LB4C. Stay Current—The Puzzle of Inheritance

2024-11-14. Meet Evo, the DNA-trained AI that creates genomes from scratch. By Mitch Leslie, Science. Excerpt: ChatGPT, the famous artificial intelligence (AI) chatbot, can summarize Moby Dick, write computer code, and serve up a recipe for chicken à la king because it has much of the written information on the internet at its silicon fingertips. What if it could do the same for DNA? That’s the advance behind a new study published today in Science. Researchers describe an AI model, schooled on billions of lines of genetic sequences, that can deduce how bacterial and viral genomes operate and use that information to design new proteins and even whole microbial genomes. The model, known as Evo, could help scientists probe evolution, investigate diseases, develop new treatments, and potentially answer a host of other biomedical questions…. Full article at https://www.science.org/content/article/meet-evo-dna-trained-ai-creates-genomes-scratch.

2024-11-13. Sweeter tomatoes are coming soon thanks to CRISPR gene editing. By Michael Le Page, New Scientist. Excerpt: …bigger tomato varieties could soon get a sweetness boost with the help of CRISPR gene editing. The bigger a tomato is, the lower its sugar content usually is, says Jinzhe Zhang at the Chinese Academy of Agricultural Sciences in Beijing. …Zhang and colleagues compared different varieties to identify genetic variants that affect sweetness. They found that two closely related genes called SlCDPK27 and SlCDPK26 are more active in large varieties. These genes code for proteins that lower the levels of an enzyme that produces sugars. When the team used CRISPR gene editing to disable these genes in a variety called Moneymaker, the levels of glucose and fructose in the fruits increased by up to 30 per cent with no decrease in yield. The fruits were also rated as sweeter in a taste test. The only other effect was fewer and smaller seeds, …. Full article at https://www.newscientist.com/article/2456025-sweeter-tomatoes-are-coming-soon-thanks-to-crispr-gene-editing/.

2024-11-04. Once thought a fantasy, effort to sequence DNA of millions of species gains momentum. By Elizabeth Pennisi, Science. Excerpt: Six years ago this month, scientists launched a massively ambitious effort to sequence the genomes of some 1.67 million plants, animals, fungi, and other microbes—essentially all known eukaryotes, or species with complex cells. It would cost an estimated $4.7 billion and take 10 years, but its leaders argued that having so many full DNA sequences would clarify life’s evolution, help with conservation, improve agriculture, and even aid human health. Today, the so-called Earth BioGenome Project (EBP) …is no longer pure aspiration, as organizers made clear at a meeting that ended last week. Its partners around the world have sequenced 3000 genomes so far, spanning 1060 eukaryotic families, and say they are on track to reach 10,000 species—the goal for the project’s first phase—by 2026. …Project leaders now hope to meet the 1.67 million species goal by 2032, and for hundreds of millions of dollars less than once predicted thanks to the faster speeds, lower costs, and greater accuracy of today’s DNA sequencing…. Full article at https://www.science.org/content/article/once-thought-fantasy-effort-sequence-dna-millions-species-gains-momentum.

2024-05-03. What a Philippine court ruling means for transgenic Golden Rice, once hailed as a dietary breakthrough. By DENNIS NORMILE, Science. Excerpt: Golden Rice seemed to be on the cusp of fulfilling its promise. Decades ago, researchers created the genetically modified (GM) rice variety to combat vitamin A deficiency, a scourge of the developing world that can cause blindness and even lead to death. But for more than 20 years activists opposed to GM crops kept Golden Rice confined to laboratories and test plots. But in 2021, the government of the Philippines granted a permit allowing the commercial planting of Malusog Rice, a Golden Rice variety tailored for local conditions and tastes. Farmers began to grow limited amounts of the grain in 2022. Officials hoped to have the variety comprise 10% of the nation’s rice harvest within 8 years, enough to meet the needs of all vitamin A deficient households. On 17 April, however, a Philippine Court of Appeals revoked the permit, bringing that plan to a halt. Ruling on a lawsuit brought by Greenpeace and other groups, the court concluded that in the absence of a scientific consensus on the safety of Golden Rice it should not be commercially cultivated. The nation’s constitution, the judges found, required the government to follow the so-called precautionary principle of waiting to approve new crops and activities until scientists reach a consensus that they are safe for humans and the environment. …the decision also blocks new field testing in greenhouses or open fields, crimping research until an approved monitoring scheme is in place. …Australia, New Zealand, Canada, and the United States have all approved Golden Rice for consumption although there is little if any cultivation of the crop…. Full article at https://www.science.org/content/article/what-philippine-court-ruling-means-transgenic-golden-rice-once-hailed-dietary.

