276 research outputs found
Mathematical Caring Relations in Action
Get PDFIn a small-scale, 8-month teaching experiment, the author aimed to establish and maintain mathematical caring relations (MCRs) (Hackenberg, 2005c) with 4 6th-grade students. From a teacher's perspective, establishing MCRs involves holding the work of orchestrating mathematical learning for students together with an orientation to monitor and respond to energetic fluctuations that may accompany student–teacher interactions. From a student's perspective, participating in an MCR involves some openness to the teacher's interventions in the student's mathematical activity and some willingness to pursue questions of interest. In this article, the author elucidates the nature of establishing MCRs with 2 of the 4 students in the study and examines what is mathematical about these caring relations. Analysis revealed that student–teacher interaction can be viewed as a linked chain of perturbations; in student–teacher interaction aimed toward the establishment of MCRs, the linked chain tends toward perturbations that are bearable (Tzur, 1995) for both students and teachers
Identification of tomato miRNAs responsive to root colonization by endophytic Pochonia chlamydosporia
No full textThe molecular mechanisms active during the endophytic phase of the fungus Pochonia chlamydosporia are still poorly understood. In particular, few data are available on the links between the endophyte and the root response, as modulated by noncoding small RNAs. In this study, we describe the microRNAs (miRNAs) that are differentially expressed (DE) in the roots of tomato, colonized by P. chlamydosporia. A genome-wide NGS expression profiling of small RNAs in roots, either colonized or not by the fungus, showed 26 miRNAs upregulated in inoculated roots. Their predicted target genes are involved in the plant information processing system, which recognizes, percepts, and transmits signals, with higher representations in processes such as apoptosis and plant defense regulation. RNAseq data showed that predicted miRNA target genes were downregulated in tomato roots after 4, 7, 10, and 21Â days post P. chlamydosporia inoculation. The differential expression of four miRNAs was further validated using qPCR analysis. The P. chlamydosporia endophytic lifestyle in tomato roots included an intricate network of miRNAs and targets. Data provide a first platform of DE tomato miRNAs after P. chlamydosporia colonization. They indicated that several miRNAs are involved in the host response to the fungus, playing important roles for its recognition as a symbiotic microorganism, allowing endophytism by modulating the host defense reaction. Data also indicated that endophytism affects tRNA fragmentation. This is the first study on miRNAs induced by P. chlamydosporia endophytism and related development regulation effects in Solanum lycopersicum
Charles Dickens and Edwin Drood: the death of the author, the rise of the reader
No full textOn June 9, 1870, Charles Dickens died, leaving his last novel, The Mystery of Edwin Drood, half completed. For decades, readers and scholars have speculated about what Dickens intended for the second half of this novel. I argue that the both Dickens and Edwin Drood have extended afterlives due to the incomplete nature of this novel: readers return to Dickens's career and his other novels in order to try to determine the fate of Edwin Drood. The case of Drood shows us that the author is not dead; Dickens stays very much alive in the continuations whether the writers of continuations choose to include him in their interpretations or whether they decide to exclude him from their interpretations but or pay homage to his writing style. Either way, Dickens is a part of the novel and its afterlives, even though other people have picked up their pens to finish what he began
CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands
Get PDFHypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.This work was supported by the Spanish Government [BIO2008-01353 to José L. Oliver and BIO2010-20219 to Michael Hackenberg], Basque country “AE” grant (to Guillermo Barturen) and Erasmus internships (to Stefanie Geisen, Francisco Dios, and E. J. Maarten Hamberg)
Thiourea priming enhances salt tolerance through co-ordinated regulation of microRNAs and hormones in Brassica juncea
Get PDFActivation of stress tolerance mechanisms demands transcriptional reprogramming. Salt stress, a
major threat to plant growth, enhances ROS production and affects transcription through modulation
of miRNAs and hormones. The present study delineates salt stress ameliorating action of thiourea
(TU, a ROS scavenger) in Brassica juncea and provides mechanistic link between redox, microRNA and
hormones. The ameliorative potential of TU towards NaCl stress was related with its ability to decrease
ROS accumulation in roots and increase Na+ accumulation in shoots. Small RNA sequencing revealed
enrichment of down-regulated miRNAs in NaCl+TU treated roots, indicating transcriptional activation.
