Scientists Have Figured out How Life Is Able to Survive


IN BRIEF
  • A new sequencing technique that maps out and analyzes DNA damage demonstrates how bacterial cells function in two critical excision repair proteins.
  • The team’s research and discovery not only heralds the use of this new mapping technique, it could also pave the way for a solution that will help address antibiotic resistance.

DNA-REPAIR SYSTEMS

Every day, the DNA in our cells gets damaged. This might sound scary, but it’s actually a normal occurrence – which makes DNA’s ability to repair itself vital to our survival. Now, scientists are beginning to better understand exactly how these repairs happen. A new sequencing technique that maps out and analyzes DNA damage demonstrates how bacterial cells function in two critical excision repair proteins: Mfd and UvrD.

The process, called nucleotide excision repair, has been used by a team from the UNC School of Medicine to gain a deeper insight into the key molecular functions of these repair systems, including the proteins’ roles in living cells. This repair process is known for fixing a common form of DNA damage called the “bulky adduct,” where a toxin or ultraviolet (UV) radiation chemically modifies the DNA.

The technique, called XR-seq lets the scientists isolate and sequence sections of DNA with the bulky adduct, thus allowing them to identify its actual locations in the genome. It has previously been used to generate a UV repair map of the human genome, as well as a map for the anticancer cisplatin drug.

For this study, scientists used the same method to repair damage caused by E. coli. As co-author of the study, Christopher P. Selby, PhD explained:

When the DNA of a bacterial gene is being transcribed into RNA, and the molecular machinery of transcription gets stuck at a bulky adduct, Mfd appears on the scene, recruits other repair proteins that snip away the damaged section of DNA, and “un-sticks” the transcription machinery so that it can resume its work. This Mfd-guided process is called transcription-coupled repair, and it accounts for a much higher rate of excision repair on strands of DNA that are being actively transcribed.

A POTENTIAL SOLUTION

f32e6aa3-7f8a-435f-b883-1a798e9616e3
Chris Selby, PhD; Aziz Sancar, MD, PhD; and Ogun Adebali, PhD

In further experiments, the researchers defined the role of an accessory excision repair protein in E. coli – UvrD, which helps clear away each excised segment of damaged DNA. Essentially, think of Mfd as the DNA “un-sticker” and UvrD as the “unwinder.” Using the XR-seq method, scientists discovered evidence of transcription-coupled repair in normal cells, but not in cells without Mfd—implying that the protein played a key role in its repair process.

The team’s research and discovery not only heralds the use of this new mapping technique, it could also pave the way for a solution that will help address the pressing, global threat of antibiotic resistance.

“If we fail to address this problem quickly and comprehensively, antimicrobial resistance will make providing high quality universal health coverage more difficult, if not impossible,” the UN Secretary-General Ban Ki-moon said. “[Antibiotic resistance] a fundamental, long-term threat to human health, sustainable food production and development.”

To support their current research, the team now plans to study XR-seq in bacterial, human and mammalian cells, to better understand the excision repair process.

Source:futurism.com

An Efficient Single-Nucleotide-Editing CRISPR


  • Since the discovery of the genome-editing tool CRISPR/Cas9, scientists have been looking to utilize the technology to make a significant impact on correcting genetic diseases. Technical challenges have made it difficult to use this method to correct disorders that are caused by single-nucleotide mutations, such as cystic fibrosis, sickle cell anemia, Huntington’s disease, and phenylketonuria. However now, researchers from the Center for Genome Engineering, within the Institute for Basic Science (IBS) in Korea, have just used a variation of CRISPR/Cas9 to produce mice with single-nucleotide differences. The findings from this new study were published recently in Nature Biotechnology in an article entitled “Highly Efficient RNA-Guided Base Editing in Mouse Embryos.”

    Comparison of the most used CRISPR system (top) vs. the newly developed editing tool (bottom). In some cases, the difference of just one nucleotide can bring serious disease consequences. Scientists hope to cure such diseases by substituting the incorrect nucleotide with the correct one.

    “Although genome editing with programmable nucleases such as CRISPR–Cas9 or Cpf1 systems holds promise for gene correction to repair genetic defects that cause genetic diseases, it is technically challenging to induce single-nucleotide substitutions in a targeted manner,” the authors wrote. “This is because most DNA double-strand breaks (DSBs) produced by programmable nucleases are repaired by error-prone non-homologous end-joining (NHEJ) rather than homologous recombination (HR) using a template donor DNA. As a result, insertion/deletions (indels) are obtained much more frequently at a nuclease target site than are single-nucleotide substitutions.”

