Monthly Archives: March 2017

Pushing the boundaries of DNA sequencing – Phys.Org

Posted: March 6, 2017 at 2:47 pm

March 6, 2017 Credit: University of New Mexico

A young company developing technology created at the University of New Mexico (UNM) is on a mission to disrupt the landscape of DNA sequencing.

Armonica Technologies, LLC, is developing a DNA sequencing platform that will sequence a complete human genome in minutes. The company's goal is to make the technology the gold standard for DNA sequencing for precision medicine research applications. Armonica has optioned a portfolio of patented and patent pending technologies from STC.UNM. The technology is called "optical nanopore sequencing" and uses nanochannels to deliver single DNA molecules through nanopores. Nanopores are very small holes with an internal diameter of 1 nanometer (one billionth of a meter). The nanopores slow down DNA translocation enough to produce massively parallel, single-base resolution using optical techniques.

Here's how nanopore sequencing works: when a nanopore is immersed in conducting fluid, voltage can be applied to produce an electric current. The current is sensitive to the size and shape of the nanopore so that if a DNA strand passes through or near the nanopore, the amount of current changes. The change in the current as the DNA molecule passes through the nanopore represents a reading of the DNA sequence.

"There is an unmet need in the fast-growing DNA sequencing market," said Armonica President & CEO Scott Goldman. "Today's standard genome sequencing approach requires extensive library preparation and creates a massive computational and bioinformatics problem related to reassembling the data set. Armonica will resolve these problems by introducing a sequencing instrument that will not require library preparation and will generate reads of up to 50,000 bases, combined with a parallelism of 1 million. This approach will net 50 billion basesmore than sufficient to sequence the entire human genome in minutes."

The innovative nanopore technology was developed by Distinguished Professor Emeritus Steve Brueck, Research Assistant Professor Yuliya Kuznetsova, and Postdoctoral Fellow Alexander Neumann from UNM's Center for High Technology Materials (CHTM) and Professor Jeremy Edwards from UNM's Department of Chemistry & Chemical Biology, in collaboration with Redondo Optics CEO Edgar Mendoza.

"Nanopore sequencing analyzes long DNA strings, with long reads that provide more accurate identification of genome variations," said Brueck. "It is an approach, therefore, that leads to a more thorough, faster, and accurate genomic analysis, allowing researchers to substantially improve the ability to make new discoveries. One of the challenges of nanopore sequencing is to improve the resolution to be able to detect single nucleotides (bases)."

"We believe our nanochannel technology will disrupt the industry because it produces very long reads for higher accuracy, very high parallelism using optical techniques, and high throughput rates for greater processing speed. It will be an affordable tool for researchers," said STC CEO Lisa Kuuttila. "This technology portfolio represents a leap in genomic sequencing technology that could be a huge benefit for the DNA sequencing industry, which is experiencing explosive growth. The company's research and development are currently being done at UNM's CHTM, a research center with a global reputation for inventing disruptive nanoscale technologies and providing outstanding scientific expertise and technical support. We are very excited about the technology's potential and believe in the company's vision."

Explore further: The gene sequencing that everyone can afford in future

DNA sequencing is important to science. While Professor Qian Linmao and his group from Tribology Research Institute, Southwest Jiaotong University, were working on the optimization of the third-generation sequencing technique ...

(Phys.org) U.K. based Oxford Nanopore Technologies has made good on a promise made two years ago to produce an inexpensive genome sequencer that is based on nanopore technology. David Jaffe, with the Broad Institute reported ...

Research published this week in Nature Nanotechnology shows a new method of enzyme-controlled movement of a single strand of DNA through a protein nanopore. The paper, by researchers at the University of California Santa ...

(Phys.org) High-speed reading of the genetic code should get a boost with the creation of the world's first graphene nanopores pores measuring approximately 2 nanometers in diameter that feature a "built-in" optical ...

Scientists at The University of Nottingham have demonstrated for the first time that it is possible to selectively sequence fragments of DNA in real time, greatly reducing the time needed to analyse biological samples.

In a future of personalized medicine, doctors may quickly glean the changes in the DNA sequences of patients that predispose them to specific diseases or determine the most appropriate therapeutic approach simply by analyzing ...

A small team of researchers with members from the University of California and the University of Michigan has found that some personality traits unique to a queen wasp are passed down to her offspring, the worker wasps. In ...

A new computational method can improve the accuracy of gene expression analyses, which are increasingly used to diagnose and monitor cancers and are a major tool for basic biological research.

