Oct

30

MicroRNAs as Potential Biomarkers in Cancer and Heart Disease

Filed Under Technical Article | 2 Comments

Heart disease and cancer represent the number one and number two killer diseases in developed countries. Identifying biomarkers to detect these and other diseases at early stages remains an important research goal and researchers are scrambling for ways to identify contributing factors to the pathogenesis of diseased cells in the body.  In recent years, research has turned to the study of microRNA (miRNA) as possible biomarkers due to their extensive role in biological processes and cell functionality in normal vs. diseased cells.  Microarrays combined with quantitative real-time PCR (qRT-PCR) validation are proving to be valuable tools for miRNA expression profiling and are predicted to play a crucial role in biomarker discovery and detection.  Read more

Oct

27

Featured Customer Publication – microRNA in Fatty Liver Disease

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untitledSteatohepatitis is a type of liver disease, characterized by inflammation and fat accumulation in the liver, which can lead to cirrhosis. Steatohepatitis is frequently seen in alcoholics and people with diabetes and/or obesity and alcoholic and nonalcoholic steatohepatitis are leading causes of liver diseases worldwide. Researchers at UMASS Medical School used LC Sciences microarray service to examine the microRNA expression profiles in mouse models of steatohepatitis of both alcoholic and non-alcoholic etiology1. The data they present about the baseline status of the microRNA profile in normal liver and upon development of steatohepatitis facilitate better understanding of this disease and opens new avenues for research its pathophysiology. 

  1. Dolganiuc A, Petrasek J, Kodys K, Catalano D, Mandrekar P, Velayudham A, Szabo G. (2009) MicroRNA Expression Profile in Lieber-DeCarli Diet-Induced Alcoholic and Methionine Choline Deficient Diet-Induced Nonalcoholic Steatohepatitis Models in Mice.  Alcohol Clin Exp Res  33(10), 1704-10.  [abstract]

Oct

26

Tools And Information for Plant Scientists Studying microRNA

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Web Links

PMRD:  plant miRNA Database
http://bioinformatics.cau.edu.cn/PMRD/

This site offers a complete list of all publicly known plant miRNA sequences.  The database is composed of a total of 8,433 sequences including all known sequences in the miRBase database.

PlantGDB
http://www.plantgdb.org/

This website is dedicated entirely to plant miRNA and provides many useful tools such as sequence browser & assemblies, genome browser, and other tools and datasets.

miRU: Plant miRNA Potential Target Finder
http://bioinfo3.noble.org/miRNA/miRU.htm

This website allows users to predict plant miRNA target genes.  By entering a small RNA sequence (19-28nt) the program will report all potential complimentary sequences.

UPC: A Resource for Predicting and Comparing Plant microRNAs
http://www3a.biotec.or.th/micropc/index.html

Here users can predict and compare plant miRNA sequences.  This site includes 128 miRNA families, 125 plant species, and 2,995 protein targets.

The UEA plant sRNA toolkit
http://srna-tools.cmp.uea.ac.uk/targets/

Users can input sequences up to 50 nucleotides in length in FASTA format to run target predictions for their sequence dataset.

  Read more

Oct

16

The Most Current Probe Content Available

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mirna_probe_contentThe most current probe content available delivering the most complete microRNA expression profile of your samples

miRBase Sequence Database Content – Release 14.0 – September 2009

The miRBase database provides a searchable online repository for published microRNA sequences and associated annotation. 

miRBase 14 Probe content is available now at LC Sciences!

  • 10883 entries representing hairpin precursor miRNAs
  • 10581 mature miRNA products
  • Verified miRNAs for 115 species

Plant MicroRNA Database (PMRD) Content – Release 1 – October 2009

The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated by the database organizers. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser.

PMRD Probe content is available now at LC Sciences!

  • 8433 miRNAs
  • 121 plant species
  • Includes model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc in this first edition of the database.

