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Posts Tagged ‘reverse engineering’


Life-work in Engineering of Improved Heart Valve

Curator and Reporter: Larry H Bernstein, MD, FCAP

 

An authority and author of the book on cardiovascular valve devices is challenged by patient’s mother to go beyond what is available.  The results are splendid after re-engineering the design to the problem.

 

Reverse Engineering A Human Heart Valve

By Jim Pomager

aortic valve - a remarkable piece of biomechanical engineering

aortic valve – a remarkable piece of biomechanical engineering

 

 

 

The aortic valve is a remarkable piece of biomechanical engineering. On any given day, the leaflets (or cusps) of a healthy aortic valve will open and close 100,000+ times, allowing the proper amount of blood to flow from the heart to the rest of the body. Over a lifetime, a healthy valve endures more than 3.4 billion heartbeats.

Unfortunately, the aortic valve doesn’t always remain healthy. (What organ does?) According to the American Heart Association, up to 1.5 million people in the United States suffer from aortic stenosis (AS), a calcification of the aortic valve that narrows its opening and restricts blood flow. In the early stages, the disease is often asymptomatic, but as it progresses, it can cause chest pain, weakness, and difficulty breathing. And in approximately 300,000 people worldwide, the condition develops into severe AS, which has a one-year survival rate of approximately 50 percent, if left untreated.

Fortunately, there are treatment options.  The most common and successful is aortic valve replacement (AVR), wherein a mechanical or tissue-based valve is substituted for the diseased valve. For decades, replacement valves were implanted via open heart surgery, which involves an extended hospital stay and months of recovery. But in recent years, a promising new approach has emerged: transcatheter aortic valve implementation (TAVI), also known as transcatheter aortic valve replacement (TAVR). In TAVI, a tissue-based artificial valve is delivered into the diseased heart valve via a blood vessel, rather than through a large incision in the chest.

TAVI has many benefits, the most obvious (and compelling) of which is its noninvasiveness, which means shorter recovery times and faster attainment of quality-of-life outcomes for the patient. Replacement of a transcatheter aortic valve (TAV) can also be a minimally invasive exercise — a second TAV can simply be implanted within the first.

On the other hand, the use of TAVI procedures in U.S. hospitals is not yet widespread (though it is growing rapidly). The longevity of current-generation TAVs also remains unknown because it is an emerging technology, compared to evidence of 15+ years for surgically implanted heart valves. Plus, TAVI is only approved in the U.S. for use in AS patients who are either ineligible for surgical valve replacement or at high risk. (TAVI has been available in Europe since 2007, and clinical trials are underway in the U.S. for its use in intermediate-risk patients.)

What’s really needed is an improved TAV — one that outperforms current transcatheter valves, is as durable as a surgical valve, and operates more like … well, a healthy human aortic valve. Such a valve would open the door to TAVI’s use in the hundreds of thousands of lower-risk (and generally younger) AS patients whose only current option is a surgically implanted valve, and who would rather not have their chest opened.

Now, a man who has dedicated his professional career to studying the aortic valve has invented a new artificial valve design that he says will revolutionize TAVI. And if everything goes according to plan, his TAV will reach European patients in 2015 and U.S. patients soon after. How did he and his startup company design such technology? By reverse engineering the aortic valve.

The Man Behind The Valve

Mano Thubrikar

Mano Thubrikar

 

 

 

Mano Thubrikar, quite literally wrote the book on heart valves and heart disease — two of them, in fact. His The Aortic Valve (1989) and Vascular Mechanics and Pathology (2007) are leading textbooks in cardiovascular studies, and the former is widely used as a guide in the design of bioprosthetic heart valves.

After earning an undergraduate degree in metallurgy, a master’s in materials science, and a Ph.D. in biomedical engineering, Dr. Thubrikar spent the first 30 years of his career exclusively in academic research. He studied the aortic valve and bioprostheses from almost every conceivable angle while working at the University of Virginia (UVA) and at the Carolinas Medical Center and the University of North Carolina (UNC) at Charlotte.

But in 2003, Dr. Thubrikar received a phone call that would change the trajectory of his career and set him on the path to develop a novel TAV technology. A woman contacted him to discuss her son, a 35-year-old athlete with a calcified aortic valve. The condition was the result of a bicuspid valve, a congenital condition where the aortic valve has two cusps, rather than the customary three. The man needed a valve replacement, and his only choice was to have a mechanical heart valve surgically implanted. However, the surgical valve meant he would have to stay on anticoagulants for the rest of his life, effectively ending his athletic pursuits. Dr. Thubrikar informed the mother that there just weren’t any treatments available that would allow her son to continue his active lifestyle.

“Didn’t you write the book on the aortic valve?” she asked. “Why didn’t you make a valve that my son could use?”

The conversation and question deeply affected the researcher. “I went home and was so disturbed,” he told me during a recent visit to his office. “I talked to my wife and said, “You know what? Years of research, writing papers, and giving presentations — that’s done. I now need to make a heart valve.”

