Debunking 11 popular GMO Myths: Part I: Frankenfoods and Franken-corporations || Part II: Do GMOs pose health and ecological dangers? by Michael Hess & Peter Hess
Happy Friday (or should we say, Fri-YAY) from CauseScience!
psgurel– Today I am miniprepping! If you remember last week, I was doing PCR to get a specific DNA construct. After doing PCR, there are several steps before you have nice clean DNA. For the DNA I’m using (plasmid DNA) the final step is to extract your DNA from bacteria. Lucky for us, several companies make “miniprep” kits that make this process super quick and easy. It takes about 30min, and then you have (hopefully) nice, clean DNA!
crestwind24– This is crazy! I am also doing mini preps of DNA this morning!! SAMESIES!! Preparing DNA is a major part of most labs, as made obvious by todays post. I am making DNA that will label synapses in neurons in C. elegans. Once I have the DNA that I want, we will inject it into developing embryos, and then I will have transgenic worms!! Hopefully with glowing synapses!! This will allow me to visualize connections between different neurons.
CauseScience Friday… more like mini prep Friday!!!
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In case you didn’t see the media coverage of an abstract from the recent meeting of the American Society of Human Genetics in Baltimore, Maryland (see Nature News stories here), an abstract presented preliminary data in the search for the genetic roots of homosexuality in human twins. Obviously this scientific presentation, and the press release about it from the conference, generated excitement, skepticism, and now controversy. Nature has a terrific editorial this week examining how this was a failure in science communication. Scientific conferences and meetings are meant to be a place to present preliminary, controversial, and incomplete studies to scientific peers to get feedback, ideas, and promote the work being done. Criticism of the work and experiments are always a part of this process, but where do we draw the line?
A few critics went so far as to argue that the authors should not have presented such preliminary work at the meeting. And at least one suggested that the authors could have provided preprints of their study when presenting it. These arguments seem to misunderstand the traditional, and still useful and relevant, role of such gatherings. Studies with small sample sizes and controversial methods are presented at conferences all the time, and many scientists already fear being scooped when they present even a bit of their data.
One might wonder how so much media coverage was generated from a scientific conference abstract, and the answer is that the conference used the abstract in a press release, unfortunately titled, ‘Epigenetic Algorithm Accurately Predicts Male Sexual Orientation.’ While this may represent the science, it opens the door for misinterpretation by non-scientists that never saw the data presented. This failure in science communication has a remedy, and it involves being careful with press releases of unpublished, non-peer-reviewed science, especially on topics that could be ‘misused’ or misinterpreted by the press.
The genetics of homosexuality is a subject that will always find media coverage, partly because of the societal interest in the topic. Neither the scientists nor the conference organizers can be held responsible for how some in the media chose to write about the study. But both could have done more to get the right message across.
Check out this podcast episode from Radiolab focusing on CRISPR and its potential applications.[tweet https://twitter.com/CauseScience1/status/611576799013769217]
Out drinking with a few biologists, Jad finds out about something called CRISPR. No, it’s not a robot or the latest dating app, it’s a method for genetic manipulation that is rewriting the way we change DNA. Scientists say they’ll someday be able to use CRISPR to fight cancer and maybe even bring animals back from the dead. Or, pretty much do whatever you want. Jad and Robert delve into how CRISPR does what it does, and consider whether we should be worried about a future full of flying pigs, or the simple fact that scientists have now used CRISPR to tweak the genes of human embryos.
As mentioned previously, a moratorium has been called on the new gene editing technique using the CRISPR/Cas9 system due to ethical concerns over altering genes. Essentially, biologists fear that this technique will be used in cilinical applications before the safety can be determined and ALSO are worried about ethical issues surrounding the technique of editing genes.
In light of all this, a new controversy has surfaced following the publication in Protein & Cell of work from Chinese scientists who essentially tried to delete a gene from human embryos that causes a fatal blood disorder. While the CRISPR/Cas9 system definitely has potential, the work from this group clearly shows that their current method of gene editing has several off target effects and is absolutely not ready for any sort of clinical trial.