    The most frequently used CRISPR/Cas9 technique works by cutting around the faulty nucleotide in both strands of the DNA and cuts out a small part of DNA. In the current study, the investigators used a variation of the Cas9 protein (nickase Cas9, or nCas9) fused with an enzyme called cytidine deaminase, which can substitute one nucleotide into another—generating single-nucleotide substitutions without DNA deletions.

  • Click Image To Enlarge +
    Example of how the IBS scientists created the single-nucleotide substituted mice using the new CRISPR system. [IBS]

    The IBS researchers were able to show the efficiency of the CRISPR–nCas9–cytidine deaminase fusion by generating mice that had changes to a single nucleotide in the dystrophin gene (Dmd) or the tyrosinase gene (Tyr). The research team provided evidence that embryos with the single-nucleotide mutation in the Dmd gene led to mice producing no dystrophin protein in their muscles; mice with the Tyr mutation showed albino traits. Mutations in the dystrophin are associated with muscular dystrophy, and tyrosinase controls the production of the skin pigment melanin. Moreover, these single-nucleotide substitutions appeared only in the target position. These results are important because they show that only the correct nucleotide was substituted.

    “We showed here for the first time that programmable deaminases efficiently induced base substitutions in animal embryos, producing mutant mice with disease phenotypes,” remarked senior study investigator Jin-Soo Kim, Ph.D., director of the Center for Genome Engineering at IBS. “This is a proof-of-principle experiment. The next goal is to correct a genetic defect in animals. Ultimately, this technique may allow gene correction in human embryos.”

CRISPR gene editing tech brings countless opportunities and challenges.


Dr. Thomas Doetschman, Ph.D., examines the embryonic cells used to study and implant mutated and disease genes; if the mutated gene successfully imbeds itself into a sperm or egg cell, the resulting rat that is born will be studied to research the effects of that same disease genes in humans. CRISPR CAS9 is technology that allows the splicing of genes to both remove and replace particular DNA strands. CRISPR can affect either just the patient or his descendants as well, depending on the technique used.

A new genome editing technology known as CRISPR has the potential to revolutionize the way scientists study diseases and genetics.

“I think it’s a really useful tool for science, in fact it’s sort of revolutionizing the speed at which we can accomplish certain things in the laboratory and it has tremendous potential for therapeutic applications,” said Kimberly McDermott, a research associate professor of medicine and an associate professor of cellular and molecular medicine, cancer biology and genetics.

Clustered Regularly Interspaced Short Palindromic Repeats, or CRISPR-Cas9, is based off a bacterial immune system, said Thomas Doetschman, professor of cancer biology, genetics and cellular and molecular medicine.

When bacteria become infected by a virus, they take pieces of the virus’s DNA and incorporate it into their own genome. This allows the bacteria to recognize and attack the virus if it ever appears again. This system allows them to destroy the virus, but it also allows them to destroy DNA, Doetschman said.

In developing CRISPR, scientists took a hint from the bacteria.

“What it [CRISPR] actually does is causes a mutation at that site, in the DNA, and then repairs it,” Doetschman said. “And you can repair it in different ways, such that you can actually modify the sequence of the DNA.”

This has enormous implications for the study of genetics and combating human diseases. And while it may sound exciting, human gene editing isn’t all fun and games.

There are two ways the CRISPR technology can be used in humans, Doetschman said. The first way is to alter somatic cells, which don’t get passed down to the next generation. This would only affect the patient who is receiving the treatment. The second way, known as the germline, can have serious long-lasting effects. Altering genes in the germline can produce permanent changes in the patient that will then be passed on to their children.

“There’s two completely different ways of doing this, and the real concern, the big concern, is that it be used by some unscrupulous people to try to change the germline of people, so that you can create progeny that will all have this kind of modification,” Doetschman said.

CRISPR isn’t just for humans; it can be used to edit plant cells as well.

“It could alter genes in a plant so that the plant either becomes resistant to or susceptible to agents that might otherwise kill the plant,” Doetschman said. This could mean disease-resistant plants or increased nutritional content.

