Category Archives: Genetic Engineering

Its been no secret that screening methods to detect prostate cancer have been woefully lacking and largely inconsistent with respect to the results they provide. Yet, with the rise in validated biomarkers and advanced diagnostics coupled with next-generation sequencing methods, new liquid biopsy assays are guiding physician treatment options. Now, a group of investigators at The Institute of Cancer Research, London, and The Royal Marsden NHS Foundation Trust have developed a three-in-one blood test that could transform the treatment of advanced prostate cancer through the use of precision drugs designed to target mutations in the BRCA genes.

"Blood tests for cancer promise to be truly revolutionary, noted Paul Workman, Ph.D., chief executive of The Institute of Cancer Research, London. They are cheap and simple to use, but most importantly, because they aren't invasive, they can be employed or applied to routinely monitor patients to spot early if treatment is failingoffering patients the best chance of surviving their disease.

The research team was able to isolate cancer DNA in a patients bloodstream and determine which men with advanced prostate cancer were likely to benefit from treatment with a new class of drugs called poly(ADP-ribose) polymerase (PARP) inhibitorsspecifically the drug olaparib. Moreover, the scientists were able to use the test to analyze DNA in the blood after treatment had started, so people who were not responding could be identified and switched to an alternative therapy in as little as four to eight weeks. The third aspect of the new test came when the research team was able to monitor a patient's blood throughout treatment, quickly picking up signs that the cancer was evolving genetically and might be becoming resistant to the drugs.

Findings from the new study were published recently in Cancer Discovery in an article entitled Circulating Free DNA to Guide Prostate Cancer Treatment with PARP Inhibition.

"Our study identifies, for the first time, genetic changes that allow prostate cancer cells to become resistant to the precision medicine olaparib, explained senior study investigator Johann de Bono, M.D., professor of cancer research at The Institute of Cancer Research, London, and consultant medical oncologist at The Royal Marsden NHS Foundation Trust. "From these findings, we were able to develop a powerful, three-in-one test that could in future be used to help doctors select treatment, check whether it is working, and monitor the cancer in the longer term. We think it could be used to make clinical decisions about whether a PARP inhibitor is working within as little as four to eight weeks of starting therapy.

The investigators are optimistic that the new test could help to extend or save lives by targeting treatment more effectively, while also reducing the side effects of treatment and ensuring patients don't receive drugs that are unlikely to do them any good. Additionally, the new study is also the first to identify which genetic mutations prostate cancers use to resist treatment with olaparib. The test could potentially be adapted to monitor treatment with PARP inhibitors for other cancers.

"Not only could the test have a major impact on the treatment of prostate cancer, but it could also be adapted to open up the possibility of precision medicine to patients with other types of cancer as well," Dr. de Bono remarked.

In the study, researchers at the ICR and The Royal Marsden collected blood samples from 49 men at The Royal Marsden with advanced prostate cancer enrolled in the TOPARP-A Phase II clinical trial of olaparib. Olaparib is good at killing cancer cells that have errors in genes that have a role in repairing damaged DNA such as BRCA1 or BRCA2. Some patients respond to the drug for years, but in other patients, the treatment either fails early, or the cancer evolves resistance. Evaluating the levels of cancer DNA circulating in the blood, the researchers found that patients who responded to the drug had a median drop in the levels of circulating DNA of 49.6% after only eight weeks of treatment, whereas cancer DNA levels rose by a median of 2.1% in patients who did not respond.

Men whose blood levels of DNA had decreased at eight weeks after treatment survived an average of 17 months, compared with only 10.1 months for men whose cancer DNA levels remained high.

"This is another important example where liquid biopsiesa simple blood test as opposed to an invasive tissue biopsycan be used to direct and improve the treatment of patients with cancer," commented David Cunningham, Ph.D., director of clinical research at The Royal Marsden NHS Foundation Trust.

The researchers also performed a detailed examination of the genetic changes that occurred in cancer DNA from patients who had stopped responding to olaparib. They found that cancer cells had acquired new genetic changes that canceled out the original errors in DNA repairparticularly in the genes BRCA2 and PALB2that had made the cancer susceptible to olaparib in the first place.

"To greatly improve the survival chances of the 47,000 men diagnosed with prostate cancer each year, it's clear that we need to move away from the current one-size-fits-all approach to much more targeted treatment methods, concluded Matthew Hobbs, Ph.D., deputy director of research at Prostate Cancer UK. The results from this study and others like it are crucial as they give an important understanding of the factors that drive certain prostate cancers, or make them vulnerable to specific treatments.

The rest is here:
Liquid Biopsy Guides New Prostate Cancer Drug Trial - Genetic Engineering & Biotechnology News

Photo: Daniel Acker / Bloomberg

With Dow-DuPont merger, food editing gets fresh start

As U.S. regulators approved last week the $130 billion merger between Dow and DuPont, a new agricultural spinoff is on the cusp of moving forward with a DuPont unit that promises to change the world with a pioneering technology designed to improve crops, both in yields and quality.