2024-04-14. Should We Change Species to Save Them? By Emily Anthes, The New York Times. Excerpt: Australia has also become a case study in what happens when people push biodiversity to the brink. Habitat degradation, invasive species, infectious diseases and climate change have put many native animals in jeopardy and given Australia one of the worst rates of species loss in the world. In some cases, scientists say, the threats are so intractable that the only way to protect Australia’s unique animals is to change them. Using a variety of techniques, including crossbreeding and gene editing, scientists are altering the genomes of vulnerable animals, hoping to arm them with the traits they need to survive. …in this human-dominated age — in which Australia is simply at the leading edge of a global biodiversity crisis — the traditional conservation playbook may no longer be enough, some scientists said…. See article at https://www.nytimes.com/2024/04/14/science/australia-wildlife-assisted-evolution.html.

2024-04-09. Bacteria is the new black: Scientists create microbes that make self-dyeing textiles. [https://www.science.org/content/article/bacteria-new-black-scientists-create-microbes-make-self-dyeing-textiles] By MADELINE REINSEL, Science. Excerpt: For sustainability-minded fashionistas, materials made by fast-growing, eco-friendly bacteria offer an appealing alternative to leather or faux plastic replacements such as “pleather.” Yet coloring or adding patterns to these bacterial textiles can still mean working with environmentally harmful dyes. A study published last week in Nature Biotechnology may offer a solution: genetically engineering bacteria to produce melanin pigment so the material can dye itself. …says Sara Molinari, a synthetic biologist at the University of Maryland who was not involved in the study. Bacteria-generated textiles are “a completely new approach in material manufacturing.” The leather substitute is made of cellulose, an essential structural material in plants that is also produced by several species of bacteria. In recent years, researchers and designers have started to produce textiles from bacterial cellulose as an alternative to leather and pleather, some of which are already on the market. …although bacterial cellulose textiles have fewer environmental impacts than leather or plastic, they are naturally beige. That means they are typically colored using traditional dyeing processes, which can use large amounts of water and release harsh chemicals into the environment. …Researchers from Imperial College London (ICL) …genetically engineered a cellulose-producing bacterium, Komagataeibacter rhaeticus—the same bacterium that helps ferment kombucha—by adding a gene from another bacterium that produces black melanin pigment. Melanin is what gives color to tissue throughout the natural world, including human skin, eyes, and hair….

2024-02-15. New biosecurity group aims to prevent biotech disasters. [https://www.science.org/content/article/new-biosecurity-group-aims-prevent-biotech-disasters] By ROBERT F. SERVICE, Science. Excerpt: Biosecurity experts today launched a new international nonprofit designed to prevent modern biotechnology from causing harm. Known as the International Biosecurity and Biosafety Initiative for Science (IBBIS), the group aims to develop technological and policy guardrails to reduce the risk that biotech tools, such as the ability to synthesize and edit DNA, are accidentally or deliberately used to create deadly toxins and pathogens. …in recent years, researchers have also shown they can build dangerous viruses and other microbes from scratch….

