Gram Slam! Teaching Contextualized Grammar through Cooperative Learning

Grammar in the classroom is often set aside as a minor part of the curriculum. This study analyzed why grammar is difficult to incorporate in the classroom as well as how that can be changed. Strategies that might impact the way grammar is taught in the classroom include cooperative learning among small groups, Student Teams-Achievement Divisions (STAD), Teams-Games-Tournament (TGT), and online quizzing formats, such as Kahoot! and No Red Ink. The mixed method study analyzed whether these strategies have an influence over student retention of grammatical rules and their usage in writing in the 9th grade Language Arts classroom. As it turns out, teaching grammar through cooperative learning and competition does not have a significant effect on student improvement on grammar skills. Students from the treatment group, however, demonstrated more enthusiasm for incorporating games in order to learn the concept

Single-cell internalization during zebrafish gastrulation

AbstractDuring gastrulation, germ layers are formed as prospective mesodermal and endodermal cells internalize and come to underlie the ectoderm [1–9]. Despite the pivotal role of gastrulation in animal development, the cellular interactions underlying this process are poorly understood. In zebrafish, mesoderm and endoderm formation requires the Nodal signals Cyclops and Squint and their cofactor One-eyed pinhead (Oep) [10–14]. We found that marginal cells in maternal-zygotic oep (MZoep) mutants do not internalize during gastrulation and acquire neural and tail fates at the expense of head and trunk mesendoderm. The lack of internalization in MZoep embryos and the cell-autonomous requirement for oep in Nodal signaling enabled us to test whether internalization can be achieved by individual cells or whether it depends on interactions within a group of cells. We found that individual MZoep mutant cells transplanted to the margin of wild-type blastula embryos initially internalize with their neighbors but are unable to contribute to the mesendoderm. In the reciprocal experiment, single wild-type cells transplanted to the margin of MZoep mutant embryos autonomously internalize and can express the mesendodermal markers axial/foxA2 and sox17. These results suggest that internalization and mesendoderm formation in zebrafish can be attained autonomously by single cells

Generating chimeric zebrafish embryos by transplantation.

One of the most powerful tools used to gain insight into complex developmental processes is the analysis of chimeric embryos. A chimera is defined as an organism that contains cells from more than one animal; mosaics are one type of chimera in which cells from more than one genotype are mixed, usually wild-type and mutant. In the zebrafish, chimeras can be readily made by transplantation of cells from a donor embryo into a host embryo at the appropriate embryonic stage. Labeled donor cells are generated by injection of a lineage marker, such as a fluorescent dye, into the one-cell stage embryo. Labeled donor cells are removed from donor embryos and introduced into unlabeled host embryos using an oil-controlled glass pipette mounted on either a compound or dissecting microscope. Donor cells can in some cases be targeted to a specific region or tissue of the developing blastula or gastrula stage host embryo by choosing a transplantation site in the host embryo based on well-established fate maps

Nonparametric survival analysis of epidemic data

This paper develops nonparametric methods for the survival analysis of epidemic data based on contact intervals. The contact interval from person i to person j is the time between the onset of infectiousness in i and infectious contact from i to j, where we define infectious contact as a contact sufficient to infect a susceptible individual. We show that the Nelson-Aalen estimator produces an unbiased estimate of the contact interval cumulative hazard function when who-infects-whom is observed. When who-infects-whom is not observed, we average the Nelson-Aalen estimates from all transmission networks consistent with the observed data using an EM algorithm. This converges to a nonparametric MLE of the contact interval cumulative hazard function that we call the marginal Nelson-Aalen estimate. We study the behavior of these methods in simulations and use them to analyze household surveillance data from the 2009 influenza A(H1N1) pandemic. In an appendix, we show that these methods extend chain-binomial models to continuous time.Comment: 30 pages, 6 figure

Auxin Input Pathway Disruptions Are Mitigated by Changes in Ausin Biosynthetic Gene Expression in Arabidopsis

