RNA editing gives organisms a way to adapt the instructions that their DNA provides for making proteins. Few people would have described RNA editing as a simple process, but a new paper in Nature Communications demonstrates the process as more complex and difficult to predict than previously assumed. The study, done in living fruit flies, discovered two new mechanisms that govern editing in a key neurodevelopmental gene. …read more
Source: FULL ARTICLE at Phys.org
Standard toxicity testing is inadequate to assess the safety of a new technology with potential for creating pesticides and genetically modifying crops, according to a Forum article published in the August issue of BioScience. The authors of the article, Jonathan G. Lundgren and Jian J. Duan of the USDA Agricultural Research Service, argue that pesticides and insect-resistant crops based on RNA interference, now in exploratory development, may have to be tested under elaborate procedures that assess effects on animals’ whole life cycles, rather than by methods that look for short-term toxicity. …read more
Source: FULL ARTICLE at Phys.org
(Phys.org) —Much of biomedical science – both mystifying and awe-inspiring to the lay public – depends on an unwavering focus on things that can’t be easily seen, like the inner-workings of cells, in order to determine how and why disease develops. New research authored by Thomas Sladewski, a University of Vermont graduate student working in the laboratory of Kathleen Trybus, Ph.D., and colleagues, provides a rare “picture” of the activity taking place at the single molecular level: visual evidence of the mechanisms involved when a cell transports mRNA (or messenger RNA) to where a protein is needed to perform a cellular function. …read more
Source: FULL ARTICLE at Phys.org
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Illumina and Kindstar Global Announce Strategic Collaboration to Facilitate Clinical Adoption of Illumina Technologies in Asia
SAN DIEGO & WUHAN, China–(BUSINESS WIRE)– Illumina, Inc. (NAS: ILMN) and Kindstar Global (Kindstar) today announced they are entering into a strategic collaboration whereby Kindstar will validate and implement molecular assays in their laboratories, leveraging Illumina’s TruSightTM content sets, Infinium® Dx CytoSNP-12 assay and NuPCRTM reagents. The collaboration will enable Kindstar to expand its esoteric and specialty testing services offerings within its network of more than 3,300 hospitals across China.
“Kindstar’s adoption of Illumina’s TruSight technology across its extensive network in China speaks to the breadth and depth of content in this innovative portfolio,” said Matt Posard, Senior Vice President and General Manager of Illumina’s Translational and Consumer Genomics business. “Next-generation sequencing is enabling a dramatic improvement in both coverage and accuracy for molecular diagnostics, and we look forward to additional partnerships that continue to drive this improvement forward.”
“Kindstar is excited to offer services in China based on Illumina’s products including the TruSight content sets,” said Dr. Shiang Huang, Founder and CEO of Kindstar. “Leveraging Illumina‘s technology will enable us to offer the highest quality and most specialized diagnostics.”
About Illumina
Illumina (www.illumina.com) is a leading developer, manufacturer, and marketer of life science tools and integrated systems for the analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA, and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare.
About Kindstar Global
Kindstar Global, with laboratory facilities in Beijing, Shanghai and Wuhan, provides esoteric diagnostic testing services to hospitals and physicians in every province of China. Kindstar is the first and largest esoteric diagnostic testing business in China, providing laboratory testing services to over 3,300 Chinese hospitals, including 930 tertiary hospitals (classification for largest leading hospitals). Kindstar is becoming the partner of choice to physicians in China for advanced diagnostics in many medical specialties including hematology, oncology, infectious diseases and medical genetics.
Forward-Looking
From: http://www.dailyfinance.com/2013/04/18/illumina-and-kindstar-global-announce-strategic-co/
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Illumina to Announce First Quarter 2013 Financial Results on Monday, April 22, 2013
SAN DIEGO–(BUSINESS WIRE)– Illumina, Inc. (NAS: ILMN) today announced that it will issue results for first quarter 2013 following the close of market on Monday, April 22, 2013.