Three species and three genera of birdeater spiders are described as new to science in a paper recently published in the open access journal ZooKeys. In their study, the Brazilian spider experts, Drs. Caroline Fukushima and ...

One of the unique and most iconic features of many modern turtles is that they can withdraw their neck and head to hide and protect them within their shells. The group name of species which do this, Cryptodira, even means ...

The scientists who uncovered why zebras have black and white stripes (to repel biting flies), took the coloration question to giant pandas in a study published this week in the journal Behavioral Ecology.

Research by the University of Southampton has found that methods used to predict the effect of species extinction on ecosystems could be producing inaccurate results. This is because current thinking assumes that when a species ...

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Pushing the boundaries of DNA sequencing - Phys.Org

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$300000 Parking Space Could Be Yours in Park Slope – DNAinfo

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The Park Slope Garage Condominium at 845 Union St., where a parking spot is on the market for $300,000. View Full Caption

DNAinfo/Leslie Albrecht

PARK SLOPE The hottest real estate in Brooklyn may be a closet-sized slab of concrete on Union Street.

A parking spot at the 845 Union St. parking garage is on the market for $300,000.

Like other condo properties, whoever buys the parking spot will have to pay monthly charges. In this case it's $240 in monthly maintenance fees, plus an extra$51 in monthly taxes.

But the monthly charges could be worth it if you sell the spot for a tidy profit in a few years. Just four years ago a spot in the same garage sold for a then eye-popping $80,000.

"Even though youre not going to be saving money monthly, its an asset thats increasing in value," said Constantine Valhouli, co-founder of the real estate analytics firm NeighborhoodX.

Parking garages are more in demand than ever as many have been converted to other uses, he said.

Valhouli likened the six-figure price tag for a parking spot to Brooklyn's rising real estate fortunes. The borough was once simply an affordable alternative to Manhattan but now attracts buyers seeking luxury housing.

"It shows how the market is maturing, where people are willing to pay an amount tagged to luxury and convenience rather than to yield," Valhouli said.

The $300,000 price tag is comparable to the asking prices for one-bedroom apartments for people, not vehicles in Rego Park, Spuyten Duyvil or Gravesend, according to a quick perusal of StreetEasy.

Garage owner Howard Pronsky of Berman Realty predicted in 2013 that prices for his parking spots would probably go up, in part because the parking garage directly across the street at 800 Union St. was being converted into condos and retail.

A 4-year-old boy was killed at the garage, which is also known by the address 841 Union St., in 2016 after falling down a 50-foot elevator shaft.

RELATED: Free Park Slope Parking up For Grabs in Lottery at Methodist Hospital

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Deep dive into dolphin genome may uncover drugs that protect human hearts, kidneys from damage – Genetic Literacy Project

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Dolphins and humans are very, very similar creatures, said NISTs Ben Neely, a member of the Marine Biochemical Sciences Group and the lead on a new project at the Hollings Marine Laboratory, a research facility in Charleston, South Carolina that includes the National Institute of Standards and Technology (NIST) as one of its partner institutions. As mammals, we share a number of proteins and our bodies function in many similar ways, even though we are terrestrial and dolphins live in the water all their lives.

Studies have recently revealed that lesser-known proteins in the blood of marine mammals may be playing a big role in the dives by protecting bottlenose dolphins kidneys and hearts from damage when blood flow and oxygen flow start and stop repeatedly during those underwater forays.

One of these proteins is known as vanin-1. Humans produce vanin-1, but in much smaller amounts. Researchers would like to gather more information on whether or not elevating levels of vanin-1 may offer protection to kidneys.

Theres this gap in the knowledge about genes and the proteins they make. We are missing a huge piece of the puzzle in how these animals do what they do, said Mike Janech from the Medical University of South Carolina. His group has been researching vanin-1 (link is external) and has identified numerous other potential biomedical applications for the dolphin genome just created by NIST.

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post:Diving deep into the dolphin genome could benefit human health

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OSU researchers sequence full beaver genome – The Daily Barometer

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Provides knowledge, information to help ecosystems and nature

A full beaver genome has been sequenced at Oregon State University using DNA derived from a beaver at the Oregon Zoo after a little more than a year of fundraising and work.

The Beaver Genome Project was first announced in September 2015, with a crowdfunding campaign launched in order to generate funds for the project. This crowdfunding project was led by Jeannine Cropley, assistant to the director of the Center for Genome Research and Biocomputing at OSU.

We were able to raise $20,000 from the crowdfunding project, Cropley said. These were all from small donations paying in increments of around $50 or $100, and there were no significantly large donors. We got the equivalent of the other $10,000 from a company, Illumina Inc. They donated all the sequencing parts needed for this project.

