Changing Practices in the Assessment of Writing a Discipline Redefining Itself

This thesis concerns how changes in the assessment of writing mirror the historical changes in the purposes and methodologies in education. We have witnessed a dramatic shift from the viewing and testing of writing as a series of sub-skills, with emphasis on error-avoidance and correctness of form, to viewing both the process of writing and its assessment as a means of discovery, reflection, and learning. New practices in the evaluation of writing reflect knowledge of how writing occurs and how it is taught. Results of a survey conducted over two years show high school students\u27 responses to traditional and new assessment methods. The important role writing may play in aiding students to better understand and learn school related materials is explored. The use of portfolios in writing classes can provide students with experiences they can carry outside of the English classroom. Creating a portfolio and portfolio assessment in the writing classroom are ways to nurture creative and critical thinking. Through the use of portfolios in the writing classroom, teaching, learning, and assessing can work together as a recursive whole. Portfolios can provide the authentic experience and the authentic assessment called for by today\u27s educational theorists, writer-researchers, and classroom teachers to prepare students for the complex world waiting for them in the twenty-first century

The chloroplast import receptor Toc34 functions as preprotein-regulated GTPase

Toc34 is a protein of the chloroplast outer envelope membrane that acts as receptor for preproteins containing a transit sequence. The recognition of preproteins by Toc34 is regulated by GTP binding and phosphorylation. The phosphorylation site of Toc34 is located at serine 113, close to the postulated triphosphate binding site. This can explain the down-regulation of Toc34 by phosphorylation, resulting in the loss of GTP binding. Vice versa, GTP but not GDP binding of Toc34 influences the phosphorylation. The nucleotide specificity of Toc34 is not only determined by the classical nucleotide binding domains but by a non-typical region at the N-terminus of the protein. As a result, the GTP binding properties are unusual, since the triphosphate moiety of GTP is bound with higher affinity than the purine base. Purified Toc34 hydrolyses GTP at a low rate, which could regulate the receptor function. The rate of hydrolysis is greatly stimulated by a precursor protein

Positively charged residues, the helical conformation and the structural flexibility of the leader sequence of pALDH are important for recognition by hTom20

AbstractTom20, a mitochondrial outer membrane receptor necessary for protein translocation, was found to interact specifically with mitochondrial preproteins. The interaction of proteins containing an N-terminal matrix targeting signal was enhanced in an hydrophobic environment and the dependence of this interaction on the alpha helical conformation of the presequence was postulated. In order to test this hypothesis and to gain insights about the features of a matrix targeting signal necessary to be recognized by the receptor machinery including Tom20, the interaction of pALDH and signal sequence mutants to Tom20 in the absence and presence of a hydrophobic environment was investigated. Here we present evidence to show that in a hydrophobic environment the interaction between Tom20 and the leader sequence is strongly dependent on the positive charges within the signal sequence as well as on the flexibility of this signal

Hubris, humility and humanity: expanding evidence approaches for improving and sustaining community health programmes

Community-based approaches are a critical foundation for many health outcomes, including reproductive, maternal, newborn and child health (RMNCH). Evidence is a vital part of strengthening that foundation, but largely focuses on the technical content of what must be done, rather than on how disparate community actors continuously interpret, implement and adapt interventions in dynamic and varied community health systems. We argue that efforts to strengthen evidence for community programmes must guard against the hubris of relying on a single approach or hierarchy of evidence for the range of research questions that arise when sustaining community programmes at scale. Moving forward we need a broader evidence agenda that better addresses the implementation realities influencing the scale and sustainability of community programmes and the partnerships underpinning them if future gains in community RMNCH are to be realised

Photosystem II core phosphorylation and photosynthetic acclimation require two different protein kinases

Illumination changes elicit modifications of thylakoid proteins and reorganization of the photosynthetic machinery. This involves, in the short term, phosphorylation of photosystem II (PSII) and light-harvesting (LHCII) proteins. PSII phosphorylation is thought to be relevant for PSII turnover1,2, whereas LHCII phosphorylation is associated with the relocation of LHCII and the redistribution of excitation energy (state transitions) between photosystems3,4. In the long term, imbalances in energy distribution between photosystems are counteracted by adjusting photosystem stoichiometry5,6. In the green alga Chlamydomonas and the plant Arabidopsis, state transitions require the orthologous protein kinases STT7 and STN7, respectively7,8. Here we show that in Arabidopsis a second protein kinase, STN8, is required for the quantitative phosphorylation of PSII core proteins. However, PSII activity under high-intensity light is affected only slightly in stn8 mutants, and D1 turnover is indistinguishable from the wild type, implying that reversible protein phosphorylation is not essential for PSII repair. Acclimation to changes in light quality is defective in stn7 but not in stn8 mutants, indicating that short-term and long-term photosynthetic adaptations are coupled. Therefore the phosphorylation of LHCII, or of an unknown substrate of STN7, is also crucial for the control of photosynthetic gene expressio

