm and coated with Li3PS4 to form the nano-scaled core-shell Li2S@Li3PS4 composite. Then nano-Li2S@Li3PS4/graphene aerogel is prepared by a simple liquid infiltration-evaporation coating process and used directly as a composite cathode without metal substrate for lithium-sulfur batteries. Electrochemical tests demonstrate that the composite delivers a high discharge capacity of 934.4 mAh g-1 in the initial cycle and retains 485.5 mAh g-1 after 100 cycles at 0.1 C rate. In addition, the composite exhibits much lower potential barrier (∼2.40 V) and overpotential compared with previous reports, indicating that Li2S needs only a little energy to be activated. The excellent electrochemical performances could be attributed to the tiny particle size of Li2S and the superionic conducting Li3PS4 coating layer, which can shorten Li-ion and electron diffusion paths, improve the ionic conductivity, as well as retarding polysulfides dissolution into the electrolyte to some extent.

Development of new USER-based cloning vectors for multiple genes expression in Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Kildegaard, Kanchana Rueksomtawin; Jensen, Niels Bjerg; Maury, Jerome

2013-01-01

auxotrophic and dominant markers for convenience of use. Our vector set also contains both integrating and multicopy vectors for stability of protein expression and high expression level. We will make the new vector system available to the yeast community and provide a comprehensive protocol for cloning...... the production strain with the proper phenotype and product yield. However, the sequential number of metabolic engineering is time-consuming. Furthermore, the number of available selectable markers is also limiting the number of genetic modifications. To overcome these limitations, we have developed a new set...... of shuttle vectors for convenience of use for high-throughput cloning and selectable marker recycling. The new USER-based cloning vectors consist of a unique USER site and a CRE-loxP-mediated marker recycling system. The USER site allows insertion of genes of interest along with a bidirectional promoter...

Degs and degu operon from Bacillus-brevis: a combination that enhances the production of commercially valuable enzymes

CSIR Research Space (South Africa)

Louw, M

1995-05-01

Full Text Available A novel method has been developed for increasing the production of commercially valuable enzymes, such as proteases, beta-glucanases, alpha-amylases and levansucrase. It is dependent on two genes cloned from Bacillus brevis, expressed on a multicopy...

Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes.

Science.gov (United States)

Singh, Nagendra K; Dalal, Vivek; Batra, Kamlesh; Singh, Binay K; Chitra, G; Singh, Archana; Ghazi, Irfan A; Yadav, Mahavir; Pandit, Awadhesh; Dixit, Rekha; Singh, Pradeep K; Singh, Harvinder; Koundal, Kirpa R; Gaikwad, Kishor; Mohapatra, Trilochan; Sharma, Tilak R

2007-01-01

The high-quality rice genome sequence is serving as a reference for comparative genome analysis in crop plants, especially cereals. However, early comparisons with bread wheat showed complex patterns of conserved synteny (gene content) and colinearity (gene order). Here, we show the presence of ancient duplicated segments in the progenitor of wheat, which were first identified in the rice genome. We also show that single-copy (SC) rice genes, those representing unique matches with wheat expressed sequence tag (EST) unigene contigs in the whole rice genome, show more than twice the proportion of genes mapping to syntenic wheat chromosome as compared to the multicopy (MC) or duplicated rice genes. While 58.7% of the 1,244 mapped SC rice genes were located in single syntenic wheat chromosome groups, the remaining 41.3% were distributed randomly to the other six non-syntenic wheat groups. This could only be explained by a background dispersal of genes in the genome through transposition or other unknown mechanism. The breakdown of rice-wheat synteny due to such transpositions was much greater near the wheat centromeres. Furthermore, the SC rice genes revealed a conserved primordial gene order that gives clues to the origin of rice and wheat chromosomes from a common ancestor through polyploidy, aneuploidy, centromeric fusions, and translocations. Apart from the bin-mapped wheat EST contigs, we also compared 56,298 predicted rice genes with 39,813 wheat EST contigs assembled from 409,765 EST sequences and identified 7,241 SC rice gene homologs of wheat. Based on the conserved colinearity of 1,063 mapped SC rice genes across the bins of individual wheat chromosomes, we predicted the wheat bin location of 6,178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 35.4% initial success. This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat

Metabolic changes in Arabidopsis thaliana plants overexpressing chalcone synthase

NARCIS (Netherlands)

Dao, Thi Thanh Hien

2010-01-01

The study has shown that it is possible to introduce the heterologous CHS gene in Arabidopsis thaliana and common multicopies of transgenes containing plants were obtained. Analysis of the change in metabolome of CHS transgenic plants, high expression transgenic lines can be identified by markers

Development of PCR-based detection methods for the quarantine phytopathogen Synchytrium endobioticum, causal agent of wart disease

NARCIS (Netherlands)

Boogert, van den P.H.J.F.; Gent-Pelzer, van M.P.E.; Bonants, P.J.M.; Boer, de S.H.; Wander, J.G.N.; Lévesque, C.A.; Leeuwen, van G.C.M.; Baayen, R.P.

2005-01-01

Abstract PCR-based methods were developed for the detection and quantification of the potato pathogen Synchytrium endobioticum in soil extracts and in planta. PCR primers, based on the internal transcribed spacer region of the multi-copy gene rDNA were tested for specificity, sensitivity and

Biology in the Dry Seed: Transcriptome Changes Associated with Dry Seed Dormancy and Dormancy Loss in the Arabidopsis GA-Insensitive sleepy1-2 Mutant

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Sven K. Nelson

2017-12-01

Full Text Available Plant embryos can survive years in a desiccated, quiescent state within seeds. In many species, seeds are dormant and unable to germinate at maturity. They acquire the capacity to germinate through a period of dry storage called after-ripening (AR, a biological process that occurs at 5–15% moisture when most metabolic processes cease. Because stored transcripts are among the first proteins translated upon water uptake, they likely impact germination potential. Transcriptome changes associated with the increased seed dormancy of the GA-insensitive sly1-2 mutant, and with dormancy loss through long sly1-2 after-ripening (19 months were characterized in dry seeds. The SLY1 gene was needed for proper down-regulation of translation-associated genes in mature dry seeds, and for AR up-regulation of these genes in germinating seeds. Thus, sly1-2 seed dormancy may result partly from failure to properly regulate protein translation, and partly from observed differences in transcription factor mRNA levels. Two positive regulators of seed dormancy, DELLA GAI (GA-INSENSITIVE and the histone deacetylase HDA6/SIL1 (MODIFIERS OF SILENCING1 were strongly AR-down-regulated. These transcriptional changes appeared to be functionally relevant since loss of GAI function and application of a histone deacetylase inhibitor led to decreased sly1-2 seed dormancy. Thus, after-ripening may increase germination potential over time by reducing dormancy-promoting stored transcript levels. Differences in transcript accumulation with after-ripening correlated to differences in transcript stability, such that stable mRNAs appeared AR-up-regulated, and unstable transcripts AR-down-regulated. Thus, relative transcript levels may change with dry after-ripening partly as a consequence of differences in mRNA turnover.

The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology

Science.gov (United States)

Mallet, François; Bouton, Olivier; Prudhomme, Sarah; Cheynet, Valérie; Oriol, Guy; Bonnaud, Bertrand; Lucotte, Gérard; Duret, Laurent; Mandrand, Bernard

2004-01-01

The definitive demonstration of a role for a recently acquired gene is a difficult task, requiring exhaustive genetic investigations and functional analysis. The situation is indeed much more complicated when facing multicopy gene families, because most or portions of the gene are conserved among the hundred copies of the family. This is the case for the ERVWE1 locus of the human endogenous retrovirus W family (HERV-W), which encodes an envelope glycoprotein (syncytin) likely involved in trophoblast differentiation. Here we describe, in 155 individuals, the positional conservation of this locus and the preservation of the envelope ORF. Sequencing of the critical elements of the ERVWE1 provirus showed a striking conservation among the 48 alleles of 24 individuals, including the LTR elements involved in the transcriptional machinery, the splice sites involved in the maturation of subgenomic Env mRNA, and the Env ORF. The functionality and tissue specificity of the 5′ LTR were demonstrated, as well as the fusogenic activity of the envelope polymorphic variants. Such functions were also shown to be preserved in the orthologous loci isolated from chimpanzee, gorilla, orangutan, and gibbon. This functional preservation among humans and during evolution strongly argued for the involvement of this recently acquired retroviral envelope glycoprotein in hominoid placental physiology. PMID:14757826

Improved detection of Candida albicans by PCR in blood of neutropenic mice with systemic candidiasis

NARCIS (Netherlands)

A.J.M. Munting-van Deventer; W.H.F. Goessens (Wil); A.F. van Belkum (Alex); H.J. van Vliet; E.W.M. van Etten (Els); H.A. Verbrugh (Henri)

1995-01-01

textabstractA PCR using primers aimed at the multicopy gene coding for the small subunit rRNA and resulting in the synthesis of a 180-bp fragment was evaluated for its use in diagnosing invasive candidiasis in comparison with blood culture. With the use of a C.

Doing new things with language: Narrative language in SLI preschoolers Ingrida Balčiūnienė, Aleksandr N. Kornev

Directory of Open Access Journals (Sweden)

Ingrida Balčiūnienė

2016-05-01

Full Text Available The paper deals with micro- and macrostructural static and dynamic narrative characteristics in specifically language-impaired (SLI Russian-speaking preschool children and their typically-developing (TD peers. The study was based on experimental data that included storytelling and retelling elicited by means of wordless picture sequences. First, individual measures of story structure, episode com- pleteness, internal state terms, story productivity, lexical diversity, and syntactic complexity, as well as the percentage of linguistic dysfluencies and errors, were evaluated and compared between the experimental and control groups. Second, the impact of such factors as session (1st vs. 2nd, story complexity, and mode (telling vs. retelling on the dynamic variation of micro- and macrostructural narrative measures was evaluated. Our results highlighted essential dynamic differences between the samples from the perspective of narrative structure, structural complexity, grammaticality, and vocabulary.

Prevalence and pathogen load estimates for the fungus Batrachochytrium dendrobatidis are impacted by ITS DNA copy number variation

DEFF Research Database (Denmark)

Rebollar, Eria A.; Woodhams, Douglas C.; LaBumbard, Brandon

2017-01-01

The ribosomal gene complex is a multi-copy region that is widely used for phylogenetic analyses of organisms from all 3 domains of life. In fungi, the copy number of the internal transcribed spacer (ITS) is used to detect abundance of pathogens causing diseases such as chytridiomycosis in amphibi...

Exome sequencing in an admixed isolated population indicates NFXL1 variants confer a risk for specific language impairment.

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Pía Villanueva

2015-03-01

Full Text Available Children affected by Specific Language Impairment (SLI fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile, who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations in the NFXL1 gene that confers a nonsynonymous change (N150K and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10-4, 8 variants tested. Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model.

Cytosine hypomethylation at CHG and CHH sites in the pleiotropic ...

Indian Academy of Sciences (India)

Ribonuclease/transcriptional repressor (R/TR). 59. MULTICOPY SUPRESSOR OF IRA1 (MSI). 60. AP2-domain DNA-binding protein (ORCA3). 61. LEAFY PETIOLE (LEP). 62. GLYCINE-RICH PROTEIN 2B (ATGRP2B). 63. LEAFY COTYLEDON 2 (LEC2). 64. YELLOW-LEAF-SPECIFIC GENE 9 (YLS9). 65. TRANSCRIPTION ...

Multidrug resistance transporters Snq2p and Pdr5p mediate caffeine efflux in Saccharomyces cerevisiae.

Science.gov (United States)

Tsujimoto, Yoshiyuki; Shimizu, Yoshihiro; Otake, Kazuya; Nakamura, Tatsuya; Okada, Ryutaro; Miyazaki, Toshitaka; Watanabe, Kunihiko

2015-01-01

SNQ2 was identified as a caffeine-resistance gene by screening a genomic library of Saccharomyces cerevisiae in a multicopy vector YEp24. SNQ2 encodes an ATP-binding cassette transporter and is highly homologous to PDR5. Multicopy of PDR5 also conferred resistance to caffeine, while its resistance was smaller than that of SNQ2. Residual caffeine contents were analyzed after transiently exposing cells to caffeine. The ratios of caffeine contents were 21.3 ± 8.8% (YEp24-SNQ2) and 81.9 ± 8.7% (YEp24-PDR5) relative to control (YEp24, 100%). In addition, multicopies of SNQ2 or PDR5 conferred resistance to rhodamine 6G (R6G), which was widely used as a substrate for transport assay. R6G was exported by both transporters, and their efflux activities were inhibited by caffeine with half-maximal inhibitory concentrations of 5.3 ± 1.9 (YEp24-SNQ2) and 17.2 ± 9.6 mM (YEp24-PDR5). These results demonstrate that Snq2p is a more functional transporter of caffeine than Pdr5p in yeast cells.

Heterogeneic dynamics of the structures of multiple gene clusters in two pathogenetically different lines originating from the same phytoplasma.

Science.gov (United States)

Arashida, Ryo; Kakizawa, Shigeyuki; Hoshi, Ayaka; Ishii, Yoshiko; Jung, Hee-Young; Kagiwada, Satoshi; Yamaji, Yasuyuki; Oshima, Kenro; Namba, Shigetou

2008-04-01

Phytoplasmas are phloem-limited plant pathogens that are transmitted by insect vectors and are associated with diseases in hundreds of plant species. Despite their small sizes, phytoplasma genomes have repeat-rich sequences, which are due to several genes that are encoded as multiple copies. These multiple genes exist in a gene cluster, the potential mobile unit (PMU). PMUs are present at several distinct regions in the phytoplasma genome. The multicopy genes encoded by PMUs (herein named mobile unit genes [MUGs]) and similar genes elsewhere in the genome (herein named fundamental genes [FUGs]) are likely to have the same function based on their annotations. In this manuscript we show evidence that MUGs and FUGs do not cluster together within the same clade. Each MUG is in a cluster with a short branch length, suggesting that MUGs are recently diverged paralogs, whereas the origin of FUGs is different from that of MUGs. We also compared the genome structures around the lplA gene in two derivative lines of the 'Candidatus Phytoplasma asteris' OY strain, the severe-symptom line W (OY-W) and the mild-symptom line M (OY-M). The gene organizations of the nucleotide sequences upstream of the lplA genes of OY-W and OY-M were dramatically different. The tra5 insertion sequence, an element of PMUs, was found only in this region in OY-W. These results suggest that transposition of entire PMUs and PMU sections has occurred frequently in the OY phytoplasma genome. The difference in the pathogenicities of OY-W and OY-M might be caused by the duplication and transposition of PMUs, followed by genome rearrangement.

The Escherichia coli cryptic prophage protein YfdR binds to DnaA and initiation of chromosomal replication is inhibited by overexpression of the gene cluster yfdQ-yfdR-yfdS-yfdT

Directory of Open Access Journals (Sweden)

Yaunori eNoguchi

2016-03-01

Full Text Available The initiation of bacterial chromosomal replication is regulated by multiple pathways. To explore novel regulators, we isolated multicopy suppressors for the cold-sensitive hda-185 ΔsfiA(sulA mutant. Hda is crucial for the negative regulation of the initiator DnaA and the hda-185 mutation causes severe replication overinitiation at the replication origin oriC. The SOS-associated division inhibitor SfiA inhibits FtsZ ring formation, an essential step for cell division during the SOS response, and ΔsfiA enhances the cold sensitivity of hda-185 cells in colony formation. One of the suppressors comprised the yfdQ-yfdR-yfdS-yfdT gene cluster carried on a cryptic prophage. Increased copy numbers of yfdQRT or yfdQRS inhibited not only hda-185-dependent overinitiation, but also replication overinitiation in a hyperactive dnaA mutant, and in a mutant lacking an oriC-binding initiation-inhibitor SeqA. In addition, increasing the copy number of the gene set inhibited the growth of cells bearing specific, initiation-impairing dnaA mutations. In wild-type cells, multicopy supply of yfdQRT or yfdQRS also inhibited replication initiation and increased hydroxyurea (HU-resistance, as seen in cells lacking DiaA, a stimulator of DnaA assembly on oriC. Deletion of the yfdQ-yfdR-yfdS-yfdT genes did not affect either HU resistance or initiation regulation. Furthermore, we found that DnaA bound specifically to YfdR in soluble protein extracts oversupplied with YfdQRST. Purified YfdR also bound to DnaA, and DnaA Phe46, an amino acid residue crucial for DnaA interactions with DiaA and DnaB replicative helicase was important for this interaction. Consistently, YfdR moderately inhibited DiaA-DnaA and DnaB-DnaA interactions. In addition, protein extracts oversupplied with YfdQRST inhibited replication initiation in vitro. Given the roles of yfdQ and yfdS in cell tolerance to specific environmental stresses, the yfdQ-yfdR-yfdS-yfdT genes might downregulate the initiator

The Escherichia coli Cryptic Prophage Protein YfdR Binds to DnaA and Initiation of Chromosomal Replication Is Inhibited by Overexpression of the Gene Cluster yfdQ-yfdR-yfdS-yfdT

Science.gov (United States)

Noguchi, Yasunori; Katayama, Tsutomu

2016-01-01

The initiation of bacterial chromosomal replication is regulated by multiple pathways. To explore novel regulators, we isolated multicopy suppressors for the cold-sensitive hda-185 ΔsfiA(sulA) mutant. Hda is crucial for the negative regulation of the initiator DnaA and the hda-185 mutation causes severe replication overinitiation at the replication origin oriC. The SOS-associated division inhibitor SfiA inhibits FtsZ ring formation, an essential step for cell division regulation during the SOS response, and ΔsfiA enhances the cold sensitivity of hda-185 cells in colony formation. One of the suppressors comprised the yfdQ-yfdR-yfdS-yfdT gene cluster carried on a cryptic prophage. Increased copy numbers of yfdQRT or yfdQRS inhibited not only hda-185-dependent overinitiation, but also replication overinitiation in a hyperactive dnaA mutant, and in a mutant lacking an oriC-binding initiation-inhibitor SeqA. In addition, increasing the copy number of the gene set inhibited the growth of cells bearing specific, initiation-impairing dnaA mutations. In wild-type cells, multicopy supply of yfdQRT or yfdQRS also inhibited replication initiation and increased hydroxyurea (HU)-resistance, as seen in cells lacking DiaA, a stimulator of DnaA assembly on oriC. Deletion of the yfdQ-yfdR-yfdS-yfdT genes did not affect either HU resistance or initiation regulation. Furthermore, we found that DnaA bound specifically to YfdR in soluble protein extracts oversupplied with YfdQRST. Purified YfdR also bound to DnaA, and DnaA Phe46, an amino acid residue crucial for DnaA interactions with DiaA and DnaB replicative helicase was important for this interaction. Consistently, YfdR moderately inhibited DiaA-DnaA and DnaB-DnaA interactions. In addition, protein extracts oversupplied with YfdQRST inhibited replication initiation in vitro. Given the roles of yfdQ and yfdS in cell tolerance to specific environmental stresses, the yfdQ-yfdR-yfdS-yfdT genes might downregulate the initiator Dna

The Escherichia coli Cryptic Prophage Protein YfdR Binds to DnaA and Initiation of Chromosomal Replication Is Inhibited by Overexpression of the Gene Cluster yfdQ-yfdR-yfdS-yfdT.

Science.gov (United States)

Noguchi, Yasunori; Katayama, Tsutomu

2016-01-01

The initiation of bacterial chromosomal replication is regulated by multiple pathways. To explore novel regulators, we isolated multicopy suppressors for the cold-sensitive hda-185 ΔsfiA(sulA) mutant. Hda is crucial for the negative regulation of the initiator DnaA and the hda-185 mutation causes severe replication overinitiation at the replication origin oriC. The SOS-associated division inhibitor SfiA inhibits FtsZ ring formation, an essential step for cell division regulation during the SOS response, and ΔsfiA enhances the cold sensitivity of hda-185 cells in colony formation. One of the suppressors comprised the yfdQ-yfdR-yfdS-yfdT gene cluster carried on a cryptic prophage. Increased copy numbers of yfdQRT or yfdQRS inhibited not only hda-185-dependent overinitiation, but also replication overinitiation in a hyperactive dnaA mutant, and in a mutant lacking an oriC-binding initiation-inhibitor SeqA. In addition, increasing the copy number of the gene set inhibited the growth of cells bearing specific, initiation-impairing dnaA mutations. In wild-type cells, multicopy supply of yfdQRT or yfdQRS also inhibited replication initiation and increased hydroxyurea (HU)-resistance, as seen in cells lacking DiaA, a stimulator of DnaA assembly on oriC. Deletion of the yfdQ-yfdR-yfdS-yfdT genes did not affect either HU resistance or initiation regulation. Furthermore, we found that DnaA bound specifically to YfdR in soluble protein extracts oversupplied with YfdQRST. Purified YfdR also bound to DnaA, and DnaA Phe46, an amino acid residue crucial for DnaA interactions with DiaA and DnaB replicative helicase was important for this interaction. Consistently, YfdR moderately inhibited DiaA-DnaA and DnaB-DnaA interactions. In addition, protein extracts oversupplied with YfdQRST inhibited replication initiation in vitro. Given the roles of yfdQ and yfdS in cell tolerance to specific environmental stresses, the yfdQ-yfdR-yfdS-yfdT genes might downregulate the initiator Dna

A strategy of gene overexpression based on tandem repetitive promoters in Escherichia coli

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Li Mingji

2012-02-01

Full Text Available Abstract Background For metabolic engineering, many rate-limiting steps may exist in the pathways of accumulating the target metabolites. Increasing copy number of the desired genes in these pathways is a general method to solve the problem, for example, the employment of the multi-copy plasmid-based expression system. However, this method may bring genetic instability, structural instability and metabolic burden to the host, while integrating of the desired gene into the chromosome may cause inadequate transcription or expression. In this study, we developed a strategy for obtaining gene overexpression by engineering promoter clusters consisted of multiple core-tac-promoters (MCPtacs in tandem. Results Through a uniquely designed in vitro assembling process, a series of promoter clusters were constructed. The transcription strength of these promoter clusters showed a stepwise enhancement with the increase of tandem repeats number until it reached the critical value of five. Application of the MCPtacs promoter clusters in polyhydroxybutyrate (PHB production proved that it was efficient. Integration of the phaCAB genes with the 5CPtacs promoter cluster resulted in an engineered E.coli that can accumulate 23.7% PHB of the cell dry weight in batch cultivation. Conclusions The transcription strength of the MCPtacs promoter cluster can be greatly improved by increasing the tandem repeats number of the core-tac-promoter. By integrating the desired gene together with the MCPtacs promoter cluster into the chromosome of E. coli, we can achieve high and stale overexpression with only a small size. This strategy has an application potential in many fields and can be extended to other bacteria.

Functional characterization of human COQ4, a gene required for Coenzyme Q10 biosynthesis

International Nuclear Information System (INIS)

Casarin, Alberto; Jimenez-Ortega, Jose Carlos; Trevisson, Eva; Pertegato, Vanessa; Doimo, Mara; Ferrero-Gomez, Maria Lara; Abbadi, Sara; Artuch, Rafael; Quinzii, Catarina; Hirano, Michio; Basso, Giuseppe; Ocana, Carlos Santos; Navas, Placido; Salviati, Leonardo

2008-01-01

Defects in genes involved in coenzyme Q (CoQ) biosynthesis cause primary CoQ deficiency, a severe multisystem disorders presenting as progressive encephalomyopathy and nephropathy. The COQ4 gene encodes an essential factor for biosynthesis in Saccharomyces cerevisiae. We have identified and cloned its human ortholog, COQ4, which is located on chromosome 9q34.13, and is transcribed into a 795 base-pair open reading frame, encoding a 265 amino acid (aa) protein (Isoform 1) with a predicted N-terminal mitochondrial targeting sequence. It shares 39% identity and 55% similarity with the yeast protein. Coq4 protein has no known enzymatic function, but may be a core component of multisubunit complex required for CoQ biosynthesis. The human transcript is detected in Northern blots as a ∼1.4 kb single band and is expressed ubiquitously, but at high levels in liver, lung, and pancreas. Transcription initiates at multiple sites, located 333-23 nucleotides upstream of the ATG. A second group of transcripts originating inside intron 1 of the gene encodes a 241 aa protein, which lacks the mitochondrial targeting sequence (isoform 2). Expression of GFP-fusion proteins in HeLa cells confirmed that only isoform 1 is targeted to mitochondria. The functional significance of the second isoform is unknown. Human COQ4 isoform 1, expressed from a multicopy plasmid, efficiently restores both growth in glycerol, and CoQ content in COQ4 null yeast strains. Human COQ4 is an interesting candidate gene for patients with isolated CoQ 10 deficiency

Advances in plant gene-targeted and functional markers: a review

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Poczai Péter

2013-02-01

Full Text Available Abstract Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information

Advances in plant gene-targeted and functional markers: a review

Science.gov (United States)

2013-01-01

Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the

A gene catalogue of the euchromatic male-specific region of the horse Y chromosome: comparison with human and other mammals.

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Nandina Paria

Full Text Available Studies of the Y chromosome in primates, rodents and carnivores provide compelling evidence that the male specific region of Y (MSY contains functional genes, many of which have specialized roles in spermatogenesis and male-fertility. Little similarity, however, has been found between the gene content and sequence of MSY in different species. This hinders the discovery of species-specific male fertility genes and limits our understanding about MSY evolution in mammals. Here, a detailed MSY gene catalogue was developed for the horse--an odd-toed ungulate. Using direct cDNA selection from horse testis, and sequence analysis of Y-specific BAC clones, 37 horse MSY genes/transcripts were identified. The genes were mapped to the MSY BAC contig map, characterized for copy number, analyzed for transcriptional profiles by RT-PCR, examined for the presence of ORFs, and compared to other mammalian orthologs. We demonstrate that the horse MSY harbors 20 X-degenerate genes with known orthologs in other eutherian species. The remaining 17 genes are acquired or novel and have so far been identified only in the horse or donkey Y chromosomes. Notably, 3 transcripts were found in the heterochromatic part of the Y. We show that despite substantial differences between the sequence, gene content and organization of horse and other mammalian Y chromosomes, the functions of MSY genes are predominantly related to testis and spermatogenesis. Altogether, 10 multicopy genes with testis-specific expression were identified in the horse MSY, and considered likely candidate genes for stallion fertility. The findings establish an important foundation for the study of Y-linked genetic factors governing fertility in stallions, and improve our knowledge about the evolutionary processes that have shaped Y chromosomes in different mammalian lineages.

A gene catalogue of the euchromatic male-specific region of the horse Y chromosome: comparison with human and other mammals.

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Paria, Nandina; Raudsepp, Terje; Pearks Wilkerson, Alison J; O'Brien, Patricia C M; Ferguson-Smith, Malcom A; Love, Charles C; Arnold, Carolyn; Rakestraw, Peter; Murphy, William J; Chowdhary, Bhanu P

2011-01-01

Studies of the Y chromosome in primates, rodents and carnivores provide compelling evidence that the male specific region of Y (MSY) contains functional genes, many of which have specialized roles in spermatogenesis and male-fertility. Little similarity, however, has been found between the gene content and sequence of MSY in different species. This hinders the discovery of species-specific male fertility genes and limits our understanding about MSY evolution in mammals. Here, a detailed MSY gene catalogue was developed for the horse--an odd-toed ungulate. Using direct cDNA selection from horse testis, and sequence analysis of Y-specific BAC clones, 37 horse MSY genes/transcripts were identified. The genes were mapped to the MSY BAC contig map, characterized for copy number, analyzed for transcriptional profiles by RT-PCR, examined for the presence of ORFs, and compared to other mammalian orthologs. We demonstrate that the horse MSY harbors 20 X-degenerate genes with known orthologs in other eutherian species. The remaining 17 genes are acquired or novel and have so far been identified only in the horse or donkey Y chromosomes. Notably, 3 transcripts were found in the heterochromatic part of the Y. We show that despite substantial differences between the sequence, gene content and organization of horse and other mammalian Y chromosomes, the functions of MSY genes are predominantly related to testis and spermatogenesis. Altogether, 10 multicopy genes with testis-specific expression were identified in the horse MSY, and considered likely candidate genes for stallion fertility. The findings establish an important foundation for the study of Y-linked genetic factors governing fertility in stallions, and improve our knowledge about the evolutionary processes that have shaped Y chromosomes in different mammalian lineages.

The contribution of p53 and Y chromosome long arm genes to regulation of apoptosis in mouse testis.

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Lech, Tomasz; Styrna, Józefa; Kotarska, Katarzyna

2018-03-01

Apoptosis of excessive or defective germ cells is a natural process occurring in mammalian testes. Tumour suppressor protein p53 is involved in this process both in developing and adult male gonads. Its contribution to testicular physiology is known to be modified by genetic background. The aim of this study was to evaluate the combined influence of the p53 and Y chromosome long arm genes on male germ cell apoptosis. Knockout of the transformation related protein 53 (Trp53) gene was introduced into congenic strains: B10.BR (intact Y chromosome) and B10.BR-Ydel (Y chromosome with a deletion in the long arm). The level of apoptosis in the testes of 19-day-old and 3-month-old male mice was determined using the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate in situ nick-end labelling (TUNEL) method. The study revealed that although p53 is involved in germ cell apoptosis in peripubertal testes, this process can also be mediated by p53-independent mechanisms. However, activation of p53-independent apoptotic pathways in the absence of the p53 protein requires engagement of the multicopy Yq genes and was not observed in gonads of B10.BR-Ydel-p53-/- males. The role of Yq genes in the regulation of testicular apoptosis seems to be restricted to the initial wave of spermatogenesis and is not evident in adult gonads. The study confirmed, instead, that p53 does participate in spontaneous apoptosis in mature testes.

Developmental cognitive genetics: How psychology can inform genetics and vice versa

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Bishop, Dorothy V. M.

2006-01-01

Developmental neuropsychology is concerned with uncovering the underlying basis of developmental disorders such as specific language impairment (SLI), developmental dyslexia, and autistic disorder. Twin and family studies indicate that genetic influences play an important part in the aetiology of all of these disorders, yet progress in identifying genes has been slow. One way forward is to cut loose from conventional clinical criteria for diagnosing disorders and to focus instead on measures of underlying cognitive mechanisms. Psychology can inform genetics by clarifying what the key dimensions are for heritable phenotypes. However, it is not a one-way street. By using genetically informative designs, one can gain insights about causal relationships between different cognitive deficits. For instance, it has been suggested that low-level auditory deficits cause phonological problems in SLI. However, a twin study showed that, although both types of deficit occur in SLI, they have quite different origins, with environmental factors more important for auditory deficit, and genes more important for deficient phonological short-term memory. Another study found that morphosyntactic deficits in SLI are also highly heritable, but have different genetic origins from impairments of phonological short-term memory. A genetic perspective shows that a search for the underlying cause of developmental disorders may be misguided, because they are complex and heterogeneous and are associated with multiple risk factors that only cause serious disability when they occur in combination. PMID:16769616

Temporal expression and localization patterns of variant surface antigens in clinical Plasmodium falciparum isolates during erythrocyte schizogony.

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Anna Bachmann

Full Text Available Avoidance of antibody-mediated immune recognition allows parasites to establish chronic infections and enhances opportunities for transmission. The human malaria parasite Plasmodium falciparum possesses a number of multi-copy gene families, including var, rif, stevor and pfmc-2tm, which encode variant antigens believed to be expressed on the surfaces of infected erythrocytes. However, most studies of these antigens are based on in vitro analyses of culture-adapted isolates, most commonly the laboratory strain 3D7, and thus may not be representative of the unique challenges encountered by P. falciparum in the human host. To investigate the expression of the var, rif-A, rif-B, stevor and pfmc-2tm family genes under conditions that mimic more closely the natural course of infection, ex vivo clinical P. falciparum isolates were analyzed using a novel quantitative real-time PCR approach. Expression patterns in the clinical isolates at various time points during the first intraerythrocytic developmental cycle in vitro were compared to those of strain 3D7. In the clinical isolates, in contrast to strain 3D7, there was a peak of expression of the multi-copy gene families rif-A, stevor and pfmc-2tm at the young ring stage, in addition to the already known expression peak in trophozoites. Furthermore, most of the variant surface antigen families were overexpressed in the clinical isolates relative to 3D7, with the exception of the pfmc-2tm family, expression of which was higher in 3D7 parasites. Immunofluorescence analyses performed in parallel revealed two stage-dependent localization patterns of RIFIN, STEVOR and PfMC-2TM. Proteins were exported into the infected erythrocyte at the young trophozoite stage, whereas they remained inside the parasite membrane during schizont stage and were subsequently observed in different compartments in the merozoite. These results reveal a complex pattern of expression of P. falciparum multi-copy gene families during

Evidence of strain structure in Plasmodium falciparum var gene repertoires in children from Gabon, West Africa.

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Day, Karen P; Artzy-Randrup, Yael; Tiedje, Kathryn E; Rougeron, Virginie; Chen, Donald S; Rask, Thomas S; Rorick, Mary M; Migot-Nabias, Florence; Deloron, Philippe; Luty, Adrian J F; Pascual, Mercedes

2017-05-16

Existing theory on competition for hosts between pathogen strains has proposed that immune selection can lead to the maintenance of strain structure consisting of discrete, weakly overlapping antigenic repertoires. This prediction of strain theory has conceptual overlap with fundamental ideas in ecology on niche partitioning and limiting similarity between coexisting species in an ecosystem, which oppose the hypothesis of neutral coexistence. For Plasmodium falciparum , strain theory has been specifically proposed in relation to the major surface antigen of the blood stage, known as Pf EMP1 and encoded by the multicopy multigene family known as the var genes. Deep sampling of the DBLα domain of var genes in the local population of Bakoumba, West Africa, was completed to define whether patterns of repertoire overlap support a role of immune selection under the opposing force of high outcrossing, a characteristic of areas of intense malaria transmission. Using a 454 high-throughput sequencing protocol, we report extremely high diversity of the DBLα domain and a large parasite population with DBLα repertoires structured into nonrandom patterns of overlap. Such population structure, significant for the high diversity of var genes that compose it at a local level, supports the existence of "strains" characterized by distinct var gene repertoires. Nonneutral, frequency-dependent competition would be at play and could underlie these patterns. With a computational experiment that simulates an intervention similar to mass drug administration, we argue that the observed repertoire structure matters for the antigenic var diversity of the parasite population remaining after intervention.

Penicillin production in industrial strain Penicillium chrysogenum P2niaD18 is not dependent on the copy number of biosynthesis genes.

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Ziemons, Sandra; Koutsantas, Katerina; Becker, Kordula; Dahlmann, Tim; Kück, Ulrich

2017-02-16

Multi-copy gene integration into microbial genomes is a conventional tool for obtaining improved gene expression. For Penicillium chrysogenum, the fungal producer of the beta-lactam antibiotic penicillin, many production strains carry multiple copies of the penicillin biosynthesis gene cluster. This discovery led to the generally accepted view that high penicillin titers are the result of multiple copies of penicillin genes. Here we investigated strain P2niaD18, a production line that carries only two copies of the penicillin gene cluster. We performed pulsed-field gel electrophoresis (PFGE), quantitative qRT-PCR, and penicillin bioassays to investigate production, deletion and overexpression strains generated in the P. chrysogenum P2niaD18 background, in order to determine the copy number of the penicillin biosynthesis gene cluster, and study the expression of one penicillin biosynthesis gene, and the penicillin titer. Analysis of production and recombinant strain showed that the enhanced penicillin titer did not depend on the copy number of the penicillin gene cluster. Our assumption was strengthened by results with a penicillin null strain lacking pcbC encoding isopenicillin N synthase. Reintroduction of one or two copies of the cluster into the pcbC deletion strain restored transcriptional high expression of the pcbC gene, but recombinant strains showed no significantly different penicillin titer compared to parental strains. Here we present a molecular genetic analysis of production and recombinant strains in the P2niaD18 background carrying different copy numbers of the penicillin biosynthesis gene cluster. Our analysis shows that the enhanced penicillin titer does not strictly depend on the copy number of the cluster. Based on these overall findings, we hypothesize that instead, complex regulatory mechanisms are prominently implicated in increased penicillin biosynthesis in production strains.

Gain of DNA methylation is enhanced in the absence of CTCF at the human retinoblastoma gene promoter

International Nuclear Information System (INIS)

Dávalos-Salas, Mercedes; Furlan-Magaril, Mayra; González-Buendía, Edgar; Valdes-Quezada, Christian; Ayala-Ortega, Erandi; Recillas-Targa, Félix

2011-01-01

Long-term gene silencing throughout cell division is generally achieved by DNA methylation and other epigenetic processes. Aberrant DNA methylation is now widely recognized to be associated with cancer and other human diseases. Here we addressed the contribution of the multifunctional nuclear factor CTCF to the epigenetic regulation of the human retinoblastoma (Rb) gene promoter in different tumoral cell lines. To assess the DNA methylation status of the Rb promoter, genomic DNA from stably transfected human erythroleukemic K562 cells expressing a GFP reporter transgene was transformed with sodium bisulfite, and then PCR-amplified with modified primers and sequenced. Single- and multi-copy integrants with the CTCF binding site mutated were isolated and characterized by Southern blotting. Silenced transgenes were reactivated using 5-aza-2'-deoxycytidine and Trichostatin-A, and their expression was monitored by fluorescent cytometry. Rb gene expression and protein abundance were assessed by RT-PCR and Western blotting in three different glioma cell lines, and DNA methylation of the promoter region was determined by sodium bisulfite sequencing, together with CTCF dissociation and methyl-CpG-binding protein incorporation by chromatin immunoprecipitation assays. We found that the inability of CTCF to bind to the Rb promoter causes a dramatic loss of gene expression and a progressive gain of DNA methylation. This study indicates that CTCF plays an important role in maintaining the Rb promoter in an optimal chromatin configuration. The absence of CTCF induces a rapid epigenetic silencing through a progressive gain of DNA methylation. Consequently, CTCF can now be seen as one of the epigenetic components that allows the proper configuration of tumor suppressor gene promoters. Its aberrant dissociation can then predispose key genes in cancer cells to acquire DNA methylation and epigenetic silencing

Physical map location of the multicopy genes coding for ammonia monooxygenase and hydroxylamine oxidoreductase in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11.

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Hirota, R; Yamagata, A; Kato, J; Kuroda, A; Ikeda, T; Takiguchi, N; Ohtake, H

2000-02-01

Pulsed-field gel electrophoresis of PmeI digests of the Nitrosomonas sp. strain ENI-11 chromosome produced four bands ranging from 1,200 to 480 kb in size. Southern hybridizations suggested that a 487-kb PmeI fragment contained two copies of the amoCAB genes, coding for ammonia monooxygenase (designated amoCAB(1) and amoCAB(2)), and three copies of the hao gene, coding for hydroxylamine oxidoreductase (hao(1), hao(2), and hao(3)). In this DNA fragment, amoCAB(1) and amoCAB(2) were about 390 kb apart, while hao(1), hao(2), and hao(3) were separated by at least about 100 kb from each other. Interestingly, hao(1) and hao(2) were located relatively close to amoCAB(1) and amoCAB(2), respectively. DNA sequence analysis revealed that hao(1) and hao(2) shared 160 identical nucleotides immediately upstream of each translation initiation codon. However, hao(3) showed only 30% nucleotide identity in the 160-bp corresponding region.

Bat white-nose syndrome: A real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructans

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Laura K Muller; Jeffrey M. Lorch; Daniel L. Lindner; Michael O' Connor; Andrea Gargas; David S. Blehert

2013-01-01

The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The...

Simultaneous and Sequential Integration by Cre/loxP Site-Specific Recombination in Saccharomyces cerevisiae.

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Choi, Ho-Jung; Kim, Yeon-Hee

2018-05-28

A Cre/ loxP -δ-integration system was developed to allow sequential and simultaneous integration of a multiple gene expression cassette in Saccharomyces cerevisiae . To allow repeated integrations, the reusable Candida glabrata MARKER ( CgMARKER ) carrying loxP sequences was used, and the integrated CgMARKER was efficiently removed by inducing Cre recombinase. The XYLP and XYLB genes encoding endoxylanase and β-xylosidase, respectively, were used as model genes for xylan metabolism in this system, and the copy number of these genes was increased to 15.8 and 16.9 copies/cell, respectively, by repeated integration. This integration system is a promising approach for the easy construction of yeast strains with enhanced metabolic pathways through multicopy gene expression.

Chromatin Structure of Epstein-Barr Virus Latent Episomes.

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Lieberman, Paul M

2015-01-01

EBV latent infection is characterized by a highly restricted pattern of viral gene expression. EBV can establish latent infections in multiple different tissue types with remarkable variation and plasticity in viral transcription and replication. During latency, the viral genome persists as a multi-copy episome, a non-integrated-closed circular DNA with nucleosome structure similar to cellular chromosomes. Chromatin assembly and histone modifications contribute to the regulation of viral gene expression, DNA replication, and episome persistence during latency. This review focuses on how EBV latency is regulated by chromatin and its associated processes.

Identification, cloning, and expression of the Escherichia coli pyrazinamidase and nicotinamidase gene, pncA.

Science.gov (United States)

Frothingham, R; Meeker-O'Connell, W A; Talbot, E A; George, J W; Kreuzer, K N

1996-06-01

Pyrazinamide (PZA) is one of the three most important drugs for treatment of Mycobacterium tuberculosis infections. The antibacterial activity of PZA requires a bacterial enzyme, pyrazinamidase (PZAase), which hydrolyzes PZA to form pyrazinoic acid and ammonia. Most PZA-resistant clinical M. tuberculosis isolates lack PZAase activity. With the goal of eventually identifying and characterizing the M.tuberculosis PZAase gene, we began with the more tractable organism, Escherichia coli, which also has PZAase activity. We screened a transposon-generated E. coli insertion mutant library, using a qualitative PZAase assay. Two PZAase-negative mutants out of 4,000 colonies screened were identified. In each mutant, the transposon interrupted the same 639-bp open reading frame (ORF), ORF1. The expression of ORF1 on a multicopy plasmid complemented a PZAase-negative mutant, leading to PZAase activity levels approximately 10-fold greater than those of the wild type. PZA has a structure similar to that of nicotinamide, a pyridine nucleotide cycle intermediate, so we tested our strains for nicotinamidase activity (EC 3.5.1.19) (genetic locus pncA). The construct with multiple plasmid copies of ORF1 had an approximately 10-fold increase in levels of nicotinamidase activity. This overexpressing strain could utilize nicotinamide as a sole nitrogen source, through wild-type E. coli cannot. We conclude that a single E. coli enzyme accounts for both PZAase and nicotinamidase activities and that ORF1 is the E.coli PZAase and nicotinamidase gene, pncA.

TTY2 genes deletions as genetic risk factor of male infertility.

Science.gov (United States)

Shaveisi-Zadeh, F; Alibakhshi, R; Asgari, R; Rostami-Far, Z; Bakhtiari, M; Abdi, H; Movafagh, A; Mirfakhraie, R

2017-02-28

Y chromosome has a number of genes that are expressed in testis and have a role in spermatogenesis. TTY2L12A and TTY2L2A are the members of testis transcript Y2 (TTY2) that are Y linked multi-copy gene families, located on Yp11 and Yq11 loci respectively. The aim of this study was to investigate frequency of TTY2L12A and TTY2L2A deletions in azoospermic patients compared with fertile males. This study was performed on 45 infertile males with idiopathic azoospermia without any AZF micro deletions (group A), 33 infertile males with azoospermia which do not screened for AZF micro deletions (group B) and 65 fertile males (group C), from October 2013 to April 2015 in west of Iran. Polymerase chain reaction (PCR) method was used for detection of TTY2L12A and TTY2L2A gene deletions in studied groups. No deletions were detected in normal fertile males of group C. 1 out of 45 azoospermic males of group A (2.22%) and 3 out of 33 azoospermic males of group B (9.09%) had TTY2L2A deletion (p= 0.409 and p= 0.036 respectively), also 1 out of 45 azoospermic males of group A (2.22%) and 4 out of 33 azoospermic males of group B (12.12%) had TTY2L12A deletion (p= 0.409 and p= 0.011 respectively).  None of azoospermic males in Group A and B had deletions in both genes. Our data showed significant correlation between non-obstructive azoospermia and TTY2L12A and TTY2L2A deletions. Thus, it seems that TTY2L12A and TTY2L2A deletions can consider as one of the genetic risk factors for non-obstructive azoospermia.

Electrical brain responses in language-impaired children reveal grammar-specific deficits.

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Elisabeth Fonteneau

2008-03-01

Full Text Available Scientific and public fascination with human language have included intensive scrutiny of language disorders as a new window onto the biological foundations of language and its evolutionary origins. Specific language impairment (SLI, which affects over 7% of children, is one such disorder. SLI has received robust scientific attention, in part because of its recent linkage to a specific gene and loci on chromosomes and in part because of the prevailing question regarding the scope of its language impairment: Does the disorder impact the general ability to segment and process language or a specific ability to compute grammar? Here we provide novel electrophysiological data showing a domain-specific deficit within the grammar of language that has been hitherto undetectable through behavioural data alone.We presented participants with Grammatical(G-SLI, age-matched controls, and younger child and adult controls, with questions containing syntactic violations and sentences containing semantic violations. Electrophysiological brain responses revealed a selective impairment to only neural circuitry that is specific to grammatical processing in G-SLI. Furthermore, the participants with G-SLI appeared to be partially compensating for their syntactic deficit by using neural circuitry associated with semantic processing and all non-grammar-specific and low-level auditory neural responses were normal.The findings indicate that grammatical neural circuitry underlying language is a developmentally unique system in the functional architecture of the brain, and this complex higher cognitive system can be selectively impaired. The findings advance fundamental understanding about how cognitive systems develop and all human language is represented and processed in the brain.