The big question is whether food activists will yield to the new engineering, after attempting to erect warning signs in Connecticut and nationally in the first wave of genetically modified foods.

In 2013, Connecticut passed a law that would require labeling of foods made with genetically modified organisms but only if neighboring states did so, as well. With Vermont following suit in 2016, Congress passed and President Barack Obama signed federal legislation a year ago preempting states from requiring GMO labeling in favor of a national standard. Fed up with waiting, opponents derisively termed the law the DARK Act as an acronym for Deny Americans the Right to Know.

As the federal law worked through Capitol Hill, back in Hartford activists had taken another crack last year at GMO labeling in Connecticut, with a bill that would have mandated GMO disclosure for baby formulas and foods. Unlike 2013, the bill did not make it to a vote.

In advance of the 2016 debate the previous November, the Food & Drug Administration issued guidance on how companies should label GMO-based foods if they choose to do so, with the FDA continuing to hone final regulations mandated by the federal law.

Among the Connecticut-based manufacturers to adopt GMO labeling on a voluntary basis included the Norwalk-based Pepperidge Farm subsidiary of Campbell Soup.

The Non-GMO Project keeps a running database online of the foodmakers who have had their products verified as GMO-free, with more than 43,600 products listed as of June in Connecticut to include Saffron Road in Stamford, Barefoot and Chocolate in Norwalk, and Reds 100% All Natural in Fairfield.

The new GE in Connecticut and beyond

In the past year, the GMO debate has faded as attention has shifted to the promise of genetically edited foods in which producers trim existing DNA in foods rather than introducing new DNA, as the case in GMO-based genetic engineering.

DuPont has emerged as a major innovation in genetic editing with a new unit called CRISPR-Cas, designed to improve seeds without incorporating DNA from other species. DuPont describes the innovation as a continuation of what people have been doing since plants were first domesticated selecting for characteristics such as better yields, resistance to diseases, shelf life and nutritional qualities.

Research on CRISPR and acronym for Clustered Regularly Interspaced Short Palindromic Repeats is being extended to mice used by Jackson Laboratory in Farmington and Maine for medical research, with one staffer calling the technology a tremendously versatile tool in engineering genetic alterations. In March, Jackson Lab received a $450,000 federal grant to improve genome editing for research, drug testing and potential future therapies.

It is one thing to tinker with DNA for medicine, it is another to do it for everyday food people put on their table. To date, genetic editing has yet to spark the universal outcry that Monsanto incurred with its early efforts to produce GMO foods, with activists still absorbing the implications of the emerging technology.

Leading the charge for both Connecticut bills was Tara Cook-Littman, who has worked to marshal support via the lobbying groups Citizens for GMO Free Labeling and GMO Free CT.

Cook-Littman told Connecticut legislators last year that her group agreed in 2013 only reluctantly to the trigger clause compromise that shifted the enabling of Connecticuts GMO labeling law to companion laws in other states. She added that in the run-up to Vermont creating its own GMO law, companies voluntarily changed their labeling there and with sales not impacted by the move.

If Vermont can do it why cant we? Cook Littman asked at the time.

Alex.Soule@scni.com; 203-842-2545; http://www.twitter.com/casoulman

Link:
With Dow-DuPont merger, food 'editing' gets fresh start - Greenwich Time

Subscribe

Get our stories in your inbox, free.

Like Caribbean Life on Facebook.

Jomo Kwame Sundaram, a former economics professor and United Nations Assistant Secretary-General for Economic Development, received the Wassily Leontief Prize for Advancing the Frontiers of Economic Thought in 2007.

KUALA LUMPUR, June 13 2017 (IPS) - To her credit, Dr. Mahaletchumy has pioneered and promoted science journalism in Malaysia. This is indeed commendable in the face of the recent resurgence of obscurantism of various types, both traditional and modern.

But she has done herself, journalism and science a great disservice by using her position of influence to lobby for her faith in genetic engineering, promoting another obscurantism in the guise of science. In her blatantly polemical GE advocacy, she uses caricature and rhetoric to misrepresent and defame those she disagrees with.

She accuses us of spreading flawed arguments and inaccurate information, demonising private industry, and making a number of sweeping statements with inaccuracies about lower yield gains with genetically engineered crops, higher usage of herbicides, decline in crop and (sic) biodiversity, rising pest resistance, carcinogenicity of glyphosate, and increase in corporate power.

To be sure, our article was never intended for a scientific journal, but rather for IPS readers to appreciate the implications of recent research. It nevertheless provided links to relevant research for those interested, which she chose to ignore while accusing us of lying (false news) in Trumpian fashion.

Most importantly, she does not directly refute any of our arguments or the evidence that the increased output from non-GE crops has exceeded the productivity growth of GE crops due to, among others, the rise of pesticide resistance our main argument. Nor does she bother to refute the mounting evidence of greater farmer reliance on commercial agrochemicals, especially herbicides.