One of CRISPR’s greatest contributions is in the realm of research, specifically for understanding normal development and disease processes, McDermott said.

For example, in the future scientists may be able to grow human organs from the patient’s own cells, using CRISPR.

Recent studies on mice and rats have introduced the possibility of using a model organism, such as a pig, to grow human organs, McDermott said.

Another exciting possibility available through CRISPR involves induced pluripotent stem cells, Doetschman said. This process essentially works as a time machine for your cells.

Doetschman describes it as the ability to put your own cells, such as skin cells, in culture and de-differentiate those cells back down to the pluripotent “master key” stem cell, using CRISPR. Once your adult cells are transformed into stem cells, you can make the genetic modifications you’d like, such as correcting a mutation, and then re-differentiate the cells back into the cell type of the tissue you want to correct.

These cells could potentially be engrafted  back into the patient’s disease tissue, Doetschman said.

Dr. Thomas Doetschman, Ph.D., describes a few of the many functions performed in the workspace pictured, which can effectively seal itself to create a sterile and airtight environment in which researchers can operate. CRISPR technology may redefine the future of genetics.

When it comes to working with human therapeutics, safety and regulations are extremely important, McDermott said.

As scientists, their primary concern is to minimize and prevent harm in every way possible. One of these regulations is a patent that was recently issued to the MIT and Harvard-affiliated Broad Institute, one of the centers responsible for creating CRISPR technology.

Despite heavy public controversy surrounding the patent, Doetschman said the patent is a good thing, because it will allow scientists to ensure that CRISPR research is carried out in a safe way, especially in regards to human use.

“I think from a scientist’s perspective, the thing that we’re really focusing on is trying to listen to our colleagues but also the public in general about what are the fears of this technology,” McDermott said. “Of course when you start to edit genes and mutate genes there’s a lot of concerns about what might happen.”

As for the future of human genetics research, both Doetschman and McDermott remain optimistic. CRISPR improves both the efficiency and the accuracy of genome research.

McDermott said while scientists may have had the ability to make mutations in cells in the past, the results were usually inefficient and could produce off-target effects.

CRISPR might not be the cure to every disease, but it is the key to unlock many avenues of research, Doetschman said.

“In terms of the research end of science and medical research, it’s expanding tremendously the scientist’s ability to ask questions about genetic disease,” Doetschman said.

What is CRISPR-Cas9?


CRISPR-Cas9 is a genome editing tool that is creating a buzz in the science world. It is faster, cheaper and more accurate than previous techniques of editing DNA and has a wide range of potential applications.

What is CRISPR-Cas9?

  • CRISPR-Cas9 is a unique technology that enables geneticists and medical researchers to edit parts of the genome? by removing, adding or altering sections of the DNA? sequence.
  • It is currently the simplest, most versatile and precise method of genetic manipulation and is therefore causing a buzz in the science world.

How does it work?

  • The CRISPR-Cas9 system consists of two key molecules that introduce a change (mutation?) into the DNA. These are:
    • an enzyme? called Cas9. This acts as a pair of ‘molecular scissors’ that can cut the two strands of DNA at a specific location in the genome so that bits of DNA can then be added or removed.
    • a piece of RNA? called  guide RNA (gRNA). This consists of a small piece of pre-designed RNA sequence (about 20 bases long) located within a longer RNA scaffold. The scaffold part binds to DNA and the pre-designed sequence ‘guides’ Cas9 to the right part of the genome. This makes sure that the Cas9 enzyme cuts at the right point in the genome.
  • The guide RNA is designed to find and bind to a specific sequence in the DNA. The guide RNA has RNA bases? that are complementary? to those of the target DNA sequence in the genome. This means that, at least in theory, the guide RNA will only bind to the target sequence and no other regions of the genome.
  • The Cas9 follows the guide RNA to the same location in the DNA sequence and makes a cut across both strands of the DNA.
  • At this stage the cell? recognises that the DNA is damaged and tries to repair it.
  • Scientists can use the DNA repair machinery to introduce changes to one or more genes? in the genome of a cell of interest.

Diagram showing how the CRISPR-Cas9 editing tool works.

How was it developed?

  • Some bacteria? have a similar, built-in, gene editing system to the CRISPR-Cas9 system that they use to respond to invading pathogens? like viruses,? much like an immune system.
  • Using CRISPR the bacteria snip out parts of the virus DNA and keep a bit of it behind to help them recognise and defend against the virus next time it attacks.
  • Scientists adapted this system so that it could be used in other cells from animals, including mice and humans.

