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GEN reports on ocular therapeutics targeting the retina

Posted: September 11, 2012 at 5:13 pm

Public release date: 10-Sep-2012 [ | E-mail | Share ]

Contact: John Sterling jsterling@genengnews.com 914-740-2196 Mary Ann Liebert, Inc./Genetic Engineering News

New Rochelle, NY, September 10, 2012-- Therapies for retinal diseases are expected to overtake those for glaucoma by 2014, reports Genetic Engineering & Biotechnology News (GEN). Because current retinal disease treatments only improve vision for six to eight weeks, there is a critical need for new remedies, according to a recent issue of GEN.

"As increasing numbers of baby-boomers continue to grow older, many will have to deal with eye diseases such as age-related macular degeneration," said John Sterling, Editor-in-Chief of GEN. "Some estimates put the current AMD and diabetic retinopathy drug segment of the market at $3 billion, and this is expected to increase to about $5 billion in two years."

Standard therapy has been Genentech's VEGF inhibitors Lucentis and the off-label use of Avastin. Regeneron, in collaboration with Bayer HealthCare, is challenging these drugs with a similar VEGF inhibitor, Eyela. The FDA approved the drug last November for wet AMD.

In another approach, Acucela is in Phase II trials using visual cycle modulators to lighten the metabolic load on the retina by reducing the activity of the rod visual system. This protects the retina from light damage, improves retinal vasculature, and reduces the accumulation of A2E and other retinal-related toxic by-products.

GlaxoSmithKline has two drugs in Phase II trials for ocular therapy: darapladib, an oral Lp-PLA2 inhibitor for diabetic macular edema, and Votrient, a multi-kinase angiogenesis inhibitor in eye drop form for AMD. Early-stage work also is under way for neovascular AMD, dry AMD, diabetic retinopathy, diabetic macula edema, uveitis, and glaucoma, as well as for technologies for drug delivery.

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Other companies covered in the GEN article include Acucela, pSiveda, Sanofi, NeuroTech, QLT, Applied Genetic Technologies, RetroSense Therapeutics, Aerie Pharmaceuticals, Kowa Pharmaceuticals America, Novartis, Senju Pharmaceutical, Can-Fite Biopharma, Inotek Pharmaceuticals, Otsuka Pharmaceutical, and Santen Pharmaceutical.

For a copy of the September 1 issue of GEN, please call (914) 740-2146, or email: pbartell@genengnews.com

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GEN reports on ocular therapeutics targeting the retina

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'Junk DNA' and the mystery of mankind's missing genes

Posted: at 5:13 pm

The lexicon of science is riddled with catchy yet misleading terms. The god particle is nothing of the sort. Genes cannot really be selfish, and when astronomers talk about metals, they usually mean something else entirely. Now, we must add junk DNA to the list of scientific misnomers.

Last week, the results of the multinational Encode Project were published across 30 papers in the journals Nature, Science, Genome Biology and Genome Research. The five-year collaboration involved some 450 scientists working in 32 institutions and took up 300 years of computer time. The goal was to analyse the vast bulk of human DNA that does not constitute a gene ie, does not directly code for the creation of particular proteins and is seemingly surplus to requirements.

The conclusion? That this DNA is not junk at all, but absolutely vital for the functioning of our cells. It turns out that as much as a fifth of the 98 per cent of our DNA that falls into this category is instead made up, among other things, of switches bits of DNA that turn some genes on and others off. It is now believed that, in order to get to grips with genetic illnesses such as hereditary heart disease, some forms of diabetes and Crohns Disease, we need to understand these regulatory elements as much as the genes themselves.

It has been clear for a long time that there is a lot more to DNA than just genes. Indeed, one of the great scientific surprises in recent decades has been the discovery that the human genome is surprisingly bereft of actual genes. When the first draft of it was published in the summer of 2001, it did not describe the 100,000 or more genes that most biologists assumed we had, but fewer than 20,000 making Homo sapiens not much more well-endowed genetically than a fruit fly or even a lump of yeast. As an editorial in Nature put it, Unless the human genome contains a lot of genes that are opaque to our computers, it is clear we do not gain our undoubted complexity over worms and plants by using many more genes.

