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News Article | May 2, 2017
Site: news.yahoo.com

Last May a seemingly commonplace meeting kicked off a firestorm of controversy. More than 100 experts in genetics and bioengineering convened at Harvard Medical School for a meeting that was closed to the public — attendees were asked not to contact news media or to post about the meeting on social media. The same group is getting back together in New York City next week. To the meeting organizers, last year's secretive measures were, counterintuitively, to make sure as many people heard about the project as possible. They were submitting a paper about the project to a scientific journal and were discouraged from sharing the information publicly before it was published. But there's another reason why this group of scientists, while encouraging debate and public involvement, would be wary of attracting too much attention. Their project is an effort to synthesize DNA, including human DNA. Researchers will start with simpler organisms, such as microbes and plants, but hope to ultimately create strands of human genetic code. One of the group's organizers, Jef Boeke, director of the Institute for Systems Genetics at NYU School of Medicine, told CNBC that incorporating synthesized DNA into mammalian (or even human) cells could happen in four to five years. This project follows in the footsteps of the Human Genome Project (HGP), the 13-year, $2.7 billion project that enabled scientists to first decode the human genome. "HGP allowed us to read the genome, but we still don't completely understand it," said Nancy Kelley, the coordinator of the new effort, dubbed GP-write. High school biology covers the basic building blocks for DNA, called nucleotides — adenine (A), cytosine (C), guanine (G) and thymine (T). Humans' 3 billion pairs provide the blueprints for how to build our cells. The intention of GP-write is to provide a better fundamental understanding of how these pieces work together. Using synthesized genomes has both pragmatic and theoretical implications — it could lead to lower cost and higher quality of DNA synthesis, discoveries about DNA assembly in cells and the ability to test many DNA variations. "If you do that, you gain a much deeper understanding of how a complicated apparatus goes," Boeke said. Boeke likens the genome to a bicycle — you can only fully understand something once you take it apart and put it back together. "Really, a synthetic genome is an engine for learning new information." More from Modern Medicine: Medical breakthroughs are way behind for the hard of hearing In the land of Vikings, an ambitious effort to find a cancer cure New guidelines for prostate cancer screening Boeke is particularly excited about what he calls an "ultrasafe cell line." Certain types of mammalian cells intended to produce certain types of large molecule drugs, called biologics. "[Cell lines] have been cultured in dishes in labs for decades. But you can't engineer the genomes — the tools for doing that are quite crude, relatively speaking," Boeke said. Sometimes these cells get infected with a virus, and it completely shuts down drug production. A synthetic cell that lacked unnecessary genetic material could, evidence suggests, be virus-resistant, consistently producing useful drugs to treat disease. The results of GP-write could also lead to stem cell therapy that doesn't run the risk of infecting the patient with another disease, which appears to be what happened to one patient who received stem cell treatment in Mexico. Or they could create a line of microorganisms that could help humans generate some of their own amino acids — nutrients we usually get from food. These outcomes, of course, won't happen overnight. Boeke, who has spent years synthesizing yeast DNA, knows there will be plenty of technical hurdles. "Getting big pieces of DNA efficiently into mammalian cells, engineering them rapidly, these will be major challenges," he said. Scientists will also have to do that without breaking the bank. Right now, Kelley estimates that it costs 10 cents to synthesize every base pair, the bonded molecules that make up the double helix of DNA (start-up GenScript advertises even higher prices, at 23 cents for "economy"). Considering that humans have 3 billion base pairs. "If we can get that [cost] down to one cent per base pair, it would really make a difference," Kelley said. Since last May's meeting, Kelley, Boeke and their collaborators have published an article in Science about the project, as well as a white paper outlining its timeline. Close to 200 researchers and collaborators around the world have expressed interest in participating, Kelley says, ranging from institutional researchers to corporate scientists. Preliminary experiments are already underway, and the project organizers are discussing the project with companies as well as federal and state agencies that might help them reach their goal of raising $100 million this year. They estimate GP-write should cost less, in total, than the $3 billion Human Genome Project, though they have not provided more specific cost projections. It might not be so bad if these advances took some time. After news broke of the May meeting, some criticized the way the rollout was handled. "Given that human genome synthesis is a technology that can completely redefine the core of what now joins all of humanity together as a species, we argue that discussions of making such capacities real ... should not take place without open and advance consideration of whether it is morally right to proceed," read one op-ed, published in Cosmos. Boeke says a public and scientific discussion is exactly what the GP-write organizers intend to have. "I think articulation of our plan not to start right off synthesizing a full human genome tomorrow was helpful. We have a four- to five-year period where there can be plenty of time for debate about the wisdom of that, whether resources should be put in that direction or in another. Whenever it's human, everyone has an opinion and wants their voice to be heard. We want to hear what people have to say," Boeke said. Up to 250 people are expected at the New York Genome Center meeting, which will include discuss of applications, ethics and logistics behind the GP-write project. New technology that can help the 360 million people with hearing loss The race is on to stop a Zika virus epidemic in the US