M6: A diploid potato inbred line for use in breeding and genetics research

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M6 is a vigorous, homozygous breeding line derived by self-pollinating the diploid wild potato relative Solanum chacoense for seven generations. While most wild Solanum species are self-incompatible, this clone is homozygous for the dominant self-incompatibility inhibitor gene Sli. It is homozygous ...

Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA) Genes in Flax (Linum usitatissimum L.).

Science.gov (United States)

Yurkevich, Olga Y; Kirov, Ilya V; Bolsheva, Nadezhda L; Rachinskaya, Olga A; Grushetskaya, Zoya E; Zoschuk, Svyatoslav A; Samatadze, Tatiana E; Bogdanova, Marina V; Lemesh, Valentina A; Amosova, Alexandra V; Muravenko, Olga V

2017-01-01

Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase ( CesA ) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum . Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG) 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.

Which Preschool Children with Specific Language Impairment Receive Language Intervention?

Science.gov (United States)

Wittke, Kacie; Spaulding, Tammie J.

2018-01-01

Purpose: Potential biases in service provision for preschool children with specific language impairment (SLI) were explored. Method: In Study 1, children with SLI receiving treatment (SLI-T) and those with SLI not receiving treatment (SLI-NT) were compared on demographic characteristics and developmental abilities. Study 2 recruited children with…

Physical and functional maps of the luminescence gene cluster in an autoinducer-deficient Vibrio fischeri strain isolated from a squid light organ.

Science.gov (United States)

Gray, K M; Greenberg, E P

1992-07-01

Vibrio fischeri ES114 is an isolate representing the specific bacterial light organ symbiont of the squid Euprymna scolopes. An interesting feature of this strain of V. fischeri is that it is visibly luminous within the light organ of the squid host but is nonluminous when grown under standard laboratory conditions. Luminescence can be restored in laboratory culture, however, by the addition of autoinducer, a species-specific inducer of the V. fischeri luminescence (lux) genes. Most other isolates of V. fischeri produce autoinducer in sufficient quantities to induce luminescence in laboratory culture. We have cloned an 8.8-kb DNA fragment from V. fischeri ES114 that encodes all of the functions necessary for luminescence in Escherichia coli in the absence of exogenous autoinducer. This DNA contains both of the recognized V. fischeri lux regulatory genes, one of which (luxI) directs E. coli to synthesize autoinducer. The organization of the individual lux genes within this DNA fragment appears to be the same as that in the other strains of V. fischeri studied; the restriction map of the V. fischeri ES114 lux DNA has diverged substantially, however, from the largely conserved maps of V. fischeri MJ1 and ATCC 7744. Although E. coli containing the V. fischeri ES114 lux DNA synthesizes considerable amounts of autoinducer, V. fischeri ES114 synthesizes autoinducer only in small amounts, even when transcription of the lux genes, including luxI, is activated by the addition of exogenous autoinducer. Nonetheless, transconjugants of V. fischeri ES114 that contain multicopy plasmids bearing the ES114 lux genes synthesize sufficient autoinducer to induce luminescence. These results suggest that V. fischeri ES11r does not lack a functional luxl, nor is it deficient in the ability to synthesize metabolic precursors for autoinducer synthesis.

Cloning and characterization of the rec2 gene of Ustilago maydis

International Nuclear Information System (INIS)

Bauchwitz, R.P.; Holloman, W.K.

1989-01-01

The authors are exploring the molecular basis for genetic recombination using the corn smut fungus Ustilago maydis, from which the first two eucaryotic DNA repair and recombination mutants, rec1 and rec2, were described. Cells mutant at the rec2 locus are unable to repair lethal damage to their DNA from UV and X irradiation or from chemical alkylating agents such as N-methyl-nitrosoguanidine. Rec2 mutants retain only a residual level of DNA-damage inducible mitotic recombination, and are unable to complete meiosis. Using an autonomously replicating plasmid vector for Ustilago, they established the first nonintegrating plasmid library of the Ustilago genome. The rec2 locus was cloned by complementation of the rec2 mutation in vivo. One clone was found to restore all of the deficient activities. Although this rec2 complementing clone is present on a multicopy plasmid, the authors observed that it fully restored but did not further increase the fifty-fold inducibility of heteroallelic recombination at the nitrate reductase and inositol loci of rec2 or wild type cells. Northern blot analysis using the rec2 complementing clone revealed three UV inducible transcripts, one of which is absent in a rec2 mutant strain. This transcript organization resembles that of the yeast rad10 and the human ERCC-1 genes (MCB 9:1794), but sequence obtained to date from rec2 does not show homology with these genes. They have also observed that the rec2 mutation may alter the level of homologous integration of transformed DNA markers. Integration of a Leu1 complementing plasmid by Scott Fotheringham of the lab has shown that while much of plasmid integration in wild type Ustilago is nonhomologous, integration in at least some rec2 strains is entirely homologous. They are using the cloned rec2 gene to confirm that rec2 is indeed involved in altering the level of homologous integration in Ustilago, and if so, they plan to clone a mammalian analogue of rec2

Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA Genes in Flax (Linum usitatissimum L.

Directory of Open Access Journals (Sweden)

Olga Y. Yurkevich

2017-08-01

Full Text Available Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase (CesA multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH-based chromosomal localization of the CesA conserved fragment (KF011584.1, 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum. Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.

DNA extraction from dry museum beetles without conferring external morphological damage

DEFF Research Database (Denmark)

Gilbert, M Thomas P; Moore, Wendy; Melchior, Linea

2007-01-01

undesirable when dealing with rare species or otherwise important specimens, such as type specimens. METHODOLOGY: We describe a method for the extraction of PCR-amplifiable mitochondrial and nuclear DNA from dry insects without causing external morphological damage. Using PCR to amplify approximately 220 bp...... of the mitochondrial gene cytochrome c oxidase I, and 250-345 bp fragments of the multi-copy, nuclear 28s ribosomal DNA gene, we demonstrate the efficacy of this method on beetles collected up to 50 years ago. CONCLUSIONS: This method offers a means of obtaining useful genetic information from rare insects without...... conferring external morphological damage. Udgivelsesdato: 2007-null...

Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

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The diversity and population-genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analyzed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, Romagnola), sequenced to 11-fold...

Analysis of Salmonella enterica serotype paratyphi A gene expression in the blood of bacteremic patients in Bangladesh.

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Alaullah Sheikh

2010-12-01

Full Text Available Salmonella enterica serotype Paratyphi A is a human-restricted cause of paratyphoid fever, accounting for up to a fifth of all cases of enteric fever in Asia.In this work, we applied an RNA analysis method, Selective Capture of Transcribed Sequences (SCOTS, and cDNA hybridization-microarray technology to identify S. Paratyphi A transcripts expressed by bacteria in the blood of three patients in Bangladesh. In total, we detected 1,798 S. Paratyphi A mRNAs expressed in the blood of infected humans (43.9% of the ORFeome. Of these, we identified 868 in at least two patients, and 315 in all three patients. S. Paratyphi A transcripts identified in at least two patients encode proteins involved in energy metabolism, nutrient and iron acquisition, vitamin biosynthesis, stress responses, oxidative stress resistance, and pathogenesis. A number of detected transcripts are expressed from PhoP and SlyA-regulated genes associated with intra-macrophage survival, genes contained within Salmonella Pathogenicity Islands (SPIs 1-4, 6, 10, 13, and 16, as well as RpoS-regulated genes. The largest category of identified transcripts is that of encoding proteins with unknown function. When comparing levels of bacterial mRNA using in vivo samples collected from infected patients to samples from in vitro grown organisms, we found significant differences for 347, 391, and 456 S. Paratyphi A transcripts in each of three individual patients (approximately 9.7% of the ORFeome. Of these, expression of 194 transcripts (4.7% of ORFs was concordant in two or more patients, and 41 in all patients. Genes encoding these transcripts are contained within SPI-1, 3, 6 and 10, PhoP-regulated genes, involved in energy metabolism, nutrient acquisition, drug resistance, or uncharacterized genes. Using quantitative RT-PCR, we confirmed increased gene expression in vivo for a subset of these genes.To our knowledge, we describe the first microarray-based transcriptional analysis of a pathogen

Modes of overinitiation, dnaA gene expression, and inhibition of cell division in a novel cold-sensitive hda mutant of Escherichia coli.

Science.gov (United States)

Fujimitsu, Kazuyuki; Su'etsugu, Masayuki; Yamaguchi, Yoko; Mazda, Kensaku; Fu, Nisi; Kawakami, Hironori; Katayama, Tsutomu

2008-08-01

The chromosomal replication cycle is strictly coordinated with cell cycle progression in Escherichia coli. ATP-DnaA initiates replication, leading to loading of the DNA polymerase III holoenzyme. The DNA-loaded form of the beta clamp subunit of the polymerase binds the Hda protein, which promotes ATP-DnaA hydrolysis, yielding inactive ADP-DnaA. This regulation is required to repress overinitiation. In this study, we have isolated a novel cold-sensitive hda mutant, the hda-185 mutant. The hda-185 mutant caused overinitiation of chromosomal replication at 25 degrees C, which most likely led to blockage of replication fork progress. Consistently, the inhibition of colony formation at 25 degrees C was suppressed by disruption of the diaA gene, an initiation stimulator. Disruption of the seqA gene, an initiation inhibitor, showed synthetic lethality with hda-185 even at 42 degrees C. The cellular ATP-DnaA level was increased in an hda-185-dependent manner. The cellular concentrations of DnaA protein and dnaA mRNA were comparable at 25 degrees C to those in a wild-type hda strain. We also found that multiple copies of the ribonucleotide reductase genes (nrdAB or nrdEF) or dnaB gene repressed overinitiation. The cellular levels of dATP and dCTP were elevated in cells bearing multiple copies of nrdAB. The catalytic site within NrdA was required for multicopy suppression, suggesting the importance of an active form of NrdA or elevated levels of deoxyribonucleotides in inhibition of overinitiation in the hda-185 cells. Cell division in the hda-185 mutant was inhibited at 25 degrees C in a LexA regulon-independent manner, suggesting that overinitiation in the hda-185 mutant induced a unique division inhibition pathway.

Modes of Overinitiation, dnaA Gene Expression, and Inhibition of Cell Division in a Novel Cold-Sensitive hda Mutant of Escherichia coli▿

Science.gov (United States)

Fujimitsu, Kazuyuki; Su'etsugu, Masayuki; Yamaguchi, Yoko; Mazda, Kensaku; Fu, Nisi; Kawakami, Hironori; Katayama, Tsutomu

2008-01-01

The chromosomal replication cycle is strictly coordinated with cell cycle progression in Escherichia coli. ATP-DnaA initiates replication, leading to loading of the DNA polymerase III holoenzyme. The DNA-loaded form of the β clamp subunit of the polymerase binds the Hda protein, which promotes ATP-DnaA hydrolysis, yielding inactive ADP-DnaA. This regulation is required to repress overinitiation. In this study, we have isolated a novel cold-sensitive hda mutant, the hda-185 mutant. The hda-185 mutant caused overinitiation of chromosomal replication at 25°C, which most likely led to blockage of replication fork progress. Consistently, the inhibition of colony formation at 25°C was suppressed by disruption of the diaA gene, an initiation stimulator. Disruption of the seqA gene, an initiation inhibitor, showed synthetic lethality with hda-185 even at 42°C. The cellular ATP-DnaA level was increased in an hda-185-dependent manner. The cellular concentrations of DnaA protein and dnaA mRNA were comparable at 25°C to those in a wild-type hda strain. We also found that multiple copies of the ribonucleotide reductase genes (nrdAB or nrdEF) or dnaB gene repressed overinitiation. The cellular levels of dATP and dCTP were elevated in cells bearing multiple copies of nrdAB. The catalytic site within NrdA was required for multicopy suppression, suggesting the importance of an active form of NrdA or elevated levels of deoxyribonucleotides in inhibition of overinitiation in the hda-185 cells. Cell division in the hda-185 mutant was inhibited at 25°C in a LexA regulon-independent manner, suggesting that overinitiation in the hda-185 mutant induced a unique division inhibition pathway. PMID:18502852

Screening for Specific Language Impairment in Preschool Children: Evaluating a Screening Procedure Including the Token Test

Science.gov (United States)

Willinger, Ulrike; Schmoeger, Michaela; Deckert, Matthias; Eisenwort, Brigitte; Loader, Benjamin; Hofmair, Annemarie; Auff, Eduard

2017-01-01

Specific language impairment (SLI) comprises impairments in receptive and/or expressive language. Aim of this study was to evaluate a screening for SLI. 61 children with SLI (SLI-children, age-range 4-6 years) and 61 matched typically developing controls were tested for receptive language ability (Token Test-TT) and for intelligence (Wechsler…

ORF Alignment: NC_002755 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available tallographic Structure Of A Relaxed ... Glutamine Synthetase From Mycobacterium Tuberculosis ... ...m Mycobacterium ... Tuberculosis pdb|1HTQ|V Chain V, Multicopy ... ...Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis pdb|... From Mycobacterium ... Tuberculosis pdb|1HTQ|T Chain T, Multicopy ... ... ... Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis

ORF Alignment: NC_002945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available tallographic Structure Of A Relaxed ... Glutamine Synthetase From Mycobacterium Tuberculosis ... ...m Mycobacterium ... Tuberculosis pdb|1HTQ|V Chain V, Multicopy ... ...Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis pdb|... From Mycobacterium ... Tuberculosis pdb|1HTQ|T Chain T, Multicopy ... ... ... Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis

ORF Alignment: NC_000962 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available tallographic Structure Of A Relaxed ... Glutamine Synthetase From Mycobacterium Tuberculosis ... ...m Mycobacterium ... Tuberculosis pdb|1HTQ|V Chain V, Multicopy ... ...Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis pdb|... From Mycobacterium ... Tuberculosis pdb|1HTQ|T Chain T, Multicopy ... ... ... Crystallographic Structure Of A Relaxed Glutamine ... Synthetase From Mycobacterium Tuberculosis

Plasmid Complement of Lactococcus lactis NCDO712 Reveals a Novel Pilus Gene Cluster.

Science.gov (United States)

Tarazanova, Mariya; Beerthuyzen, Marke; Siezen, Roland; Fernandez-Gutierrez, Marcela M; de Jong, Anne; van der Meulen, Sjoerd; Kok, Jan; Bachmann, Herwig

2016-01-01

Lactococcus lactis MG1363 is an important gram-positive model organism. It is a plasmid-free and phage-cured derivative of strain NCDO712. Plasmid-cured strains facilitate studies on molecular biological aspects, but many properties which make L. lactis an important organism in the dairy industry are plasmid encoded. We sequenced the total DNA of strain NCDO712 and, contrary to earlier reports, revealed that the strain carries 6 rather than 5 plasmids. A new 50-kb plasmid, designated pNZ712, encodes functional nisin immunity (nisCIP) and copper resistance (lcoRSABC). The copper resistance could be used as a marker for the conjugation of pNZ712 to L. lactis MG1614. A genome comparison with the plasmid cured daughter strain MG1363 showed that the number of single nucleotide polymorphisms that accumulated in the laboratory since the strains diverted more than 30 years ago is limited to 11 of which only 5 lead to amino acid changes. The 16-kb plasmid pSH74 was found to contain a novel 8-kb pilus gene cluster spaCB-spaA-srtC1-srtC2, which is predicted to encode a pilin tip protein SpaC, a pilus basal subunit SpaB, and a pilus backbone protein SpaA. The sortases SrtC1/SrtC2 are most likely involved in pilus polymerization while the chromosomally encoded SrtA could act to anchor the pilus to peptidoglycan in the cell wall. Overexpression of the pilus gene cluster from a multi-copy plasmid in L. lactis MG1363 resulted in cell chaining, aggregation, rapid sedimentation and increased conjugation efficiency of the cells. Electron microscopy showed that the over-expression of the pilus gene cluster leads to appendices on the cell surfaces. A deletion of the gene encoding the putative basal protein spaB, by truncating spaCB, led to more pilus-like structures on the cell surface, but cell aggregation and cell chaining were no longer observed. This is consistent with the prediction that spaB is involved in the anchoring of the pili to the cell.

Non-Invasive Gene Therapy of Experimental Parkinson’s Disease

Science.gov (United States)

2006-09-01

11. Naeser P. Insulin receptors in human ocular tissues. Immunohis- tochemical demonstration in normal and diabetic eyes. Ups J Med Sci 1997; 102:35-40...Sly) GUSB NM_000181 Fabry disease GLA NM_000169 Neuronal ceroid lipofuscinosis (NCL1) PPT NM_000310 NCL2, late infantile (Jansky-Bielschowsky) CLN2...immunohistochemical demonstration in normal and diabetic eyes. Upsala J Med Sci 1997; 102: 35–40. 16. Haruta M, Kosaka M, Kanegae Y, et al. Induction of

The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains

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Wang Yiguo

2008-10-01

Full Text Available Abstract Background Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs. Accurate prediction of SLiMs has been difficult because they are short (often Results Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. Conclusion The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains.

Is Weak Oral Language Associated with Poor Spelling in School-Age Children with Specific Language Impairment, Dyslexia, or Both?

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McCarthy, Jillian H.; Hogan, Tiffany P.; Catts, Hugh W.

2013-01-01

The purpose of this study was to test the hypothesis that word reading accuracy, not oral language, is associated with spelling performance in school-age children. We compared fourth grade spelling accuracy in children with specific language impairment (SLI), dyslexia, or both (SLI/dyslexia) to their typically developing grade-matched peers. Results of the study revealed that children with SLI performed similarly to their typically developing peers on a single word spelling task. Alternatively, those with dyslexia and SLI/dyslexia evidenced poor spelling accuracy. Errors made by both those with dyslexia and SLI/dyslexia were characterized by numerous phonologic, orthographic, and semantic errors. Cumulative results support the hypothesis that word reading accuracy, not oral language, is associated with spelling performance in typically developing school-age children and their peers with SLI and dyslexia. Findings are provided as further support for the notion that SLI and dyslexia are distinct, yet co-morbid, developmental disorders. PMID:22876769

P300 as a measure of processing capacity in auditory and visual domains in specific language impairment.

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Evans, Julia L; Selinger, Craig; Pollak, Seth D

2011-05-10

This study examined the electrophysiological correlates of auditory and visual working memory in children with Specific Language Impairments (SLI). Children with SLI and age-matched controls (11;9-14;10) completed visual and auditory working memory tasks while event-related potentials (ERPs) were recorded. In the auditory condition, children with SLI performed similarly to controls when the memory load was kept low (1-back memory load). As expected, when demands for auditory working memory were higher, children with SLI showed decreases in accuracy and attenuated P3b responses. However, children with SLI also evinced difficulties in the visual working memory tasks. In both the low (1-back) and high (2-back) memory load conditions, P3b amplitude was significantly lower for the SLI as compared to CA groups. These data suggest a domain-general working memory deficit in SLI that is manifested across auditory and visual modalities. Copyright © 2010 Elsevier B.V. All rights reserved.

Getting complete genomes from complex samples using nanopore sequencing

DEFF Research Database (Denmark)

Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

Short read sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes, as they are mostly...... fragmented, incomplete and often contaminated with foreign DNA and with no robust strategies to validate the quality. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and the uncertainty of what is missing. The genetic material most often...... missed is important multi-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. We demonstrate that using nanopore long reads it is now possible to overcome these issues and make complete genomes from...

Getting complete genomes from complex samples using nanopore sequencing

DEFF Research Database (Denmark)

Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

Background Short read DNA sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes......, as they are mostly fragmented, incomplete and often contaminated with foreign DNA. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and there is some uncertainty of what is missing1. The genetic material most often missed is important multi......-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. However, long read sequencing technologies are emerging promising an end to fragmented genome assemblies2. Experimental design We extracted DNA from a full...

Deficits in Coordinative Bimanual Timing Precision in Children With Specific Language Impairment.

Science.gov (United States)

Vuolo, Janet; Goffman, Lisa; Zelaznik, Howard N

2017-02-01

Our objective was to delineate components of motor performance in specific language impairment (SLI); specifically, whether deficits in timing precision in one effector (unimanual tapping) and in two effectors (bimanual clapping) are observed in young children with SLI. Twenty-seven 4- to 5-year-old children with SLI and 21 age-matched peers with typical language development participated. All children engaged in a unimanual tapping and a bimanual clapping timing task. Standard measures of language and motor performance were also obtained. No group differences in timing variability were observed in the unimanual tapping task. However, compared with typically developing peers, children with SLI were more variable in their timing precision in the bimanual clapping task. Nine of the children with SLI performed greater than 1 SD below the mean on a standardized motor assessment. The children with low motor performance showed the same profile as observed across all children with SLI, with unaffected unimanual and impaired bimanual timing precision. Although unimanual timing is unaffected, children with SLI show a deficit in timing that requires bimanual coordination. We propose that the timing deficits observed in children with SLI are associated with the increased demands inherent in bimanual performance.

Are children with Specific Language Impairment competent with the pragmatics and logic of quantification?

Science.gov (United States)

Katsos, Napoleon; Roqueta, Clara Andrés; Estevan, Rosa Ana Clemente; Cummins, Chris

2011-04-01

Specific Language Impairment (SLI) is understood to be a disorder that predominantly affects phonology, morphosyntax and/or lexical semantics. There is little conclusive evidence on whether children with SLI are challenged with regard to Gricean pragmatic maxims and on whether children with SLI are competent with the logical meaning of quantifying expressions. We use the comprehension of statements quantified with 'all', 'none', 'some', 'some…not', 'most' and 'not all' as a paradigm to study whether Spanish-speaking children with SLI are competent with the pragmatic maxim of informativeness, as well as with the logical meaning of these expressions. Children with SLI performed more poorly than a group of age-matched typically-developing peers, and both groups performed more poorly with pragmatics than with logical meaning. Moreover, children with SLI were disproportionately challenged by pragmatic meaning compared to their age-matched peers. However, the performance of children with SLI was comparable to that of a group of younger language-matched typically-developing children. The findings document that children with SLI do face difficulties with employing the maxim of informativeness, as well as with understanding the logical meaning of quantifiers, but also that these difficulties are in keeping with their overall language difficulties rather than exceeding them. The implications of these findings for SLI, linguistic theory, and clinical practice are discussed. Copyright © 2010 Elsevier B.V. All rights reserved.

Learning trajectories for speech motor performance in children with specific language impairment.

Science.gov (United States)

Richtsmeier, Peter T; Goffman, Lisa

2015-01-01

Children with specific language impairment (SLI) often perform below expected levels, including on tests of motor skill and in learning tasks, particularly procedural learning. In this experiment we examined the possibility that children with SLI might also have a motor learning deficit. Twelve children with SLI and thirteen children with typical development (TD) produced complex nonwords in an imitation task. Productions were collected across three blocks, with the first and second blocks on the same day and the third block one week later. Children's lip movements while producing the nonwords were recorded using an Optotrak camera system. Movements were then analyzed for production duration and stability. Movement analyses indicated that both groups of children produced shorter productions in later blocks (corroborated by an acoustic analysis), and the rate of change was comparable for the TD and SLI groups. A nonsignificant trend for more stable productions was also observed in both groups. SLI is regularly accompanied by a motor deficit, and this study does not dispute that. However, children with SLI learned to make more efficient productions at a rate similar to their peers with TD, revealing some modification of the motor deficit associated with SLI. The reader will learn about deficits commonly associated with specific language impairment (SLI) that often occur alongside the hallmark language deficit. The authors present an experiment showing that children with SLI improved speech motor performance at a similar rate compared to typically developing children. The implication is that speech motor learning is not impaired in children with SLI. Copyright © 2015 Elsevier Inc. All rights reserved.

Music identification skills of children with specific language impairment.

Science.gov (United States)

Mari, Giorgia; Scorpecci, Alessandro; Reali, Laura; D'Alatri, Lucia

2016-03-01

To date very few studies have investigated the musical skills of children with specific language impairment (SLI). There is growing evidence that SLI affects areas other than language, and it is therefore reasonable to hypothesize that children with this disorder may have difficulties in perceiving musical stimuli appropriately. To compare melody and song identification skills in a group of children with SLI and in a control group of children with typical language development (TD); and to study possible correlations between music identification skills and language abilities in the SLI group. This is a prospective case control study. Two groups of children were enrolled: one meeting DSM-IV-TR(®) diagnostic criteria for SLI and the other comprising an age-matched group of children with TD. All children received a melody and a song identification test, together with a test battery assessing receptive and productive language abilities. 30 children with SLI (mean age = 56 ± 9 months) and 23 with TD (mean age = 60 ± 10 months) were included. Melody and song identification scores among SLI children were significantly lower than those of TD children, and in both groups song identification scores were significantly higher than melody identification scores. Song identification skills bore a significant correlation to chronological age in both groups (TD: r = 0.529, p = 0.009; SLI: r = 0.506, p = 0.004). Whereas no other variables were found explaining the variability of melody or song identification scores in either group, the correlation between language comprehension and song identification in the SLI group approached significance (r = 0.166, p = 0.076). The poorer music perception skills of SLI children as compared with TD ones suggests that SLI may also affect music perception. Therefore, training programmes that simultaneously stimulate via language and music may prove useful in the rehabilitation of children affected by SLI. © 2015 Royal College of Speech and

Dicty_cDB: SLH218 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available SL (Link to library) SLH218 (Link to dictyBase) - - - Contig-U16325-1 SLH218F (Link to Original site) SLH2...18F 419 - - - - - - Show SLH218 Library SL (Link to library) Clone ID SLH218 (Link to...ycdb.biol.tsukuba.ac.jp/CSM/SL/SLH2-A/SLH218Q.Seq.d/ Representative seq. ID SLH21...8F (Link to Original site) Representative DNA sequence >SLH218 (SLH218Q) /CSM/SL/SLH2-A/SLH218Q.Seq.d/ CCATG...) /CSM/SL/SLI3-C/SLI370Q.Seq.d/ 831 0.0 SLI170 (SLI170Q) /CSM/SL/SLI1-C/SLI170Q.Seq.d/ 831 0.0 SLH218 (SLH218Q) /CSM/SL/SLH2-A/SLH2

An anther- and petal-specific gene SlMF1 is a multicopy gene with homologous sequences on sex chromosomes

Czech Academy of Sciences Publication Activity Database

Matsunaga, S.; Lebel-Hardenack, S.; Kejnovský, Eduard; Vyskot, Boris; Grant, Sarah R.; Kawano, S.

2005-01-01

Roč. 80, - (2005), s. 395-401 ISSN 1341-7568 R&D Projects: GA ČR(CZ) GA204/05/2097 Institutional research plan: CEZ:AV0Z50040507 Keywords : dioecious plant * male flower * sex chromosomes Subject RIV: BO - Biophysics Impact factor: 1.081, year: 2005

Reconstruction of phylogenetic relationships in a highly reticulate group with deep coalescence and recent speciation (Hieracium, Asteraceae).

Science.gov (United States)

Krak, K; Caklová, P; Chrtek, J; Fehrer, J

2013-02-01

Phylogeny reconstruction based on multiple unlinked markers is often hampered by incongruent gene trees, especially in closely related species complexes with high degrees of hybridization and polyploidy. To investigate the particular strengths and limitations of chloroplast DNA (cpDNA), low-copy nuclear and multicopy nuclear markers for elucidating the evolutionary history of such groups, we focus on Hieracium s.str., a predominantly apomictic genus combining the above-mentioned features. Sequences of the trnV-ndhC and trnT-trnL intergenic spacers were combined for phylogenetic analyses of cpDNA. Part of the highly variable gene for squalene synthase (sqs) was applied as a low-copy nuclear marker. Both gene trees were compared with previous results based on the multicopy external transcribed spacer (ETS) of the nuclear ribosomal DNA. The power of the different markers to detect hybridization varied, but they largely agreed on particular hybrid and allopolyploid origins. The same crown groups of species were recognizable in each dataset, but basal relationships were strongly incongruent among cpDNA, sqs and ETS trees. The ETS tree was considered as the best approximation of the species tree. Both cpDNA and sqs trees showed basal polytomies as well as merging or splitting of species groups of non-hybrid taxa. These patterns can be best explained by a rapid diversification of the genus with ancestral polymorphism and incomplete lineage sorting. A hypothetical scenario of Hieracium speciation based on all available (including non-molecular) evidence is depicted. Incorporation of seemingly contradictory information helped to better understand species origins and evolutionary patterns in this notoriously difficult agamic complex.

The Collagen-Binding Adhesin Is a Virulence Factor in Staphylococcus aureus Keratitis

Science.gov (United States)

Rhem, Marcus N.; Lech, Elizabeth M.; Patti, Joseph M.; McDevitt, Damien; Höök, Magnus; Jones, Dan B.; Wilhelmus, Kirk R.

2000-01-01

A collagen-binding strain of Staphylococcus aureus produced suppurative inflammation in a rabbit model of soft contact lens-associated bacterial keratitis more often than its collagen-binding-negative isogenic mutant. Reintroduction of the cna gene on a multicopy plasmid into the mutant helped it regain its corneal adherence and infectivity. The topical application of a collagen-binding peptide before bacterial challenge decreased S. aureus adherence to deepithelialized corneas. These data suggest that the collagen-binding adhesin is involved in the pathogenesis of S. aureus infection of the cornea. PMID:10816547

Screening for Specific Language Impairment in Preschool Children: Evaluating a Screening Procedure Including the Token Test.

Science.gov (United States)

Willinger, Ulrike; Schmoeger, Michaela; Deckert, Matthias; Eisenwort, Brigitte; Loader, Benjamin; Hofmair, Annemarie; Auff, Eduard

2017-10-01

Specific language impairment (SLI) comprises impairments in receptive and/or expressive language. Aim of this study was to evaluate a screening for SLI. 61 children with SLI (SLI-children, age-range 4-6 years) and 61 matched typically developing controls were tested for receptive language ability (Token Test-TT) and for intelligence (Wechsler Preschool-and-Primary-Scale-of-Intelligence-WPPSI). Group differences were analyzed using t tests, as well as direct and stepwise discriminant analyses. The predictive value of the WPPSI with respect to TT performance was analyzed using regression analyses. SLI-children performed significantly worse on both TT and WPPSI ([Formula: see text]). The TT alone yielded an overall classification rate of 79%, the TT and the WPPSI together yielded an overall classification rate of 80%. TT performance was significantly predicted by verbal intelligence in SLI-children and nonverbal intelligence in controls whilst WPPSI subtest arithmetic was predictive in both groups. Without further research, the Token Test cannot be seen as a valid and sufficient tool for the screening of SLI in preschool children but rather as a tool for the assessment of more general intellectual capacities. SLI-children at this age already show impairments typically associated with SLI which indicates the necessity of early developmental support or training. Token Test performance is possibly an indicator for a more general developmental factor rather than an exclusive indicator for language difficulties.

Executive functions and language in children with different subtypes of specific language impairment.

Science.gov (United States)

Acosta Rodríguez, V; Ramírez Santana, G M; Hernández Expósito, S

The marked heterogeneity among children diagnosed with specific language impairment (SLI) highlights the importance of studying and describing cases based on the distinction between the expressive and receptive-expressive SLI subtypes. The main objective of this study was to examine neuropsychological, linguistic, and narrative behaviours in children with different SLI subtypes. A comprehensive battery of language and neuropsychological tests was administered to a total of 58 children (29 with SLI and 29 normal controls) between 5.60 and 11.20 years old. Both SLI subtypes performed more poorly than the control group in language skills, narrative, and executive function. Furthermore, the expressive SLI group demonstrated substantial ungrammaticality, as well as problems with verbal fluency and both verbal and spatial working memory, while the receptive-expressive SLI subtype displayed poorer neuropsychological performance in general. Our findings showed that children with either SLI subtype displayed executive dysfunctions that were not limited to verbal tasks but rather extended to nonverbal measures. This could reflect a global cognitive difficulty which, along with declining linguistic and narrative skills, illustrates the complex profile of this impairment. Copyright © 2016 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

When words lead to solutions: executive function deficits in preschool children with specific language impairment.

Science.gov (United States)

Roello, Mara; Ferretti, Maria Letizia; Colonnello, Valentina; Levi, Gabriel

2015-02-01

Several studies indicate that school-age children with specific language impairment (SLI) have difficulties with tasks that rely on executive functions. Whether executive function deficits in children with SLI emerge during preschool age remains unclear. Our aim was to fill this gap by investigating executive function performances in two age groups of preschoolers with and without SLI. Children with SLI (N=60; young: 53.6±5.3 months; old: 65.4±3.8 months) and age-matched control children (N=58) were tested for problem-representation ability, using the Flexible Item Selection Task (FIST), rule-use skills, using a Stroop-like Day-Night test (D/N), and planning skills, using the Tower of London test (TOL). Older children performed better than younger children did across tasks. Children with SLI had poorer performance, compared to typically developing children, on measures of problem representation, planning skills, and use of rules. Our results clearly indicate that executive function impairment is evident during the preschool period. Although old children with SLI performed better than young children with SLI, their performances were still poor, compared to those of control peers. These findings suggest that children with SLI have altered executive functioning at 53.6 months. Copyright © 2014. Published by Elsevier Ltd.

What do children with specific language impairment do with multiple forms of DO?

Science.gov (United States)

Rice, Mabel L; Blossom, Megan

2013-02-01

This study was designed to examine the early usage patterns of multiple grammatical functions of DO in children with and without specific language impairment (SLI). Children's use of this plurifunctional form is informative for evaluation of theoretical accounts of the deficit in SLI. Spontaneous uses of multiple functions of DO were analyzed in language samples from 89 children: 37 children with SLI, ages 5;0-5;6 (years;months); 37 age-equivalent children; and 15 language-equivalent children, ages 2;8-4;10. Proportion correct and types of errors produced were analyzed for each function of DO. Children with SLI had significantly lower levels of proportion correct auxiliary DO use compared to both control groups, with omissions of the DO form as the primary error type. Children with SLI had near-ceiling performance on lexical DO and elliptical DO, similar to both control groups. Plurifunctionality is not problematic: Children acquire each function of DO separately. Grammatical properties of the function, rather than surface properties of the form, dictate whether children with SLI will have difficulty using the word. Overall, these results support the extended optional infinitive account of SLI and the use of auxiliary DO omissions as part of a clinical marker for SLI.

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

DEFF Research Database (Denmark)

Kröger, Carsten; Dillon, Shane C.; Cameron, Andrew D. S.

2012-01-01

More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required......-thirds of these TSSs were associated with σ70 (including phoP, slyA, and invF) from which we identified the −10 and −35 motifs of σ70-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium...

Evaluation of the efficiency and utility of recombinant enzyme-free seamless DNA cloning methods

Directory of Open Access Journals (Sweden)

Ken Motohashi

2017-03-01

Full Text Available Simple and low-cost recombinant enzyme-free seamless DNA cloning methods have recently become available. In vivo Escherichia coli cloning (iVEC can directly transform a mixture of insert and vector DNA fragments into E. coli, which are ligated by endogenous homologous recombination activity in the cells. Seamless ligation cloning extract (SLiCE cloning uses the endogenous recombination activity of E. coli cellular extracts in vitro to ligate insert and vector DNA fragments. An evaluation of the efficiency and utility of these methods is important in deciding the adoption of a seamless cloning method as a useful tool. In this study, both seamless cloning methods incorporated inserting DNA fragments into linearized DNA vectors through short (15–39 bp end homology regions. However, colony formation was 30–60-fold higher with SLiCE cloning in end homology regions between 15 and 29 bp than with the iVEC method using DH5α competent cells. E. coli AQ3625 strains, which harbor a sbcA gene mutation that activates the RecE homologous recombination pathway, can be used to efficiently ligate insert and vector DNA fragments with short-end homology regions in vivo. Using AQ3625 competent cells in the iVEC method improved the rate of colony formation, but the efficiency and accuracy of SLiCE cloning were still higher. In addition, the efficiency of seamless cloning methods depends on the intrinsic competency of E. coli cells. The competency of chemically competent AQ3625 cells was lower than that of competent DH5α cells, in all cases of chemically competent cell preparations using the three different methods. Moreover, SLiCE cloning permits the use of both homemade and commercially available competent cells because it can use general E. coli recA− strains such as DH5α as host cells for transformation. Therefore, between the two methods, SLiCE cloning provides both higher efficiency and better utility than the iVEC method for seamless DNA plasmid

Contemporary evolution of resistance at the major insecticide target site gene Ace-1 by mutation and copy number variation in the malaria mosquito Anopheles gambiae

Science.gov (United States)

Weetman, David; Mitchell, Sara N; Wilding, Craig S; Birks, Daniel P; Yawson, Alexander E; Essandoh, John; Mawejje, Henry D; Djogbenou, Luc S; Steen, Keith; Rippon, Emily J; Clarkson, Christopher S; Field, Stuart G; Rigden, Daniel J; Donnelly, Martin J

2015-01-01

Functionally constrained genes are ideal insecticide targets because disruption is often fatal, and resistance mutations are typically costly. Synaptic acetylcholinesterase (AChE) is an essential neurotransmission enzyme targeted by insecticides used increasingly in malaria control. In Anopheles and Culex mosquitoes, a glycine–serine substitution at codon 119 of the Ace-1 gene confers both resistance and fitness costs, especially for 119S/S homozygotes. G119S in Anopheles gambiae from Accra (Ghana) is strongly associated with resistance, and, despite expectations of cost, resistant 119S alleles are increasing significantly in frequency. Sequencing of Accra females detected only a single Ace-1 119S haplotype, whereas 119G diversity was high overall but very low at non-synonymous sites, evidence of strong purifying selection driven by functional constraint. Flanking microsatellites showed reduced diversity, elevated linkage disequilibrium and high differentiation of 119S, relative to 119G homozygotes across up to two megabases of the genome. Yet these signals of selection were inconsistent and sometimes weak tens of kilobases from Ace-1. This unexpected finding is attributable to apparently ubiquitous amplification of 119S alleles as part of a large copy number variant (CNV) far exceeding the size of the Ace-1 gene, whereas 119G alleles were unduplicated. Ace-1 CNV was detectable in archived samples collected when the 119S allele was rare in Ghana. Multicopy amplification of resistant alleles has not been observed previously and is likely to underpin the recent increase in 119S frequency. The large CNV compromised localization of the strong selective sweep around Ace-1, emphasizing the need to integrate CNV analysis into genome scans for selection. PMID:25865270

Biocontrol of the Sugarcane Borer Eldana saccharina by Expression of the Bacillus thuringiensis cry1Ac7 and Serratia marcescens chiA Genes in Sugarcane-Associated Bacteria

Science.gov (United States)

Downing, Katrina J.; Leslie, Graeme; Thomson, Jennifer A.

2000-01-01

The cry1Ac7 gene of Bacillus thuringiensis strain 234, showing activity against the sugarcane borer Eldana saccharina, was cloned under the control of the tac promoter. The fusion was introduced into the broad-host-range plasmid pKT240 and the integration vector pJFF350 and without the tac promoter into the broad-host-range plasmids pML122 and pKmM0. These plasmids were introduced into a Pseudomonas fluorescens strain isolated from the phylloplane of sugarcane and the endophytic bacterium Herbaspirillum seropedicae found in sugarcane. The ptac-cry1Ac7 construct was introduced into the chromosome of P. fluorescens using the integration vector pJFF350 carrying the artificial interposon Omegon-Km. Western blot analysis showed that the expression levels of the integrated cry1Ac7 gene were much higher under the control of the tac promoter than under the control of its endogenous promoter. It was also determined that multicopy expression in P. fluorescens and H. seropedicae of ptac-cry1Ac7 carried on pKT240 caused plasmid instability with no detectable protein expression. In H. seropedicae, more Cry1Ac7 toxin was produced when the gene was cloned under the control of the Nmr promoter on pML122 than in the opposite orientation and bioassays showed that the former resulted in higher mortality of E. saccharina larvae than the latter. P. fluorescens 14::ptac-tox resulted in higher mortality of larvae than did P. fluorescens 14::tox. An increased toxic effect was observed when P. fluorescens 14::ptac-tox was combined with P. fluorescens carrying the Serratia marcescens chitinase gene chiA, under the control of the tac promoter, integrated into the chromosome. PMID:10877771

Gray-white matter and cerebrospinal fluid volume differences in children with Specific Language Impairment and/or Reading Disability.

Science.gov (United States)

Girbau-Massana, Dolors; Garcia-Marti, Gracian; Marti-Bonmati, Luis; Schwartz, Richard G

2014-04-01

We studied gray-white matter and cerebrospinal fluid (CSF) alterations that may be critical for language, through an optimized voxel-based morphometry evaluation in children with Specific Language Impairment (SLI), compared to Typical Language Development (TLD). Ten children with SLI (8;5-10;9) and 14 children with TLD (8;2-11;8) participated. They received a comprehensive language and reading test battery. We also analyzed a subgroup of six children with SLI+RD (Reading Disability). Brain images from 3-Tesla MRIs were analyzed with intelligence, age, gender, and total intracranial volume as covariates. Children with SLI or SLI+RD exhibited a significant lower overall gray matter volume than children with TLD. Particularly, children with SLI showed a significantly lower volume of gray matter compared to children with TLD in the right postcentral parietal gyrus (BA4), and left and right medial occipital gyri (BA19). The group with SLI also exhibited a significantly greater volume of gray matter in the right superior occipital gyrus (BA19), which may reflect a brain reorganization to compensate for their lower volumes at medial occipital gyri. Children with SLI+RD, compared to children with TLD, showed a significantly lower volume of: (a) gray matter in the right postcentral parietal gyrus; and (b) white matter in the right inferior longitudinal fasciculus (RILF), which interconnects the temporal and occipital lobes. Children with TLD exhibited a significantly lower CSF volume than children with SLI and children with SLI+RD respectively, who had somewhat smaller volumes of gray matter allowing for more CSF volume. The significant lower gray matter volume at the right postcentral parietal gyrus and greater cerebrospinal fluid volume may prove to be unique markers for SLI. We discuss the association of poor knowledge/visual representations and language input to brain development. Our comorbid study showed that a significant lower volume of white matter in the right

Novel genetic tools for diaminopimelic acid selection in virulence studies of Yersinia pestis.

Science.gov (United States)

Bland, David M; Eisele, Nicholas A; Keleher, Lauren L; Anderson, Paul E; Anderson, Deborah M

2011-03-02

Molecular studies of bacterial virulence are enhanced by expression of recombinant DNA during infection to allow complementation of mutants and expression of reporter proteins in vivo. For highly pathogenic bacteria, such as Yersinia pestis, these studies are currently limited because deliberate introduction of antibiotic resistance is restricted to those few which are not human treatment options. In this work, we report the development of alternatives to antibiotics as tools for host-pathogen research during Yersinia pestis infections focusing on the diaminopimelic acid (DAP) pathway, a requirement for cell wall synthesis in eubacteria. We generated a mutation in the dapA-nlpB(dapX) operon of Yersinia pestis KIM D27 and CO92 which eliminated the expression of both genes. The resulting strains were auxotrophic for diaminopimelic acid and this phenotype was complemented in trans by expressing dapA in single and multi-copy. In vivo, we found that plasmids derived from the p15a replicon were cured without selection, while selection for DAP enhanced stability without detectable loss of any of the three resident virulence plasmids. The dapAX mutation rendered Y. pestis avirulent in mouse models of bubonic and septicemic plague which could be complemented when dapAX was inserted in single or multi-copy, restoring development of disease that was indistinguishable from the wild type parent strain. We further identified a high level, constitutive promoter in Y. pestis that could be used to drive expression of fluorescent reporters in dapAX strains that had minimal impact to virulence in mouse models while enabling sensitive detection of bacteria during infection. Thus, diaminopimelic acid selection for single or multi-copy genetic systems in Yersinia pestis offers an improved alternative to antibiotics for in vivo studies that causes minimal disruption to virulence.

Novel genetic tools for diaminopimelic acid selection in virulence studies of Yersinia pestis.

Directory of Open Access Journals (Sweden)

David M Bland

2011-03-01

Full Text Available Molecular studies of bacterial virulence are enhanced by expression of recombinant DNA during infection to allow complementation of mutants and expression of reporter proteins in vivo. For highly pathogenic bacteria, such as Yersinia pestis, these studies are currently limited because deliberate introduction of antibiotic resistance is restricted to those few which are not human treatment options. In this work, we report the development of alternatives to antibiotics as tools for host-pathogen research during Yersinia pestis infections focusing on the diaminopimelic acid (DAP pathway, a requirement for cell wall synthesis in eubacteria. We generated a mutation in the dapA-nlpB(dapX operon of Yersinia pestis KIM D27 and CO92 which eliminated the expression of both genes. The resulting strains were auxotrophic for diaminopimelic acid and this phenotype was complemented in trans by expressing dapA in single and multi-copy. In vivo, we found that plasmids derived from the p15a replicon were cured without selection, while selection for DAP enhanced stability without detectable loss of any of the three resident virulence plasmids. The dapAX mutation rendered Y. pestis avirulent in mouse models of bubonic and septicemic plague which could be complemented when dapAX was inserted in single or multi-copy, restoring development of disease that was indistinguishable from the wild type parent strain. We further identified a high level, constitutive promoter in Y. pestis that could be used to drive expression of fluorescent reporters in dapAX strains that had minimal impact to virulence in mouse models while enabling sensitive detection of bacteria during infection. Thus, diaminopimelic acid selection for single or multi-copy genetic systems in Yersinia pestis offers an improved alternative to antibiotics for in vivo studies that causes minimal disruption to virulence.

