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Literacy coaching: Research & practice
No full textCopyright © 2010 Center for Educational Development, Evaluation, and Research; Texas A&M University-Corpus Christi College of EducationThe chapters in this volume are based on presentations from the First National Literacy Coaching Summit held at Texas A&M University-Corpus Christi on April 3 and 4, 2009. The conference drew more than 400 participants from 21 states, the Virgin Islands, Canada, and Washington, D.C. Keynote speakers included Dr. Nancy Shanklin of the University of Colorado, then-head of the Literacy Coaching Clearinghouse; Dr. Rita Bean of the University of Pittsburgh, a longtime researcher on the role of the reading specialist/literacy professional; Dr. MaryEllen Vogt of California State University Long Beach, an expert on teaching English language learners; and Gary Soto, a noted children’s author. Literacy coaching has been a hot topic in the field for most of the past decade (Cassidy & Cassidy, 2009-10). A literacy coach should be a well-qualified and highly-regarded classroom teacher with advanced training in literacy. Ideally, the literacy coach is assigned to one school and primarily works as a staff developer. However, the International Reading Association recognized the “changing roles … and variety of new titles, such as reading coach and literacy coach, and …the variability in the job descriptions for these coaches” (2004, p. 2). Chapters included in this book represent both research and practice in the field of literacy coaching. The 26 authors hail from 10 different states. These chapter authors are both school-based and university-based professionals. Each of the articles was blindly peer reviewed by at least two literacy professionals. Like the authors, Jack Cassidy & Sherrye Dee Garrett, these peer reviewers were both school-based and university based and came from ten different states. The first chapter introduces the major coaching themes and research presented in this book. The second chapter provides an overview provides an overview of the history and precursors of current literacy coaching. The next five chapters represent some of the research conducted on literacy coaching. Nancy Shanklin’s article begins the research section, and it highlights some of the most significant research on literacy coaching. The second section of the book focuses on specific practices associated with literacy coaching. This chapter opens with a piece by Rita Bean, delineating five lessons from her years working with and observing literacy coaching in schools. The remaining five chapters address specific programs and strategies that have proven effective
Essential Features and Rational Design of CRISPR RNAs That Function With the Cas RAMP Module Complex to Cleave RNAs
No full textSmall RNAs target invaders for silencing in the CRISPR-Cas pathways that protect bacteria and archaea from viruses and plasmids. The CRISPR RNAs (crRNAs) contain sequence elements acquired from invaders that guide CRISPR-associated (Cas) proteins back to the complementary invading DNA or RNA. Here, we have analyzed essential features of the crRNAs associated with the Cas RAMP module (Cmr) effector complex, which cleaves targeted RNAs. We show that Cmr crRNAs contain an 8-nucleotide 5’ sequence tag (also found on crRNAs associated with other CRISPR-Cas pathways) that is critical for crRNA function and can be used to engineer crRNAs that direct cleavage of novel targets. We also present data that indicates that the Cmr complex cleaves an endogenous complementary RNA in Pyrococcus furiosus, providing direct in vivo evidence of RNA targeting by the CRISPR-Cas system. Our findings indicate that the CRISPR RNA-Cmr protein pathway may be exploited to cleave RNAs of interest
Transcriptome Analysis Reveals Strain-Specific and Conserved Stemness Genes in Schmidtea Mediterranea
No full textThe planarian Schmidtea mediterranea is a powerful model organism for studying stem cell biology due to its extraordinary regenerative ability mediated by neoblasts, a population of adult somatic stem cells. Elucidation of the S. mediterranea transcriptome and the dynamics of transcript expression will increase our understanding of the gene regulatory programs that regulate stem cell function and differentiation. Here, we have used RNA-Seq to characterize the S. mediterranea transcriptome in sexual and asexual animals and in purified neoblast and differentiated cell populations. Our analysis identified many uncharacterized genes, transcripts, and alternatively spliced isoforms that are differentially expressed in a strain or cell type-specific manner. Transcriptome profiling of purified neoblasts and differentiated cells identified neoblast-enriched transcripts, many of which likely play important roles in regeneration and stem cell function. Strikingly, many of the neoblast-enriched genes are orthologs of genes whose expression is enriched in human embryonic stem cells, suggesting that a core set of genes that regulate stem cell function are conserved across metazoan species
Loss of DNA mismatch repair imparts a selective advantage in planarian adult stem cells.
