Genetics  

CRISPR gene drives allow scientists to change sequences of DNA and make that the resulting edited genetic trait is inherited by future generations, opening up the possibility of altering entire species forever. More than anything, the technology has led to questions: How will this new power affect humanity? What are we going to use it to change?

CRISPR genetic engineering now gives scientists the ability to change sequences of DNA and guarantee that the resulting edited genetic trait is inherited by future generations, opening up the possibility of altering entire species forever. More than anything, the technology has led to questions: How will this new power affect humanity? What are we going to use it to change?

At a recent TED talk, Jennifer Kahn questions and shares a potentially powerful application of gene drives: the development of disease-resistant mosquitoes that could knock out malaria and Zika.

Kahn talks about the work of Kevin Esvelt, the scientist behind gene drives. Gene drive systems are capable of altering the traits of wild populations and associated ecosystems.

"It's like a global search and replace, or in science terms, it makes a heterozygous trait homozygous.."

Named for the ability to "drive" themselves and nearby genes through populations of organisms over many generations, these genetic elements can spread even if they reduce the fitness of individual organisms. They do this by ensuring that they will be inherited by most - rather than only half - of offspring. Preferential inheritance can more than offset costs to the organism, permitting rapid spread through the population. CRISPR-based genome editing allows us to build gene drive systems capable of spreading different useful changes, including those that will eventually suppress or eliminate the target population.

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So, what does this mean asks Kahn? For one thing, it means we have a very powerful, but also somewhat alarming new tool. "Up until now, the fact that gene drives didn't work very well was actually kind of a relief. Normally when we mess around with an organism's genes, we make that thing less evolutionarily fit. So biologists can make all the mutant fruit flies they want without worrying about it. If some escape, natural selection just takes care of them."

Gene drives might not stay confined to what we call the target species, says Kahn. That's because of gene flow, or species interbreeding. If that happens, it's possible a gene drive could cross over, like Asian carp could infect some other kind of carp. That's not so bad if your drive just promotes a trait, like eye color. In fact, there's a decent chance that we'll see a wave of very weird fruit flies in the near future. But it could be a disaster if your drive is deigned to eliminate the species entirely.

Science journalist Kahn likes to seek out complex stories, with the goal of illuminating their nuances. She teaches in the magazine program at the UC Berkeley Graduate School of Journalism, and is a contributing writer for the New York Times Magazine; she has written features and cover stories for The New Yorker, National Geographic, Outside, Wired and many more.

Her work has appeared in the Best American Science Writing anthology series four times, most recently for the New Yorker story “A Cloud of Smoke,” a story on the complicated death of a policeman after 9/11.

SOURCE  TED

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Medicine  

Medical testing technology has developed a lot in the last few years. New scientific discoveries, technology, and knowledge available are helping medical professionals keep us healthy and living longer. Here are a few examples.

The field of medical testing has exploded in the last few years with new scientific discoveries, technology, and knowledge available. It is hard for the average person to imagine how so many advances have been developed so quickly, but we know how important these advancements are in our health and in the lives of medical professionals who use them daily. Below are some of the most amazing advancements and what they mean for medical testing in the future.

Autoclaves and DNA Sequencers

Improved autoclaves and DNA sequencers allow for fetal DNA testing. Recent non-invasive autosomal testing methods lessen common dangers and reduce the risk of miscarriage, which was of great concern in earlier testing methods.

DNA testing now has the potential to eliminate several genetic diseases through Clustered Regularly Interspaced Short Palindromic Repeats or CRISPR therapy which searches for unwanted or defective genes. These can then be cut and discarded, repaired, or even replaced. Cell-free fetal DNA testing for missing or extra chromosomes can prevent serious birth defects such as Down Syndrome as well. This new development has made pregnancy and birth a much safer experience for women and can help in long-term family planning.

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Molecular Microscopes and Super Scanners

Although tests for rare diseases have been somewhat neglected of late, some researchers have continued to work in these areas. Molecular microscopes have led to blood and urine tests being developed for, among others, metachromatic leukodystrophy. This disease affects growth and development of myelin, which is the covering that insulates nerves.