What other techniques are there for altering genes?

  • Over the years scientists have learned about genetics? and gene function by studying the effects of changes in DNA.
  • If you can create a change in a gene, either in a cell line or a whole organism, it is possible to then study the effect of that change to understand what the function of that gene is.
  • For a long time geneticists used chemicals or radiation to cause mutations. However, they had no way of controlling where in the genome the mutation would occur.
  • For several years scientists have been using ‘gene targeting’ to introduce changes in specific places in the genome, by removing or adding either whole genes or single bases.
  • Traditional gene targeting has been very valuable for studying genes and genetics, however it takes a long time to create a mutation and is fairly expensive.
  • Several ‘gene editing’ technologies have recently been developed to improve gene targeting methods, including CRISPR-Cas systems, transcription activator-like effector nucleases (TALENs) and zinc-finger nucleases (ZFNs).
  • The CRISPR-Cas9 system currently stands out as the fastest, cheapest and most reliable system for ‘editing’ genes.

What are the applications and implications?

  • CRISPR-Cas9 has a lot of potential as a tool for treating a range of medical conditions that have a genetic component, including cancer?, hepatitis B or even high cholesterol.
  • Many of the proposed applications involve editing the genomes of somatic? (non-reproductive) cells but there has been a lot of interest in and debate about the potential to edit germline?(reproductive) cells.
  • Because any changes made in germline cells will be passed on from generation to generation it has important ethical implications.
  • Carrying out gene editing in germline cells is currently illegal in the UK and most other countries.
  • By contrast, the use of CRISPR-Cas9 and other gene editing technologies in somatic cells is uncontroversial. Indeed they have already been used to treat human disease on a small number of exceptional and/or life-threatening cases.

A sperm and egg cell. Carrying out gene editing in germline cells is currently illegal in the UK.

What’s the future of CRISPR-Cas9?

  • It is likely to be many years before CRISPR-Cas9 is used routinely in humans.
  • Much research is still focusing on its use in animal models or isolated human cells, with the aim to eventually use the technology to routinely treat diseases in humans.
  • There is a lot of work focusing on eliminating ‘off-target’ effects, where the CRISPR-Cas9 system cuts at a different gene to the one that was intended to be edited.

Better targeting of CRISPR-Cas9

  • In most cases the guide RNA consists of a specific sequence of 20 bases. These are complementary to the target sequence in the gene to be edited. However, not all 20 bases need to match for the guide RNA to be able to bind.
  • The problem with this is that a sequence with, for example, 19 of the 20 complementary bases may exist somewhere completely different in the genome. This means there is potential for the guide RNA to bind there instead of or as well as at the target sequence.
  • The Cas9 enzyme will then cut at the wrong site and end up introducing a mutation in the wrong location. While this mutation may not matter at all to the individual, it could affect a crucial gene or another important part of the genome.
  • Scientists are keen to find a way to ensure that the CRISPR-Cas9 binds and cuts accurately. Two ways this may be achieved are through:
    • the design of better, more specific guide RNAs using our knowledge of the DNA sequence of the genome and the ‘off-target’ behaviour of different versions of the Cas9-gRNA complex.
    • the use of a Cas9 enzyme that will only cut a single strand of the target DNA rather than the double strand. This means that two Cas9 enzymes and two guide RNAs have to be in the same place for the cut to be made. This reduces the probability of the cut being made in the wrong place.

Cystic fibrosis, sickle-cell anemia could be corrected in embryos with new CRISPR variant.


Since the discovery of the genome-editing tool CRISPR/Cas9, scientists have been looking to utilize the technology to make a significant impact on correcting genetic diseases. Technical challenges have made it difficult to use this method to correct disorders that are caused by single-nucleotide mutations, such as cystic fibrosis, sickle-cell anemia, Huntington’s disease, and phenylketonuria. … [Researchers] have just used a variation of CRISPR/Cas9 to produce mice with single-nucleotide differences. The findings from this new study were published recently in Nature Biotechnology in an article entitled “Highly Efficient RNA-Guided Base Editing in Mouse Embryos.