The Phytophthora sojae avirulence locus Avr3c encodes a multi-copy RXLR effector with sequence polymorphisms among pathogen strains.

Directory of Open Access Journals (Sweden)

Suomeng Dong

Full Text Available Root and stem rot disease of soybean is caused by the oomycete Phytophthora sojae. The avirulence (Avr genes of P. sojae control race-cultivar compatibility. In this study, we identify the P. sojae Avr3c gene and show that it encodes a predicted RXLR effector protein of 220 amino acids. Sequence and transcriptional data were compared for predicted RXLR effectors occurring in the vicinity of Avr4/6, as genetic linkage of Avr3c and Avr4/6 was previously suggested. Mapping of DNA markers in a F(2 population was performed to determine whether selected RXLR effector genes co-segregate with the Avr3c phenotype. The results pointed to one RXLR candidate gene as likely to encode Avr3c. This was verified by testing selected genes by a co-bombardment assay on soybean plants with Rps3c, thus demonstrating functionality and confirming the identity of Avr3c. The Avr3c gene together with eight other predicted genes are part of a repetitive segment of 33.7 kb. Three near-identical copies of this segment occur in a tandem array. In P. sojae strain P6497, two identical copies of Avr3c occur within the repeated segments whereas the third copy of this RXLR effector has diverged in sequence. The Avr3c gene is expressed during the early stages of infection in all P. sojae strains examined. Virulent alleles of Avr3c that differ in amino acid sequence were identified in other strains of P. sojae. Gain of virulence was acquired through mutation and subsequent sequence exchanges between the two copies of Avr3c. The results illustrate the importance of segmental duplications and RXLR effector evolution in the control of race-cultivar compatibility in the P. sojae and soybean interaction.

Information processing speed as a predictor of IQ in children with and without specific language impairment in grades 3 and 8.

Science.gov (United States)

Park, Jisook; Mainela-Arnold, Elina; Miller, Carol A

2015-01-01

This study investigated (1) whether nonlinguistic processing speed predicts nonverbal IQ in TD children and children with SLI and (2) if the proposed relationship is different at two time points. The participants consisted of a subset of a longitudinal dataset, 55 typically developing children and 55 children with SLI. Children completed four nonverbal speed tasks and four subtests of the WISC-III. The WISC-III subtests requiring timed and untimed responses were examined separately. Linear mixed model analyses indicated that in both groups, processing speed predicted nonverbal IQ subtests that reward speedy responses, but not IQ subtests that do not. The relationships between processing speed and IQ with speed bonuses did not differ at grades 3 and 8, and these relationships also were not significantly different in children with SLI and their TD peers. The results suggest that the presence of processing speed limitations in many children with SLI raises questions about the utility of timed nonverbal IQ measures as tools for diagnosis of SLI. Future studies should investigate other cognitive assessments that could be used as inclusionary criteria for SLI. The reader will be able to (1) describe the relationship between processing speed and nonverbal IQ in children with TD and SLI and (2) discuss problems using an IQ criterion to diagnose children as having SLI. Copyright © 2014 Elsevier Inc. All rights reserved.

Specific Language Impairment, Nonverbal IQ, Attention-Deficit/Hyperactivity Disorder, Autism Spectrum Disorder, Cochlear Implants, Bilingualism, and Dialectal Variants: Defining the Boundaries, Clarifying Clinical Conditions, and Sorting Out Causes.

Science.gov (United States)

Rice, Mabel L

2016-02-01

The purpose of this research forum article is to provide an overview of a collection of invited articles on the topic "specific language impairment (SLI) in children with concomitant health conditions or nonmainstream language backgrounds." Topics include SLI, attention-deficit/hyperactivity disorder, autism spectrum disorder, cochlear implants, bilingualism, and dialectal language learning contexts. The topic is timely due to current debates about the diagnosis of SLI. An overarching comparative conceptual framework is provided for comparisons of SLI with other clinical conditions. Comparisons of SLI in children with low-normal or normal nonverbal IQ illustrate the unexpected outcomes of 2 × 2 comparison designs. Comparative studies reveal unexpected relationships among speech, language, cognitive, and social dimensions of children's development as well as precise ways to identify children with SLI who are bilingual or dialect speakers. The diagnosis of SLI is essential for elucidating possible causal pathways of language impairments, risks for language impairments, assessments for identification of language impairments, linguistic dimensions of language impairments, and long-term outcomes. Although children's language acquisition is robust under high levels of risk, unexplained individual variations in language acquisition lead to persistent language impairments.

Virulence genes and genetic diversity of Streptococcus suis serotype 2 isolates from Thailand.

Science.gov (United States)

Maneerat, K; Yongkiettrakul, S; Kramomtong, I; Tongtawe, P; Tapchaisri, P; Luangsuk, P; Chaicumpa, W; Gottschalk, M; Srimanote, P

2013-11-01

Isolates of Streptococcus suis from different Western countries as well as those from China and Vietnam have been previously well characterized. So far, the genetic characteristics and relationship between S. suis strains isolated from both humans and pigs in Thailand are unknown. In this study, a total of 245 S. suis isolates were collected from both human cases (epidemic and sporadic) and pigs (diseased and asymptomatic) in Thailand. Bacterial strains were identified by biochemical tests and PCR targeting both, the 16S rRNA and gdh genes. Thirty-six isolates were identified as serotype 2 based on serotyping and the cps2-PCR. These isolates were tested for the presence of six virulence-associated genes: an arginine deiminase (arcA), a 38-kDa protein and protective antigen (bay046), an extracellular factor (epf), an hyaluronidase (hyl), a muramidase-released protein (mrp) and a suilysin (sly). In addition, the genetic diversities of these isolates were studied by RAPD PCR and multilocus sequence typing (MLST) analysis. Four virulence-associated gene patterns (VAGP 1 to 4) were obtained, and the majority of isolates (32/36) carried all genes tested (VAGP1). Each of the three OPB primers used provided 4 patterns designated RAPD-A to RAPD-D. Furthermore, MLST analysis could also distinguish the 36 isolates into four sequence types (STs): ST1 (n = 32), ST104 (n = 2), ST233 (n = 1) and a newly identified ST, ST336 (n = 1). Dendrogram constructions based on RAPD patterns indicated that S. suis serotype 2 isolates from Thailand could be divided into four groups and that the characteristics of the individual groups were in complete agreement with the virulence gene profiles and STs. The majority (32/36) of isolates recovered from diseased pigs, slaughterhouse pigs or human patients could be classified into a single group (VAGP1, RAPD-A and ST1). This genetic information strongly suggests the transmission of S. suis isolates from pigs to humans in Thailand. Our findings are

Theory of Mind deficits and social emotional functioning in preschoolers with Specific Language Impairment

Directory of Open Access Journals (Sweden)

Constance Vissers

2016-11-01

Full Text Available Children with Specific Language Impairment (SLI often experience emotional and social difficulties. In general, problems in social emotional functioning can be cognitively explained in terms of Theory of Mind (ToM. In this mini-review, an overview is provided of studies on social-emotional functioning and ToM in preschoolers (average age from 2.3 to 6.2 years with SLI. It is concluded that, similar to school-aged children with SLI, preschoolers with SLI have several social-emotional problems and that both cognitive and affective aspects of ToM are impaired in those children. Based hereon, three possible causal models for the interrelation between language, ToM and social emotional functioning are put forward. It is proposed that future research on the construct and measurement of early ToM, social emotional functioning and language development in preschoolers with SLI is needed to achieve early detection, tailored treatment, and ultimately insight into the pathogenesis of SLI.

Prosodic constraints on inflected words: an area of difficulty for German-speaking children with specific language impairment?

Science.gov (United States)

Kauschke, Christina; Renner, Lena; Domahs, Ulrike

2013-08-01

Recent studies suggest that morphosyntactic difficulties may result from prosodic problems. We therefore address the interface between inflectional morphology and prosody in typically developing children (TD) and children with SLI by testing whether these groups are sensitive to prosodic constraints that guide plural formation in German. A plural elicitation task was designed consisting of 60 words and 20 pseudowords. The performance of 14 German-speaking children with SLI (mean age 7.5) was compared to age-matched controls and to younger children matched for productive vocabulary. TD children performed significantly better than children with SLI. Error analyses revealed that children with SLI produced more forms that did not meet the optimal shape of a noun plural. Beyond the fact that children with SLI have deficits in plural marking, the findings suggest that they also show reduced sensitivity to prosodic requirements. In other words, the prosodic structure of inflected words seems to be vulnerable in children with SLI.

Lactose/whey utilization and ethanol production by transformed Saccharomyces cerevisiae cells.

Science.gov (United States)

Porro, D; Martegani, E; Ranzi, B M; Alberghina, L

1992-04-05

Strains of Saccharomyces cerevisiae transformed with a multicopy expression vector bearing both the Escherichia coli beta-galactosidase gene under the control of the upstream activating sequence of the GAL1-10 genes and the GAL4 activator gene release part of beta-galactosidase in the growth medium. This release is due to cell lysis of the older mother cells; the enzyme maintains its activity in buffered growth media. Fermentation studies with transformed yeast strains showed that the release of beta-galactosidase allowed an efficient growth on buffered media containing lactose as carbon source as well as on whey-based media. The transformed strains utilized up to 95% of the lactose and a high growth yield was obtained in rich media. High productions of ethanol were also observed in stationary phase after growth in lactose minimal media.

Different expression patterns of genes from the exo-xis region of bacteriophage λ and Shiga toxin-converting bacteriophage Ф24B following infection or prophage induction in Escherichia coli.

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Sylwia Bloch

Full Text Available Lambdoid bacteriophages serve as useful models in microbiological and molecular studies on basic biological process. Moreover, this family of viruses plays an important role in pathogenesis of enterohemorrhagic Escherichia coli (EHEC strains, as they are carriers of genes coding for Shiga toxins. Efficient expression of these genes requires lambdoid prophage induction and multiplication of the phage genome. Therefore, understanding the mechanisms regulating these processes appears essential for both basic knowledge and potential anti-EHEC applications. The exo-xis region, present in genomes of lambdoid bacteriophages, contains highly conserved genes of largely unknown functions. Recent report indicated that the Ea8.5 protein, encoded in this region, contains a newly discovered fused homeodomain/zinc-finger fold, suggesting its plausible regulatory role. Moreover, subsequent studies demonstrated that overexpression of the exo-xis region from a multicopy plasmid resulted in impaired lysogenization of E. coli and more effective induction of λ and Ф24B prophages. In this report, we demonstrate that after prophage induction, the increase in phage DNA content in the host cells is more efficient in E. coli bearing additional copies of the exo-xis region, while survival rate of such bacteria is lower, which corroborated previous observations. Importantly, by using quantitative real-time reverse transcription PCR, we have determined patterns of expressions of particular genes from this region. Unexpectedly, in both phages λ and Ф24B, these patterns were significantly different not only between conditions of the host cells infection by bacteriophages and prophage induction, but also between induction of prophages with various agents (mitomycin C and hydrogen peroxide. This may shed a new light on our understanding of regulation of lambdoid phage development, depending on the mode of lytic cycle initiation.

Using electronic storybooks to support word learning in children with severe language impairments

NARCIS (Netherlands)

Smeets, Daisy J. H.; van Dijken, Marianne J.; Bus, Adriana G

2012-01-01

Novel word learning is reported to be problematic for children with severe language impairments (SLI). In this study, we tested electronic storybooks as a tool to support vocabulary acquisition in SLI children. In Experiment 1, 29 kindergarten SLI children heard four e-books each four times: (a) two

Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS using chemogenomics

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Jaime Maria DLA

2012-06-01

Full Text Available Abstract Background Chitosan oligosaccharide (COS, a deacetylated derivative of chitin, is an abundant, and renewable natural polymer. COS has higher antimicrobial properties than chitosan and is presumed to act by disrupting/permeabilizing the cell membranes of bacteria, yeast and fungi. COS is relatively non-toxic to mammals. By identifying the molecular and genetic targets of COS, we hope to gain a better understanding of the antifungal mode of action of COS. Results Three different chemogenomic fitness assays, haploinsufficiency (HIP, homozygous deletion (HOP, and multicopy suppression (MSP profiling were combined with a transcriptomic analysis to gain insight in to the mode of action and mechanisms of resistance to chitosan oligosaccharides. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified are involved in processes such as RNA biology (transcription, translation and regulatory mechanisms, membrane functions (e.g. signalling, transport and targeting, membrane structural components, cell division, and proteasome processes. The transcriptomes of control wild type and 5 suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the Ras signal transduction pathway. Down-regulated transcripts included those encoding protein folding components and respiratory chain proteins. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress and pre-treatment with these well characterized environmental stressors provided little or any resistance to COS. Conclusions Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane

Non-word repetition in children with specific language impairment: a deficit in phonological working memory or in long-term verbal knowledge?

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Casalini, Claudia; Brizzolara, Daniela; Chilosi, Anna; Cipriani, Paola; Marcolini, Stefania; Pecini, Chiara; Roncoli, Silvia; Burani, Cristina

2007-08-01

In this study we investigated the effects of long-term memory (LTM) verbal knowledge on short-term memory (STM) verbal recall in a sample of Italian children affected by different subtypes of specific language impairment (SLI). The aim of the study was to evaluate if phonological working memory (PWM) abilities of SLI children can be supported by LTM linguistic representations and if PWM performances can be differently affected in the various subtypes of SLI. We tested a sample of 54 children affected by Mixed Receptive-Expressive (RE), Expressive (Ex) and Phonological (Ph) SLI (DSM-IV - American Psychiatric Association, 1994) by means of a repetition task of words (W) and non-words (NW) differing in morphemic structure [morphological non-words (MNW), consisting of combinations of roots and affixes - and simple non-words - with no morphological constituency]. We evaluated the effects of lexical and morpho-lexical LTM representations on STM recall by comparing the repetition accuracy across the three types of stimuli. Results indicated that although SLI children, as a group, showed lower repetition scores than controls, their performance was affected similarly to controls by the type of stimulus and the experimental manipulation of the non-words (better repetition of W than MNW and NW, and of MNW than NW), confirming the recourse to LTM verbal representations to support STM recall. The influence of LTM verbal knowledge on STM recall in SLI improved with age and did not differ among the three types of SLI. However, the three types of SLI differed in the accuracy of their repetition performances (PMW abilities), with the Phonological group showing the best scores. The implications for SLI theory and practice are discussed.

Specific language impairment in a bilingual context : the acquisition of Dutch inflection by Turkish-Dutch learners

NARCIS (Netherlands)

Orgassa, A.

2009-01-01

With the aim of specifying the relationship between SLI and L2 acquisition, production data of various groups of L1 and L2 learners with and without SLI were compared. The experiments centered on the application of morphosyntactic rules in Dutch that were considered vulnerable in SLI and L2

Individual differences in the production of word classes in eight specific language-impaired preschoolers.

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Le Normand, M T; Chevrie-Muller, C

1991-01-01

The production of word classes in eight 53-62-month-old specific language-impaired (SLI) children was described and compared with that of 30 normal 24-33-month-old children in the same play situation. SLI subjects and nonimpaired children were selected within specified mean length of utterance ranges (low MLU versus high MLU). Production of word classes by subjects was evaluated in order to determine (1) whether SLI children showed a similar or a different word-class profile among themselves and when compared with non-impaired children and (2) whether MLU related to word classes would be useful as a single clinical index in assessment of language acquisition. Results showed that scores of SLI children in production of word classes reflect important individual differences among subjects. In the high-MLU sample, all SLI children produced each word class relatively within the same range as the nonimpaired group. In the low-MLU sample two SLI children were very different in their word-class profile and individual differences were further confirmed by a discriminant function analysis. Correlations between MLU and word classes were significant in nonimpaired children for all variables except Questions and Onomatopoeia and were only significant in SLI children for Verbs, Prepositions, and Personal Pronouns. Such findings contribute support to the view that there is "deviant" pattern of language in SLI children and once again questions whether MLU is one of the best discriminating indicators to use in the clinical assessment of language organization.

Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits

Science.gov (United States)

2011-01-01

Background Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. Results A total of 404 protein families, present in all cyanobacterial genomes, were identified. Two of these are unique to the phylum, corresponding to an AbrB family transcriptional regulator and a gene that escapes functional annotation although its genomic neighbourhood is conserved among the organisms examined. The evolution of cyanobacterial genome sizes involves a mix of gains and losses in the clade encompassing complex cyanobacteria, while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. Orthologs unique to cyanobacteria exhibiting specific characteristics, such as filament formation, heterocyst differentiation, diazotrophy and symbiotic competence, were also identified. An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genes, 4%-6% of which are unique to cyanobacteria today. Conclusions The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the history of cyanobacteria. The expansion strategy is driven by gene-family enlargment and generates a broad adaptive potential; while the genome streamlining strategy imposes adaptations to highly specific niches, also reflected in their different functional capacities. A few

Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits

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Nylander Johan AA

2011-06-01

Full Text Available Abstract Background Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. Results A total of 404 protein families, present in all cyanobacterial genomes, were identified. Two of these are unique to the phylum, corresponding to an AbrB family transcriptional regulator and a gene that escapes functional annotation although its genomic neighbourhood is conserved among the organisms examined. The evolution of cyanobacterial genome sizes involves a mix of gains and losses in the clade encompassing complex cyanobacteria, while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. Orthologs unique to cyanobacteria exhibiting specific characteristics, such as filament formation, heterocyst differentiation, diazotrophy and symbiotic competence, were also identified. An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genes, 4%-6% of which are unique to cyanobacteria today. Conclusions The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the history of cyanobacteria. The expansion strategy is driven by gene-family enlargment and generates a broad adaptive potential; while the genome streamlining strategy imposes adaptations to highly specific niches, also reflected in their different

Learning and Overnight Retention in Declarative Memory in Specific Language Impairment

Science.gov (United States)

Lukács, Ágnes; Kemény, Ferenc; Lum, Jarrad A. G.; Ullman, Michael T.

2017-01-01

We examined learning and retention in nonverbal and verbal declarative memory in Hungarian children with (n = 21) and without (n = 21) SLI. Recognition memory was tested both 10 minutes and one day after encoding. On nonverbal items, only the children with SLI improved overnight, with no resulting group differences in performance. In the verbal domain, the children with SLI consistently showed worse performance than the typically-developing children, but the two groups showed similar overnight changes. The findings suggest the possibility of spared or even enhanced declarative memory consolidation in SLI. PMID:28046095

The relationship between mathematics and language: academic implications for children with specific language impairment and English language learners.

Science.gov (United States)

Alt, Mary; Arizmendi, Genesis D; Beal, Carole R

2014-07-01

The present study examined the relationship between mathematics and language to better understand the nature of the deficit and the academic implications associated with specific language impairment (SLI) and academic implications for English language learners (ELLs). School-age children (N = 61; 20 SLI, 20 ELL, 21 native monolingual English [NE]) were assessed using a norm-referenced mathematics instrument and 3 experimental computer-based mathematics games that varied in language demands. Group means were compared with analyses of variance. The ELL group was less accurate than the NE group only when tasks were language heavy. In contrast, the group with SLI was less accurate than the groups with NE and ELLs on language-heavy tasks and some language-light tasks. Specifically, the group with SLI was less accurate on tasks that involved comparing numerical symbols and using visual working memory for patterns. However, there were no group differences between children with SLI and peers without SLI on language-light mathematics tasks that involved visual working memory for numerical symbols. Mathematical difficulties of children who are ELLs appear to be related to the language demands of mathematics tasks. In contrast, children with SLI appear to have difficulty with mathematics tasks because of linguistic as well as nonlinguistic processing constraints.

Cognitive functions in preschool children with specific language impairment.

Science.gov (United States)

Reichenbach, Katrin; Bastian, Laura; Rohrbach, Saskia; Gross, Manfred; Sarrar, Lea

2016-07-01

A growing body of research has focused on executive functions in children with specific language impairment (SLI). However, results show limited convergence, particularly in preschool age. The current neuropsychological study compared performance of cognitive functions focused on executive components and working memory in preschool children with SLI to typically developing controls. Performance on the measures cognitive flexibility, inhibition, processing speed and phonological short-term memory was assessed. The monolingual, Caucasian study sample consisted of 30 children with SLI (Mage = 63.3 months, SD = 4.3 months) and 30 healthy controls (Mage = 62.2 months, SD = 3.7 months). Groups were matched for age and nonverbal IQ. Socioeconomic status of the participating families was included. Children with SLI had significantly poorer abilities of phonological short-term memory than matched controls. A tendency of poorer abilities in the SLI group was found for inhibition and processing speed. We confirmed phonological short-term memory to be a reliable marker of SLI in preschoolers. Our results do not give definite support for impaired executive function in SLI, possibly owing to limited sensitivity of test instruments in this age group. We argue for a standardization of executive function tests for research use. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Discrimination and identification of long vowels in children with typical language development and specific language impairment

Science.gov (United States)

Datta, Hia; Shafer, Valerie; Kurtzberg, Diane

2004-05-01

Researchers have claimed that children with specific language impairment (SLI) have particular difficulties in discriminating and identifying phonetically similar and brief speech sounds (Stark and Heinz, 1966; Studdert-Kennedy and Bradley, 1997; Sussman, 1993). In a recent study (Shafer et al., 2004), children with SLI were reported to have difficulty in processing brief (50 ms), phonetically similar vowels (/I-E/). The current study investigated perception of long (250 ms), phonetically similar vowels (/I-E/) in 8- to 10-year-old children with SLI and typical language development (TLD). The purpose was to examine whether phonetic similarity in vowels leads to poorer speech-perception in the SLI group. Behavioral and electrophysiological methods were employed to examine discrimination and identification of a nine-step vowel continuum from /I/ to /E/. Similar performances in discrimination were found for both groups, indicating that lengthening vowel duration indeed improves discrimination of phonetically similar vowels. However, these children with SLI showed poor behavioral identification, demonstrating that phonetic similarity of speech sounds, irrespective of their duration, contribute to the speech perception difficulty observed in SLI population. These findings suggest that the deficit in these children with SLI is at the level of working memory or long term memory representation of speech.

Effect of Co-overexpression of Nisin Key Genes on Nisin Production Improvement in Lactococcus lactis LS01.

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Ni, Zhi-Jian; Zhang, Xiao-Yuan; Liu, Fei; Wang, Miao; Hao, Rong-Hua; Ling, Pei-Xue; Zhu, Xi-Qiang

2017-06-01

Nisin is a small antimicrobial peptide produced by several subset strains of Lactococcus lactis. To improve nisin yield in the producer L. lactis LS01, we proposed a successive fusion of nisA with nisRK and nisFEG into a single shuttle expression vector pMG36e under the control of the native strong constitutive promoter p32. Subsequently, the recombinant vectors were transplanted into the producer cell through electroporation. Nisin productivity was determined through sodium dodecyl sulfate-polyacrylamide gel electrophoresis and bioactivity assays. Expression of nisin peptide was detected by agar diffusion bioassay, and the transcriptional levels of the target genes involved in nisin biosynthesis were investigated via semi-quantitative reverse transcription PCR expression analysis using 16S ribosomal RNA (rRNA) as an internal control. Results suggested that the introduction of empty plasmid did not affect nisin production of L. lactis LS01, whereas by our rational construction and screening, the engineered strain co-overexpressing nisA, nisRK, and nisFEG achieved a maximum increment in bioactive nisin production with a yield of 2470 IU/ml in shake flasks and 4857 IU/ml in 1.0-l fermenters, which increased by approximately 66.3 and 52.6% (P < 0.05), respectively, compared with that of the original strain under the given fermentation conditions. Meanwhile, the transcriptional analysis revealed that the expression of most of these multicopy genes except nisE at transcriptional level were upregulated in the two recombinant strains (LS01/pAR and LS01/pARF), possibly contributing to the improved nisin production. Therefore, this study would provide a potential strategy to improve the economic benefits of nisin manufacture for large-scale industrial production.

Elicited Production of Relative Clauses in German: Evidence from Typically Developing Children and Children with Specific Language Impairment

Science.gov (United States)

Adani, Flavia; Stegenwallner-Schütz, Maja; Haendler, Yair; Zukowski, Andrea

2016-01-01

We elicited the production of various types of relative clauses in a group of German-speaking children with specific language impairment (SLI) and typically developing controls in order to test the movement optionality account of grammatical difficulty in SLI. The results show that German-speaking children with SLI are impaired in relative clause…

MBA1 encodes a mitochondrial membrane-associated protein required for biogenesis of the respiratory chain.

Science.gov (United States)

Rep, M; Grivell, L A

1996-06-17

The yeast MBA 1 gene (Multi-copy Bypass of AFG3) is one of three genes whose overexpression suppresses afg3-null and rca1-null mutations. Bypass of AFG3 and RCA1, whose products are essential for assembly of mitochondrial inner membrane enzyme complexes, suggests a related role for MBA1. The predicted translation product is a 30 kDa hydrophilic protein with a putative mitochondrial targeting sequence and no homology to any sequence in protein or EST databases. Gene disruption leads to a partial respiratory growth defect, which is more pronounced at temperatures above 30 degrees C. Concomitantly, amounts of cytochromes b and aa3 are reduced. A C-terminal c-myc-tagged MBA1 gene product is functional and is found associated with the mitochondrial inner membrane, from which it can he extracted by carbonate, but not by high salt. These observations give further support to a role of MBA1 in assembly of the respiratory chain.

The relation between receptive grammar and procedural, declarative, and working memory in specific language impairment.

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Conti-Ramsden, Gina; Ullman, Michael T; Lum, Jarrad A G

2015-01-01

What memory systems underlie grammar in children, and do these differ between typically developing (TD) children and children with specific language impairment (SLI)? Whilst there is substantial evidence linking certain memory deficits to the language problems in children with SLI, few studies have investigated multiple memory systems simultaneously, examining not only possible memory deficits but also memory abilities that may play a compensatory role. This study examined the extent to which procedural, declarative, and working memory abilities predict receptive grammar in 45 primary school aged children with SLI (30 males, 15 females) and 46 TD children (30 males, 16 females), both on average 9;10 years of age. Regression analyses probed measures of all three memory systems simultaneously as potential predictors of receptive grammar. The model was significant, explaining 51.6% of the variance. There was a significant main effect of learning in procedural memory and a significant group × procedural learning interaction. Further investigation of the interaction revealed that procedural learning predicted grammar in TD but not in children with SLI. Indeed, procedural learning was the only predictor of grammar in TD. In contrast, only learning in declarative memory significantly predicted grammar in SLI. Thus, different memory systems are associated with receptive grammar abilities in children with SLI and their TD peers. This study is, to our knowledge, the first to demonstrate a significant group by memory system interaction in predicting grammar in children with SLI and their TD peers. In line with Ullman's Declarative/Procedural model of language and procedural deficit hypothesis of SLI, variability in understanding sentences of varying grammatical complexity appears to be associated with variability in procedural memory abilities in TD children, but with declarative memory, as an apparent compensatory mechanism, in children with SLI.

Music Perception Influences Language Acquisition: Melodic and Rhythmic-Melodic Perception in Children with Specific Language Impairment.

Science.gov (United States)

Sallat, Stephan; Jentschke, Sebastian

2015-01-01

Language and music share many properties, with a particularly strong overlap for prosody. Prosodic cues are generally regarded as crucial for language acquisition. Previous research has indicated that children with SLI fail to make use of these cues. As processing of prosodic information involves similar skills to those required in music perception, we compared music perception skills (melodic and rhythmic-melodic perception and melody recognition) in a group of children with SLI (N = 29, five-year-olds) to two groups of controls, either of comparable age (N = 39, five-year-olds) or of age closer to the children with SLI in their language skills and about one year younger (N = 13, four-year-olds). Children with SLI performed in most tasks below their age level, closer matching the performance level of younger controls with similar language skills. These data strengthen the view of a strong relation between language acquisition and music processing. This might open a perspective for the possible use of musical material in early diagnosis of SLI and of music in SLI therapy.

Inflectional and derivational morphological spelling abilities of children with Specific Language Impairment.

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Critten, Sarah; Connelly, Vincent; Dockrell, Julie E; Walter, Kirsty

2014-01-01

Children with Specific Language Impairment (SLI) are known to have difficulties with spelling but the factors that underpin these difficulties, are a matter of debate. The present study investigated the impact of oral language and literacy on the bound morpheme spelling abilities of children with SLI. Thirty-three children with SLI (9-10 years) and two control groups, one matched for chronological age (CA) and one for language and spelling age (LA) (aged 6-8 years) were given dictated spelling tasks of 24 words containing inflectional morphemes and 18 words containing derivational morphemes. There were no significant differences between the SLI group and their LA matches in accuracy or error patterns for inflectional morphemes. By contrast when spelling derivational morphemes the SLI group was less accurate and made proportionately more omissions and phonologically implausible errors than both control groups. Spelling accuracy was associated with phonological awareness and reading; reading performance significantly predicted the ability to spell both inflectional and derivational morphemes. The particular difficulties experienced by the children with SLI for derivational morphemes are considered in relation to reading and oral language.

Music Perception Influences Language Acquisition: Melodic and Rhythmic-Melodic Perception in Children with Specific Language Impairment

Science.gov (United States)

Sallat, Stephan; Jentschke, Sebastian

2015-01-01

Language and music share many properties, with a particularly strong overlap for prosody. Prosodic cues are generally regarded as crucial for language acquisition. Previous research has indicated that children with SLI fail to make use of these cues. As processing of prosodic information involves similar skills to those required in music perception, we compared music perception skills (melodic and rhythmic-melodic perception and melody recognition) in a group of children with SLI (N = 29, five-year-olds) to two groups of controls, either of comparable age (N = 39, five-year-olds) or of age closer to the children with SLI in their language skills and about one year younger (N = 13, four-year-olds). Children with SLI performed in most tasks below their age level, closer matching the performance level of younger controls with similar language skills. These data strengthen the view of a strong relation between language acquisition and music processing. This might open a perspective for the possible use of musical material in early diagnosis of SLI and of music in SLI therapy. PMID:26508812

Music Perception Influences Language Acquisition: Melodic and Rhythmic-Melodic Perception in Children with Specific Language Impairment

Directory of Open Access Journals (Sweden)

Stephan Sallat

2015-01-01

Full Text Available Language and music share many properties, with a particularly strong overlap for prosody. Prosodic cues are generally regarded as crucial for language acquisition. Previous research has indicated that children with SLI fail to make use of these cues. As processing of prosodic information involves similar skills to those required in music perception, we compared music perception skills (melodic and rhythmic-melodic perception and melody recognition in a group of children with SLI (N=29, five-year-olds to two groups of controls, either of comparable age (N=39, five-year-olds or of age closer to the children with SLI in their language skills and about one year younger (N=13, four-year-olds. Children with SLI performed in most tasks below their age level, closer matching the performance level of younger controls with similar language skills. These data strengthen the view of a strong relation between language acquisition and music processing. This might open a perspective for the possible use of musical material in early diagnosis of SLI and of music in SLI therapy.

The effect of spatio-temporal distance between visual stimuli on information processing in children with Specific Language Impairment.

Science.gov (United States)

Dispaldro, Marco; Corradi, Nicola

2015-01-01

The purpose of this study is to evaluate whether children with Specific Language Impairment (SLI) have a deficit in processing a sequence of two visual stimuli (S1 and S2) presented at different inter-stimulus intervals and in different spatial locations. In particular, the core of this study is to investigate whether S1 identification is disrupted due to a retroactive interference of S2. To this aim, two experiments were planned in which children with SLI and children with typical development (TD), matched by age and non-verbal IQ, were compared (Experiment 1: SLI n=19; TD n=19; Experiment 2: SLI n=16; TD n=16). Results show group differences in the ability to identify a single stimulus surrounded by flankers (Baseline level). Moreover, children with SLI show a stronger negative interference of S2, both for temporal and spatial modulation. These results are discussed in the light of an attentional processing limitation in children with SLI. Copyright © 2015 Elsevier Ltd. All rights reserved.

Developmental cognitive genetics: How psychology can inform genetics and vice versa

OpenAIRE

Bishop, Dorothy V. M.

2006-01-01

Developmental neuropsychology is concerned with uncovering the underlying basis of developmental disorders such as specific language impairment (SLI), developmental dyslexia, and autistic disorder. Twin and family studies indicate that genetic influences play an important part in the aetiology of all of these disorders, yet progress in identifying genes has been slow. One way forward is to cut loose from conventional clinical criteria for diagnosing disorders and to focus instead on measures ...

Contemporary evolution of resistance at the major insecticide target site gene Ace-1 by mutation and copy number variation in the malaria mosquito Anopheles gambiae.

Science.gov (United States)

Weetman, David; Mitchell, Sara N; Wilding, Craig S; Birks, Daniel P; Yawson, Alexander E; Essandoh, John; Mawejje, Henry D; Djogbenou, Luc S; Steen, Keith; Rippon, Emily J; Clarkson, Christopher S; Field, Stuart G; Rigden, Daniel J; Donnelly, Martin J

2015-06-01

Functionally constrained genes are ideal insecticide targets because disruption is often fatal, and resistance mutations are typically costly. Synaptic acetylcholinesterase (AChE) is an essential neurotransmission enzyme targeted by insecticides used increasingly in malaria control. In Anopheles and Culex mosquitoes, a glycine-serine substitution at codon 119 of the Ace-1 gene confers both resistance and fitness costs, especially for 119S/S homozygotes. G119S in Anopheles gambiae from Accra (Ghana) is strongly associated with resistance, and, despite expectations of cost, resistant 119S alleles are increasing significantly in frequency. Sequencing of Accra females detected only a single Ace-1 119S haplotype, whereas 119G diversity was high overall but very low at non-synonymous sites, evidence of strong purifying selection driven by functional constraint. Flanking microsatellites showed reduced diversity, elevated linkage disequilibrium and high differentiation of 119S, relative to 119G homozygotes across up to two megabases of the genome. Yet these signals of selection were inconsistent and sometimes weak tens of kilobases from Ace-1. This unexpected finding is attributable to apparently ubiquitous amplification of 119S alleles as part of a large copy number variant (CNV) far exceeding the size of the Ace-1 gene, whereas 119G alleles were unduplicated. Ace-1 CNV was detectable in archived samples collected when the 119S allele was rare in Ghana. Multicopy amplification of resistant alleles has not been observed previously and is likely to underpin the recent increase in 119S frequency. The large CNV compromised localization of the strong selective sweep around Ace-1, emphasizing the need to integrate CNV analysis into genome scans for selection. © 2015 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Developing Plugin e-DDC as an Additional Application for Senayan Library Management System with PHP Language Programming and MySQL Database

Directory of Open Access Journals (Sweden)

Mohamad Rotmianto

2018-01-01

Full Text Available Between Senayan Library Management System or usually called SLiMS and e-DDC (electronic Dewey Decimal Classification now is the most popular library application software which has a lot of user, because it is simple to use, has an updating guarantee from its developers and off course both of them are free of charge. Although SLiMS and e-DDC are different application at all, as practically they are recommended to be used togather for library management. SLiMS is used for library automation and e-DDC is to find collection’s classification. Many users of SLiMS and e-DDC ever give suggestions about developing SLiMS with e-DDC include in its database, and then librarians will be easier to manage their libraries. Because of that suggestion, finally a plugin as an additional application for SLiMS has been created and developed. That plugin was build with PHP language programming and MySQL database. The purpose of this paper is to enrich about reference of development of library application, especially those based on Free Open Source Software (FOSS. This paper use Research and Development Methods. And the result of this paper is Plugin e-DDC for SLiMS which has released on May, 2nd 2015, in order to celebrate “National Education Day”.

Developing Plugin e-DDC as an Additional Application for Senayan Library Management System with PHP Language Programming and MySQL Database

Directory of Open Access Journals (Sweden)

Mohamad Rotmianto

2016-07-01

Full Text Available Senayan Library Management System, usually called as SLiMS dan e-DDC (electronic Dewey Decimal Classification, is an application for library that now is used widely because it is easy to use, guaranteed of updating from the provider, and free. SLiMs and e-DDC is actually two separated application, but in the practice, it is possible and recommended to be used together. SLiMS is used as a tool of library automation, meanwhile e-DDC functions to help finding collection classification number. Some users of SLiMS and e-DDC have suggested to develop SLiMS that is integral with e-DDC, so the use of both application can be practical which can make the librarian easier to manage the library. Based on the suggestion, the writer and e-DDC team finally created and designed additional application which is called plugin in SLiMS automation system that contained e-DDC. The plugin was created using PHP MySQL and MySQL database. The purpose of this paper is to enrich the reference of library application development, especially that is based on Free Open Source Software (FOSS. The method used is Research and Development method. The result was the Plugin e-DDC for SLiMS was finished and released on May 2, 2015 to celebrate National Education Day.

The relationship between phonological short-term memory, receptive vocabulary, and fast mapping in children with specific language impairment.

Science.gov (United States)

Jackson, Emily; Leitao, Suze; Claessen, Mary

2016-01-01

Children with specific language impairment (SLI) often experience word-learning difficulties, which are suggested to originate in the early stage of word learning: fast mapping. Some previous research indicates significantly poorer fast mapping capabilities in children with SLI compared with typically developing (TD) counterparts, with a range of methodological factors impacting on the consistency of this finding. Research has explored key issues that might underlie fast mapping difficulties in children with SLI, with strong theoretical support but little empirical evidence for the role of phonological short-term memory (STM). Additionally, further research is required to explore the influence of receptive vocabulary on fast mapping capabilities. Understanding the factors associated with fast mapping difficulties that are experienced by children with SLI may lead to greater theoretically driven word-learning intervention. To investigate whether children with SLI demonstrate significant difficulties with fast mapping, and to explore the related factors. It was hypothesized that children with SLI would score significantly lower on a fast mapping production task compared with TD children, and that phonological STM and receptive vocabulary would significantly predict fast mapping production scores in both groups of children. Twenty-three children with SLI (mean = 64.39 months, SD = 4.10 months) and 26 TD children (mean = 65.92 months, SD = 2.98) were recruited from specialist language and mainstream schools. All participants took part in a unique, interactive fast-mapping task whereby nine novel objects with non-word labels were presented and production accuracy was assessed. A non-word repetition test and the Peabody Picture Vocabulary Test-Fourth Edition (PPVT-IV) were also administered as measures of phonological STM capacity and receptive vocabulary, respectively. Results of the fast-mapping task indicated that children with SLI had significantly poorer fast

Grammatical morphology is not a sensitive marker of language impairment in Icelandic in children aged 4-14 years.

Science.gov (United States)

Thordardottir, Elin

2016-01-01

Grammatical morphology continues to be widely regarded as an area of extraordinary difficulty in children with Specific Language Impairment (SLI). A main argument for this view is the purported high diagnostic accuracy of morphological errors for the identification of SLI. However, findings are inconsistent across age groups and across languages. Studies show morphological difficulty to be far less pronounced in more highly inflected languages and the diagnostic accuracy of morphology in such languages is largely unknown. This study examines the morphological use of Icelandic children with and without SLI in a cross-sectional sample of children ranging from preschool age to adolescence and assesses the usefulness of morphology as a clinical marker to identify SLI. Participants were 57 monolingual Icelandic-speaking children age 4-14 years; 31 with SLI and 26 with typical language development (TD). Spontaneous language samples were coded for correct and incorrect use of grammatical morphology. The diversity of use of grammatical morphemes was documented for each group at different age and MLU levels. Individual accuracy scores were plotted against age as well as MLU and diagnostic accuracy was calculated. MLU and morphological accuracy increased with age for both children with SLI and TD, with the two groups gradually approaching each other. Morphological diversity and sequence of acquisition was similar across TD and SLI groups compared based on age or MLU. Morphological accuracy was overall high, but was somewhat lower in the SLI group, in particular at ages below 12 years and MLU levels below 6.0. However, overlap between the groups was important in all age groups, involving a greater tendency for errors in both groups at young ages and scores close to or at ceiling at older ages. Sensitivity rates as well as likelihood ratios for each morpheme were all below the range considered acceptable for clinical application, whereas better specificity rates in some age

An Escherichia coli strain deficient for both exonuclease 5 and deoxycytidine triphosphate deaminase shows enhanced sensitivity to ionizing radiation

International Nuclear Information System (INIS)

Estevenon, A.M.; Kooistra, J.; Sicard, N.

1995-01-01

An Escherichia coli mutant lacking deoxycytidine triphosphate deaminase (Dcd) activity and an unknown function encoded by a gene designated ior exhibits sensitivity to ionizing radiation whereas dcd mutants themselves are not sensitive. A DNA fragment from an E. coli genomic library that restores the wild type level of UV and gamma ray resistance to this mutant has been cloned in the multicopy vector pBR322. Comparison of its restriction map with the physical map of the E. coli chromosome revealed complete identity to the recBD genes. ior affects ATP-dependent exonuclease activity, suggesting that it is an allele of recB. This mutation alone does not confer sensitivity to UV and gamma radiation, indicating that lack of Dcd activity is also required for expression of radiation sensitivity

Comparative genomic analysis reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in Cryptosporidium parvum.

Science.gov (United States)

Guo, Yaqiong; Tang, Kevin; Rowe, Lori A; Li, Na; Roellig, Dawn M; Knipe, Kristine; Frace, Michael; Yang, Chunfu; Feng, Yaoyu; Xiao, Lihua

2015-04-18

Cryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis-associated outbreaks in Europe and Australia, and is a dominant outbreak subtype in the United States. In recent yearsIaA28R4 is becoming a major new subtype in the United States. In this study, we sequenced the genomes of two field specimens from each of the two subtypes and conducted a comparative genomic analysis of the obtained sequences with those from the only fully sequenced Cryptosporidium parvum genome. Altogether, 8.59-9.05 Mb of Cryptosporidium sequences in 45-767 assembled contigs were obtained from the four specimens, representing 94.36-99.47% coverage of the expected genome. These genomes had complete synteny in gene organization and 96.86-97.0% and 99.72-99.83% nucleotide sequence similarities to the published genomes of C. parvum and C. hominis, respectively. Several major insertions and deletions were seen between C. hominis and C. parvum genomes, involving mostly members of multicopy gene families near telomeres. The four C. hominis genomes were highly similar to each other and divergent from the reference IaA25R3 genome in some highly polymorphic regions. Major sequence differences among the four specimens sequenced in this study were in the 5' and 3' ends of chromosome 6 and the gp60 region, largely the result of genetic recombination. The sequence similarity among specimens of the two dominant outbreak subtypes and genetic recombination in chromosome 6, especially around the putative virulence determinant gp60 region, suggest that genetic recombination plays a potential role in the emergence of hyper-transmissible C. hominis subtypes. The high sequence conservation between C. parvum and C. hominis genomes and significant differences in copy numbers of MEDLE family secreted proteins and insulinase-like proteases indicate that telomeric gene duplications could potentially contribute to

Which are the best predictors of theory of mind delay in children with specific language impairment?

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Andrés-Roqueta, Clara; Adrian, Juan E; Clemente, Rosa A; Katsos, Napoleon

2013-01-01

The relationship between language and theory of mind (ToM) development in participants with specific language impairment (SLI) it is far from clear due to there were differences in study design and methodologies of previous studies. This research consisted of an in-depth investigation of ToM delay in children with SLI during the typical period of acquisition, and it studied whether linguistic or information-processing variables were the best predictors of this process. It also took into account whether there were differences in ToM competence due to the degree of pragmatic impairment within the SLI group. Thirty-one children with SLI (3;5-7;5 years old) and two control groups (age matched and language matched) were assessed with False Belief (FB) tasks, a wide battery of language measures and additional information-processing measures. The members of the SLI group were less competent than their age-matched peers at solving FB tasks, but they performed similarly to the language-matched group. Regression analysis showed that overall linguistic skills of children with SLI were the best predictor of ToM performance, and especially grammar abilities. No differences between SLI subgroups were found according to their pragmatic level. A delay in ToM development in children with SLI around the critical period of acquisition is confirmed more comprehensively, and it is shown to be more strongly related to their general linguistic level than to their age and other information-processing faculties. This finding stresses the importance of early educational and clinical programmes aimed at reducing deleterious effects in later development. © 2013 Royal College of Speech and Language Therapists.

Self-reported lactose intolerance in clinic patients with functional gastrointestinal symptoms: prevalence, risk factors, and impact on food choices.