Recently researchers at Johns Hopkins have engineered lab tests for a rare genetic blood cell disorder called HELLP, named for hemolysis, elevated liver enzymes and low platelet count. This is a life-threatening complication of pregnancy which can result in high blood pressure and end organ damage.

At University of Virginia, studies have led to the development of a blood test for ischemic stroke. This condition results from blocked blood flow to the brain. Position emission tomography or PET scanning has been used for years in diagnosing numerous diseases as well. Medical professionals require a bachelor of radiation science technology to operate this machine, but now PET is being used to diagnose the presence of brain plaque associated with Alzheimer's disease. This is great news for many people who weren’t sure how to get a clear diagnosis before.

Nano Enclosures

Perhaps the most exciting medical testing today is being developed in the field of nanotechnology. Diagnostic tests based on the use of Nano enclosures allow for much earlier discovery of disease processes than previous methods.

In brain cancer research, scientists are using magnetic nanoparticles and nuclear magnetic resonance (NMR) imaging to make very early diagnosis of the disease. Nanoparticles release biomarkers which alert the tester to the presence of cancer cells.

Modern scanners, high-level computers, and astonishingly powerful camera-microscopes will allow even faster and better medical testing. Prevention and cure may be available in years, not decades, for formerly untreatable diseases.

By Brooke Chaplan

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Author Bio - 33rd Square contributor Brooke Chaplan is recent graduate of New Mexico University where she studied journalism. She loves to hike, bike, run and explore around her home in Los Lunas, New Mexico. She also enjoys blogging about health, fitness, fashion and many other topics.

Biotech  

New research into molecular biology is increasing our scientific understanding of diseases, genetic processes, and many health problems. Here are five advances in microbiology and the impacts they have had on scientific knowledge and today’s disease treatment options.

Recent breakthroughs in microbiology and new research are increasing scientific understanding of diseases, genetic processes, and many maladies which have long plagued us. In this article we discuss five advances in microbiology and the impacts they have had on scientific knowledge and today’s disease treatment options.

Clustered Regularly Interspaced Short Palindromic Repeats

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a DNA editing tool transforming biology and genetics. CRISPR is actually one component of the immune system of bacteria. Bacteria use this mechanism by maintaining small pieces of viruses that are harmful to them. The bacteria use this as a recognition tool, enabling them to spot these bacteria when they are nearby. CRISPR works in conjunction with CRISPR Associated Proteins (CAS), a tool that enables the bacteria to precisely cut the DNA of the invading virus.

Microbiologists use this mechanism to edit the genomes of higher level organisms with extreme accuracy. CRISPR has been used to create human cells that are resistant to infection from the HIV virus and to correct genetic defects with an unprecedented precision.

Pluripotent Stem Cells

An induced pluripotent stem cell (IPSC) is a cell taken from an organism that is genetically modified to function as an embryonic stem cell.

IPSCs are used in modeling diseases and creating drugs. A promising field of application involves using the IPSCs to transport DNA expression treatments in-vitro to treat genetically-based disorders, as IPSCs represent a safer approach than viral delivery methods, which can increase the risks of developing certain cancers.

Recent innovations involving IPSCs come from Jacob Hanna of Israel’s Weizmann Institute of Science, who along with his research colleagues were able to disable a cell gene that resists pluripotency conversion, increasing the production success to 100 percent. Previous IPSC creation techniques had a success rate of approximately 10 percent.

Hydrogel Microparticles

Hydrogels are a category of polymeric materials, having structures with strong affinities for water, allowing them to store large amounts of water in 3-dimensional networks. Their highly bio-compatible and tunable characteristics have increased their attractiveness in many bio-tech applications. Their solution-like environments make them suited for use in bio-sensing applications. Hydrogels have been used in immunoassay and nucleic acid assaying applications. Because of their very sensitive nature, these applications have presented many challenges using previous coating and substrate techniques. Hydrogels have also been the material of choice in tissue regenerative medicine.