The most frequently used CRISPR/Cas9 technique works by cutting around the faulty nucleotide in both strands of the DNA and cuts out a small part of DNA. In the current study, the investigators used a variation of the Cas9 protein (nickase Cas9, or nCas9) fused with an enzyme called cytidine deaminase, which can substitute one nucleotide into another—generating single-nucleotide substitutions without DNA deletions

“The next goal is to correct a genetic defect in animals. Ultimately, this technique may allow gene correction in human embryos,” [remarked senior study investigator Jin-Soo Kim].

HIV Can Mutate to Evade Attempts To Modify It With CRISPR Gene Editing


IN BRIEF

HIV can defeat efforts to cripple it with CRISPR gene editing technology, researchers say. And the very act of editing – involving snipping at the virus’s genome – may introduce mutations that help it resist attack.

There’s a negative side to the news that a second team of scientists successfully modified human embryos, making them HIV-resistant. The team was able to modify some but not all embryos in the study. And it seems that HIV can actually defeat our efforts to cripple it with CRISPR gene-editing technology.

Ultimately, it seems that CRISPR itself may introduce mutations that help HIV resist attack; however, the team behind the work thinks that these problems may be surmountable.

RESISTING ATTACK

When HIV infects a T cell, its genome is inserted into the cell’s DNA, and it hijacks its DNA-replicating machinery to churn out more copies of the virus. But a T cell equipped with a DNA-shearing enzyme called Cas9 can find, cut, and cripple the invader’s genome.

That method did seem to work, at least for a short period of time, when a team led by virologist Chen Liang, at McGill University in Montreal, Canada, infected T cells that had been given the tools to stop HIV. But two weeks later, Liang’s group saw that the T cells were pumping out copies of virus particles that had escaped the CRISPR attack.

Liang’s team believes that the mutations occurred when Cas9 cut the viral DNA. When DNA is cut, its host cell tries to repair the break; in doing so, it sometimes introduces or deletes DNA letters. These ‘indels’ usually inactivate the gene that was cut — which is how CRISPR works. But sometimes this doesn’t happen.

Occasionally, Liang thinks, some of the indels made by the T cell’s machinery leave the genome of the invading HIV able to replicate and infect other cells. And worse, the change in sequence means the virus can’t be recognized and targeted by T cells with the same machinery. This means it becomes resistant to any future attack.

ALTERING HUMAN GENES

Liang thinks that the challenges seen in this study can be overcome. He suggests inactivating several essential HIV genes at once, or using CRISPR in combination with HIV-attacking drugs. Gene editing therapies that make T cells resistant to HIV invasion (by altering human, not viral, genes) would also be harder for the virus to combat.

A clinical trial is under way to test this approach using another gene-editing tool, zinc-finger nucleases.

The First Results of Gene Editing in Normal Embryos Have Been Released


Viable Editing

One of the most fascinating and promising developments in genetics is the CRISPR genome editing technique. Basically, CRISPR is a mechanism by which geneticists can treat disease by either disrupting genetic code by splicing in a mutation or repairing genes by splicing out mutations and replacing them with healthy code.

Researchers in China at the Third Affiliated Hospital of Guangzhou Medical University have successfully edited genetic mutations in viable human embryos for the first time. Typically, to avoid ethical concerns, researchers opt to use non-viable embryos that could not possibly develop into a child.

*5* Researchers Release Successful Results of First Genetic Edit of Viable Embryos

Previous research using these non-viable embryos has not produced promising results. The very first attempt to repair genes in any human embryos used these abnormal embryos. The study ended with abysmal results, with fewer than ten percent of cells being repaired. Another study published last year also had a low rate of success, showing that the technique still has a long way to go before becoming a reliable medical tool.

However, after experiencing similar results with using the abnormal embryos again, the scientists decided to see if they would fare better with viable embryos. The team collected immature eggs from donors undergoing IVF treatment. Under normal circumstances, these cells would be discarded, as they are less likely to successfully develop. The eggs were matured and fertilized with sperm from men carrying hereditary diseases.

Disease Sniper

While the results of this round of study were not perfect, they were much more promising than the previous studies done with the non-viable embryos. The team used six embryos, three of which had the mutation that causes favism (a disease leading to red blood cell breakdown in response to certain stimuli), and the other three had the mutation that results in a blood disease called beta-thalassemia.