Customer Defined Content

These are not spotted arrays.  Each microarray is custom synthesized when ordered.  That means we can add custom content to any of our standard microRNA microarrays with no delay in data delivery. There is no charge for addition of up to 100 of your custom sequences.  Furthermore, the entire contents of the arrays are completely customizable according to the customer’s design at a very affordable price.  Customers may add up to 3,918 sequences of their own selection for various applications.

  • Screen for new microRNAs by adding predicted mature microRNA sequences or performing tiling along a certain section of genome.
  • Combine microRNA sequences of different species to identify cross-species conservations.
  • 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.

Oct

15

LC Sciences

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Oct

15

Press Release – LC Sciences First miRNA Microarray Service Provider to Offer Plant MicroRNA Database (PMRD) Probe Content

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Houston, TX – October 15, 2009 – Taking full advantage of its flexible µParaflo® Biochip Technology, Houston based LC Sciences today announced immediate availability of probe content from the newly created Plant MicroRNA Database (PMRD) for their microRNA (miRNA) microarray customers. This announcement comes immediately following a publication in Nucleic Acids Research introducing the public database1. The PMRD integrates available plant miRNA data deposited in other public databases, gleaned from the recent literature, and data generated by the database organizers. It is freely available at http://bioinformatics.cau.edu.cn/PMRD. Read more

Oct

14

Integrating microRNA and mRNA expression profiles for identification of regulatory networks

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The discovery of microRNA as an additional regulatory mechanism has been a revolution to the field of Developmental Biology. While early research has focused on the identification of miRNAs using a combination of experimental and computational techniques, subsequent studies have focused on identification of miRNA-target mRNA pairs as a means of identifying regulatory networks. It has been shown that the relationship between messenger RNA and microRNA (often an inverse relationship) plays a large role in cell functionality, especially in the early stages of cell development.  Read more

Oct

8

Plant MicroRNA Database Arrays Now Available

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LC Sciences now has standard arrays available for all species listed in the newly created Plant MicroRNA Database (PMRD). 

The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated by the database organizers. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser.

In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, the possible target genes for each miRNA with a predicted interaction site are included in the database.  

In addition, miRNA expression profiles are provided in the PMRD, including some data generated with previous versions of  LC Sciences’ Plants microRNA Microarray.

The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD.

  1. Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z.  (2009) PMRD: plant microRNA database.  Nucleic Acids Res  [Epub ahead of print]

Oct

7

New Customer Publication – miRNA Target Identification

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1756-0500-2-169.fm

Identifying the target mRNA against miRNA is essential to understanding cellular regulatory networks. However, due to the low complementarity between a miRNA and its target mRNAs in mammals, identification of mammalian miRNA targets has been a challenge and only a few have been reported to date. Researchers at the Genome Research Laboratories, Wako Pure Chemical Industries, Japan propose that the ability to isolate and profile both the mRNA and miRNA components of the RISC complex has the potential to aid in the identification of miRNA targets. They have developed a protocol for isolation of endogenous RISC-associated miRNAs and mRNAs by immunoprecipitation with antibodies specific for Ago2, an Argonaute family protein that is the central RISC component. They used LC Sciences microRNA microarray service to compare the profile the immunopurified RNA with that of total RNA. Microarray results suggested that Ago2-immunopurification could trap almost all expressed miRNA species.  Subsequent cloning and analysis of both miRNAs and mRNAs correctly correlated a well-characterized miRNA with its target.

  1. Hayashida Y, Nishibu T, Inoue K, Kurokawa T. (2009) A useful approach to total analysis of RISC-associated RNA. BMC Res Notes 2,169.  [abstract]

Oct

6

UTMB Seminar – Microfluidic Technology Enabling Advances in microRNA Research

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Presented by Christoph Eicken Ph.D. – LC Sciences LLC

An advanced microfluidic biochip system designed to produce high quality data, stay current with the rapidly evolving microRNA field, and perform diverse small RNA discovery experiments is presented. This technology’s unique flexibility allows for miRBase synchronicity and design of customized biochips adapted to each researcher’s specific needs. Applications featuring disease marker discovery, drug treatment, microRNA target screening, and small RNA discovery are highlighted.


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