2024-02-07. European Parliament votes to ease regulation of gene-edited crops. [https://www.science.org/content/article/european-parliament-votes-ease-regulation-gene-edited-crops] By ERIK STOKSTAD, Science. Excerpt: Europe has long been a bastion of skepticism about genetically engineered organisms, but today the European Parliament voted to lessen regulatory oversight of crops created through one type of DNA manipulation: gene editing. …[Oana] Dima says several factors have lessened the resistance recently. The success of messenger RNA vaccines for COVID-19 has improved the reputation of biotechnology, she notes. …Although the Parliament is now supportive of greenlighting gene-edited crops, some members want to prohibit patents on NGTs, arguing this would help keep costs low for farmers. Conventionally bred plants in Europe cannot be patented in Europe. Dima says the issue of patent protection should be discussed apart from the NGT legislation, and within the EU’s patent regulatory framework. …The Parliament also wants all NGT plants to be labeled when sold to consumers, whereas the Commission thinks biotech crops exempt from the GMO regulation should only have seeds labeled, so that farmers can be sure of what they are planting….

2024-01-09. How CRISPR could yield the next blockbuster crop. [https://www.nature.com/articles/d41586-024-00015-w?et_rid=40179168&et_cid=5059475] By Michael Marshall, Nature. Excerpt: In the space of just a few years, Jiayang Li is trying to achieve something that once took people centuries. He wants to turn a wild rice species into a domesticated crop by hacking its genome. And he is already part of the way there. …Li and his co-workers sequenced the [Oryza] alta genome and compared it with that of domestic rice, searching for genes similar to those that control important traits in the conventional crop, such as stem diameter, grain size and seed shattering. They then targeted these genes with customized gene-editing tools, trying to recapitulate some of the genetic changes that make domesticated rice easy to farm¹. All the traits improved to some degree, says Li, although the plants still drop their grains too soon. …The modification of this rice is one of a growing number of efforts to rapidly domesticate new crops using genome editing. Through this process, known as de novo domestication, transformations that took the world’s early farmers millennia could be achieved in just a handful of years. The work might improve the resilience of the global food supply: many wild relatives of staple crops have useful traits that could prove valuable when climate change puts stress on global agriculture. …But the technical challenges of de novo domestication are immense. …Targeted gene editing, using tools such as CRISPR–Cas9, is a powerful approach, but it cannot fully replicate the thousands of mutations that have fine-tuned modern domestic crops for growing and harvest….

2023-12-14. Pangolin-poaching hot spots revealed by DNA tests. [https://www.science.org/content/article/pangolin-poaching-hot-spots-revealed-dna-tests] By RIK STOKSTAD, Scioence. Excerpt: Using DNA tests, researchers have exposed smuggling routes and traced the remains of African pangolins back to specific forest populations. Since 2012, poaching of these endangered animals has shifted eastward from Sierra Leone to Cameroon, they report today in Science. The tests could help law enforcement agents more quickly identify the source of untold numbers of hunted pangolins, possibly millions of which are illegally shipped around the world each year. …Pangolins—also called scaly anteaters—are the only mammals with reptilelike scales, which grow from modified hair follicles. When threatened, the nocturnal animals will roll up into a ball, a ploy that provides no protection when humans hunt them for their meat. Their scales are also in demand, mainly in China, for use in traditional medicine, even though there’s no evidence that they provide effective remedies. As Asian pangolins have become scarce, hunting has increased elsewhere….

2023-12-08. F.D.A. Approves Sickle Cell Treatments, Including One That Uses CRISPR. [https://www.nytimes.com/2023/12/08/health/fda-sickle-cell-crispr.html] By Gina Kolata, , The New York Times. Excerpt: On Friday, the Food and Drug Administration approved the first gene editing therapy ever to be used in humans, for sickle cell disease, a debilitating blood disorder caused by a single mutated gene. …For the 100,000 Americans with the disease, most of them Black, the approvals offer hope for finally living without an affliction that causes excruciating pain, organ damage and strokes. While patients, their families and their doctors welcome the F.D.A.’s approvals, getting either therapy will be difficult, and expensive. …Vertex says its price to edit a patient’s genes will be $2.2 million; for, Bluebird it will be $3.1 million. But living with the disease is also extremely costly: On average, $1.7 million for those with commercial insurance over a patient’s lifetime….

