|THe AtSCL26 transcription factor controls cross-talk between GA and N root architecture in Arabidopsis thaliana roots|
Beatriz Lagunas, Anthony D. Carter, Dafyd Jenkins and Miriam Gifford
Phenotypic and molecular evidence supports the hypothesis that developmental program enabling nodule formation arose during evolution from a lateral root ‘blueprint’ pre-existing in all higher plants . We reasoned that analyzing Arabidopsis genes orthologous to regulators of nodulation could shed insight on control of lateral root development. This led us to the discovery that an Arabidopsis GRAS family transcription factor controls lateral root development under specific nitrogen conditions.
|LOHA Comprehensive Assay for Single Nucleotide Polymorphism, Copy Number Variants and Loss of Heterozygosity Using SureSelect Target Enrichment|
Kyeong Soo Jeong, Arjun Vadapalli, Ashutosh Ashutosh, Paula Costa, Brian Peter, Stephanie Fulmer-Smentek, Magnus Isaksson, Jayati Ghosh, Douglas Roberts, Holly Hogrefe
Here we describe a comprehensive assay that enables researchers to identify SNP, INDEL, CNV, and LOH using SureSelect target enrichment. This design can be employed as a standalone entity or in concert with other bait designs for SNP and INDEL detection. We also describe methods for data analysis and visualization.
|The Power Decoder simulator for the evaluation of pooled shRNA screen performance|
Jesse Stombaugh, Abel Licon, Žaklina Strezoska, Joshua Stahl, Sarah Bael Anderson, Michael Banos, Anja van Brabant Smith, Amanda Birmingham, Annaleen Vermeulen
Power Decoder (written in R and Python) simulates shRNA pooled screening experiments in silico to allow for the estimation of a screen’s statistical power. Populations of shRNAs were engineered in such a way that the magnitude of depletion and enrichment was known, then using the negative binomial distribution, an in silico model was developed to successfully resemble data from an actual laboratory experiment.
|Polymer Microarrays for Biomaterial Development|
Simmonte, M.J.1, Dhaliwal, K.2, Cuschieri, K.3, Graham, S.V.4, Bradley, M.1
The application of polymer microarrays in the discovery of biocompatible and bioactive substrates. Progress towards biomaterial development for the treatment of SIRS (systemic inflammatory response syndrome), and improving cervical cytology.
|Knockdown of long noncoding RNAs in breast cancer |
1 Jennii Luu, 2 Jesper Maag, 1 Yanny Handoko, 3 Richard Redvers, 3,4 Robin L. Anderson, 5 Maren M. Gross , 2 Marcel E. Dinger, and 1,3 Kaylene J. Simpson 1 Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre; 2 Genome Informatics, The Kinghorn Cancer Centre, The Garvan Institute of Medical Research; 3 Metastasis Research Laboratory, Peter MacCallum Cancer Centre, 4 Sir Peter MacCallum Department of Oncology, University of Melbourne;
RNAi global collaboration study using Lincode siRNA in a primary screen of tumor and nontumor breast cell lines. Hundreds of lncRNAs are found to affect viability and cell morphology of breast cancer. Presented at Keystone Symposia on Long Noncoding RNAs: From Evolution to Function, Mar 15 - Mar 20, 2015.
|Human iPSC-derived hepatocytes and cardiomyocytes for drug toxicity testing|
AnnandRR; Vardaro R; Hamilton B; Akakira R; Tamura K; Yoshida S; Lin YC; Toyoda D; Kogami H; Okuda Y; Watanabe T; Inamura M
Human iPS-derived hepatocytes (ReproHepato™) and cardiomyocytes (ReproCardio 2™) are useful for in vitro toxicity assays.
|Improved Small RNA Library Preparation Workflow for Next-Generation Sequencing|
Sabrina Shore, Jordana Henderson, Anton McCaffrey, Gerald Zon, Richard Hogrefe
We describe an optimized small RNA NGS library prep workflow using chemically modified adapters which suppresses adapter dimers, allows for RNA inputs down to 1 ng and eliminates the need for a gel purification step, thus allowing full automation not previously possible.
|Flexible automated platform for blood group genotyping on DNA microarrays|
S. Paris1, D. Rigal1, V. Barlet1, M. Verdier1, N. Coudurier2, P. Bailly3, J.-C. Brès1,4
The purpose of this project was to set up and validate a flexible robotic platform using 96-well DNA microarray for multiplex blood group genotyping.
|Specificity of highly potent miRNA inhibitors|
Barbara Robertson, Andrew Dalby, Yuriy Fedorov, Jon Karpilow, Anastasia Khvorova1, Devin Leake, Annaleen Vermeulen
miRNA inhibitors are invaluable tools for elucidating the roles of miRNAs. However, potent inhibitors may also affect other miRNAs. To understand the potential cross-reactivity of miRNA inhibitors, various miRNA inhibitor designs were systematically tested. We demonstrate that mismatches both within and outside the seed region of the miRNA interfere with inhibition. Our findings indicate that features important for natural miRNA target recognition are also important for inhibitor specificity.