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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.

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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.

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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.

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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.

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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.

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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.

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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.

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Alternative miRNA design for therapeutic RNAi applications
Anja van Brabant Smith, Barb Robertson, Annaleen Vermeulen, Christina Yamada, Angela Reynolds, Anastasia Khvorova, Devin Leake

For in vivo applications, the design of miRNA inhibitors and miRNA mimics must be optimized for stability and potency. However, stabilized miRNA mimic molecules can lose functionality compared to standard miRNA mimic molecules due, in part, to the activity of the stabilized passenger strand acting as a miRNA inhibitor. We discuss how mismatches affect the activity of the stabilized miRNA mimics, perhaps by generating a passenger strand that is less functional as an inhibitor molecule.

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Cas9 driven by an optimal promoter improves gene editing in eukaryotic cell lines when paired with synthetic crRNA and tracrRNA
Amanda Haupt, Emily Anderson, Žaklina Strezoska, Hidevaldo Machado, Shawn McClelland, Maren Mayer, Adam Rocker, Annaleen Vermeulen, Amanda Birmingham, Melissa Kelley, Anja Smith

Presented here are results on the efficiency of using synthetic crRNA and tracrRNA to introduce gene editing events when co-transfected with a plasmid expressing Cas9. We explored the use of antibiotic and fluorescence activated cell sorting (FACS) methods for enrichment of cells that have undergone gene editing, and the use of multiple promoters to increase efficiency of gene editing with Cas9 and synthetic tracrRNA and crRNAs.

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Showing Results 31 - 40 of 218
Scientific News
A Guide to CRISPR Gene Activation
A comparison of synthetic gene-activating Cas9 proteins can help guide research and development of therapeutic approaches.
Gene That Lowers Heart Attack Risk Identified
Individuals with a rare twelve-letter deletion from a gene on chromosome 17 have significantly reduced non-HDL cholesterol levels and a 35% lower than average risk of heart disease.
"Sunscreen" Gene May Guard Against Melanoma
USC-led study reveals that melanoma patients with deficient or mutant copies of the gene are less protected from harmful ultraviolet rays.
Myeloid-Derived Suppressor Cells Play Role in Tumor Growth
Researchers at Baylor College of Medicine have reported a new mechanism that helps cancer cells engage myeloid-derived suppressor cells.
Transcription Factor Isoforms Implicated in Colon Diseases
UC Riverside study explains how distribution of two forms of a transcription factor in the colon influence risk of disease.
Roundup Impacts Gene Expression
Study published on the impact of low-dose toxicity of Roundup weed-killer on gene expression profiles.
US-India Collab Finds Molecular Signatures of Severe Malaria
Study may be a significant advancement in understanding the causes of severe malaria.
Big Data Can Save Lives
The sharing of genetic information from millions of cancer patients around the world could be key to revolutionising cancer prevention and care, according to a leading cancer expert from Queen's University Belfast.
Triple-Negative Breast Cancer Target Is Found
Researchers at UC Berkeley discover a target that drives cancer metabolism in triple-negative breast cancer.
Gene Expression Controls Revealed
Researchers have modelled every atom in a key part of the process for switching on genes, revealing a whole new area for potential drug targets.
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