2023-11-16. United Kingdom approves first-ever CRISPR treatment, a cure for sickle cell disease and beta thalassemia. [https://www.science.org/content/article/united-kingdom-approves-first-ever-crispr-treatment-cure-sickle-cell-disease-and-beta] By JOCELYN KAISER, Science. Excerpt: …In a world first, U.K. regulators yesterday approved a therapy that uses the gene-editing technique CRISPR. The approach treats two inherited blood disorders, including sickle cell disease, which afflicts mostly people of African ancestry, by modifying a patient’s blood stem cells in the lab and returning them. …The treatment “has the potential to significantly improve the quality of life for so many,” said an official from the United Kingdom’s Medicines and Healthcare products Regulatory Agency in a press release today. The agency approved the therapy, which the companies have called Casgevy, for patients ages 12 or older with sickle cell disease or beta thalassemia. …Questions will arise about whether the U.K.’s National Health Service and U.S. insurance companies will pay for the CRISPR treatment, also expected to be millions of dollars. Also clouding Casgevy’s approval is that most people with sickle cell disease live in Africa, which has few medical facilities that can offer the complex care needed to deliver the treatment. Those steps include chemotherapy to wipe out a patient’s existing blood cells and make room for the edited ones….

2023-11-06. The Scottish wildcat has been wiped out by breeding with domestic cats. [https://www.science.org/content/article/scottish-wildcat-has-been-wiped-out-breeding-domestic-cats] By DAVID GRIMM, Science. Excerpt: …A study published today in Current Biology finds that even though European wildcats and domestic cats overlapped in Great Britain for more than 2000 years—including at sites such as Kilton—they appear to have almost never interbred. That changed suddenly about 70 years ago, when domestic cats began to mate with wildcats in Scotland. In the span of mere decades, the genome of the Scottish wildcat—the last remaining wildcat in Great Britain—has become so corrupted that the animal is now effectively extinct, a second study in the same issue finds. The findings could complicate ongoing efforts to save the most endangered mammalian carnivore in Great Britain….

2023-10-27. Gene therapy restores hearing in children with rare form of deafness. [https://www.science.org/content/article/gene-therapy-restores-hearing-children-rare-form-deafness] By JOCELYN KAISER, Science. Excerpt: Several deaf children can hear after receiving gene therapy—a first for the approach—a team at Fudan University reported today at a meeting in Belgium. The children were born deaf because they inherited two defective copies of the gene for a protein called otoferlin that helps the inner ear’s hair cells transmit sound to the brain. …researchers injected harmless viruses carrying DNA for a working copy of the otoferlin gene into the children’s ears. Four of five patients treated now have some hearing, the MIT Technology Review reports. …The U.S. company Regeneron yesterday reported similar success for the first patient treated with its otoferlin gene therapy. Otoferlin-related deafness is very rare—it explains only 1% to 3% of cases of inherited deafness, the MIT Technology Review writes—but the results offer hope for treating other genetic forms of hearing loss….

2023-09-20. Worms with spider genes spin silk tougher than bulletproof Kevlar. [https://www.science.org/content/article/worms-spider-genes-spin-silk-tougher-bulletproof-kevlar] By KATHERINE BOURZAC, Science. Excerpt: …researchers have used gene editing to make silkworms that can spin spider fibers tougher than the Kevlar used in bulletproof vests. The material, described today in Matter, is “a really high-performance fiber,” says Justin Jones, a biologist who engineers spider silks at Utah State University but who was not involved with the research. It could be used to make lightweight but tough structural materials for fuel-efficient planes and cars, he says, wound dressings for faster healing, and superthin but tough sutures for eye surgeries. …researchers have tried for years to genetically engineer silkworms to make spider fibers. But spider silk proteins are large, and the correspondingly large genes have been difficult to insert in the genomes of other animals. So in the new study, Junpeng Mi, a biotechnologist at Donghua University, and colleagues chose to work with a relatively small spider silk protein. Called MiSp, it’s found in Araneus ventricosus, an orb-weaving spider found in East Asia. The scientists used CRISPR to insert MiSp in place of the gene in silkworms that codes for their primary silk protein. But the scientists retained some silkworm sequences in their MiSp gene construct, Mi says, in order to ensure the worm’s internal machinery could still work with the spider protein….