GE advocates cannot have it both ways. One cannot insist that only GE can increase output and productivity as well as improve farmers net incomes and the environment without offering or citing systematic evidence, and simply reject inconvenient evidence to the contrary.

Dr. Mahaletchumy fails to actually quote anything we actually wrote or to show how the sources we use are wrong. Her effort to discredit us resorts to innuendo and insinuation. While accusing us of selective citation, she has little hesitation to do what she condemns, citing only one person, Graham Brookes, not once, but twice, to make her case.

Instead of creating false news, as she claims we did, inter alia, we relied on and provided links to the US National Academy of Sciences report on Genetically Engineered Crops. The report provides an authoritative review of the now very considerable and diverse research on related issues. While the encyclopaedic volume admittedly includes a bland summary, the report itself offers a richly textured survey of evidence from many peer-reviewed studies.

She also refuses to recognize that most people go hungry in the world because they cannot afford access to the food they need and not because there is not enough food grown in the world.

Meanwhile, government and philanthropic funding of public research and development has declined while private corporate interests have been promoting GE, not exactly for charitable reasons.

We draw conclusions which other science journalists have also drawn, but instead of critically addressing our arguments, she lumps us together with GE critics, and invokes the same arguments and sources of the heavily corporate funded GE lobby.

Let me be very clear. We are keen supporters of technological progress, including biotechnology. And as we made clear, genetic modification is as old as nature itself. Unlike GE opponents, we remain open-minded about it.

Dr. Mahaletchumy is correct that there continues to be some debate over whether glyphosates are carcinogenic. This is partly why we insist on adherence to long established scientific ethics, including the precautionary principle.

But one cannot go authority shopping by dismissing the World Health Organization when it is inconvenient, and citing any body saying otherwise, especially when its authority is not relevant as she does.

We have previously shown how misleading research findings funded by the US Sugar Foundation had damaging consequences for world health for half a century.

We are also concerned about the unintended consequences of scientific progress. For example, the excessive use of cheap antibiotics for both humans and animals has generated antibiotic-resistant bacteria for every class of antibiotics, with annual mortality rates due to antibiotic resistant diseases expected to rise exponentially to ten million by mid-century.

One wonders why a journalist resorts to fraudulent misrepresentation in the cause of any advocacy, or in this case, to deceptively insist that her faith that GE is the only way forward is irrefutable science.

Updated 4:45 pm, June 15, 2017

2017 Community News Group

Subscribe

Get our stories in your inbox, free.

Like Caribbean Life on Facebook.

Continued here:
Genetic engineering lobbyist's Trumpian methods - Caribbean Life

In science and medicine, the terminology applied can be the difference between life and death, success and failure. Words have precise meanings, and a productive dialogue in the sciences requires adherence to a common set of mutually recognized terms. Shared meaning is like a verbal handshake that ensures a positive connection where information can flow.

Genetic engineering, familiarly known by the slippery colloquialism GMO, has been central to the production of drugs like insulin, enzymes used in cheese making, and laboratory-produced fibers. The widest-recognized successes have been the adoption of the technology by 20 million farmers onto almost half a billion acres of farmland, most of those in the developing world. Some 70 percent of grocery store products now contain ingredients from genetically engineered plants. And while scientists and farmers acknowledge concerns arising from the overuse of the technology, such as weed and insect resistance, there remains zero credible evidence of health-related concerns.

Still, the most beautiful and altruistic applications of this technology remain to be deployed. The innovations geared to solve specific issues in hunger, environment or consumer health have not left university laboratories or government greenhouses.

This cutting edge has not been dulled due to technical problems or clandestine dangers. Instead, technology has been stalled because of high deregulation costs and negative public perception founded on misinformation.

Could part of the problem simply be the bad branding of a good technology? Our social psyche has been saturated with fear-based manufactured risk and misinformation. Could cleaning up our vocabulary advance the publics understanding of the science and help illuminate its actual risks and benefits, while curing the tales of fear mongering?

Take for instance the abbreviation GMO. The term appears to have been first used thirty-three years ago this week, appropriately in the New York Times, a venue that regularly uses language to blur scientific reality in food space. Over the last decades the term has been adopted as nomenclature of derision; after all, who would want to feed their child an alien organism?

GMO is not a scientific term. Scientifically speaking, genetic modification is ambiguous, applying to many situations. Genetic modification is what happens upon a sexual crossing, mutation, multiplication of chromosomes (like in a seedless watermelon or banana), introduction of a single new gene from an unrelated species or the tweaking a genome with new gene editing techniques. These are all examples of genetic modification, but not all offer the predictability and precision of the process of genetic engineering.