Partly as a result, the idea that scanning a persons genome can tell us pretty much everything about them their likely intelligence, the chance of criminal tendencies, their probable age and cause of death is now seen as a simplistic fantasy. Indeed, the more we learn about our genome, the more complex the story becomes. We have genes that tell our bodies to make proteins, genes that affect other genes, genes that are influenced by the environment, segments of DNA that switch certain genes on and off, as well as our RNA, the still-not-fully understood messenger molecule that conveys information from our DNA to protein factories in the cells.

Despite the fanfare with which the Encode findings were greeted last week, biologists have known for years that junk DNA, a term coined in 1972 by the Japanese-American geneticist Susumu Ohno, performs a host of functions, among them gene regulation. Indeed, it was always obvious that much of our DNA must be tasked with the activation or suppression of other parts of itself: genes that make bone tissue are present in all cells but are only switched on in bone cells; heart muscle genes are present but inactive in your teeth and liver and everywhere else.

Furthermore, as Ohno pointed out, a great deal of the genome consists of pseudogenes non-functioning copies of active genes that form the raw material of evolution. Without this spare genetic material, natural selection would have nothing to act upon. We have also known for some time that the dark part of our genome contains what are known as human endogenous retroviruses: bits of the genetic code from viruses that are a legacy of our long battle with these microbes. In millennia to come, it is likely that bits of the genome for HIV will become similarly incorporated into our DNA, as a legacy of the Aids epidemic.

The more we learn, the more the recipe book of life turns out to resemble less a single tome than a well-organised library, complete with a sophisticated index and with the ability to lend and borrow books. Some of the volumes are crucial a mix-up in the code could kill or cripple us while others moulder in the stacks. There is probably a lot of built-in redundancy, which is not surprising considering that the genomes of any species are the result of three billion years of evolution. Perhaps the most amazing thing is that we can make any sense of it at all.

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Genetics Breakthrough Changes Thinking About DNA

Posted: at 5:13 pm

A Massive Research Effort Now Shows How the Genome Works

By Daniel J. DeNoon WebMD Health News

Reviewed by Louise Chang, MD

Sept. 7, 2012 -- In what scientists call the biggest breakthrough in genetics since the unraveling of the human genome, a massive research effort now shows how the genome works.

The human genome contains 3 billion letters of code containing a person's complete genetic makeup.

The biggest surprise is that most of the DNA in the genome -- which had been called "junk DNA" because it didn't seem to do anything -- turns out to play a crucial role. While only 2% of the genome encodes actual genes, at least 80% of the genome contains millions of "switches" that not only turn genes on and off, but also tell them what to do and when to do it.

Eleven years ago, the Human Genome Project discovered the blueprint carried by every cell in the body. The new ENCODE project now has opened the toolbox each cell uses to follow its individual part of the blueprint. The effort is the work of more than 400 researchers who performed more than 1,600 experiments.

The genome, with its 3-billion-letter code, reads from beginning to end like a book. But in real life, the genome isn't read like a book. The ENCODE data shows it's an intricate dance, with each step carefully choreographed.

Ewan Birney, PhD, associate director of the European Molecular Biology Laboratory, was one of the leaders of the Human Genome Project. He also helped lead the ENCODE project.

"The ENCODE data is just amazing. It shows how complex the human genome is," Birney said at a news conference. "This is the science for this century. We are going to be working out how we make humans, starting out from a simple instruction manual."

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Genome research given a boost with opening of bioscience facility

Posted: at 5:13 pm

By Joe Dermody

Tuesday, September 11, 2012

Irish genome research has been given a welcome boost with the opening of a Teagasc Animal Bioscience Facility at Grange, Co Meath.

The facility will optimise research into animal breeding. It will also be used to assist in the commercial development of new meat and milk products.

Officially opened by Agriculture Minister Simon Coveney, the Animal Bioscience Facility was developed as part of the Teagasc vision programme initiated in 2006, with the objective of establishing centres of excellence in the sciences that underpin agriculture. The tech-nologies being developed have the potential to accelerate the rate of gain in efficiency and quality.

Teagasc director Professor Gerry Boyle said: "The publication of the genome sequence for cattle in 2009 has opened up the possibility to use DNA-based approaches to study commercially important traits. These include milk and meat production, immunity and disease, nutrition, and reproduction."