NPR summarizes the whole ordeal:
For the first time, scientists have edited DNA in human embryos, a highly controversial step long considered off limits.
Junjiu Huang and his colleagues at the Sun Yat-sen University in Guangzhou, China, performed a series of experiments involving 86 human embryos to see if they could make changes in a gene known as HBB, which causes the sometimes fatal blood disorder beta-thalassemia.
The report, in the journal Protein & Cell, was immediately condemned by other scientists and watchdog groups, who argue the research is unsafe, premature and raises disturbing ethical concerns.
“No researcher should have the moral warrant to flout the globally widespread policy agreement against modifying the human germline,” Marcy Darnovsky of the Center for Genetics and Society, a watchdog group, wrote in an email to Shots. “This paper demonstrates the enormous safety risks that any such attempt would entail, and underlines the urgency of working to forestall other such efforts. The social dangers of creating genetically modified human beings cannot be overstated.”
George Daley, a stem cell researcher at Harvard, agreed.
“Their data reinforces the wisdom of the calls for a moratorium on any clinical practice of embryo gene editing, because current methods are too inefficient and unsafe,” he wrote in an email. “Further, there needs to be careful consideration not only of the safety but also of the social and ethical implications of applying this technology to alter our germ lines.”
Scientists have been able to manipulate DNA for years. But it’s long been considered taboo to make changes in the DNA in a human egg, sperm or embryo because those changes could become a permanent part of the human genetic blueprint. One concern is that it would be unsafe: Scientists could make a mistake, which could introduce a new disease that would be passed down for generations. And there’s also fears it this could lead to socially troubling developments, such as “designer babies,” in which parents can pick and choose the traits of their children.
The Chinese researchers say they tried this to try to refine a new technique called CRISPR/Cas9, which many scientists are excited about it because it makes it much easier to edit DNA. The procedure could enable scientists to do all sorts of things, including possibly preventing and curing diseases. So the Chinese scientists tried using CRISPR/Cas9 to fix a gene known as the HBB gene, which causes beta thallasemia.
The work was done on 86 very early embryos that weren’t viable, in order to minimize some of the ethical concerns. Only 71 of the embryos survived, and just 28 were successfully edited. But the process also frequently created unintended mutations in the embryos’ DNA.
“Taken together, our data underscore the need to more comprehensively understand the mechanisms of CRISPR/Cas9-mediated genome editing in human cells, and support the notion that clinical applications of the CRISPR system may be premature at this stage,” the Chinese scientists wrote.
Rumors about this research have been circulating for weeks, prompting several prominent groups of scientists to publish appeals for a moratorium on doing this sort of thing.
In the wake of the report from the Chinese scientists, several of these researchers reiterated their call for a moratorium. Some said they hoped the difficulties that Huang and his colleagues encountered might discourage other scientists from attempting anything similar.
“The study simply underscores the point that the technology is not ready for clinical application in the human germline,” Jennifer Doudna, the University of California, Berkeley, scientist who developed CRISPR, wrote in an email. “And that application of the technology needs to be on hold pending a broader societal discussion of the scientific and ethical issues surrounding such use.”
But there are already reports that Huang’s group and possibly others in China continue to try editing the genes in human embryos.
“We should brace for a wave of these papers, and I worry that if one is published with a more positive spin, it might prompt some IVF clinics to start practicing it, which in my opinion would be grossly premature and dangerous,” Daley says.
What do YOU think about the CRISPR/Cas9 technology? Should a moratorium be placed? Does the technology show promise for curing disease in the future? Or is this whole thing unethical? Share your opinions in the comments or tweet at us @CauseScience1.
Not all GMO plants are created equally: it’s the trait, not the method, that’s important
Many people have strong opinions about genetically modified plants, also known as genetically modified organisms or GMOs. But sometimes there’s confusion around what it means to be a GMO. It also may be much more sensible to judge a plant by its specific traits rather than the way it was produced – GMO or not.
