Inter-generational transmission in a minority language setting: Stop consonant production by Bangladeshi heritage children and adults

Aims and objectives: The purpose of this study was to gain a better understanding of speech development across successive generations of heritage language users, examining how cross-linguistic, developmental and socio-cultural factors affect stop consonant production. Design: To this end, we recorded Sylheti and English stop productions of two sets of Bangladeshi heritage families: (1) first-generation adult migrants from Bangladesh and their (second-generation) UK-born children, and (2) second-generation UK-born adult heritage language users and their (third-generation) UK-born children. Data and analysis: The data were analysed auditorily, using whole-word transcription, and acoustically, examining voice onset time. Comparisons were then made in both languages across the four groups of participants, and cross-linguistically. Findings: The results revealed non-native productions of English stops by the first-generation migrants but largely target-like patterns by the remaining sets of participants. The Sylheti stops exhibited incremental changes across successive generations of speakers, with the third-generation children’s productions showing the greatest influence from English. Originality: This is one of few studies to examine both the host and heritage language in an ethnic minority setting, and the first to demonstrate substantial differences in heritage language accent between age-matched second- and third-generation children. The study shows that current theories of bilingual speech learning do not go far enough in explaining how speech develops in heritage language settings. Implications: These findings have important implications for the maintenance, transmission and long-term survival of heritage languages, and show that investigations need to go beyond second-generation speakers, in particular in communities that do not see a steady influx of new migrants

Computing and applying atomic regulons to understand gene expression and regulation

The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb.2016.01819/full#supplementary-materialUnderstanding gene function and regulation is essential for the interpretation prediction and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets Atomic Regulons ARs represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes and to enable rational genetic engineering of cellular systems. Here we describe an approach for inferring ARs that leverages large-scale expression data sets gene context and functional relationships among genes. We computed ARs for Escherichia coli based on 907 gene expression experiments and compared our results with gene clusters produced by two prevalent data-driven methods: hierarchical clustering and k-means clustering. We compared ARs and purely data-driven gene clusters to the curated set of regulatory interactions for E. coli found in RegulonDB showing that ARs are more consistent with gold standard regulons than are data-driven gene clusters. We further examined the consistency of ARs and data-driven gene clusters in the context of gene interactions predicted by Context Likelihood of Relatedness CLR analysis finding that the ARs show better agreement with CLR predicted interactions. We determined the impact of increasing amounts of expression data on AR construction and find that while more data improve ARs it is not necessary to use the full set of gene expression experiments available for E. coli to produce high quality ARs. In order to explore the conservation of co-regulated gene sets across different organisms we computed ARs for Shewanella oneidensis Pseudomonas aeruginosa Thermus thermophilus and Staphylococcus aureus each of which represents increasing degrees of phylogenetic distance from E. coli. Comparison of the organism-specific ARs showed that the consistency of AR gene membership correlates with phylogenetic distance but there is clear variability in the regulatory networks of closely related organisms. As large scale expression data sets become increasingly common for model and non-model organisms comparative analyses of atomic regulons will provide valuable insights into fundamental regulatory modules used across the bacterial domain.JF acknowledges funding from [SFRH/BD/70824/2010] of the FCT (Portuguese Foundation for Science and Technology) PhD program. CH and PW were supported by the National Science Foundation under grant number EFRI-MIKS-1137089. RT was supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), U.S. Department of Energy(DOE),and his work is a contribution of the Pacific North west National Laboratory (PNNL) Foundational Scientific Focus Area. This work was partially supported by an award from the National Science Foundation to MD, AB, NT, and RO (NSFABI-0850546). This work was also supported by the United States National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Service [Contract No. HHSN272201400027C]

Binding-Induced Folding of a Natively Unstructured Transcription Factor

Transcription factors are central components of the intracellular regulatory networks that control gene expression. An increasingly recognized phenomenon among human transcription factors is the formation of structure upon target binding. Here, we study the folding and binding of the pKID domain of CREB to the KIX domain of the co-activator CBP. Our simulations of a topology-based Go¯-type model predict a coupled folding and binding mechanism, and the existence of partially bound intermediates. From transition-path and W-value analyses, we find that the binding transition state resembles the unstructured state in solution, implying that CREB becomes structured only after committing to binding. A change of structure following binding is reminiscent of an induced-fit mechanism and contrasts with models in which binding occurs to pre-structured conformations that exist in the unbound state at equilibrium. Interestingly, increasing the amount of structure in the unbound pKID reduces the rate of binding, suggesting a ‘‘fly-casting’’-like process. We find that the inclusion of attractive non-native interactions results in the formation of non-specific encounter complexes that enhance the on-rate of binding, but do not significantly change the binding mechanism. Our study helps explain how being unstructured can confer an advantage in protein target recognition. The simulations are in general agreement with the results of a recently reported nuclear magnetic resonance study, and aid in the interpretation of the experimental binding kinetics.Fil: Turjanski, Adrian. National Institutes of Health; Estados Unidos. National Institute of Dental and Craniofacial Research; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gutkind, J. Silvio. National Institute of Dental and Craniofacial Research; Estados Unidos. National Institutes of Health; Estados UnidosFil: Best, Robert B.. National Institute of Diabetes and Digestive and Kidney Diseases; Estados Unidos. National Institutes of Health; Estados UnidosFil: Hummer, Gerhard. National Institutes of Health; Estados Unidos. National Institute of Diabetes and Digestive and Kidney Diseases; Estados Unido