The facilities include molecular biology laboratories, and labs for DNA/RNA preparation, immunology, biochemistry, microbiology, cell culture, and flow cytometry.

Head of the Teagasc Animal and Bioscience Department, Dr Richard Dewhurst, said: "We are developing the optimal breeding programmes to maximise genetic gain in the long term. Our main research activities include the development of multi-breed genetic and genomic evaluations, breeding objectives, and breeding programmes for dairy cattle, beef cattle, and sheep.

"We also aim to identify genes, pathways, and biological processes mediating resistance to infectious diseases in cattle and sheep and how these genes interact with pathogens and the environment."

The Teagasc Animal and Bioscience Department carries out research in the areas of animal breeding and genomics, animal health and welfare, infection and disease, computational and systems biology, fertility and reproduction, feed efficiency, and product quality.

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Genome research given a boost with opening of bioscience facility

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Re-Imagining Our Genes: ENCODE Project Reveals Genome as an Information Processing System

Posted: at 5:13 pm

Thirty-one papers simultaneously published by the ENCODE (Encyclopedia of DNA Elements) project indelibly repaint the picture of the human genome, throwing its information-processing characteristics into even sharper relief. (The whole collectionsix papers in Nature, 18 in Genome Research, four in Genome Biology, and one in BioMed Central Geneticsis posted with open access at Nature Encode. The lead article, Architecture of the human regulatory network derived from ENCODE data, is must reading for information-systems designers.)

Just a few years ago, the prevailing wisdom said that the genome comprises 3 percent or so genes and 97 percent junk (with 2 or 3 percent of that junk consisting of the fossilized remains of retroviruses that infected our ancestors somewhere along the line). After a decade of painstaking analysis by more than 200 scientists, the new ENCODE data show that indeed 2.94 percent ofthe genome isprotein-coding genes, while 80.4 percent of sequences regulate how those genes get turned on, turned off, expressed, processed, and modified.

This fundamentally changes how most biologists understand the master instruction set of life: we are, in short, 3 percent input/output and 80 percent logic. (Though perhaps a surprise to biologists, the finding will hardly astound anyone who has designed a complex interactive system.)

And though only 3 percent of the genomes three-billion-odd base pairs of DNA code for proteins directly, 62 percent of your DNA is, at some time or another, transcribed into RNA, which has relatively recently been revealed to have myriad functions beyond directing the assembly of amino acids into proteins.

It will take years to analyze the healthcare implications of the ENCODE vision of the genome.Stanford University biologist Michael Snyder told theNew York Times that,Most of the changes that affect disease dont lie in the genes themselves; they lie in the switches.

The Times also quoted Massachusetts General Hospital researcher Bradley Bernstein, who said: I dont think anyone predicted that would be the case. I cant resist pointing out that some folks did predict exactly this. In 1991, for example, the editor of Nature Biotechnologythen called Bio/Technologypointed out that even simple communications programs available then were 75 percent logic and 25 percent input/output. He added that, [R]esearchers are announcing new disciplines whose names are redolent of bits and bytesgenomics, bio-informatics. Maybe they will see past the junk epithet to discover whether the logic lies within the genome, but beyond the gene.

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Illumina Announces Expedited Individual Genome Sequencing Service (IGS)

Posted: at 5:13 pm

SAN DIEGO--(BUSINESS WIRE)--

Illumina, Inc. (ILMN) today announced the introduction of its rapid Individual Genome Sequencing (IGS) service with a turnaround time in as little as two weeks. Rapid turnaround whole genome sequencing services were announced by Illumina in June 2012, enabled by technology innovations to the HiSeq platform. Now these advancements have been implemented in Illuminas CLIA-certified laboratory to enable the same fast turnaround for the IGS service.

The IGS service is only available through a physicians order and is designed to assist clinicians with diagnosis and treatment decisions. As the only CLIA-certified, CAP-accredited whole genome sequencing service laboratory in the world, Illumina continues to increase access and lay the foundation for routine clinical use of whole-genome sequencing.

Illumina has long believed that sequencing will become a mainstream practice in the clinical setting. By delivering a whole human genome in as little as two weeks, we have taken significant strides towards that goal, said Illumina President and CEO Jay Flatley. Whole genome sequencing is quickly gaining recognition for its potential in diagnostics and treatment decisions, particularly in cases where physicians are challenged with identifying a disorder based on symptoms that don't quite fit with a known disease. When this happens, rapid whole-genome sequencing can provide big-picture information about genetic makeup, enabling physicians to make more informed decisions and patients to obtain answers more quickly.