Auxin is a phytohormone involved in cell elongation and division. Levels of indole-3-acetic acid (IAA), the primary auxin, are tightly regulated through biosynthesis, degradation, sequestration, and transport. IAA is sequestered in reversible processes by adding amino acids, polyol or simple alcohols, or sugars, forming IAA conjugates, or through a two-carbon elongation forming indole-3-butyric acid. These sequestered forms of IAA alter hormone activity. To gain a better understanding of how auxin homeostasis is maintained, we have generated Arabidopsis (Arabidopsis tlnaliana) mutants that combine disruptions in the pathways, converting IAA conjugates and indole-3-butyric acid to free IAA. These mutants show phenotypes indicative of low auxin levels, including delayed germination, abnormal vein patterning, and decreased apical dominance. Root phenotypes include changes in root length, root branching, and root hair growth. IAA levels are reduced in the cotyledon tissue but not meristems or hypocotyls. In the combination mutants, auxin biosynthetic gene expression is increased, particularly in the YUCCA/Tryptophan Aminotransferase of Arabidopsisl pathway, providing a feedback mechanism that allows the plant to compensate for changes in IAA input pathways and maintain cellular homeostasis

Compensatory Mutations in Predicted Metal Transporters Modulate Auxin Conjugate Responsiveness in Arabidopsis

Levels of the phytohormone indole-3-acetic acid (IAA) can be altered by the formation and hydrolysis of IAA conjugates. The isolation and characterization of Arabidopsis thaliana mutants with reduced IAA-conjugate sensitivity and wild-type IAA responses is advancing the understanding of auxin homeostasis by uncovering the factors needed for conjugate metabolism. For example, the discovery that the IAA-Ala-resistant mutant iar1 is defective in a protein in the ZIP family of metal transporters uncovered a link between metal homeostasis and IAA-conjugate sensitivity. To uncover additional factors impacting auxin conjugate metabolism, we conducted a genetic modifier screen and isolated extragenic mutations that restored IAA-amino acid conjugate sensitivity to the iar1 mutant. One of these suppressor mutants is defective in a putative cation diffusion facilitator, MTP5 (At3g12100; formerly known as MTPc2). Loss of MTP5 function restored IAA conjugate sensitivity to iar1 but not to mutants defective in IAA-amino acid conjugate amidohydrolases. Our results are consistent with a model in which MTP5 and IAR1 transport metals in an antagonistic fashion to regulate metal homeostasis within the subcellular compartment in which the IAA-conjugate amidohydrolases reside, and support previous suggestions that the ion composition in this compartment influences hydrolase activity

The coat protein of Alfalfa mosaic virus interacts and interferes with the transcriptional activity of the bHLH transcription factor ILR3 promoting salicylic acid-dependent defence signalling response

