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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.

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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.

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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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Scientific News
Women’s Immune System Genes Operate Differently from Men’s
A new technology reveals that immune system genes switch on and off differently in women and men, and the source of that variation is not primarily in the DNA.
Long Telomeres Associated with Increased Lung Cancer Risk
Genetic predisposition for long telomeres predicts increased lung adenocarcinoma risk.
Expanding the Brain
A team of researchers has identified more than 40 new “imprinted” genes, in which either the maternal or paternal copy of a gene is expressed while the other is silenced.
Study Uncovers Target for Preventing Huntington’s Disease
Scientists from Cardiff University believe that a treatment to prevent or delay the symptoms of Huntington’s disease could now be much closer, following a major breakthrough.
The Genetic Roots of Adolescent Scoliosis
Scientists at the RIKEN Center for Integrative Medical Sciences in collaboration with Keio University in Japan have discovered a gene that is linked to susceptibility of Scoliosis.
A Gene-Sequence Swap Using CRISPR to Cure Haemophilia
For the first time chromosomal defects responsible for hemophilia have been corrected in patient-specific iPSCs using CRISPR-Cas9 nucleases
How a Kernel Got Naked and Corn Became King
Ten thousand years ago, a golden grain got naked, brought people together and grew to become one of the top agricultural commodities on the planet.
New Tool For Investigating RNA Gone Awry
A new technology – called “Sticky-flares” – developed by nanomedicine experts at Northwestern University offers the first real-time method to track and observe the dynamics of RNA distribution as it is transported inside living cells.
Access Denied: Leukemia Thwarted by Cutting Off Link to Environmental Support
A new study reveals a protein’s critical – and previously unknown -- role in the development and progression of acute myeloid leukemia (AML), a fast-growing and extremely difficult-to-treat blood cancer.
Oxitec ‘Self-Limiting Gene’ Offers Hope for Controlling Invasive Moth
A new pesticide-free and environmentally-friendly way to control insect pests has moved ahead with the publication of results showing that Oxitec diamondback moths (DBM) with a ‘self-limiting gene’ can dramatically reduce populations of DBM.
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