On the same day, at 2:00 pm Pacific Time (5:00 pm Eastern Time), Jay Flatley, President and Chief Executive Officer, Marc Stapley, Senior Vice President and Chief Financial Officer, and Christian Henry, Senior Vice President and General Manager, Genomic Solutions, will host a conference call with analysts, investors, and other interested parties to discuss financial and operating results.
Conference Call Details
The conference call will begin at 2:00 pm Pacific Time (5:00 pm Eastern Time) on Monday, April 22, 2013. Interested parties may listen to the call by dialing 888.679.8033 (passcode: 58226131), or if outside North America, by dialing +1.617.213.4846 (passcode: 58226131). Individuals may access the live teleconference in the Investor Relations section of Illumina’s web site under the “Company” tab at www.illumina.com.
A replay of the conference call will be available from 4:00 pm Pacific Time (7:00 pm Eastern Time) on April 22, 2013 through April 29, 2013 by dialing 888.286.8010 (passcode: 31374623), or if outside North America, by dialing +1.617.801.6888 (passcode: 31374623).
About Illumina
Illumina (http://www.illumina.com) is a leading developer, manufacturer, and marketer of life science tools and integrated systems for the analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA, and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare.
Illumina, Inc.
Investors:
Rebecca Chambers
858-255-5243
rchambers@illumina.com
or
Media:
Jennifer Temple
858-882-6822
pr@illumina.com
KEYWORDS: United States North America California
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The article Illumina to Announce First Quarter 2013 Financial Results on Monday, April 22, 2013 originally appeared on Fool.com.
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Rexahn Pharmaceuticals to Present data on the Mechanism of action of RX-5902: A first-in-class inhibitor of p68 helicase for the treatment of solid tumors at AACR Annual Meeting 2013
ROCKVILLE, Md.–(BUSINESS WIRE)– Rexahn Pharmaceuticals, Inc. (NYSE MKT: RNN), a clinical stage biopharmaceutical company developing potential best-in-class oncology therapies, today announced that it will present mechanism of action data on RX-5902 during a poster session at the American Association for Cancer Research (AACR) 104th Annual Meeting being held in Washington, DC, April 6-10, 2013, at the Washington Convention Center.
The Company will present the mechanism data of RX-5902 in a poster (abstract #5507) entitled, “Mechanistic study of a new 4-(3, 5-dimethoxyphenyl)-N-(7-fluoro-3-methoxyquinoxalin-2-yl)piperazine-1-carboxamide compound (RX-5902),” on Wednesday, April 10, 2013, during the “Chemotherapy and Cancer Dependencies” poster session from 8:00 am – 12:00 pm EDT in Exhibit Hall A-C, Poster Section 37.
For more information on the AACR conference, please visit www.aacr.org.
About RX-5902
RX-5902 is an orally bioavailable, first-in-class inhibitor of p68 RNA helicase for the treatment of various solid tumors, such as melanoma and cancers of the ovary, kidney and pancreas. Rexahn has filed an IND for RX-5902 and anticipates initiating Phase I clinical development in the second quarter of 2013.
RX-5902 has been shown to produce potent anti-tumor effects, increased survival in xenograft models, anti-proliferative activity in drug-resistance cancer cell lines and synergistic effects with known anti-cancer drugs.
RX-5902 is part of a growing pipeline of clinical stage oncology compounds that Rexahn is developing to potentially provide improved efficacy and reduced toxicity, resulting in improved survival and quality of life for patients.
About Rexahn Pharmaceuticals, Inc.
Rexahn Pharmaceuticals is a clinical stage biopharmaceutical company dedicated to developing best-in-class therapeutics for the treatment of cancer. Rexahn currently has three clinical stage oncology candidates, Archexin®, RX-3117, and RX-5902 and a robust pipeline of preclinical compounds to treat multiple types of cancer. Rexahn has also developed proprietary drug discovery platform technologies in the areas of nano-medicines, 3D-GOLD, and TIMES. For more information, please visit www.rexahn.com.
