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Category Archives: Transhuman News

Short and Sweet: Why Modern Molecular Biology Needs Oligos

Posted: March 31, 2015 at 10:44 pm

DNA sequencing and synthesis are two sides of the same coin, the read and write functions of genetic material. The field and its requisite technology took off in the 1990s with the Human Genome Projects effort to sequence billions of bases and unlock a new era of genetically informed medicine. The resulting science is still a work in progress it turns out the genetic code is more complicated than anticipated but the technologies and companies it helped spawn are an impressive legacy.

Integrated DNA Technologies (IDT) got its start during the Human Genome Project, as it produced single nucleotides (the As, Ts, Cs, and Gs that comprise the genetic code) and short oligonucleotide chains (or oligos) to help facilitate a massive sequencing effort around the world. Of course, sequencing technology has advanced dramatically in the intervening decades, but you still need oligos to do the sequencing, explains Jerry Steele, IDTs Director of Marketing, especially in the next gen sequencing space. Sequencing and DNA synthesis go hand in hand.

The current sequencing method of choice is Illumina, a process that frequently returns millions of bases of DNA sequence by reading distinct stepwise fluorescent signals associated with each base in a massively parallel array. To distinguish genetic material from different samples (a few hundred are often run on the same plate), scientists label each samples DNA extract with a distinct barcode. With each barcode comprised of about ten nucleotides, the demand for synthetic DNA chains in the sequencing process is substantial.

Unlike other biotech companies prioritizing longer constructs or gene variants, IDT specializes in relatively short oligos. These chains are used not only in Illumina barcoding, but also as primers consistent patches of sequence that may border unknown regions and facilitate PCR-based amplification. Both techniques next gen Illumina sequencing and primer-based amplification are staples of any self-respecting applied or research-based microbiology laboratory, as they allow researchers to identify constituent organisms or confirm a genes presence.

With such short sequences, a single nucleotide discrepancy could mean the difference between two Illumina samples from opposite ends of the world, or between a gene native to the Firmicutes or the Proteobacteria. Its a small margin for error, so every base better be right, explains Steele. As weve grown, its just a matter of maintaining that consistency on a larger scale. In the spirit of not fixing something that needs no repairs, IDT shipped an entire fabrication room from its headquarters in Des Moines to Belgium when that facility was being built.

Fundamental as they are to modern biology, oligos are used every day in thousands of laboratories around the world, often in innovative ways that the company itself may not have predicted. The things that people are doing with DNA are really inspiring, notes Steele. One of his favorite use cases involves low-impact prenatal tests: rather than a painful and invasive amniosyntesis, weve discovered that now because of sequencing, we can see the babys DNA in a blood draw from the mother. Improved sequencing fidelity and throughput are expanding the resolution of the technique, and Steele soon envisions scientists using next gen sequencing to detect cancer cells from the blood stream as an early diagnosis tool. Biology is really leaving the lab and coming into the real world, Steele explains, and its going to improve a lot of lives.

*This article is part of a special series on DNA synthesis and was previously published at SynBioBeta, the activity hub for the synthetic biology industry.

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Short and Sweet: Why Modern Molecular Biology Needs Oligos

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The Deeper Genome – Video

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The Deeper Genome
John Parrington, author of The Deeper Genome, looks at the latest research about human DNA and why it is far more complex and more dynamically changing -- than we initially believed. http://ukc...

By: Oxford Academic (Oxford University Press)

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The Deeper Genome - Video

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Thyroid Cancer: Biomarkers and Lessons from The Cancer Genome Atlas.Dr. Giordano. ThyCa Conference – Video

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Thyroid Cancer: Biomarkers and Lessons from The Cancer Genome Atlas.Dr. Giordano. ThyCa Conference
241 Biomarkers in Thyroid Cancer: Lessons From The Cancer Genome Atlas (TCGA). 241 Thomas J. Giordano, M.D., Ph.D., Pathologist Biomarkers in Thyroid Cancer: Lessons From The Cancer ...

By: ThyCa: Thyroid Cancer Survivors #39; Association, Inc.

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Thyroid Cancer: Biomarkers and Lessons from The Cancer Genome Atlas.Dr. Giordano. ThyCa Conference - Video

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251pp osu! Daidai Genome [Insane] NC – Video

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251pp osu! Daidai Genome [Insane] NC
player https://osu.ppy.sh/u/3021716.

By: Res wery

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251pp osu! Daidai Genome [Insane] NC - Video

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STI Genome Subaru Legacy B4 2007 BL9 2.5i – Video

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STI Genome Subaru Legacy B4 2007 BL9 2.5i
STI Genome Subaru Legacy B4 2007 BL9 2.5i Subaru Legacy B4 BLE 3.0 . ...

