Monthly Archives: September 2014

September 29, 2014 - In DNA SMART ChIP-Seq Kit, adaptation of template switching technology is used to add Illumina-specific adapters directly to DNA. This produces ChIP-seq libraries without additional ligation or clean-up steps. Kit generates libraries with good complexity and low redundancy from low-input samples (100 pg-10 ng) using simple protocol. SMART (Switching Mechanism at 5' End of RNA Template) technology, when applied to RNA, allows for full-length cDNA synthesis with direct addition of PCR adapter. Clontech Laboratories, Inc. 1020 E. Meadow Circle Palo Alto, CA, 94303 USA Press release date: September 22, 2014

MOUNTAIN VIEW, Calif., -- Clontech Laboratories, Inc., a wholly-owned subsidiary of Takara Bio Inc., today announced the launch of the DNA SMART ChIP-Seq Kit. This kit adapts Clontech's patented SMART technology in an innovative manner for use with low-input samples, including both dsDNA and ssDNA templates, to generate ChIP-seq libraries for NGS.

SMART (Switching Mechanism at 5' End of RNA Template) technology, when applied to RNA, allows for full-length cDNA synthesis with direct addition of a PCR adaptor. In the DNA SMART ChIP-Seq Kit, a novel, patent-pending adaptation of template switching technology is used to add Illumina-specific adaptors directly to DNA. This produces ChIP-seq libraries without additional ligation or clean-up steps. The process has resulted in the simplification of library generation, cutting down protocol time significantly compared to traditional, ligation-based methods of adapter addition. The DNA SMART ChIP-Seq Kit generates libraries with good complexity and low redundancy from low-input samples (100 pg-10 ng) using a simple protocol that can be completed in half a day.

"Clontech is known as a leader in cDNA synthesis, and in recent years SMART technology has been widely acclaimed as the gold standard for sensitive transcriptome analysis from low-input samples, including single cells," said Carol Lou, General Manager of Clontech Laboratories, Inc. "With the DNA SMART ChIP-Seq Kit we are able to expand the benefits of SMART technology into other NGS applications. Our focus has been providing new solutions to customers, enabling them to work with challenging samples. This kit allows us to address the needs of those researchers working with low inputs of either dsDNA or ssDNA for NGS applications."

The launch of the DNA SMART ChIP-Seq Kit continues the Clontech tradition of supporting good science by providing new tools to meet the ever-changing needs of life science researchers. For more information about Clontech products for NGS, please visit: http://www.clontech.com/NGS.

About Clontech Laboratories, Inc. Clontech Laboratories, Inc., a wholly-owned subsidiary of Takara Bio Inc., develops, manufactures, and distributes a wide range of life science research reagents under the Clontech and Takara brands. Key products include SMARTer cDNA synthesis kits for a variety of samples and applications, including NGS; high-performance qPCR and PCR reagents (including the TaKaRa Ex Taq, TaKaRa LA Taq, Titanium, and Advantage enzymes); RT enzymes and SMART library construction kits; the innovative In-Fusion cloning system; Tet-based inducible gene expression systems; Living Colors fluorescent proteins; and a range of Macherey-Nagel nucleic acid purification tools. These and other products support applications including NGS, gene discovery, regulation, and function; protein expression and purification; RNAi and stem cell studies; and plant and food research. For more information, visit http://www.clontech.com.

About Takara Bio Inc. Takara Bio Inc. is an innovative biotechnology company based in Shiga, Japan. As a world leader in biotechnology research and development, Takara Bio was the first company to market PCR technology in Japan and is also the developer of the RetroNectin reagent, which is used as a world standard in gene therapy protocols. In addition to providing research reagents and equipment to the life science research market, Takara Bio has active research and product development activities in the fields of gene and cell-based therapy and agricultural biotechnology; and is committed to preventing disease and improving the quality of life for all people through the use of biotechnology. Through strategic alliances with other industry leaders, Takara Bio aims to extend its reach around the world. More information is available at http://www.takara-bio.com.