The crowdfunding project brought in a lot of publicity when the project was first introduced, which was necessary in order to raise enough funds for the project.

I think a lot of it is school pride, with alumni wanting to support their beaver and whatnot, Cropley said. But its also due to the fact that this project is pretty cool; the beaver genome could help with a lot of scientific research.

If it wasnt for the help of many of the younger participants of the Beaver Genome Project, the crowdfunding campaign wouldnt have reached out to the public as much as it did, according to Cropley. They were taught to use social media platforms, such as Twitter.

This beaver genome project was inspired by previous sequencing of genomes, including the well-known Human Genome Project, in which all the genes of human beings were completely mapped and understood. In the same way, the beaver genome was sequenced by collecting the complete set of DNA of a beaver. The goal is to uncover knowledge about beavers that could tie directly to helping ecosystems and nature, according to Brent Kronmiller, the bioinformatics scientist of CGRB.

There was a period of time when beavers were almost extinct due to people hunting (them) for their fur, but fortunately they were rehabilitated and are adapting back to normal, Kronmiller said. We really want to focus on a couple things, including how beavers are able to build dams, how they are a keystone species in terms of modifying ecosystems. Beavers can be a crucial part to learning more about survival within animals.

While the crowdfunding project went on from September through October 2015, there were many other components necessary to complete the overall project. The DNA was first derived from Filbert, a beaver at the Oregon Zoo.

There are many steps, Kronmiller said. First, we had to sequence the DNA and record the giga basepairs received from it. This didnt take that long, maybe a couple weeks. But then we also had to assemble a genome draft, collect RNA samples, which can take a while because we have to do many trials in order to be precise. Theres a whole process involved, and afterwards we have to create presentations and compile all the data together.

Other than the many involved in the crowdfunding campaign, there were also 20 others involved in the actual research and scientific investigations tied to the project. Adelaide Rhodes, an undergraduate researcher, represents one of the many.

Genomes are an extremely interesting topic to me, so being a part of this project is extremely fulfilling, Rhodes said. Although this project took a long time to complete, Ive learned so much from it, all the way from DNA sequencing to acquiring tissues. There were a lot of us part of this project, and I think we were all important in making this project complete.

The beaver genome project was finished by the beginning of January, and received its first accolades at the 25th annual Plant and Animal Genome Conference in San Diego.

This is a really big conference in which many, many genomic scientists gather around to talk about their findings in genome research, Kronmiller said. It was rewarding that we were able to be a part of it this year and provide our own presentations about the beaver species.

This project is special, not just because its the first beaver genome to be sequenced, according to Rhodes.

Oregon State University represents the first Pac-12 university to sequence their mascots genome, which is pretty cool, Rhodes said. Theres a lot of school spirit involved in this, and as we continue to research, more publicity will be coming along the way.

Now that the project is complete, scientists at Oregon State University can use the full genome to conduct research. Because the research is so new, many questions have yet to be answered.

All of our research is still pretty new, but essentially there are multitudes of things we can test using this new genome, Kronmiller said. Were looking for potential genes to see how the beaver adapts to its unique lifestyle. Were looking for relations between beavers and other animals and comparing their characteristics. Weve found that the kangaroo rat is most closely related to the beaver, out of the 19 species that we compared.

Because the DNA samples were collected from just one beaver, Filbert, there may be a few raw factors that are unaccounted for.

Im not too familiar with the specific characteristics and personality traits of Filbert, Rhodes said. But depending on what kind of traits Filbert may have, the genome may not represent all beavers the same way.

All of the completed research will be available online, according to Cropley.

Were not trying to make any money from this, Cropley said. There are websites and databases in which results from studies are posted, and theres one specifically for genomic research. These will all be made public and available for everyone to see.

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In Largest Whole Genome Sequence Analysis Study, Human Longevity, Inc.-Led Team Identifies Common-to-Rare … – PR Newswire (press release)

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The HLI-led team conducted whole genome analysis and comprehensive metabolite profiling on 1,960 adults, including 413 monozygotic twin pairs and 552 dizygotic twin pairs focusing on 644 specific blood metabolites. The study group had been seen in three clinical visits over an 18-year period. The team uncovered that 113 people or 10% of the 1,054 non-related people in the study, carried heterozygous rare variants that influence the function of 17 genes. Of these 17 genes 13 are associated with inborn metabolic errors and other pediatric genetic disorders.