Protein-Induced Modulation of Chloroplast Membrane Morphology

Organelles are surrounded by membranes with a distinct lipid and protein composition. While it is well established that lipids affect protein functioning and vice versa, it has been only recently suggested that elevated membrane protein concentrations may affect the shape and organization of membranes. We therefore analyzed the effects of high chloroplast envelope protein concentrations on membrane structures using an in vivo approach with protoplasts. Transient expression of outer envelope proteins or protein domains such as CHUP1-TM–GFP, outer envelope protein of 7 kDa–GFP, or outer envelope protein of 24 kDa–GFP at high levels led to the formation of punctate, circular, and tubular membrane protrusions. Expression of inner membrane proteins such as translocase of inner chloroplast membrane 20, isoform II (Tic20-II)–GFP led to membrane protrusions including invaginations. Using increasing amounts of DNA for transfection, we could show that the frequency, size, and intensity of these protrusions increased with protein concentration. The membrane deformations were absent after cycloheximide treatment. Co-expression of CHUP1-TM–Cherry and Tic20-II–GFP led to membrane protrusions of various shapes and sizes including some stromule-like structures, for which several functions have been proposed. Interestingly, some structures seemed to contain both proteins, while others seem to contain one protein exclusively, indicating that outer and inner envelope dynamics might be regulated independently. While it was more difficult to investigate the effects of high expression levels of membrane proteins on mitochondrial membrane shapes using confocal imaging, it was striking that the expression of the outer membrane protein Tom20 led to more elongate mitochondria. We discuss that the effect of protein concentrations on membrane structure is possibly caused by an imbalance in the lipid to protein ratio and may be involved in a signaling pathway regulating membrane biogenesis. Finally, the observed phenomenon provides a valuable experimental approach to investigate the relationship between lipid synthesis and membrane protein expression in future studies

A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase

Ribosome biogenesis in yeast requires 75 small nucleolar RNAs (snoRNAs) and a myriad of cofactors for processing, modification, and folding of the ribosomal RNAs (rRNAs). For the 19 RNA helicases implicated in ribosome synthesis, their sites of action and molecular functions have largely remained unknown. Here, we have used UV cross-linking and analysis of cDNA (CRAC) to reveal the pre-rRNA binding sites of the RNA helicase Rok1, which is involved in early small subunit biogenesis. Several contact sites were identified in the 18S rRNA sequence, which interestingly all cluster in the “foot” region of the small ribosomal subunit. These include a major binding site in the eukaryotic expansion segment ES6, where Rok1 is required for release of the snR30 snoRNA. Rok1 directly contacts snR30 and other snoRNAs required for pre-rRNA processing. Using cross-linking, ligation and sequencing of hybrids (CLASH) we identified several novel pre-rRNA base-pairing sites for the snoRNAs snR30, snR10, U3, and U14, which cluster in the expansion segments of the 18S rRNA. Our data suggest that these snoRNAs bridge interactions between the expansion segments, thereby forming an extensive interaction network that likely promotes pre-rRNA maturation and folding in early pre-ribosomal complexes and establishes long-range rRNA interactions during ribosome synthesis

Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins

<p>Abstract</p> <p>Background</p> <p>The outer membranes of mitochondria are thought to be homologous to the outer membranes of Gram negative bacteria, which contain 100's of distinct families of <it>β</it>-barrel membrane proteins (BOMPs) often forming channels for transport of nutrients or drugs. However, only four families of mitochondrial BOMPs (MBOMPs) have been confirmed to date. Although estimates as high as 100 have been made in the past, the number of yet undiscovered MBOMPs is an open question. Fortunately, the recent discovery of a membrane integration signal (the <it>β</it>-signal) for MBOMPs gave us an opportunity to look for undiscovered MBOMPs.</p> <p>Results</p> <p>We present the results of a comprehensive survey of eukaryotic protein sequences intended to identify new MBOMPs. Our search employs recent results on <it>β</it>-signals as well as structural information and a novel BOMP predictor trained on both bacterial and mitochondrial BOMPs. Our principal finding is circumstantial evidence suggesting that few MBOMPs remain to be discovered, if one assumes that, like known MBOMPs, novel MBOMPs will be monomeric and <it>β</it>-signal dependent. In addition to this, our analysis of MBOMP homologs reveals some exceptions to the current model of the <it>β</it>-signal, but confirms its consistent presence in the C-terminal region of MBOMP proteins. We also report a <it>β</it>-signal independent search for MBOMPs against the yeast and Arabidopsis proteomes. We find no good candidates MBOMPs in yeast but the Arabidopsis results are less conclusive.</p> <p>Conclusions</p> <p>Our results suggest there are no remaining MBOMPs left to discover in yeast; and if one assumes all MBOMPs are <it>β</it>-signal dependent, few MBOMP families remain undiscovered in any sequenced organism.</p

Individualized markers optimize class prediction of microarray data

BACKGROUND: Identification of molecular markers for the classification of microarray data is a challenging task. Despite the evident dissimilarity in various characteristics of biological samples belonging to the same category, most of the marker – selection and classification methods do not consider this variability. In general, feature selection methods aim at identifying a common set of genes whose combined expression profiles can accurately predict the category of all samples. Here, we argue that this simplified approach is often unable to capture the complexity of a disease phenotype and we propose an alternative method that takes into account the individuality of each patient-sample. RESULTS: Instead of using the same features for the classification of all samples, the proposed technique starts by creating a pool of informative gene-features. For each sample, the method selects a subset of these features whose expression profiles are most likely to accurately predict the sample's category. Different subsets are utilized for different samples and the outcomes are combined in a hierarchical framework for the classification of all samples. Moreover, this approach can innately identify subgroups of samples within a given class which share common feature sets thus highlighting the effect of individuality on gene expression. CONCLUSION: In addition to high classification accuracy, the proposed method offers a more individualized approach for the identification of biological markers, which may help in better understanding the molecular background of a disease and emphasize the need for more flexible medical interventions