Validated for laboratory use in accordance with CLIA and CAP regulations and guidelines, Illuminas fast IGS service uses Illuminas HiSeq 2500 sequencing system, which is capable of completing a sequencing run on a whole human genome in one day. The service will continue to deliver the highest quality, most comprehensive data with the broadest coverage of exomic, promoter, and regulatory regions, as well as fully annotated variants to facilitate clinical interpretation, now available faster. Illumina is also working on a suite of analytic tools and professional services in collaboration with physicians and medical geneticists to improve clinical interpretation.

Illumina has delivered on the promise of personalized healthcare by notonly enabling clinical interrogation of the whole genome, but also providing theresults in a turnaround time consistent with the demands of patient care. This is a game-changer that will revolutionize our field, saidDr. Leonard Sender, Medical Director, CHOC Hyundai Cancer Institute and Director of the Young Adult Cancer Program at the Universityof California, Irvine Chao Family Comprehensive Cancer Center.

Initially, the rapid turnaround option is available with limited capacity, and cases will be prioritized by severity in consultation with ordering physicians. Later this year, Illumina will begin offering focused clinical interpretation for CLIA services, working closely with ordering physicians and leveraging bioinformatics tools and internal medical genetics expertise.

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.

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The New Yorker Got Temporarily Banned From Facebook for Posting Cartoon Boobs [Censorship]

Posted: at 5:13 pm

The venerable New Yorker is the latest casualty in Facebook's senseless war on boobs. The Facebook page for the New Yorker's cartoon department was temporarily disabled after they posted the cartoon above featuring a topless lady, according to a blog post by New Yorker cartoon editor Bob Mankoff.

After the ban, the cartoon was even redrawn by its author, Mick Stevens, to feature a clothed couple, though "the gain in clothes caused too great a loss in humor," Mankoff writes.

Mankoff believes Facebook temporarily axed the New Yorker's cartoon page because the cartoon broke content guidelines that prohibit "naked 'private parts' including female nipple bulges and naked butt cracks." (We obtained and published Facebook's detailed content guidelines earlier this year.) This would make sense. The social network mercilessly hunts down and censors pictures of bare breasts like Iranian computer scientists going after Stuxnet, even when they appear in the innocuous context of breastfeeding.

However, Facebook has voiced acceptance of artistic representations of breasts. Last year an art school got banned for posting a nude sketch. After a public outcry Facebook admitted they made a mistake and said they had an "unwritten policy that allows drawings or sculptures of nudes." So why did The New Yorker's cartoon department get heat for posting a minimalist cartoon featuring breasts? Who knows. Maybe one of the poorly-paid Third World moderators who help police Facebook just didn't get it.

[Cartoon via The New Yorker]

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Stockman: "Ron Paul Is Right: The Fed, And The Lunatics That Run It, Are The Heart Of The Problem"

Posted: at 5:13 pm

Former Reagan OMB Director David Stockman was 'allowed' on CNBC this morning - much to their chagrin now we suspect - and espoused his own brand of truthiness, starting with this epic tirade:

"Ron Paul is the only one who is right about the Fed, and the Fed is the heart of the problem. They have destroyed the capital markets and the money markets; interest rates mean nothing; everything is trading off the Fed and Wall Street isn't even home - as it's now a bunch of computers trading word-clouds emitted by this central banker and that"

In this environment, he goes on, everyone is being given the wrong signal - i.e. the Ryan/Romney campaign is abnout restoring vibrant capitalism; how can you do that when the financial markets are dead - the lifeblood of a capitalist system. And that is the problem today.

An excellent discussion ensues diving into the lack of fiscal discipline (that is enabled by a Fed ZIRP) as "[politicians] will never do it when you can keep borrowing free-money forever" and summed up nicely with this subtle sentence:

"The Fed (and the lunatics that run it) are telling the whole world untruths about the cost of money and the price of risk."