Ranking analysis identified three key genes including BRX4, CBL10 and PHO1, showing inverse
relationship with corresponding miRNA expression, which were responsible for TU mediated stress
mitigation. Additionally, ABA level was consistently higher till 24h in NaCl, while NaCl+TU treated
roots showed only transient increase at 4h suggesting an effective stress management. Jasmonate and
auxin levels were also increased, which prioritized defence and facilitated root growth, respectively.
Thus, the study highlights redox as one of the “core” components regulating miRNA and hormone
levels, and also strengthens the use of TU as a redox priming agent for imparting crop resilience to salt
stres
Identification and characterisation of a previously unknown drought tolerance‐associated micro <scp>RNA</scp> in barley
No full textDrought is the most serious abiotic stress, and causes crop losses on a worldwide scale. The present study identified a previously unknown microRNA (designated as hvu-miRX) of 21 nucleotides (nt) in length in barley. Its precursor (designated pre-miRX) and primary transcript (designated pri-miRX) were also identified, with lengths of 73 and 559 nt, respectively. The identified upstream sequence of pri-miRX contained both the TATA box and the CAAT box, which are both required for initiation of transcription. Transient promoter activation assays showed that the core promoter region of pri-miRX ranged 500 nt from the transcription start site. In transgenic barley overexpression of the wheat DREB3 transcription factor (TaDREB3) caused hvu-miRX to be highly expressed as compared with the same miRNA in non-transgenic barley. However, the high expression was not directly associated with TaDREB3. Genomic analysis revealed that the hvu-miRX gene was a single copy located on the short arm of chromosome 2 and appeared to be only conserved in Triticeae, but not in other plant species. Notably, transgenic barley that overexpressed hvu-miRX showed drought tolerance. Degradome library analysis and other tests showed that hvu-miRX targeted various genes including transcription factors via the cleavage mode. Our data provides an excellent opportunity to develop drought stress tolerant cereals using hvu-miRX.Hui Zhou, Syed S. Hussain, Michael Hackenberg, Natalia Bazanova, Omid Eini, Jie Li, Perry Gustafson, Bujun Sh
Characterization of phosphorus-regulated miR399 and miR827 and their isomirs in barley under phosphorus-sufficient and phosphorus-deficient conditions
Get PDF17 p.BACKGROUND: miR399 and miR827 are both involved in conserved phosphorus (P) deficiency signalling pathways. miR399 targets the PHO2 gene encoding E2 enzyme that negatively regulates phosphate uptake and root-to-shoot allocation, while miR827 targets SPX-domain-containing genes that negatively regulate other P-responsive genes. However, the response of miR399 and miR827 to P conditions in barley has not been investigated. RESULTS: In this study, we investigated the expression profiles of miR399 and miR827 in barley (Hordeum vulagre L.) under P-deficient and P-sufficient conditions. We identified 10 members of the miR399 family and one miR827 gene in barley, all of which were significantly up-regulated under deficient P. In addition, we found many isomirs of the miR399 family and miR827, most of which were also significantly up-regulated under deficient P. Several isomirs of miR399 members were found to be able to cleave their predicted targets in vivo. Surprisingly, a few small RNAs (sRNAs) derived from the single-stranded loops of the hairpin structures of MIR399b and MIR399e-1 were also found to be able to cleave their predicted targets in vivo. Many antisense sRNAs of miR399 and a few for miR827 were also detected, but they did not seem to be regulated by P. Intriguingly, the lowest expressed member, hvu-miR399k, had four-fold more antisense sRNAs than sense sRNAs, and furthermore under P sufficiency, the antisense sRNAs are more frequent than the sense sRNAs. We identified a potential regulatory network among miR399, its target HvPHO2 and target mimics HvIPS1 and HvIPS2 in barley under P-deficient and P-sufficient conditions. CONCLUSIONS: Our data provide an important insight into the mechanistic regulation and function of miR399, miR827 and their isomirs in barley under different P conditions.Michael Hackenberg, Bu-Jun Shi, Perry Gustafson and Peter Langridg