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Zheng, X; Chu, H; Cong, Y; Deng, Y; Long, Y; Zhu, Y; Pohl, D; Fried, M; Dai, N; Fox, M

2015-08-01

Many patients complain of abdominal symptoms with dairy products; however, clinical and psychosocial factors associated with self-reported lactose intolerance (SLI) have not been assessed in large studies. In particular, data are lacking from lactase deficient populations. This prospective cohort study assessed the prevalence of, and risk factors for, SLI in Chinese patients attending a gastroenterology clinic. Consecutive patients completed questionnaires to assess digestive health (Rome III), psychological state (HADS), life event stress (LES), food intake, and quality-of-life (SF-8). A representative sample completed genetic studies and hydrogen breath testing (HBT) at the clinically relevant dose of 20 g lactose. SLI was present in 411/910 (45%) clinic patients with functional abdominal symptoms. The genotype in all subjects was C/C-13910. A small number of novel SNPs in lactase promoter region were identified, including C/T-13908 which appeared to confer lactase persistence. Over half of the patients (54%) completed the 20 g lactose HBT with 58% (285/492) reporting typical symptoms. Positive and negative predictive values of SLI for abdominal symptoms during HBT were 60% and 44%, respectively. Psychological state and stress were not associated with SLI in clinic patients. SLI impacted on physical quality-of-life and was associated with reduced ingestion of dairy products, legumes, and dried fruit (p ≤ 0.05). In a lactase deficient population, approximately half of patients attending clinic with functional gastrointestinal symptoms reported intolerance to dairy products; however, SLI did not predict findings on 20 g lactose HBT. Independent of psychosocial factors, SLI impacted on quality-of-life and impacted on food choices with restrictions not limited to dairy products. © 2015 John Wiley & Sons Ltd.

Analogical reasoning in children with specific language impairment: Evidence from a scene analogy task.

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Krzemien, Magali; Jemel, Boutheina; Maillart, Christelle

2017-01-01

Analogical reasoning is a human ability that maps systems of relations. It develops along with relational knowledge, working memory and executive functions such as inhibition. It also maintains a mutual influence on language development. Some authors have taken a greater interest in the analogical reasoning ability of children with language disorders, specifically those with specific language impairment (SLI). These children apparently have weaker analogical reasoning abilities than their aged-matched peers without language disorders. Following cognitive theories of language acquisition, this deficit could be one of the causes of language disorders in SLI, especially those concerning productivity. To confirm this deficit and its link to language disorders, we use a scene analogy task to evaluate the analogical performance of SLI children and compare them to controls of the same age and linguistic abilities. Results show that children with SLI perform worse than age-matched peers, but similar to language-matched peers. They are more influenced by increased task difficulty. The association between language disorders and analogical reasoning in SLI can be confirmed. The hypothesis of limited processing capacity in SLI is also being considered.

Mirror-drawing skill in children with specific language impairment: Improving generalization by incorporating variability into the practice session.

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Desmottes, Lise; Maillart, Christelle; Meulemans, Thierry

2017-05-01

This study aimed to investigate the procedural deficit hypothesis (PDH) in children with specific language impairment (SLI) by using a mirror-drawing task, a sensorimotor adaptation paradigm that does not involve sequence learning and has never before been used in SLI. A total of 30 school-aged children with SLI matched to 30 typically developing (TD) control children had to trace several figures seen only in mirror-reversed view in two practice sessions separated by a one-week interval. Two practice conditions were compared: a constant condition in which children had to trace the same figure throughout the learning trials, and a variable one in which they had to trace different figures in each trial. The results revealed a similar learning pattern between SLI and TD children in both practice conditions, suggesting that initial learning for a non-sequential procedural task is preserved in SLI. However, the children with SLI generalized the mirror-drawing skill in the same way as the TD children only if there was variability in the way the material was trained (variable practice). No significant schedule effects were observed in the control group.

Influence of Language Load on Speech Motor Skill in Children With Specific Language Impairment.

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Saletta, Meredith; Goffman, Lisa; Ward, Caitlin; Oleson, Jacob

2018-03-15

Children with specific language impairment (SLI) show particular deficits in the generation of sequenced action: the quintessential procedural task. Practiced imitation of a sequence may become rote and require reduced procedural memory. This study explored whether speech motor deficits in children with SLI occur generally or only in conditions of high linguistic load, whether speech motor deficits diminish with practice, and whether it is beneficial to incorporate conditions of high load to understand speech production. Children with SLI and typical development participated in a syntactic priming task during which they generated sentences (high linguistic load) and, then, practiced repeating a sentence (low load) across 3 sessions. We assessed phonetic accuracy, speech movement variability, and duration. Children with SLI produced more variable articulatory movements than peers with typical development in the high load condition. The groups converged in the low load condition. Children with SLI continued to show increased articulatory stability over 3 practice sessions. Both groups produced generated sentences with increased duration and variability compared with repeated sentences. Linguistic demands influence speech motor production. Children with SLI show reduced speech motor performance in tasks that require language generation but not when task demands are reduced in rote practice.

Assessment of second language proficiency in bilingual children with specific language impairment: a clinical perspective.

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Verhoeven, Ludo; Steenge, Judit; van Weerdenburg, Marjolijn; van Balkom, Hans

2011-01-01

The goal of this study was to examine to what extent the conditions of restricted input of L2 and SLI have an additive impact on language acquisition. Therefore, the Dutch language achievement of 6-, 7-, and 8-year-old bilingual children with SLI was compared with that of typically developing monolingual Dutch children, typically developing bilingual children, and monolingual Dutch children with SLI. Assuming that speaking a language in varying environments involves distinct subskills that can be acquired in differential patterns, the achievement of phonological, lexical, morphosyntactic and textual abilities were assessed separately. For each of these abilities, it was determined to what extent the conditions of restricted input (first vs. second language) and language deficit (typically developing vs. SLI) cause stagnation or a delay in language acquisition. Bilingual children with SLI perform at a lower level than the other groups in almost all aspects of achievement in Dutch. For language tasks related to the mental lexicon and grammar, an additional disadvantage was evidenced as a result of the combination of learning Dutch as second language and having SLI. Copyright © 2011 Elsevier Ltd. All rights reserved.

Sequence-specific procedural learning deficits in children with specific language impairment.

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Hsu, Hsinjen Julie; Bishop, Dorothy V M

2014-05-01

This study tested the procedural deficit hypothesis of specific language impairment (SLI) by comparing children's performance in two motor procedural learning tasks and an implicit verbal sequence learning task. Participants were 7- to 11-year-old children with SLI (n = 48), typically developing age-matched children (n = 20) and younger typically developing children matched for receptive grammar (n = 28). In a serial reaction time task, the children with SLI performed at the same level as the grammar-matched children, but poorer than age-matched controls in learning motor sequences. When tested with a motor procedural learning task that did not involve learning sequential relationships between discrete elements (i.e. pursuit rotor), the children with SLI performed comparably with age-matched children and better than younger grammar-matched controls. In addition, poor implicit learning of word sequences in a verbal memory task (the Hebb effect) was found in the children with SLI. Together, these findings suggest that SLI might be characterized by deficits in learning sequence-specific information, rather than generally weak procedural learning. © 2014 The Authors. Developmental Science Published by John Wiley & Sons Ltd.

Growth of reading skills in children with a history of specific language impairment: the role of autistic symptomatology and language-related abilities.

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St Clair, Michelle C; Durkin, Kevin; Conti-Ramsden, Gina; Pickles, Andrew

2010-03-01

Individuals with a history of specific language impairment (SLI) often have subsequent problems with reading skills, but there have been some discrepant findings as to the developmental time course of these skills. This study investigates the developmental trajectories of reading skills over a 9-year time-span (from 7 to 16 years of age) in a large sample of individuals with a history of SLI. Relationships among reading skills, autistic symptomatology, and language-related abilities were also investigated. The results indicate that both reading accuracy and comprehension are deficient but that the development of these skills progresses in a consistently parallel fashion to what would be expected from a normative sample of same age peers. Language-related abilities were strongly associated with reading skills. Unlike individuals with SLI only, those with SLI and additional autistic symptomatology had adequate reading accuracy but did not differ from the individuals with SLI only in reading comprehension. They exhibited a significant gap between what they could read and what they could understand when reading. These findings provide strong evidence that individuals with SLI experience continued, long-term deficits in reading skills from childhood to adolescence.

Nonword repetition--a clinical marker for specific language impairment in Swedish associated with parents' language-related problems.

Directory of Open Access Journals (Sweden)

Nelli Kalnak

Full Text Available First, we explore the performance of nonword repetition (NWR in children with specific language impairment (SLI and typically developing children (TD in order to investigate the accuracy of NWR as a clinical marker for SLI in Swedish-speaking school-age children. Second, we examine the relationship between NWR, family aggregation, and parental level of education in children with SLI. A sample of 61 children with SLI, and 86 children with TD, aged 8-12 years, were administered an NWR test. Family aggregation, measured as the prevalence of language and/or literacy problems (LLP in parents of the children with SLI, was based on family history interviews. The sensitivity and specificity of nonword repetition was analyzed in a binary logistic regression, cut-off values were established with ROC curves, and positive and negative likelihood ratios reported. Results from the present study show that NWR distinguishes well between Swedish-speaking school-children with and without SLI. We found 90.2% sensitivity and 97.7% specificity at a cut-off level of -2 standard deviations for binary scoring of nonwords. Differences between the SLI and TD groups showed large effect sizes for the two scoring measures binary (d = 2.11 and percent correct consonants (PCC (d = 1.79. The children with SLI were split into two subgroups: those with no parents affected with LLP (n = 12, and those with one or both parents affected (n = 49. The subgroup consisting of affected parents had a significantly lower score on NWR binary (p = .037, and there was a great difference between the subgroups (d = 0.7. When compared to the TD group, the difference from the subgroup with affected parents was almost one standard deviation larger (d = 2.47 than the difference from the TD to the subgroup consisting of non-affected parents (d = 1.57. Our study calls for further exploration of the complex interaction between family aggregation, language input, and

Lexical spelling in children and adolescents with specific language impairment: variations with the writing situation.

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Broc, Lucie; Bernicot, Josie; Olive, Thierry; Favart, Monik; Reilly, Judy; Quémart, Pauline; Uzé, Joël

2013-10-01

The goal of this study was to compare the lexical spelling performance of children and adolescents with specific language impairment (SLI) in two contrasting writing situations: a dictation of isolated words (a classic evaluative situation) and a narrative of a personal event (a communicative situation). Twenty-four children with SLI and 48 typically developing children participated in the study, split into two age groups: 7-11 and 12-18 years of age. Although participants with SLI made more spelling errors per word than typically developing participants of the same chronological age, there was a smaller difference between the two groups in the narratives than in the dictations. Two of the findings are particularly noteworthy: (1) Between 12 and 18 years of age, in communicative narration, the number of spelling errors of the SLI group was not different from that of the typically developing group. (2) In communicative narration, the participants with SLI did not make specific spelling errors (phonologically unacceptable), contrary to what was shown in the dictation. From an educational perspective or that of a remediation program, it must be stressed that the communicative narration provides children-and especially adolescents-with SLI an opportunity to demonstrate their improved lexical spelling abilities. Furthermore, the results encourage long-term lexical spelling education, as adolescents with SLI continue to show improvement between 12 and 18 years of age. Copyright © 2013 Elsevier Ltd. All rights reserved.

Linguistic and pragmatic aspects of narration in Finnish typically developing children and children with specific language impairment.

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Mäkinen, Leena; Loukusa, Soile; Laukkanen, Päivi; Leinonen, Eeva; Kunnari, Sari

2014-06-01

This study investigates narratives of Finnish children with specific language impairment (SLI) from linguistic and pragmatic perspectives, in order to get a comprehensive overview of these children's narrative abilities. Nineteen children with SLI (mean age 6;1 years) and 19 typically developing age-matched children participated in the study. Their picture-elicited narrations were analysed for linguistic productivity and complexity, grammatical and referential accuracy, event content, the use of mental state expressions and narrative comprehension. Children with SLI showed difficulties in every aspect of narration in comparison to their peers. Only one measure of productivity, the number of communication units, did not reach statistical significance. Not only was linguistic structure fragile but also pragmatic aspects of storytelling (referencing, event content, mental state expressions and inferencing) were demanding for children with SLI. Results suggest that pragmatic aspects of narration should be taken into account more often when assessing narrative abilities of children with SLI.

Adjective production by Russian-speaking children with specific language impairment.

Science.gov (United States)

Tribushinina, Elena; Dubinkina, Elena

2012-06-01

Research on specific language impairment (SLI) has primarily focused on the acquisition of nouns and verbs. Less attention has been given to other content-word classes, such as adjectives and adverbs. This article investigates adjective production by 7- to 10-year-old Russian-speaking children with SLI and their typically developing (TD) peers and focuses on the production of antonymous adjectives and degree markers in an elicitation experiment. The results show that degree morphology is more impaired in SLI than antonymy. In antonym production, children with SLI were able to catch up with their TD peers by age 8. In the domain of degree, however, the SLI group lagged behind the TD controls across all ages studied. Error analysis indicates that language-impaired children have particular difficulty with agreement inflection and affixal negations. They also substitute adjectives with specific meanings by more general terms. The implications of this study for the morphological-richness hypothesis are discussed.

Social stress in young people with specific language impairment

OpenAIRE

Wadman, Ruth; Durkin, Kevin; Conti-Ramsden, Gina

2010-01-01

Social interactions can be a source of social stress for adolescents. Little is known about how adolescents with developmental difficulties, such as specific language impairment (SLI), feel when interacting socially. Participants included 28 adolescents with SLI and 28 adolescents with typical language abilities (TL). Self-report measures of social stress, social skills and social acceptance were obtained. Participants with SLI reported experiencing significantly more social stress than did p...

The comprehension of Italian relative clauses in poor readers and in children with Specific Language Impairment

Directory of Open Access Journals (Sweden)

Fabrizio Arosio

2017-02-01

Full Text Available Children with Specific Language Impairment (SLI and children with Developmental Dyslexia (DD have problems comprehending relative clauses (RCs and find object RCs more difficult than subject RCs, as do typically developing children. Few studies have compared these groups directly, leaving it unclear whether the problems observed in children with DD are similar to those described in SLI. Work with typically developing children has shown that the comprehension of passive RCs is less challenging than that of object RCs. It is argued that this asymmetry depends on intervention effects as modelized in a Relativized Minimality framework. Since movement is challenging for children with SLI and those with DD, examining and comparing their comprehension of object RCs and passive RCs can broaden our understanding of their language deficits. In fact, both structures involve movement, but the moved element and the movement configuration are different. In our study we investigated the comprehension of subject RCs, object RCs and passive RCs in 12 Italian monolingual children with SLI (mean age: 7;6, 13 Italian monolingual children with DD (mean age: 10;7 and 50 typically developing controls matched for age, grammar and vocabulary. Results from a picture selection task show that: (i subject RCs are unproblematic for all children; (ii object RCs are challenging for children with SLI, children with DD and younger typically developing controls; (iii passive RCs are better understood than object RCs in all groups, but still problematic for children with SLI and younger typically developing controls. Our data show that intervention effects are found in children with SLI and children with DD and that those with SLI have a deficit in transferring thematic roles to moved elements. Our results point out that some of the children with DD have a mild grammatical deficit that was undetected or escaped standardized tests.

Novel-word learning deficits in Mandarin-speaking preschool children with specific language impairments.

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Chen, Yuchun; Liu, Huei-Mei

2014-01-01

Children with SLI exhibit overall deficits in novel word learning compared to their age-matched peers. However, the manifestation of the word learning difficulty in SLI was not consistent across tasks and the factors affecting the learning performance were not yet determined. Our aim is to examine the extent of word learning difficulties in Mandarin-speaking preschool children with SLI, and to explore the potent influence of existing lexical knowledge on to the word learning process. Preschool children with SLI (n=37) and typical language development (n=33) were exposed to novel words for unfamiliar objects embedded in stories. Word learning tasks including the initial mapping and short-term repetitive learning were designed. Results revealed that Mandarin-speaking preschool children with SLI performed as well as their age-peers in the initial form-meaning mapping task. Their word learning difficulty was only evidently shown in the short-term repetitive learning task under a production demand, and their learning speed was slower than the control group. Children with SLI learned the novel words with a semantic head better in both the initial mapping and repetitive learning tasks. Moderate correlations between stand word learning performances and scores on standardized vocabulary were found after controlling for children's age and nonverbal IQ. The results suggested that the word learning difficulty in children with SLI occurred in the process of establishing a robust phonological representation at the beginning stage of word learning. Also, implicit compound knowledge is applied to aid word learning process for children with and without SLI. We also provide the empirical data to validate the relationship between preschool children's word learning performance and their existing receptive vocabulary ability. Copyright © 2013 Elsevier Ltd. All rights reserved.

Awareness of rhythm patterns in speech and music in children with specific language impairments

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Ruth eCumming

2015-12-01

Full Text Available Children with specific language impairments (SLIs show impaired perception and production of language, and also show impairments in perceiving auditory cues to rhythm (amplitude rise time [ART] and sound duration and in tapping to a rhythmic beat. Here we explore potential links between language development and rhythm perception in 45 children with SLI and 50 age-matched controls. We administered three rhythmic tasks, a musical beat detection task, a tapping-to-music task, and a novel music/speech task, which varied rhythm and pitch cues independently or together in both speech and music. Via low-pass filtering, the music sounded as though it was played from a low-quality radio and the speech sounded as though it was muffled (heard behind the door. We report data for all of the SLI children (N = 45, IQ varying, as well as for two independent subgroupings with intact IQ. One subgroup, Pure SLI, had intact phonology and reading (N=16, the other, SLI PPR (N=15, had impaired phonology and reading. When IQ varied (all SLI children, we found significant group differences in all the rhythmic tasks. For the Pure SLI group, there were rhythmic impairments in the tapping task only. For children with SLI and poor phonology (SLI PPR, group differences were found in all of the filtered speech/music AXB tasks. We conclude that difficulties with rhythmic cues in both speech and music are present in children with SLIs, but that some rhythmic measures are more sensitive than others. The data are interpreted within a ‘prosodic phrasing’ hypothesis, and we discuss the potential utility of rhythmic and musical interventions in remediating speech and language difficulties in children.

Dosage compensation and demasculinization of X chromosomes in Drosophila.

Science.gov (United States)

Bachtrog, Doris; Toda, Nicholas R T; Lockton, Steven

2010-08-24

The X chromosome of Drosophila shows a deficiency of genes with male-biased expression, whereas mammalian X chromosomes are enriched for spermatogenesis genes expressed premeiosis and multicopy testis genes. Meiotic X-inactivation and sexual antagonism can only partly account for these patterns. Here, we show that dosage compensation (DC) in Drosophila may contribute substantially to the depletion of male genes on the X. To equalize expression between X-linked and autosomal genes in the two sexes, male Drosophila hypertranscribe their single X, whereas female mammals silence one of their two X chromosomes. We combine fine-scale mapping data of dosage compensated regions with genome-wide expression profiles and show that most male-biased genes on the D. melanogaster X are located outside dosage compensated regions. Additionally, X-linked genes that have newly acquired male-biased expression in D. melanogaster are less likely to be dosage compensated, and parental X-linked genes that gave rise to an autosomal male-biased retrocopy are more likely located within compensated regions. This suggests that DC contributes to the observed demasculinization of X chromosomes in Drosophila, both by limiting the emergence of male-biased expression patterns of existing X genes, and by contributing to gene trafficking of male genes off the X. Copyright 2010 Elsevier Ltd. All rights reserved.

Dicty_cDB: SLH211 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available SL (Link to library) SLH211 (Link to dictyBase) - - - Contig-U16162-1 SLH211Z (Link... to Original site) - - SLH211Z 427 - - - - Show SLH211 Library SL (Link to library) Clone ID SLH211 (Link to...ycdb.biol.tsukuba.ac.jp/CSM/SL/SLH2-A/SLH211Q.Seq.d/ Representative seq. ID SLH21...1Z (Link to Original site) Representative DNA sequence >SLH211 (SLH211Q) /CSM/SL/SLH2-A/SLH211Q.Seq.d/ XXXXX...equences producing significant alignments: (bits) Value SLI277 (SLI277Q) /CSM/SL/SLI2-D/SLI277Q.Seq.d/ 767 0.0 SLH211 (SLH2

A pilot study of the effects of RightStart instruction on early numeracy skills of children with specific language impairment.

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Mononen, Riikka; Aunio, Pirjo; Koponen, Tuire

2014-05-01

This pilot study investigated the effects of an early numeracy program, RightStart Mathematics (RS), on Finnish kindergartners with specific language impairment (SLI). The study applied a pre-test-instruction-post-test design. The children with SLI (n=9, Mage=82.11 months) received RS instruction two to three times a week for 40 min over seven months, which replaced their business-as-usual mathematics instruction. Mathematical skill development among children with SLI was examined at the individual and group levels, and compared to the performance of normal language-achieving age peers (n=32, Mage=74.16 months) who received business-as-usual kindergarten mathematics instruction. The children with SLI began kindergarten with significantly weaker early numeracy skills compared to their peers. Immediately after the instruction phase, there was no significant difference between the groups in counting skills. In Grade 1, the children with SLI performed similarly to their peers in addition and subtraction skills (accuracy) and multi-digit number comparison, but showed weaker skills in arithmetical reasoning and in matching spoken and printed multi-digit numbers. Our pilot study showed encouraging signs that the early numeracy skills of children with SLI can be improved successfully in a kindergarten small-classroom setting with systematic instruction emphasizing visualization. Copyright © 2014 Elsevier Ltd. All rights reserved.

Behavior problems and social competence in Brazilian children with specific language impairment

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Marina Leite Puglisi

2016-01-01

Full Text Available Abstract This study aimed to investigate the behavior and social profile of Brazilian children with specific language impairment (SLI and explore whether the severity of language deficits was associated with behavioral problems and low social competence. Twenty-four children with SLI aged from 6 to 11 years who showed substantial expressive language problems and were receiving speech-language therapy were assessed through the Child Behavior Checklist (CBCL. Children with SLI showed high rates of behavioral problems and low levels of social competence. With the exception of two subscales (“somatic” and “rule breaker”, the percentage of children with SLI at risk of behavioral problems was significantly higher than the same proportion in the general population; and almost all children with SLI (95.2 % demonstrated problems with social competence. The severity of language deficits was associated with the risk of behavioral problems according to only one criterion. No associations were found between the severity of language problems and social competence. The study provides cross-cultural evidence to support the existence of behavior problems and reduced social competence in children with SLI. Our findings point to the need of using a combination of measures to classify the severity of language problems rather than a single dimension.

Effects of Sustained Lung Inflation, a lung recruitment maneuver in primary acute respiratory distress syndrome, in respiratory and cerebral outcomes in preterm infants.

Science.gov (United States)

Grasso, Chiara; Sciacca, Pietro; Giacchi, Valentina; Carpinato, Caterina; Mattia, Carmine; Palano, Grazia Maria; Betta, Pasqua

2015-01-01

Sustained Lung Inflation (SLI) is a maneuver of lung recruitment in preterm newborns at birth that can facilitate the achieving of larger inflation volumes, leading to the clearance of lung fluid and formation of functional residual capacity (FRC). To investigate if Sustained Lung Inflation (SLI) reduces the need of invasive procedures and iatrogenic risks. 78 newborns (gestational age≤34 weeks, weighing≤2000 g) who didn't breathe adequately at birth and needed to receive SLI in addition to other resuscitation maneuvers (2010 guidelines). 78 preterm infants born one after the other in our department of Neonatology of Catania University from 2010 to 2012. The need of intubation and surfactant, the ventilation required, radiological signs, the incidence of intraventricular hemorrhage (IVH), periventricular leukomalacia, retinopathy in prematurity from III to IV plus grades, bronchopulmonary dysplasia, patent ductus arteriosus, pneumothorax and necrotizing enterocolitis. In the SLI group infants needed less intubation in the delivery room (6% vs 21%; phemorrhage in the SLI group (23% vs 14%; p=0.15; OR=1.83). SLI is easier to perform even with a single operator, it reduces the necessity of more complicated maneuvers and surfactant without statistically evident adverse effects. Copyright © 2014. Published by Elsevier Ireland Ltd.

Later learning stages in procedural memory are impaired in children with Specific Language Impairment.

Science.gov (United States)

Desmottes, Lise; Meulemans, Thierry; Maillart, Christelle

2016-01-01

According to the Procedural Deficit Hypothesis (PDH), difficulties in the procedural memory system may contribute to the language difficulties encountered by children with Specific Language Impairment (SLI). Most studies investigating the PDH have used the sequence learning paradigm; however these studies have principally focused on initial sequence learning in a single practice session. The present study sought to extend these investigations by assessing the consolidation stage and longer-term retention of implicit sequence-specific knowledge in 42 children with or without SLI. Both groups of children completed a serial reaction time task and were tested 24h and one week after practice. Results showed that children with SLI succeeded as well as children with typical development (TD) in the early acquisition stage of the sequence learning task. However, as training blocks progressed, only TD children improved their sequence knowledge while children with SLI did not appear to evolve any more. Moreover, children with SLI showed a lack of the consolidation gains in sequence knowledge displayed by the TD children. Overall, these results were in line with the predictions of the PDH and suggest that later learning stages in procedural memory are impaired in SLI. Copyright © 2015 Elsevier Ltd. All rights reserved.

The complexity of narrative interferes in the use of conjunctions in children with specific language impairment.

Science.gov (United States)

Gonzalez, Deborah Oliveira; Cáceres, Ana Manhani; Bento-Gaz, Ana Carolina Paiva; Befi-Lopes, Debora Maria

2012-01-01

To verify the use of conjunctions in narratives, and to investigate the influence of stimuli's complexity over the type of conjunctions used by children with specific language impairment (SLI) and children with typical language development. Participants were 40 children (20 with typical language development and 20 with SLI) with ages between 7 and 10 years, paired by age range. Fifteen stories with increasing of complexity were used to obtain the narratives; stories were classified into mechanical, behavioral and intentional, and each of them was represented by four scenes. Narratives were analyzed according to occurrence and classification of conjunctions. Both groups used more coordinative than subordinate conjunctions, with significant decrease in the use of conjunctions in the discourse of SLI children. The use of conjunctions varied according to the type of narrative: for coordinative conjunctions, both groups differed only between intentional and behavioral narratives, with higher occurrence in behavioral ones; for subordinate conjunctions, typically developing children's performance did not show differences between narratives, while SLI children presented fewer occurrences in intentional narratives, which was different from other narratives. Both groups used more coordinative than subordinate conjunctions; however, typically developing children presented more conjunctions than SLI children. The production of children with SLI was influenced by stimulus, since more complex narratives has less use of subordinate conjunctions.

Atypical audio-visual speech perception and McGurk effects in children with specific language impairment.

Science.gov (United States)

Leybaert, Jacqueline; Macchi, Lucie; Huyse, Aurélie; Champoux, François; Bayard, Clémence; Colin, Cécile; Berthommier, Frédéric

2014-01-01

Audiovisual speech perception of children with specific language impairment (SLI) and children with typical language development (TLD) was compared in two experiments using /aCa/ syllables presented in the context of a masking release paradigm. Children had to repeat syllables presented in auditory alone, visual alone (speechreading), audiovisual congruent and incongruent (McGurk) conditions. Stimuli were masked by either stationary (ST) or amplitude modulated (AM) noise. Although children with SLI were less accurate in auditory and audiovisual speech perception, they showed similar auditory masking release effect than children with TLD. Children with SLI also had less correct responses in speechreading than children with TLD, indicating impairment in phonemic processing of visual speech information. In response to McGurk stimuli, children with TLD showed more fusions in AM noise than in ST noise, a consequence of the auditory masking release effect and of the influence of visual information. Children with SLI did not show this effect systematically, suggesting they were less influenced by visual speech. However, when the visual cues were easily identified, the profile of responses to McGurk stimuli was similar in both groups, suggesting that children with SLI do not suffer from an impairment of audiovisual integration. An analysis of percent of information transmitted revealed a deficit in the children with SLI, particularly for the place of articulation feature. Taken together, the data support the hypothesis of an intact peripheral processing of auditory speech information, coupled with a supra modal deficit of phonemic categorization in children with SLI. Clinical implications are discussed.

Phytoplasma PMU1 exists as linear chromosomal and circular extrachromosomal elements and has enhanced expression in insect vectors compared with plant hosts.

Science.gov (United States)

Toruño, Tania Y; Musić, Martina Seruga; Simi, Silvia; Nicolaisen, Mogens; Hogenhout, Saskia A

2010-09-01

Phytoplasmas replicate intracellularly in plants and insects and are dependent on both hosts for dissemination in nature. Phytoplasmas have small genomes lacking genes for major metabolic pathways. Nevertheless, their genomes harbour multicopy gene clusters that were named potential mobile units (PMUs). PMU1 is the largest most complete repeat among the PMUs in the genome of Aster Yellows phytoplasma strain Witches' Broom (AY-WB). PMU1 is c. 20 kb in size and contains 21 genes encoding DNA replication and predicted membrane-targeted proteins. Here we show that AY-WB has a chromosomal linear PMU1 (L-PMU1) and an extrachromosomal circular PMU1 (C-PMU1). The C-PMU1 copy number was consistently higher by in average approximately fivefold in insects compared with plants and PMU1 gene expression levels were also considerably higher in insects indicating that C-PMU1 synthesis and expression are regulated. We found that the majority of AY-WB virulence genes lie on chromosomal PMU regions that have similar gene content and organization as PMU1 providing evidence that PMUs contribute to phytoplasma host adaptation and have integrated into the AY-WB chromosome. © 2010 Blackwell Publishing Ltd.

Desempeño en lectura inicial de escolares con TEL que presentan problemas fonológicos o morfosintácticos

Directory of Open Access Journals (Sweden)

Carmen Julia Coloma

2010-01-01

Full Text Available The objective of this study is to give more information about the impact of primary school student's phonological problems and morphosyntactic problems in initial reading with Specific Language Impairment (SLI. We used a study group of 18 school students with SLI. and a control group of 30 individuals with typical language development. Among the children with SLI, twelve presented phonological problems and the other six had morpho-syntactical problems. All were evaluated in phonology, morphosyntax and initial reading. The results indicate that children with SLI have a significantly lower performance in initial reading when compared with the control group. Moreover, it was noted that the initial reading problems and word decoding problems were mainly in school students with morphosyntactic problems.

Dicty_cDB: SLH242 [Dicty_cDB

Lifescience Database Archive (English)

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Dicty_cDB: SLH222 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available SL (Link to library) SLH222 (Link to dictyBase) - - - Contig-U16475-1 SLH222Z (Link... to Original site) - - SLH222Z 433 - - - - Show SLH222 Library SL (Link to library) Clone ID SLH222 (Link to...ycdb.biol.tsukuba.ac.jp/CSM/SL/SLH2-A/SLH222Q.Seq.d/ Representative seq. ID SLH22...2Z (Link to Original site) Representative DNA sequence >SLH222 (SLH222Q) /CSM/SL/SLH2-A/SLH222Q.Seq.d/ XXXXX...603Q.Seq.d/ 728 0.0 SLI537 (SLI537Q) /CSM/SL/SLI5-B/SLI537Q.Seq.d/ 728 0.0 SLH222 (SLH222Q) /CSM/SL/SLH2

Verbal declarative memory impairments in specific language impairment are related to working memory deficits

OpenAIRE

Lum, Jarrad A.G.; Ullman, Michael T.; Conti-Ramsden, Gina

2015-01-01

This study examined verbal declarative memory functioning in SLI and its relationship to working memory. Encoding, recall, and recognition of verbal information was examined in children with SLI who had below average working memory (SLILow WM), children with SLI who had average working memory (SLIAvg. WM) and, a group of non-language impaired children with average working memory (TDAvg. WM). The SLILow WM group was significantly worse than both the SLIAvg. WM and TDAvg. WM groups at encoding ...

Operational experience with synchrotron light interferometers for CEBAF experimental beam lines

Energy Technology Data Exchange (ETDEWEB)

Pavel Chevtsov

2006-10-24

Beam size and energy spread monitoring systems based on Synchrotron Light Interferometers (SLI) have been in operations at Jefferson Lab for several years. A non-invasive nature and a very high (a few mm) resolution of SLI make these instruments valuable beam diagnostic tools for the CEBAF accelerator. This presentation describes the evolution of the Synchrotron Light Interferometer at Jefferson Lab and highlights our extensive experience in the installation and operation of the SLI for CEBAF experimental beam lines.

The representation of roots in the spelling of children with specific language impairment.

Science.gov (United States)

Deacon, S Hélène; Cleave, Patricia L; Baylis, Julia; Fraser, Jillian; Ingram, Elizabeth; Perlmutter, Signy

2014-01-01

Children with Specific Language Impairment (SLI) have demonstrated general spelling and writing difficulties. We investigated the sensitivity of children with SLI to the consistent spelling of root morphemes, a feature to which young typically developing children demonstrate sensitivity. We asked children with SLI and two groups of typically developing children (n = 17 in each group) to spell the same letter-sound sequence (e.g., win) as a root, and as a component of inflected, derived, and control words (e.g., win, wins, winner, wink). Children with SLI and spelling-age-matched children (mean age of 9 and 7 years, respectively) were more accurate and more consistent in spelling the initial sections of the inflected and derived words than of the control words, a pattern that suggests sensitivity to the representation of roots in spelling. The absence of a group-level interaction suggests comparable sensitivity in the two groups. Our results suggest that elementary-school-aged children with SLI are sensitive to the consistent spelling of roots, at least to the extent predicted by their general spelling abilities.

First-order and higher order sequence learning in specific language impairment.

Science.gov (United States)

Clark, Gillian M; Lum, Jarrad A G

2017-02-01

A core claim of the procedural deficit hypothesis of specific language impairment (SLI) is that the disorder is associated with poor implicit sequence learning. This study investigated whether implicit sequence learning problems in SLI are present for first-order conditional (FOC) and higher order conditional (HOC) sequences. Twenty-five children with SLI and 27 age-matched, nonlanguage-impaired children completed 2 serial reaction time tasks. On 1 version, the sequence to be implicitly learnt comprised a FOC sequence and on the other a HOC sequence. Results showed that the SLI group learned the HOC sequence (η p ² = .285, p = .005) but not the FOC sequence (η p ² = .099, p = .118). The control group learned both sequences (FOC η p ² = .497, HOC η p 2= .465, ps < .001). The SLI group's difficulty learning the FOC sequence is consistent with the procedural deficit hypothesis. However, the study provides new evidence that multiple mechanisms may underpin the learning of FOC and HOC sequences. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Impact of specific language impairment and type of school on different language subsystems.

Science.gov (United States)

Puglisi, Marina Leite; Befi-Lopes, Debora Maria

2016-01-01

This study aimed to explore quantitative and qualitative effects of type of school and specific language impairment (SLI) on different language abilities. 204 Brazilian children aged from 4 to 6 years old participated in the study. Children were selected to form three groups: 1) 63 typically developing children studying in private schools (TDPri); 2) 102 typically developing children studying in state schools (TDSta); and 39 children with SLI studying in state schools (SLISta). All individuals were assessed regarding expressive vocabulary, number morphology and morphosyntactic comprehension. All language subsystems were vulnerable to both environmental (type of school) and biological (SLI) effects. The relationship between the three language measures was exactly the same to all groups: vocabulary growth correlated with age and with the development of morphological abilities and morphosyntactic comprehension. Children with SLI showed atypical errors in the comprehension test at the age of 4, but presented a pattern of errors that gradually resembled typical development. The effect of type of school was marked by quantitative differences, while the effect of SLI was characterised by both quantitative and qualitative differences.

Effect of polyvinylpyrrolidone and sodium lauroyl isethionate on kaolinite suspension in an aqueous phase.

Science.gov (United States)

Kwan, Chang-Chin; Chu, Wen-Hweu; Shimabayashi, Saburo

2006-08-01

Suspension of concentrated kaolinite (20 g/30 ml-medium) in the presence of polyvinylpyrrolidone (PVP) and sodium lauroyl isethionate (SLI) was allowed to evaluate its degree of dispersion based on their rheological studies. Flow curves at low shear rate, measured by means of cone-plate method, showed a non-Newtonian flow. Plastic viscosity and Bingham yield value were derived from the flow curves. Relative viscosity, effective volume fraction and void fraction of secondary particle were also obtained. Results of dispersity and fluidity of the suspension were explained. PVP acted as a flocculant at a concentration lower than 0.1% but as a dispersant at a higher concentration. The presence of SLI could decrease both the Bingham yield value and suspension viscosity. Cooperative and competitive effects of PVP and SLI were found. Results indicated that SLI enhanced the degree of dispersion of kaolinite when PVP was less than 0.1%. The suspension, however, showed a maximum flocculation (i.e., aggregation) at 4 mM SLI when the concentration of PVP was higher than 0.1%.

Association between language development and auditory processing disorders

Directory of Open Access Journals (Sweden)

Caroline Nunes Rocha-Muniz

2014-06-01

Full Text Available INTRODUCTION: It is crucial to understand the complex processing of acoustic stimuli along the auditory pathway ;comprehension of this complex processing can facilitate our understanding of the processes that underlie normal and altered human communication. AIM: To investigate the performance and lateralization effects on auditory processing assessment in children with specific language impairment (SLI, relating these findings to those obtained in children with auditory processing disorder (APD and typical development (TD. MATERIAL AND METHODS: Prospective study. Seventy-five children, aged 6-12 years, were separated in three groups: 25 children with SLI, 25 children with APD, and 25 children with TD. All went through the following tests: speech-in-noise test, Dichotic Digit test and Pitch Pattern Sequencing test. RESULTS: The effects of lateralization were observed only in the SLI group, with the left ear presenting much lower scores than those presented to the right ear. The inter-group analysis has shown that in all tests children from APD and SLI groups had significantly poorer performance compared to TD group. Moreover, SLI group presented worse results than APD group. CONCLUSION: This study has shown, in children with SLI, an inefficient processing of essential sound components and an effect of lateralization. These findings may indicate that neural processes (required for auditory processing are different between auditory processing and speech disorders.

Using electronic storybooks to support word learning in children with severe language impairments.

Science.gov (United States)

Smeets, Daisy J H; van Dijken, Marianne J; Bus, Adriana G

2014-01-01

Novel word learning is reported to be problematic for children with severe language impairments (SLI). In this study, we tested electronic storybooks as a tool to support vocabulary acquisition in SLI children. In Experiment 1, 29 kindergarten SLI children heard four e-books each four times: (a) two stories were presented as video books with motion pictures, music, and sounds, and (b) two stories included only static illustrations without music or sounds. Two other stories served as the control condition. Both static and video books were effective in increasing knowledge of unknown words, but static books were most effective. Experiment 2 was designed to examine which elements in video books interfere with word learning: video images or music or sounds. A total of 23 kindergarten SLI children heard 8 storybooks each four times: (a) two static stories without music or sounds, (b) two static stories with music or sounds, (c) two video stories without music or sounds, and (d) two video books with music or sounds. Video images and static illustrations were equally effective, but the presence of music or sounds moderated word learning. In children with severe SLI, background music interfered with learning. Problems with speech perception in noisy conditions may be an underlying factor of SLI and should be considered in selecting teaching aids and learning environments. © Hammill Institute on Disabilities 2012.

An Investigation to Validate the Grammar and Phonology Screening (GAPS) Test to Identify Children with Specific Language Impairment

Science.gov (United States)

van der Lely, Heather K. J.; Payne, Elisabeth; McClelland, Alastair

2011-01-01

Background The extraordinarily high incidence of grammatical language impairments in developmental disorders suggests that this uniquely human cognitive function is “fragile”. Yet our understanding of the neurobiology of grammatical impairments is limited. Furthermore, there is no “gold-standard” to identify grammatical impairments and routine screening is not undertaken. An accurate screening test to identify grammatical abilities would serve the research, health and education communities, further our understanding of developmental disorders, and identify children who need remediation, many of whom are currently un-diagnosed. A potential realistic screening tool that could be widely administered is the Grammar and Phonology Screening (GAPS) test – a 10 minute test that can be administered by professionals and non-professionals alike. Here we provide a further step in evaluating the validity and accuracy (sensitivity and specificity) of the GAPS test in identifying children who have Specific Language Impairment (SLI). Methods and Findings We tested three groups of children; two groups aged 3;6–6:6, a typically developing (n = 30) group, and a group diagnosed with SLI: (n = 11) (Young (Y)-SLI), and a further group aged 6;9–8;11 with SLI (Older (O)-SLI) (n = 10) who were above the test age norms. We employed a battery of language assessments including the GAPS test to assess the children's language abilities. For Y-SLI children, analyses revealed a sensitivity and specificity at the 5th and 10th percentile of 1.00 and 0.98, respectively, and for O-SLI children at the 10th and 15th percentile .83 and .90, respectively. Conclusions The findings reveal that the GAPS is highly accurate in identifying impaired vs. non-impaired children up to 6;8 years, and has moderate-to-high accuracy up to 9 years. The results indicate that GAPS is a realistic tool for the early identification of grammatical abilities and impairment in young children. A larger

Executive and intellectual functioning in school-aged children with specific language impairment.

Science.gov (United States)

Kuusisto, Marika A; Nieminen, Pirkko E; Helminen, Mika T; Kleemola, Leenamaija

2017-03-01

Earlier research and clinical practice show that specific language impairment (SLI) is often associated with nonverbal cognitive deficits and weakened skills in executive functions (EFs). Executive deficits may have a remarkable influence on a child's everyday activities in the home and school environments. However, research information is still limited on EFs in school-aged children with SLI, mostly conducted among English- and Dutch-speaking children. To study whether there are differences in EFs between Finnish-speaking children with SLI and typically developing (TD) peers at school age. EFs are compared between the groups with and without controlling for nonverbal intelligence. Parents and teachers of children with SLI (n = 22) and age- and gender-matched TD peers (n = 22) completed The Behavior Rating Inventory of Executive Functions (BRIEF). The mean age of the children was 8,2 years. BRIEF ratings of parents and teachers were compared between the children with SLI and with TD peers by paired analysis using conditional logistic regression models with and without controlling for nonverbal IQ. Intellectual functioning was assessed with the Wechsler Intelligence Scale for Children. Children with SLI had weaker scores in all parent and teacher BRIEF scales compared with TD peers. Statistically significant differences between the groups were found in BRIEF scales Shift, Emotional Control, Initiate, Working Memory, Plan/Organize and Monitor. Differences between the groups were statistically significant also in intellectual functioning. On BRIEF scales some group differences remained statistically significant after controlling for nonverbal IQ. This study provides additional evidence that also Finnish-speaking school-aged children with SLI are at risk of having deficits in EFs in daily life. EFs have been proposed to have an impact on developmental outcomes later in life. In clinical practice it is important to pay attention to EFs in school-aged children with SLI

Gesture-speech integration in children with specific language impairment.

Science.gov (United States)

Mainela-Arnold, Elina; Alibali, Martha W; Hostetter, Autumn B; Evans, Julia L

2014-11-01

Previous research suggests that speakers are especially likely to produce manual communicative gestures when they have relative ease in thinking about the spatial elements of what they are describing, paired with relative difficulty organizing those elements into appropriate spoken language. Children with specific language impairment (SLI) exhibit poor expressive language abilities together with within-normal-range nonverbal IQs. This study investigated whether weak spoken language abilities in children with SLI influence their reliance on gestures to express information. We hypothesized that these children would rely on communicative gestures to express information more often than their age-matched typically developing (TD) peers, and that they would sometimes express information in gestures that they do not express in the accompanying speech. Participants were 15 children with SLI (aged 5;6-10;0) and 18 age-matched TD controls. Children viewed a wordless cartoon and retold the story to a listener unfamiliar with the story. Children's gestures were identified and coded for meaning using a previously established system. Speech-gesture combinations were coded as redundant if the information conveyed in speech and gesture was the same, and non-redundant if the information conveyed in speech was different from the information conveyed in gesture. Children with SLI produced more gestures than children in the TD group; however, the likelihood that speech-gesture combinations were non-redundant did not differ significantly across the SLI and TD groups. In both groups, younger children were significantly more likely to produce non-redundant speech-gesture combinations than older children. The gesture-speech integration system functions similarly in children with SLI and TD, but children with SLI rely more on gesture to help formulate, conceptualize or express the messages they want to convey. This provides motivation for future research examining whether interventions

Semantic Differences of Definitional skills between Persian Speaking Children with Specific Language Impairment and Normal Language Developing Children

Directory of Open Access Journals (Sweden)

Mehri Mohammadi

2011-07-01

Full Text Available Objective: Linguistic and metalinguistic knowledge are the effective factors for definitional skills. This study investigated definitional skills both content and form in children with specific language impairment. Materials and Method: The participants were 32 Children in two groups of 16 SLI and 16 normal children, matched with age, sex and educational level. The SLI group was referred from Learning Difficulties Centers and Zarei Rehabilitation Center in Tehran, as well as the control group who was selected by randomized sampling from normal primary schools. The stimuli were 14 high frequency nouns from seven different categories. The reliability was calculated by interjudge agreement and the validity was assessed by content. Data was analyzed using independent T-test. Results: There were significant differences between mean scores of content and form of the definitional skills in two groups. The mean and SD scores of the content of word definition were M= 45.87, SD=12.22 in control group and M=33.18, SD= 17.60 for SLI one, out of possible 70 points (P= 0.025. The mean and SD scores of the form of word definition were M= 48.87, SD= 9.49 in control group and M= 38.18, SD= 12.85 for SLI one, out of 70 points (P= 0.012. Conclusion: Based on the results, it was concluded that, language problems of the SLI children may not let them semantic represention in order to form and present a complete process of word definition. Although this skill in children with SLI is inadequate, all the definitions given by SLI children were consistent with the categories of content and form of word definition used in this study. Therefore, an exact planning and intervention by speech and language pathologist can be effective for this skill. Linguistic intervention especially in semantic and grammatical aspects not only improves the definition of familiar words but also it might be useful for the definition of new words, consequently lead to educational and

Multilingual home environment and specific language impairment: a case-control study in Chinese children.