This is why actual scientists rarely (if ever) use the GMO designation in technical parlance. It first regularly was highlighted in rhetoric opposing the technology, and since has sadly been adopted by mainstream media. Works that apply the term tend to disparage the technology, and opt for GMO rather than a scientifically precise term to stoke the negative perception.

For instance, the term GMO is prominently presented in the 2012 publication (retracted) by French biologist Gilles-Erich Seralini and colleagues, juxtaposed with tumor-ridden suffering animals. Their intent was to label the sad and grotesque figures of suffering animals with the three letters, G-M-O. A valid scientific effort would have labeled a figure with the gene installed that made the plant unique, not a catch-all term for an engineered plant. Seralinis work met tremendous outcry from a scientific community that saw this as being a political and manipulative use of the scientific literature to advance an agenda.

The use of the term GMO in the figures is consistent with that interpretation.

In order to help advance the public discussion, we should agree to abandon the meaningless term GMO. This is especially important for academics, scientists, farmers, dietitians and physicians professionals the public relies upon to answer questions about food and farming.

It is time for the science-minded community to adopt a common vocabulary to enhance effective discussion and enjoy more meaningful dialogue.

Here are my suggestions for how we can adopt a common vocabulary to make sure were all speaking the same language about these technologies.

1. Stop using GMO. It is imprecise. Everything not arising as a clone is genetically modified from previous forms, as is anything changed by mutation. You are a unique genetic modification of your parents combined genes. A dachshund is a genetic modification of an ancestral gray wolf.

Instead, we should replace GMO with Genetic Engineering. Genetic engineering is adding, subtracting, or adjusting genes in the lab that change a trait in the resulting plant, animal or microbe. It satisfies the very definition of engineering the application of science and mathematics to affect properties of matter or the sources of energy in nature to be made useful to people.

The term GMO term is intended to detract from the precision of the science.

However, the term GMO is something people recognize. Effective communication depends on shared meaning, so scientists or journalists should use the term once in a presentation or article parenthetically, then switch to genetic engineering. Experts should make it clear that GMO is not an acceptable term when discussing science.

The flawed GMO must also still be included in keywords, image tags, or in any online content. If it is not present, someone searching the internet for credible information with this non-scientific term may encounter a higher proportion of scientifically questionable information. Providing a parenthetical mention or brief reference ensures that those seeking science-based answers can find them.

2. An All-Encompassing Term. A better term for the scientific processes used to produce new varieties or breeds, or the intermediate steps, would be best referred to as crop or animal genetic improvement. In other words, when we use traditional breeding methods to make plants or animals better, it takes many steps and lots of selection. Thats genetic improvement, whether it is done by sexual exchange, breaking DNA strands with radiation or doubling chromosomes with chemistry.

3. The Newest Technologies. New technologies are now being used that allow scientists to make incredibly specific changes to DNA sequence, without leaving foreign DNA sequences (that some find objectionable) behind. These techniques should be collectively referred to as gene editing. Especially avoid referring to the technology by its technical name like CRISPR/Cas 9 or TALEN, which are specific types of gene editing. It is important because the list of gene editing methods is inevitably growing. Gene editing is also more precise than the often used genome editing.

The hierarchy of plant genetic improvement techniques. Those techniques mediated through the laboratory should be noted as genetic engineering even though gene editing and traditional breeding may result in identical final products. These are methods of improvement, and do not speak to the safety or efficacy of the final products produced.

The purpose of this brief new glossary is not to provide a mandate based on my narrow experience and observations. Instead, my goal is to offer a proposal so a scientific community eager to precisely engage the public can challenge the pros and cons of these terms to hone an optimal vocabulary. My hope is to ultimately derive an agreed-upon terminology that can be adopted and consistently applied by experts in science, medicine and agriculture. Journalists and science communications may then adopt the precise wording of the discipline for improved precision in communication.

Concrete, unambiguous terms can help curious and concerned people understand the realities of genetic engineering. Certainly, medicine has benefited from precise language, such as how childhood cognitive disabilities are now characterized with greater sensitivity and improved medical precision. This change improved social stigma of various developmental disorders, brought compassionate understanding to the conditions, and enhanced treatment for those affected.

Better scientific literacy and precision in terminology around genetic engineering would lead to a more productive discourse that ultimately could enable more rapid deployment of safe technologies that can help people and the planet. The individuals that insist on adhering to antiquated, divisive and imprecise terms will be automatically characterized as antiquated, divisive and imprecise.

The first step is to stop using the archaic, imprecise term GMO.

A version of this article appeared on Medium as Please say no to GMO and has been republished here with permission from the authors and the original publisher.