Group Discounting and the Peanuts Effect
No full texthttps://rdc.reed.edu/v1/resources/109eb7c9-eb78-45d3-b20d-229ba12a39dd/thumb/128.jpgThe present study examined how public goods judgments are discounted as group size increases by applying methods derived from social discounting to groups. Dubbed group discounting, we measured participants’ willingness to forgo money for themselves to give a fixed amount to a group with social distance held constant. In Experiment 1, participants discounted money to a group of others as that group size increased. Additionally, as the amount of money involved increased, participants discounted more steeply, showing a magnitude effect akin to that shown in the social discounting literature. In the largest group size condition, maximal discounting occurred when the money amount was lowest, akin to previous results in non-social tasks known as the ‘peanuts effect.’ Experiment 2 analyzed this outcome by comparing preferences for distributing finite amounts of money to different-sized groups over different magnitudes. The results suggest that people devalue inconsequential amounts of money. Together, the results of the two experiments show that participants heavily discount prosocial behavior when the benefits are distributed over large groups and have negligible individual benefits
A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs
Get PDFTranscription factors (TFs), microRNAs (miRNAs), small interfering RNAs (siRNAs) and other functional non-coding small RNAs (sRNAs) are important gene regulators. Comparison of sRNA expression profiles between transgenic barley overexpressing a drought tolerant TF (TaDREB3) and non-transgenic control barley revealed many group-specific sRNAs. In addition, 42% of the shared sRNAs were differentially expressed between the two groups (|log2|>1). Furthermore, TaDREB3- derived sRNAs were only detected in transgenic barley despite the existence of homologous genes in non-transgenic barley. These results demonstrate that the TF strongly affects the expression of sRNAs and siRNAs could in turn affect the TF stability. The TF also affects size distribution and abundance of sRNAs including miRNAs. About half of the sRNAs in each group were derived from chloroplast. A sRNA derived from tRNA-His(GUG) encoded by the chloroplast genome is the most abundant sRNA, accounting for 42.2% of the total sRNAs in transgenic barley and 28.9% in non-transgenic barley. This sRNA, which targets a gene (TC245676) involved in biological processes, was only present in barley leaves but not roots. 124 and 136 miRNAs were detected in transgenic and non-transgenic barley, respectively. miR156 was the most abundant miRNA and up-regulated in transgenic barley, while miR168 was the most abundant miRNA and up-regulated in non-transgenic barley. Eight out of 20 predicted novel miRNAs were differentially expressed between the two groups. All the predicted novel miRNA targets were validated using a degradome library. Our data provide an insight into the effect of TF on the expression of sRNAs in barley.Michael Hackenberg, Bu-Jun Shi, Perry Gustafson and Peter Langridg
Vienna, but fair - Influence of architectural measures on a socially just city
Get PDFDie Entstehung sozialer Ungleichheit und Segregation in einer Stadt ist das Ergebnis komplexer und vielschichtiger Faktoren. Diese Arbeit zielt darauf ab, diese Ungleichheitsfaktoren zu analysieren und stellt folgende zentrale Fragen: Identifizierung von Ungleichheiten - Welche systemischen, sozialen und räumlichen Ungleichheiten liegen in einer Stadt vor? Inwieweit kann eine Stadt als fair erachtet werden? Rolle der Architektur - Wie kann die Architektur dazu beitragen, diesen Ungleichheiten entgegenzuwirken? In dieser Arbeit dient die Stadt Wien als zentrales Untersuchungsobjekt. Eine eingehende Analyse der Stadt verdeutlicht, dass der 10. Wiener Gemeindebezirk, Favoriten, in besonderem Maße von sozialer Ungleichheit betroffen ist. Diese Ungleichheit hat nicht nur soziale, sondern auch räumliche Dimensionen, die auf politische Entscheidungen zurückzuführen sind und durch die Industrialisierung sowie nachfolgende