Fritz D.,King Abdullah University of Science and Technology | Cai L.,GenScript INC. | Stefanovic L.,Florida State University | Stefanovic B.,Florida State University
Current Medicinal Chemistry | Year: 2011

Type I collagen is the most abundant protein in human body. Fibrosis is characterized by excessive synthesis of type I collagen in parenchymal organs. It is a leading cause of morbidity and mortality worldwide, about 45% of all natural deaths are attributable to some fibroproliferative disease. There is no cure for fibrosis. To find specific antifibrotic therapy targeting type I collagen, critical molecular interactions regulating its synthesis must be elucidated. Type I and type III collagen mRNAs have a unique sequence element at the 5' end, the 5' stem-loop. This stem-loop is not found in any other mRNA. We cloned LARP6 as the protein which binds collagen 5' stem-loop with high affinity and specificity. Mutation of the 5' stem-loop or knock down of LARP6 greatly diminishes collagen expression. Mice with mutation of the 5' stem-loop are resistant to development of liver fibrosis. LARP6 associates collagen mRNAs with filaments composed of nonmuscle myosin; disruption of these filaments abolishes synthesis of type I collagen. Thus, LARP6 dependent collagen synthesis is the specific mechanism of high collagen expression seen in fibrosis. We developed fluorescence polarization (FP) method to screen for drugs that can inhibit binding of LARP6 to 5' stem-loop RNA. FP is high when LARP6 is bound, but decreases to low levels when the binding is competed out. Thus, by measuring decrease in FP it is possible to identify chemical compounds that can dissociate LARP6 from the 5' stem-loop. The method is simple, fast and suitable for high throughput screening. © 2011 Bentham Science Publishers Ltd.

Liang G.,Molecular Therapeutics | Chen X.,Molecular Therapeutics | Aldous S.,Fibrosis and Wound Repair | Pu S.-F.,Global Pharmacovigilance and Epidemiology | And 11 more authors.
ACS Medicinal Chemistry Letters | Year: 2012

A series of compounds with an amidinothiophene P1 group and a pyrrolidinone-sulphonamide scaffold linker was identified as potent inhibitors of human kallikrein 6 by structure-based virtual screening based on the union accessible binding space of serine proteases. As the first series of potent nonmechanism-based hK6 inhibitors, they may be used as tool compounds for target validation. An X-ray structure of a representative compound complexed with hK6, resolved at a resolution of 1.88 Å, revealed that the amidinothiophene moiety bound in the S1 pocket and the pyrrolidinone-sulphonamide linker projected the aromatic tail into the S' pocket. © 2012 American Chemical Society.