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Signaling Protein Discoveries

Signaling proteins function as organic clocks that cause biological events to occur in specific orders. Their role in organic processes and mechanisms is highly complex and not well understood. Proteins called receptors exist on cells throughout the body. These bind to molecules that function in signaling capacities thereby initiating biological responses. Receptors are molecule specific and will not bind to non-compatible sites.

A recent breakthrough by researchers at the University of Tennessee, Knoxville involves the specific signaling protein Cdc42, a molecule crucial to the final phase of cellular division. The discovery increased understanding of how Cdc42 works in the cell division process. This understanding can play a critical role in understanding and ultimately treating cancer, a disease in which Cdc42 signaling is defective.

Redox Signaling Molecules

Redox signaling molecules are primarily produced in the mitochondria of cells. The mitochondria simultaneously produces Adenosine Tri-Phosphate (ATP), and two Redox signaling molecules, Reactive Oxygen Species (ROS) and Reduced Species(RS). The specific roles of ROS and RS were not well understood for years following their discovery. Popular opinion regarded them as waste products generated in the production of ATP.

However, ROS has a crucial role in signaling the immune system with determining whether damaged cells can be repaired or should be destroyed. Additionally, ROS is used to attack pathogens in the body by a mechanism known as oxidative burst, creating an environment hostile to the invading microorganism. Additionally, RS molecules play a role in activating antioxidant molecules used by the body to scavenge harmful free radicals.

A novel consumer-based technology implemented by ASEA Science Based Medicine involves solutions and skin care products containing redox signaling molecules to promote their health benefits.

Advances in microbiology have benefited understanding of processes involved in cancer, DNA molecule splicing, stem cell generation, tissue regeneration and cellular signaling molecules.

By Brooke Chaplan

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Author Bio - 33rd Square contributor Brooke Chaplan is recent graduate of New Mexico University where she studied journalism. She loves to hike, bike, run and explore around her home in Los Lunas, New Mexico. She also enjoys blogging about health, fitness, fashion and many other topics.

HIV/AIDS  

Using the CRISPR/Cas9 gene editing technique, scientists at Temple University have eliminated HIV-1 DNA from T cell genomes in the lab experiments, a move that would prevent reinfection after the cells were re-exposed to the virus.

New research is paving the way to an eventual cure for patients infected with HIV, the virus that causes AIDS. In a study published in the Nature journal, Scientific Reports, researchers have shown that they can both effectively and safely eliminate the virus from the DNA of human cells grown in culture.

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Using the CRISPR/Cas9 gene editing technique, the scientists from Temple University eliminated HIV-1 DNA from T cell genomes in lab experiments, and prevented reinfection after the cells were re-exposed to the virus.

The senior investigator on the new study, Kamel Khalili, says “Antiretroviral drugs are very good at controlling HIV infection. But patients on antiretroviral therapy who stop taking the drugs suffer a rapid rebound in HIV replication.” The presence of numerous copies of HIV weakens the immune system and eventually causes acquired immune deficiency syndrome, or AIDS.

Curing HIV/AIDS – which has claimed the lives of more than 25 million people since it was first discovered in the 1980s – is the ultimate goal in HIV research. Eliminating the virus after it has become integrated into CD4+ T-cells, the cells primarily infected with HIV, has proven difficult. Recent attempts have focused on intentionally reactivating HIV, aiming to stimulate a robust immune response capable of eradicating the virus from infected cells. However, to date, none of these “shock and kill” approaches has been successful.

Khalili and colleagues decided to try a different approach, specifically targeting HIV-1 proviral DNA (the integrated viral genome) using uniquely tailored gene editing technology. Their system includes a guide RNA that specifically locates HIV-1 DNA in the T-cell genome, and a nuclease enzyme, which cuts the strands of T-cell DNA. Once the nuclease has edited out the HIV-1 DNA sequence, the loose ends of the genome are reunited by the cell's own DNA repair machinery.

"These experiments had not been performed previously to this extent but the questions they address are critical, and the results allow us to move ahead with this technology."

