Science Driving Value Creation Much of the science driving biotechnology is still in its earliest stages. We are only at the beginning of finding ways of apply it to medical advances leading to curing disease. Scientists are just scratching the surface in many areas of Hi-Tech medical science, for example researchers [...]
by Graham D. Hamblin,Janane F. Rahbani& Hanadi F. Sleiman
DNA strands of well-defined sequence are valuable in synthetic biology and nanostructure assembly. Drawing inspiration from solid-phase synthesis, here we describe a DNA assembly method that uses time, or order of addition, as a parameter to define structural complexity. DNA building blocks are sequentially added with in-situ ligation, then enzymatic enrichment and isolation. This yields a monodisperse, single-stranded long product (for example, 1,000 bases) with user-defined length and sequence pattern. The building blocks can be repeated with different order of addition, giving different DNA patterns. We organize DNA nanostructures and quantum dots using these backbones. Generally, only a small portion of a DNA structure needs to be addressable, while the rest is purely structural. Scaffolds with specifically placed unique sites in a repeating motif greatly minimize the number of components used, while maintaining addressability. This combination of symmetry and site-specific asymmetry within a DNA strand is easily accomplished with our method."
by Asaf Levy,Moran G. Goren,Ido Yosef,Oren Auster,Miriam Manor,Gil Amitai,Rotem Edgar, Udi Qimron& Rotem Sorek
"CRISPR–Cas (clustered, regularly interspaced short palindromic repeats coupled with CRISPR-associated proteins) is a bacterial immunity system that protects against invading phages or plasmids. In the process of CRISPR adaptation, short pieces of DNA (‘spacers’) are acquired from foreign elements and integrated into the CRISPR array. So far, it has remained a mystery how spacers are preferentially acquired from the foreign DNA while the self chromosome is avoided. Here we show that spacer acquisition is replication-dependent, and that DNA breaks formed at stalled replication forks promote spacer acquisition. Chromosomal hotspots of spacer acquisition were confined by Chi sites, which are sequence octamers highly enriched on the bacterial chromosome, suggesting that these sites limit spacer acquisition from self DNA. We further show that the avoidance of self is mediated by the RecBCD double-stranded DNA break repair complex. Our results suggest that, in Escherichia coli, acquisition of new spacers largely depends on RecBCD-mediated processing of double-stranded DNA breaks occurring primarily at replication forks, and that the preference for foreign DNA is achieved through the higher density of Chi sites on the self chromosome, in combination with the higher number of forks on the foreign DNA. This model explains the strong preference to acquire spacers both from high copy plasmids and from phages."
by Bogumil J. Karas,Rachel E. Diner,Stephane C. Lefebvre,Jeff McQuaid,Alex P.R. Phillips,Chari M. Noddings,John K. Brunson,Ruben E. Valas,Thomas J. Deerinck,Jelena Jablanovic,Jeroen T.F. Gillard,Karen Beeri,Mark H. Ellisman,John I. Glass,Clyde A. Hutchison III,Hamilton O. Smith,J. Craig Venter,Andrew E. Allen,Christopher L. Dupont& Philip D. Weyman
"Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify a yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research."
Recent advances in synthetic biology have provided tools to efficiently construct complex DNA molecules which are an important part of many molecular biology and biotechnology projects. The planning of such constructs has traditionally been done manually using a DNA sequence editor which becomes error-prone as scale and complexity of the construction increase. A human-readable formal description of cloning and assembly strategies, which also allows for automatic computer simulation and verification, would therefore be a valuable tool.
The iPhone could become a new tool in genetic studies.
Socrates Logos's insight:
A very interesting move in respect to personalized medicine. BTW I am working on such an app working in the iPhone, Apple watch environment. I use blockchain technology (Ethereum) to secure DNA data transfer. I will make the App in the first place only available in the US, as there are major legal problems in countries such as Germany. The German government does not trust a citizen to understand his/her medical DNA test results. So, according to the letter of the law: A person who sends his/her DNA to a DNA testing laboratory without the involvement of a Physician will be punished by 1 to 2 year in prison. http://www.gesetze-im-internet.de/gendg/index.html
"U.S. biotech startup BioBots sits at the intersection between computer science and chemistry. Its debut product, a desktop 3D printer for biomaterials, which was just demoed on stage at TechCrunch Disrupt NY — printing Van Gogh’s ear in replica, no less — combines hardware, software and wetware. It’s the latter area where the core innovation sits, says co-founder Danny Cabrera.
Biofabrication, the process of artificially building living tissue structures, is not a new field — there is more than a decade of research in this area already. But Cabrera and his co-founders believe they have spotted an opportunity to overhaul expensive (circa $100,000+), large, complex legacy devices — taking inspiration from the small, low-cost desktop 3D printers being used by the maker movement to extrude plastic.
Instead of plastic, BioBots’ 3D printer uses a special ink that can be combined with biomaterials and living cells to build 3D living tissue and miniature human organs. The use-case at this point is for research and pre-clinical screening, such as drug testing (as a replacement for animal testing). It’s not about 3D printing replacement organs from a person’s own cells — albeit developments in this area are heading (incrementally) in that direction. More near term future potential for the tech is to help foster bespoke disease therapies, according to Cabrera...."