Kevin Folta is professor and chairman of the Horticultural Sciences Department at the University of Florida, Gainesville. Dr. Folta researches the functional genomics of small fruit crops, the plant transformation, the genetic basis of flavors, andstudies at photomorphogenesis and flowering. He has also written many publications and edited books, most recently the 2011 Genetics, Genomics, and Breeding of Berries. Follow him on Twitter@kevinfolta

Read the original:
Words matter: Goodbye 'GMO'? - Genetic Literacy Project

= By ANGELA OKETCH More by this Author 2 hoursago

The chemicals that farmers spray on their crops in form of pesticides to kill pests and prevent diseases have always been a bone of contention, with researchers trying to find safer alternatives. A new variety of rice that fights multiple pathogens with no effect on the yield of the crop, is thus a welcome relief for both farmers and scientists.

The discovery is based on a study of the plants immune system. Plants use receptors on the outside of their cells to identify molecules that signal a microbial invasion, and respond by releasing antimicrobial compounds. Therefore, identifying genes that kickstart this immune response yields disease-resistant plants.

Just like sick humans who are unproductive at work, plants grow poorly and produce unfavourable yields when their immune systems are overloaded. For a long time, scientists have focused on the NPR1 gene from a small, woody plant called Arabidopsis thaliana, to boost the immune systems of rice, wheat, tomatoes and apples.

However, NPR1 is not very useful for agriculture because it has negative effects on plants. To make it useful, researchers needed a better gene that would activate the immune response only when the plant is under attack. Rice with the gene was able to combat rice blast which often causes an estimated 30 per cent loss of rice crop worldwide, every year.

A segment of DNA called the TBF1 cassette acted as a control switch for the plants immune response. When the TBF1 cassette from the Arabidopsis genome was copied and pasted alongside and in front of the NPR1 gene in rice plants, it resulted in a strain of rice that could fend off offending pathogens without causing stunted growth seen in previously engineered crops.

The researchers tested the superiority of engineered rice over regular rice by inoculating crop leaves with the bacterial pathogens that cause rice blight and leaf streak, as well as the fungus responsible for blast disease. Whereas the infections spread on the leaves of wild rice plants, the engineered plants confined the invaders to a small area.

The researchers say this innovation could come in handy in the developing world where farmers with no access to fungicide often lose their entire crop to disease. The study was published in Nature.

open close

Read more:
Genetic engineering boosts immunity against crop disease - Daily Nation

Prof John Shine in 2015. Shine discovering a sequence of DNA now called the Shine-Dalgarno sequence which allows cells to produce proteins the basis for how all our cells operate. Photograph: Mal Fairclough/AAP

A man whose discovery was essential for the development of genetic engineering, and used that technology to create several therapies now helping many thousands of people, says receiving a Queens Birthday honour is a great recognition from the community of the value of scientific research.

John Shine started his career by discovering a sequence of DNA now called the Shine-Dalgarno sequence as part of his PhD in the mid 1970s.

That sequence, while a minuscule part of the human genome, allows cells to produce proteins the basis for how all our cells operate.

The discovery was essential for genetic engineering, spawned an entire biotech industry, and has now been used to produce therapies that have helped millions of people. In his own work, Shine used those techniques to clone of human insulin and growth hormone for the first time.

Other scientists honoured on Monday included astronomer Ken Freeman, who founded the field of galactic archaeology, and ethnobotanist Beth Gott.

Shine, who was appointed a Companion of the Order of Australia today, told the Guardian he has been unusually lucky in his career to have been able to oversee discoveries he made in basic sciences, be translated into real therapies and become commercialised.

My PhD was really esoteric research, he said, referring to his discovery of the Shine-Dalgarno sequence . But then I went over to San Francisco when gene cloning was just beginning right place, right time.

Shine had discovered how to clone the human gene that produces insulin, but to make that useful, it needed to be inserted into another organism that could be farmed in this case, bacteria, which would be farmed in large vats.

But if you want to put [the gene] into bacteria to make human insulin, you needed to trick the bacteria into thinking the gene was one of its own, he said.

It turned out Shines earlier discovery of the Shine-Dalgarno sequence was essential for making that final leap. Although the genetic code is the same in animals and bacteria, the regulatory code was very different. Thats where the Shine-Dalgarno sequence comes in, Shine said.

He needed to find the bacterias version of the Shine-Dalgarno sequence, and put that on either side of the human insulin gene, inside the bacteria.

You needed to put the right Shine-Dalgarno sequence just in front in the right place in the insulin gene to make the bacteria produce human insulin.

The fact that both problems were so closely related was mostly an accident, Shine says.

But throughout the rest of his career, Shine continued to be involved in the translation of his discoveries in esoteric science, all the way through to commercialisation.

Since stepping down as the head of the Garvan Institute in 2011 one of Australias top medical research institutes Shine has been the chair of the biotech giant CSL, one of Australasias largest companies.

So Ive come full circle, Shine said. CSL ... in more recent years, were moving into genetic engineering and weve released several genetically modified proteins for haemophilia that are changing the lives of thousands of people around the world.

Ive been very lucky to be able to go through the basic research in my career, and now see a lot of these real health care products come to fruition and improve the lives of thousands of people. Its wonderful when you can have all the excitement of research but also the satisfaction of seeing something very good coming out of it.