This article is not about judging whether GMOs are good or bad, but rather an explanation of how plants with modified genomes are made. (There are non-plant GMOs, but in this article we will only refer to plant GMOs.) First of all, it’s necessary to define what we mean by a GMO. For the purposes of this discussion, I’m defining GMOs as plants whose genetic information (found in their genomes) has been modified by human activity.
Humans have changed the genomes of virtually all the plants in the grocery store
If we think of GMOs as plants that have genomes modified by humans, then quite a lot of the plants sold in any grocery store fit that description. But many of these modifications didn’t occur in the lab. Farmers select plants with superior, desirable traits to cultivate in a process known as agricultural evolution. Thousands of years of traditional agricultural breeding has changed plant genomes from those of their original wild ancestors.
Broccoli, for example, is not a naturally occurring plant. It’s been bred from undomesticated Brassica oleracea or ‘wild cabbage’; domesticated varieties of B. oleracea include both broccoli and cauliflower. Broccoli, along with any seedless variety of fruit (including what you think of as bananas), and most of the crops grown on farms today would not exist without human intervention.
However, these aren’t the plants that people typically think of when they think of GMOs. It’s easy to understand how farmers can breed better plants on farms (by choosing to plant seeds from the biggest or best-yielding plants, for example, imposing artificial selection on the crop species) so even though this activity changes plant genomes in ways nature wouldn’t have, most people don’t consider these plants GMOs.
Creating “lab” GMOs
Once plant genes had been studied enough, researchers could turn to backcrossing. This technique involves breeding the offspring back with the parents to try to get a desired, stable combination of parental traits. Genes previously linked to desirable plant traits, such as higher yield or pest-resistance, could be identified and screened for using molecular biology techniques and linkage maps. These maps lay out the relative position of genes along a chromosome, based on how often they are passed along together to offspring. Closer genes tend to travel together.
Researchers used molecular markers – specific, known gene sequences, present in the linkage maps – to select individual plants that contained both the new marker gene and the greatest proportion of other favorable genes from the parents. The combinations of genes passed to offspring are always due to random recombination of the parents’ genes. Researchers weren’t able to drive particular combinations themselves, they had to work with what arose naturally; so in this marker-assisted selection approach, there’s a lot of effort and time spent trying to find plants with the best combinations of genes.
In this system, a laboratory needs to screen the genomes, using molecular biology methods to look for particular gene sequences for desirable traits in the bred offspring. Sometimes a lab even breeds the plants in cases using tissue culture – a way to propagate many plants simultaneously while minimizing the resources needed to grow them.
Inserting non-plant genes into GMOs
In the early 1980s, the plant biotechnology era began with Agrobacterium tumifaciens. This bacterium naturally infects plants and, in the wild, creates tumors by transferring DNA between itself and the plant it has infected. Scientists use this natural property to transfer genes to plant cells from an A. tumifaciens bacterium modified to contain a gene of interest.
For the first time, it was possible to insert specific genes into a plant genome, even genes that do not come from that species – or even from a plant. A. tumifaciens does not affect all plants, however, so researchers went on to develop DNA-transferring methods inspired by this system which would work without it. They include microinjection and “gene guns,” where the desired DNA was physically injected into the plant, or covered tiny particles that were literally shot into the nuclei of plant cells.
A recent review summarizes eight new methods for altering genes in plants. These are molecular biology techniques that use different enzymes or nucleic acid molecules (DNA and RNA) to make changes to a plant’s genes. One route is to alter the sequence of a plant’s DNA. Another is to leave the sequence alone but make other epigenetic modifications to the structure of a plant’s DNA. For instance, scientists could add arrangements of atoms called methyl groups to some of the nucleotide building blocks of DNA. These epigenetic modifications, while not altering the order of the DNA or of genes, change how genes can be expressed and thus the observable traits a plant has.