[EN] During virus infection, specific viral component-host factor interaction elicits the transcriptional reprogramming of diverse cellular pathways. Alfalfa mosaic virus (AMV) can establish a compatible interaction in tobacco and Arabidopsis hosts. We show that the coat protein (CP) of AMV interacts directly with transcription factor (TF) ILR3 of both species. ILR3 is a basic helix-loop-helix (bHLH) family member of TFs, previously proposed to participate in diverse metabolic pathways. ILR3 has been shown to regulate NEET in Arabidopsis, a critical protein in plant development, senescence, iron metabolism and reactive oxygen species (ROS) homeostasis. We show that the AMV CP-ILR3 interaction causes a fraction of this TF to relocate from the nucleus to the nucleolus. ROS, pathogenesis-related protein 1 (PR1) mRNAs, salicylic acid (SA) and jasmonic acid (JA) contents are increased in healthy Arabidopsis loss-of-function ILR3 mutant (ilr3.2) plants, which implicates ILR3 in the regulation of plant defence responses. In AMV-infected wild-type (wt) plants, NEET expression is reduced slightly, but is induced significantly in ilr3.2 mutant plants. Furthermore, the accumulation of SA and JA is induced in Arabidopsis wt-infected plants. AMV infection in ilr3.2 plants increases JA by over 10-fold, and SA is reduced significantly, indicating an antagonist crosstalk effect. The accumulation levels of viral RNAs are decreased significantly in ilr3.2 mutants, but the virus can still systemically invade the plant. The AMV CP-ILR3 interaction may down-regulate a host factor, NEET, leading to the activation of plant hormone responses to obtain a hormonal equilibrium state, where infection remains at a level that does not affect plant viability.F.A. was the recipient of a contract Ramon y Cajal (RYC-2010-06169) program of the Ministerio de Educacion, Cultura y Deporte of Spain. We thank L. Corachan for excellent technical assistance. This work was supported by Grants BIO2014-54862-R from the Spanish grant agency Direccion General de Investigacion Cientifica y Tecnica (DGICT) the Prometeo Program GV2015/010 from the Generalitat Valenciana and PAID-06-10-1496 from the Universitat Politecnica de Valencia (Spain).Aparicio Herrero, F.; Pallás Benet, V. (2017). The coat protein of Alfalfa mosaic virus interacts and interferes with the transcriptional activity of the bHLH transcription factor ILR3 promoting salicylic acid-dependent defence signalling response. 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Molecular Plant-Microbe Interactions®, 19(3), 350-358. doi:10.1094/mpmi-19-0350Kim, K.-C., Lai, Z., Fan, B., & Chen, Z. (2008). Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense. The Plant Cell, 20(9), 2357-2371. doi:10.1105/tpc.107.055566Kim, S. A., Punshon, T., Lanzirotti, A., Li, L., Alonso, J. M., Ecker, J. R., … Guerinot, M. L. (2006). Localization of Iron in Arabidopsis Seed Requires the Vacuolar Membrane Transporter VIT1. Science, 314(5803), 1295-1298. doi:10.1126/science.1132563Liu, Z., Zhang, Z., Faris, J. D., Oliver, R. P., Syme, R., McDonald, M. C., … Friesen, T. L. (2012). The Cysteine Rich Necrotrophic Effector SnTox1 Produced by Stagonospora nodorum Triggers Susceptibility of Wheat Lines Harboring Snn1. PLoS Pathogens, 8(1), e1002467. doi:10.1371/journal.ppat.1002467Long, T. A., Tsukagoshi, H., Busch, W., Lahner, B., Salt, D. E., & Benfey, P. N. (2010). The bHLH Transcription Factor POPEYE Regulates Response to Iron Deficiency in Arabidopsis Roots. The Plant Cell, 22(7), 2219-2236. doi:10.1105/tpc.110.074096Lukhovitskaya, N. I., Solovieva, A. D., Boddeti, S. K., Thaduri, S., Solovyev, A. G., & Savenkov, E. I. (2013). An RNA Virus-Encoded Zinc-Finger Protein Acts as a Plant Transcription Factor and Induces a Regulator of Cell Size and Proliferation in Two Tobacco Species. The Plant Cell, 25(3), 960-973. doi:10.1105/tpc.112.106476Mandadi, K. K., & Scholthof, K.-B. G. (2013). Plant Immune Responses Against Viruses: How Does a Virus Cause Disease? The Plant Cell, 25(5), 1489-1505. doi:10.1105/tpc.113.111658Maule, A. J., Escaler, M., & Aranda, M. A. (2000). Programmed responses to virus replication in plants. Molecular Plant Pathology, 1(1), 9-15. doi:10.1046/j.1364-3703.2000.00002.xNechushtai, R., Conlan, A. R., Harir, Y., Song, L., Yogev, O., Eisenberg-Domovich, Y., … Mittler, R. (2012). Characterization of Arabidopsis NEET Reveals an Ancient Role for NEET Proteins in Iron Metabolism. The Plant Cell, 24(5), 2139-2154. doi:10.1105/tpc.112.097634Nelson, B. K., Cai, X., & Nebenführ, A. (2007). A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. The Plant Journal, 51(6), 1126-1136. doi:10.1111/j.1365-313x.2007.03212.xNemeth, K., Salchert, K., Putnoky, P., Bhalerao, R., Koncz-Kalman, Z., Stankovic-Stangeland, B., … Koncz, C. (1998). Pleiotropic control of glucose and hormone responses by PRL1, a nuclear WD protein, in Arabidopsis. Genes & Development, 12(19), 3059-3073. doi:10.1101/gad.12.19.3059Ni, P., & Cheng Kao, C. (2013). Non-encapsidation activities of the capsid proteins of positive-strand RNA viruses. Virology, 446(1-2), 123-132. doi:10.1016/j.virol.2013.07.023Olsen, A. N., Ernst, H. A., Leggio, L. L., & Skriver, K. (2005). NAC transcription factors: structurally distinct, functionally diverse. 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An Arabidopsis Basic Helix-Loop-Helix Leucine Zipper Protein Modulates Metal Homeostasis and Auxin Conjugate Responsiveness. Genetics, 174(4), 1841-1857. doi:10.1534/genetics.106.061044Ren, T., Qu, F., & Morris, T. J. (2005). The nuclear localization of the Arabidopsis transcription factor TIP is blocked by its interaction with the coat protein of Turnip crinkle virus. Virology, 331(2), 316-324. doi:10.1016/j.virol.2004.10.039Rodrigo, G., Carrera, J., Ruiz-Ferrer, V., del Toro, F. J., Llave, C., Voinnet, O., & Elena, S. F. (2012). A Meta-Analysis Reveals the Commonalities and Differences in Arabidopsis thaliana Response to Different Viral Pathogens. PLoS ONE, 7(7), e40526. doi:10.1371/journal.pone.0040526Sanchez-Navarro, J., Miglino, R., Ragozzino, A., & Bol, J. F. (2001). Engineering of Alfalfa mosaic virus RNA 3 into an expression vector. Archives of Virology, 146(5), 923-939. doi:10.1007/s007050170125Sánchez-Navarro, J. A., Carmen Herranz, M., & Pallás, V. (2006). 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7-rhamnosylated flavonols modulate homeostasis of the plant hormone auxin and affect plant development