Liang G.,Molecular Therapeutics | Chen X.,Molecular Therapeutics | Aldous S.,Sanofi S.A. | Pu S.-F.,Sanofi S.A. | And 5 more authors.
Bioorganic and Medicinal Chemistry Letters | Year: 2012

A series of hK6 inhibitors with a para-amidobenzylamine P1 group and a 2-hydroxybenzamide scaffold linker was discovered through virtual screening. The X-ray structure of hK6 complexed with compound 9b was determined to a resolution of 1.68 . The tertiary folding of the hK6 complexed with the inhibitor is conserved relative to the structure of the apo-protein, whereas the interaction between hK6 and the inhibitor is consistent with both the SAR and the in silico model used in the virtual screening. © 2011 Elsevier Ltd. All rights reserved.

Li J.,PharmaSeq, Inc. | Wang Z.,PharmaSeq, Inc. | Wang Z.,GenScript Corporation | Gryczynski I.,University of North Texas Health Science Center | Mandecki W.,PharmaSeq, Inc.
Analytical and Bioanalytical Chemistry | Year: 2010

The aim of this study is to improve assay sensitivity in common solid-phase bioassay configurations as the result of using silver nanoparticles. The solid phase was provided by numerically indexed, silicon-based electronic chips, microtransponders (p-Chips) that have previously been used in multiplexed assays. Assay configurations investigated included an ELISA-type immunoassay and a DNA hybridization assay. The surface of p-Chips was derivatized with the silver island film (SIF) and a polymer, and then characterized with AFM and SEM. Silver nanoparticle sizes were in the range of 100 to 200 nm. Four fluorophores were tested for fluorescence enhancement; namely, green fluorescent protein, phycoerythrin, Cy3 and Alexa Fluor 555. We consistently observed significant fluorescence enhancement and sensitivity improvement in the p-Chip-based assays: the sensitivity in the cytokine IL-6 immunoassay was 4.3 pg/ml, which represented a 25-fold increase over the method not involving a SIF; and 50 pM in the hybridization assay, a 38-fold increase. The greatest enhancement was obtained for p-Chip surfaces derivatized first with the polymer and then coated with SIF. In conclusion, we show that the SIF-p-Chip-based platform is a highly sensitive method to quantify low-abundance biomolecules in nucleic acid-based assays and immunoassays. © 2010 Springer-Verlag.

Kalwat M.A.,Indiana University | Wiseman D.A.,Indiana University | Luo W.,GenScript Corporation | Wang Z.,Indiana University | Thurmond D.C.,Indiana University
Molecular Endocrinology | Year: 2012

The plasma membrane soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) protein syntaxin (Syn)4 is required for biphasic insulin secretion, although how it regulates each phase remains unclear. In a screen to identify new Syn4-interacting factors, the calcium-activated F-actin-severing protein gelsolin was revealed. Gelsolin has been previously implicated as a positive effector of insulin secretion, although a molecular mechanism to underlie this function is lacking. Toward this, our in vitro binding studies showed the Syn4-gelsolin interaction to be direct and mediated by the N-terminal Ha domain (amino acid residues 39-70) of Syn4. Syn4-gelsolin complexes formed under basal conditions and dissociated upon acute glucose or KCl stimulation; nifedipine blocked dissociation. The dissociating action of secretagogues could be mimicked by expression of the N-terminal Ha domain of Syn4 fused to green fluorescent protein (GFP) (GFP-39-70). Furthermore, GFP-39-70 expression in isolated mouse islet and clonal MIN6 β-cells initiated insulin release in the absence of appropriate stimuli. Consistent with this, the inhibitory GFP-39-70 peptide also initiated Syn4 activation in the absence of stimuli. Moreover, although MIN6 β-cells expressing the GFP-39-70 peptide maintained normal calcium influx in response to KCl, KCl-stimulated insulin secretion and the triggering pathway of insulin secretion were significantly impaired. Taken together, these data support a mechanistic model for gelsolin's role in insulin exocytosis: gelsolin clamps unsolicited soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE)-regulated exocytosis through direct association with Syn4 in the absence of appropriate stimuli, which is relieved upon stimulus-induced calcium influx to activate gelsolin and induce its dissociation from Syn4 to facilitate insulin exocytosis. © 2012 by The Endocrine Society.

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