CONTACT: Clontech Laboratories, Inc., Lorna Neilson, Ph.D., Director, Business Development, Clontech Laboratories, Inc., A Takara Bio Company, lorna_neilson@clontech.com, 650.919.7372

Excerpt from:
DNA Sequencing Kit generates ChIP-seq libraries for NGS.

PUBLIC RELEASE DATE:

29-Sep-2014

Contact: Florence Meney florence.meney@douglas.mcgill.ca Douglas Mental Health University Institute

This news release is available in French.

Montreal, September 29th, 2014 - The number of days an expectant mother was deprived of electricity during Quebec's Ice Storm (1998) predicts the epigenetic profile of her child, a new study finds.

Scientists from the Douglas Mental Health University Institute and McGill University have detected a distinctive 'signature' in the DNA of children born in the aftermath of the massive Quebec ice storm. Five months after the event, researchers recruited women who had been pregnant during the disaster and assessed their degrees of hardship and distress in a study called Project Ice Storm.

Thirteen years later, the researchers found that DNA within the T cells - a type of immune system cell - of 36 children showed distinctive patterns in DNA methylation.

The researchers concluded for the first time that maternal hardship, predicted the degree of methylation of DNA in the T cells. The "epigenetic" signature plays a role in the way the genes express themselves. This study is also the first to show that it is the objective stress exposure (such as days without electricity) and not the degree of emotional distress in pregnant women that causes long lasting changes in the epigenome of their babies.

The health impacts on these children is less clear, but changes in the family of genes related to immunity and sugar metabolism detected in these babies, now teenagers, may put them at a greater risk to develop asthma, diabetes or obesity.

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DNA signature found in ice storm babies

By Douglas Walker and Keith Roysdon 8:09 p.m. EDT September 29, 2014

Brianna DiBattiste(Photo: Provided photo)

MUNCIE The search for Brianna DiBattiste is officially over.

Jay County Prosecutor Wesley Schemenaur on Monday evening said DNA tests confirmed that a body found in southwestern Jay County on Sept. 1 is that of DiBattiste.

The 25-year-old Dunkirk woman had been missing since June 16. Indiana State Police submitted their report on the DNA analysis on Monday.

"Testing took longer than initially anticipated due to the condition of the body," Schemenaur said in a prepared statement. "Investigators were confident upon discovery of the body that it was in fact Ms. DiBattiste based on artifacts found near the body at the scene and the family was informed accordingly.

"Having the DNA results confirms those initial observations."

Authorities have said it might be several more weeks before tests that could reveal the cause of DiBattiste's death are completed.

THESTARPRESS

DNA still out, but dad's class ring helped ID

See more here:
DNA confirms remains are missing woman

PUBLIC RELEASE DATE:

29-Sep-2014

Contact: Jocelyn Duffy jhduffy@andrew.cmu.edu 412-268-9982 Carnegie Mellon University @CMUScience

PITTSBURGHMany double-stranded DNA viruses infect cells by ejecting their genetic information into a host cell. But how does the usually rigid DNA packaged inside a virus' shell flow from the virus to the cell?

In two separate studies, Carnegie Mellon University biophysicist Alex Evilevitch has shown that in viruses that infect both bacteria and humans, a phase transition at the temperature of infection allows the DNA to change from a rigid crystalline structure into a fluid-like structure that facilitates infection.

The findings, published in Nature Chemical Biology and the Proceedings of the National Academy of Sciences (PNAS), provide a promising new target for antiviral therapies. Most antiviral drugs work by deactivating viral proteins, but viruses often evolve and become drug resistant. Evilevitch believes that researchers now have a possible new way to prevent infection blocking the phase transition. Such a therapy could be generalizable across all types of Herpes viruses, and wouldn't be prone to developing resistance.