It is not the first time Shine has been recognised publicly for his work. In 2010 he won the prime ministers prize for science something his brother Rick Shine won in 2016.

Apart from the obvious personal honour, its a demonstration that the community does appreciate the benefits that come from research, Shine said. The wellbeing of any society is intimately linked to good healthcare.

Another winner of the prime ministers science prize, astronomer Ken Freeman, was appointed a Companion of the Order of Australia for his founding contributions to the field of galactic archaeology and his teaching work at the Australian National Universitys Mount Stromlo Observatory.

Honours were also awarded to Royal Melbourne hospitals Peter Grahame Colman (AM), for his work in endocrinology and diabetes research; aeronautical engineer Graeme Bird (AO), the former department head at the University of Sydney and a NASA consultant for 40 years; and Peter Klinken (AC), the chief scientist of Western Australia.

Ethnobotanist Beth Gott was made a Member of the Order of Australia for her work studying native plants and their use by Indigenous people. Gott founded Monash Universitys Aboriginal education garden in 1986 and has assembled databases of native plants in south-eastern Australia.

A paper she wrote in 2005 for the Journal of Biogreography found Indigenous fire-farming was crucial to the growth of plant tubers in southeastern Australia, allowing them to make up half of the local peoples diet.

Read more from the original source:
Scientist John Shine honoured for discovery that formed basis of genetic engineering - The Guardian

Bioenergy production techniques that are already available could be used to supply up to 30 percent of the worlds energy by 2050, according to a 2015 report by The Scientific Committee on Problems of the Environment (SCOPE), a global network of scientists from 24 countries that reviews scientific knowledge on the environment.

To find out why scientists are so optimistic about biofuel production in the developing world, SciDev.Net spoke with Glaucia Mendes Souza, researcher at the Chemistry Institute of the University of So Paulo.

Souza is also coordinator of the Bioenergy Research Program at the Brazilian research foundation FAPESP, and co-editor of the report.

What is the potential for expanding biofuel production in Latin America and Africa?

Huge! There are at least 500 million hectares of land available for biofuel production around the world. Much of that is in Latin America and sub-Saharan Africa, and is currently being used for low-intensity grazing.

What are the main scientific and technological advances related to biofuel production in Brazil?

Thanks to the ethanol programme and research carried out by the private sector, as well as public research entities, Brazil has obtained genetically improved varieties of sugar cane and managed to increase its productivity from 49 tonnes per hectare in 1970 to 85 tons per hectare in 2010.

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post: Q&A: Boosting bioenergy in Africa and Latin America

See the original post here:
How genetic engineering could boost biofuel production in Africa and Latin America - Genetic Literacy Project

Last month, researchers announced some astonishing findings in Nature Genetics: Theyd found 40 genes that play a role in shaping human intelligence, bringing the total number of known intelligence genes up to 52.

This study was a big deal because while weve known intelligence is largely heritable, we havent understood the specifics of the biology of IQ why it can be so different between people, and why we can lose it near the end of life.

The Nature Genetics study was a key early step toward understanding this, hailed as an enormous success in the New York Times.

And there are many more insights like this to come. The researchers used a design called a genome-wide association study. In it, computers comb through enormous data sets of human genomes to find variations among them that point to disease or traits like intelligence. As more people have their genomes sequenced, and as computers become more sophisticated at seeking out patterns in data, these types of studies will proliferate.

But theres also a deep uneasiness at the heart of this research it is easily misused by people who want to make claims about racial superiority and differences between groups. Such concerns prompted Nature to run an editorial stressing that the new science of genetics and intelligence comes to no such conclusions. Environment is crucial, too, Nature emphasized. The existence of genes for intelligence would not imply that education is wasted on people without those genes. Geneticists burned down that straw man long ago.

Also, nothing in this work suggests there are genetic difference in intelligence when comparing people of different ancestries. If anything, it suggests that the genetics that give rise to IQ are more subtle and intricate than we can ever really understand.

Were going to keep getting better at mapping the genes that make us smart, make us sick, or even make us lose our hair. But old fears and myths about genetics and determinism will rear their heads. So will fears about mapping ideal human genes that will lead to designer babies, where parents can pick traits for their children la carte.

To walk through the science, and to bust its myths, I spoke to Danielle Posthuma, a statistical geneticist at Vrije Universiteit in Amsterdam, who was the senior author on the latest Nature study.

Theres a simple understanding of genetics were all taught in high school. We learn, as Gregor Mendel discovered with pea plants, that we can inherit multiple forms of the same gene. One variation of the gene makes wrinkled peas; the other makes for round peas. Its true, but its hardly the whole story.

In humans, a few traits and illnesses work like this. Whether the bottom of your earlobes stick to the side of your face or hang free is the result of one gene. Huntingtons disease which deteriorates nerve cells in the brain is the result of a single gene.