No full textLynch syndrome (LS) leads to an increased risk of early-onset colorectal and other types of cancer and is caused by germline mutations in DNA mismatch repair (MMR) genes. Loss of MMR function results in a mutator phenotype that likely underlies its role in tumorigenesis. However, loss of MMR also results in the elimination of a DNA damage-induced checkpoint/apoptosis activation barrier that may allow damaged cells to grow unchecked. A fundamental question is whether loss of MMR provides pre-cancerous stem cells an immediate selective advantage in addition to establishing a mutator phenotype. To test this hypothesis in an in vivo system, we utilized the planarian Schmidtea mediterranea which contains a significant population of identifiable adult stem cells. We identified a planarian homolog of human MSH2, a MMR gene which is mutated in 38% of LS cases. The planarian Smed-msh2 is expressed in stem cells and some progeny. We depleted Smed-msh2 mRNA levels by RNA-interference and found a striking survival advantage in these animals treated with a cytotoxic DNA alkylating agent compared to control animals. We demonstrated that this tolerance to DNA damage is due to the survival of mitotically active, MMR-deficient stem cells. Our results suggest that loss of MMR provides an in vivo survival advantage to the stem cell population in the presence of DNA damage that may have implications for tumorigenesis
Gaps in affiliation indexing in Scopus and PubMed
No full textObjective: The authors sought to determine whether unexpected gaps existed in Scopus’s author affiliation indexing of publications written by the University of Nebraska Medical Center or Nebraska Medicine (UNMC/NM) authors during 2014.
Methods: First, we compared Scopus affiliation identifier search results to PubMed affiliation keyword search results. Then, we searched Scopus using affiliation keywords (UNMC, etc.) and compared the results to PubMed affiliation keyword and Scopus affiliation identifier searches.
Results: We found that Scopus’s records for approximately 7% of UNMC/NM authors’ publications lacked appropriate UNMC/NM author affiliation identifiers, and many journals’ publishers were supplying incomplete author affiliation information to PubMed.
Conclusions: Institutions relying on Scopus to track their impact should determine whether Scopus’s affiliation identifiers will, in fact, identify all articles published by their authors and investigators
In search of a new paradigm for protective immunity to TB
No full textAuthor ManuscriptClinical trials of vaccines against Mycobacterium tuberculosis are well under way and results are starting to come in. Some of these results are not so encouraging, as exemplified by the latest Aeras-422 and MVA85A trials. Other than empirically determining whether a vaccine reduces the number of cases of active tuberculosis, which is a daunting prospect given the chronic nature of the disease, we have no way of assessing vaccine efficacy. Therefore, investigators seek to identify biomarkers that predict vaccine efficacy. Historically, focus has been on the production of interferon-γ by CD4(+) T cells, but this has not been a useful correlate of vaccine-induced protection. In this Opinion article, we discuss recent advances in our understanding of the immune control of M. tuberculosis and how this knowledge could be used for vaccine design and evaluation.The authors are supported by the following grants from the US National Institutes of Heath (NIH) and US National Institute of Allergy and Infectious Diseases (NIAID): R21AI100766, R01AI085669, R01AI098637, and R01AI10672
THE SELF-REFLECTION OF EMIGRANT IN AYN RAND’S ART WORKS
No full textThe article is devoted to the research of exile elements in Ayn Rand’s art works (the American
writer and philosopher from Russia Alissa Rozenbaum). The hypothesis of the survey is in the fact that Ayn
Rand in the texts takes the self-reflection as an emigrant. The author formulated two stages of Ayn Rand’s
reflection as an emigrant in the art works. The first stage encompasses the period when Ayn Rand freshly
emigrated in the USA and the trauma of the October revolution was actual. As a reflection of this emotions she wrote the novel We The Living (1936) that (as the author of the article demonstrates gradually) fits
organically in the exile literature of the first wave (M. Aldanov, I. Shmelev). The author concentrated on the