Flavonols are a group of secondary metabolites that affect diverse cellular processes. They are considered putative negative regulators of the transport of the phytohormone auxin, by which they influence auxin distribution and concomitantly take part in the control of plant organ development. Flavonols are accumulating in a large number of glycosidic forms. Whether these have distinct functions and diverse cellular targets is not well understood. The rol1-2 mutant of Arabidopsis thaliana is characterized by a modified flavonol glycosylation profile that is inducing changes in auxin transport and growth defects in shoot tissues. To determine whether specific flavonol glycosides are responsible for these phenotypes, a suppressor screen was performed on the rol1-2 mutant, resulting in the identification of an allelic series of UGT89C1, a gene encoding a flavonol 7-O-rhamnosyltransferase. A detailed analysis revealed that interfering with flavonol rhamnosylation increases the concentration of auxin precursors and auxin metabolites, whereas auxin transport is not affected. This finding provides an additional level of complexity to the possible ways by which flavonols influence auxin distribution and suggests that flavonol glycosides play an important role in regulating plant development

Causes of unrest at silicic calderas in the East African Rift: new constraints from InSAR and soil-gas chemistry at Aluto volcano, Ethiopia

This work is a contribution to the Natural Environment Research Council (NERC) funded RiftVolc project (NE/L013932/1, Rift volcanism: past, present, and future). W.H., J.B., T.A.M., and D.M.P. are supported by and contribute to the NERC Centre for the Observation and Modelling of Earthquakes, Volcanoes, and Tectonics (COMET). Envisat data were provided by ESA. ALOS data were provided through ESA third party mission. W.H. funded by NERC studentship, NE/J5000045/1. Additional funding for fieldwork was provided by University College (University of Oxford), the Geological Remote Sensing Group, the Edinburgh Geological Society, and the Leverhulme Trust. Analytical work at the University of New Mexico was supported by the Volcanic and Geothermal Volatiles Lab at the Center for Stable Isotopes and an NSF grant EAR-1113066 to T.P.F.Restless silicic calderas present major geological hazards, and yet many also host significant untapped geothermal resources. In East Africa this poses a major challenge, although the calderas are largely unmonitored their geothermal resources could provide substantial economic benefits to the region. Understanding what causes unrest at these volcanoes is vital for weighing up the opportunities against the potential risks. Here we bring together new field and remote sensing observations to evaluate causes of ground deformation at Aluto, a restless silicic volcano located in the Main Ethiopian Rift (MER). Interferometric Synthetic Aperture Radar (InSAR) data reveal the temporal and spatial characteristics of a ground deformation episode that took place between 2008 and 2010. Deformation time-series reveal pulses of accelerating uplift that transition to gradual long-term subsidence, and analytical models support inflation source depths of ∼5 km. Gases escaping along the major fault zone of Aluto show high CO2 flux, and a clear magmatic carbon signature (CO2–δ13C of −4.2 to −4.5 ‰). This provides compelling evidence that the magmatic and hydrothermal reservoirs of the complex are physically connected. We suggest that a coupled magmatic-hydrothermal system can explain the uplift-subsidence signals. We hypothesize that magmatic fluid injection and/or intrusion in the cap of the magmatic reservoir drives edifice wide inflation while subsequent deflation is related to magmatic degassing and depressurization of the hydrothermal system. These new constraints on the plumbing of Aluto yield important insights into the behaviour of rift volcanic systems and will be crucial for interpreting future patterns of unrest.Publisher PDFPeer reviewe