But most of the traits that make you you your height, your personality, your intellect arise out of a complex constellation of genes. There might be 1,000 genes that influence intelligence, for example. Same goes for the genes that lead to certain disorders. Theres no one gene for schizophrenia, for obesity, for depression.

A single gene for one of these things also wont have an appreciable impact on behavior. If you have the bad variant of one gene for IQ, maybe your IQ score ... is 0.001 percent lower than it would have been, Posthuma says.

But if you have 100 bad variants, or 1,000, then that might make a meaningful difference.

Genome-wide association studies allow scientists to start to see how combinations of many, many genes interact in complicated ways. And it takes huge data sets to sort through all the genetic noise and find variants that truly make a difference on traits like intelligence.

The researchers had one: the UK Biobank, a library that contains genetic, health, and behavioral information on 500,000 Britons. For the study, they pulled complete genome information on 78,000 individuals who had also undergone intelligence testing. Then a computer program combed through millions of sites on the gene code where people tend to variate from one another, and singled out the areas that correlated with smarts.

The computer processing power needed for this kind of research this study had to crunch 9.3 million DNA letters from 78,000 people hasnt been available very long. But now that it is, researchers have been starting to piece together the puzzle that links genes to behaviors.

A recent genome-wide analysis effort identified 250 gene sites that predicted male pattern baldness in a sample of 52,000 men. (Would you really want to know if you had them?) And theres been progress identifying genes that signal risk for diabetes, schizophrenia, and depression.

And these studies dont just look at traits, diseases, and behavior. Theyre also starting to analyze genetic associations to life outcomes. A 2016 paper in Nature reported on 74 gene sites that correlate with educational attainment. (These genes, the study authors note, seem to have something to do with the formation of neurons.) Again, these associations are tiny the study found that these 74 gene variants could only explain 3 percent of the difference between any two people on what level of education they achieve. Its hardly set in stone that youll flunk school if you dont have these gene variants.

But still, they make a small significant difference once you start looking at huge numbers of people.

Its important to note that Posthumas study was only on people of European ancestry. Whatever we find for Europeans doesnt necessarily [extrapolate] for Asians or South Americans, [or any other group] she says. Those things are often misused.

Which is to say: The gene variations that produce the differences between Europeans arent necessarily the same variations that produce differences among groups of different ancestry. So if you were to test the DNA of someone of African origin, and saw they lacked these genes, it would be incredibly irresponsible to conclude they had a lower capacity for intelligence. (Again, there are also likely hundreds of more genetic sites that have something to do with intellect that have yet to be discovered.)

Posthumas work identifying genes associated with intelligence isnt about making predictions about how smart a baby might grow up to be. She doesnt think you can reliably predict educational or intelligence outcomes from DNA alone. This is all really about reverse-engineering the biology of intelligence.

Genes code for proteins. Proteins then interact with other proteins. Researchers can trace this pathway all the way up to the level of behavior. And somewhere along that path, there just might be a place where we can intervene and stop age-related cognitive decline, for instance, and Alzheimers.

We're finally starting to see robust reliable associations from genes with their behavior, she says. The next step is how do we prove that this gene is actually evolved in a disorder, and how does it work?

Understanding the biology of intelligence could also lead the way for personalized approaches to treating neurodegenerative diseases. Its possible that two people with Alzheimers may have different underlying genetic causes. Knowing which genes are causing the disease, then, you might be able to tailor the treatment, Posthuma says.

As more and more genome-wide studies are conducted, the more researchers will be able to assign people polygenic risk scores for how susceptible they might be for certain traits and diseases. That can lead to early interventions. (Or, perhaps in the wrong hands, a cruel and unfair sorting of society. Have you seen the movie Gattaca?)

And there are some worries about abusing this data, especially as more and more people get their genomes analyzed by commercial companies like 23&Me.

Many people are concerned that insurance companies will use it, she says. That they will look into people's DNA and say, Well, you have a very high risk of being a nicotine addict. So we want you to pay more. Or, You have a high risk of dying early from cancer. So you have to pay more early in life. And of course, that's all nonsense. Its still too complicated to make such precise predictions.

We now have powerful tools to edit genes. CRISPR/Cas9 makes it possible to cut out any specific gene and replace it with another. Genetic engineering has advanced to the point where scientists are building whole organisms from the ground up with custom DNA.

Its easy to indulge our imaginations here: Genome-wide studies are going to make it easier to predict what set of genes leads to certain life outcomes. Genetic engineering is making it easier to assemble whatever genes we want in an individual. Is this the perfect recipe for designer babies?

Posthuma urges caution here, and says this conclusion is far afield from the actual state of the research.

Lets say you wanted to design a human with superior intelligence. Could you just select the right variants of the 52 intelligence genes, and wham-o, we have our next Einstein?

No. Genetics is so, so much more complicated than that.