By: Genome

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Breaking the Human Genome Code – Opening Pandora’s Box – Video

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Breaking the Human Genome Code - Opening Pandora #39;s Box
Recent technology advances have resulted in the ability to sequence anyone #39;s genome cheaply and quickly, but we are only just beginning the journey to discover the true meaning of our individual...

By: The University of Sheffield

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Genome Canada to create innovation network of 10 research centres

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Citing the need to keep up with a rapidly changing field of science, Canadas principal entity for supporting research in genomics is changing its approach.

On Tuesday, Genome Canada is expected to announce it will spend $15.5-million over the next two years to jump-start the creation of what it calls an innovation network by doling out funds to 10 research centres across the country. Matching funds from other public and private sources will bring the initial investment in the network to $31-million. In addition, the centres will compete with one another to divide a $15-million pot earmarked for technology development.

The funding replaces an earlier five-centre model and puts more emphasis on collaboration between centres to avoid building up silos that cannot talk to each other, said Genome Canada president Pierre Meulien.

The expanded network represents a pivot for the non-profit organization, which channels federal money toward the branch of science that deals with the decoding and analysis of DNA sequences.

When Genome Canada was established in February, 2000, the price tag for sequencing a single human genome was about $100-million. Since then, a revolution in sequencing technology has pushed the price down to just more than $1,000 per genome and the field is increasingly concerned with comparing genetic differences among populations (of humans and many other organisms).

To reflect the change, Dr. Meulien said that the new network will include substantial investments in Canadas capacity to do bioinformatics, which marries computing power with the reams of data now available as genetic sequences accumulate. Analysis of such data has already yielded important breakthroughs in identifying the causes of genetically inherited diseases and in spotting genetically based susceptibilities to more complex maladies such as cancer and diabetes.

Data generation is getting easier, but in the end you have to interpret and analyze all of that data, said Guillaume Borque, co-director of the Canadian Centre for Computational Genomics, a collaboration between McGill Univeristy and the University of Toronto and one of the new centres in the expanded network.

Other new centres that will be included for the first time under the Genome Canada funding umbrella demonstrate a broader trend in the field to link genes identified through sequencing to their biological functions and health implications. For example, the Toronto Centre of Phenogenomics, another of the nodes, specializes in creating strains of mice with specific genetic mutations. that can be used in the development of new approaches for disease.

Its the whole picture thats going to give rise to new treatments and diagnostics, said Dr. Meulien.

The new network amounts to a retooling of the countrys genomics infrastructure, he added, marking a shift from the era when Genome Canada was needed to ensure that Canadian scientists had access to an expensive but crucially important new technology for biomedical research. Now, the research that the organization funds has expanded beyond health, with applications in agriculture and environmental science, among other areas.

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Genome editing poses ethical problems that we cannot ignore

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14 hours ago by Anthony Wrigley And Ainsley Newson, The Conversation In the future, our DNA could be different by design. Credit: http://www.shutterstock.com

The ability to precisely and accurately change almost any part of any genome, even in complex species such as humans, may soon become a reality through genome editing. But with great power comes great responsibility and few subjects elicit such heated debates about moral rights and wrongs.

Although genetic engineering techniques have been around for some time, genome editing can achieve this with lower error rates, more simply and cheaply than ever although the technology is certainly not yet perfect.

Genome editing offers a greater degree of control and precision in how specific DNA sequences are changed. It could be used in basic science, for human health, or improvements to crops. There are a variety of techniques but clustered regularly inter-spaced short palindromic repeats, or CRISPR, is perhaps the foremost.

CRISPR has prompted recent calls for a genome editing moratorium from a group of concerned US academics. Because it is the easiest technique to set up and so could be quickly and widely adopted, the fear is that it may be put into use far too soon outstripping our understanding of its safety implications and preventing any opportunity to think about how such powerful tools should be controlled.

The ethics of genetics, revisited

Ethical concerns over genetic modification are not new, particularly when it comes to humans. While we don't think genome editing gives rise to any completely new ethical concerns, there is more to gene editing than just genetic modification.

First, there is no clear consensus as to whether genome editing is just an incremental step forward, or whether it represents a disruptive technology capable of overthrowing the current orthodoxy. If this is the case and it's a very real prospect then we will need to carefully consider genome editing's ethical implications, including whether current regulation is adequate.

Second, there are significant ethical concerns over the potential scope and scale of genome editing modifications. As more researchers use CRISPR to achieve more genome changes, the implications shift. Our consideration of a technology that is rarely used and then only in specific cases will differ from one that is widely used and put to all sorts of uses.