Science.gov (United States)

Cheuk, Daniel Ka Leung; Wong, Virginia; Leung, Gabriel Matthew

2005-07-01

Specific language impairment (SLI) is a common developmental disorder in young children. To investigate the association between multilingual home environment and SLI, we conducted a case-control study in Hong Kong Chinese children over a 4-year period in the Duchess of Kent Children's Hospital. Consecutive medical records of all new referrals below 5 years of age were reviewed and children diagnosed with SLI (case) were compared with those referred with other developmental and behavioural problems who had been assessed as having normal language and overall development (control) using the Griffiths Mental Developmental Scale. SLI was defined as those with a language quotient more than one standard deviation below the mean and below the general developmental quotient in children with normal general developmental quotient, but without neurological or other organic diseases. We used binary and ordinal logistic regression to assess any association between SLI and multilingual exposure at home, adjusting for age and gender of subjects, parental age, education level and occupational status, number of siblings, family history of language delay and main caregiver at home. Multivariable linear regression was used to examine the effect of covariates on the language comprehension and expression standard scores assessed by the Reynell Developmental Language Scale. A total of 326 cases and 304 controls were included. The mean ages of cases and controls were 2.56 and 2.89 years respectively. Boys predominated in both groups (cases, 75.2%; controls, 60.2%). The children were exposed to between one and four languages at home, the major ones being Cantonese Chinese followed by English. The adjusted odds ratio (OR) of SLI was 2.94; [95% confidence interval (CI) 1.82, 4.74] for multilingual compared with monolingual exposure. A significant linear dose-response relationship was found (OR of SLI = 2.58 [1.72, 3.88] for each additional language to which the child was exposed). Male

Methods for Identifying Specific Language Impairment in Bilingual Populations in Germany

Directory of Open Access Journals (Sweden)

Cornelia Hamann

2017-10-01

Full Text Available This study investigates the performance of 22 monolingual and 54 bilingual children with and without specific language impairment (SLI, in a non-word repetition task (NWRT and a sentence repetition task (SRT. Both tasks were constructed according to the principles for LITMUS tools (Language Impairment Testing in Multilingual Settings developed within COST Action IS0804 and incorporated phonological or syntactic structures that are linguistically complex and have been shown to be difficult for children with SLI across languages. For phonology these are in particular (nonwords containing consonant clusters. In morphosyntax, complexity has been attributed to factors such as embedding and/or syntactic movement. Tasks focusing on such structures are expected to identify SLI in bilinguals across language combinations. This is notoriously difficult because structures that are problematic for typically developing bilinguals (BiTDs and monolingual children with SLI (MoSLI often overlap. We show that the NWRT and the SRT are reliable tools for identification of SLI in bilingual contexts. However, interpretation of the performance of bilingual children depends on background information as provided by parental questionnaires. To evaluate the accuracy of our tasks, we recruited children in ordinary kindergartens or schools and in speech language therapy centers and verified their status with a battery of standardized language tests, assessing bilingual children in both their languages. We consider a bilingual child language impaired if she shows impairments in two language domains in both her languages. For assessment, we used tests normed for monolinguals (with one exception and adjusted the norms for bilingualism and for language dominance. This procedure established the following groups: 10 typical monolinguals (MoTD, 12 MoSLI, 46 BiTD, and 8 bilingual children with SLI (BiSLI. Our results show that both tasks target relevant structures: monolingual

Dicty_cDB: SLH286 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available SL (Link to library) SLH286 (Link to dictyBase) - - - Contig-U16366-1 SLH286Z (Link... to Original site) - - SLH286Z 386 - - - - Show SLH286 Library SL (Link to library) Clone ID SLH286 (Link to...ycdb.biol.tsukuba.ac.jp/CSM/SL/SLH2-D/SLH286Q.Seq.d/ Representative seq. ID SLH28...6Z (Link to Original site) Representative DNA sequence >SLH286 (SLH286Q) /CSM/SL/SLH2-D/SLH286Q.Seq.d/ XXXXX...Seq.d/ 646 0.0 SLK513 (SLK513Q) /CSM/SL/SLK5-A/SLK513Q.Seq.d/ 646 0.0 SLI160 (SLI160Q) /CSM/SL/SLI1-C/SLI160Q.Seq.d/ 646 0.0 SLH2

Gene capture from across the grass family in the allohexaploid Elymus repens (L.) Gould (Poaceae, Triticeae) as evidenced by ITS, GBSSI, and molecular cytogenetics.

Science.gov (United States)

Mahelka, Václav; Kopecký, David

2010-06-01

Four accessions of hexaploid Elymus repens from its native Central European distribution area were analyzed using sequencing of multicopy (internal transcribed spacer, ITS) and single-copy (granule-bound starch synthase I, GBSSI) DNA in concert with genomic and fluorescent in situ hybridization (GISH and FISH) to disentangle its allopolyploid origin. Despite extensive ITS homogenization, nrDNA in E. repens allowed us to identify at least four distinct lineages. Apart from Pseudoroegneria and Hordeum, representing the major genome constituents, the presence of further unexpected alien genetic material, originating from species outside the Triticeae and close to Panicum (Paniceae) and Bromus (Bromeae), was revealed. GBSSI sequences provided information complementary to the ITS. Apart from Pseudoroegneria and Hordeum, two additional gene variants from within the Triticeae were discovered: One was Taeniatherum-like, but the other did not have a close relationship with any of the diploids sampled. GISH results were largely congruent with the sequence-based markers. GISH clearly confirmed Pseudoroegneria and Hordeum as major genome constituents and further showed the presence of a small chromosome segment corresponding to Panicum. It resided in the Hordeum subgenome and probably represents an old acquisition of a Hordeum progenitor. Spotty hybridization signals across all chromosomes after GISH with Taeniatherum and Bromus probes suggested that gene acquisition from these species is more likely due to common ancestry of the grasses or early introgression than to recent hybridization or allopolyploid origin of E. repens. Physical mapping of rDNA loci using FISH revealed that all rDNA loci except one minor were located on Pseudoroegneria-derived chromosomes, which suggests the loss of all Hordeum-derived loci but one. Because homogenization mechanisms seem to operate effectively among Pseudoroegneria-like copies in this species, incomplete ITS homogenization in our samples

The impact of specific language impairment on working memory in children with ADHD combined type

OpenAIRE

Jondottir, S.; Bouma, A.; Sergeant, J.A.; Scherder, E.J.A.

2005-01-01

The objective of this study was to examine the impact of comorbid specific language impairment (SLI) on verbal and spatial working memory in children with DSM-IV combined subtype Attention Deficit Hyperactivity Disorder (ADHD-C). Participants were a clinical sample of 81/2- to 121/2-year-old children diagnosed with ADHD-C. A group of ADHD-C with SLI was compared to a group of ADHD-C without SLI, and a group of normal children, matched on age and nonverbal intelligence. The results show that A...

The impact of specific language impairment on working memory children with ADHD combined subtype

OpenAIRE

Jonsdottir, S.; Bouma, A.; Sergeant, J.A.; Scherder, E.J.A.

2005-01-01

The objective of this study was to examine the impact of comorbid specific language impairment (SLI) on verbal and spatial working memory in children with DSM-IV combined subtype Attention Deficit Hyperactivity Disorder (ADHD-C). Participants were a clinical sample of 81/2- to 121/2-year-old children diagnosed with ADHD-C. A group of ADHD-C with SLI was compared to a group of ADHD-C without SLI, and a group of normal children, matched on age and nonverbal intelligence. The results show that A...

Health-Related Quality of Life for Children and Adolescents with Specific Language Impairment: A Cohort Study by a Learning Disabilities Reference Center.

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Gaëlle Hubert-Dibon

Full Text Available To assess the health-related quality of life (HRQOL of children with specific language impairment (SLI.In a prospective sample at a Learning Disabilities Reference Center, proxy-rated HRQOL (KIDSCREEN-27 was assessed for children with SLI and unaffected children from January 1, 2014 to March 31, 2015. Quality of life predictors for children with SLI were evaluated by recording the length and number of speech therapy and psychotherapy sessions and the specific school organization that the children had participated in. The KIDSCREEN scores of the two groups were compared using nonparametric statistics.The questionnaires were completed by the parents of 67 children with SLI and 67 unaffected children. For children with SLI, the mean HRQOL scores were significantly lower for physical and psychological well-being, autonomy and parent relation, social support, and school environment compared to the reference group, controlling for age and parental education (β = -6.7 (-12.7;-.7 P = 0.03, β = -4.9 (-9.5;-.3 P = 0.04, β = -8.4 (-14.2;-2.6 P = 0.005, β = -11.6 (-19.5;-3.7 P = 0.004, β = -7.1(-12.4;-1.7 P = 0.010, respectively. Multivariate analyses in the group of children with SLI found that children who had undergone psychotherapy sessions or who had been enrolled in specific schooling programs had reduced HRQOL scores in social support and school environment and that children who were in a special class had higher scores in physical well-being.Children with SLI had significantly lower HRQOL scores as compared to unaffected children. Measurement of HRQOL could serve as one of the strategies employed throughout the follow-up of these individuals to provide them with the most appropriate and comprehensive care possible.

Health-Related Quality of Life for Children and Adolescents with Specific Language Impairment: A Cohort Study by a Learning Disabilities Reference Center.

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Hubert-Dibon, Gaëlle; Bru, Marie; Gras Le Guen, Christèle; Launay, Elise; Roy, Arnaud

2016-01-01

To assess the health-related quality of life (HRQOL) of children with specific language impairment (SLI). In a prospective sample at a Learning Disabilities Reference Center, proxy-rated HRQOL (KIDSCREEN-27) was assessed for children with SLI and unaffected children from January 1, 2014 to March 31, 2015. Quality of life predictors for children with SLI were evaluated by recording the length and number of speech therapy and psychotherapy sessions and the specific school organization that the children had participated in. The KIDSCREEN scores of the two groups were compared using nonparametric statistics. The questionnaires were completed by the parents of 67 children with SLI and 67 unaffected children. For children with SLI, the mean HRQOL scores were significantly lower for physical and psychological well-being, autonomy and parent relation, social support, and school environment compared to the reference group, controlling for age and parental education (β = -6.7 (-12.7;-.7) P = 0.03, β = -4.9 (-9.5;-.3) P = 0.04, β = -8.4 (-14.2;-2.6) P = 0.005, β = -11.6 (-19.5;-3.7) P = 0.004, β = -7.1(-12.4;-1.7) P = 0.010, respectively). Multivariate analyses in the group of children with SLI found that children who had undergone psychotherapy sessions or who had been enrolled in specific schooling programs had reduced HRQOL scores in social support and school environment and that children who were in a special class had higher scores in physical well-being. Children with SLI had significantly lower HRQOL scores as compared to unaffected children. Measurement of HRQOL could serve as one of the strategies employed throughout the follow-up of these individuals to provide them with the most appropriate and comprehensive care possible.

Statistical Learning in Specific Language Impairment and Autism Spectrum Disorder: A Meta-Analysis

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Rita Obeid

2016-08-01

Full Text Available Impairments in statistical learning might be a common deficit among individuals with Specific Language Impairment (SLI and Autism Spectrum Disorder (ASD. Using meta-analysis, we examined statistical learning in SLI (14 studies, 15 comparisons and ASD (13 studies, 20 comparisons to evaluate this hypothesis. Effect sizes were examined as a function of diagnosis across multiple statistical learning tasks (Serial Reaction Time, Contextual Cueing, Artificial Grammar Learning, Speech Stream, Observational Learning, Probabilistic Classification. Individuals with SLI showed deficits in statistical learning relative to age-matched controls g = .47, 95% CI [.28, .66], p < .001. In contrast, statistical learning was intact in individuals with ASD relative to controls, g = –.13, 95% CI [–.34, .08], p = .22. Effect sizes did not vary as a function of task modality or participant age. Our findings inform debates about overlapping social-communicative difficulties in children with SLI and ASD by suggesting distinct underlying mechanisms. In line with the procedural deficit hypothesis (Ullman & Pierpont, 2005, impaired statistical learning may account for phonological and syntactic difficulties associated with SLI. In contrast, impaired statistical learning fails to account for the social-pragmatic difficulties associated with ASD.

Delay or deficit? Spelling processes in children with specific language impairment.

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Larkin, Rebecca F; Williams, Gareth J; Blaggan, Samarita

2013-01-01

Few studies have explored the phonological, morphological and orthographic spellings skills of children with specific language impairment (SLI) simultaneously. Fifteen children with SLI (mean age=113.07 months, SD=8.61) completed language and spelling tasks alongside chronological-age controls and spelling-age controls. While the children with SLI showed a deficit in phonological spelling, they performed comparably to spelling-age controls on morphological spelling skills, and there were no differences between the three groups in producing orthographically legal spellings. The results also highlighted the potential importance of adequate non-word repetition skills in relation to effective spelling skills, and demonstrated that not all children with spoken language impairments show marked spelling difficulties. Findings are discussed in relation to theory, educational assessment and practice. As a result of this activity, readers will describe components of spoken language that predict children's morphological and phonological spelling performance. As a result of this activity, readers will describe how the spelling skills of children with SLI compare to age-matched and spelling age-matched control children. Readers will be able to interpret the variability in spelling performance seen in children with SLI. Copyright © 2013 Elsevier Inc. All rights reserved.

Low-level neural auditory discrimination dysfunctions in specific language impairment—A review on mismatch negativity findings

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Teija Kujala

2017-12-01

Full Text Available In specific language impairment (SLI, there is a delay in the child’s oral language skills when compared with nonverbal cognitive abilities. The problems typically relate to phonological and morphological processing and word learning. This article reviews studies which have used mismatch negativity (MMN in investigating low-level neural auditory dysfunctions in this disorder. With MMN, it is possible to tap the accuracy of neural sound discrimination and sensory memory functions. These studies have found smaller response amplitudes and longer latencies for speech and non-speech sound changes in children with SLI than in typically developing children, suggesting impaired and slow auditory discrimination in SLI. Furthermore, they suggest shortened sensory memory duration and vulnerability of the sensory memory to masking effects. Importantly, some studies reported associations between MMN parameters and language test measures. In addition, it was found that language intervention can influence the abnormal MMN in children with SLI, enhancing its amplitude. These results suggest that the MMN can shed light on the neural basis of various auditory and memory impairments in SLI, which are likely to influence speech perception. Keywords: Specific language impairment, Auditory processing, Mismatch negativity (MMN

Frequency of educational computer use as a longitudinal predictor of educational outcome in young people with specific language impairment.

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Kevin Durkin

Full Text Available Computer use draws on linguistic abilities. Using this medium thus presents challenges for young people with Specific Language Impairment (SLI and raises questions of whether computer-based tasks are appropriate for them. We consider theoretical arguments predicting impaired performance and negative outcomes relative to peers without SLI versus the possibility of positive gains. We examine the relationship between frequency of computer use (for leisure and educational purposes and educational achievement; in particular examination performance at the end of compulsory education and level of educational progress two years later. Participants were 49 young people with SLI and 56 typically developing (TD young people. At around age 17, the two groups did not differ in frequency of educational computer use or leisure computer use. There were no associations between computer use and educational outcomes in the TD group. In the SLI group, after PIQ was controlled for, educational computer use at around 17 years of age contributed substantially to the prediction of educational progress at 19 years. The findings suggest that educational uses of computers are conducive to educational progress in young people with SLI.

The production of direct object clitics in pre-school- and primary school-aged children with specific language impairments.

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Guasti, Maria Teresa; Palma, Silvia; Genovese, Elisabetta; Stagi, Paolo; Saladini, Gabriella; Arosio, Fabrizio

2016-01-01

Third-person direct object (DO) clitic pronoun production is examined through an elicited production method in pre-school- and primary school-aged groups of Italian children with specific language impairment (SLI) to establish whether there is an improvement from age 5 years to age 7 years and whether there are qualitative differences in the two groups' responses. It was found that 5- and 7-year-old Italian children with SLI produce fewer third-person DO clitics than same-age peers. The kind of responses they provide changes: at 5 years, children with SLI tend to omit clitics, while at 7 years, they use a full noun. Production of third-person DO clitics is a persistent challenge for children with SLI and is confirmed to be a good clinical marker both at 5 and 7 years of age.

Generalized motor abilities and timing behavior in children with specific language impairment.

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Zelaznik, Howard N; Goffman, Lisa

2010-04-01

To examine whether children with specific language impairment (SLI) differ from normally developing peers in motor skills, especially those skills related to timing. Standard measures of gross and fine motor development were obtained. Furthermore, finger and hand movements were recorded while children engaged in 4 different timing tasks, including tapping and drawing circles in time with a metronome or a visual target. Fourteen children with SLI (age 6 to 8 years) and 14 age-matched peers who were typically developing participated. As expected, children with SLI showed poorer performance on a standardized test of gross and fine motor skill than did their normally developing peers. However, timing skill in the manual domain was equivalent to that seen in typically developing children. Consistent with earlier findings, relatively poor gross and fine motor performance is observed in children with SLI. Surprisingly, rhythmic timing is spared.

Interactivity in prosodic representations in children.

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Goffman, Lisa; Westover, Stefanie

2013-11-01

The aim of this study was to determine, using speech error and articulatory analyses, whether the binary distinction between iambs and trochees should be extended to include additional prosodic subcategories. Adults, children who are normally developing, and children with specific language impairment (SLI) participated. Children with SLI were included because they exhibit prosodic and motor deficits. Children, especially those with SLI, showed the expected increase in omission errors in weak initial syllables. Movement patterning analyses revealed that speakers produced differentiated articulatory templates beyond the broad categories of iamb and trochee. Finally, weak-weak prosodic sequences that crossed word boundaries showed increased articulatory variability when compared with strong-weak alternations. The binary distinction between iamb and trochee may be insufficient, with additional systematic prosodic subcategories evident, even in young children with SLI. Findings support increased interactivity in language processing.

Language and executive functioning in the context of specific language impairment and bilingualism

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Laloi, A.

2015-01-01

The present thesis has investigated how French-speaking monolingual and bilingual children with SLI (specific language impairment) performed on various tasks examining language and executive functioning (EF) abilities, in comparison to monolingual and bilingual peers without SLI. Language was

The cost of copy number in a selfish genetic element: the 2-μm plasmid of Saccharomyces cerevisiae.

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Harrison, Ellie; Koufopanou, V; Burt, A; MacLean, R C

2012-11-01

Many autonomously replicating genetic elements exist as multiple copies within the cell. The copy number of these elements is often assumed to have important fitness consequences for both element and host, yet the forces shaping its evolution are not well understood. The 2 μm is a multicopy plasmid of Saccharomyces yeasts, encoding just four genes that are solely involved in plasmid replication. One simple model for the fitness relationship between yeasts and 2 μm is that plasmid copy number evolves as a trade-off between selection for increased vertical transmission, favouring high copy number, and selection for decreased virulence, favouring low copy number. To test this model, we experimentally manipulated the copy number of the plasmid and directly measured the fitness cost, in terms of growth rate reduction, associated with high plasmid copy number. We find that the fitness burden imposed by the 2 μm increases with plasmid copy number, such that each copy imposes a fitness burden of 0.17% (± 0.008%), greatly exceeding the cost expected for it to be stably maintained in yeast populations. Our results demonstrate the crucial importance of copy number in the evolution of yeast per 2 μm associations and pave the way for future studies examining how selection can shape the cost of multicopy elements. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Training understanding of reversible sentences: a study comparing language-impaired children with age-matched and grammar-matched controls.

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Hsu, Hsinjen Julie; Bishop, Dorothy V M

2014-01-01

Introduction. Many children with specific language impairment (SLI) have problems with language comprehension, and little is known about how to remediate these. We focused here on errors in interpreting sentences such as "the ball is above the cup", where the spatial configuration depends on word order. We asked whether comprehension of such short reversible sentences could be improved by computerized training, and whether learning by children with SLI resembled that of younger, typically-developing children. Methods. We trained 28 children with SLI aged 6-11 years, 28 typically-developing children aged from 4 to 7 years who were matched to the SLI group for raw scores on a test of receptive grammar, and 20 typically-developing children who were matched to the SLI group on chronological age. A further 20 children with SLI were given pre- and post-test assessments, but did not undergo training. Those in the trained groups were given training on four days using a computer game adopting an errorless learning procedure, during which they had to select pictures to correspond to spoken sentences such as "the cup is above the drum" or "the bird is below the hat". Half the trained children heard sentences using above/below and the other half heard sentences using before/after (with a spatial interpretation). A total of 96 sentences was presented over four sessions. Half the sentences were unique, whereas the remainder consisted of 12 repetitions of each of four sentences that became increasingly familiar as training proceeded. Results. Age-matched control children performed near ceiling (≥ 90% correct) in the first session and were excluded from the analysis. Around half the trained SLI children also performed this well. Training effects were examined in 15 SLI and 16 grammar-matched children who scored less than 90% correct on the initial training session. Overall, children's scores improved with training. Memory span was a significant predictor of improvement, even

Training understanding of reversible sentences: a study comparing language-impaired children with age-matched and grammar-matched controls

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Hsinjen Julie Hsu

2014-11-01

Full Text Available Introduction. Many children with specific language impairment (SLI have problems with language comprehension, and little is known about how to remediate these. We focused here on errors in interpreting sentences such as “the ball is above the cup”, where the spatial configuration depends on word order. We asked whether comprehension of such short reversible sentences could be improved by computerized training, and whether learning by children with SLI resembled that of younger, typically-developing children.Methods. We trained 28 children with SLI aged 6–11 years, 28 typically-developing children aged from 4 to 7 years who were matched to the SLI group for raw scores on a test of receptive grammar, and 20 typically-developing children who were matched to the SLI group on chronological age. A further 20 children with SLI were given pre- and post-test assessments, but did not undergo training. Those in the trained groups were given training on four days using a computer game adopting an errorless learning procedure, during which they had to select pictures to correspond to spoken sentences such as “the cup is above the drum” or “the bird is below the hat”. Half the trained children heard sentences using above/below and the other half heard sentences using before/after (with a spatial interpretation. A total of 96 sentences was presented over four sessions. Half the sentences were unique, whereas the remainder consisted of 12 repetitions of each of four sentences that became increasingly familiar as training proceeded.Results. Age-matched control children performed near ceiling (≥ 90% correct in the first session and were excluded from the analysis. Around half the trained SLI children also performed this well. Training effects were examined in 15 SLI and 16 grammar-matched children who scored less than 90% correct on the initial training session. Overall, children’s scores improved with training. Memory span was a significant

Theory of mind and emotion recognition skills in children with specific language impairment, autism spectrum disorder and typical development: group differences and connection to knowledge of grammatical morphology, word-finding abilities and verbal working memory.

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Loukusa, Soile; Mäkinen, Leena; Kuusikko-Gauffin, Sanna; Ebeling, Hanna; Moilanen, Irma

2014-01-01

Social perception skills, such as understanding the mind and emotions of others, affect children's communication abilities in real-life situations. In addition to autism spectrum disorder (ASD), there is increasing knowledge that children with specific language impairment (SLI) also demonstrate difficulties in their social perception abilities. To compare the performance of children with SLI, ASD and typical development (TD) in social perception tasks measuring Theory of Mind (ToM) and emotion recognition. In addition, to evaluate the association between social perception tasks and language tests measuring word-finding abilities, knowledge of grammatical morphology and verbal working memory. Children with SLI (n = 18), ASD (n = 14) and TD (n = 25) completed two NEPSY-II subtests measuring social perception abilities: (1) Affect Recognition and (2) ToM (includes Verbal and non-verbal Contextual tasks). In addition, children's word-finding abilities were measured with the TWF-2, grammatical morphology by using the Grammatical Closure subtest of ITPA, and verbal working memory by using subtests of Sentence Repetition or Word List Interference (chosen according the child's age) of the NEPSY-II. Children with ASD scored significantly lower than children with SLI or TD on the NEPSY-II Affect Recognition subtest. Both SLI and ASD groups scored significantly lower than TD children on Verbal tasks of the ToM subtest of NEPSY-II. However, there were no significant group differences on non-verbal Contextual tasks of the ToM subtest of the NEPSY-II. Verbal tasks of the ToM subtest were correlated with the Grammatical Closure subtest and TWF-2 in children with SLI. In children with ASD correlation between TWF-2 and ToM: Verbal tasks was moderate, almost achieving statistical significance, but no other correlations were found. Both SLI and ASD groups showed difficulties in tasks measuring verbal ToM but differences were not found in tasks measuring non-verbal Contextual ToM. The

Understanding Conservation Delays in Children with Specific Language Impairment: Task Representations Revealed in Speech and Gesture

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Mainela-Arnold, Elina; Evans, Julia L.; Alibali, Martha W.

2006-01-01

Purpose: The authors investigated mental representations of Piagetian conservation tasks in children with specific language impairment (SLI) and typically developing peers. Children with SLI have normal nonverbal intelligence; however, they exhibit difficulties in Piagetian conservation tasks. The authors tested the hypothesis that conservation…

Identification of a common cyanobacterial symbiont associated with Azolla spp. through molecular and morphological characterization of free-living and symbiotic cyanobacteria.

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Gebhardt, J S; Nierzwicki-Bauer, S A

1991-01-01

Symbiotically associated cyanobacteria from Azolla mexicana and Azolla pinnata were isolated and cultured in a free-living state. Morphological analyses revealed differences between the free-living isolates and their symbiotic counterparts, as did restriction fragment length polymorphism (RFLP) analyses with both single-copy glnA and rbcS gene probes and a multicopy psbA gene probe. RFLP analyses with Anabaena sp. strain PCC 7120 nifD excision element probes, including an xisA gene probe, detected homologous sequences in DNA extracted from the free-living isolates. Sequences homologous to these probes were not detected in DNA from the symbiotically associated cyanobacteria. These analyses indicated that the isolates were not identical to the major cyanobacterial symbiont species residing in leaf cavities of Azolla spp. Nevertheless, striking similarities between several free-living isolates were observed. In every instance, the isolate from A. pinnata displayed banding patterns virtually identical to those of free-living cultures previously isolated from Azolla caroliniana and Azolla filiculoides. These results suggest the ubiquitous presence of a culturable minor cyanobacterial symbiont in at least three species of Azolla. Images PMID:1685078

Yeast Sgf73/Ataxin-7 serves to anchor the deubiquitination module into both SAGA and Slik(SALSA HAT complexes

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Lee Kenneth K

2009-02-01

Full Text Available Abstract Spinocerebellar ataxia (SCA is a physically devastating, genetically inherited disorder characterized by abnormal brain function that results in the progressive loss of the ability to coordinate movements. There are many types of SCAs as there are various gene mutations that can cause this disease. SCA types 1–3, 6–10, 12, and 17 result from a trinucleotide repeat expansion in the DNA-coding sequence. Intriguingly, recent work has demonstrated that increased trinucleotde expansions in the SCA7 gene result in defect in the function of the SAGA histone acetyltransferase complex. The SCA7 gene encodes a subunit of the SAGA complex. This subunit is conserved in yeast as the SGF73 gene. We demonstrate that Sgf73 is required to recruit the histone deubiquitination module into both SAGA and the related SliK(SALSA complex, and to maintain levels of histone ubiquitination, which is necessary for regulation of transcription at a number of genes.

Pragmatic language impairment and associated behavioural problems

NARCIS (Netherlands)

Ketelaars, M.P.; Cuperus, J.; Jansonius, K.; Verhoeven, L.

2010-01-01

Background: Specific language impairment (SLI) is diagnosed when a child shows isolated structural language problems. The diagnosis of pragmatic language impairment (PLI) is given to children who show difficulties with the use of language in context. Unlike children with SLI, these children tend to

Persistent grammatical difficulties in Specific Language Impairment : Deficits in knowledge or in knowledge implementation?

NARCIS (Netherlands)

Duinmeijer, I.

2017-01-01

This study examines the grammatical abilities of children and adolescents with Specific Language Impairment (SLI). There were two research goals. Firstly, the persistence of grammatical problems over time was examined by comparing a younger group of children with SLI and an older group of

Among perinatal factors, only the Apgar score is associated with specific language impairment

NARCIS (Netherlands)

Diepeveen, F.B.; de Kroon, M.L.A.; Dusseldorp, E.; Snik, A.F.M.

2013-01-01

Aim: The purpose of this study was to assess the relation of perinatal risk factors with later development of specific language impairment (SLI). Method: In a case-control study, 179 children attending special needs schools for SLI were matched with non-affected children attending mainstream

Among perinatal factors, only the Apgar score is associated with specific language impairment

NARCIS (Netherlands)

Diepeveen, F.B.; Kroon, M.L. De; Dusseldorp, E.; Snik, A.F.M.

2013-01-01

AIM: The purpose of this study was to assess the relation of perinatal risk factors with later development of specific language impairment (SLI). METHOD: In a case-control study, 179 children attending special needs schools for SLI were matched with non-affected children attending mainstream

Among perinatal factors, only the Apgar score is associated with specific language impairment

NARCIS (Netherlands)

Diepeveen, F.B.; Kroon, M.L. de; Dusseldorp, E.; Snik, A.F.

2013-01-01

The purpose of this study was to assess the relation of perinatal risk factors with later development of specific language impairment (SLI). METHOD: In a case-control study, 179 children attending special needs schools for SLI were matched with non-affected children attending mainstream schools.

75 FR 30013 - South Feather Water and Power Agency; Notice of Availability of Environmental Assessment

Science.gov (United States)

2010-05-28

... Water and Power Agency; Notice of Availability of Environmental Assessment May 20, 2010. In accordance... assessment (EA) regarding South Feather Water and Power Agency's (SFWPA) request to raise the dam crest and... Project (FERC No. 2088). Sly Creek is located on Sly Creek [[Page 30014

Children’s Marking of Verbal –s by Nonmainstream English Dialect and Clinical Status

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Cleveland, Lesli H.; Oetting, Janna B.

2015-01-01

Purpose Children’s marking of verbal –s was examined by their dialect (African American English [AAE] vs. Southern White English [SWE]) and clinical status (specific language impairment [SLI] vs. typically developing [TD]) and as a function of 4 linguistic variables (verb regularity, negation, expression of a habitual activity, and expression of historical present tense). Method The data were language samples from 57 six-year-olds who varied by their dialect and clinical status (AAE: SLI = 14, TD = 12; SWE: SLI = 12, TD = 19). Results The AAE groups produced lower rates of marking than did the SWE groups, and the SWE SLI group produced lower rates of marking than did the SWE TD group. Although low numbers of verb contexts made it difficult to evaluate the linguistic variables, there was evidence of their influence, especially for verb regularity and negation. The direction and magnitude of the effects were often (but not always) consistent with what has been described in the adult dialect literature. Conclusion Verbal –s can be used to help distinguish children with and without SLI in SWE but not in AAE. Clinicians can apply these findings to other varieties of AAE and SWE and other dialects by considering rates of marking and the effects of linguistic variables on marking. PMID:23813205

Input Distribution Influences Degree of Auxiliary Use by Children with Specific Language Impairment.

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Leonard, Laurence B; Deevy, Patricia

2011-04-01

Children with specific language impairment (SLI) show a protracted period of inconsistent use of tense/agreement morphemes. The purpose of this investigation was to determine whether this inconsistent use could be attributed to the children's misinterpretations of particular syntactic structures in the input. In Study 1, preschool-aged children with SLI and typically developing peers heard sentences containing novel verbs preceded by auxiliary was or sentences in which the novel verb formed part of a nonfinite subject-verb sequence within a larger syntactic structure (e.g., We saw the dog relling ). The children were then tested on their use of the novel verbs in contexts that obligated use of auxiliary is . The children with SLI were less accurate than their peers and more likely to produce the novel verb without is if the verb had been heard in a nonfinite subject-verb sequence. In Study 2, children with SLI and typically developing peers were tested on their comprehension of sentences such as The cow sees the horse eating. The children with SLI were less accurate than their peers and were disproportionately influenced by the nonfinite subject-verb clause at the end of the sentence. We interpret these findings within the framework of construction learning.

Do children with dyslexia and/or specific language impairment compensate for place assimilation? Insight into phonological grammar and representations.

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Marshall, Chloe R; Ramus, Franck; van der Lely, Heather

2011-10-01

English speakers have to recognize, for example, that te[m] in te[m] pens is a form of ten, despite place assimilation of the nasal consonant. Children with dyslexia and specific language impairment (SLI) are commonly proposed to have a phonological deficit, and we investigate whether that deficit extends to place assimilation, as a way of probing phonological representations and phonological grammar. Children with SLI plus dyslexia, SLI only, and dyslexia only listened to sentences containing a target word in different assimilatory contexts-viable, unviable, and no change-and pressed a button to report hearing the target. The dyslexia-only group did not differ from age-matched controls, but the SLI groups showed more limited ability to accurately identify words within sentences. Once this factor was taken into account, the groups did not differ in their ability to compensate for assimilation. The results add to a growing body of evidence that phonological representations are not necessarily impaired in dyslexia. SLI children's results suggest that they too are sensitive to this aspect of phonological grammar, but are more liberal in their acceptance of alternative phonological forms of words. Furthermore, these children's ability to reject alternative phonological forms seems to be primarily limited by their vocabulary size and phonological awareness abilities.

Don't speak too fast! Processing of fast rate speech in children with specific language impairment.

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Hélène Guiraud

Full Text Available Perception of speech rhythm requires the auditory system to track temporal envelope fluctuations, which carry syllabic and stress information. Reduced sensitivity to rhythmic acoustic cues has been evidenced in children with Specific Language Impairment (SLI, impeding syllabic parsing and speech decoding. Our study investigated whether these children experience specific difficulties processing fast rate speech as compared with typically developing (TD children.Sixteen French children with SLI (8-13 years old with mainly expressive phonological disorders and with preserved comprehension and 16 age-matched TD children performed a judgment task on sentences produced 1 at normal rate, 2 at fast rate or 3 time-compressed. Sensitivity index (d' to semantically incongruent sentence-final words was measured.Overall children with SLI perform significantly worse than TD children. Importantly, as revealed by the significant Group × Speech Rate interaction, children with SLI find it more challenging than TD children to process both naturally or artificially accelerated speech. The two groups do not significantly differ in normal rate speech processing.In agreement with rhythm-processing deficits in atypical language development, our results suggest that children with SLI face difficulties adjusting to rapid speech rate. These findings are interpreted in light of temporal sampling and prosodic phrasing frameworks and of oscillatory mechanisms underlying speech perception.

Don't speak too fast! Processing of fast rate speech in children with specific language impairment.

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Guiraud, Hélène; Bedoin, Nathalie; Krifi-Papoz, Sonia; Herbillon, Vania; Caillot-Bascoul, Aurélia; Gonzalez-Monge, Sibylle; Boulenger, Véronique

2018-01-01

Perception of speech rhythm requires the auditory system to track temporal envelope fluctuations, which carry syllabic and stress information. Reduced sensitivity to rhythmic acoustic cues has been evidenced in children with Specific Language Impairment (SLI), impeding syllabic parsing and speech decoding. Our study investigated whether these children experience specific difficulties processing fast rate speech as compared with typically developing (TD) children. Sixteen French children with SLI (8-13 years old) with mainly expressive phonological disorders and with preserved comprehension and 16 age-matched TD children performed a judgment task on sentences produced 1) at normal rate, 2) at fast rate or 3) time-compressed. Sensitivity index (d') to semantically incongruent sentence-final words was measured. Overall children with SLI perform significantly worse than TD children. Importantly, as revealed by the significant Group × Speech Rate interaction, children with SLI find it more challenging than TD children to process both naturally or artificially accelerated speech. The two groups do not significantly differ in normal rate speech processing. In agreement with rhythm-processing deficits in atypical language development, our results suggest that children with SLI face difficulties adjusting to rapid speech rate. These findings are interpreted in light of temporal sampling and prosodic phrasing frameworks and of oscillatory mechanisms underlying speech perception.

Oral language and narrative skills in children with specific language impairment with and without literacy delay: a three-year longitudinal study.

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Vandewalle, Ellen; Boets, Bart; Boons, Tinne; Ghesquière, Pol; Zink, Inge

2012-01-01

This longitudinal study compared the development of oral language and more specifically narrative skills (storytelling and story retelling) in children with specific language impairment (SLI) with and without literacy delay. Therefore, 18 children with SLI and 18 matched controls with normal literacy were followed from the last year of kindergarten (mean age=5 years 5 months) until the beginning of grade 3 (mean age=8 years 1 month). Oral language tests measuring vocabulary, morphology, sentence and text comprehension and narrative skills were administered yearly. Based on first and third grade reading and spelling achievement, both groups were divided into a group with and a group without literacy problems. Results showed that the children with SLI and literacy delay had persistent oral language problems across all assessed language domains. The children with SLI and normal literacy skills scored also persistently low on vocabulary, morphology and story retelling skills. Only on listening comprehension and storytelling, they evolved towards the level of the control group. In conclusion, oral language skills in children with SLI and normal literacy skills remained in general poor, despite their intact literacy development during the first years of literacy instruction. Only for listening comprehension and storytelling, they improved, probably as a result of more print exposure. Copyright © 2012 Elsevier Ltd. All rights reserved.

Adaptation to the deep-sea hydrothermal vents and cold seeps: Insights from the transcriptomes of Alvinocaris longirostris in both environments

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Hui, Min; Cheng, Jiao; Sha, Zhongli

2018-05-01

Alvinocaris longirostris Kikuchi and Ohta, 1995 is one of the few species co-distributed in deep-sea hydrothermal vent and cold seep environments. We performed the transcriptome analysis for A. longirostris and identified differentially expressed genes (DEGs) between samples from the Iheya North hydrothermal vent (HV) and a methane seep in the South China Sea (MS). From the 57,801 annotated unigenes, multi-copies of enzyme family members for eliminating toxic xenobiotics were isolated and seven putatively duplicated gene clusters of cytochrome P450s were discovered, which may contribute to adaptation to the harsh conditions. Eight single amino acid substitutions of a Rhodopsin gene with low expression in two deep-sea alvinocaridid species were positively selected when compared with shallow water shrimps, which may be the result of adaptation to the dim-light environment in deep sea. 408 DEGs were identified with 53 and 355 up-regulated in HV and MS, respectively. Various genes associated with sulfur metabolism, detoxification and mitochondria were included, revealing different mechanisms of adaptation to the two types of extreme environments. All results are expected to serve as important basis for the further study.

Auditory Perception and Word Recognition in Cantonese-Chinese Speaking Children with and without Specific Language Impairment

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Kidd, Joanna C.; Shum, Kathy K.; Wong, Anita M.-Y.; Ho, Connie S.-H.

2017-01-01

Auditory processing and spoken word recognition difficulties have been observed in Specific Language Impairment (SLI), raising the possibility that auditory perceptual deficits disrupt word recognition and, in turn, phonological processing and oral language. In this study, fifty-seven kindergarten children with SLI and fifty-three language-typical…

The Relationship between Phonological Short-Term Memory, Receptive Vocabulary, and Fast Mapping in Children with Specific Language Impairment

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Jackson, Emily; Leitao, Suze; Claessen, Mary

2016-01-01

Background: Children with specific language impairment (SLI) often experience word-learning difficulties, which are suggested to originate in the early stage of word learning: fast mapping. Some previous research indicates significantly poorer fast mapping capabilities in children with SLI compared with typically developing (TD) counterparts, with…

Divergence of Verbal Expression and Embodied Knowledge: Evidence from Speech and Gesture in Children with Specific Language Impairment.

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Evans, Julia L.; Alibali, Martha W.; McNeil, Nicole M.

2001-01-01

Explores the extent to which children with specific language impairment (SLI) with severe phonological working memory deficits express knowledge uniquely in gesture as compared to speech. Using a paradigm in which gesture-speech relationships have been studied extensively, children with SLI and conversation judgment-matched, typically developing…

Linguistic and other cognitive abilities in children with Specific Language Impairment as compared to children with High-Functioning Autism

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Schaeffer, J.

2018-01-01

This study investigates the question as to whether and how the linguistic and other cognitive abilities of children with Specific Language Impairment (SLI) differ from those of children with High-Functioning Autism (HFA). To this end, 27 Dutch-speaking elementary-school-age children with SLI, 27

Exploration of a "Double-Jeopardy" Hypothesis within Working Memory Profiles for Children with Specific Language Impairment

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Briscoe, J.; Rankin, P. M.

2009-01-01

Background: Children with specific language impairment (SLI) often experience difficulties in the recall and repetition of verbal information. Archibald and Gathercole (2006) suggested that children with SLI are vulnerable across two separate components of a tripartite model of working memory (Baddeley and Hitch 1974). However, the hierarchical…

Specific Language Impairment, Nonverbal IQ, Attention-Deficit/Hyperactivity Disorder, Autism Spectrum Disorder, Cochlear Implants, Bilingualism, and Dialectal Variants: Defining the Boundaries, Clarifying Clinical Conditions, and Sorting out Causes

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Rice, Mabel L.

2016-01-01

Purpose: The purpose of this research forum article is to provide an overview of a collection of invited articles on the topic "specific language impairment (SLI) in children with concomitant health conditions or nonmainstream language backgrounds." Topics include SLI, attention-deficit/hyperactivity disorder, autism spectrum disorder,…

Interaction of language processing and motor skill in children with specific language impairment.

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DiDonato Brumbach, Andrea C; Goffman, Lisa

2014-02-01

To examine how language production interacts with speech motor and gross and fine motor skill in children with specific language impairment (SLI). Eleven children with SLI and 12 age-matched peers (4-6 years) produced structurally primed sentences containing particles and prepositions. Utterances were analyzed for errors and for articulatory duration and variability. Standard measures of motor, language, and articulation skill were also obtained. Sentences containing particles, as compared with prepositions, were less likely to be produced in a priming task and were longer in duration, suggesting increased difficulty with this syntactic structure. Children with SLI demonstrated higher articulatory variability and poorer gross and fine motor skills compared with aged-matched controls. Articulatory variability was correlated with generalized gross and fine motor performance. Children with SLI show co-occurring speech motor and generalized motor deficits. Current theories do not fully account for the present findings, though the procedural deficit hypothesis provides a framework for interpreting overlap among language and motor domains.

Syntactic comprehension and working memory in children with specific language impairment, autism or Down syndrome.

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Fortunato-Tavares, Talita; Andrade, Claudia R F; Befi-Lopes, Debora; Limongi, Suelly O; Fernandes, Fernanda D M; Schwartz, Richard G

2015-07-01

This study examined syntactic assignment for predicates and reflexives as well as working memory effects in the sentence comprehension of children with Specific Language Impairment (SLI), Down syndrome (DS), high functioning Autism (HFA) and Typical Language Development (TLD). Fifty-seven children (35 boys and 22 girls) performed a computerised picture-selection sentence comprehension task. Predicate attachment and reflexive antecedent assignment (with working memory manipulations) were investigated. The results showed that SLI, HFA and DS children exhibited poorer overall performance than TLD children. Children with SLI exhibited similar performance to the DS and HFA children only when working memory demands were higher. We conclude that children with SLI, HFA and DS differ from children with TLD in their comprehension of predicate and reflexive structures where the knowledge of syntactic assignment is required. Working memory manipulation had different effects on syntactic comprehension depending on language disorder. Intelligence was not an explanatory factor for the differences observed in performance.

Partial amino acid sequence of the branched chain amino acid aminotransferase (TmB) of E. coli JA199 pDU11

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Feild, M.J.; Armstrong, F.B.

1987-01-01

E. coli JA199 pDU11 harbors a multicopy plasmid containing the ilv GEDAY gene cluster of S. typhimurium. TmB, gene product of ilv E, was purified, crystallized, and subjected to Edman degradation using a gas phase sequencer. The intact protein yielded an amino terminal 31 residue sequence. Both carboxymethylated apoenzyme and [ 3 H]-NaBH-reduced holoenzyme were then subjected to digestion by trypsin. The digests were fractionated using reversed phase HPLC, and the peptides isolated were sequenced. The borohydride-treated holoenzyme was used to isolate the cofactor-binding peptide. The peptide is 27 residues long and a comparison with known sequences of other aminotransferases revealed limited homology. Peptides accounting for 211 of 288 predicted residues have been sequenced, including 9 residues of the carboxyl terminus. Comparison of peptides with the inferred amino acid sequence of the E. coli K-12 enzyme has helped determine the sequence of the amino terminal 59 residues; only two differences between the sequences are noted in this region

Validation of qPCR Methods for the Detection of Mycobacterium in New World Animal Reservoirs.