GMO doesn’t mean glyphosate-resistant
Calling a plant a genetically modified organism means only that – its genome has been modified by the activity of humans. But lots of people conflate the idea of a GMO plant with one that’s been created to be resistant to the herbicide glyphosate, also known by the brand name Roundup. It’s true that the most well-known GMO crops currently grown contain a gene that makes them resistant to glyphosate, which allows farmers to spray the chemical to kill weeds while allowing their crop to grow. But that’s just one example of a gene inserted into a plant.
It’s sensible to evaluate GMOs not on how they are made, but rather on what new traits the modified plants have. For instance, while it can be argued that glyphosate resistance in plants is not good for the environment because of increased use of the pesticide, other GMOs are unlikely to cause this problem.
For example, it’s difficult see how the controversial golden rice, which has been engineered to produce vitamin A in the rice grains to be more nutritious, is worse for the environment than ordinary rice. GMOs have been developed to express a pesticide permitted in organic farming: Bt toxin, an insecticide naturally produced by the bacterium Bacillus thuringiensis. While this may reduce pesticide use, it may also lead to the evolution of Bt-resistant insects. And there are GMOs which have improved storage characteristics or nutritional content, like “Flavr Savr” tomatoes, or pineapples that contain lycopene, and tomatoes that contain anthocyanins. These compounds are ordinarily found in other fruits and are thought to have health benefits.
The so-called “fish tomato” contains an antifreeze protein (gene name afa3), found naturally in winter flounder, that increases frost tolerance in the tomato plant. The tomato doesn’t actually contain fish tissue, or even necessarily DNA taken from fish tissue – just DNA of the same sequence present in the fish genome. The Afa3 protein is produced from the afa3 gene in the tomato cells using the same machinery as other tomato proteins.
Is there any fish in the tomato plant? Whether DNA taken from one organism and put into another can change the species of the recipient organism is an interesting philosophical debate. If a single gene from a fish can make a “fish tomato” a non-plant, are we human beings, who naturally contain over a hundred non-human genes, truly human?
Ode to the fruit fly: tiny lab subject crucial to basic research
The world around us is full of amazing creatures. My favorite is an animal the size of a pinhead, that can fly and land on the ceiling, that stages an elaborate (if not beautiful) courtship ritual, that can learn and remember… I am talking about the humble fruit fly, Drosophila melanogaster. By day, a tiny bug content to live on our food scraps. By night, the superhero that contributes to saving millions of human lives as one of the key model systems of modern biomedical research.
Fruit flies entered the laboratory almost through the back window a little more than 100 years ago. The excitement was still fresh after rediscovery of Gregor Mendel’s work on the genetics of peas in 1900. It was an outlandish notion at the time that Mendel’s simple laws of inheritance could apply even to animals. To test this revolutionary idea, scientists were looking for an animal they could keep easily in the lab and reproduce in large numbers.
Thomas Hunt Morgan struck gold when he decided to use the fruit fly as a model. He and his students pushed this prolific little animal to great success. They furthered Mendel’s work to discover that genes are located on chromosomes, where they are arranged, in Morgan’s words, like “beads on a string” – a breakthrough that was recognized with the Nobel prize in 1933. With the success of Morgan’s “flyroom,” the humble fruit fly was set on its way to becoming one of the leading models in modern biology, contributing vast amounts of knowledge to many areas – including genetics, embryology, cell biology, neuroscience. Additional fly Nobel prizes were awarded in 1946, 1995, 2006 and 2011.
A tiny fly stands in for us in basic research
If you ask a geneticist, humans are brothers to mice and just first cousins to flies, sharing 99% and 60% of protein-coding genes, respectively. Our anatomy and physiology are also related, so that we can use these laboratory animals to design powerful experiments, hoping what we find will be of significance to animals and humans alike. It’s undeniable that the research on animal models – such as nematodes, flies, fish and mice – has contributed immensely to what we know about our own body and as a result is helping us tackle the diseases that plague us. On this front, the services of the fruit fly will certainly be required for some time to come.