In previous work, Dr. Khalili's team had demonstrated the ability of their technology to snip out HIV-1 DNA from human cell lines. In their latest study, however, they concentrated on latently and productively infected CD4+ T cells to show not only that the technology eliminates the virus from cells but also that its persistent presence in HIV-1-eradicated cells actually protects them against reinfection. More importantly, they carried their work over to ex vivo experiments, in which T-cells from patients infected with HIV were grown in cell culture, showing that treatment with the gene editing system can suppress viral replication and dramatically reduce viral load in patient cells.

In another major component of the study, Dr. Khalili's team addressed questions about off-target effects and toxicity. Using an approach known as ultra-deep whole-genome sequencing, which is considered the gold standard for genomic assessment, the researchers analyzed the genomes of HIV-1-eradicated cells for mutations in genes outside the region targeted by the guide RNA. Their analyses ruled out off-target effects on genes, including potential collateral effects on cellular gene expression. Studies of cell viability and proliferation showed that HIV-1-eradicated cells were growing and functioning normally.

“The findings are important on multiple levels,” Dr. Khalili said. “They demonstrate the effectiveness of our gene editing system in eliminating HIV from the DNA of CD4 T-cells and, by introducing mutations into the viral genome, permanently inactivating its replication. Further, they show that the system can protect cells from reinfection and that the technology is safe for the cells, with no toxic effects.”

“These experiments had not been performed previously to this extent,” he added. “But the questions they address are critical, and the results allow us to move ahead with this technology.”

More work is needed to adapt the techniques into  human treatments, but the promise is there, and according to many associated in the field, the work is only a sign of things to come in terms of CRISPR breakthroughs.

SOURCE  Temple University

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Health  

Scientists have discovered the mechanism underlying the genomic region most strongly associated with obesity. The research, that uses CRISPR methods, has uncovered a genetic pathway that controls whether our bodies burn or store fat. Manipulating that genetic circuit could offer a new approach for obesity treatments.

Obesity is one of the biggest public health challenges today. Wih more than 500 million people affected worldwide, obesity costs at least $200 billion each year in the United States alone, and contributes to potentially fatal disorders such as cardiovascular disease, diabetes, and cancer.

Now a new approach to prevent and even cure obesity may soon be available, after a study led by researchers at MIT and Harvard Medical School and published in the New England Journal of Medicine.

By analyzing the cellular circuitry underlying the strongest genetic association with obesity, the researchers have unveiled a new pathway that controls human metabolism by prompting our adipocytes, or fat cells, to store fat or burn it away.

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“Obesity has traditionally been seen as the result of an imbalance between the amount of food we eat and how much we exercise, but this view ignores the contribution of genetics to each individual’s metabolism,” says senior author Manolis Kellis, a professor of computer science and a member of MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) and of the Broad Institute.

"Our results indicate that the obesity-associated region acts primarily in adipocyte progenitor cells in a brain-independent way."

The strongest association with obesity resides in a gene region known as “FTO,” which has been the focus of intense scrutiny since its discovery in 2007. However, previous studies have failed to find a mechanism to explain how genetic differences in the region lead to obesity.

“Many studies attempted to link the FTO region with brain circuits that control appetite or propensity to exercise,” says first author Melina Claussnitzer, a visiting professor at CSAIL and instructor in medicine at Beth Israel Deaconess Medical Center and Harvard Medical School. “Our results indicate that the obesity-associated region acts primarily in adipocyte progenitor cells in a brain-independent way.”

To recognize the cell types where the obesity-associated region may act, the researchers used annotations of genomic control switches across more than 100 tissues and cell types. They found evidence of a major control switchboard in human adipocyte progenitor cells, suggesting that genetic differences may affect the functioning of human fat stores.

The researchers that the risk version activated a major control region in adipocyte progenitor cells, which turned on two distant genes, IRX3 and IRX5.

Follow-up experiments showed that IRX3 and IRX5 act as master controllers of a process known as thermogenesis, whereby adipocytes dissipate energy as heat, instead of storing it as fat.