Directory of Open Access Journals (Sweden)

Genevieve Housman

2015-11-01

Full Text Available Zoonotic pathogens that cause leprosy (Mycobacterium leprae and tuberculosis (Mycobacterium tuberculosis complex, MTBC continue to impact modern human populations. Therefore, methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats. Here we tested for mycobacterial-specific single- and multi-copy loci using qPCR. In a trial study in which armadillos were artificially infected with M. leprae, these techniques were specific and sensitive to pathogen detection, while more traditional ELISAs were only specific. These assays were then employed in a case study to detect M. leprae as well as MTBC in wild marmosets. All marmosets were negative for M. leprae DNA, but 14 were positive for the mycobacterial rpoB gene assay. Targeted capture and sequencing of rpoB and other MTBC genes validated the presence of mycobacterial DNA in these samples and revealed that qPCR is useful for identifying mycobacterial-infected animal hosts.

Effect of ventriculectomy versus ventriculocordectomy on upper airway noise in draught horses with recurrent laryngeal neuropathy.

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Cramp, P; Derksen, F J; Stick, J A; Nickels, F A; Brown, K E; Robinson, P; Robinson, N E

2009-11-01

Little is known about the efficacy of bilateral ventriculectomy (VE) or bilateral ventriculocordectomy (VCE) in draught horses. To compare the effect of VE and VCE on upper airway noise in draught horses with recurrent laryngeal neuropathy (RLN) by use of quantitative sound analysis techniques. In competitive draught horses with grade 4 RLN, VE and VCE reduce upper airway noise during exercise, but VCE is more effective. Thirty competitive hitch or pulling draught horses with grade 4 RLN were evaluated for upper airway sound during exercise. Respiratory rate (RR), inspiratory (Ti) and expiratory time (Te), the ratio between Ti and Te (Ti/Te), inspiratory (Sli) and expiratory sound levels (Sle), the ratio between Sli and Sle (Sli/Sle), and peak sound intensity of the second formant (F2) were calculated. Eleven horses were treated with VE and 19 with VCE. After 90 days of voice and physical rest and 30 days of work, the horses returned for post operative upper airway sound evaluation and resting videoendoscopy. VE significantly reduced Ti/Te, Sli, Sli/Sle and the sound intensity of F2. Respiratory rate, Ti, Te and Sle were unaffected by VE. VCE significantly reduced Ti/Te, Ti, Te, Sli, Sli/Sle and the sound intensity of F2, while RR and Sle were unaffected. The reduction in sound intensity of F2 following VCE was significantly greater than following VE. After VE and VCE, 7/11 (64%) and 15/18 (83%) owners, respectively, concluded that the surgery improved upper airway sound in their horses sufficiently for successful competition. VE and VCE significantly reduce upper airway noise and indices of airway obstruction in draught horses with RLN, but VCE is more effective than VE. The procedures have few post operative complications. VCE is recommended as the preferred treatment for RLN in draught horses. Further studies are required to evaluate the longevity of the procedure's results.

Health-related quality of life in school-age children with speech-language-impairment

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Flapper, B.C.; Van Den Heuvel, M.

Speech-language-impairment (SLI) as well as behavioral-dysfunction and school-type might influence health-related-quality-of-life. Patients and methods: Cross-sectional study in 124 children aged 5-8 years with SLI, in 4 special education (SE) and 7 mainstream ambulatory care (AC) schools, and 35

Spoken Word Recognition in Adolescents with Autism Spectrum Disorders and Specific Language Impairment

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Loucas, Tom; Riches, Nick; Baird, Gillian; Pickles, Andrew; Simonoff, Emily; Chandler, Susie; Charman, Tony

2013-01-01

Spoken word recognition, during gating, appears intact in specific language impairment (SLI). This study used gating to investigate the process in adolescents with autism spectrum disorders plus language impairment (ALI). Adolescents with ALI, SLI, and typical language development (TLD), matched on nonverbal IQ listened to gated words that varied…

Declarative and Procedural Memory in Danish Speaking Children with Specific Language Impairment

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Lum, Jarrad A. G.; Bleses, Dorthe

2012-01-01

It has been proposed that the language problems in specific language impairment (SLI) arise from basal ganglia abnormalities that lead to impairments with procedural and working memory but not declarative memory. In SLI, this profile of memory functioning has been hypothesized to underlie grammatical impairment but leave lexical knowledge…

Influence of Language Load on Speech Motor Skill in Children with Specific Language Impairment

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Saletta, Meredith; Goffman, Lisa; Ward, Caitlin; Oleson, Jacob

2018-01-01

Purpose: Children with specific language impairment (SLI) show particular deficits in the generation of sequenced action--the quintessential procedural task. Practiced imitation of a sequence may become rote and require reduced procedural memory. This study explored whether speech motor deficits in children with SLI occur generally or only in…

Complex Sentence Comprehension and Working Memory in Children with Specific Language Impairment

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Montgomery, James W.; Evans, Julia L.

2009-01-01

Purpose: This study investigated the association of 2 mechanisms of working memory (phonological short-term memory [PSTM], attentional resource capacity/allocation) with the sentence comprehension of school-age children with specific language impairment (SLI) and 2 groups of control children. Method: Twenty-four children with SLI, 18 age-matched…

Working Memory Functioning in Children with Learning Disorders and Specific Language Impairment

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Schuchardt, Kirsten; Bockmann, Ann-Katrin; Bornemann, Galina; Maehler, Claudia

2013-01-01

Purpose: On the basis of Baddeley's working memory model (1986), we examined working memory functioning in children with learning disorders with and without specific language impairment (SLI). We pursued the question whether children with learning disorders exhibit similar working memory deficits as children with additional SLI. Method: In…

(Dis)connections between Specific Language Impairment and Dyslexia in Chinese

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Wong, Anita M.-Y.; Ho, Connie S.-H.; Au, Terry K.-F.; Kidd, Joanna C.; Ng, Ashley K.-H.; Yip, Lesley P.-W.; Lam, Catherine C.-C.

2015-01-01

Specific language impairment (SLI) and dyslexia are found to co-occur in school-aged children learning Chinese, a non-alphabetic language (Wong, Kidd, Ho, & Au in "Sci Stud Read" 14:30--57, 2010). This paper examined the "Distinct" hypothesis--that SLI and dyslexia have different cognitive deficits and behavioural…

Production and Processing of Subject-Verb Agreement in Monolingual Dutch Children with Specific Language Impairment

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Blom, Elma; Vasic, Nada; de Jong, Jan

2014-01-01

Purpose: In this study, the authors investigated whether errors with subject-verb agreement in monolingual Dutch children with specific language impairment (SLI) are influenced by verb phonology. In addition, the productive and receptive abilities of Dutch acquiring children with SLI regarding agreement inflection were compared. Method: An SLI…

Social Stress in Young People with Specific Language Impairment

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Wadman, Ruth; Durkin, Kevin; Conti-Ramsden, Gina

2011-01-01

Social interactions can be a source of social stress for adolescents. Little is known about how adolescents with developmental difficulties, such as specific language impairment (SLI), feel when interacting socially. Participants included 28 adolescents with SLI and 28 adolescents with typical language abilities (TL). Self-report measures of…

Postschool Educational and Employment Experiences of Young People with Specific Language Impairment

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Conti-Ramsden, Gina; Durkin, Kevin

2012-01-01

Purpose: This study examined the postschool educational and employment experiences of young people with and without specific language impairment (SLI). Method: Nineteen-year-olds with (n = 50) and without (n = 50) SLI were interviewed on their education and employment experiences since finishing compulsory secondary education. Results: On average,…

Hypertext comprehension of deaf and hard-of-hearing students and students with specific language impairment

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Blom, H.C.; Segers, P.C.J.; Hermans, D.; Knoors, H.E.T.; Verhoeven, L.T.W.

2017-01-01

This paper provides insight into the reading comprehension of hierarchically structured hypertexts within D/HH students and students with SLI. To our knowledge, it is the first study on hypertext comprehension in D/HH students and students with SLI, and it also considers the role of working memory.

The role of social cognition and prosocial behaviour in relation to the socio-emotional functioning of primary aged children with specific language impairment.

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Bakopoulou, Ioanna; Dockrell, Julie E

2016-01-01

Children with language impairments often experience difficulties with their socio-emotional functioning and poorly developed prosocial behaviour. However, the nature of the association between language impairment and difficulties with socio-emotional functioning remains unclear. The social cognition skills of a group of primary-aged children (6-11 years old) with Specific Language Impairment (SLI) were examined in relation to their teachers' ratings of socio-emotional functioning. Forty-two children with SLI were individually matched with 42 children for chronological age and non-verbal cognitive ability, and 42 children for receptive language ability. The children all attended mainstream primary schools or one Language Unit. Four aspects of social cognition were directly assessed: emotion identification, emotion labelling, inferring the causes of emotions, and knowledge of conflict resolution strategies. The children's socio-emotional functioning was assessed using the Strengths and Difficulties questionnaire (SDQ), a standardised measure, completed by their teachers. Associations between children's performance on tasks of social cognition and children's socio-emotional functioning were explored. Significant group differences were found for all social cognition tasks. The SLI group was rated to experience significantly more problems with socio-emotional functioning by their teachers than both control groups, indicating problems with all aspects of socio-emotional functioning. Social cognition and prosocial behaviour, but not language ability, predicted teacher-rated behavioural, emotional and social difficulties for the SLI group. The results challenge current understanding of socio-emotional functioning in children with SLI by pointing to the crucial role of social cognition and prosocial behaviour. Factors other than expressive and receptive language play a role in the socio-emotional functioning of children with SLI. Copyright © 2015 Elsevier Ltd. All rights

Exploration of a 'double-jeopardy' hypothesis within working memory profiles for children with specific language impairment.

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Briscoe, J; Rankin, P M

2009-01-01

Children with specific language impairment (SLI) often experience difficulties in the recall and repetition of verbal information. Archibald and Gathercole (2006) suggested that children with SLI are vulnerable across two separate components of a tripartite model of working memory (Baddeley and Hitch 1974). However, the hierarchical relationship between the 'slave' systems (temporary storage) and the central executive components places a particular challenge for interpreting working memory profiles within a tripartite model. This study aimed to examine whether a 'double-jeopardy' assumption is compatible with a hierarchical relationship between the phonological loop and central executive components of the working memory model in children with SLI. If a strong double-jeopardy assumption is valid for children with SLI, it was predicted that raw scores of working memory tests thought to tap phonological loop and central executive components of tripartite working memory would be lower than the scores of children matched for chronological age and those of children matched for language level, according to independent sources of constraint. In contrast, a hierarchical relationship would imply that a weakness in a slave component of working memory (the phonological loop) would also constrain performance on tests tapping a super-ordinate component (central executive). This locus of constraint would predict that scores of children with SLI on working memory tests that tap the central executive would be weaker relative to the scores of chronological age-matched controls only. Seven subtests of the Working Memory Test Battery for Children (Digit recall, Word recall, Non-word recall, Word matching, Listening recall, Backwards digit recall and Block recall; Pickering and Gathercole 2001) were administered to 14 children with SLI recruited via language resource bases and specialist schools, as well as two control groups matched on chronological age and vocabulary level

A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

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Bloom-Ackermann, Zohar; Navon, Sivan; Gingold, Hila; Towers, Ruth; Pilpel, Yitzhak; Dahan, Orna

2014-01-01

Deciphering the architecture of the tRNA pool is a prime challenge in translation research, as tRNAs govern the efficiency and accuracy of the process. Towards this challenge, we created a systematic tRNA deletion library in Saccharomyces cerevisiae, aimed at dissecting the specific contribution of each tRNA gene to the tRNA pool and to the cell's fitness. By harnessing this resource, we observed that the majority of tRNA deletions show no appreciable phenotype in rich medium, yet under more challenging conditions, additional phenotypes were observed. Robustness to tRNA gene deletion was often facilitated through extensive backup compensation within and between tRNA families. Interestingly, we found that within tRNA families, genes carrying identical anti-codons can contribute differently to the cellular fitness, suggesting the importance of the genomic surrounding to tRNA expression. Characterization of the transcriptome response to deletions of tRNA genes exposed two disparate patterns: in single-copy families, deletions elicited a stress response; in deletions of genes from multi-copy families, expression of the translation machinery increased. Our results uncover the complex architecture of the tRNA pool and pave the way towards complete understanding of their role in cell physiology. PMID:24453985

Trastorno Específico del Desarrollo del Lenguaje en una población infantil colombiana

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LILIANA HINCAPIÉ-HENAO

2008-03-01

Full Text Available The Neuroscience Group of Antioquia evaluated two hundred and fourchildren from 6 to 16 years old with speech and language problems and 51 of them meet the inclusion and exclusion criteria for Specific Language Impairment (SLI. The SLI group underwent a neuropsychological and linguistic test to compare their cognitive and linguistic skills with a control group of asymptomatic children. When compared to the control group, SLI children showed significant differences in comprehension tests, particularly in complex morphosyntactic structures and elaborated sentences; in verbal expression, especially formulated sentences; repetition test ofnon-sense words; naming errors and marked disadvantages in readingwriting sub-tests.

'MetaTaal': enhancing complex syntax in children with specific language impairment--a metalinguistic and multimodal approach.

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Zwitserlood, Rob; Wijnen, Frank; van Weerdenburg, Marjolijn; Verhoeven, Ludo

2015-01-01

Currently, most research on the effective treatment of morphosyntax in children with specific language impairment (SLI) pertains to younger children. In the last two decades, several studies have provided evidence that intervention for older school-age children with SLI can be effective. These metalinguistic intervention approaches teach grammatical rules explicitly and use shapes and colours as two-dimensional visual support. Reading or writing activities form a substantial part of these interventions. However, some children with SLI are poor readers and might benefit more from an approach that is less dependent on literacy skills. To examine the effectiveness of a combined metalinguistic and multimodal approach in older school-age children with SLI. The intervention was adapted to suit poor readers and targeted the improvement of relative clause production, because relative clauses still pose difficulties for older children with SLI. Participants were 12 monolingual Dutch children with SLI (mean age 11;2). All children visited a special school for children with speech and language disorders in the Netherlands. A quasi-experimental multiple-baseline design was chosen to evaluate the effectiveness of the intervention. A set of tasks was constructed to test relative clause production and comprehension. Two balanced versions were alternated in order to suppress a possible learning effect from multiple presentations of the tasks. After 3 monthly baseline measurements, the children received individual treatment with a protocolled intervention programme twice a week during 5 weeks. The tests were repeated directly post-therapy and at a retention measurement 3 months later. During the intervention programme, the speech therapist delivering the treatment remained blind to the test results. No significant changes were found during the baseline measurements. However, measurement directly post-therapy showed that 5 h of intervention produced significant improvement on the

Do Adolescents with Specific Language Impairment Understand Driving Terminology?

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Pandolfe, Jessica M.; Wittke, Kacie; Spaulding, Tammie J.

2016-01-01

Purpose: This study examined if adolescents with specific language impairment (SLI) understand driving vocabulary as well as their typically developing (TD) peers. Method: A total of 16 adolescents with SLI and 16 TD comparison adolescents completed a receptive vocabulary task focused on driving terminology derived from statewide driver's manuals.…

Dynamic Assessment of Sentence Structure (DASS): Design and Evaluation of a Novel Procedure for the Assessment of Syntax in Children with Language Impairments

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Hasson, Natalie; Dodd, Barbara; Botting, Nicola

2012-01-01

Background: Sentence construction and syntactic organization are known to be poor in children with specific language impairments (SLI), but little is known about the way in which children with SLI approach language tasks, and static standardized tests contribute little to the differentiation of skills within the population of children with…

Lipreading Ability and Its Cognitive Correlates in Typically Developing Children and Children with Specific Language Impairment

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Heikkilä, Jenni; Lonka, Eila; Ahola, Sanna; Meronen, Auli; Tiippana, Kaisa

2017-01-01

Purpose: Lipreading and its cognitive correlates were studied in school-age children with typical language development and delayed language development due to specific language impairment (SLI). Method: Forty-two children with typical language development and 20 children with SLI were tested by using a word-level lipreading test and an extensive…

Information Processing and Proactive Interference in Children with and without Specific Language Impairment

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Marton, Klara; Campanelli, Luca; Eichorn, Naomi; Scheuer, Jessica; Yoon, Jungmee

2014-01-01

Purpose: Increasing evidence suggests that children with specific language impairment (SLI) have a deficit in inhibition control, but research isolating specific abilities is scarce. The goal of this study was to examine whether children with SLI differ from their peers in resistance to proactive interference under different conditions. Method: An…

Effects of Explicit Vocabulary Videos Delivered through iPods on Students with Language Impairments

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Lowman, J. Joneen; Dressler, Emily V.

2016-01-01

Poor word learning is a hallmark characteristic of students with specific language impairment (SLI). Explicit vocabulary instruction has shown to positively improve word learning in this population. Mobile technology has many advantages making it conducive for addressing the word learning needs of students with SLI. The current study utilized a…

Co-Localisation of Abnormal Brain Structure and Function in Specific Language Impairment

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Badcock, Nicholas A.; Bishop, Dorothy V. M.; Hardiman, Mervyn J.; Barry, Johanna G.; Watkins, Kate E.

2012-01-01

We assessed the relationship between brain structure and function in 10 individuals with specific language impairment (SLI), compared to six unaffected siblings, and 16 unrelated control participants with typical language. Voxel-based morphometry indicated that grey matter in the SLI group, relative to controls, was increased in the left inferior…

Interaction of Language Processing and Motor Skill in Children with Specific Language Impairment

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DiDonato Brumbach, Andrea C.; Goffman, Lisa

2014-01-01

Purpose: To examine how language production interacts with speech motor and gross and fine motor skill in children with specific language impairment (SLI). Method: Eleven children with SLI and 12 age-matched peers (4-6 years) produced structurally primed sentences containing particles and prepositions. Utterances were analyzed for errors and for…

Working Memory Capacity and Language Processes in Children with Specific Language Impairment

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Marton, Klara; Schwartz, Richard G.

2003-01-01

This study examined the interaction between working memory and language comprehension in children with specific language impairment (SLI), focusing on the function of the central executive component and its interaction with the phonological loop (A. D. Baddeley, 1986) in complex working memory tasks. Thirteen children with SLI and 13 age-matched…

Auxiliary BE Production by African American English-Speaking Children with and without Specific Language Impairment

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Garrity, April W.; Oetting, Janna B.

2010-01-01

Purpose: To examine 3 forms ("am," "is," "are") of auxiliary BE production by African American English (AAE)-speaking children with and without specific language impairment (SLI). Method: Thirty AAE speakers participated: 10 six-year-olds with SLI, 10 age-matched controls, and 10 language-matched controls. BE production was examined through…

Sustained Selective Attention Skills of Preschool Children with Specific Language Impairment: Evidence for Separate Attentional Capacities

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Spaulding, Tammie J.; Plante, Elena; Vance, Rebecca

2008-01-01

Purpose: The present study was designed to investigate the performance of preschool children with specific language impairment (SLI) and their typically developing (TD) peers on sustained selective attention tasks. Method: This study included 23 children diagnosed with SLI and 23 TD children matched for age, gender, and maternal education level.…

School Processes That Can Drive Scaling-Up of an Innovation or Contribute to Its Abandonment

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Newman, Denis; Zacamy, Jenna; Lazarev, Valeriy; Lin, Li

2017-01-01

This five-year study focused on school processes that promoted the scaling-up of a high school academic literacy framework, Reading Apprenticeship, developed by WestEd's Strategic Literacy Initiative (SLI). Implementing an innovative strategy for scaling-up involving school-based cross-disciplinary teacher teams, SLI brought the framework to 274…

Visual Fast Mapping in School-Aged Children with Specific Language Impairment

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Alt, Mary

2013-01-01

Purpose: To determine whether children with specific language impairment (SLI) demonstrate impaired visual fast mapping skills compared with unimpaired peers and to test components of visual working memory that may contribute to a visual working memory deficit. Methods: Fifty children (25 SLI) played 2 computer-based visual fast mapping games…

Assessing bilingual Chinese-English young children in Malaysia using language sample measures.

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Ooi, Carmen C-W; Wong, Anita M-Y

2012-12-01

One reason why specific language impairment (SLI) is grossly under-identified in Malaysia is the absence of locally- developed norm-referenced language assessment tools for its multilingual and multicultural population. Spontaneous language samples provide quantitative information for language assessment, and useful descriptive information on child language development in complex language and cultural environments. This research consisted of two studies and investigated the use of measures obtained from English conversational samples among bilingual Chinese-English Malaysian preschoolers. The research found that the language sample measures were sensitive to developmental changes in this population and could identify SLI. The first study examined the relationship between age and mean length of utterance (MLU(w)), lexical diversity (D), and the index of productive syntax (IPSyn) among 52 typically-developing (TD) children aged between 3;4-6;9. Analyses showed a significant linear relationship between age and D (r = .450), the IPsyn (r = .441), and MLU(w) (r = .318). The second study compared the same measures obtained from 10 children with SLI, aged between 3;8-5;11, and their age-matched controls. The children with SLI had significantly shorter MLU(w) and lower IPSyn scores than the TD children. These findings suggest that utterance length and syntax production can be potential clinical markers of SLI in Chinese-English Malaysian children.

Kindergarten Children’s Growth Trajectories in Reading and Mathematics: Who Falls Increasingly Behind?

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Morgan, Paul L.; Farkas, George; Wu, Qiong

2015-01-01

We used a large sample of children (N ≈ 7,400) participating in the Early Childhood Longitudinal Study – Kindergarten Cohort to estimate kindergarten children’s academic achievement growth trajectories in reading and mathematics. We were particularly interested in whether the growth trajectories of children with learning disabilities (LD) or speech language impairments (SLI)—as well as those of other groups of children—were consistent with a cumulative or compensatory developmental cycle. Both LD and SLI children displayed significantly lower levels of kindergarten reading achievement than non-disabled children. However, and over the subsequent five years of elementary school, only children with SLI lagged increasingly behind non-disabled peers in their reading skills growth. We observed a different pattern for mathematics achievement. Children with LD, but not SLI, lagged increasingly behind non-disabled children in their mathematics skills growth. We also observed some consistency in “poor-get-poorer” effects across reading and mathematic achievement for additional population subgroups. Those kindergarten children who were from lower socio-economic status (SES) families, who were African-American, and who more frequently displayed learning-related behaviors problems initially had lower levels of reading and mathematics achievement and also lagged increasingly behind in their acquisition of these skills over time. Some groups of children, including those with SLI, experience a cumulative rather than compensatory cycle of achievement growth. PMID:21856991

Sentence Repetition in Deaf Children with Specific Language Impairment in British Sign Language

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Marshall, Chloë; Mason, Kathryn; Rowley, Katherine; Herman, Rosalind; Atkinson, Joanna; Woll, Bencie; Morgan, Gary

2015-01-01

Children with specific language impairment (SLI) perform poorly on sentence repetition tasks across different spoken languages, but until now, this methodology has not been investigated in children who have SLI in a signed language. Users of a natural sign language encode different sentence meanings through their choice of signs and by altering…

Examining the Language Phenotype in Children with Typical Development, Specific Language Impairment, and Fragile X Syndrome

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Haebig, Eileen; Sterling, Audra; Hoover, Jill

2016-01-01

Purpose: One aspect of morphosyntax, finiteness marking, was compared in children with fragile X syndrome (FXS), specific language impairment (SLI), and typical development matched on mean length of utterance (MLU). Method: Nineteen children with typical development (mean age = 3.3 years), 20 children with SLI (mean age = 4.9 years), and 17 boys…

Using Pupillometry to Investigate Sentence Comprehension in Children with and without Specific Language Impairment

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Lum, Jarrad A. G.; Youssef, George J.; Clark, Gillian M.

2017-01-01

Purpose: In this study pupillometry was used to investigate the allocation of attentional resources associated with sentence comprehension in children with and without specific language impairment (SLI). Method: Eighteen children with SLI (age: M = 6.4 years) and 18 typically developing (TD) children (age: M = 6.3 years) participated in the study.…

Tense Marking and Spontaneous Speech Measures in Spanish Specific Language Impairment: A Discriminant Function Analysis

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Grinstead, John; Baron, Alisa; Vega-Mendoza, Mariana; De la Mora, Juliana; Cantu-Sanchez, Myriam; Flores, Blanca

2013-01-01

Purpose: To test the proposal that the tense deficit that has been demonstrated for children with specific language impairment (SLI) in other languages is also found in child Spanish and that low performance on tense-related measures can distinguish Spanish-speaking children with SLI from those without. Method: The authors evaluated evidence from…

RALLI: An Internet Campaign for Raising Awareness of Language Learning Impairments

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Bishop, Dorothy V. M.; Clark, Becky; Conti-Ramsden, Gina; Norbury, Courtenay Frazier; Snowling, Margaret J

2012-01-01

In contrast to dyslexia and autism, specific language impairment (SLI) is a neglected condition not only in research, but also in debates about policy and practice. A recent analysis of research publications and grants confirmed this impression, showing that SLI attracted far less research funding and led to fewer publications than many other…

The Relationship between Phonological Memory, Receptive Vocabulary, and Fast Mapping in Young Children with Specific Language Impairment

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Gray, Shelley

2006-01-01

Purpose: This study assessed the fast mapping performance of children with specific language impairment (SLI) across the preschool to kindergarten age span in relation to their phonological memory and vocabulary development. Method: Fifty-three children diagnosed with SLI and 53 children with normal language (NL) matched for age and gender (30…

Working, declarative and procedural memory in specific language impairment

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Lum, Jarrad A.G.; Conti-Ramsden, Gina; Page, Debra; Ullman, Michael T.

2012-01-01

According to the Procedural Deficit Hypothesis (PDH), abnormalities of brain structures underlying procedural memory largely explain the language deficits in children with specific language impairment (SLI). These abnormalities are posited to result in core deficits of procedural memory, which in turn explain the grammar problems in the disorder. The abnormalities are also likely to lead to problems with other, non-procedural functions, such as working memory, that rely at least partly on the affected brain structures. In contrast, declarative memory is expected to remain largely intact, and should play an important compensatory role for grammar. These claims were tested by examining measures of working, declarative and procedural memory in 51 children with SLI and 51 matched typically-developing (TD) children (mean age 10). Working memory was assessed with the Working Memory Test Battery for Children, declarative memory with the Children’s Memory Scale, and procedural memory with a visuo-spatial Serial Reaction Time task. As compared to the TD children, the children with SLI were impaired at procedural memory, even when holding working memory constant. In contrast, they were spared at declarative memory for visual information, and at declarative memory in the verbal domain after controlling for working memory and language. Visuo-spatial short-term memory was intact, whereas verbal working memory was impaired, even when language deficits were held constant. Correlation analyses showed neither visuo-spatial nor verbal working memory was associated with either lexical or grammatical abilities in either the SLI or TD children. Declarative memory correlated with lexical abilities in both groups of children. Finally, grammatical abilities were associated with procedural memory in the TD children, but with declarative memory in the children with SLI. These findings replicate and extend previous studies of working, declarative and procedural memory in SLI. Overall, we

Subordinate clause comprehension and tense/agreement inconsistency in children with specific language impairment.

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Souto, Sofía M; Leonard, Laurence B; Deevy, Patricia; Fey, Marc E; Bredin-Oja, Shelley L

2016-01-01

Several recent studies have suggested that the production errors of children with specific language impairment (SLI) such as The girl singing may be explained by a misinterpretation of grammatical adult input containing a similar structure (e.g., The boy hears the girl singing). Thirteen children with SLI and 13 younger typically developing children with comparable sentence comprehension test scores (TD-COMP) completed a comprehension task to assess their understanding of sentences involving a nonfinite subject-verb sequence in a subordinate clause such as The dad sees the boy running. TD-COMP children were more accurate on subordinate clause items than children with SLI despite similar performance on simple transitive (e.g., The horse sees the cow) and simple progressive (e.g., The cow is eating) items. However, no relationship was found between the SLI group's specific subordinate clause comprehension level and their specific level of auxiliary is production, casting some doubt on this type of structure as a source for inconsistent use of auxiliary is. The reader will learn that children with specific language impairment (SLI): (1) have difficulty understanding complex sentences that include nonfinite subject-verb sequences; (2) that this difficulty is apparent in comparison to younger typically developing peers who have similar scores not only on a sentence comprehension test, but also on simple sentences that correspond to the component parts of the complex sentences; and (3) that this weakness is concurrent with these children's inconsistent use of auxiliary is in production. Although novel verb studies show a clear connection between how children with SLI hear new verbs and how they use them, we do not yet have evidence that this connection is tied to a poor understanding of the input sentences that house the verbs. Copyright © 2016 Elsevier Inc. All rights reserved.

Utility of the Spelling Sensitivity Score to Analyze Spellings of Children with Specific Language Impairment

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Werfel, Krystal L.; Krimm, Hannah

2015-01-01

The purpose of this study was to examine the utility of the Spelling Sensitivity Score (SSS) beyond percentage correct scoring in analyzing the spellings of children with specific language impairment (SLI). Participants were 31 children with SLI and 28 children with typical language in grades 2-4. Spellings of individual words were scored using…

Linguistic and Cognitive Abilities in Children with Specific Language Impairment as Compared to Children with High-Functioning Autism

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Schaeffer, Jeannette

2018-01-01

This study investigates the question as to whether and how the linguistic and other cognitive abilities of children with Specific Language Impairment (SLI) differ from those of children with High-Functioning Autism (HFA). To this end, 27 Dutch-speaking elementary-school-age children with SLI, 27 age-matched children with HFA, and a control group…

Developmental Coordination Disorder in children with specific language impairment : Co-morbidity and impact on quality of life

NARCIS (Netherlands)

Flapper, Boudien C.T.; Schoemaker, Marina M.

Co-morbidity of Developmental Coordination Disorder (DCD) in children with specific language impairment (SLI) and the impact of DCD on quality-of-life (QOL) was investigated in 65 5-8 year old children with SLI (43 boys, age 6.8 +/- 0.8; 22 girls, age 6.6 +/- 0.8). The prevalence of DCD was assessed

Empirical Implications of Matching Children with Specific Language Impairment to Children with Typical Development on Nonverbal IQ

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Earle, F. Sayako; Gallinat, Erica L.; Grela, Bernard G.; Lehto, Alexa; Spaulding, Tammie J.

2017-01-01

This study determined the effect of matching children with specific language impairment (SLI) and their peers with typical development (TD) for nonverbal IQ on the IQ test scores of the resultant groups. Studies published between January 2000 and May 2012 reporting standard nonverbal IQ scores for SLI and age-matched TD controls were categorized…

Sensitivity to Audiovisual Temporal Asynchrony in Children with a History of Specific Language Impairment and Their Peers with Typical Development: A Replication and Follow-Up Study

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Kaganovich, Natalya

2017-01-01

Purpose: Earlier, my colleagues and I showed that children with a history of specific language impairment (H-SLI) are significantly less able to detect audiovisual asynchrony compared with children with typical development (TD; Kaganovich & Schumaker, 2014). Here, I first replicate this finding in a new group of children with H-SLI and TD and…

Theory of mind and specific language impairment in school-age children.

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Spanoudis, George

2016-01-01

Research on the relationship between aspects of language development and Theory of Mind (ToM) in children with language impairments suggests that children with language impairment show a delay in ToM development. This study aimed to examine the relationships of the syntactic, semantic, and pragmatic skills with ToM in school-age children. Twenty children with Specific Language Impairment (SLI) aged 9-12 years and two control groups, one matched for chronological age (CA) and one for language ability (LA) (aged 8-10 years) were compared on a set of language tasks tapping syntactic, semantic, and pragmatic skills and on an advanced test of ToM. Results showed that children with SLI performed poorly on the ToM task compared to the CA matches. Also, analysis showed that language skills and ToM are related and that syntactic and pragmatic abilities contributed significantly to the prediction of ToM performance in the SLI group. It is concluded that the syntax/pragmatic aspects of the language impact on ToM understanding in children with SLI. Copyright © 2016 Elsevier Inc. All rights reserved.

Perception of audio-visual speech synchrony in Spanish-speaking children with and without specific language impairment.

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Pons, Ferran; Andreu, Llorenç; Sanz-Torrent, Monica; Buil-Legaz, Lucía; Lewkowicz, David J

2013-06-01

Speech perception involves the integration of auditory and visual articulatory information, and thus requires the perception of temporal synchrony between this information. There is evidence that children with specific language impairment (SLI) have difficulty with auditory speech perception but it is not known if this is also true for the integration of auditory and visual speech. Twenty Spanish-speaking children with SLI, twenty typically developing age-matched Spanish-speaking children, and twenty Spanish-speaking children matched for MLU-w participated in an eye-tracking study to investigate the perception of audiovisual speech synchrony. Results revealed that children with typical language development perceived an audiovisual asynchrony of 666 ms regardless of whether the auditory or visual speech attribute led the other one. Children with SLI only detected the 666 ms asynchrony when the auditory component preceded [corrected] the visual component. None of the groups perceived an audiovisual asynchrony of 366 ms. These results suggest that the difficulty of speech processing by children with SLI would also involve difficulties in integrating auditory and visual aspects of speech perception.

Imitation of Body Postures and Hand Movements in Children with Specific Language Impairment

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Marton, Klara

2009-01-01

Within the domain-general theory of language impairment, this study examined body posture and hand movement imitation in children with specific language impairment (SLI) and in their age-matched peers. Participants included 40 children with SLI (5 years 3 months to 6 years 10 months of age) and 40 children with typical language development (5…

Mining Concept Maps from News Stories for Measuring Civic Scientific Literacy in Media

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Tseng, Yuen-Hsien; Chang, Chun-Yen; Rundgren, Shu-Nu Chang; Rundgren, Carl-Johan

2010-01-01

Motivated by a long-term goal in education for measuring Taiwanese civic scientific literacy in media (SLiM), this work reports the detailed techniques to efficiently mine a concept map from 2 years of Chinese news articles (901,446 in total) for SLiM instrument development. From the Chinese news stories, key terms (important words or phrases),…

An Initial Investigation of the Neural Correlates of Word Processing in Preschoolers With Specific Language Impairment.

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Haebig, Eileen; Leonard, Laurence; Usler, Evan; Deevy, Patricia; Weber, Christine

2018-03-15

Previous behavioral studies have found deficits in lexical-semantic abilities in children with specific language impairment (SLI), including reduced depth and breadth of word knowledge. This study explored the neural correlates of early emerging familiar word processing in preschoolers with SLI and typical development. Fifteen preschoolers with typical development and 15 preschoolers with SLI were presented with pictures followed after a brief delay by an auditory label that did or did not match. Event-related brain potentials were time locked to the onset of the auditory labels. Children provided verbal judgments of whether the label matched the picture. There were no group differences in the accuracy of identifying when pictures and labels matched or mismatched. Event-related brain potential data revealed that mismatch trials elicited a robust N400 in both groups, with no group differences in mean amplitude or peak latency. However, the typically developing group demonstrated a more robust late positive component, elicited by mismatch trials. These initial findings indicate that lexical-semantic access of early acquired words, indexed by the N400, does not differ between preschoolers with SLI and typical development when highly familiar words are presented in isolation. However, the typically developing group demonstrated a more mature profile of postlexical reanalysis and integration, indexed by an emerging late positive component. The findings lay the necessary groundwork for better understanding processing of newly learned words in children with SLI.

Fetal head circumference growth in children with specific language impairment.

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Whitehouse, Andrew J O; Zubrick, Stephen R; Blair, Eve; Newnham, John P; Hickey, Martha

2012-01-01

To characterise fetal brain growth in children with specific language impairment (SLI). A nested case-control study. Perth, Western Australia. Thirty children meeting criteria for SLI at age 10 years were individually matched with a typically developing comparison child on sex, non-verbal ability, fetal gestational age, maternal age at conception, smoking and alcohol intake during pregnancy. Occipitofrontal head circumference (HC) was measured using ultrasonography at approximately 18 weeks gestation. Femur length provided a measure of fetal length. Occipitofrontal HC was measured at birth and at the 1-year postnatal follow-up using a precise paper tape measure, while crown-heel length acted as an index of body length at both time points. Raw data were transformed to z-scores using reference norms. The SLI group had a significantly smaller mean HC than the typically developing comparison children at birth, but there was no group difference at 18 weeks gestation or at the 1-year postnatal follow-up. Individual analyses found that 12 SLI children had an HC z-score less than -1 at birth, with three of these cases meeting criteria for microcephaly. There was no group difference in the indices of overall body size at any time point. Children with SLI are more likely to have a small HC at birth but not at 18 weeks gestation or infancy, suggesting growth asynchrony in brain development during the second half of pregnancy.

[Specific language impairment and electroencephalogram: which recommendations in clinical practice? A cohort of 24 children].

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Billard, C; Hassairi, I; Delteil, F

2010-04-01

Electroencephalographic recording (electroencephalogram [EEG]) is frequent in specific language impairment (SLI), whereas the relations between epileptiform activity (EA) and language disorders remain uncertain and the therapeutic approach undetermined. The aim of this prospective study was to clarify EEG indications and interpretation in SLI. We present a prospective study of cognitive (speech-language measures, psychological assessments) and electroencephalographic data on 24 children (20 males, 4 females; mean age: 4 years 5 months; range: 3 years to 4 years 8 months) with a diagnosis of SLI, defined as a pathologic score on at least 2 speech-language measures and IQ performance of at least 80 points, within epileptic seizures. All participants had an EEG after partial deprivation of sleep at night. When nonsporadic EA was found, 24-h EEG was performed. Antiepileptic treatment was prescribed depending on the frequency of discharges and the SLI profile. The follow-up lasted 2 years. All patients reached stage II sleep during their EEG. Seven children had abnormal electroencephalography results, including 5 children with EA. Two patients with mixed SLI prevailing on expression presented a left centrotemporal spike focus on EEG becoming subcontinuous during sleep. In the first case, the language progressed without antiepileptic treatment. The 2nd case was treated with ethosuximide; the EEG normalized on subsequent recordings, but the language disorder remained severe. The lexical and syntactic understanding and syntactic production scores were not different for children presented EA (5 cases) or without (19 cases) (Wilcoxon's test). Finally, the progression of the various linguistic skills was similar whether or not the children had EA (pactivity is more frequent in SLI than in normal children. It can be seen in all types of SLI but preferentially in the mixed forms. The longitudinal systematic evaluation of all the children with or without EA has never been

Terbinafine Resistance Mediated by Salicylate 1-Monooxygenase in Aspergillus nidulans

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Graminha, Marcia A. S.; Rocha, Eleusa M. F.; Prade, Rolf A.; Martinez-Rossi, Nilce M.

2004-01-01

Resistance to antifungal agents is a recurring and growing problem among patients with systemic fungal infections. UV-induced Aspergillus nidulans mutants resistant to terbinafine have been identified, and we report here the characterization of one such gene. A sib-selected, 6.6-kb genomic DNA fragment encodes a salicylate 1-monooxygenase (salA), and a fatty acid synthase subunit (fasC) confers terbinafine resistance upon transformation of a sensitive strain. Subfragments carrying salA but not fasC confer terbinafine resistance. salA is present as a single-copy gene on chromosome VI and encodes a protein of 473 amino acids that is homologous to salicylate 1-monooxygenase, a well-characterized naphthalene-degrading enzyme in bacteria. salA transcript accumulation analysis showed terbinafine-dependent induction in the wild type and the UV-induced mutant Terb7, as well as overexpression in a strain containing the salA subgenomic DNA fragment, probably due to the multicopy effect caused by the transformation event. Additional naphthalene degradation enzyme-coding genes are present in fungal genomes, suggesting that resistance could follow degradation of the naphthalene ring contained in terbinafine. PMID:15328121

Serratamolide is a hemolytic factor produced by Serratia marcescens.

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Robert M Q Shanks

Full Text Available Serratia marcescens is a common contaminant of contact lens cases and lenses. Hemolytic factors of S. marcescens contribute to the virulence of this opportunistic bacterial pathogen. We took advantage of an observed hyper-hemolytic phenotype of crp mutants to investigate mechanisms of hemolysis. A genetic screen revealed that swrW is necessary for the hyper-hemolysis phenotype of crp mutants. The swrW gene is required for biosynthesis of the biosurfactant serratamolide, previously shown to be a broad-spectrum antibiotic and to contribute to swarming motility. Multicopy expression of swrW or mutation of the hexS transcription factor gene, a known inhibitor of swrW expression, led to an increase in hemolysis. Surfactant zones and expression from an swrW-transcriptional reporter were elevated in a crp mutant compared to the wild type. Purified serratamolide was hemolytic to sheep and murine red blood cells and cytotoxic to human airway and corneal limbal epithelial cells in vitro. The swrW gene was found in the majority of contact lens isolates tested. Genetic and biochemical analysis implicate the biosurfactant serratamolide as a hemolysin. This novel hemolysin may contribute to irritation and infections associated with contact lens use.

Inducible pathway is required for mutagenesis in Salmonella typhimurium LT2

International Nuclear Information System (INIS)

Orrego, C.; Eisenstadt, E.

1987-01-01

UV mutability of Salmonella typhimurium LT2 was eliminated in the presence of a multicopy plasmid carrying the Escherichia coli lexA + gene. This result suggests that inducible, SOS-like functions are required for UV mutagenesis in S. typhimurium. S. typhimurium strains carrying either point or deletion mutations in topA had previously been shown to lose their mutability by UV or methyl methanesulfonate. Mitomycin C induction of the Phi(mucB'-lacZ') fusion (a DNA damage-inducible locus carried on plasmid pSE205) in S. typhimurium topA was normal, suggesting that RecA is activated in topA mutants. These observations lead the authors deduce that S. typhimurium has at least one DNA damage-inducible locus in addition to recA that is required for UV mutability

Common skate (Raja kenojei) secretes pentraxin into the cutaneous secretion: The first skin mucus lectin in cartilaginous fish.

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Tsutsui, Shigeyuki; Yamaguchi, Motoki; Hirasawa, Ai; Nakamura, Osamu; Watanabe, Tasuku

2009-08-01

A lactose-specific lectin with a molecular mass of about 25 kDa was purified from the skin mucus of a cartilaginous fish-the common skate (Raja kenojei). The complementary DNA sequence of the lectin was 1540 bp long and contained a reading frame encoding 226 amino acids, which showed approximately 38% identity to pentraxins of mammals and teleosts. Gene expression was observed in the skin, gill, stomach and intestine in the healthy skate. We also identified an isotype gene from the liver whose deduced amino-acid sequence shared 69.0% identity with the skin type gene. The antiserum detected protein in the skin, where the lectin is localized in the epidermal cells, and in the blood plasma. The lectin genes are multicopied in the common skate genome. Although pentraxins are acute phase proteins, mRNAs of both the isotypes were not upregulated after the in vivo challenge with formalin-killed Escherichia coli, which suggests that they are constantly present in the skin mucus and blood plasma to protect against pathogenic invasion. This lectin is the fifth type of lectin found in the cutaneous secretions of fish, demonstrating that skin mucus lectins have evolved with marked molecular diversity in fish.

Optimal multicopy asymmetric Gaussian cloning of coherent states

International Nuclear Information System (INIS)

Fiurasek, Jaromir; Cerf, Nicolas J.

2007-01-01

We investigate the asymmetric Gaussian cloning of coherent states which produces M copies from N input replicas in such a way that the fidelity of each copy may be different. We show that the optimal asymmetric Gaussian cloning can be performed with a single phase-insensitive amplifier and an array of beam splitters. We obtain a simple analytical expression characterizing the set of optimal asymmetric Gaussian cloning machines and prove the optimality of these cloners using the formalism of Gaussian completely positive maps and semidefinite programming techniques. We also present an alternative implementation of the asymmetric cloning machine where the phase-insensitive amplifier is replaced with a beam splitter, heterodyne detector, and feedforward

Optimal multicopy asymmetric Gaussian cloning of coherent states

Science.gov (United States)

Fiurášek, Jaromír; Cerf, Nicolas J.

2007-05-01

We investigate the asymmetric Gaussian cloning of coherent states which produces M copies from N input replicas in such a way that the fidelity of each copy may be different. We show that the optimal asymmetric Gaussian cloning can be performed with a single phase-insensitive amplifier and an array of beam splitters. We obtain a simple analytical expression characterizing the set of optimal asymmetric Gaussian cloning machines and prove the optimality of these cloners using the formalism of Gaussian completely positive maps and semidefinite programming techniques. We also present an alternative implementation of the asymmetric cloning machine where the phase-insensitive amplifier is replaced with a beam splitter, heterodyne detector, and feedforward.

Incidence and presence of virulence factors of Streptococcus suis infection in slaughtered pigs from Chiang Mai, Thailand.

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Padungtod, Pawin; Tharavichitkul, Prasit; Junya, Supansa; Chaisowong, Warangkhana; Kadohira, Mutsuyo; Makino, Souichi; Sthitmatee, Nattawooti

2010-11-01

This study was designed to determine the incidence of Streptococcus suis infection in slaughtered pigs raised in industrial facility and backyard system in Chiang Mai City, Thailand. A total of 90 tonsils and submaxillary salivary gland/lymph node samples from slaughtered pigs raised in industrial facility and 122 samples from slaughtered pigs raised in backyard system were collected. Isolation and identification of S. suis were conducted using standard bacteriological methods. Farm management and risk factor data were collected by a questionnaire. Serotyping and presence of virulence factor genes, epf, mrp and sly, were determined by multiplex PCR assay. The overall incidence of S. suis in this study was 9% (n = 212) and the incidence is significantly higher in districts located at a greater distance south of Chiang Mai City. S. suis serotype 2 was present more in healthy pigs (43%) than ill pigs (10%). Every S. suis isolate carried mrp and sly and ill pigs carried epf (80%) more than healthy pigs (57%). However, the probability of S. suis serotype 2 with epf+ (0.245) detected in healthy pigs was higher than in ill pigs (0.08) indicating people may have a higher risk of being infected with S. suis from healthy than ill pigs.