Studying fly brains to understand our own
A recent renaissance in neuroscience is also bringing the fly to the forefront of our efforts to understand the brain. One of the things we least understand is how our own brain produces our emotions and behavior. Scientists are naturally attracted by the unknown, making this one of the most exciting open frontiers in biology. Perhaps, our brain, the ultimate Narcissus, cannot resist the temptation to study itself. Can the humble fly really contribute to our understanding of how our own brain works?
The fruit fly brain is a miracle of miniaturization. It deals with an incredible flow of sensory information: an obstacle approaching, the enticing smell of overripe banana, a hot windowsill to stay away from, a sexy potential mate. And it does this literally on-the-fly, as the little marvel is computing suitable trajectories around the room. Yet the fly brain is composed of only about 100,000 neurons (compared with nearly 100 billion for human beings) and can fit easily through the eye of the finest needle.
The relatively small number of cells is a key advantage for brain mapping, and large efforts are under way to label, trace and catalog every single neuron in the fly brain. Combine this with the unique wealth of information on the genetics of this little animal, and you will see how we are now able to design incredibly powerful experiments in which we alter the “software” (that is, introduce specific changes in the genome) to create animals with unique and predictable changes in the “hardware” (the brain circuits) to ask questions about brain function.
Following this playbook are recent experiments demonstrating, for example:
- how sleep enhances memory formation (yes, even in flies!)
- how a few sexually dimorphic neurons in the male fly brain promote male-vs-male fights
- how specific ‘moonwalker’ neurons in the brain control backward walking
- how the brain processes simple hot and cold stimuli to keep this little animal away from danger (my own area of research)
- and many more.
Of course, we can do these kinds of experiments in a number of animal models. But the unique advantage of the fly is that we can pinpoint every single neuron that’s important for a particular response or behavior, precisely map how they connect to each other and silence or activate each one to figure out how the whole thing works.
Don’t forget the flies
Just a few weeks back, Chicago hosted the Genetics Society of America’s annual “fly meeting,” bringing together thousands of fly scientists from around the world. One of the topics discussed was that, in this tough economic climate, funding cuts to public agencies are disproportionately hurting research on fruit flies in favor of more “translational” approaches – that is, research that has more immediate practical applications.
It’s worth remembering that neither Mendel nor Morgan expected that their work could have a direct impact on medicine. Yet when, hopefully soon, we manage to “cure” cancer – a genetic disease par excellence – they should be among the very first people receiving a thank you note from humanity.
Flies still have a lot to contribute to our understanding of all aspects of biology. As with much basic research, the direct benefits from this work may be around the corner, or may take a little longer to find. It would be a big mistake to curb fruit fly research now that the flies are just getting warmed up to tackle some of the most interesting questions in biology.
Explainer: CRISPR technology brings precise genetic editing – and raises ethical questions
A group of leading biologists earlier this month called for a halt to the use of a powerful new gene editing technique on humans. Known by the acronym CRISPR, the method allows precise editing of genes for targeted traits, which can be passed down to future generations.
With this explainer, we’ll look at where this technique came from, its potential and some of the issues it raises.
CRISPR stands for clustered regularly interspaced short palindromic repeats, which is the name for a natural defense system that bacteria use to fend off harmful infections.
Bacteria are infected by other microorganisms, called bacteriophages, or phages. The intricate details of the mechanism were elucidated around 2010 by two research groups led by Dr Doudna of the University of California Berkeley and Dr Charpentier of Umeå University in Sweden.
The CRISPR system recognizes specific patterns of DNA from the foreign invaders and decapacitates them by cutting the invader’s DNA into pieces. The way that the bacteria target specific DNA and cleave it gave scientists a hint of its potential in other applications.
In 2013, two research groups, one lead by Dr Zhang of Massachusetts of Institute of Technology and the other by Dr Church of Harvard University, successfully modified this basic mechanism and turned it into a powerful tool that can now cut human genomic DNA at any desired location.