The team concluded that these rare variants associated with abnormal blood metabolite profiles are higher than thought in adult populations and could be important factors in adult health. The researchers believe that much more research should be done to further examine the clinical consequences and significance of these rare variants.

Dr. Telenti stated, "The collection of small molecules and chemicals in blood called the metabolome reflect the intimate workings of our body. It was very surprising to us that so many adults would display abnormalities in blood metabolites, and that a high proportion would be the result of genetic defects. We believe the metabolome should be a continued area of research, and our findings today highlight the importance of looking holistically at the human body and all the components that factor into our health and potential for disease."

About Human Longevity, IncHuman Longevity, Inc. (HLI) is the genomic-based, health intelligence company empowering proactive healthcare and enabling a life better lived. HLI combines the largest database of genomic and phenotypic data with machine learning to drive discoveries and revolutionize the practice of medicine. HLI's business areas include the HLI Health Nucleus, a genomic powered clinical research center which uses whole genome sequence analysis, advanced clinical imaging and innovative machine learning, along with curated personal health information, to deliver the most complete picture of individual health; HLIQ Whole Genome and HLIQ Oncology. For more information, please visit http://www.humanlongevity.comor http://www.healthnucleus.com.

To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/in-largest-whole-genome-sequence-analysis-study-human-longevity-inc-led-team-identifies-common-to-rare-variants-in-the-human-blood-metabolome-300418556.html

SOURCE Human Longevity, Inc.

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Get ready to live 140 years; maybe even 1000! – Trade Arabia

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Scientists gathered in Abu Dhabi for a forum on human longevity said humans may live up to 140 years within the next two generations with one expert arguing that the first person to live 1,000 years is probably already born.

Speaking at the Aspen Abu Dhabi Ideas Forum, Dr Brad Perkins, chief medical officer, Human Longevity, said: Right now the most daunting and expensive human health problem that the world is facing is age related chronic disease. Our hypothesis at Human Longevity is that genomics and the technologies that support its application in medicine and drug discovery are going to be the next accelerant in extending a high performance human lifespan.

The two-day part private conference, part public festival aims to tackle some of the worlds largest moonshot challenges.

Dr Maha Barakat, director general, Health Authority Abu Dhabi, argued that the world is in a transition phase, and on the cusp of major improvements in medicine that will help people live longer.

Once we have gone through this phase and through this research we are hearing about, we will be heading towards a phase where we can live longer without disease. And that I would say is the Holy Grail. This is the utopian society that we are heading towards, where we can live much longer.

Speakers shared some of the current developments in medicine which will help to achieve this goal, such as regenerative medicine, which is already a reality.

Dr Anthony Atala, director of the Institute for Regenerative Medicine at Wake Forest University, spoke about strategies that exist to promote regeneration include using cells alone, using cells and scaffolds together for structural defects, alongside bio-printing to create human organoid microchips which can be used to test the effectiveness of drugs.

He said challenges exist surrounding cost, scale and regulation, but the goal is to keep bringing these technologies to more patients.

Dr Aubrey de Grey, a biomedical gerontologist based in Mountain View, California, US, and chief science officer of SENS Research Foundation, a California-based biomedical research charity that performs and funds laboratory research dedicated to combating the aging process, argued that the first person to live to 1,000 years is already probably alive today.

He further commented that fixing ageing is difficult, but not impossible and the only way in which people are going to stay alive a long time is by staying healthy a long time.

He further concluded: We won World War II and World War I. World War III hasnt happened yet. But World War 0 which we have been fighting against nature since the dawn of civilization is still there to be won.

The Aspen Abu Dhabi Ideas Forum is a collaboration between Tamkeen, a Government of Abu Dhabi-owned company, and the Aspen Institute, an educational and policy studies organisation based in the US.

The event was held in partnership with McKinsey & Company, the UAE Space Agency, Mohammed bin Rashid Space Centre, Health Authority Abu Dhabi, Cleveland Clinic Abu Dhabi, US-UAE Business Council, NYUAD, The National, Al Ittihad, DubaiEye and Park Hyatt Abu Dhabi Hotel and Villas. -TradeArabia News Service

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Decoding death: Craig Venter’s quest to uncover secret to immortality in our DNA – Genetic Literacy Project

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Craig Venter, the man in the late 1990s who, frustrated by the slow progress of the government-funded Human Genome Project, launched an effort that sequenced human DNA two years earlier than planned[is] back with his most ambitious project since his historic breakthrough 17 years ago. Hes raised $300 million from investors including Celgene and GE Ventures for a new firm, Human Longevity, thats trying to take the DNA information he helped unlock and figure out how to leverage it to cheat death for years, or even decades.