[Progress in transgenic fish techniques and application].

Science.gov (United States)

Ye, Xing; Tian, Yuan-Yuan; Gao, Feng-Ying

2011-05-01

Transgenic technique provides a new way for fish breeding. Stable lines of growth hormone gene transfer carps, salmon and tilapia, as well as fluorescence protein gene transfer zebra fish and white cloud mountain minnow have been produced. The fast growth characteristic of GH gene transgenic fish will be of great importance to promote aquaculture production and economic efficiency. This paper summarized the progress in transgenic fish research and ecological assessments. Microinjection is still the most common used method, but often resulted in multi-site and multi-copies integration. Co-injection of transposon or meganuclease will greatly improve the efficiency of gene transfer and integration. "All fish" gene or "auto gene" should be considered to produce transgenic fish in order to eliminate misgiving on food safety and to benefit expression of the transferred gene. Environmental risk is the biggest obstacle for transgenic fish to be commercially applied. Data indicates that transgenic fish have inferior fitness compared with the traditional domestic fish. However, be-cause of the genotype-by-environment effects, it is difficult to extrapolate simple phenotypes to the complex ecological interactions that occur in nature based on the ecological consequences of the transgenic fish determined in the laboratory. It is critical to establish highly naturalized environments for acquiring reliable data that can be used to evaluate the environ-mental risk. Efficacious physical and biological containment strategies remain to be crucial approaches to ensure the safe application of transgenic fish technology.

COMPARATIVE ANALISYS OF ARTICULATION AND PHONOLOGY DISORDERS IN FUNCTION OF DIFFERENTIAL DIAGNOSIS

Directory of Open Access Journals (Sweden)

Ana POPOSKA

2010-04-01

Full Text Available Sound expression is the first impression of speech and language. Whatever its origin, false pronunciation is the first sign. In the early school years of developmental speech – if a language disorder appears, it is often followed by the disruption of the phonological – articulation segment.This research aims to establish and compare frequency, type, and every articulate and acoustic characteristics of the disordered sound in both children with Dyslalia, as well as those with SLI.This micro investigation was done using 71 examinees ages 6 to 8. Thirty-five examinees were with Dyslalia and 36 had SLI. Their achievements are underlined using comparative analysis, tested with two relevant tests.Some of the more important conclusions are:Children with Dyslalia mostly showed distorted sounds, while those with SLI mostly substituted the disordered sound. In Dyslalia, fricatives were most affected, but in the case of SLI, all sound groups were disordered usually. In both tested groups, the type of disorder was due to the misplacement of sound formation. All children having articulation disorders while also having sound discrimination have not only phonetic contrasts, but were also being influenced by the rest of the linguistic aspects.

Preschool language profiles of children at family risk of dyslexia: continuities with specific language impairment

Science.gov (United States)

Nash, Hannah M.; Hulme, Charles; Gooch, Debbie; Snowling, Margaret J.

2015-01-01

Background Children at family risk of dyslexia have been reported to show phonological deficits as well as broader language delays in the preschool years. Method The preschool language skills of 112 children at family risk of dyslexia (FR) at ages 3½ and 4½ were compared with those of children with SLI and typically developing (TD) controls. Results Children at FR showed two different profiles: one third of the group resembled the children with SLI and scored poorly across multiple domains of language including phonology. As a group, the remaining children had difficulties on tasks tapping phonological skills at T1 and T2. At the individual level, we confirmed that some FR children had both phonological and broader oral language difficulties (compared with TD controls), some had only phonological difficulties and some appeared to be developing typically. Conclusions We have highlighted the early overlap between family risk of dyslexia and SLI. A family history of dyslexia carries an increased risk for SLI and the two disorders both show an increased incidence of phonological deficits which appear to a proximal risk factor for developing a reading impairment. PMID:23772651

Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

KAUST Repository

Alam, Tanvir

2018-03-11

Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.

Hypertext comprehension of deaf and hard-of-hearing students and students with specific language impairment.

Science.gov (United States)

Blom, Helen; Segers, Eliane; Hermans, Daan; Knoors, Harry; Verhoeven, Ludo

2017-02-01

This paper provides insight into the reading comprehension of hierarchically structured hypertexts within D/HH students and students with SLI. To our knowledge, it is the first study on hypertext comprehension in D/HH students and students with SLI, and it also considers the role of working memory. We compared hypertext versus linear text comprehension in D/HH students and students with SLI versus younger students without language problems who had a similar level of decoding and vocabulary. The results demonstrated no difference in text comprehension between the hierarchically structured hypertext and the linear text. Text comprehension of D/HH students and students with SLI was comparable to that of the students without language problems. In addition, there was a similar positive predictive value of visuospatial and not verbal working memory on hypertext comprehension for all three groups. The findings implicate that educational settings can make use of hierarchically structured hypertexts as well as linear texts and that children can navigate in the digital world from young age on, even if language or working memory problems are present. Copyright © 2016 Elsevier Ltd. All rights reserved.

A multicopy phr-plasmid increases the ultraviolet resistance of a recA strain of Escherichia coli

International Nuclear Information System (INIS)

Yamamoto, K.; Satake, M.; Shinagawa, H.

1984-01-01

It has been previously reported that the ultraviolet sensitivity of recA strains of Escherichia coli in the dark is suppressed by a plasmid pKY1 which carries the phr gene, suggesting that this is due to a novel effect of photoreactivating enzyme (PRE) of E. coli in the dark. In this work, it is observed that an increase of UV-resistance by pKY1 in the dark is not apparent in strains with a mutation in either uvrA, uvrB, uvrC, lexA, recBC or recF. The sensitivity of recA lexA and recA recBC multiple mutants to UV is suppressed by the plasmid but that of recA uvrA, recA uvrB and recA uvrC is not. Host-cell reactivation of UV-irradiated lambda phage is slightly more efficient in the recA/pKY1 strain compared with the parental recA strain. On the other hand, the recA and recA/pKY1 strains do not differ significantly in the following properties: Hfr recombination, induction of lambda by UV, and mutagenesis. It is suggested that dark repair of PRE is correlated with its capacity of excision repair. (Auth.)

Thinking or feeling? An exploratory study of maternal scaffolding, child mental state talk, and emotion understanding in language-impaired and typically developing school-aged children.

Science.gov (United States)

Yuill, Nicola; Little, Sarah

2018-06-01

Mother-child mental state talk (MST) supports children's developing social-emotional understanding. In typically developing (TD) children, family conversations about emotion, cognition, and causes have been linked to children's emotion understanding. Specific language impairment (SLI) may compromise developing emotion understanding and adjustment. We investigated emotion understanding in children with SLI and TD, in relation to mother-child conversation. Specifically, is cognitive, emotion, or causal MST more important for child emotion understanding and how might maternal scaffolding support this? Nine 5- to 9-year-old children with SLI and nine age-matched typically developing (TD) children, and their mothers. We assessed children's language, emotion understanding and reported behavioural adjustment. Mother-child conversations were coded for MST, including emotion, cognition, and causal talk, and for scaffolding of causal talk. Children with SLI scored lower than TD children on emotion understanding and adjustment. Mothers in each group provided similar amounts of cognitive, emotion, and causal talk, but SLI children used proportionally less cognitive and causal talk than TD children did, and more such child talk predicted better child emotion understanding. Child emotion talk did not differ between groups and did not predict emotion understanding. Both groups participated in maternal-scaffolded causal talk, but causal talk about emotion was more frequent in TD children, and such talk predicted higher emotion understanding. Cognitive and causal language scaffolded by mothers provides tools for articulating increasingly complex ideas about emotion, predicting children's emotion understanding. Our study provides a robust method for studying scaffolding processes for understanding causes of emotion. © 2017 The British Psychological Society.

Individual differences in the shape bias in preschool children with specific language impairment and typical language development: theoretical and clinical implications.

Science.gov (United States)

Collisson, Beverly Anne; Grela, Bernard; Spaulding, Tammie; Rueckl, Jay G; Magnuson, James S

2015-05-01

We investigated whether preschool children with specific language impairment (SLI) exhibit the shape bias in word learning: the bias to generalize based on shape rather than size, color, or texture in an object naming context ('This is a wek; find another wek') but not in a non-naming similarity classification context ('See this? Which one goes with this one?'). Fifty-four preschool children (16 with SLI, 16 children with typical language [TL] in an equated control group, and 22 additional children with TL included in individual differences analyses but not group comparisons) completed a battery of linguistic and cognitive assessments and two experiments. In Experiment 1, children made generalization choices in object naming and similarity classification contexts on separate days, from options similar to a target object in shape, color, or texture. On average, TL children exhibited the shape bias in an object naming context, but children with SLI did not. In Experiment 2, we tested whether the failure to exhibit the shape bias might be linked to ability to detect systematicities in the visual domain. Experiment 2 supported this hypothesis, in that children with SLI failed to learn simple paired visual associations that were readily learned by children with TL. Analyses of individual differences in the two studies revealed that visual paired-associate learning predicted degree of shape bias in children with SLI and TL better than any other measure of nonverbal intelligence or standard assessments of language ability. We discuss theoretical and clinical implications. © 2014 John Wiley & Sons Ltd.

Community-based participatory research projects and policy engagement to protect environmental health on St Lawrence Island, Alaska

Directory of Open Access Journals (Sweden)

Pamela K. Miller

2013-08-01

Full Text Available Objectives . This article synthesizes discussion of collaborative research results, interventions and policy engagement for St Lawrence Island (SLI, Alaska, during the years 2000–2012. Methods . As part of on-going community-based participatory research (CBPR studies on SLI, 5 discrete exposure-assessment projects were conducted: (a a biomonitoring study of human blood serum; (b–d 3 investigations of levels of contaminants in environmental media at an abandoned military site at Northeast Cape – using sediment cores and plants, semi-permeable membrane devices and blackfish, respectively; and (e a study of traditional foods. Results . Blood serum in residents of SLI showed elevated levels of polychlorinated biphenyls (PCBs with higher levels among those exposed to the military site at Northeast Cape, an important traditional subsistence-use area. Environmental studies at the military site demonstrated that the site is a continuing source of PCBs to a major watershed, and that clean-up operations at the military site generated PCB-contaminated dust on plants in the region. Important traditional foods eaten by the people of SLI showed elevated concentrations of PCBs, which are primarily derived from the long-range transport of persistent pollutants that are transported by atmospheric and marine currents from more southerly latitudes to the north. Interventions . An important task for all CBPR projects is to conduct intervention strategies as needed in response to research results. Because of the findings of the CBPR projects on SLI, the CBPR team and the people of the Island are actively engaging in interventions to ensure cleanup of the formerly used military sites; reform chemicals policy on a national level; and eliminate persistent pollutants internationally. The goal is to make the Island and other northern/Arctic communities safe for themselves and future generations. Conclusions . As part of the CBPR projects conducted from 2000 to 2012

Statistical word learning in children with autism spectrum disorder and specific language impairment.

Science.gov (United States)

Haebig, Eileen; Saffran, Jenny R; Ellis Weismer, Susan

2017-11-01

Word learning is an important component of language development that influences child outcomes across multiple domains. Despite the importance of word knowledge, word-learning mechanisms are poorly understood in children with specific language impairment (SLI) and children with autism spectrum disorder (ASD). This study examined underlying mechanisms of word learning, specifically, statistical learning and fast-mapping, in school-aged children with typical and atypical development. Statistical learning was assessed through a word segmentation task and fast-mapping was examined in an object-label association task. We also examined children's ability to map meaning onto newly segmented words in a third task that combined exposure to an artificial language and a fast-mapping task. Children with SLI had poorer performance on the word segmentation and fast-mapping tasks relative to the typically developing and ASD groups, who did not differ from one another. However, when children with SLI were exposed to an artificial language with phonemes used in the subsequent fast-mapping task, they successfully learned more words than in the isolated fast-mapping task. There was some evidence that word segmentation abilities are associated with word learning in school-aged children with typical development and ASD, but not SLI. Follow-up analyses also examined performance in children with ASD who did and did not have a language impairment. Children with ASD with language impairment evidenced intact statistical learning abilities, but subtle weaknesses in fast-mapping abilities. As the Procedural Deficit Hypothesis (PDH) predicts, children with SLI have impairments in statistical learning. However, children with SLI also have impairments in fast-mapping. Nonetheless, they are able to take advantage of additional phonological exposure to boost subsequent word-learning performance. In contrast to the PDH, children with ASD appear to have intact statistical learning, regardless of

Silicone líquido industrial para transformar o corpo: prevalência e fatores associados ao seu uso entre travestis e mulheres transexuais em São Paulo, Brasil

Directory of Open Access Journals (Sweden)

Thiago Pestana Pinto

Full Text Available O objetivo deste trabalho foi estimar a prevalência do uso de silicone líquido industrial (SLI entre pessoas travestis e mulheres transexuais e identificar os fatores relacionados a esta prática. Trata-se de estudo transversal realizado em sete municípios do Estado de São Paulo, Brasil, com dados coletados entre 2014 e 2015, em uma amostra de 576 pessoas. Na análise dos fatores associados, utilizamos o modelo de Poisson com variância robusta para estimar as razões de prevalências bruta e ajustada. A prevalência do uso de SLI foi de 49%, a média de idade para a primeira colocação de SLI foi de 22 (± 5,3 anos e aproximadamente 43% informaram a ocorrência de problemas de saúde decorrente do uso. No modelo múltiplo ter escolaridade menor que o nível superior, estar em faixa etária a partir dos 20 anos, identificar-se como travesti e exercer a prostituição foram associados positivamente com a utilização de SLI. Houve uma elevada prevalência do uso de SLI e de problemas decorrentes desta prática, indicando um desafio acerca da prevenção do uso e da redução dos danos à saúde provocados pelo SLI. Dessa forma, torna-se fundamental assegurar o acesso aos recursos necessários para a realização das modificações corporais ao longo do percurso de transição por meio de uma atenção integral à saúde das pessoas travestis e transexuais no Sistema Único de Saúde. Finalmente, incluir nas políticas de saúde as demandas por modificações corporais como parte da construção da identidade de gênero, respeitando as necessidades singulares de cada pessoa neste processo de transição.

Identifying language impairment in bilingual children in France and in Germany.

Science.gov (United States)

Tuller, Laurice; Hamann, Cornelia; Chilla, Solveig; Ferré, Sandrine; Morin, Eléonore; Prevost, Philippe; Dos Santos, Christophe; Abed Ibrahim, Lina; Zebib, Racha

2018-05-23

The detection of specific language impairment (SLI) in children growing up bilingually presents particular challenges for clinicians. Non-word repetition (NWR) and sentence repetition (SR) tasks have proven to be the most accurate diagnostic tools for monolingual populations, raising the question of the extent of their usefulness in different bilingual populations. To determine the diagnostic accuracy of NWR and SR tasks that incorporate phonological/syntactic complexity as discussed in recent linguistic theory. The tasks were developed as part of the Language Impairment Testing in Multilingual Settings (LITMUS) toolkit, in two different national settings, France and Germany, and investigated children with three different home languages: Arabic, Portuguese and Turkish. NWR and SR tasks developed in parallel were administered to 151 bilingual children, aged 5;6-8;11, in France and in Germany, to 64 children in speech-language therapy (SLT) and to 87 children not in SLT, whose first language (L1) was Arabic, Portuguese or Turkish. Children were also administered standardized language tests in each of their languages to determine likely clinical status (typical development (TD) or SLI), and parents responded to a questionnaire including questions about early and current language use (bilingualism factors) and early language development (risk factors for SLI). Monolingual controls included 47 TD children and 29 children with SLI. Results were subjected to inter-group comparisons, to diagnostic accuracy calculation, and to correlation and multiple regression analyses. In accordance with previous studies, NWR and SR identified SLI in the monolingual children, yielding good to excellent diagnostic accuracy. Diagnostic accuracy in bilingual children was fair to good, generally distinguishing children likely to have SLI from children likely to have TD. Accuracy was necessarily linked to the determination of clinical status, which was based on standardized assessment in each

Genes and Gene Therapy

Science.gov (United States)

... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

Non-adjacent dependency learning in Cantonese-speaking\\ud children with and without a history of specific language\\ud impairment

OpenAIRE

Iao, L-S; Ng, LY; Wong, AMY; Lee, OT

2017-01-01

Purpose: This study investigated non-adjacent dependency learning in Cantonese-speaking children with and without a history of Specific Language Impairment (SLI) in an artificial linguistic context.\\ud \\ud Method: Sixteen Cantonese-speaking children with SLI history and 16 Cantonese-speaking children with typical language development (TLD) were tested with a non-adjacent dependency learning task using artificial languages that mimic Cantonese.\\ud \\ud Results: Children with TLD performed above...

The relation between receptive grammar and procedural, declarative, and working memory in specific language impairment

OpenAIRE

Conti-Ramsden, Gina; Ullman, Michael T.; Lum, Jarrad A. G.

2015-01-01

What memory systems underlie grammar in children, and do these differ between typically developing children and children with specific language impairment (SLI)? Whilst there is substantial evidence linking certain memory deficits to the language problems in children with SLI, few studies have investigated multiple memory systems simultaneously, examining not only possible memory deficits but also memory abilities that may play a compensatory role. This study examined the extent to which proc...

Autistic symptomatology and language ability in autism spectrum disorder and specific language impairment.

Science.gov (United States)

Loucas, Tom; Charman, Tony; Pickles, Andrew; Simonoff, Emily; Chandler, Susie; Meldrum, David; Baird, Gillian

2008-11-01

Autism spectrum disorders (ASD) and specific language impairment (SLI) are common developmental disorders characterised by deficits in language and communication. The nature of the relationship between them continues to be a matter of debate. This study investigates whether the co-occurrence of ASD and language impairment is associated with differences in severity or pattern of autistic symptomatology or language profile. Participants (N = 97) were drawn from a total population cohort of 56,946 screened as part of study to ascertain the prevalence of ASD, aged 9 to 14 years. All children received an ICD-10 clinical diagnosis of ASD or No ASD. Children with nonverbal IQ > or =80 were divided into those with a language impairment (language score of 77 or less) and those without, creating three groups: children with ASD and a language impairment (ALI; N = 41), those with ASD and but no language impairment (ANL; N = 31) and those with language impairment but no ASD (SLI; N = 25). Children with ALI did not show more current autistic symptoms than those with ANL. Children with SLI were well below the threshold for ASD. Their social adaptation was higher than the ASD groups, but still nearly 2 SD below average. In ALI the combination of ASD and language impairment was associated with weaker functional communication and more severe receptive language difficulties than those found in SLI. Receptive and expressive language were equally impaired in ALI, whereas in SLI receptive language was stronger than expressive. Co-occurrence of ASD and language impairment is not associated with increased current autistic symptomatology but appears to be associated with greater impairment in receptive language and functional communication.

[Use of the 2D:4D digit ratio as a biological marker of specific language disorders].

Science.gov (United States)

Font-Jordà, Antònia; Gamundí, Antoni; Nicolau Llobera, María Cristina; Aguilar-Mediavilla, Eva

2018-04-03

The finding of biological markers of specific language impairment would facilitate their detection and early intervention. In this sense, the 2D:4D finger ratio is considered an indirect indicator of prenatal exposure to testosterone. Previous studies have related it to linguistic competence and aggressive behaviour, and could be a candidate for a biological marker of language impairment. The aim was to compare the value of the 2D:4D ratio in children with Specific Language Impairment (SLI) with those of children with typical language development, as well as to establish to what extent this biological index correlates with the behaviour (linguistic, cognitive, social,...) in both groups. 2D:4D ratio, language, cognition and social behaviour were compared in a group of children with SLI (n=15), with a group of children without language difficulties (n=16) of the same age (between 5-8 years), gender (male), and socio-cultural level. Children with SLI showed significantly higher values of 2D:4D ratio of the right hand, and a negative correlation between this ratio and their linguistic competence. Although the children with SLI showed impaired adaptive abilities, but not more aggressive behaviour, these measurements did not correlate with the 2D:4D index. Nevertheless, social behaviour correlated with language and cognition competence. A higher value of the biological 2D:4D ration (lower intrauterine exposure to testosterone) seems to be associated with language difficulties in boys with SLI, but not with their behavioural difficulties. Their behavioural difficulties seem to be a consequence of their linguistic difficulties and their level of cognition. Copyright © 2018. Publicado por Elsevier España, S.L.U.

Sustained versus intermittent lung inflation for resuscitation of preterm infants: a randomized controlled trial.

Science.gov (United States)

El-Chimi, Mohamed S; Awad, Hisham A; El-Gammasy, Tarek M; El-Farghali, Ola G; Sallam, Mohamed T; Shinkar, Dina M

2017-06-01

To evaluate efficacy and safety of delivery room (DR) sustained lung inflation (SLI) in resuscitation of preterm neonates. Randomized Controlled Trial including 112 preterm infants randomized to either SLI (n = 57) using T-piece resuscitator [maximum three inflations with maximum pressure of 30 cmH 2 O for 15 s followed by continuous positive airway pressure (CPAP) of 5-7 cmH 2 O] or conventional bag/mask inflation (CBMI) (n = 55) using traditional self-inflating bag (maximum pressure of 40 cmH 2 O at a rate of 40-60 per min). Failure was defined as the need for DR or first 72 h intubation. Cord and 2-h post-resuscitation blood samples were collected to measure interleukin (IL)-1β and tumor necrosis factor-α levels before and after intervention. SLI was associated with significantly higher success rate compared to CBMI [75.4 versus 54.5%; p = 0.017], lower need for DR intubation [5.3% versus 23.6%; (X 2  =   7.7; p = 0.005)], higher 5-min-Apgar score (median 8 versus 7; p = 0.018), shorter duration on nasal-CPAP (p = 0.017), and non-significantly different air leak (7% versus 11%; p = 0.3) and bronchopulmonary dysplasia rates among survivors (2% versus 11%; p = 0.09). Post-resuscitation IL-1β plasma levels increased significantly in CBMI (p = 0.009) and not in SLI group. Delivery room SLI is more effective than intermittent bag and mask inflation for improving short-term respiratory outcome in preterm infants, without significant adverse effects.

Motor skills, haptic perception and social abilities in children with mild speech disorders.

Science.gov (United States)

Müürsepp, Iti; Aibast, Herje; Gapeyeva, Helena; Pääsuke, Mati

2012-02-01

The aim of the study was to evaluate motor skills, haptic object recognition and social interaction in 5-year-old children with mild specific expressive language impairment (expressive-SLI) and articulation disorder (AD) in comparison of age- and gender matched healthy children. Twenty nine children (23 boys and 6 girls) with expressive-SLI, 27 children (20 boys and 7 girls) with AD and 30 children (23 boys and 7 girls) with typically developing language as controls participated in our study. The children were examined for manual dexterity, ball skills, static and dynamic balance by M-ABC test, haptic object recognition and for social interaction by questionnaire completed by teachers. Children with mild expressive-SLI demonstrated significantly poorer results in all subtests of motor skills (psocial interaction (p0.05) in measured parameters between children with AD and controls. Children with expressive-SLI performed considerably poorer compared to AD group in balance subtest (psocial interaction are considerably more affected than in children with AD. Although motor difficulties in speech production are prevalent in AD, it is localised and does not involve children's general motor skills, haptic perception or social interaction. Copyright © 2011 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

Depletion of somatostatin-like immunoreactivity in the rat central nervous system by cysteamine

International Nuclear Information System (INIS)

Sagar, S.M.; Landry, D.; Millard, W.J.; Badger, T.M.; Arnold, M.A.; Martin, J.B.

1982-01-01

Selective neurotoxins have been of value in providing a means for specifically interfering with the actions of endogenous neurotransmitter candidates. Others have shown cysteamine (CSH) to deplete the gastrointestinal tract and hypothalamus of rats of immunoreactive somatostatin, suggesting a toxic action of that compound directed against somatostatin-containing cells. The present study further defines the actions of cysteamine on somatostatin in the central nervous system. (CNS). Cysteamine hydrochloride administered subcutaneously results in a depletion of somatostatin-like immunoreactivity (SLI) in the retina, brain, and cervical spinal cord of rats. The effect is demonstrable at doses of 30 mg/kg of body weight and above, occurs within 2 to 4 hr of a single injection of the drug, and is largely reversible within 1 week. The mean depletion of SLI observed within the CNS varies from 38% in cerebral cortex to 65% in cervical spinal cord 24 hr following administration of CSH, 300 mg/kg of body weight, s.c. By gel permeation chromatography, all molecular weight forms of SLI are affected, with the largest reductions in those forms that co-chromatograph with synthetic somatostatin-14 and somatostatin-28. These results indicate that CSH has a generalized, rapid, and largely reversible effect in depleting SLI from the rat CNS

Control of Auditory Attention in Children With Specific Language Impairment.

Science.gov (United States)

Victorino, Kristen R; Schwartz, Richard G

2015-08-01

Children with specific language impairment (SLI) appear to demonstrate deficits in attention and its control. Selective attention involves the cognitive control of attention directed toward a relevant stimulus and simultaneous inhibition of attention toward irrelevant stimuli. The current study examined attention control during a cross-modal word recognition task. Twenty participants with SLI (ages 9-12 years) and 20 age-matched peers with typical language development (TLD) listened to words through headphones and were instructed to attend to the words in 1 ear while ignoring the words in the other ear. They were simultaneously presented with pictures and asked to make a lexical decision about whether the pictures and auditory words were the same or different. Accuracy and reaction time were measured in 5 conditions, in which the stimulus in the unattended channel was manipulated. The groups performed with similar accuracy. Compared with their peers with TLD, children with SLI had slower reaction times overall and different within-group patterns of performance by condition. Children with TLD showed efficient inhibitory control in conditions that required active suppression of competing stimuli. Participants with SLI had difficulty exerting control over their auditory attention in all conditions, with particular difficulty inhibiting distractors of all types.

Applying an Integrative Framework of Executive Function to Preschoolers With Specific Language Impairment.

Science.gov (United States)

Kapa, Leah L; Plante, Elena; Doubleday, Kevin

2017-08-16

The first goal of this research was to compare verbal and nonverbal executive function abilities between preschoolers with and without specific language impairment (SLI). The second goal was to assess the group differences on 4 executive function components in order to determine if the components may be hierarchically related as suggested within a developmental integrative framework of executive function. This study included 26 4- and 5-year-olds diagnosed with SLI and 26 typically developing age- and sex-matched peers. Participants were tested on verbal and nonverbal measures of sustained selective attention, working memory, inhibition, and shifting. The SLI group performed worse compared with typically developing children on both verbal and nonverbal measures of sustained selective attention and working memory, the verbal inhibition task, and the nonverbal shifting task. Comparisons of standardized group differences between executive function measures revealed a linear increase with the following order: working memory, inhibition, shifting, and sustained selective attention. The pattern of results suggests that preschoolers with SLI have deficits in executive functioning compared with typical peers, and deficits are not limited to verbal tasks. A significant linear relationship between group differences across executive function components supports the possibility of a hierarchical relationship between executive function skills.

Extending Use of the NRT to Preschool-Aged Children with and without Specific Language Impairment

Science.gov (United States)

Deevy, Patricia; Weil, Lisa Wisman; Leonard, Laurence B.; Goffman, Lisa

2009-01-01

Purpose The purpose of this study was to assess the diagnostic accuracy of the Nonword Repetition Test (NRT; Dollaghan & Campbell, 1998) in a sample of four- and five-year-olds with and without specific language impairment (SLI), and to evaluate its feasibility for use in universal screening. Method The NRT was administered to 29 children with SLI and 47 age-matched children with typical development (TD). Diagnostic accuracy was computed using alternative scoring methods, which treated out-of-inventory phonemes either as errors or as unscorable. To estimate accuracy in a universal screening context, probability of identifying a child at risk for language impairment was computed using the prevalence of SLI (7%) as the base rate. Results Diagnostic accuracy was acceptable using both scoring methods. The resulting likelihood ratios (LR+ = 22.66, 19.43; LR- = .05, .05) were similar to those reported for older children. The probability of accurate detection of children with SLI in the general population increased from 7% to 61%. However this value suggests that many false positives could be expected. Conclusions The NRT yielded results similar to those reported for older children. However, despite its strengths, the NRT is not sufficient for screening the general population of four- and five-year-olds. PMID:20421612

Extending use of the NRT to preschool-age children with and without specific language impairment.

Science.gov (United States)

Deevy, Patricia; Weil, Lisa Wisman; Leonard, Laurence B; Goffman, Lisa

2010-07-01

The purpose of this study was to assess the diagnostic accuracy of the Nonword Repetition Test (NRT; Dollaghan & Campbell, 1998) using a sample of 4- and 5-year-olds with and without specific language impairment (SLI) and to evaluate its feasibility for use in universal screening. The NRT was administered to 29 children with SLI and 47 age-matched children with typical development. Diagnostic accuracy was computed using alternative scoring methods, which treated out-of-inventory phonemes either as errors or as unscorable. To estimate accuracy in a universal screening context, the probability of identifying a child at risk for language impairment was computed using the prevalence of SLI (7%) as the base rate. Diagnostic accuracy was acceptable using both scoring methods. The resulting likelihood ratios (LR+ = 22.66, 19.43; LR- = .05, .05) were similar to those reported for older children. The probability of accurate detection of children with SLI in the general population increased from 7% to 61%. However, this value suggests that many false positives could be expected. The NRT yielded results similar to those reported for older children. However, despite its strengths, the NRT is not sufficient for screening the general population of 4- and 5-year-olds.

Applying an Integrative Framework of Executive Function to Preschoolers With Specific Language Impairment

Science.gov (United States)

Plante, Elena; Doubleday, Kevin

2017-01-01

Purpose The first goal of this research was to compare verbal and nonverbal executive function abilities between preschoolers with and without specific language impairment (SLI). The second goal was to assess the group differences on 4 executive function components in order to determine if the components may be hierarchically related as suggested within a developmental integrative framework of executive function. Method This study included 26 4- and 5-year-olds diagnosed with SLI and 26 typically developing age- and sex-matched peers. Participants were tested on verbal and nonverbal measures of sustained selective attention, working memory, inhibition, and shifting. Results The SLI group performed worse compared with typically developing children on both verbal and nonverbal measures of sustained selective attention and working memory, the verbal inhibition task, and the nonverbal shifting task. Comparisons of standardized group differences between executive function measures revealed a linear increase with the following order: working memory, inhibition, shifting, and sustained selective attention. Conclusion The pattern of results suggests that preschoolers with SLI have deficits in executive functioning compared with typical peers, and deficits are not limited to verbal tasks. A significant linear relationship between group differences across executive function components supports the possibility of a hierarchical relationship between executive function skills. PMID:28724132

Theory of Mind in Children With Specific Language Impairment: A Systematic Review and Meta-Analysis.

Science.gov (United States)

Nilsson, Kristine Kahr; de López, Kristine Jensen

2016-01-01

The relation between language and theory of mind (ToM) has been debated for more than two decades. In a similar vein, ToM has been examined in children with specific language impairment (SLI), albeit with inconsistent results. This meta-analysis of 17 studies with 745 children between the ages of 4 and 12 found that children with SLI had substantially lower ToM performance compared to age-matched typically developing children (d = .98). This effect size was not moderated by age and gender. By revealing that children with SLI have ToM impairments, this finding emphasizes the need for further investigation into the developmental interface between language and ToM as well as the extended consequences of atypical language development. © 2015 The Authors. Child Development © 2015 Society for Research in Child Development, Inc.

Rates of auxiliary is and are in African American English speaking children with specific language impairment following language treatment.

Science.gov (United States)

Smith, Shana; Bellon-Harn, Monica L

2015-02-01

The purpose of this exploratory study is to examine rates of auxiliary is and are across dialect patterns produced by African American English with specific language impairment (AAE-SLI) children following language treatment. The following research question is asked: Do AAE-SLI children exhibit rates of auxiliary is and are across dialect patterns consistent with previous reports of typically developing children and adult AAE speakers? A pre-/post-test design was used to identify patterns in which auxiliary is and are were produced at significant levels. Individual performance was included to examine variable rates of use across patterns. Group and individual results suggest children used auxiliary is and are in dialect patterns at rates consistent with typically developing child and adult AAE speakers. We conclude that rates of use may contribute to evidence-based guidelines for morphological intervention with AAE-SLI children.

The role of verbal and nonverbal memory in the Family Pictures Subtest: Data from children with specific language impairment

OpenAIRE

Lum, Jarrad A. G.; Conti-Ramsden, Gina; Ullman, Michael T.

2012-01-01

This study examined the contribution of verbal and visual memory to performance on the Family Pictures subtest of the Children's Memory Scale. This subtest purports to assess declarative memory functioning in the visual/nonverbal domain. A total of 115 nine-year-old children participated in this study. Fifty-eight had specific language impairment (SLI), whilst the remaining 57 were typically developing (TD), with no history of language difficulties. Results showed that the children with SLI, ...

The acquisition of nouns in children with Specific Language Impairment

OpenAIRE

Krzemien, Magali; Thibaut, Jean-Pierre; Zghonda, Hela; Maillart, Christelle

2017-01-01

Specific Language Impairment (SLI) is a neurodevelopmental disorder that affects the language development of children with a normal nonverbal intelligence and no history of neurological disorder nor auditory deficit (Leonard, 2014). A difficulty linked to SLI is the poor language productivity and the input dependency that children display compared with their peers: they tend to use a limited variety of verbal forms compared to younger siblings (Conti-Ramsden & Jones, 1997) and use a high prop...

Second Generation RLV Space Vehicle Concept

Science.gov (United States)

Bailey, M. D.; Daniel, C. C.

2002-01-01

NASA has a long history of conducting development programs and projects in a consistant fashion. Systems Engineering within those programs and projects has also followed a given method outlined by such documents as the NASA Systems Engineering Handbook. The relatively new NASA Space Launch Initiative (SLI) is taking a new approach to developing a space vehicle, with innovative management methods as well as new Systems Engineering processes. With the program less than a year into its life cycle, the efficacy of these new processes has yet to be proven or disproven. At 776M for phase I, SLI represents a major portion of the NASA focus; however, the new processes being incorporated are not reflected in the training provided by NASA to its engineers. The NASA Academy of Program and Project Leadership (APPL) offers core classes in program and project management and systems engineering to NASA employees with the purpose of creating a "knowledge community where ideas, skills, and experiences are exchanged to increase each other's capacity for strong leadership". The SLI program is, in one sense, a combination of a conceptual design program and a technology program. The program as a whole doesn't map into the generic systems engineering project cycle as currently, and for some time, taught. For example, the NASA APPL Systems Engineering training course teaches that the "first step in developing an architecture is to define the external boundaries of the system", which will require definition of the interfaces with other systems and the next step will be to "define all the components that make up the next lower level of the system hierarchy" where fundamental requirements are allocated to each component. Whereas, the SLI technology risk reduction approach develops architecture subsystem technologies prior to developing architectures. The higher level architecture requirements are not allowed to fully develop and undergo decomposition and allocation down to the subsystems

NRI and SLI Status Map

Data.gov (United States)

Farm Service Agency, Department of Agriculture — The National Resource Inventory (NRI) program acquires aerial photos of small 1/4 section sites nationwide. It is special purpose photography for government land-use...

Gene expression and gene therapy imaging

International Nuclear Information System (INIS)

Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

2007-01-01

The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

Children with Specific Language Impairment and Their Families: A Future View of Nature Plus Nurture and New Technologies for Comprehensive Language Intervention Strategies.

Science.gov (United States)

Rice, Mabel L

2016-11-01

Future perspectives on children with language impairments are framed from what is known about children with specific language impairment (SLI). A summary of the current state of services is followed by discussion of how these children can be overlooked and misunderstood and consideration of why it is so hard for some children to acquire language when it is effortless for most children. Genetic influences are highlighted, with the suggestion that nature plus nurture should be considered in present as well as future intervention approaches. A nurture perspective highlights the family context of the likelihood of SLI for some of the children. Future models of the causal pathways may provide more specific information to guide gene-treatment decisions, in ways parallel to current personalized medicine approaches. Future treatment options can build on the potential of electronic technologies and social media to provide personalized treatment methods available at a time and place convenient for the person to use as often as desired. The speech-language pathologist could oversee a wide range of treatment options and monitor evidence provided electronically to evaluate progress and plan future treatment steps. Most importantly, future methods can provide lifelong language acquisition activities that maintain the privacy and dignity of persons with language impairment, and in so doing will in turn enhance the effectiveness of speech-language pathologists. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Lactose intolerance in infants with gluten-sensitive enteropathy: Frequency and clinical characteristics

Directory of Open Access Journals (Sweden)

Radlović Nedeljko

2009-01-01

Full Text Available Introduction. Secondary lactose intolerance (SLI belongs to the rarer manifestations of gluten-sensitive enteropathy (GSE. It occurs in more severe forms of the disease and its presence contributes significantly to the degree of its expression. Objective. The goal of the study was to determine the frequency of SLI in infants with clinically classic form of GSE, as well as its relationship with the duration, severity and age at the diagnosis of the basic disease and the degree of small bowel mucosa damage. Methods. The study was based on a sample of 42 infants, 30 female and 12 male, aged 7-12 months (x=9.98±1.69, with a clinically classic form of GSE. The diagnosis of GSE was established based on the characteristic pathohistological appearance of small bowel mucosa and clinical improvement of patients on gluten-free diet, while SLI on pathological lactose or milk tolerance test. The assessment of basic disease severity was based on body mass divergence in relation to the standard value, as well as on Hb and serum iron levels, while the degree of small bowel mucosa damage was determined according to the modified Marsh criteria. Results. SLI was verified in 8/42 or 19.05% of patients. In addition to the symptoms and clinical signs of GSE, all the patients with SLI also featured the problems characteristic of lactose tolerance disorders, i.e. watery diarrhoea, borborygmus and meteorism occurring after milk meals. In addition, all had perianal erythema (6 with erosive changes, as well as destructive enteropathy (5 subtotal and 3 total. The difference in the duration of the basic disease, age at diagnosis, as well as in the degree of body mass deviation from the standard value between the lactose-tolerant and lactose-intolerant infants was not found. In addition, no difference in Hb and serum iron levels or in the degree of small bowel mucosa damage was found between the two groups. Conclusion. Our findings indicate that SLI presents a relatively

Grammar predicts procedural learning and consolidation deficits in children with Specific Language Impairment.

Science.gov (United States)

Hedenius, Martina; Persson, Jonas; Tremblay, Antoine; Adi-Japha, Esther; Veríssimo, João; Dye, Cristina D; Alm, Per; Jennische, Margareta; Bruce Tomblin, J; Ullman, Michael T

2011-01-01

The Procedural Deficit Hypothesis (PDH) posits that Specific Language Impairment (SLI) can be largely explained by abnormalities of brain structures that subserve procedural memory. The PDH predicts impairments of procedural memory itself, and that such impairments underlie the grammatical deficits observed in the disorder. Previous studies have indeed reported procedural learning impairments in SLI, and have found that these are associated with grammatical difficulties. The present study extends this research by examining consolidation and longer-term procedural sequence learning in children with SLI. The Alternating Serial Reaction Time (ASRT) task was given to children with SLI and typically developing (TD) children in an initial learning session and an average of three days later to test for consolidation and longer-term learning. Although both groups showed evidence of initial sequence learning, only the TD children showed clear signs of consolidation, even though the two groups did not differ in longer-term learning. When the children were re-categorized on the basis of grammar deficits rather than broader language deficits, a clearer pattern emerged. Whereas both the grammar impaired and normal grammar groups showed evidence of initial sequence learning, only those with normal grammar showed consolidation and longer-term learning. Indeed, the grammar-impaired group appeared to lose any sequence knowledge gained during the initial testing session. These findings held even when controlling for vocabulary or a broad non-grammatical language measure, neither of which were associated with procedural memory. When grammar was examined as a continuous variable over all children, the same relationships between procedural memory and grammar, but not vocabulary or the broader language measure, were observed. Overall, the findings support and further specify the PDH. They suggest that consolidation and longer-term procedural learning are impaired in SLI, but that these

Grammar Predicts Procedural Learning and Consolidation Deficits in Children with Specific Language Impairment

Science.gov (United States)

Hedenius, Martina; Persson, Jonas; Tremblay, Antoine; Adi-Japha, Esther; Veríssimo, João; Dye, Cristina D.; Alm, Per; Jennische, Margareta; Tomblin, J. Bruce; Ullman, Michael T.

2011-01-01

The Procedural Deficit Hypothesis (PDH) posits that Specific Language Impairment (SLI) can be largely explained by abnormalities of brain structures that subserve procedural memory. The PDH predicts impairments of procedural memory itself, and that such impairments underlie the grammatical deficits observed in the disorder. Previous studies have indeed reported procedural learning impairments in SLI, and have found that these are associated with grammatical difficulties. The present study extends this research by examining the consolidation and longer-term procedural sequence learning in children with SLI. The Alternating Serial Reaction Time (ASRT) task was given to children with SLI and typically-developing (TD) children in an initial learning session and an average of three days later to test for consolidation and longer-term learning. Although both groups showed evidence of initial sequence learning, only the TD children showed clear signs of consolidation, even though the two groups did not differ in longer-term learning. When the children were re-categorized on the basis of grammar deficits rather than broader language deficits, a clearer pattern emerged. Whereas both the grammar impaired and normal grammar groups showed evidence of initial sequence learning, only those with normal grammar showed consolidation and longer-term learning. Indeed, the grammar-impaired group appeared to lose any sequence knowledge gained during the initial testing session. These findings held even when controlling for vocabulary or a broad non-grammatical language measure, neither of which were associated with procedural memory. When grammar was examined as a continuous variable over all children, the same relationships between procedural memory and grammar, but not vocabulary or the broader language measure, were observed. Overall, the findings support and further specify the PDH. They suggest that consolidation and longer-term procedural learning are impaired in SLI, but that

Nonadjacent Dependency Learning in Cantonese-Speaking Children With and Without a History of Specific Language Impairment.

Science.gov (United States)

Iao, Lai-Sang; Ng, Lai Yan; Wong, Anita Mei Yin; Lee, Oi Ting

2017-03-01

This study investigated nonadjacent dependency learning in Cantonese-speaking children with and without a history of specific language impairment (SLI) in an artificial linguistic context. Sixteen Cantonese-speaking children with a history of SLI and 16 Cantonese-speaking children with typical language development (TLD) were tested with a nonadjacent dependency learning task using artificial languages that mimic Cantonese. Children with TLD performed above chance and were able to discriminate between trained and untrained nonadjacent dependencies. However, children with a history of SLI performed at chance and were not able to differentiate trained versus untrained nonadjacent dependencies. These findings, together with previous findings from English-speaking adults and adolescents with language impairments, suggest that individuals with atypical language development, regardless of age, diagnostic status, language, and culture, show difficulties in learning nonadjacent dependencies. This study provides evidence for early impairments to statistical learning in individuals with atypical language development.

Characteristics of early spelling of children with Specific Language Impairment.

Science.gov (United States)

Cordewener, Kim A H; Bosman, Anna M T; Verhoeven, Ludo

2012-01-01

The present study investigated active grapheme knowledge and early spelling of 59 first grade children with Specific Language Impairment (SLI). Speed, nature, and knowledge transfer of spelling acquisition were taken into account. Four orthographic characteristics that influence early spelling, namely, 'Type of Grapheme', 'Grapheme Position', 'Number of Graphemes', and 'Word Structure' were examined at the middle and at the end of first grade. At the beginning of first grade when children were between 71 and 97 months, they performed well below national norms on assessment of active grapheme knowledge. The delay in word spelling persisted, but decreased between the middle and the end of first grade. Despite this delay, the findings suggest that characteristics of early spelling for children with SLI are rather similar to those of children with typical language development. For example, children with SLI represented more graphemes at the end of first grade than at the middle of first grade, found it easier to represent the initial grapheme in words than the final or medial grapheme (Grapheme Position), were more successful spelling shorter than longer words (Number of Graphemes), and spelled words with simple structures (CVC) more accurately than those with complex structures (CVCC and CCVC; Word Structure). Finally, participants demonstrated that they can use known graphemes to spell words, but the transfer between active grapheme knowledge and word spelling was not always stable. As a result of this activity, readers will be able to explain the speed and the nature of spelling acquisition of children with SLI. As a result of this activity, readers will be able to explain what skills are most important for teachers to practice with children with SLI to improve the spelling skills of these children. Copyright © 2012 Elsevier Inc. All rights reserved.