The ability to cut DNA or genes at specific locations is the basic requirement to modify the genome structure. Changes can be made in the DNA around the cleavage site which alter the biological features of the resulting cells or organisms. It is the equivalent of a surgical laser knife, which allows a surgeon to cut out precisely defective body parts and replace them with new or repaired ones.
Tool for gene discovery
Scientists have long sought after this sort of genome editing tools for living cells. Two other technologies, called zinc-finger nucleases and TALEN (transcription activator-like effector nuclease) are available to achieve the same result. However, the CRISPR technology is much easier to generate and manipulate. This means that most biological research laboratories can carry out the CRISPR experiments.
As a result, CRISPR technology has been quickly adopted by scientists all over the world and put it into various tests. It has been demonstrated to be effective in genome editing of most experimental organisms, including cells derived from insects, plants, fish, mice, monkeys and humans.
Such broad successes in a short period of time imply we’ve arrived at a new genome editing era, promising fast-paced development in biomedical research that will bring about new therapeutic treatments for various human diseases.
The CRISPR technology offers a novel tool for scientists to address some of the most fundamental questions that were difficult, if not impossible, to address before.
For instance, the whole human genomic DNA sequence had been deciphered many years ago, but the majority of information embedded on the DNA fragments are largely unknown. Now, the CRISPR technology is enabling scientists to study those gene functions. By eliminating or replacing specific DNA fragments and observing the consequences in the resulting cells, we can now link particular DNA fragments to their biological functions.
Recently, cells and even whole animals with desired genome alterations have successfully been generated using the CRISPR technology. This has proven highly valuable in various biomedical research studies, such as understanding the cause and effect relationship between specific DNA changes and human diseases. Studying DNA in this way also sheds light on the mechanisms underlying how diseases develop and provides insights for developing new drugs that eliminate specific disease symptoms.
With such profound implications in medical sciences, many biotech and pharmaceutical companies have now licensed the CRISPR technology to develop commercial products.
For example, a biotech company, Editas Medicine, was founded in 2013 with the specific goal of creating treatments for hereditary human diseases employing the CRISPR technology.
However, products derived from the use of CRISPR technology are yet to hit the market with FDA approval.
Call for ethical guidelines
With the CRISPR technology, scientists can now alter the genome composition of whole organisms, including humans, through manipulating reproductive cells and fertilized eggs or embryos. Those particular genetic traits are then passed down through generations. This brings hope to cure genetic defects that cause various hereditary human diseases, such as cystic fibrosis, haemophilia, sickle-cell anemia, Down syndrome and so on.
Unlike the current approaches of gene therapy which temporarily fix defective cells or organs through the introduction of corrected or functional genes, the CRISPR technology promises to correct the defect in the reproductive cells, producing progenies that are free of the defective gene. In other words, it can eliminate the root causes of hereditary human diseases.
In theory,then, hereditary features that people consider advantageous, such as higher intelligence, better body appearance and longevity, can be introduced into an individual’s genome through CRISPR mediated reproductive cell modifications as well.
However, scientists do not yet fully understand all the possible side effects of editing human genomes. It is also the case, that there is no clear law to regulate such attempts.
That’s why groups of prominent scientists in the field have recently initiated calls for ethical guidelines for doing such modifications of reproductive cells. The fear being that uncontrolled practice might bring about unforeseen disastrous outcomes in long run.
The guidelines call for a strong discouragement of any attempts at genome modification of reproductive cells for clinical application in humans, until the social, environmental, and ethical implications of such operations are broadly discussed among scientific and governmental organizations.
There is no doubt that the exciting and revolutionary CRISPR technology, under the guidance of carefully drafted and broadly accepted rules, will serve well for the well-being of human kind.
Epigenome: The symphony in your cells
Almost every cell in your body has the same DNA sequence. So how come a heart cell is different from a brain cell? Cells use their DNA code in different ways, depending on their jobs. Just like orchestras can perform one piece of music in many different ways. A cell’s combined set of changes in gene expression is called its epigenome. This week Nature publishes a slew of new data on the epigenomic landscape in lots of different cells. Learn how epigenomics works in this video.