The researchers were able to correct two of the favism embryos. In the other, the mutation was turned off, as not all of the cells were corrected. This means that the mutation was effectively shut down, but not eliminated. It created what is called a mosaic. In the other set, the mutation was fully corrected in one of the embryos and only some cells were corrected in the other two.

These results are not perfect, but experts still do find potential in them. “It does look more promising than previous papers,” says Fredrik Lanner of the Karolinska Institute. However, they do understand that results from a test of only six embryos are far from definitive.

Gene editing with CRISPR truly has the possibility to revolutionize medicine. Just looking at the development in terms of disease treatment, and not the other more ethically murky possible applications, it is an extremely exciting achievement.

Not only could CRISPR help eradicate hereditary disease, but it is also a tool that could help fight against diseases like malaria. There is a long road ahead for both the scientific and ethical aspects of the tech. Still, the possible benefits are too great to give up now.

CRISPR Gene Editing Has Repaired a Blood-Borne Disease


IN BRIEF
  • Researchers from Stanford have used the CRISPR-Cas9 gene editing technique to fix the gene defects that cause sickle cell disease.
  • Approximately 70,000 – 100,000 individuals in the United States have sickle cell disease and 3 million have sickle cell trait.

GENE THERAPY

Gene editing remains a widely controversial topic due to the large potential for both benefit and “accidents.” Despite this, scientists are still hard at work developing gene edits that can solve a wide variety of diseases.

A new study may have found the key to solving a painful, and potentially fatal, genetic defect. Researchers from Stanford used the CRISPR-Cas9 gene editing technique to fix the gene defects that cause sickle cell disease.

Sickle cell disease is actually a group of related diseases that cause the formation of hemoglobin S, or sickle-shaped hemoglobin. That shape results in red blood cells becoming tangled in each other. Enough tangling, and blood vessels could be blocked, causing pain and even death.

To correct the issue, one has to repair the genes that code for abnormal hemoglobin. Using CRISPR, the researchers were able to do this. They took hematopoietic stem cells from patients that have the disease and edited them to repair their genome.

After, the repaired stem cells are concentrated and injected to healthy mice. Once there, the stem cells find their way into bone marrow and start producing more of their healthy variants. Sixteen weeks after injection, the researchers found healthy red blood cells thriving in the bone marrow.

ONE OF MANY

This is just one of the increasing number of diseases that have met their match thanks to CRISPR. The gene editing technique is composed of an enzyme that can splice DNA sequences and guide RNA that take them to the specific sequences that need splicing.

“There’s already a lot of active research going on using the CRISPR technology to fix diseases like Duchenne muscular dystrophy or cystic fibrosis or Huntington’s disease,” says Jennifer Doudna, a pioneer of the technology, to CNBC.

But even if ways to cure using CRISPR are abound, researchers are treading lightly on implementation, since editing genes is risky and can have disastrous consequences. Ultimately, we will need to have a serious debate on how to go about the changing the very blueprint of our bodies.

A CRISPR first: editing normal human embryos.


In the first ever report of the CRISPR-Cas9 genome-editing tool being used on normal human embryos, a team of Chinese scientists had mixed results, New Scientist writes. The team first created embryos with genetic mutations that caused two different diseases: β-thalassemia and favism (an anemia caused by eating fava beans). When they tried correcting the mutations using CRISPR-Cas9, their success rate was one in four for β-thalassemia and two in two for favism, they report this month in Molecular Genetics and Genomics. That’s better than the 10% success rate for genetically abnormal embryos, but far more work needs to be done before the technique is ready for prime time, say other scientists.

CRISPR debate fueled by publication of second human embryo–editing paper

Synthetic Yeast Genome A Step Closer To Reality.


Colored scanning electron micrograph of baker’s yeast, conventionally grown in the lab. So far, researchers have been able to synthesize six of the yeast’s 16 chromosomes from scratch, and think they may be able to complete all 16 by 2018.

Scientists have taken another important step toward creating different types of synthetic life in the laboratory.

An international research consortium reports Thursday that it has figured out an efficient method for synthesizing a substantial part of the genetic code of yeast.

“We are absolutely thrilled,” says Jef Boeke, a geneticist at New York University School of Medicine, who is leading the project. “This is a significant step toward our goal.”

The milestone is the latest development in the intensifying quest to create living, complex organisms from scratch in the lab. This group previously reported it had completely synthesized one of yeast’s 16 chromosomes, which are the molecular structures that carry all of an organism’s genes.