more detail comparative analysis of Ayn Rand’s first novel and the novel The Sun of Deads (1923) by another
Russian emigrant writer I. Shmelev. The author discovered the familiarity of the art images in these texts that reflected the pain of both
emigrants. Having different ideological opinions, Rand and Shmelev nevertheless are close to each other in the traumatic experience
of the October revolution. The second stage of Ayn Rand’s emigrant self-reflection is the period of “American novels” that (as it is believed) have no common with Russian reality. But in the novels The Fountainhead (1943) and Atlas Shrugged (1957) the layer of exile subtext
is evolved. It contains the allusion on the Soviet reality comprehended by the writer as the warning to the American capitalism. As the
result the author made the conclusion that Ayn Rand’s art texts ate the complicated mix of two mentalities (Russian and American ones)
that generates a new art model and is perspective for the research as an exile literature too. The results of the research can be used in
the practice of teaching at higher school education, on the special courses about the literature of Russian abroad. The methods of the
research are caused by its tasks and contains such traditional for the literary studies methods as biographical, cultural-historical, sociological, comparative-historical
Evolution of alternative and constitutive regions of mammalian 5'UTRs
No full textAbstract Background Alternative splicing (AS) in protein-coding sequences has emerged as an important mechanism of regulation and diversification of animal gene function. By contrast, the extent and roles of alternative events including AS and alternative transcription initiation (ATI) within the 5'-untranslated regions (5'UTRs) of mammalian genes are not well characterized. Results We evaluated the abundance, conservation and evolution of putative regulatory control elements, namely, upstream start codons (uAUGs) and open reading frames (uORFs), in the 5'UTRs of human and mouse genes impacted by alternative events. For genes with alternative 5'UTRs, the fraction of alternative sequences (those present in a subset of the transcripts) is much greater than that in the corresponding coding sequence, conceivably, because 5'UTRs are not bound by constraints on protein structure that limit AS in coding regions. Alternative regions of mammalian 5'UTRs evolve faster and are subject to a weaker purifying selection than constitutive portions. This relatively weak selection results in over-abundance of uAUGs and uORFs in the alternative regions of 5'UTRs compared to constitutive regions. Nevertheless, even in alternative regions, uORFs evolve under a stronger selection than the rest of the sequences, indicating that some of the uORFs are conserved regulatory elements; some of the non-conserved uORFs could be involved in species-specific regulation. Conclusion The findings on the evolution and selection in alternative and constitutive regions presented here are consistent with the hypothesis that alternative events, namely, AS and ATI, in 5'UTRs of mammalian genes are likely to contribute to the regulation of translation.</p
Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea.
No full textThe planarian Schmidtea mediterranea is a powerful model organism for studying stem cell biology due to its extraordinary regenerative ability mediated by neoblasts, a population of adult somatic stem cells. Elucidation of the S. mediterranea transcriptome and the dynamics of transcript expression will increase our understanding of the gene regulatory programs that regulate stem cell function and differentiation. Here, we have used RNA-Seq to characterize the S. mediterranea transcriptome in sexual and asexual animals and in purified neoblast and differentiated cell populations. Our analysis identified many uncharacterized genes, transcripts, and alternatively spliced isoforms that are differentially expressed in a strain or cell type-specific manner. Transcriptome profiling of purified neoblasts and differentiated cells identified neoblast-enriched transcripts, many of which likely play important roles in regeneration and stem cell function. Strikingly, many of the neoblast-enriched genes are orthologs of genes whose expression is enriched in human embryonic stem cells, suggesting that a core set of genes that regulate stem cell function are conserved across metazoan species
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