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Stockman: "Ron Paul Is Right: The Fed, And The Lunatics That Run It, Are The Heart Of The Problem"

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Dan Halloran Keeps Up the Good Fight for Ron Paul Supporters

Posted: at 5:13 pm

Dan Halloran speaking before the crowd at the Rebel.

GOP Councilman Dan Halloran is an underdog congressional campaign in a staunchly Democratic district where his opponent has repeatedly attacked him for his support of Ron Pauls presidential campaign, but Mr. Halloran has no plans to slow down his advocacy in Mr. Pauls political movement any time soon. To that end, he was among the supporters of Mr. Paul who gathered in Mainea couple weeks ago, and last night, he addressed a crowd that had gathered for Mr. Pauls son, Kentucky Senator Rand Paul,near Penn Station last night.

Problem is, we aint getting Ron in the White House. We have a choice: Do we keep what we have, or do we trade it in? Mr. Halloran said to the enthusiastic crowd, making the case for Mitt Romneys campaign. We cant afford to have four more years of Barack Hussein Obama. We cant afford it. Our country cant economically. Our people cant afford it. If you think people are out of work today, when the real depression hits us, and theres no leadership in the White House, theres going to be nowhere to hide.This country will come to a grinding halt. The Constitution, you can just forget about it.

Mr. Halloran said some of that erosion of liberty has already begun at home with Mayor Michael Bloombergs various restrictive proposals as well as nationally, with President Barack Obamas healthcare reform bill and Mitt Romneys presidential campaign making life difficult for supporters of Mr. Paul. However, Mr. Halloran encouraged the crowd not to lose hope.

If we have people like Rand Paul in the Senate of the United States speaking up for us, if we have men like that doing what needs to be done, then this Republic is not dead, he said. Dont be disparaged at what happened this year with the Ron Paul campaign. Dont be disparaged by some of the things that have gone on.Keep momentum alive!

He added, I implore all of you, continue the fight.

Overall, Mr. Halloran seemed a little less assertive than some of his other recent appearances before conservative crowds where he had directly engaged his Democratic opponent, Assemblywoman Grace Meng and her father, who was arrested on bribery charges earlier this summer. For example, on one occasion,he tossed out a number for what Mr. Meng might have raised on his daughters behalf, and on another,he insinuated she would have been complicit in her fathers crime had it been carried out. For her part, Ms. Meng has maintained that she has nothing to do with the allegations.

Last night, however, Mr. Halloran only referred to my opponent, and only in the context of her outraising him and soliciting contributions from Hollywood, who use their money to tell the blind sheep how to vote.

Additionally, his appearance was in no way as fiery as his speech to another crowd of Ron Paul supporters atLiberty Fest NYC last year. Watch that address below.

Follow Colin Campbell on Twitter or via RSS. ccampbell@observer.com

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Mandatory GM Labeling Would Require Major Change

Posted: September 10, 2012 at 11:10 am

CPG manufacturers may be on the cusp of monumental change as voters in California contemplate a hotly contested ballot initiative to require labeling of genetically modified foods.

Food marketers will face tough choices should the measure pass, as about 70% of processed foods sold in supermarkets contain GM ingredients like corn and soy. Some estimate that 100,000 or more foods sold in California contain some level of GE ingredients and would therefore be affected.

The mandate would be limited to the Golden State, but the implications for companies that choose not to move away from GM ingredients in advance of the July 1, 2014, deadline could be as far-reaching as consumer awareness spreads.

While the government deems genetically modified organisms safe, Californians want to judge for themselves. A Pepperdine University poll found that if the election were held last month, Californians would pass the proposition by a 3-1 margin.

To avoid the partially produced with genetic engineering label and possible consumer backlash, suppliers will likely reformulate product with more costly non-GE foods or organic ingredients, just as theyve done in countries where genetic modification disclosure is required.

Read more: Prop 37 Battle Rages in California

A recent study commissioned by the No on 37, Stop the Deceptive Food Labeling Scheme campaign, of which the Grocery Manufacturers Association is a chief sponsor, bears this out.

It projects that reformulations to non-GE and organic ingredients, which by law cannot be genetically modified, will be the most likely course taken by food producers.

Read more: California GMO Bill Is Top Priority for GMA

Retailers might also adjust their sourcing policies to gain consumer favor by incorporating more organic foods and those that have been verified under the Non-GMO Project and labeled with its seal.

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