Craig Venter

With Human Longevity, Venter hopes to solve the problem that ultimately limited the efficacy of Celera and the Human Genome Project. Those two groups produced an average DNA sequence. Thats incredibly important for a science textbook, but for individuals, its the differenceshow one persons genes are different from anothers, leading to different noses, eye colors and, yes, diseasesthat matter.

Human Longevity initially sequenced DNA from 40,000 people who had participated in clinical trials for the pharmaceutical companies Roche and AstraZeneca. Venter says this work has led to the discovery of genetic variations that can be found in young people but not older onesmeaning the young folks had genes incompatible with surviving into old age. Figuring out what these genes do could be the kind of breakthrough that would turn the promise of genome sequencing into a lifesaver.

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post:Craig Venter Mapped The Genome. Now Hes Trying To Decode Death

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Intramuscular Flu Vaccination Recommended for Patients With Eczema – Infectious Disease Advisor (registration)

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Intramuscular Flu Vaccination Recommended for Patients With Eczema
Infectious Disease Advisor (registration)
Intramuscular rather than intradermal flu vaccination is preferred in patients with S aureus colonized atopic dermatitis. HealthDay News For patients with moderate/severe atopic dermatitis (AD), those colonized with Staphylococcus aureus have a ...

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Celgene’s Otezla successful in late-stage study in expanded psoriasis population – Seeking Alpha

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Results from a Phase 4 clinical trial, UNVEIL. evaluating Celgene's (CELG -0.6%) Otezla (apremilast) in patients with moderate plaque psoriasis with a body surface area of 5 - 10% showed a significant treatment benefit compared to placebo. The results were presented at the American Academy of Dermatology's Annual Meeting in Orlando, FL.

UNVEIL evaluated oral OTEZLA (30 mg twice daily) compared to placebo at week 16 in 221 subjects with moderate plaque psoriasis who had not been treated with systemic or biologic therapy. At baseline, 80% (n=177) had received topical therapy. The primary endpoint was the mean percent change from baseline in the product of PGA and BSA scores (two measures of psoriasis severity) at week 16.

The mean changes for the Otezla and placebo cohorts were -48.1% and -10.2%, respectively (p<0.0001). The proportions of patients who achieved at least a 75% improvement in symptoms were 35.1% and 12.3%, respectively (p<0.0001). The proportions of patients who achieved clear or almost clear skin were 30.4% and 9.6%, respectively (p<0.0001).

The most common treatment-relate adverse events were diarrhea (29%), headache (20%), nausea (18%), upper respiratory tract infection (7%) and vomiting (6%).

Otezla is currently approved to treat moderate-to-severe plaque psoriasis.

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3 breakthroughs that will change medicine – FierceHealthcare

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From brain implants to a map of human cells, the Massachusetts Institute of Technology is out with its annual list of 10 breakthrough technologies. And although its peppered with cool stuff like face-detecting tech that can authorize payments and 360-degree selfies, three healthcare breakthroughs made this years list.

Scientists are making remarkable progress at using brain implants to restore the freedom of movement that spinal cord injuries take away, according to the report.

In recent years, lab animals and a few people have controlled computer cursors or robotic arms with their thoughts, thanks to a brain implant wired to machines, the authors write. Now researchers are taking a significant next step toward reversing paralysis once and for all. They are wirelessly connecting the brain-reading technology directly to electrical stimulators on the body so that peoples thoughts can again move their limbs.

Researchers have been chasing the dream of gene therapy for decades. Until recently it had produced more disappointments than successes. But now, crucial puzzles have been solved and gene therapies are on the verge of curing devastating genetic disorders.

Fixing rare diseases, impressive in its own right, could be just the start, according to the article.

RELATED:Hype surrounds precision medicine, but significant challenges remain

The first comprehensive map of human cells should reveal, for the first time, what human bodies are made of, providing scientists with a sophisticated new model of biology that could speed the search for drugs, according to the article.

We will see some things that we expect, things we know to exist, but Im sure there will be completely novel things, Mike Stubbington, head of the cell atlas team at the Sanger Institute in the U.K., tells the publication. I think there will be surprises.

RELATED:C-suiters: Keep an eye on these technologies in 2017

Practical quantum computers, reinforcement learning and the botnet of things also made this years list. Connected devices in the home, an item of interest to healthcare organizations, are particularly vulnerable to hackers, the article notes. And that makes it easier than ever to build huge botnets that take down much more than one site at a time.

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