Skill tests of three-dimensional tidal currents in a global ocean model: A look at the North Atlantic

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/92458/1/jgr_timkoetal_northatlatnictidalcurrentskilltest_2012.pd

Disordered RNA chaperones can enhance nucleic acid folding via local charge screening

This work is licensed under a Creative Commons Attribution 4.0 International License.RNA chaperones are proteins that aid in the folding of nucleic acids, but remarkably, many of these proteins are intrinsically disordered. How can these proteins function without a well-defined three-dimensional structure? Here, we address this question by studying the hepatitis C virus core protein, a chaperone that promotes viral genome dimerization. Using single-molecule fluorescence spectroscopy, we find that this positively charged disordered protein facilitates the formation of compact nucleic acid conformations by acting as a flexible macromolecular counterion that locally screens repulsive electrostatic interactions with an efficiency equivalent to molar salt concentrations. The resulting compaction can bias unfolded nucleic acids towards folding, resulting in faster folding kinetics. This potentially widespread mechanism is supported by molecular simulations that rationalize the experimental findings by describing the chaperone as an unstructured polyelectrolyte.Swiss National Science FoundationEuropean Molecular Biology OrganizationIntramural Research Program of the NIDDK at the National Institutes of Healt

Atomistic mechanism of transmembrane helix association

Transmembrane helix association is a fundamental step in the folding of helical membrane proteins. The prototypical example of this association is formation of the glycophorin dimer. While its structure and stability have been well-characterized experimentally, the detailed assembly mechanism is harder to obtain. Here, we use all-atom simulations within phospholipid membrane to study glycophorin association. We find that initial association results in the formation of a non-native intermediate, separated by a significant free energy barrier from the dimer with a native binding interface. We have used transition-path sampling to determine the association mechanism. We find that the mechanism of the initial bimolecular association to form the intermediate state can be mediated by many possible contacts, but seems to be particularly favoured by formation of non-native contacts between the C-termini of the two helices. On the other hand, the contacts which are key to determining progression from the intermediate to the native state are those which define the native binding interface, reminiscent of the role played by native contacts in determining folding of globular proteins. As a check on the simulations, we have computed association and dissociation rates from the transition-path sampling. We obtain results in reasonable accord with available experimental data, after correcting for differences in native state stability. Our results yield an atomistic description of the mechanism for a simple prototype of helical membrane protein folding

Diffusion of intrinsically disordered proteins within viscoelastic membraneless droplets

In living cells, intrinsically disordered proteins (IDPs), such as FUS and DDX4, undergo phase separation, forming biomolecular condensates. Using molecular dynamics simulations, we investigate their behavior in their respective homogenous droplets. We find that the proteins exhibit transient subdiffusion due to the viscoelastic nature and confinement effects in the droplets. The conformation and the instantaneous diffusivity of the proteins significantly vary between the interior and the interface of the droplet, resulting in non-Gaussianity in the displacement distributions. This study highlights key aspects of IDP behavior in biomolecular condensates

The influence of contextual factors on healthcare quality improvement initiatives:what works, for whom and in what setting? Protocol for a realist review

Background  Context shapes the effectiveness of knowledge implementation and influences health improvement. Successful healthcare quality improvement (QI) initiatives frequently fail to transfer to different settings, with local contextual factors often cited as the cause. Understanding and overcoming contextual barriers is therefore crucial to implementing effective improvement; yet context is still poorly understood. There is a paucity of information on the mechanisms underlyinghowandwhyQI projects succeed or fail in given settings. A realist review of empirical studies of healthcare QI initiatives will be undertaken to examine the influence and impact of contextual factors on quality improvement in healthcare settings and explore whether QI initiatives can work in all contexts.  Methods  The review will explore which contextual factors are important, and how, why, when and for whom they are important, within varied settings. The dynamic nature of context and change over time will be explored by examining which aspects of context impact at key points in the improvement trajectory. The review will also consider the influence of context on improvement outcomes (provider- and patient-level), spread and sustainability. The review process will follow five iterative steps: (1) clarify scope, (2) search for evidence, (3) appraise primary studies and extract data, (4) synthesise evidence and draw conclusions and (5) disseminate findings. The reviewers will consult with experts and stakeholders in the early stages to focus the review and develop a programme theory consisting of explanatory ‘context–mechanism–outcome’ configurations. Searches for primary evidence will be conducted iteratively. Data will be extracted and tested against the programme theory. A review advisory group will oversee the review process. Review findings will follow RAMESES guidelines and will be disseminated via a report, presentations and peer-reviewed publications.  Discussion  The review will update and consolidate evidence on the contextual conditions for effective improvement and distil new knowledge to inform the design and development of context-sensitive QI initiatives. This review ties in with the study of improvement programmes as vehicles of change and the development of an evidence base around healthcare improvement by addressing whether QI initiatives can work in all contexts.  Systematic review registration  PROSPERO CRD4201706213