stadtplanerische Eingriffe verstärkt wurden. Als Forschungsmethodik werden mit den Mitteln der Fotografie, der Bezirk kartiert und Lebensumstände dokumentiert. Aus einer multispektralen, interdisziplinären Perspektive werden über Gespräche mit den Bewohner*innen sowie den relevanten Akteur*innen der lokalen Institutionen, darunter Polizei und Sozialarbeit, Lebensrealitäten abgebildet. Die gesammelten Informationen werden einer theoretisch fundierten Reflexion unterzogen, wobei soziologische Ansätze von Bourdieu und Wacquant als Leitfaden dienen. Eine Hypothese dieser Arbeit ist, dass die vorhandene soziale Ungleichheit in Wien eng mit institutionellem und strukturellem Rassismus verknüpft ist. Zugangsbeschränkungen und Diskriminierung auf dem Wohnungsmarkt tragen zur Verdrängung sozial benachteiligter Bevölkerungsgruppen in einen strukturell isolierten, dicht besiedelten Bezirk bei. Zusätzlich beleuchtet die Analyse der Medienberichterstattung eine Tendenz zur Kriminalisierung von Armut, was ein negatives Image schafft und bei anderen Stadtbewohner*innen verstärkt Unsicherheit und Angst auslöst. In interdisziplinärer Zusammenarbeit mit einer Rechtspsychologin wird deutlich, dass Stigmatisierung und Vorurteile individuelles Verhalten beeinflussen können. Der Wert, der einem Ort zugesprochen wird, überträgt sich also auch auf seine Bewohner*innen. Abschließend werden auf verschiedenen Maßstäben konkrete, architektonische Einflussfaktoren aufgezeigt, die die Lebensqualität, soziale Mobilität und das Zusammengehörigkeitsgefühl langfristig verbessern. Es handelt sich dabei um ein konkretes Kooperationsprojekt mit dem lokalen Jugendzentrum, eine Reaktivierung impulsgebender Stadtbausteine und um eine großflächige Umgestaltung der Verkehrshierachie und des öffentlichen Raums.The development of social inequality and segregation in a city is the result of complex and multi-layered factors. This thesis aims to analyze these inequality factors and poses the following central questions: Identification of inequalities - What systemic, social and spatial inequalities are present in a city? To what extent can a city be considered fair? Role of architecture - How can architecture contribute to counteracting these inequalities? In this thesis, Vienna serves as the central object of study. An in-depth analysis of the city reveals that Vienna's 10th district, Favoriten, is particularly affected by social inequality. This inequality has not only social but also spatial dimensions, which can be traced back to political decisions and have been reinforced by industrialization and subsequent urban planning interventions. The research method combines photography with comprehensive mapping of the district and documentation of living conditions. From a multispectral, interdisciplinary perspective, realities of life are mapped through interviews with residents as well as relevant actors of local institutions, including police and social work. The collected information will be subjected to a theoretically grounded reflection, using sociological approaches by Bourdieu and Wacquant as a guide. A central hypothesis of this thesis is that existing social inequality in Vienna is closely linked to institutional and structural racism. Restrictions on access and discrimination in the housing market contribute to the displacement of socially disadvantaged populations into an exclusive, densely populated and structurally isolated district. In addition, the analysis of media coverage sheds light on a tendency to criminalize poverty, which creates a negative image and triggers increased insecurity and fear among other city residents. In interdisciplinary collaboration with a legal psychologist, it becomes clear that stigmatization and prejudice can influence individual behavior. The reputation of a place is thus also transmitted to its inhabitants. Finally, concrete architectural interventions are proposed at various levels to improve the quality of life, social mobility and sense of belonging in the long term. These measures include a cooperation project with the local youth center, the reactivation of impulse-giving urban building blocks, and large-scale redesigns of the traffic structure and public space
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