*Chinese scientists genetically modify human embryos*
by David Cyranoski& Sara Reardon
"Rumours of germline modification prove true — and look set to reignite an ethical debate.
In a world first, Chinese scientists have reported editing the genomes of human embryos. The results are published1 in the online journal Protein & Cell and confirm widespread rumours that such experiments had been conducted—rumours that sparked a high-profile debate last month2, 3 about the ethical implications of such work.
In the paper, researchers led by Junjiu Huang, a gene-function researcher at Sun Yat-sen University in Guangzhou, tried to head off such concerns by using 'non-viable' embryos, which cannot result in a live birth, that were obtained from local fertility clinics. The team attempted to modify the gene responsible for β-thalassaemia, a potentially fatal blood disorder, using a gene-editing technique known as CRISPR/Cas9. The researchers say that their results reveal serious obstacles to using the method in medical applications.
"I believe this is the first report of CRISPR/Cas9 applied to human pre-implantation embryos and as such the study is a landmark, as well as a cautionary tale," says George Daley, a stem-cell biologist at Harvard Medical School in Boston. "Their study should be a stern warning to any practitioner who thinks the technology is ready for testing to eradicate disease genes.
Some say that gene editing in embryos could have a bright future because it could eradicate devastating genetic diseases before a baby is born. Others say that such work crosses an ethical line: researchers warned in Nature2 in March that because the genetic changes to embryos, known as germline modification, are heritable, they could have an unpredictable effect on future generations. Researchers have also expressed concerns that any gene-editing research on human embryos could be a slippery slope towards unsafe or unethical uses of the technique.
The paper by Huang's team looks set to reignite the debate on human-embryo editing — and there are reports that other groups in China are also experimenting on human embryos.
The technique used by Huang’s team involves injecting embryos with the enzyme complex CRISPR/Cas9, which binds and splices DNA at specific locations. The complex can be programmed to target a problematic gene, which is then replaced or repaired by another molecule introduced at the same time. The system is well studied in human adult cell and in animal embryos. But there had been no published reports of its use in human embryos.
Huang and his colleagues set out to see if the procedure could replace a gene in a single-cell fertilized human embryo; in principle, all cells produced as the embryo developed would then have the repaired gene. The embryos they obtained from the fertility clinics had been created for use in in vitro fertilization but had an extra set of chromosomes, following fertilization by two sperm. This prevents the embryos from resulting in a live birth, though they do undergo the first stages of development.
Huang’s group studied the ability of the CRISPR/Cas9 system to edit the gene called HBB, which encodes the human β-globin protein. Mutations in the gene are responsible for β-thalassaemia.
The team injected 86 embryos and then waited 48 hours, enough time for the CRISPR/Cas9 system and the molecules that replace the missing DNA to act — and for the embryos to grow to about eight cells each. Of the 71 embryos that survived, 54 were genetically tested. This revealed that just 28 were successfully spliced, and that only a fraction of those contained the replacement genetic material. “If you want to do it in normal embryos, you need to be close to 100%,” Huang says. “That’s why we stopped. We still think it’s too immature.”
His team also found a surprising number of ‘off-target’ mutations assumed to be introduced by the CRISPR/Cas9 complex acting on other parts of the genome. This effect is one of the main safety concerns surrounding germline gene editing because these unintended mutations could be harmful. The rates of such mutations were much higher than those observed in gene-editing studies of mouse embryos or human adult cells. And Huang notes that his team likely only detected a subset of the unintended mutations because their study looked only at a portion of the genome, known as the exome. “If we did the whole genome sequence, we would get many more,” he says.
Huang says that the paper was rejected by Nature and Science, in part because of ethical objections; both journals declined to comment on the claim (Nature’s news team is editorially independent of its research editorial team.)
He adds that critics of the paper have noted that the low efficiencies and high number of off-target mutations could be specific to the abnormal embryos used in the study. Huang acknowledges the critique, but because there are no examples of gene editing in normal embryos he says that there is no way to know if the technique operates differently in them.
Still, he maintains that the embryos allow for a more meaningful model — and one closer to a normal human embryo — than an animal model or one using adult human cells. “We wanted to show our data to the world so people know what really happened with this model, rather than just talking about what would happen without data,” he says.
But Edward Lanphier, one of the scientists who sounded the warning in Nature last month, says: "It underlines what we said before: we need to pause this research and make sure we have a broad based discussion about which direction we’re going here." Lanphier is president of Sangamo Biosciences in Richmond, California, which applies gene-editing techniques to adult human cells.
"At Advances in Genome Biology and Technology, a conference for genomic scientists held earlier this year, one speaker told attendees that the use of genome sequencing to improve patient care is no longer a far-off goal—it’s happening today. While you won’t encounter genome sequencing on an average visit to the ER, there are certain clinical areas where this technology has indeed become routine: cancer, pediatric care, the diagnosis and treatment of ultra rare diseases, and a few others.
During that same conference, other scientists and doctors recounted impressive cases, from leukemia patients whose cancer was accurately monitored with sequencing to epilepsy patients whose symptoms were successfully treated with a normally unrelated medication chosen because of DNA data. An infant with life-threatening liver failure was restored to health after emergency genome sequencing pinpointed the problem....."
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