Safe Harbor
To the extent any statements made in this press release deal with information that is not historical, these are forward-looking statements under the Private Securities Litigation Reform Act of 1995. Such statements include, …read more
Source: FULL ARTICLE at DailyFinance
By empyrean
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Source: FULL ARTICLE at The UNIX and Linux Forums
(Phys.org) —The discovery of the Rosetta Stone resolved a longstanding puzzle, permitting the translation of Egyptian hieroglyphs into Ancient Greek. John Chaput, a researcher at Arizona State University’s Biodesign Institute has been hunting for a biological Rosetta Stone—an enzyme allowing DNA‘s 4-letter language to be written into a simpler (and potentially more ancient) molecule that may have existed as a genetic pathway to DNA and RNA in the prebiotic world. …read more
Source: FULL ARTICLE at Phys.org
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Illumina Announces Favorable Outcome of Its Patent Litigation Against Life Technologies, Inc.
SAN DIEGO–(BUSINESS WIRE)– Illumina, Inc. (NAS: ILMN) announced today that District Court Judge Cathy Ann Bencivengo of the U.S. District Court for the Southern District of California granted Illumina’s motion for summary judgment that its sequencing systems do not infringe U.S. Patent Nos. 5,616,478; 5,958,698 and 6,001,568, being asserted by Life Technologies Corporation in a lawsuit filed against Illumina in 2009. The Court ruled that, “Life Tech cannot establish, as a matter of law, that the accused Illumina systems infringe” the patents.
Jay Flatley, Illumina’s President and CEO, stated, “We are obviously very pleased with the favorable outcome of this suit. Since Life Technologies filed this patent infringement suit against Illumina in 2009, we have consistently believed and strongly argued that our sequencing technology does not infringe any of the patents Life Technologies asserted against us in this case. The federal court’s ruling has now vindicated our position. While our policy is to respect the valid and enforceable intellectual property rights of others, and take licenses where appropriate, this case demonstrates we are determined to defend vigorously any unfounded claims of infringement.”
About Illumina
Illumina (www.illumina.com) is a leading developer, manufacturer, and marketer of life science tools and integrated systems for the analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA, and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare.
Forward-Looking Statements
This release may contain forward-looking statements that involve risks and uncertainties. Important factors that could cause actual results to differ materially from those in any forward-looking statements are detailed in our filings with the Securities and Exchange Commission, including our most recent filings on Forms 10-K and 10-Q, or in information disclosed in public conference calls, the date and time of which are released beforehand. We do not intend to update any forward-looking statements after the date of this release.
Scientists have cracked a 35-year-old mystery about the workings of the natural motors that are serving as models for development of a futuristic genre of synthetic nanomotors that pump therapeutic DNA, RNA or drugs into individual diseased cells. Their report revealing the innermost mechanisms of these nanomotors in a bacteria-killing virus—and a new way to move DNA through cells—is being published online today in the journal ACS Nano. …read more
Source: FULL ARTICLE at Phys.org
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Illumina Announces Outcome of Its Patent Litigation Against Syntrix Biosystems, Inc.
SAN DIEGO–(BUSINESS WIRE)– Illumina, Inc. (NAS: ILMN) today announced that a federal jury in Tacoma, Washington found that Illumina’s BeadChip array product infringed U.S. Patent No. 6,951, 682, asserted by Syntrix Biosystems, Inc. The federal jury ordered Illumina to pay approximately $96 million in damages to Syntrix based on a royalty rate of six percent for BeadChip products sold by Illumina from 2005 through May 2012. United States District Court Judge Benjamin H. Settle, however, dismissed from the case claims that Illumina’s alleged infringement was willful and that Illumina misappropriated Syntrix’s trade secrets. The Syntrix patent expires on September 17, 2019.
Illumina continues to believe that Syntrix’s claims are without merit. Illumina intends to file post-trial motions asking the court to vacate the jury’s finding and to rule as a matter of law that the BeadChip does not infringe Syntrix’s patent.