Now, in a series of seven papers published in the journal Science, the group reports it has completed five more, and is on track to having a fully synthetic yeast genome finished by the end of the year.

“We’re chugging along toward that goal,” Boeke says.

The advance is being praised by many biologists, geneticists and others as an important advance. And even bioethicists and environmentalists who are worried about possible ethical and environmental implications praised the project for its careful approach.

But the increasing ability to manipulate the basic building blocks of life is stirring concerns about someday using this technology to create synthetic genomes of other organisms, especially humans.

The yeast project is significant because it provides insights into how human cells work, Boeke says.

Geneticist Jef Boeke of New York University studies DNA sequences from baker’s yeast.

Though single-celled, yeast are among the complicated group of organisms called eukaryotes. That means, like humans, yeast contain organelles, and package their DNA inside a nucleus.

“They are a great model for understanding the basic wiring of higher cells,” Boeke says.

The project enlisted labs around the world to painstakingly assemble yeast chromosomes from the four basic chemical building blocks of DNA — adenine, cytosine, guanine and thymine.

“We’re essentially swapping out the code, if you will, in a living yeast cell with sort of a 21st Century version of the operating system,” he says.

The team has shown that all six of the chromosomes assembled so far function inside yeast cells, even when several are simultaneously inserted into the same cell. That’s true even when significant portions of individual chromosomes have been rewritten.

“We can kind of torture the genome of the yeast in some pretty extreme ways and the yeast sort of shrugs its shoulders and doesn’t seem to care that much about it,” Boeke says.

That bodes well for one of the goals of the project: creating synthetic yeast that could be used like tiny factories to produce more than bread, beer and wine. The scientists hope to use yeast to produce new drugs to treat diseases as well as for other purposes, possibly including manufacturing new forms of fuel.

“We’re also developing some really practical tools for improving the yeast so that it can do a much better job at making useful products for us,” Boeke says.

Others experts agree.

“This is really going to allow us to understand how to design cells from the bottom up that can be reprogrammed for many applications,” says Daniel Gibson, vice president of DNA technologies at Synthetic Genomics, of La Jolla, Calif., who wrote an article accompanying the new research

Another goal is to learn new things about basic biology, Boeke says.

“A great quote from Richard Feynman of the Feynman lectures on physics is: ‘What I cannot create, I cannot understand,’ ” says Boeke. “And that’s kind of a motto for our field, I guess you would say.”

The techniques the scientists are developing could also be used to synthesize from scratch the genomes of other much more complex organisms, Boeke says. For example, the group has developed an efficient way to identify and fix errors in thegenomes they’re working on, similar to the way computer programmers debug computer programs.

“This is absolutely setting the stage for being able to do these kinds of manipulations on a much larger scale in much larger genomes, such as those of plants and animals and even of the human genome,” Boeke says.

That includes synthesizing the whole human genome. Boeke is already working on that with George Church, a prominent Harvard University geneticist.

“This is a whole new era where we’re moving beyond little edits on single genes to being able to write whatever we want throughout the genome,” Church says. “The goal is to be able to change it as radically as our understanding permits.”

That prospect worries some biologists, environmentalists, bioethicists and others. The concern is that synthetic microbes, plants or animals might damage the environment in unpredictable ways if they’re released either accidentally or on purpose.

“You can think of it of like introducing an invasive species into a different environment,” says Todd Kuiken, a senior research scholar at North Carolina State University’s Genetic Engineering and Society Center. “It will have some type of impact to the system.”

Others fear terrorists could use this technology to brew new biological weapons.

Boeke says the yeast project is being done with careful safeguards and tight ethical scrutiny. But he acknowledges that the possibility of creating a synthetic human genome stirs alarm.

“The biggest concern, of course, is people are worried that our goal is to make a synthetic human — a human powered by a synthetic genome,” he says. “And this is why we are very adamant that our applications are in engineering of cells that could be used as therapies for humans. Don’t make an organism from it.”

But others think society is nowhere near ready for the manufacturing of a synthetic human genome.

“Having that kind of knowledge and that kind of power over the human genome in a world as riven by injustice as the world in which we currently live would not be a good way to go — would not be a justifiable direction,” says Laurie Zoloth, a bioethicist at Northwestern University. But she praises the yeast project.

%d bloggers like this: