MiR-103a-3p targets the 5\u27 UTR of GPRC5A in pancreatic cells.

MicroRNAs (miRNAs) are short noncoding RNAs that regulate the expression of their targets in a sequence-dependent manner. For protein-coding transcripts, miRNAs regulate expression levels through binding sites in either the 3\u27 untranslated region (3\u27 UTR) or the amino acid coding sequence (CDS) of the targeted messenger RNA (mRNA). Currently, for the 5\u27 untranslated region (5\u27 UTR) of mRNAs, very few naturally occurring examples exist whereby the targeting miRNA down-regulates the expression of the corresponding mRNA in a seed-dependent manner. Here we describe and characterize two miR-103a-3p target sites in the 5\u27 UTR of GPRC5A, a gene that acts as a tumor suppressor in some cancer contexts and as an ongocene in other cancer contexts. In particular, we show that the interaction of miR-103a-3p with each of these two 5\u27 UTR targets reduces the expression levels of both GPRC5A mRNA and GPRC5A protein in one normal epithelial and two pancreatic cancer cell lines. By ectopically expressing sponges that contain instances of the wild-type 5\u27 UTR targets we also show that we can reduce miR-103a-3p levels and increase GPRC5A mRNA and protein levels. These findings provide some first knowledge on the post-transcriptional regulation of this tumor suppressor/oncogene and present additional evidence for the participation of 5\u27 UTRs in miRNA driven post-transcriptional regulatory control

Pattern-based phylogenetic distance estimation and tree reconstruction

We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au), we have created a dataset of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees. We find our pattern-based method statistically superior to all other tested alignment-free methods on this dataset. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.Comment: 21 pages, 3 figures, 2 table

MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.

Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analyze RNA-seq data when studying microRNAs (miRNAs) or messenger RNAs (mRNAs). Here we present MINTmap (for MItochondrial and Nuclear TRF mapping), a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNA-seq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs. Furthermore, to ensure specificity, MINTmap identifies the subset of discovered tRFs that could be originating outside of tRNA space and flags them as candidate false positives. Our comparative analysis shows that MINTmap exhibits superior sensitivity and specificity to other available methods while also being exceptionally fast. The MINTmap codes are available through https://github.com/TJU-CMC-Org/MINTmap/ under an open source GNU GPL v3.0 license

Gurses' Type (b) Transformations are Neighborhood-Isometries

Following an idea close to one given by C. G. Torre (private communication), we prove that Riemannian spaces (M,g) and (M,h) that are related by a Gurses type (b) transformation [M. Gurses, Phys. Rev. Lett. 70, 367 (1993)] or, equivalently, by a Torre-Anderson generalized diffeomorphism [C. G. Torre and I. M. Anderson, Phys. Rev. Lett. xx, xxx (1993)] are neighborhood-isometric, i.e., every point x in M has a corresponding diffeomorphism phi of a neighborhood V of x onto a generally different neighborhood W of x such that phi*(h|W) = g|V.Comment: 10 pages, LATEX, FJE-93-00

Une expérience réussie d'approche par projets pour favoriser l'intégration des apprentissages /

Bibliogr

Une approche de prise en charge intégrant le contrôle social et la thérapie : analyse et réflexion

On présente ici une initiative novatrice découlant des adaptations nécessitées par l'entrée en scène de la Loi sur la protection de la jeunesse. L'auteur décrit d'abord une expérience de prise en charge se déroulant dans un centre de psychiatrie infantile et juvénile; il démontre ensuite comment cette expérience peut apporter une solution à certaines situations intenables dans la prise en charge habituelle ; il termine enfin par un retour aux assises théoriques de cette expérimentation

UNBLACKBOXING TECHNOLOGY THROUGH THE RHETORIC OF TECHNICAL COMMUNICATION: BIOMETRIC TECHNOLOGY AND GHANA\u27S 2012 ELECTION

In this project, I seek to “unblackbox” technology; by which I mean, I seek to, in the words of Latour, “open up” or “debug” the biometric technology used by Ghana for its 2012 presidential and parliamentary elections. Through the process of “unblackboxing,” I demonstrate the value of technical communicators to technology studies by analyzing technical documents that accompanied the biometric verification device which was adopted and used by Ghana to conduct its 2012 presidential and parliamentary elections. I argue in this dissertation that technical documentation does not merely accommodate users to technologies, but also it provides avenues to articulate broader issues like localization, ideology, subjectivity, and the social justice implications of the various technologies we adopt and use. We are also positioned to understand how a society reacts to issues that are historically, politically, culturally rooted in their context. I maintain that documentation writing is one of the defining activities of technical communication. Thus, it is important to continue to build upon and expand the analyses of these types of documents to critically assess the role they can play in discussions about technology especially in international contexts. By performing a rhetorical-cultural analysis of various technical documents that accompanied the biometric device used in Ghana, I hope to aid technical communicators to reconsider received knowledge about the purposes and uses of technical documentation, such as instructional manuals. More importantly, by embarking on this project, I am able to: interrogate the “international” in international technical communication; discuss documentation design in international context; expand research on the importance of technical documentation to technology studies in a non-Western context (Ghana); demonstrate how rhetorical and cultural theories can be combined to study technology in international contexts