Jay Flatley, Illumina’s President and CEO, stated, “We strongly disagree with this verdict and plan to appeal the present finding of infringement. In the meantime, we will continue to sell the products that are the subject of this suit and no damages will be payable to Syntrix until all appropriate appeals have been taken, which may take a number of years.” Mr. Flatley continued, “Our BeadChip products are based on Dr. David Walt‘s technology that was licensed from Tufts University when Illumina was founded in 1998. Like many other companies, we respect the valid and enforceable intellectual property rights of others. Consistent with our policy, we believe we acted properly with respect to the Syntrix ‘682 patent. We continue to feel very strongly about our position that Syntrix’s allegations are without merit and that, ultimately, our position will be vindicated.”
About Illumina
Illumina (www.illumina.com) is a leading developer, manufacturer, and marketer of life science tools and integrated systems for the analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA, and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare.
Forward-Looking Statements
By Business Wirevia The Motley Fool
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RXi Pharmaceuticals to Present at the 25th Annual ROTH Conference
WESTBOROUGH, Mass.–(BUSINESS WIRE)– RXi Pharmaceuticals Corporation (OTC: RXII), a biotechnology company focused on discovering, developing and commercializing innovative therapies addressing major unmet medical needs using RNA-targeted technologies, today announced that the Company’s President and Chief Executive Officer, Dr. Geert Cauwenbergh, will present at the 25th Annual ROTH Conference on Tuesday, March 19th at 1:30pm PT. Dr. Cauwenbergh will discuss the development of RXI-109, a self-delivering RNAi compound designed to reduce dermal scarring, as well as business development opportunities with RXi’s sd-rxRNA® technology platform.
A live webcast of the presentation will be available on the “Investors” section of the Company’s website, www.rxipharma.com. A replay of the presentation will be available 90 days.
This conference is being held March 17-20, 2013 at the Ritz-Carlton Laguna Niguel in Dana Point, CA. For more information visit: http://www.roth.com.
About RXi Pharmaceuticals Corporation
RXi Pharmaceuticals Corporation (OTC: RXII) is a biotechnology company focused on discovering, developing and commercializing innovative therapies based on its proprietary, self-delivering RNAi platform. Therapeutics that use RNA interference, or “RNAi,” have great promise because of their ability to down-regulate, the expression of a specific gene that may be over-expressed in a disease condition. Building on the pioneering work of scientific founder and Nobel Laureate Dr. Craig Mello, a member of the RXi Scientific Advisory Board, RXi’s first RNAi product candidate, RXI-109, which targets CTGF, entered into human clinical development in June 2012. For more information, please visit www.rxipharma.com.
Forward-Looking Statements
This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Such statements include, but are not limited to, statements about future expectations, planned and future development of RXi Pharmaceuticals Corporation’s products and technologies. Forward-looking statements about expectations and development plans of RXi’s products involve significant risks, and uncertainties: risks that RXi may not be able to successfully develop its candidates, or that development of RNAi-based therapeutics may be delayed or not proceed as planned, or that we may not develop any RNAi-based product; risks that the development process for our product candidates may be delayed, risks related to development and commercialization of products by our competitors, risks related to our ability to control timing and terms of collaborations with third parties, and the possibility that other companies or organizations may assert …read more
Source: FULL ARTICLE at DailyFinance
New research shows that a tiny piece of RNA has an essential role in ensuring that embryonic tissue segments form properly. …read more
Source: FULL ARTICLE at Phys.org
In order to build and maintain cells, DNA is copied into ribonucleic acid (RNA) molecules, also called transcripts. Transcripts are often like a recipe for making proteins, and a collection of all the transcripts in a cell is called a transcriptome. …read more
Source: FULL ARTICLE at Phys.org
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Alnylam to Webcast Presentation at Barclays Global Healthcare Conference
CAMBRIDGE, Mass.–(BUSINESS WIRE)– Alnylam Pharmaceuticals, Inc. (NAS: ALNY) , a leading RNAi therapeutics company, today announced that management will present a company overview at the Barclays Global Healthcare Conference on Tuesday, March 12, 2013 at 10:15 a.m. ET at the Loews Miami Hotel in Miami, Florida.