"The exciting part of this is that the physical properties of packaged DNA play a very important role in the spread of a viral infection, and those properties are universal," said Evilevitch, an associate professor in Carnegie Mellon's Department of Physics. "This could lead to a therapy that isn't linked to the virus' gene sequence or protein structure, which would make developing resistance to the therapy highly unlikely."

Most viruses, whether they infect bacteria, plants or animals, have fairly similar structures. They consist of an outer shell called a capsid that contains the viral genome either DNA or RNA. In many DNA viruses the long strands of nucleic acid are tightly wound in a crystalline structure. The repulsive forces formed by the layered strands of genetic material exert a large amount of pressure on the capsid, and according to previous research done by Evilevitch, this pressure is ultimately what propels DNA out of a small porthole in the virus's capsid and into a host cell. That hole is no larger than the width of a DNA chain.

In order to find out how DNA could easily escape through such a tiny opening in the capsid, Evilevitch did separate studies on Herpes Simplex virus type 1 (HSV-1), which infects humans, and bacteriophage lambda, which infects bacteria.

In the HSV-1 study, which was published in Nature Chemical Biology, Evilevitch set out to see what physical conditions lead to successful viral infection. Using atomic force microscopy and small angle x-ray scattering (SAXS), he found that both ionic conditions in the cell and temperature could change the fluidity and mobility of the DNA inside a virus. The viral DNA was much more fluid at temperatures close to that of infection (37 degrees Celsius) and at ionic conditions similar to that of neuronal and epithelial cells the same cells that HSV-1 infects.

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Viral infection might just be a phase... transition

The number of days an expectant mother was deprived of electricity during Quebec's Ice Storm (1998) predicts the epigenetic profile of her child, a new study finds.

Scientists from the Douglas Mental Health University Institute and McGill University have detected a distinctive 'signature' in the DNA of children born in the aftermath of the massive Quebec ice storm. Five months after the event, researchers recruited women who had been pregnant during the disaster and assessed their degrees of hardship and distress in a study called Project Ice Storm.

Thirteen years later, the researchers found that DNA within the T cells -- a type of immune system cell -- of 36 children showed distinctive patterns in DNA methylation. The researchers concluded for the first time that maternal hardship, predicted the degree of methylation of DNA in the T cells. The "epigenetic" signature plays a role in the way the genes express themselves. This study is also the first to show that it is the objective stress exposure (such as days without electricity) and not the degree of emotional distress in pregnant women that causes long lasting changes in the epigenome of their babies.

The health impacts on these children is less clear, but changes in the family of genes related to immunity and sugar metabolism detected in these babies, now teenagers, may put them at a greater risk to develop asthma, diabetes or obesity.

Among the team of scientists who conducted this study are Lei Cao-Lei, Psychological Research Division, Douglas Institute Research Center and Department of Psychiatry, McGill University, Moshe Szyf, Department of Pharmacology and Therapeutics, Sackler Program for Epigenetics and Developmental Psychobiology, McGill University, and Suzanne King, Psychological Research Division, Douglas Institute Research Center and Department of Psychiatry, McGill University. Results of this study have been published in the international online publication PLOS ONE on September 19th, 2014 In June 2014, Project Ice Storm results reported in the journals BioMed Research International and Psychiatry Research showed links between prenatal maternal stress (PNMS) and the development of symptoms of asthma and autism, respectively, in the children.

About Project Ice Storm

When the ice storms of January 1998 plunged more than 3 million Quebecers into darkness for as long as 45 days, the team seized the opportunity to study the effects of stress on pregnant women, their pregnancies, and their unborn children. The team has been following a group of about 150 families, in which the mother was pregnant during the ice storm or became pregnant shortly thereafter, in order to observe the immediate effects of different levels and types of stress on the unborn children. It continues to follow these children, who are now teenagers.

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The above story is based on materials provided by Douglas Mental Health University Institute. Note: Materials may be edited for content and length.

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DNA signature found in Ice Storm babies: Prenatal maternal stress exposure to natural disasters predicts epigenetic ...