Thermogenesis can be triggered by exercise, diet, or exposure to cold, and occurs both in mitochondria-rich brown adipocytes that are developmentally related to muscle, and in beige adipocytes that are instead related to energy-storing white adipocytes.

“Early studies of thermogenesis focused primarily on brown fat, which plays a major role in mice, but is virtually nonexistent in human adults,” Claussnitzer says. “This new pathway controls thermogenesis in the more abundant white fat stores instead, and its genetic association with obesity indicates it affects global energy balance in humans.”

The researchers predicted that a genetic difference of only one nucleotide is responsible for the obesity association. In risk individuals, a thymine (T) is replaced by a cytosine (C) nucleobase, which disrupts repression of the control region and turns on IRX3 and IRX5. This then turns off thermogenesis, leading to lipid accumulation and ultimately obesity.

By editing a single nucleotide position using the CRISPR/Cas9 system — a technology that allows researchers to make precise changes to a DNA sequence — the researchers could switch between lean and obese signatures in human pre-adipocytes.

Switching the C to a T in risk individuals turned off IRX3 and IRX5, restored thermogenesis to non-risk levels, and switched off lipid storage genes.

“Knowing the causal variant underlying the obesity association may allow somatic genome editing as a therapeutic avenue for individuals carrying the risk allele,” Kellis says. “But more importantly, the uncovered cellular circuits may allow us to dial a metabolic master switch for both risk and non-risk individuals, as a means to counter environmental, lifestyle, or genetic contributors to obesity.”

"Our results point to a pathway for adipocyte thermogenesis regulation involving ARID5B, rs1421085, IRX3, and IRX5, which, when manipulated, had pronounced pro-obesity and anti-obesity effects," conclude the researchers in their paper.

The researchers work could lead to therapies that manipulate this new pathway to reverse the signatures of obesity in both human cells and mice.

“By manipulating this new pathway, we could switch between energy storage and energy dissipation programs at both the cellular and the organismal level, providing new hope for a cure against obesity,” Kellis says.

SOURCE  MIT News

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 Genetic Engineering  

Researchers have developed a way to program DNA in such a way that genes can be turned on or off in living cells. The new tool can affect two different genes at the same time, an advance that will allow scientists to treat even the most complex genetic disorders.

Bioengineers at Stanford and other universities have developed a sort of programmable genetic code that allows them to preferentially activate or deactivate genes in living cells.

The research is published in the current issue of Cell, and could help usher in a new generation of gene therapies.

The technique is an adaptation of CRISPR, itself a relatively new genetic tool that makes use of a natural defense mechanism that bacteria evolved over millions of years to slice up infectious virus DNA.

Standard CRISPR consists of two components: a short RNA that matches a particular spot in the genome, and a protein called Cas9 that snips the DNA in that location. For the purposes of gene editing, scientists can control where the protein snips the genome, insert a new gene into the cut and patch it back together.

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Inserting new genetic code, however, is just one way to influence how the genome is expressed. Another involves telling the cell how much or how little to activate a particular gene, thus controlling how much protein a cell produces from that gene and altering its behavior.

"We could eventually synthesize tens of thousands of RNA molecules to control the genome over a whole organism."

It's this action that Lei Stanley Qi, an assistant professor of bioengineering and of chemical and systems biology at Stanford, and his colleagues aim to manipulate.

In the new work, the researchers describe how they have designed the CRISPR molecule to include a second piece of information on the RNA, instructing the molecule to either increase (upregulate) or decrease (downregulate) a target gene's activity, or turn it on/off entirely.

They also designed it so that it could affect two different genes at once. In a cell, the order or degree in which multiple genes are activated can produce different metabolic products.

"It's like driving a car. You control the wheel to control direction, and the engine to control the speed, and how you balance the two determines how the car moves," Qi said. "We can do the same thing in the cell by up- or downregulating genes, and produce different outcomes."

To prove the principle, the scientists used the technique to take control of a yeast metabolic pathway, turning genes on and off in various orders to produce four different end products. They then tested it on two mammalian genes that are important in cell mobility, and were able to control the cell's direction and how fast it moved.