A live audio webcast of the presentation will be available on the News & Investors section of the company’s website, www.alnylam.com. A replay of the presentation will be available on the Alnylam website within 48 hours after the event.
About Alnylam Pharmaceuticals
Alnylam is a biopharmaceutical company developing novel therapeutics based on RNA interference, or RNAi. The company is leading the translation of RNAi as a new class of innovative medicines with a core focus on RNAi therapeutics for the treatment of genetically defined diseases, including ALN-TTR for the treatment of transthyretin-mediated amyloidosis (ATTR), ALN-AT3 for the treatment of hemophilia and rare bleeding disorders (RBD), ALN-AS1 for the treatment of acute intermittent porphyria, ALN-PCS for the treatment of hypercholesterolemia, and ALN-TMP for the treatment of hemoglobinopathies. As part of its “Alnylam 5×15TM” strategy, the company expects to have five RNAi therapeutic products for genetically defined diseases in clinical development, including programs in advanced stages, on its own or with a partner by the end of 2015. Alnylam has additional partnered programs in clinical or development stages, including ALN-RSV01 for the treatment of respiratory syncytial virus (RSV) infection and ALN-VSP for the treatment of liver cancers. The company’s leadership position on RNAi therapeutics and intellectual property have enabled it to form major alliances with leading companies including Merck, Medtronic, Novartis, Biogen Idec, Roche, Takeda, Kyowa Hakko Kirin, Cubist, Ascletis, Monsanto, Genzyme, and The Medicines Company. In addition, Alnylam holds a significant equity position in Regulus Therapeutics Inc., a company focused on discovery, development, and commercialization of microRNA therapeutics. Alnylam has also formed Alnylam Biotherapeutics, a division of the company focused on the development of RNAi technologies for applications in biologics manufacturing, including recombinant proteins and monoclonal antibodies. Alnylam’s VaxiRNA™ platform applies RNAi technology to improve the manufacturing processes for vaccines; GlaxoSmithKline is a collaborator in this effort. Alnylam scientists and collaborators have published their research on RNAi therapeutics in over 100 peer-reviewed papers, including many in the world’s top scientific journals such as Nature, Nature Medicine, Nature Biotechnology, and Cell. Founded in 2002, Alnylam maintains headquarters in Cambridge, Massachusetts. For more information, please visit www.alnylam.com.
By evelibertine
I have a file of fasta headers that looks like the following:
>gi|28476830|ref|NR_001281.1| Homo sapiens protocadherin beta 18 pseudogene (PCDHB18), non-coding RNA
>gi|187937204|ref|NR_023342.1| Homo sapiens keratin associated protein 20-4 (KRTAP20-4), non-coding RNA
>gi|221139737|ref|NR_024072.2| Homo sapiens MRS2 magnesium homeostasis factor homolog (S. cerevisiae) pseudogene 2 (MRS2P2), non-coding RNA
>gi|219881533|ref|NR_003932.2| Homo sapiens ribosomal protein L13a pseudogene 20 (RPL13AP20), non-coding RNA
>gi|93204855|ref|NR_003024.1| Homo sapiens eukaryotic translation initiation factor 3, subunit I pseudogene 1 (EIF3IP1), non-coding RNA
>gi|222831626|ref|NR_026740.1| Homo sapiens placenta-specific 9 pseudogene (LOC389033), non-coding RNA
I want to write a code to extract the string inside parantheses in each line. The difficulty is some of the lines how more than two strings inside parantheses (i.e. line 3) In such cases, I only want to extract the string inside the second paranthesis. My output should look like:
PCDHB18
KRTAP20-4
MRS2P2
RPL13AP20
EIF3IP1
LOC389033
How do I go about doing this? Thanks!