Should we reach this tipping point, we will have to revisit the conclusions of the first few decades of the genetic modification debate. Currently modifying plants, some animals, and non-inheritable cells in humans is allowed under strict controls. But modifications that alter the human germ-line are not allowed, with the exception of the recent decision in the UK to allow mitochondrial replacement.

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Long-lived lemurs could hold secret to human aging

Posted: at 10:44 pm

March 31, 2015

Jonas, the world's oldest known dwarf lemur, died this January just months shy of his 30th birthday. Duke researchers are using lemurs like Jonas to study the biology of aging. (Credit: Photo by David Haring, Duke Lemur Center)

Chuck Bednar for redOrbit.com @BednarChuck

Conventional wisdom indicates that larger species live longer than smaller ones, but lemurs are on notable exception to that rule, and researchers from Duke University believe that the secrets of their longevity could lead to new insights into the aging process.

In January, the worlds oldest known dwarf lemur, Jonas, passed away, and inspired Sarah Zehr and Marina Blanco of the Duke Lemur Center in Durham, North Carolina to analyze over 50 years worth of medical records pertaining to his species and three other types of lemurs.

Suspended animation, suspended life

Dwarf lemurs live two to three times longer than similar-sized animals, they explained, and the duo was searching for clues to help explain their longevity. They found that these hamster-sized creatures are actually capable of placing their bodies in suspended animation to prevent aging.

How long the animals live and how quickly they age directly correlates with the amount of time they spend in this state, which is known as torpor and is comparable to the standby or sleep mode feature found in many modern electronic devices. Lemurs that enter this state and put their body functions on hold can outlive those that dont by up to 10 years, the data revealed.

[STORY: Lemurs match scent to voice]

Jonas was one of the most extreme examples found in the study, the researchers said. While in the wild, he spent up to half the year in this state of deep hibernation. Most dwarf lemurs go into a semi-hibernation state for no more than three months in captivity, Zehr said, but that was still enough to give them added longevity.

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Dr. Nir Barzilai Presents Study on Longevity at DOROT

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New York, NY (PRWEB) March 31, 2015

On the evening of Monday, March 16th, DOROT, a nonprofit organization working to prevent social isolation among older adults in New York, hosted Dr. Nir Barzilai, the Director of the Institute for Aging Research at the Albert Einstein College of Medicine and the Director of the Glenn Center for the Biology of Human Aging and of the Nathan Shock Center of excellence in biology of aging. Dr. Barzilai spoke to a crowd of 65 DOROT supporters about his current study on the genetics of longevity and the biology of aging.

Dr. Barzilai is studying Ashkenazi Jews who are approaching or exceeding age 100, and their offspring, to identify genetic markers that may indicate or lead to longer lifespan. He opened his talk by pointing out that many illnesses that humans experience in their lives are experienced at old age, and so if one could eliminate the factor of aging, one could possibly eliminate those illnesses. He went on to explain that he does not want to stop aging, but he wants to increase the ability of individuals to age healthfully and well. Dr. Barzilai spoke of research participants who were siblings in their early 100s and had been partaking in risky behaviors (cigarette smoking, poor diet, etc.) for decades, but who had still experienced good quality of life at advanced age. He used these individuals as examples of how long lifespan could possibly be genetically linked. He also identified a number of other possible factors for longevity, including: shorter stature, heavier frame, hormones, and nutrition.

Guests asked thoughtful questions such as whether Dr. Barzilai had taken happiness into consideration, or whether the longevity genes were more predominant on maternal or paternal sides. After the talk, guests were able to individually ask the presenter more personal questions. Attendees were delighted at the opportunity. One guest said, The lecture by Dr. Barzilai was the best lecture I have ever heard on the aging process. I went up to him after his lecture and told him I was the son of a centenarian. He told me to contact him; I did and have been accepted into his current study! I am so excited to be part of a study that could improve the health of people as they age.

In addition to a thought-provoking lecture, guests got to meet one another and learn more about DOROT as well as about upcoming volunteer opportunities. One told us, The whole experience of the evening at DOROT was one of dignity and beauty! My wife and I plan to participate in some of your volunteer programs.

DOROT became connected to Dr. Barzilai through a volunteer who brought the study to the attention of Executive Director, Mark Meridy. Meridy met with Dr. Barzilai and agreed to help him find participants for his study, as both the doctor and DOROT have similar missions: to help older adults live well and independently long into advanced age.

It was an honor to host Dr. Barzilai at DOROT, Meridy said. Our guests found his talk engaging and thought-provoking, and we look forward to a continued relationship with him and the rest of the team at the Albert Einstein College of Medicine.

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