Overproduction of Geranylgeraniol by Metabolically Engineered Saccharomyces cerevisiae▿

Science.gov (United States)

Tokuhiro, Kenro; Muramatsu, Masayoshi; Ohto, Chikara; Kawaguchi, Toshiya; Obata, Shusei; Muramoto, Nobuhiko; Hirai, Masana; Takahashi, Haruo; Kondo, Akihiko; Sakuradani, Eiji; Shimizu, Sakayu

2009-01-01

(E, E, E)-Geranylgeraniol (GGOH) is a valuable starting material for perfumes and pharmaceutical products. In the yeast Saccharomyces cerevisiae, GGOH is synthesized from the end products of the mevalonate pathway through the sequential reactions of farnesyl diphosphate synthetase (encoded by the ERG20 gene), geranylgeranyl diphosphate synthase (the BTS1 gene), and some endogenous phosphatases. We demonstrated that overexpression of the diacylglycerol diphosphate phosphatase (DPP1) gene could promote GGOH production. We also found that overexpression of a BTS1-DPP1 fusion gene was more efficient for producing GGOH than coexpression of these genes separately. Overexpression of the hydroxymethylglutaryl-coenzyme A reductase (HMG1) gene, which encodes the major rate-limiting enzyme of the mevalonate pathway, resulted in overproduction of squalene (191.9 mg liter−1) rather than GGOH (0.2 mg liter−1) in test tube cultures. Coexpression of the BTS1-DPP1 fusion gene along with the HMG1 gene partially redirected the metabolic flux from squalene to GGOH. Additional expression of a BTS1-ERG20 fusion gene resulted in an almost complete shift of the flux to GGOH production (228.8 mg liter−1 GGOH and 6.5 mg liter−1 squalene). Finally, we constructed a diploid prototrophic strain coexpressing the HMG1, BTS1-DPP1, and BTS1-ERG20 genes from multicopy integration vectors. This strain attained 3.31 g liter−1 GGOH production in a 10-liter jar fermentor with gradual feeding of a mixed glucose and ethanol solution. The use of bifunctional fusion genes such as the BTS1-DPP1 and ERG20-BTS1 genes that code sequential enzymes in the metabolic pathway was an effective method for metabolic engineering. PMID:19592534

Hygromycin B and apramycin antibiotic resistance cassettes for use in Campylobacter jejuni.

Directory of Open Access Journals (Sweden)

Andrew Cameron

Full Text Available Campylobacter jejuni genetic manipulation is restricted by the limited number of antibiotic resistance cassettes available for use in this diarrheal pathogen. In this study, two antibiotic resistance cassettes were developed, encoding for hygromycin B and apramycin resistance, for use in mutagenesis or for selection of gene expression and complementation constructs in C. jejuni. First, the marker genes were successfully modified to allow for insertional mutagenesis or deletion of a gene-of-interest, and were bracketed with restriction sites for the facilitation of site-specific cloning. These hygromycin B and apramycin markers are encoded by plasmids pAC1H and pAC1A, respectively. We also modified an insertional gene-delivery vector to create pRRH and pRRA, containing the hygromycin B and apramycin resistance genes, and 3 unique restriction sites for the directional introduction of genes into the conserved multi-copy rRNA gene clusters of the C. jejuni chromosome. We determined the effective antibiotic concentrations required for selection, and established that no harmful effects or fitness costs were associated with carrying hygromycin B or apramycin resistance under standard C. jejuni laboratory conditions. Using these markers, the arylsulfatase reporter gene astA was deleted, and the ability to genetically complement the astA deletion using pRRH and pRRA for astA gene insertion was demonstrated. Furthermore, the relative levels of expression from the endogenous astA promoter were compared to that of polycistronic mRNA expression from the constitutive promoter upstream of the resistance gene. The development of additional antibiotic resistance cassettes for use in Campylobacter will enable multiple gene deletion and expression combinations as well as more in-depth study of multi-gene systems important for the survival and pathogenesis of this important bacterium.

Imaging gene expression in gene therapy

International Nuclear Information System (INIS)

Wiebe, Leonard I.

1997-01-01

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on 'suicide gene therapy' of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k + ) has been use for 'suicide' in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k + gene expression where the H S V-1 t k + gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([ 18 F]F H P G; [ 18 F]-A C V), and pyrimidine- ([ 123 / 131 I]I V R F U; [ 124 / 131I ]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [ 123 / 131I ]I V R F U imaging with the H S V-1 t k + reporter gene will be presented

Chromosome End Repair and Genome Stability in Plasmodium falciparum.

Science.gov (United States)

Calhoun, Susannah F; Reed, Jake; Alexander, Noah; Mason, Christopher E; Deitsch, Kirk W; Kirkman, Laura A

2017-08-08

The human malaria parasite Plasmodium falciparum replicates within circulating red blood cells, where it is subjected to conditions that frequently cause DNA damage. The repair of DNA double-stranded breaks (DSBs) is thought to rely almost exclusively on homologous recombination (HR), due to a lack of efficient nonhomologous end joining. However, given that the parasite is haploid during this stage of its life cycle, the mechanisms involved in maintaining genome stability are poorly understood. Of particular interest are the subtelomeric regions of the chromosomes, which contain the majority of the multicopy variant antigen-encoding genes responsible for virulence and disease severity. Here, we show that parasites utilize a competitive balance between de novo telomere addition, also called "telomere healing," and HR to stabilize chromosome ends. Products of both repair pathways were observed in response to DSBs that occurred spontaneously during routine in vitro culture or resulted from experimentally induced DSBs, demonstrating that both pathways are active in repairing DSBs within subtelomeric regions and that the pathway utilized was determined by the DNA sequences immediately surrounding the break. In combination, these two repair pathways enable parasites to efficiently maintain chromosome stability while also contributing to the generation of genetic diversity. IMPORTANCE Malaria is a major global health threat, causing approximately 430,000 deaths annually. This mosquito-transmitted disease is caused by Plasmodium parasites, with infection with the species Plasmodium falciparum being the most lethal. Mechanisms underlying DNA repair and maintenance of genome integrity in P. falciparum are not well understood and represent a gap in our understanding of how parasites survive the hostile environment of their vertebrate and insect hosts. Our work examines DNA repair in real time by using single-molecule real-time (SMRT) sequencing focused on the subtelomeric

iELM—a web server to explore short linear motif-mediated interactions

Science.gov (United States)

Weatheritt, Robert J.; Jehl, Peter; Dinkel, Holger; Gibson, Toby J.

2012-01-01

The recent expansion in our knowledge of protein–protein interactions (PPIs) has allowed the annotation and prediction of hundreds of thousands of interactions. However, the function of many of these interactions remains elusive. The interactions of Eukaryotic Linear Motif (iELM) web server provides a resource for predicting the function and positional interface for a subset of interactions mediated by short linear motifs (SLiMs). The iELM prediction algorithm is based on the annotated SLiM classes from the Eukaryotic Linear Motif (ELM) resource and allows users to explore both annotated and user-generated PPI networks for SLiM-mediated interactions. By incorporating the annotated information from the ELM resource, iELM provides functional details of PPIs. This can be used in proteomic analysis, for example, to infer whether an interaction promotes complex formation or degradation. Furthermore, details of the molecular interface of the SLiM-mediated interactions are also predicted. This information is displayed in a fully searchable table, as well as graphically with the modular architecture of the participating proteins extracted from the UniProt and Phospho.ELM resources. A network figure is also presented to aid the interpretation of results. The iELM server supports single protein queries as well as large-scale proteomic submissions and is freely available at http://i.elm.eu.org. PMID:22638578

A Case of Specific Language Impairment in a Deaf Signer of American Sign Language.

Science.gov (United States)

Quinto-Pozos, David; Singleton, Jenny L; Hauser, Peter C

2017-04-01

This article describes the case of a deaf native signer of American Sign Language (ASL) with a specific language impairment (SLI). School records documented normal cognitive development but atypical language development. Data include school records; interviews with the child, his mother, and school professionals; ASL and English evaluations; and a comprehensive neuropsychological and psychoeducational evaluation, and they span an approximate period of 7.5 years (11;10-19;6) including scores from school records (11;10-16;5) and a 3.5-year period (15;10-19;6) during which we collected linguistic and neuropsychological data. Results revealed that this student has average intelligence, intact visual perceptual skills, visuospatial skills, and motor skills but demonstrates challenges with some memory and sequential processing tasks. Scores from ASL testing signaled language impairment and marked difficulty with fingerspelling. The student also had significant deficits in English vocabulary, spelling, reading comprehension, reading fluency, and writing. Accepted SLI diagnostic criteria exclude deaf individuals from an SLI diagnosis, but the authors propose modified criteria in this work. The results of this study have practical implications for professionals including school psychologists, speech language pathologists, and ASL specialists. The results also support the theoretical argument that SLI can be evident regardless of the modality in which it is communicated. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The Development of English as a Second Language With and Without Specific Language Impairment: Clinical Implications.

Science.gov (United States)

Paradis, Johanne

2016-02-01

The purpose of this research forum article is to provide an overview of typical and atypical development of English as a second language (L2) and to present strategies for clinical assessment with English language learners (ELLs). A review of studies examining the lexical, morphological, narrative, and verbal memory abilities of ELLs is organized around 3 topics: timeframe and characteristics of typical English L2 development, comparison of the English L2 development of children with and without specific language impairment (SLI), and strategies for more effective assessment with ELLs. ELLs take longer than 3 years to converge on monolingual norms and approach monolingual norms asynchronously across linguistic subdomains. Individual variation is predicted by age, first language, language learning aptitude, length of exposure to English in school, maternal education, and richness of the English environment outside school. ELLs with SLI acquire English more slowly than ELLs with typical development; their morphological and nonword repetition abilities differentiate them the most. Use of strategies such as parent questionnaires on first language development and ELL norm referencing can result in accurate discrimination of ELLs with SLI. Variability in the language abilities of ELLs presents challenges for clinical practice. Increased knowledge of English language learning development with and without SLI together with evidence-based alternative assessment strategies can assist in overcoming these challenges.

Imaging gene expression in gene therapy

Energy Technology Data Exchange (ETDEWEB)

Wiebe, Leonard I. [Alberta Univ., Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

1997-12-31

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on `suicide gene therapy` of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k{sup +}) has been use for `suicide` in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k{sup +} gene expression where the H S V-1 t k{sup +} gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([{sup 18} F]F H P G; [{sup 18} F]-A C V), and pyrimidine- ([{sup 123}/{sup 131} I]I V R F U; [{sup 124}/{sup 131I}]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [{sup 123}/{sup 131I}]I V R F U imaging with the H S V-1 t k{sup +} reporter gene will be presented

Serotype- and virulence-associated gene profile of Streptococcus suis isolates from pig carcasses in Chiang Mai Province, Northern Thailand.

Science.gov (United States)

Wongsawan, Kanruethai; Gottschalk, Marcelo; Tharavichitkul, Prasit

2015-02-01

In this present study, the serotype of 40 Streptococcus suis isolates from submaxillary glands of pig carcasses sold in wet markets in Chiang Mai Province, northern Thailand, was investigated. Eleven serotypes, including types 2, 3, 4, 5, 7, 8, 9, 17, 21, 22 and 31, were found in the isolates by a Multiplex PCR combined with serum agglutination. Of the eleven serotypes present, type 3 was the most prevalent, while types 2, 4, 5 and 21 were of primary interest due to their human isolate serotype. The mrp+/epf - /sly - genotype was found to be the most prevalent genotype. This study indicates the importance of effective control of human S. suis infection due to raw pork or pig carcass handling in northern Thailand.

Evaluation of Amplification Targets for the Specific Detection of Bordetella pertussis Using Real-Time Polymerase Chain Reaction

Directory of Open Access Journals (Sweden)

Mohammad Rubayet Hasan

2014-01-01

Full Text Available BACKGROUND: Bordetella pertussis infections continue to be a major public health challenge in Canada. Polymerase chain reaction (PCR assays to detect B pertussis are typically based on the multicopy insertion sequence IS481, which offers high sensitivity but lacks species specificity.

Insertion-Sequence-Mediated Mutations Isolated During Adaptation to Growth and Starvation in Lactococcus lactis.

NARCIS (Netherlands)

Visser, de J.A.G.M.; Akkermans, A.D.L.; Hoekstra, R.F.; Vos, de W.M.

2004-01-01

We studied the activity of three multicopy insertion sequence (IS) elements in 12 populations of Lactococcus lactis IL1403 that evolved in the laboratory for 1000 generations under various environmental conditions (growth or starvation and shaken or stationary). Using RFLP analysis of single-clone

TRE5-A retrotransposition profiling reveals putative RNA polymerase III transcription complex binding sites on the Dictyostelium extrachromosomal rDNA element.

Directory of Open Access Journals (Sweden)

Thomas Spaller

Full Text Available The amoeba Dictyostelium discoideum has a haploid genome in which two thirds of the DNA encodes proteins. Consequently, the space available for selfish mobile elements to expand without excess damage to the host genome is limited. The non-long terminal repeat retrotransposon TRE5-A maintains an active population in the D. discoideum genome and apparently adapted to this gene-dense environment by targeting positions ~47 bp upstream of tRNA genes that are devoid of protein-coding regions. Because only ~24% of tRNA genes are associated with a TRE5-A element in the reference genome, we evaluated whether TRE5-A retrotransposition is limited to this subset of tRNA genes. We determined that a tagged TRE5-A element (TRE5-Absr integrated at 384 of 405 tRNA genes, suggesting that expansion of the current natural TRE5-A population is not limited by the availability of targets. We further observed that TRE5-Absr targets the ribosomal 5S gene on the multicopy extrachromosomal DNA element that carries the ribosomal RNA genes, indicating that TRE5-A integration may extend to the entire RNA polymerase III (Pol III transcriptome. We determined that both natural TRE5-A and cloned TRE5-Absr retrotranspose to locations on the extrachromosomal rDNA element that contain tRNA gene-typical A/B box promoter motifs without displaying any other tRNA gene context. Based on previous data suggesting that TRE5-A targets tRNA genes by locating Pol III transcription complexes, we propose that A/B box loci reflect Pol III transcription complex assembly sites that possess a function in the biology of the extrachromosomal rDNA element.

GoGene: gene annotation in the fast lane.

Science.gov (United States)

Plake, Conrad; Royer, Loic; Winnenburg, Rainer; Hakenberg, Jörg; Schroeder, Michael

2009-07-01

High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4,000,000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.

Contention aware mobility prediction routing for intermittently connected mobile networks

KAUST Repository

Elwhishi, Ahmed; Ho, Pin-Han; Shihada, Basem

2013-01-01

This paper introduces a novel multi-copy routing protocol, called predict and forward (PF), for delay tolerant networks, which aims to explore the possibility of using mobile nodes as message carriers for end-to-end delivery of the messages. With PF, the message forwarding decision is made by manipulating the probability distribution of future inter-contact and contact durations based on the network status, including wireless link condition and nodal buffer availability. In particular, PF is based on the observations that the node mobility behavior is semi-deterministic and could be predicted once there is sufficient mobility history information. We implemented the proposed protocol and compared it with a number of existing encounter-based routing approaches in terms of delivery delay, delivery ratio, and the number of transmissions required for message delivery. The simulation results show that PF outperforms all the counterpart multi-copy encounter-based routing protocols considered in the study.

Contention aware mobility prediction routing for intermittently connected mobile networks

KAUST Repository

Elwhishi, Ahmed

2013-04-26

This paper introduces a novel multi-copy routing protocol, called predict and forward (PF), for delay tolerant networks, which aims to explore the possibility of using mobile nodes as message carriers for end-to-end delivery of the messages. With PF, the message forwarding decision is made by manipulating the probability distribution of future inter-contact and contact durations based on the network status, including wireless link condition and nodal buffer availability. In particular, PF is based on the observations that the node mobility behavior is semi-deterministic and could be predicted once there is sufficient mobility history information. We implemented the proposed protocol and compared it with a number of existing encounter-based routing approaches in terms of delivery delay, delivery ratio, and the number of transmissions required for message delivery. The simulation results show that PF outperforms all the counterpart multi-copy encounter-based routing protocols considered in the study.

Deletion of GOLGA2P3Y but not GOLGA2P2Y is a risk factor for oligozoospermia.

Science.gov (United States)

Sen, Sanjukta; Agarwal, Rupesh; Ambulkar, Prafulla; Hinduja, Indira; Zaveri, Kusum; Gokral, Jyotsna; Pal, Asoke; Modi, Deepak

2016-02-01

The AZFc locus on the human Y chromosome harbours several multicopy genes, some of which are required for spermatogenesis. It is believed that deletion of one or more copies of these genes is a cause of infertility in some men. GOLGA2LY is one of the genes in the AZFc locus and it exists in two copies, GOLGA2P2Y and GOLGA2P3Y. The involvement of GOLGA2LY gene copy deletions in male infertility, however, is unknown. This study aimed to investigate the association of deletions of GOLGA2P2Y and GOLGA2P3Y gene copies with male infertility and with sperm concentration and motility. The frequency of GOLGA2P3Y deletion was significantly higher in oligozoospermic men compared with normozoospermic men (7.7% versus 1.2%; P = 0.0001), whereas the frequency of GOLGA2P2Y deletion was comparable between oligozoospermic and normozoospermic men (10.3% versus 11.3%). The deletion of GOLGA2P3Y but not GOLGA2P2Y was significantly higher (P = 0.03) in men with gr/gr rearrangements, indicating that GOLGA2P3Y deletions increase the susceptibility of men with gr/gr rearrangements to oligozoospermia. Furthermore, men with GOLGA2P3Y deletion had reduced sperm concentration and motility compared with men without deletion or with deletion of GOLGA2P2Y. These findings indicate GOLGA2P3Y gene copy may be candidate AZFc gene for male infertility. Copyright © 2015 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Radionuclide reporter gene imaging for cardiac gene therapy

International Nuclear Information System (INIS)

Inubushi, Masayuki; Tamaki, Nagara

2007-01-01

In the field of cardiac gene therapy, angiogenic gene therapy has been most extensively investigated. The first clinical trial of cardiac angiogenic gene therapy was reported in 1998, and at the peak, more than 20 clinical trial protocols were under evaluation. However, most trials have ceased owing to the lack of decisive proof of therapeutic effects and the potential risks of viral vectors. In order to further advance cardiac angiogenic gene therapy, remaining open issues need to be resolved: there needs to be improvement of gene transfer methods, regulation of gene expression, development of much safer vectors and optimisation of therapeutic genes. For these purposes, imaging of gene expression in living organisms is of great importance. In radionuclide reporter gene imaging, ''reporter genes'' transferred into cell nuclei encode for a protein that retains a complementary ''reporter probe'' of a positron or single-photon emitter; thus expression of the reporter genes can be imaged with positron emission tomography or single-photon emission computed tomography. Accordingly, in the setting of gene therapy, the location, magnitude and duration of the therapeutic gene co-expression with the reporter genes can be monitored non-invasively. In the near future, gene therapy may evolve into combination therapy with stem/progenitor cell transplantation, so-called cell-based gene therapy or gene-modified cell therapy. Radionuclide reporter gene imaging is now expected to contribute in providing evidence on the usefulness of this novel therapeutic approach, as well as in investigating the molecular mechanisms underlying neovascularisation and safety issues relevant to further progress in conventional gene therapy. (orig.)

Assessment of short-term memory in Arabic speaking children with specific language impairment.

Science.gov (United States)

Kaddah, F A; Shoeib, R M; Mahmoud, H E

2010-12-15

Children with Specific Language Impairment (SLI) may have some kind of memory disorder that could increase their linguistic impairment. This study assessed the short-term memory skills in Arabic speaking children with either Expressive Language Impairment (ELI) or Receptive/Expressive Language Impairment (R/ELI) in comparison to controls in order to estimate the nature and extent of any specific deficits in these children that could explain the different prognostic results of language intervention. Eighteen children were included in each group. Receptive, expressive and total language quotients were calculated using the Arabic language test. Assessment of auditory and visual short-term memory was done using the Arabic version of the Illinois Test of Psycholinguistic Abilities. Both groups of SLI performed significantly lower linguistic abilities and poorer auditory and visual short-term memory in comparison to normal children. The R/ELI group presented an inferior performance than the ELI group in all measured parameters. Strong association was found between most tasks of auditory and visual short-term memory and linguistic abilities. The results of this study highlighted a specific degree of deficit of auditory and visual short-term memories in both groups of SLI. These deficits were more prominent in R/ELI group. Moreover, the strong association between the different auditory and visual short-term memories and language abilities in children with SLI must be taken into account when planning an intervention program for these children.

Normal and sublethally irradiated stem and granulocyte progenitor cell regeneration in an in vivo culture system. The cellular response to humoral factors released through the action of cyclophosphamide

International Nuclear Information System (INIS)

MacVittie, T.

1977-01-01

The in vivo diffusion chamber (DC) method of marrow culture was used to determine if the injection of host mice with cyclophosphamide (CY) caused, through its cytoxic action, the release of a humoral factor(s) capable of initiating stem cell (CFU-s) and granulocyte-macrophage progenitor cell (CFU-c) proliferation. Host mice were injected with CY 1-4 days prior to 800 rad of 60 Co WBI and implantation of DCs containing normal or 400 rad sublethally irradiated (SLI) marrow cells. The greatest proliferative response within CFU-s and CFU-c populations occurred in those mice injected with CY 3 days prior to implant. The marked CFU-s and CFU-c regeneration was initiated during the initial 24 hr of culture in both normal and SLI marrow cells. Thereafter growth rates were approximately the same. SLI marrow, however, showed a greater response to the humoral effects of CY injection than did normal marrow. These data provided evidence that CY induced the release of a diffusible factor(s) capable of accelerating regeneration of normal and sublethally irradiated CFU-s and CFU-c, the magnitude of which was dependent upon the time elapsed between CY injected and implantation of DCs. The marked proliferative response of the SLI stem and progenitor cells to the humoral stimulation may be indicative of the heterogeneity of both CFU-s and CFU-c populations surviving sublethal radiation exposure. The target cells may have possessed a differential sensitivity to the factor(s) initiating cell proliferation

Gene cluster statistics with gene families.

Science.gov (United States)

Raghupathy, Narayanan; Durand, Dannie

2009-05-01

Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data

Gene therapy prospects--intranasal delivery of therapeutic genes.

Science.gov (United States)

Podolska, Karolina; Stachurska, Anna; Hajdukiewicz, Karolina; Małecki, Maciej

2012-01-01

Gene therapy is recognized to be a novel method for the treatment of various disorders. Gene therapy strategies involve gene manipulation on broad biological processes responsible for the spreading of diseases. Cancer, monogenic diseases, vascular and infectious diseases are the main targets of gene therapy. In order to obtain valuable experimental and clinical results, sufficient gene transfer methods are required. Therapeutic genes can be administered into target tissues via gene carriers commonly defined as vectors. The retroviral, adenoviral and adeno-associated virus based vectors are most frequently used in the clinic. So far, gene preparations may be administered directly into target organs or by intravenous, intramuscular, intratumor or intranasal injections. It is common knowledge that the number of gene therapy clinical trials has rapidly increased. However, some limitations such as transfection efficiency and stable and long-term gene expression are still not resolved. Consequently, great effort is focused on the evaluation of new strategies of gene delivery. There are many expectations associated with intranasal delivery of gene preparations for the treatment of diseases. Intranasal delivery of therapeutic genes is regarded as one of the most promising forms of pulmonary gene therapy research. Gene therapy based on inhalation of gene preparations offers an alternative way for the treatment of patients suffering from such lung diseases as cystic fibrosis, alpha-1-antitrypsin defect, or cancer. Experimental and first clinical trials based on plasmid vectors or recombinant viruses have revealed that gene preparations can effectively deliver therapeutic or marker genes to the cells of the respiratory tract. The noninvasive intranasal delivery of gene preparations or conventional drugs seems to be very encouraging, although basic scientific research still has to continue.

Gene-gene interactions and gene polymorphisms of VEGFA and EG-VEGF gene systems in recurrent pregnancy loss.

Science.gov (United States)

Su, Mei-Tsz; Lin, Sheng-Hsiang; Chen, Yi-Chi; Kuo, Pao-Lin

2014-06-01

Both vascular endothelial growth factor A (VEGFA) and endocrine gland-derived vascular endothelial growth factor (EG-VEGF) systems play major roles in angiogenesis. A body of evidence suggests VEGFs regulate critical processes during pregnancy and have been associated with recurrent pregnancy loss (RPL). However, little information is available regarding the interaction of these two major major angiogenesis-related systems in early human pregnancy. This study was conducted to investigate the association of gene polymorphisms and gene-gene interaction among genes in VEGFA and EG-VEGF systems and idiopathic RPL. A total of 98 women with history of idiopathic RPL and 142 controls were included, and 5 functional SNPs selected from VEGFA, KDR, EG-VEGF (PROK1), PROKR1 and PROKR2 were genotyped. We used multifactor dimensionality reduction (MDR) analysis to choose a best model and evaluate gene-gene interactions. Ingenuity pathways analysis (IPA) was introduced to explore possible complex interactions. Two receptor gene polymorphisms [KDR (Q472H) and PROKR2 (V331M)] were significantly associated with idiopathic RPL (P<0.01). The MDR test revealed that the KDR (Q472H) polymorphism was the best loci to be associated with RPL (P=0.02). IPA revealed EG-VEGF and VEGFA systems shared several canonical signaling pathways that may contribute to gene-gene interactions, including the Akt, IL-8, EGFR, MAPK, SRC, VHL, HIF-1A and STAT3 signaling pathways. Two receptor gene polymorphisms [KDR (Q472H) and PROKR2 (V331M)] were significantly associated with idiopathic RPL. EG-VEGF and VEGFA systems shared several canonical signaling pathways that may contribute to gene-gene interactions, including the Akt, IL-8, EGFR, MAPK, SRC, VHL, HIF-1A and STAT3.

Gene doping: gene delivery for olympic victory

OpenAIRE

Gould, David

2012-01-01

With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

FunGene: the functional gene pipeline and repository.

Science.gov (United States)

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

FunGene: the Functional Gene Pipeline and Repository

Directory of Open Access Journals (Sweden)

Jordan A. Fish

2013-10-01

Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.

Science.gov (United States)

Li, Jin; Wang, Limei; Guo, Maozu; Zhang, Ruijie; Dai, Qiguo; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Xuan, Ping; Zhang, Mingming

2015-01-01

In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.

Gene-gene, gene-environment, gene-nutrient interactions and single nucleotide polymorphisms of inflammatory cytokines.

Science.gov (United States)

Nadeem, Amina; Mumtaz, Sadaf; Naveed, Abdul Khaliq; Aslam, Muhammad; Siddiqui, Arif; Lodhi, Ghulam Mustafa; Ahmad, Tausif

2015-05-15

Inflammation plays a significant role in the etiology of type 2 diabetes mellitus (T2DM). The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury, oxidative stress and beta cell apoptosis in T2DM. Among the recognized markers are interleukin (IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha (TNF-α), C-reactive protein, resistin, adiponectin, tissue plasminogen activator, fibrinogen and heptoglobins. Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance. Many single nucleotide polymorphisms (SNPs) in various genes including those of pro and anti-inflammatory cytokines have been reported as a risk for T2DM. Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups. The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene, gene-environment and gene-nutrient interactions. This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6, TNF-α, resistin and adiponectin in pathogenesis of T2DM.

The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens

Energy Technology Data Exchange (ETDEWEB)

Aklujkar, Muktak; Krushkal, Julia; DiBartolo, Genevieve; Lapidus, Alla; Land, Miriam L.; Lovley, Derek R.

2008-12-01

Background: The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. Results: The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE) regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes. Conclusion: The genomic evidence suggests that metabolism, physiology and regulation of gene expression in G. metallireducens may be dramatically different from other Geobacteraceae.

Self-esteem of adolescents with specific language impairment as they move from compulsory education.

Science.gov (United States)

Lindsay, Geoff; Dockrell, Julie; Palikara, Olympia

2010-01-01

Children with specific language impairment (SLI) are at risk of low self-esteem during their school years. However, there is a lack of evidence of the self-esteem of young people with a history of SLI during adolescence, as they transfer from compulsory schooling to post-compulsory education, employment or training. To examine the self-esteem of young people with a history of SLI at the transition from compulsory education (16 years) to the first year of post-compulsory education, employment and training (17 years) in England. A total of 54 young people identified as having SLI at 8 years were followed up at 16 and at 17 years. The young people completed two measures of self-esteem: the Self-perception Profile for Adolescents (16 years) and the Self-perception Profile for College Students (17 years). Assessments of language, literacy and non-verbal ability were also conducted. Perceptions of scholastic competence were significantly lower than the norm at 16 years; the female students also had lower self-esteem in the social and physical appearance domains and global self-worth. However, at 17 years there were no significant differences from the norm for these self-esteem domains. There was evidence of stability within self-esteem domains over this period but also an improvement in self-perceptions of scholastic and job competence, physical appearance and athletic competence, and also global self-worth, but not the three social domains. Non-verbal cognitive ability was not correlated with any measures of self-esteem, at 16 or 17 years. Language and literacy ability, especially spelling, were correlated with scholastic and job competence at 16 years but only spelling correlated at 17 years. This study has provided evidence for improvements in self-esteem for young people with SLI after they leave school and enter the world of non-compulsory education (typically at a college), employment and training. The study has also indicated the importance of addressing self

Calibration and analysis of a multimodal micro-CT and structured light imaging system for the evaluation of excised breast tissue

Science.gov (United States)

McClatchy, David M., III; Rizzo, Elizabeth J.; Meganck, Jeff; Kempner, Josh; Vicory, Jared; Wells, Wendy A.; Paulsen, Keith D.; Pogue, Brian W.

2017-12-01

A multimodal micro-computed tomography (CT) and multi-spectral structured light imaging (SLI) system is introduced and systematically analyzed to test its feasibility to aid in margin delineation during breast conserving surgery (BCS). Phantom analysis of the micro-CT yielded a signal-to-noise ratio of 34, a contrast of 1.64, and a minimum detectable resolution of 240 μm for a 1.2 min scan. The SLI system, spanning wavelengths 490 nm to 800 nm and spatial frequencies up to 1.37 mm-1 , was evaluated with aqueous tissue simulating phantoms having variations in particle size distribution, scatter density, and blood volume fraction. The reduced scattering coefficient, μs\\prime and phase function parameter, γ, were accurately recovered over all wavelengths independent of blood volume fractions from 0% to 4%, assuming a flat sample geometry perpendicular to the imaging plane. The resolution of the optical system was tested with a step phantom, from which the modulation transfer function was calculated yielding a maximum resolution of 3.78 cycles per mm. The three dimensional spatial co-registration between the CT and optical imaging space was tested and shown to be accurate within 0.7 mm. A freshly resected breast specimen, with lobular carcinoma, fibrocystic disease, and adipose, was imaged with the system. The micro-CT provided visualization of the tumor mass and its spiculations, and SLI yielded superficial quantification of light scattering parameters for the malignant and benign tissue types. These results appear to be the first demonstration of SLI combined with standard medical tomography for imaging excised tumor specimens. While further investigations are needed to determine and test the spectral, spatial, and CT features required to classify tissue, this study demonstrates the ability of multimodal CT/SLI to quantify, visualize, and spatially navigate breast tumor specimens, which could potentially aid in the assessment of tumor margin status during

Parental phonological memory contributes to prediction of outcome of late talkers from 20 months to 4 years: a longitudinal study of precursors of specific language impairment

Directory of Open Access Journals (Sweden)

Bishop Dorothy VM

2012-02-01

Full Text Available Abstract Background Many children who are late talkers go on to develop normal language, but others go on to have longer-term language difficulties. In this study, we considered which factors were predictive of persistent problems in late talkers. Methods Parental report of expressive vocabulary at 18 months of age was used to select 26 late talkers and 70 average talkers, who were assessed for language and cognitive ability at 20 months of age. Follow-up at 4 years of age was carried out for 24 late and 58 average talkers. A psychometric test battery was used to categorize children in terms of language status (unimpaired or impaired and nonverbal ability (normal range or more than 1 SD below average. The vocabulary and non-word repetition skills of the accompanying parent were also assessed. Results Among the late talkers, seven (29% met our criteria for specific language impairment (SLI at 4 years of age, and a further two (8% had low nonverbal ability. In the group of average talkers, eight (14% met the criteria for SLI at 4 years, and five other children (8% had low nonverbal ability. Family history of language problems was slightly better than late-talker status as a predictor of SLI.. The best predictors of SLI at 20 months of age were score on the receptive language scale of the Mullen Scales of Early Learning and the parent's performance on a non-word repetition task. Maternal education was not a significant predictor of outcome. Conclusions In this study, around three-quarters of late talkers did not have any language difficulties at 4 years of age, provided there was no family history of language impairment. A family history of language-literacy problems was found to be a significant predictor for persisting problems. Nevertheless, there are children with SLI for whom prediction is difficult because they did not have early language delay.

Suicide genes or p53 gene and p53 target genes as targets for cancer gene therapy by ionizing radiation

International Nuclear Information System (INIS)

Liu Bing; Chinese Academy of Sciences, Beijing; Zhang Hong

2005-01-01

Radiotherapy has some disadvantages due to the severe side-effect on the normal tissues at a curative dose of ionizing radiation (IR). Similarly, as a new developing approach, gene therapy also has some disadvantages, such as lack of specificity for tumors, limited expression of therapeutic gene, potential biological risk. To certain extent, above problems would be solved by the suicide genes or p53 gene and its target genes therapies targeted by ionizing radiation. This strategy not only makes up the disadvantage from radiotherapy or gene therapy alone, but also promotes success rate on the base of lower dose. By present, there have been several vectors measuring up to be reaching clinical trials. This review focused on the development of the cancer gene therapy through suicide genes or p53 and its target genes mediated by IR. (authors)

Neighboring Genes Show Correlated Evolution in Gene Expression

Science.gov (United States)

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructanstructans.

Science.gov (United States)

Muller, Laura K.; Lorch, Jeffrey M.; Lindner, Daniel L.; O'Connor, Michael; Gargas, Andrea; Blehert, David S.

2013-01-01

The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg of genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was further qualified by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific, and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research.

Genomic portrait of population of Jharkhand, India, drawn with 15 autosomal STRs and 17 Y-STRs.

Science.gov (United States)

Imam, Jahangir; Reyaz, Romana; Singh, Rama Shankar; Bapuly, Arun Kumar; Shrivastava, Pankaj

2018-01-01

We analysed 15 autosomal STRs in 200 unrelated individuals (102 males and 98 females) and 17 Y-STRs in 102 unrelated males living in Jharkhand, India, to establish parameters of forensic interest. The examined autosomal STRs revealed high combined power of exclusion (CPE) and combined power of discrimination (CPD) as equal to 0.9999 and greater than 0.99999, respectively. The combined probability of match (CP m ) and combined paternity index (CPI) for all 15 autosomal STR loci were found to be 5.15 × 10 -18 and 6.83 × 10 5 , respectively. A total of 97 unique haplotypes were obtained, of which 93 were observed only once. The haplotype diversity, discrimination capacity and matching probability for 17 Y-STR loci were 0.999, 0.951 and 1.09 × 10 -2 , respectively. The highest gene diversity values at the single copy locus DYS635 and multi-copy locus DYS385 a/b were 0.785 and 0.823, respectively.

Gene Therapy

Science.gov (United States)

Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

Imaging reporter gene for monitoring gene therapy

International Nuclear Information System (INIS)

Beco, V. de; Baillet, G.; Tamgac, F.; Tofighi, M.; Weinmann, P.; Vergote, J.; Moretti, J.L.; Tamgac, G.

2002-01-01

Scintigraphic images can be obtained to document gene function at cellular level. This approach is presented here and the use of a reporter gene to monitor gene therapy is described. Two main ways are presented: either the use of a reporter gene coding for an enzyme the action of which will be monitored by radiolabeled pro-drug, or a cellular receptor gene, the action of which is documented by a radio labeled cognate receptor ligand. (author)

Gene-Gene and Gene-Environment Interactions in the Etiology of Breast Cancer

National Research Council Canada - National Science Library

Adegoke, Olufemi

2003-01-01

The objective of this CDA is to evaluate the gene-gene and gene-environment interactions in the etiology of breast cancer in two ongoing case-control studies, the Shanghai Breast Cancer Study (SBCS...

Emergent literacy profiles of preschool-age children with specific language impairment.

Science.gov (United States)

Cabell, Sonia Q; Lomax, Richard G; Justice, Laura M; Breit-Smith, Allison; Skibbe, Lori E; McGinty, Anita S

2010-12-01

The primary aim of the present study was to explore the heterogeneity of emergent literacy skills among preschool-age children with specific language impairment (SLI) through examination of profiles of performance. Fifty-nine children with SLI were assessed on a battery of emergent literacy skills (i.e., alphabet knowledge, print concepts, emergent writing, rhyme awareness) and oral language skills (i.e., receptive/expressive vocabulary and grammar). Cluster analysis techniques identified three emergent literacy profiles: (1) Highest Emergent Literacy, Strength in Alphabet Knowledge; (2) Average Emergent Literacy, Strength in Print Concepts; and (3) Lowest Emergent Literacy across Skills. After taking into account the contribution of child age, receptive and expressive language skills made a small contribution to the prediction of profile membership. The present findings, which may be characterized as exploratory given the relatively modest sample size, suggest that preschool-age children with SLI display substantial individual differences with regard to their emergent literacy skills and that these differences cannot be fully determined by children's age or oral language performance. Replication of the present findings with a larger sample of children is needed.

Selective lymphoid irradiation: III. Prolongation of cardiac xenografts and allografts in presensitized rats

International Nuclear Information System (INIS)

Hardy, M.A.; Oluwole, S.; Fawwaz, R.; Satake, K.; Nowygrod, R.; Reemtsma, K.

1982-01-01

Selective lymphoid irradiation (SLI) with palladium-109-hematoporphyrin (Pd-H) combined with antilymphocyte globulin (ALG) induces either donor-specific permanent rat heart allograft acceptance or significant allograft prolongation depending on the degree of donor-recipient matching. The purpose of this study was to determine if SLI combined with ALG can affect ACI heart allograft survival in Lewis recipients presensitized to ACI, and of hamster heart xenografts of Lewis rats. SLI combined with ALG delays allograft and xenograft rejection in the presence of induced or preformed antidonor antibodies, and converts primarily a humoral rejection into a cellular rejection by mechanisms as yet uncertain. Such peritransplant treatment had significant effect on the levels of antidonor complement-dependent cytotoxic antibody titers but did not correlate directly with graft survival. Histological analysis of rejected hearts in all groups demonstrated primarily a humoral hyperacute rejection in control animals and in recipients treated with ALG alone, while peritransplant treatment with Pd-H and ALG resulted not only in prolonged graft survival but histologically, primarily a cellular rejection of the graft

Gene doping: gene delivery for olympic victory.

Science.gov (United States)

Gould, David

2013-08-01

With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called 'gene doping'. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted from the engineered cells or is retained locally to, or inside engineered cells will, to some extent, determine the likelihood of detection. It is clear that effective gene delivery technologies now exist and it is important that detection and prevention plans are in place. © 2012 The Author. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

Genes2FANs: connecting genes through functional association networks

Science.gov (United States)

2012-01-01

Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Conclusions Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our finding that disease genes in

Pathway to future sustainable land imaging: the compact hyperspectral prism spectrometer

Science.gov (United States)

Kampe, Thomas U.; Good, William S.

2017-09-01

NASA's Sustainable Land Imaging (SLI) program, managed through the Earth Science Technology Office, aims to develop technologies that will provide future Landsat-like measurements. SLI aims to develop a new generation of smaller, more capable, less costly payloads that meet or exceed current imaging capabilities. One projects funded by this program is Ball's Compact Hyperspectral Prism Spectrometer (CHPS), a visible-to-shortwave imaging spectrometer that provides legacy Landsat data products as well as hyperspectral coverage suitable for a broad range of land science products. CHPS exhibits extremely low straylight and accommodates full aperture, full optical path calibration needed to ensure the high radiometric accuracy demanded by SLI measurement objectives. Low polarization sensitivity in visible to near-infrared bands facilitates coastal water science as first demonstrated by the exceptional performance of the Operational Land Imager. Our goal is to mature CHPS imaging spectrometer technology for infusion into the SLI program. Our effort builds on technology development initiated by Ball IRAD investment and includes laboratory and airborne demonstration, data distribution to science collaborators, and maturation of technology for spaceborne demonstration. CHPS is a three year program with expected exiting technology readiness of TRL-6. The 2013 NRC report Landsat and Beyond: Sustaining and Enhancing the Nations Land Imaging Program recommended that the nation should "maintain a sustained, space-based, land-imaging program, while ensuring the continuity of 42-years of multispectral information." We are confident that CHPS provides a path to achieve this goal while enabling new science measurements and significantly reducing the cost, size, and volume of the VSWIR instrument.

Quantifying repetitive speech in autism spectrum disorders and language impairment.

Science.gov (United States)

van Santen, Jan P H; Sproat, Richard W; Hill, Alison Presmanes

2013-10-01

We report on an automatic technique for quantifying two types of repetitive speech: repetitions of what the child says him/herself (self-repeats) and of what is uttered by an interlocutor (echolalia). We apply this technique to a sample of 111 children between the ages of four and eight: 42 typically developing children (TD), 19 children with specific language impairment (SLI), 25 children with autism spectrum disorders (ASD) plus language impairment (ALI), and 25 children with ASD with normal, non-impaired language (ALN). The results indicate robust differences in echolalia between the TD and ASD groups as a whole (ALN + ALI), and between TD and ALN children. There were no significant differences between ALI and SLI children for echolalia or self-repetitions. The results confirm previous findings that children with ASD repeat the language of others more than other populations of children. On the other hand, self-repetition does not appear to be significantly more frequent in ASD, nor does it matter whether the child's echolalia occurred within one (immediate) or two turns (near-immediate) of the adult's original utterance. Furthermore, non-significant differences between ALN and SLI, between TD and SLI, and between ALI and TD are suggestive that echolalia may not be specific to ALN or to ASD in general. One important innovation of this work is an objective fully automatic technique for assessing the amount of repetition in a transcript of a child's utterances. © 2013 International Society for Autism Research, Wiley Periodicals, Inc.

Population coding of forelimb joint kinematics by peripheral afferents in monkeys.

Directory of Open Access Journals (Sweden)

Tatsuya Umeda

Full Text Available Various peripheral receptors provide information concerning position and movement to the central nervous system to achieve complex and dexterous movements of forelimbs in primates. The response properties of single afferent receptors to movements at a single joint have been examined in detail, but the population coding of peripheral afferents remains poorly defined. In this study, we obtained multichannel recordings from dorsal root ganglion (DRG neurons in cervical segments of monkeys. We applied the sparse linear regression (SLiR algorithm to the recordings, which selects useful input signals to reconstruct movement kinematics. Multichannel recordings of peripheral afferents were performed by inserting multi-electrode arrays into the DRGs of lower cervical segments in two anesthetized monkeys. A total of 112 and 92 units were responsive to the passive joint movements or the skin stimulation with a painting brush in Monkey 1 and Monkey 2, respectively. Using the SLiR algorithm, we reconstructed the temporal changes of joint angle, angular velocity, and acceleration at the elbow, wrist, and finger joints from temporal firing patterns of the DRG neurons. By automatically selecting a subset of recorded units, the SLiR achieved superior generalization performance compared with a regularized linear regression algorithm. The SLiR selected not only putative muscle units that were responsive to only the passive movements, but also a number of putative cutaneous units responsive to the skin stimulation. These results suggested that an ensemble of peripheral primary afferents that contains both putative muscle and cutaneous units encode forelimb joint kinematics of non-human primates.

Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning

Directory of Open Access Journals (Sweden)

Tsatsoulis Costas

2010-05-01

Full Text Available Abstract Background There is increasing evidence that gene location and surrounding genes influence the functionality of genes in the eukaryotic genome. Knowing the Gene Ontology Slim terms associated with a gene gives us insight into a gene's functionality by informing us how its gene product behaves in a cellular context using three different ontologies: molecular function, biological process, and cellular component. In this study, we analyzed if we could classify a gene in Saccharomyces cerevisiae to its correct Gene Ontology Slim term using information about its location in the genome and information from its nearest-neighbouring genes using classification learning. Results We performed experiments to establish that the MultiBoostAB algorithm using the J48 classifier could correctly classify Gene Ontology Slim terms of a gene given information regarding the gene's location and information from its nearest-neighbouring genes for training. Different neighbourhood sizes were examined to determine how many nearest neighbours should be included around each gene to provide better classification rules. Our results show that by just incorporating neighbour information from each gene's two-nearest neighbours, the percentage of correctly classified genes to their correct Gene Ontology Slim term for each ontology reaches over 80% with high accuracy (reflected in F-measures over 0.80 of the classification rules produced. Conclusions We confirmed that in classifying genes to their correct Gene Ontology Slim term, the inclusion of neighbour information from those genes is beneficial. Knowing the location of a gene and the Gene Ontology Slim information from neighbouring genes gives us insight into that gene's functionality. This benefit is seen by just including information from a gene's two-nearest neighbouring genes.

Je li periodni sustav elemenata doista periodičan?

Directory of Open Access Journals (Sweden)

Nenad Raos

2016-12-01

Full Text Available Periodni sustav elemenata je po imenu i naravi periodičan, no njegova se periodičnost ne može jednostavno, matematički definirati. Uz osnovnu periodičnost po skupinama uočavaju se i druge vrste pravilnosti, poput dijagonalne sličnosti, sličnosti među skupinama (n i (n + 10 te povezanosti elemenata “konjićevim skokom”. Složenost PSE-a odražava se i u njegovim mnogobrojnim i raznovrsnim grafičkim prikazima (“tablicama” koji naglašavaju specifične odnose među elementima.