The ability to control genes is an attractive approach in designing genetic therapies for complex diseases that involve multiple genes, Qi said, and the new system may overcome several of the challenges of existing experimental therapies.

"Our technique allows us to directly control multiple specific genes and pathways in the genome without expressing new transgenes or uncontrolled behaviors, such as producing too much of a protein, or doing so in the wrong cells," Qi said.

Next, Qi plans to test the technique in mice and refine the delivery method. Currently the scientists use a virus to insert the molecule into a cell, but he would eventually like to simply inject the molecules into an organism's blood. "I'm optimistic because everything about this system comes naturally from cells, and should be compatible with any organism."


SOURCE  Stanford University

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 Gene Therapy  

By using a a new gene-editing system based on bacterial proteins, researchers have effectively cured mice of a rare liver disorder caused by a single genetic mutation.

Using a new gene-editing system based on bacterial proteins, MIT researchers have cured mice of a rare liver disorder caused by a single genetic mutation.

The findings, described in Nature Biotechnology, offer the first evidence that this gene-editing technique, known as CRISPR, can reverse disease symptoms in living animals.

CRISPR, which offers an easy way to snip out mutated DNA and replace it with the correct sequence, holds potential for treating many genetic disorders, according to the research team.

“What’s exciting about this approach is that we can actually correct a defective gene in a living adult animal,” says Daniel Anderson, the Samuel A. Goldblith Associate Professor of Chemical Engineering at MIT, a member of the Koch Institute for Integrative Cancer Research, and the senior author of the paper.

The recently developed CRISPR system relies on cellular machinery that bacteria use to defend themselves from viral infection. Researchers have copied this cellular system to create gene-editing complexes that include a DNA-cutting enzyme called Cas9 bound to a short RNA guide strand that is programmed to bind to a specific genome sequence, telling Cas9 where to make its cut.

At the same time, the researchers also deliver a DNA template strand. When the cell repairs the damage produced by Cas9, it copies from the template, introducing new genetic material into the genome. Scientists envision that this kind of genome editing could one day help treat diseases such as hemophilia, Huntington’s disease, and others that are caused by single mutations.

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Scientists have developed other gene-editing systems based on DNA-slicing enzymes, also known as nucleases, but those complexes can be expensive and difficult to assemble.

“The CRISPR system is very easy to configure and customize,” says Anderson, who is also a member of MIT’s Institute for Medical Engineering and Science. He adds that other systems “can potentially be used in a similar way to the CRISPR system, but with those it is much harder to make a nuclease that’s specific to your target of interest.”

"What’s exciting about this approach is that we can actually correct a defective gene in a living adult animal."

For this study, the researchers designed three guide RNA strands that target different DNA sequences near the mutation that causes type I tyrosinemia, in a gene that codes for an enzyme called FAH. Patients with this disease, which affects about 1 in 100,000 people, cannot break down the amino acid tyrosine, which accumulates and can lead to liver failure. Current treatments include a low-protein diet and a drug called NTCB, which disrupts tyrosine production.

In experiments with adult mice carrying the mutated form of the FAH enzyme, the researchers delivered RNA guide strands along with the gene for Cas9 and a 199-nucleotide DNA template that includes the correct sequence of the mutated FAH gene.

Using this approach, the correct gene was inserted in about one of every 250 hepatocytes — the cells that make up most of the liver. Over the next 30 days, those healthy cells began to proliferate and replace diseased liver cells, eventually accounting for about one-third of all hepatocytes. This was enough to cure the disease, allowing the mice to survive after being taken off the NCTB drug.
“We can do a one-time treatment and totally reverse the condition,” says Hao Yin, a postdoc at the Koch Institute and one of the lead authors of the Nature Biotechnology paper.

Gene therapy is one area of science that has consistently failed to achieve its therapeutic potential. Now, our abilities may finally be able to unlock some of the promise of real-world DNA manipulation, making hereditary and acquired genetic disease much more treatable. This study marks the beginning of a new era of usability in genetic manipulation, and everyone with DNA stands to benefit.


SOURCE  MIT News Top Image - Christine Daniloff/MIT

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