Soon after, Dr. Thubrikar left Carolinas Medical Center to embark on his new mission. He joined artificial heart valve pioneer Edwards Lifesciences as a Distinguished Scientist, but left after it became clear that the company’s plans for him didn’t align with his own.

So in 2007 — coincidentally, the same year Edwards launched the first commercially available TAV device — Dr. Thubrikar returned to academia, joining the staff at the South Dakota School of Mines & Technology. There he spent the next three years working on a new artificial valve design — one based on decades of research on the physics behind the human aortic valve.

Looking To The Human Body For Design Output
According to Dr. Thubrikar’s research, the natural aortic valve follows four strong design principles for maximum longevity and optimal hemodynamic performance. Those criteria are:

1. A specific coaptation height — When the valve’s three leaflets come together to close the valve, there is some surface-to-surface contact between the leaflets, rather than an edge-to-edge seal. This safety margin helps prevent against blood leakage back into the left ventricle.

2. No folds in the leaflets — Natural aortic valve cusps flex without folding. Folds would crease the tissue and cause unwanted stress on the leaflets, negatively impacting durability.

3. Minimum overall height — Extra height would produce dead space, which can lead to a variety of issues.

4. Minimum leaflet flexion — The human aortic valve manages to open completely with the leaflets moving only 70 degrees, not the 90 degrees you might expect. Again, this improves the valve’s longevity.

“You almost need to be a solid geometry design engineer to understand the math and the equations behind these principles,” he explained. “With these criteria, however, you have design parameters for the aortic valve. The mathematical equations give you the output of how an artificial valve should be designed.”

Dimensions of the natural aortic valve

Dimensions of the natural aortic valve

Dimensions of the natural aortic valve

 

 

Based on these four principles, Dr. Thubrikar reverse engineered the aortic heart valve, developing a new artificial valve design that mimics the aortic valve’s precise geometry. In October 2010, he launched a startup company called Thubrikar Aortic Valve, Inc. to commercialize his new creation, which he calls Optimum TAV and touts as “nature’s valve by design.”

“When someone asks me, ‘How does your valve compare with Edwards’?’ or ‘How does your valve compare with Medtronic’s?’, I say ‘We don’t compare our valve to them,'” Dr. Thubrikar told me. “We compare our valve with the natural aortic valve.”

On the surface, Optimum TAV looks similar to other artificial heart valves on the market, with three leaflets of bovine pericardium tissue mounted on a metal stent-frame. (In fact, the design is often mistaken for another widely used surgical valve.) But according to Dr. Thubrikar, it has a unique combination of features that will help it overcome the major design limitations of current-generation TAVs (if we’re going to compare). Those design limitations include:

  • Suture holes in the leaflet body — While all TAVs (including Optimum TAV) are constructed by sewing animal tissue to a metal frame, piercing the flexion zone of the leaflets leads to potential wear. Optimum TAV does not have a single suture hole in the working portion of the leaflet body.
  • Blood flow through frame — Some TAV frames are as tall as 5 cm in height, extending up into the aorta once implanted. As a result, blood must pass through the frame to enter the coronary arteries. Proteins in the blood will accumulate on the frame, and can eventually break loose and cause thromboembolisms (blood clots).  Optimum TAV is only 2 cm in height. (Related, the low height of the Thubrikar valve also makes it less likely to require a pacemaker.)
  • Thick outer frame — The thicker the frame, the smaller the valve opening will be, allowing less blood to pass through. This opening is referred to as the valve’s EOA, or effective orifice area. The average EOA of a surgical valve is around 1.9 cm2, and some TAVs have EOAs as small as 1.5 cm2(technically, a mild form of stenosis). In bench tests, Optimum TAV’s EOA was 2.3 to 2.4 cm2. (A healthy aortic valve has an EOA of approximately 2.7 cm2.)
  • Clipped calcified leaflets — Some current TAVs are anchored to the patient’s original valve using a paper-clip like mechanism. In this design, there is the potential that the TAVs leaflets will come into contact with the old, calcified leaflets during the operation, causing wear. Optimum TAV’s design eliminates the possibility of contact between the leaflets and native valve.
  • Paravalvular leakage — In some cases, a space forms between the outside of a TAV and the surrounding heart tissue, and blood can leak through. Optimum TAV has a high skirt to prevent this type of gap from developing. In addition, Optimum TAV’s novel frame architecture allows it to conform to and seal off either a round or elliptical annulus (the ring-shaped base of the original valve). This is particularly helpful in minimizing or eliminating leakage in bicuspid patients, who often have an irregularly shaped annulus.
  • Balloon expansion — TAV frames made of stainless steel must be forced open by a balloon. The TAV’s tissue can get caught between the balloon and the frame and potentially tear. Optimum TAV’s frame is made of nitinol, which automatically expands once deployed from the catheter.

 

optimum TAV

optimum TAV

 

 

Optimum TAV

“Other technologies have built-in issues,” Dr. Thubrikar said. “To be able to avoid those problems in a comprehensive fashion is no small feat.”

Trial By Fire
During the two and a half years following the establishment of Thubrikar Aortic Valve, Optimum TAV seemed to be moving steadily toward market. The company raised enough funding to get started, primarily from friends, family, physicians, entrepreneurs, and technology industry executives. Patent applications were filed, suppliers were selected, valves were painstakingly produced (by hand, over one-and-a-half to two days each), and preclinical testing began.

Members of the Thubrikar Aortic Valve team

Members of the Thubrikar Aortic Valve team

 

 

Members of the Thubrikar Aortic Valve team (left to right): Deodatt Wadke, member of the board of directors and cofounder; Samir Wadke, executive director of business development and cofounder; Dr. Mano Thubrikar, president and founder; Samuel Evans, research engineer II; and Nikhil Heble, counsel, secretary, and cofounder

But the fledgling company was dealt a major setback in April 2013, when a fire destroyed the Horsham, Pa. office building to which the Thubrikar Aortic Valve laboratory had recently relocated (from South Dakota). All of its equipment was destroyed and needed to be replaced. The company had to relocate to nearby Norristown, Pa. Not an ideal scenario for a startup trying to make the most of extremely limited resources.

The company was undeterred by the fire, and the last year has been a successful one for Thubrikar. The company completed most of its preclinical testing (including implants in 12 animals and two diseased human cadaver hearts), reached design freeze on Optimum TAV, filed a provisional patent application for its proprietary delivery catheter, and achieved almost $2 million in total funding. Perhaps the biggest milestone came in August 2013, when Optimum TAV met the International Organization for Standardization’s (ISO’s) durability requirements by surpassing 200 million cycles in a third-party ISO certified laboratory.

The durability testing has continued, and Optimum TAV continues to function beyond 390 million cycles, which approximates 11 years in vivo. Surgical valves typically last anywhere from 12 to 18 years, and Thubrikar expects his valve to last at least that long.

“I would not be surprised if it surpasses the longevity of even the surgical valve,” he said.

The company also received its first institutional investment, from Delaware Crossing Investor Group (DCIG), in 2014. The primary DCIG investor, Marv Woodall, led the commercialization of the world’s first stents as president of Johnson & Johnson Interventional Systems (now Cordis) and was on the board of director of the first TAV company, Percutaneous Valve Technologies (PVT, now part of Edwards Lifesciences). Thubrikar has recruited him as its business advisor.

What Lies Ahead
Like many other developers of novel medical devices, Thubrikar Aortic Valve has decided to take its product to market through Europe initially, given European regulators’ comfort level with TAV and the FDA’s steep requirement for clinical trials. “We have spoken to the FDA and will continue to do so on a regular basis,” according to Dr. Thubrikar. “But they asked for a lot more preclinical testing than the European Notified Bodies to start a clinical trial.”

The company is now working to raise an additional $2 million to $10 million, and expects the granting of its patent for Optimum TAV in 2014. The finances will enable Thubrikar to not only conduct a first-in-human (FIH) feasibility study in up to 15 patients this year, but also to expand to a full European clinical trial of about 65 additional patients in 2015. If all goes well, a 2015 CE Mark for Optimum TAV isn’t out of the question.

However, trial success is vital, since today’s investors — and large companies in search of technology acquisitions — wait for significant clinical data to accumulate before backing a medical device. “We realize that until we actually implant the valve in a patient, other companies will think, ‘You don’t know what can go wrong,'” Dr. Thubrikar explained. “We had one big company say, ‘We will pay you four times as much once the product is in a patient.’ They want you to de-risk everything, to work out all the bugs yourself on your own dime.”

Yet Dr. Thubrikar thinks its only a matter of time until his life’s work finally arrives in the hands of interventional cardiologists, who he said have been “knocking at his door” since he first presented a paper on the technology in 2012. Since then, he has spoken at several of the largest interventional cardiology conferences, and word continues to spread about Optimum TAV. Like many other researchers-turned-entreprenuers, he steadfastly believes that his invention will eventually reach the market, where it can begin helping patients — like the one whose mother contacted him a decade ago.

“If hell freezes over, if we don’t get any money, I don’t care,” he said. “I don’t care how it happens. We are going to make a heart valve. That’s the only mission in my life.”

For more information on Thubrikar Aortic Valve and Optimum TAV, visit http://tavi.us/.

 

 

 

 

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Summary of Translational Medicine – e-Series A: Cardiovascular Diseases, Volume Four – Part 1


Summary of Translational Medicine – e-Series A: Cardiovascular Diseases, Volume Four – Part 1

Author and Curator: Larry H Bernstein, MD, FCAP

and

Curator: Aviva Lev-Ari, PhD, RN

 

Part 1 of Volume 4 in the e-series A: Cardiovascular Diseases and Translational Medicine, provides a foundation for grasping a rapidly developing surging scientific endeavor that is transcending laboratory hypothesis testing and providing guidelines to:

  • Target genomes and multiple nucleotide sequences involved in either coding or in regulation that might have an impact on complex diseases, not necessarily genetic in nature.
  • Target signaling pathways that are demonstrably maladjusted, activated or suppressed in many common and complex diseases, or in their progression.
  • Enable a reduction in failure due to toxicities in the later stages of clinical drug trials as a result of this science-based understanding.
  • Enable a reduction in complications from the improvement of machanical devices that have already had an impact on the practice of interventional procedures in cardiology, cardiac surgery, and radiological imaging, as well as improving laboratory diagnostics at the molecular level.
  • Enable the discovery of new drugs in the continuing emergence of drug resistance.
  • Enable the construction of critical pathways and better guidelines for patient management based on population outcomes data, that will be critically dependent on computational methods and large data-bases.

What has been presented can be essentially viewed in the following Table:

 

Summary Table for TM - Part 1

Summary Table for TM – Part 1

 

 

 

There are some developments that deserve additional development:

1. The importance of mitochondrial function in the activity state of the mitochondria in cellular work (combustion) is understood, and impairments of function are identified in diseases of muscle, cardiac contraction, nerve conduction, ion transport, water balance, and the cytoskeleton – beyond the disordered metabolism in cancer.  A more detailed explanation of the energetics that was elucidated based on the electron transport chain might also be in order.

2. The processes that are enabling a more full application of technology to a host of problems in the environment we live in and in disease modification is growing rapidly, and will change the face of medicine and its allied health sciences.

 

Electron Transport and Bioenergetics

Deferred for metabolomics topic

Synthetic Biology

Introduction to Synthetic Biology and Metabolic Engineering

Kristala L. J. Prather: Part-1    <iBiology > iBioSeminars > Biophysics & Chemical Biology >

http://www.ibiology.org Lecturers generously donate their time to prepare these lectures. The project is funded by NSF and NIGMS, and is supported by the ASCB and HHMI.
Dr. Prather explains that synthetic biology involves applying engineering principles to biological systems to build “biological machines”.

Dr. Prather has received numerous awards both for her innovative research and for excellence in teaching.  Learn more about how Kris became a scientist at
Prather 1: Synthetic Biology and Metabolic Engineering  2/6/14IntroductionLecture Overview In the first part of her lecture, Dr. Prather explains that synthetic biology involves applying engineering principles to biological systems to build “biological machines”. The key material in building these machines is synthetic DNA. Synthetic DNA can be added in different combinations to biological hosts, such as bacteria, turning them into chemical factories that can produce small molecules of choice. In Part 2, Prather describes how her lab used design principles to engineer E. coli that produce glucaric acid from glucose. Glucaric acid is not naturally produced in bacteria, so Prather and her colleagues “bioprospected” enzymes from other organisms and expressed them in E. coli to build the needed enzymatic pathway. Prather walks us through the many steps of optimizing the timing, localization and levels of enzyme expression to produce the greatest yield. Speaker Bio: Kristala Jones Prather received her S.B. degree from the Massachusetts Institute of Technology and her PhD at the University of California, Berkeley both in chemical engineering. Upon graduation, Prather joined the Merck Research Labs for 4 years before returning to academia. Prather is now an Associate Professor of Chemical Engineering at MIT and an investigator with the multi-university Synthetic Biology Engineering Reseach Center (SynBERC). Her lab designs and constructs novel synthetic pathways in microorganisms converting them into tiny factories for the production of small molecules. Dr. Prather has received numerous awards both for her innovative research and for excellence in teaching.

VIEW VIDEOS

https://www.youtube.com/watch?feature=player_embedded&v=ndThuqVumAk#t=0

https://www.youtube.com/watch?feature=player_embedded&v=ndThuqVumAk#t=12

https://www.youtube.com/watch?feature=player_embedded&v=ndThuqVumAk#t=74

https://www.youtube.com/watch?feature=player_embedded&v=ndThuqVumAk#t=129

https://www.youtube.com/watch?feature=player_embedded&v=ndThuqVumAk#t=168

https://www.youtube.com/watch?feature=player_embedded&v=ndThuqVumAk

 

II. Regulatory Effects of Mammalian microRNAs

Calcium Cycling in Synthetic and Contractile Phasic or Tonic Vascular Smooth Muscle Cells

in INTECH
Current Basic and Pathological Approaches to
the Function of Muscle Cells and Tissues – From Molecules to HumansLarissa Lipskaia, Isabelle Limon, Regis Bobe and Roger Hajjar
Additional information is available at the end of the chapter
http://dx.doi.org/10.5772/48240
1. Introduction
Calcium ions (Ca ) are present in low concentrations in the cytosol (~100 nM) and in high concentrations (in mM range) in both the extracellular medium and intracellular stores (mainly sarco/endo/plasmic reticulum, SR). This differential allows the calcium ion messenger that carries information
as diverse as contraction, metabolism, apoptosis, proliferation and/or hypertrophic growth. The mechanisms responsible for generating a Ca signal greatly differ from one cell type to another.
In the different types of vascular smooth muscle cells (VSMC), enormous variations do exist with regard to the mechanisms responsible for generating Ca signal. In each VSMC phenotype (synthetic/proliferating and contractile [1], tonic or phasic), the Ca signaling system is adapted to its particular function and is due to the specific patterns of expression and regulation of Ca.
For instance, in contractile VSMCs, the initiation of contractile events is driven by mem- brane depolarization; and the principal entry-point for extracellular Ca is the voltage-operated L-type calcium channel (LTCC). In contrast, in synthetic/proliferating VSMCs, the principal way-in for extracellular Ca is the store-operated calcium (SOC) channel.
Whatever the cell type, the calcium signal consists of  limited elevations of cytosolic free calcium ions in time and space. The calcium pump, sarco/endoplasmic reticulum Ca ATPase (SERCA), has a critical role in determining the frequency of SR Ca release by upload into the sarcoplasmic
sensitivity of  SR calcium channels, Ryanodin Receptor, RyR and Inositol tri-Phosphate Receptor, IP3R.
Synthetic VSMCs have a fibroblast appearance, proliferate readily, and synthesize increased levels of various extracellular matrix components, particularly fibronectin, collagen types I and III, and tropoelastin [1].
Contractile VSMCs have a muscle-like or spindle-shaped appearance and well-developed contractile apparatus resulting from the expression and intracellular accumulation of thick and thin muscle filaments [1].
Schematic representation of Calcium Cycling in Contractile and Proliferating VSMCs

Schematic representation of Calcium Cycling in Contractile and Proliferating VSMCs

 

Figure 1. Schematic representation of Calcium Cycling in Contractile and Proliferating VSMCs.

Left panel: schematic representation of calcium cycling in quiescent /contractile VSMCs. Contractile re-sponse is initiated by extracellular Ca influx due to activation of Receptor Operated Ca (through phosphoinositol-coupled receptor) or to activation of L-Type Calcium channels (through an increase in luminal pressure). Small increase of cytosolic due IP3 binding to IP3R (puff) or RyR activation by LTCC or ROC-dependent Ca influx leads to large SR Ca IP3R or RyR clusters (“Ca -induced Ca SR calcium pumps (both SERCA2a and SERCA2b are expressed in quiescent VSMCs), maintaining high concentration of cytosolic Ca and setting the sensitivity of RyR or IP3R for the next spike.
Contraction of VSMCs occurs during oscillatory Ca transient.
Middle panel: schematic representa tion of atherosclerotic vessel wall. Contractile VSMC are located in the media layer, synthetic VSMC are located in sub-endothelial intima.
Right panel: schematic representation of calcium cycling in quiescent /contractile VSMCs. Agonist binding to phosphoinositol-coupled receptor leads to the activation of IP3R resulting in large increase in cytosolic Ca calcium pumps (only SERCA2b, having low turnover and low affinity to Ca depletion leads to translocation of SR Ca sensor STIM1 towards PM, resulting in extracellular Ca influx though opening of Store Operated Channel (CRAC). Resulted steady state Ca transient is critical for activation of proliferation-related transcription factors ‘NFAT).
Abbreviations: PLC – phospholipase C; PM – plasma membrane; PP2B – Ca /calmodulin-activated protein phosphatase 2B (calcineurin); ROC- receptor activated channel; IP3 – inositol-1,4,5-trisphosphate, IP3R – inositol-1,4,5- trisphosphate receptor; RyR – ryanodine receptor; NFAT – nuclear factor of activated T-lymphocytes; VSMC – vascular smooth muscle cells; SERCA – sarco(endo)plasmic reticulum Ca sarcoplasmic reticulum.

 

Time for New DNA Synthesis and Sequencing Cost Curves

By Rob Carlson

I’ll start with the productivity plot, as this one isn’t new. For a discussion of the substantial performance increase in sequencing compared to Moore’s Law, as well as the difficulty of finding this data, please see this post. If nothing else, keep two features of the plot in mind: 1) the consistency of the pace of Moore’s Law and 2) the inconsistency and pace of sequencing productivity. Illumina appears to be the primary driver, and beneficiary, of improvements in productivity at the moment, especially if you are looking at share prices. It looks like the recently announced NextSeq and Hiseq instruments will provide substantially higher productivities (hand waving, I would say the next datum will come in another order of magnitude higher), but I think I need a bit more data before officially putting another point on the plot.

 

cost-of-oligo-and-gene-synthesis

cost-of-oligo-and-gene-synthesis

Illumina’s instruments are now responsible for such a high percentage of sequencing output that the company is effectively setting prices for the entire industry. Illumina is being pushed by competition to increase performance, but this does not necessarily translate into lower prices. It doesn’t behoove Illumina to drop prices at this point, and we won’t see any substantial decrease until a serious competitor shows up and starts threatening Illumina’s market share. The absence of real competition is the primary reason sequencing prices have flattened out over the last couple of data points.

Note that the oligo prices above are for column-based synthesis, and that oligos synthesized on arrays are much less expensive. However, array synthesis comes with the usual caveat that the quality is generally lower, unless you are getting your DNA from Agilent, which probably means you are getting your dsDNA from Gen9.

Note also that the distinction between the price of oligos and the price of double-stranded sDNA is becoming less useful. Whether you are ordering from Life/Thermo or from your local academic facility, the cost of producing oligos is now, in most cases, independent of their length. That’s because the cost of capital (including rent, insurance, labor, etc) is now more significant than the cost of goods. Consequently, the price reflects the cost of capital rather than the cost of goods. Moreover, the cost of the columns, reagents, and shipping tubes is certainly more than the cost of the atoms in the sDNA you are ostensibly paying for. Once you get into longer oligos (substantially larger than 50-mers) this relationship breaks down and the sDNA is more expensive. But, at this point in time, most people aren’t going to use longer oligos to assemble genes unless they have a tricky job that doesn’t work using short oligos.

Looking forward, I suspect oligos aren’t going to get much cheaper unless someone sorts out how to either 1) replace the requisite human labor and thereby reduce the cost of capital, or 2) finally replace the phosphoramidite chemistry that the industry relies upon.

IDT’s gBlocks come at prices that are constant across quite substantial ranges in length. Moreover, part of the decrease in price for these products is embedded in the fact that you are buying smaller chunks of DNA that you then must assemble and integrate into your organism of choice.

Someone who has purchased and assembled an absolutely enormous amount of sDNA over the last decade, suggested that if prices fell by another order of magnitude, he could switch completely to outsourced assembly. This is a potentially interesting “tipping point”. However, what this person really needs is sDNA integrated in a particular way into a particular genome operating in a particular host. The integration and testing of the new genome in the host organism is where most of the cost is. Given the wide variety of emerging applications, and the growing array of hosts/chassis, it isn’t clear that any given technology or firm will be able to provide arbitrary synthetic sequences incorporated into arbitrary hosts.

 TrackBack URL: http://www.synthesis.cc/cgi-bin/mt/mt-t.cgi/397

 

Startup to Strengthen Synthetic Biology and Regenerative Medicine Industries with Cutting Edge Cell Products

28 Nov 2013 | PR Web

Dr. Jon Rowley and Dr. Uplaksh Kumar, Co-Founders of RoosterBio, Inc., a newly formed biotech startup located in Frederick, are paving the way for even more innovation in the rapidly growing fields of Synthetic Biology and Regenerative Medicine. Synthetic Biology combines engineering principles with basic science to build biological products, including regenerative medicines and cellular therapies. Regenerative medicine is a broad definition for innovative medical therapies that will enable the body to repair, replace, restore and regenerate damaged or diseased cells, tissues and organs. Regenerative therapies that are in clinical trials today may enable repair of damaged heart muscle following heart attack, replacement of skin for burn victims, restoration of movement after spinal cord injury, regeneration of pancreatic tissue for insulin production in diabetics and provide new treatments for Parkinson’s and Alzheimer’s diseases, to name just a few applications.

While the potential of the field is promising, the pace of development has been slow. One main reason for this is that the living cells required for these therapies are cost-prohibitive and not supplied at volumes that support many research and product development efforts. RoosterBio will manufacture large quantities of standardized primary cells at high quality and low cost, which will quicken the pace of scientific discovery and translation to the clinic. “Our goal is to accelerate the development of products that incorporate living cells by providing abundant, affordable and high quality materials to researchers that are developing and commercializing these regenerative technologies” says Dr. Rowley

 

Life at the Speed of Light

http://kcpw.org/?powerpress_pinw=92027-podcast

NHMU Lecture featuring – J. Craig Venter, Ph.D.
Founder, Chairman, and CEO – J. Craig Venter Institute; Co-Founder and CEO, Synthetic Genomics Inc.

J. Craig Venter, Ph.D., is Founder, Chairman, and CEO of the J. Craig Venter Institute (JVCI), a not-for-profit, research organization dedicated to human, microbial, plant, synthetic and environmental research. He is also Co-Founder and CEO of Synthetic Genomics Inc. (SGI), a privately-held company dedicated to commercializing genomic-driven solutions to address global needs.

In 1998, Dr. Venter founded Celera Genomics to sequence the human genome using new tools and techniques he and his team developed.  This research culminated with the February 2001 publication of the human genome in the journal, Science. Dr. Venter and his team at JVCI continue to blaze new trails in genomics.  They have sequenced and a created a bacterial cell constructed with synthetic DNA,  putting humankind at the threshold of a new phase of biological research.  Whereas, we could  previously read the genetic code (sequencing genomes), we can now write the genetic code for designing new species.

The science of synthetic genomics will have a profound impact on society, including new methods for chemical and energy production, human health and medical advances, clean water, and new food and nutritional products. One of the most prolific scientists of the 21st century for his numerous pioneering advances in genomics,  he  guides us through this emerging field, detailing its origins, current challenges, and the potential positive advances.

His work on synthetic biology truly embodies the theme of “pushing the boundaries of life.”  Essentially, Venter is seeking to “write the software of life” to create microbes designed by humans rather than only through evolution. The potential benefits and risks of this new technology are enormous. It also requires us to examine, both scientifically and philosophically, the question of “What is life?”

J Craig Venter wants to digitize DNA and transmit the signal to teleport organisms

https://pharmaceuticalintelligence.com/2013/11/01/j-craig-venter-wants-to-digitize-dna-and-transmit-the-signal-to-teleport-organisms/

2013 Genomics: The Era Beyond the Sequencing of the Human Genome: Francis Collins, Craig Venter, Eric Lander, et al.

https://pharmaceuticalintelligence.com/2013/02/11/2013-genomics-the-era-beyond-the-sequencing-human-genome-francis-collins-craig-venter-eric-lander-et-al/

Human Longevity Inc (HLI) – $70M in Financing of Venter’s New Integrative Omics and Clinical Bioinformatics

https://pharmaceuticalintelligence.com/2014/03/05/human-longevity-inc-hli-70m-in-financing-of-venters-new-integrative-omics-and-clinical-bioinformatics/

 

 

Where Will the Century of Biology Lead Us?

By Randall Mayes

A technology trend analyst offers an overview of synthetic biology, its potential applications, obstacles to its development, and prospects for public approval.

  • In addition to boosting the economy, synthetic biology projects currently in development could have profound implications for the future of manufacturing, sustainability, and medicine.
  • Before society can fully reap the benefits of synthetic biology, however, the field requires development and faces a series of hurdles in the process. Do researchers have the scientific know-how and technical capabilities to develop the field?

Biology + Engineering = Synthetic Biology

Bioengineers aim to build synthetic biological systems using compatible standardized parts that behave predictably. Bioengineers synthesize DNA parts—oligonucleotides composed of 50–100 base pairs—which make specialized components that ultimately make a biological system. As biology becomes a true engineering discipline, bioengineers will create genomes using mass-produced modular units similar to the microelectronics and computer industries.

Currently, bioengineering projects cost millions of dollars and take years to develop products. For synthetic biology to become a Schumpeterian revolution, smaller companies will need to be able to afford to use bioengineering concepts for industrial applications. This will require standardized and automated processes.

A major challenge to developing synthetic biology is the complexity of biological systems. When bioengineers assemble synthetic parts, they must prevent cross talk between signals in other biological pathways. Until researchers better understand these undesired interactions that nature has already worked out, applications such as gene therapy will have unwanted side effects. Scientists do not fully understand the effects of environmental and developmental interaction on gene expression. Currently, bioengineers must repeatedly use trial and error to create predictable systems.

Similar to physics, synthetic biology requires the ability to model systems and quantify relationships between variables in biological systems at the molecular level.

The second major challenge to ensuring the success of synthetic biology is the development of enabling technologies. With genomes having billions of nucleotides, this requires fast, powerful, and cost-efficient computers. Moore’s law, named for Intel co-founder Gordon Moore, posits that computing power progresses at a predictable rate and that the number of components in integrated circuits doubles each year until its limits are reached. Since Moore’s prediction, computer power has increased at an exponential rate while pricing has declined.

DNA sequencers and synthesizers are necessary to identify genes and make synthetic DNA sequences. Bioengineer Robert Carlson calculated that the capabilities of DNA sequencers and synthesizers have followed a pattern similar to computing. This pattern, referred to as the Carlson Curve, projects that scientists are approaching the ability to sequence a human genome for $1,000, perhaps in 2020. Carlson calculated that the costs of reading and writing new genes and genomes are falling by a factor of two every 18–24 months. (see recent Carlson comment on requirement to read and write for a variety of limiting  conditions).

Startup to Strengthen Synthetic Biology and Regenerative Medicine Industries with Cutting Edge Cell Products

https://pharmaceuticalintelligence.com/2013/11/28/startup-to-strengthen-synthetic-biology-and-regenerative-medicine-industries-with-cutting-edge-cell-products/

Synthetic Biology: On Advanced Genome Interpretation for Gene Variants and Pathways: What is the Genetic Base of Atherosclerosis and Loss of Arterial Elasticity with Aging

https://pharmaceuticalintelligence.com/2013/05/17/synthetic-biology-on-advanced-genome-interpretation-for-gene-variants-and-pathways-what-is-the-genetic-base-of-atherosclerosis-and-loss-of-arterial-elasticity-with-aging/

Synthesizing Synthetic Biology: PLOS Collections

https://pharmaceuticalintelligence.com/2012/08/17/synthesizing-synthetic-biology-plos-collections/

Capturing ten-color ultrasharp images of synthetic DNA structures resembling numerals 0 to 9

https://pharmaceuticalintelligence.com/2014/02/05/capturing-ten-color-ultrasharp-images-of-synthetic-dna-structures-resembling-numerals-0-to-9/

Silencing Cancers with Synthetic siRNAs

https://pharmaceuticalintelligence.com/2013/12/09/silencing-cancers-with-synthetic-sirnas/

Genomics Now—and Beyond the Bubble

Futurists have touted the twenty-first century as the century of biology based primarily on the promise of genomics. Medical researchers aim to use variations within genes as biomarkers for diseases, personalized treatments, and drug responses. Currently, we are experiencing a genomics bubble, but with advances in understanding biological complexity and the development of enabling technologies, synthetic biology is reviving optimism in many fields, particularly medicine.

BY MICHAEL BROOKS    17 APR, 2014     http://www.newstatesman.com/

Michael Brooks holds a PhD in quantum physics. He writes a weekly science column for the New Statesman, and his most recent book is The Secret Anarchy of Science.

The basic idea is that we take an organism – a bacterium, say – and re-engineer its genome so that it does something different. You might, for instance, make it ingest carbon dioxide from the atmosphere, process it and excrete crude oil.

That project is still under construction, but others, such as using synthesised DNA for data storage, have already been achieved. As evolution has proved, DNA is an extraordinarily stable medium that can preserve information for millions of years. In 2012, the Harvard geneticist George Church proved its potential by taking a book he had written, encoding it in a synthesised strand of DNA, and then making DNA sequencing machines read it back to him.

When we first started achieving such things it was costly and time-consuming and demanded extraordinary resources, such as those available to the millionaire biologist Craig Venter. Venter’s team spent most of the past two decades and tens of millions of dollars creating the first artificial organism, nicknamed “Synthia”. Using computer programs and robots that process the necessary chemicals, the team rebuilt the genome of the bacterium Mycoplasma mycoides from scratch. They also inserted a few watermarks and puzzles into the DNA sequence, partly as an identifying measure for safety’s sake, but mostly as a publicity stunt.

What they didn’t do was redesign the genome to do anything interesting. When the synthetic genome was inserted into an eviscerated bacterial cell, the new organism behaved exactly the same as its natural counterpart. Nevertheless, that Synthia, as Venter put it at the press conference to announce the research in 2010, was “the first self-replicating species we’ve had on the planet whose parent is a computer” made it a standout achievement.

Today, however, we have entered another era in synthetic biology and Venter faces stiff competition. The Steve Jobs to Venter’s Bill Gates is Jef Boeke, who researches yeast genetics at New York University.

Boeke wanted to redesign the yeast genome so that he could strip out various parts to see what they did. Because it took a private company a year to complete just a small part of the task, at a cost of $50,000, he realised he should go open-source. By teaching an undergraduate course on how to build a genome and teaming up with institutions all over the world, he has assembled a skilled workforce that, tinkering together, has made a synthetic chromosome for baker’s yeast.

 

Stepping into DIYbio and Synthetic Biology at ScienceHack

Posted April 22, 2014 by Heather McGaw and Kyrie Vala-Webb

We got a crash course on genetics and protein pathways, and then set out to design and build our own pathways using both the “Genomikon: Violacein Factory” kit and Synbiota platform. With Synbiota’s software, we dragged and dropped the enzymes to create the sequence that we were then going to build out. After a process of sketching ideas, mocking up pathways, and writing hypotheses, we were ready to start building!

The night stretched long, and at midnight we were forced to vacate the school. Not quite finished, we loaded our delicate bacteria, incubator, and boxes of gloves onto the bus and headed back to complete our bacterial transformation in one of our hotel rooms. Jammed in between the beds and the mini-fridge, we heat-shocked our bacteria in the hotel ice bucket. It was a surreal moment.

While waiting for our bacteria, we held an “unconference” where we explored bioethics, security and risk related to synthetic biology, 3D printing on Mars, patterns in juggling (with live demonstration!), and even did a Google Hangout with Rob Carlson. Every few hours, we would excitedly check in on our bacteria, looking for bacterial colonies and the purple hue characteristic of violacein.

Most impressive was the wildly successful and seamless integration of a diverse set of people: in a matter of hours, we were transformed from individual experts and practitioners in assorted fields into cohesive and passionate teams of DIY biologists and science hackers. The ability of everyone to connect and learn was a powerful experience, and over the course of just one weekend we were able to challenge each other and grow.

Returning to work on Monday, we were hungry for more. We wanted to find a way to bring the excitement and energy from the weekend into the studio and into the projects we’re working on. It struck us that there are strong parallels between design and DIYbio, and we knew there was an opportunity to bring some of the scientific approaches and curiosity into our studio.

 

 

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