For one, there could be thousands of genes that influence intelligence that have yet to be discovered. And they interact with each other in unpredictable ways. A gene that increases your smarts could also increase your risk for schizophrenia. Or change some other trait slightly. There are trade-offs and feedback loops everywhere you look in the genome.

If you would have to start constructing a human being from scratch, and you would have to build in all these little effects, I think we wouldn't be able to do that, Posthuma says. It's very difficult to understand the dynamics.

There are about 20,000 human genes, made up of around 3 billion base pairs. We will never be able to fully predict how a person will turn out based on the DNA, she says. Its just too intricate, too complicated, and also influenced heavily by our environment.

So you could have a very high liability for depression, but it will only happen if you go through a divorce, she says. And who can predict that?

And, Posthuma cautions, there are some things that genome-wide studies cant do. They cant, for instance, find very, very rare gene variations. (Think about it: If one person in 50,000 has a gene that causes a disease, its just going to look like noise.) For schizophrenia, she says, we know that there's some [gene] variants that decrease or increase your risk of schizophrenia 20-fold, but they're very rare in the population.

And they cant be used to make generalizations about differences between large groups of people.

Last year, I interviewed Paul Glimcher, a New York University social scientist whose research floored me. Glimcher plans to recruit 10,000 New Yorkers and track everything about them for decades. Everything: full genome data, medical records, diet, credit card transactions, physical activity, personality test scores, you name it. The idea, he says, is to create a dense, longitudinal database of human life that machine learning programs can mine for insights. Its possible this approach will elucidate the complex interactions of genetics, behavior, and environment that put us at risk for diseases like Alzheimers.

Computer science and biology are converging to make these audacious projects easier. And to some degree, the results of these projects may help us align our genes and our environments for optimal well-being.

Again, Posthuma cautions: Not all the predictions this research makes will be meaningful.

Do we care if we find a gene that only increases our height or our BMI or our intelligence with less than 0.0001 percent? she asks. It doesn't have any clinical relevance. But it will aid our scientific understanding of how intellect arises nonetheless.

And thats the bottom line. The scientists doing this work arent in it to become fortune tellers. Theyre in it to understand basic science.

What most people focus on, when they hear about genes for IQ, they say: Oh, no. You can look at my DNA. You can tell me what my IQ score will be, Posthuma says. They probably dont know its much better if you just take the IQ test. Much faster.

Read the original here:
Scientists are finding more genes linked to IQ. This doesn't mean we can predict intelligence. - Vox

Cottons environmental footprint is much less noticeable today than was the case in the early 1960s, thanks largely to science and technology.

Ryan Kurtz, director of agricultural research, Cotton Incorporated, says the highly successful Boll Weevil Eradication Program, genetic engineering, innovations in tillage, and changes in farm size and efficiency combined to reduce cottons impact on the environment over the past 35 years.

[Kurtz] said cotton farming has evolved from horses to robots and drones. Weve seen great strides in reduced soil loss, water use, and pesticide use.

Biotechnology now protects plants from insect damage, Kurtz said. Herbicide tolerant varieties also allow a more efficient weed management system. Cotton farmers also reduce energy consumption because of biotech, he added.

Genetic engineering has improved varieties in other ways. We have more water efficient varieties, which improves on a plant already known for drought tolerance.

[T]he success of the Boll Weevil Eradication Program and the introduction of Bt cotton revolutionized insect control in cotton. At one time, cotton farmers in some areas were spraying as many as 15 times in a season. The average was seven. Following boll weevil eradication, the average dropped to five, and after Bt cotton was introduced the average dipped to two.

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post: Cottons effect on the environment continues to diminish

Read this article:
How genetic engineering helped reduce cotton's environmental footprint - Genetic Literacy Project

The 20th century veggie burger was a beige patty packed with whole grains and carrot chunks, sold in a brown paper wrapper. The 21st century version? Its bloody-pink and fleshy, thanks to heme, an ingredient created via genetic engineering.

To those steeped in the natural-food movement, the acronym GMO for genetically modified organisms has traditionally been almost as taboo as a plate of braised veal. However, that view could be changing as a new generation of Bay Area entrepreneurs upends the alternative meat and dairy industry, using biotechnology to create vegetarian foods that taste more like meat and promise ecological advantages to boot.

As somebody who has my entire life been a hard-core environmentalist I went vegan for a large part for that reason genetic engineering is one of the most important tools we can use in terms of environmental conservation, said Mike Selden, co-founder and CEO of Finless Foods in San Francisco, which is replicating fish fillets out of stem cells, though not currently with genetic engineering.

Not everyone agrees, and as these products hit the market including the aforementioned veggie burger that bleeds from Impossible Foods consumer and environmental groups have called for greater oversight and testing than whats currently required by the federal government.

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post:Meatless, tasty and genetically modified: a healthy debate

Original post:
21st century veggie burger: 'Bloody-pink and fleshy' thanks to genetic engineering - Genetic Literacy Project