May

28

microRNA Study in Non-Model Species

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LC Sciences’ custom microRNA microarray service is based on the flexible µParaflo® microfluidic chip technology which enables us to produce custom synthesized microarrays when ordered. (vs. an off-the-shelf spotted array)  Therefore, researchers are not limited to the species (and sequences) listed in miRBase.  They can add any sequence of their design to the standard miRBase probe content.

Customizable features include – sequence design, varying chain lengths, chip layout, synthesis chemistry, and more.   Each µParaflo® microfluidic chip has room for thousands of sequences of your design.  Add sequences for various applications:

  • Screen for new microRNAs by adding predicted mature microRNA sequences or perform sequence tiling along certain sequences sections.
  • Combine microRNA sequences of different species to identify cross-species conservations or host-parasite interaction.
  • Add controls of customer’s choice for the detection of customer-added spiking RNA sequences and use as customer-selected internal controls.
  • Add probes for the detection of siRNAs and/or other small non-coding RNAs.
  1. Liu G, Fang Y, Zhang H, Li Y, Li X, Yu J, Wang X. (2010) Computational identification and microarray-based validation of microRNAs in Oryctolagus cuniculus.  Mol Biol Rep [Epub ahead of print]  [abstract]
  2. Legeai F, Rizk G, Walsh T, Edwards O, Gordon K, Lavenier D, Leterme N, Mereau A, Nicolas J, Tagu D, Jaubert-Possamai S. (2010) Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum. BMC Genomics 11(1), 281.  [abstract]
  3. Gundersen-Rindal DE, Pedroni MJ. (2010) Larval stage Lymantria dispar microRNAs differentially expressed in response to parasitization by Glyptapanteles flavicoxis parasitoid. Arch Virol (5), 783-87.  [abstract]
  4. Dongdong L, Yusheng Zheng, Li Wan, Xiaoming Zhu and Zhekui Wang. (2009) Differentially expressed microRNAs during solid endosperm development in coconut (Cocos nucifera L.). Scientia Horticulturae 122(4), 666-69.  [abstract]
  5. Sehm T, Sachse C, Frenzel C, Echeverri K. (2009) miR-196 is an essential early-stage regulator of tail regeneration, upstream of key spinal cord patterning events. Dev Biol 334(2), 468-80.  [abstract]

May

26

Seq-Array: microRNA Discovery and Profiling Using a Customizable Workflow

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Seq-ArraySM provides an efficient pathway from an initial broad search to focused biological insights.

Seq-ArraySM offers a customized solution to high-throughput genome-wide microRNA discovery and profiling, especially in species with limited or no microRNA sequence information available. This unique combination of the latest deep sequencing technology, advanced bioinformatics, and our innovative µParaflo® custom microarray platform leverages all these technologies to form a comprehensive service package tailored to your specific research needs.

May

25

miRBase Updates Keep Coming

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mirbase_graphAfter  couple of years with nominal growth in the number of database entries, miRBase growth has turned to exponential over the last four to five updates.  The latest deep sequencing technologies have palyed a key role in the discovery of new miRNAs.  A full 30% increase in the number of entries and a 48% increase in the number of experimentally verified functional mature sequences in the single most recent miRBase update gives little doubt that there are many more as yet undiscovered miRNAs.

May

25

Cancer Research Tech Guide

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cancer_research_thumbCancer Research Tech Guide – From Genome Technology

Download Your Copy Here

Letter from the Editor

Cancer is tricky. But equipped with a vast arsenal of tools, investigators are on the offensive against the duplicitous disease. Still, even the most robust cancer research techniques come with their own sets of challenges. From sequencing to interrogating microRNAs, this technical guide aims to give you a fresh look at what a number of cancer researchers are doing to improve their day-to-day results at the bench in an effort to supply optimal diagnostics and care at the bedside.

The following pages contain tips for genome sequence analysis, optimizing qRT-PCR procedures for the investigation of miRNAs, the merits of various methylation interrogation techniques, isolating RNA from paraffin-embedded tissues, and what to do when gene expression microarray data is inconsistent with the clinical presentation in diagnosing cancers of unknown primary site. Be sure to consult the list of resources at the end of this guide for citations to the methods and research papers our experts have referred to in their responses.

— Tracy Vence

May

24

LC Sciences Presents a Poster at PEGS 2010

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Epitope Mapping on a Flexible High-Density Microfluidic Chip – Peparray™

Ailing Hong1, Qi Zhu2, Yulu Zhang3, Xiaochuan Zhou1,2, Christoph Eicken2, Xiaolian Gao3,

1Atactic Technologies, and 2LC Sciences, Houston, TX 77054, 3Dept of Biology and Biochemistry, University of Houston, Houston, TX 77004

Although a number of proteomics technologies are well-developed, the demand for reliable, sensitive, accurate, and comprehensive measurements of epitope binding remains unfulfilled. Through the use of overlapping peptides as epitopes on a custom synthesized addressable peptide microarray (PepArray™), we can systematically screen thousands of epitope sequences in a single experiment.  A proprietary microarray platform and advanced microfluidic technologies ensure quantitative measurements of binding events. This combination of high-throughput capacity with quantitative measurement enables us to quickly and efficiently identify high affinity and high specificity target binding compounds. We have a novel, in situ, on-microchip synthesis technology (mParaflo®) that allows us to perform in situ synthesis of high-density peptide arrays according to custom designs. Forty-one 96-well titer plate experiments (i.e. conventional experiments) can be accomplished simultaneously on one chip. We also apply this flexible peptide array technology for rapid and reliable quantitative measurements for phosphorylation and protein binding. Our ultimate goal is to provide new, powerful research and clinical study tools to address the critical needs in proteomic research, clinical diagnosis, and therapeutic treatment.

Download the poster

May

5

Featured Customer Publication: Phloem small RNAs, nutrient stress responses, and systemic mobility

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Phloem small RNAs, nutrient stress responses, and systemic mobility

The authors used LC Sciences’ custom miRNA microarrays containing all known plant miRNAs and a set of unknown small (s) RNAs earlier cloned from Brassica phloem sap, to comprehensively analyze the phloem response to nutrient deficiency by removing sulfate, copper or iron, respectively, from the growth medium. They show that phloem sap contains a specific set of sRNAs that is distinct from leaves and roots, and that the phloem also responds specifically to stress. They further demonstrate that under nutrient starvation miR399 and miR395 can be translocated through graft unions from wild type scions to rootstocks of the miRNA processing hen1-1 mutant. In contrast, miR171 was not transported. Translocation of miR395 led to a down-regulation of one of its targets in rootstocks, suggesting that this transport is of functional relevance, and that miR395, in addition to the well characterized miR399, could potentially act as a long-distance information transmitter.

Buhtz A, Pieritz J, Springer F, Kehr J. (2010) Phloem small RNAs, nutrient stress responses, and systemic mobility. BMC Plant Biol 10(1), 64. [Article]