…read more
Source: FULL ARTICLE at The UNIX and Linux Forums
By Business Wirevia The Motley Fool
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Arrowhead Receives Notice of Patent Allowance for New Protease Sensitive Masking Chemistry for DPC siRNA Delivery System
PASADENA, Calif.–(BUSINESS WIRE)– Arrowhead Research Corporation (NAS: ARWR) , a targeted therapeutics company, today announced that it has received a Notice of Allowance from the U.S. Patent and Trademark Office for U.S. Patent Application Number 13/336,028 entitled, “In Vivo Polynucleotide Delivery Conjugates Having Enzyme Sensitive Linkages.” This new IP expands the Dynamic Polyconjugate (DPC) platform, broadly protecting Arrowhead’s next generation DPC polymer masking technology. Using this masking technology, DPCs can be engineered for long circulation times and improved tissue-targeting characteristics. In addition, hepatocyte-targeted DPCs formulated using this new masking technology have shown to be highly potent upon subcutaneous administration. The company has previously reported target gene knockdown of 99% in monkeys after a single subcutaneous injection of 1 mg/kg, with >80% knockdown for 3 months. Additional data will be reported at upcoming scientific conferences and through peer-reviewed publications.
“This patent protects a new masking chemistry that broadens the reach of DPC-enabled RNAi therapeutics. It enables efficient subcutaneous delivery of siRNA and opens up new therapeutic area targets including oncology,” said Dr. Chris Anzalone, President and CEO of Arrowhead. “Arrowhead scientists continue to discover innovative solutions for siRNA delivery and we look forward to providing updates on how these technologies are being deployed to create new drug candidates.”
About Arrowhead Research Corporation
Arrowhead Research Corporation is a clinical stage targeted therapeutics company with development programs in oncology, obesity, and chronic hepatitis B virus infection. The company is leveraging its platform technologies to design and develop peptide-drug conjugates (PDCs) that specifically home to cell types of interest while sparing off-target tissues, create targeted drugs based on the gene silencing RNA interference (RNAi) mechanism, and work with partners to create improved versions of traditional small molecule drugs.
For more information please visit http://www.arrowheadresearch.com, or follow us on Twitter @ArrowRes. To be added to the Company’s email list to receive news directly, please send an email to ir@arrowres.com.
Safe Harbor Statement under the Private Securities Litigation Reform Act:
This news release contains forward-looking statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995. These statements are based upon our current expectations and speak only …read more
Source: FULL ARTICLE at DailyFinance
(Phys.org)—The base pairs that hold together two pieces of RNA, the older cousin of DNA, are some of the most important molecular interactions in living cells. Many scientists believe that these base pairs were part of life from the very beginning and that RNA was one of the first polymers of life. But there is a problem. The RNA bases don’t form base pairs in water unless they are connected to a polymer backbone, a trait that has baffled origin-of-life scientists for decades. If the bases don’t pair before they are part of polymers, how would the bases have been selected out from the many molecules in the “prebiotic soup” so that RNA polymers could be formed? …read more
Source: FULL ARTICLE at Phys.org
By genGirl23
Unique alignments
Non-unique alignments
original read files
I want to extract only the unique alignments by pulling out alignments that have “IH:i:1″ (indicates this read had only one alignment).
I have tried…. grep “IH:i:1″ file.sam > filtered.sam
but this will also return “IH:i:11 IH:i:12″ etc etc. I have also tried “IH:i:1 ” which returns nothing (I believe it’s tab delimited)
Any suggestions?
…read more
Source: FULL ARTICLE at The UNIX and Linux Forums
Whitehead Institute researchers have determined that DNA transcription, the process that produces messenger RNA (mRNA) templates used in protein production, also runs in the opposite direction along the DNA to create corresponding long noncoding RNAs (lncRNAs). Moreover, the mRNAs and lncRNAs are transcribed coordinately as stem cells differentiate into other cell types. This surprising finding could redefine our understanding of gene organization and its regulation.
Source: FULL ARTICLE at Phys.org