2023-08-28. Once rhabdomyosarcoma, now muscle. [https://www.cshl.edu/once-rhabdomyosarcoma-now-muscle/] By Luis Sandoval, Cold Spring Harbor Laboratory. Excerpt: Cold Spring Harbor Laboratory Professor Christopher Vakoc …has been on a mission to transform sarcoma cells into regularly functioning tissue cells. Sarcomas are cancers that form in connective tissues like muscle. …A devastating and aggressive type of pediatric cancer, rhabdomyosarcoma (RMS) resembles children’s muscle cells. …Vakoc and his team created a new genetic screening technique. Using genome-editing technology, they hunted down genes that, when disrupted, would force RMS cells to become muscle cells. That’s when a protein called NF-Y emerged. With NF-Y impaired, the scientists witnessed an astonishing transformation. Vakoc recounts: “The cells literally turn into muscle. The tumor loses all cancer attributes. They’re switching from a cell that just wants to make more of itself to cells devoted to contraction. Because all its energy and resources are now devoted to contraction, it can’t go back to this multiplying state.”….

2023-08-10. Engineered bacteria detect tumor DNA. [https://www.science.org/doi/10.1126/science.adf3974] By Robert M. Cooper et al, Science. Excerpt: Bacteria have been previously engineered to detect diseases by responding to specific metabolites or pathogens. Cooper et al. have now engineered a species of bacteria to detect specific mutations in human DNA. These bacteria, Acinetobacter baylyi, are normally nonpathogenic and naturally competent to take up DNA by horizontal gene transfer. The authors took advantage of this property, engineering these bacteria to become resistant to a specific drug only when they took up DNA containing a cancer-associated mutation in a specific oncogene, but not its wild-type counterpart. The bacteria detected their target both in culture and in mice bearing tumors with the relevant mutation after the bacteria were delivered by rectal enema, suggesting a potential clinical application….

2023-07-13. Genetically edited wood could make paper more sustainable. [https://www.science.org/content/article/genetically-edited-wood-could-make-paper-more-sustainable] By Robert F. Service, Science. Excerpt: Paper products may seem like the ultimate green technology. They are recyclable, biodegradable, and renewable. Their main ingredient, cellulose fibers, literally grows on trees. But separating the cellulose from other substances in the plant, such as the stiff, woody material called lignin, comes with a heavy environmental toll. Every year, paper mills generate millions of tons of chemical waste and more than 150 million tons of greenhouse gas emissions. Today in Science, researchers report they have found a way to reduce that burden. By using CRISPR gene-editing tools, they grew engineered poplar trees with far less lignin than usual. Milling these trees, they argue, could lower papermaking pollution while saving the industry billions of dollars….

2023-05-15. Privacy concerns sparked by human DNA accidentally collected in studies of other species. [https://www.science.org/content/article/privacy-concerns-sparked-human-dna-accidentally-collected-studies-other-species] By Gretchen Vogel, Science. Excerpt: Everywhere they go, humans leave stray DNA. Police have used genetic sequences retrieved from cigarette butts and coffee cups to identify suspects; archaeologists have sifted DNA from cave dirt to identify ancient humans. But for scientists aiming to capture genetic information not about people, but about animals, plants, and microbes, the ubiquity of human DNA and the ability of even partial sequences to reveal information most people would want to keep private is a growing problem, researchers from two disparate fields warn this week. Both groups are calling for safeguards to prevent misuse of such human genomic “bycatch.” Genetic sequences recovered from water, soil, and even air can reveal plant and animal diversity, identify pathogens, and trace past environments, sparking a boom in studies of this environmental DNA (eDNA). But the samples can also contain significant amounts of human genes, researchers report today in Nature Ecology & Evolution. In some cases, the DNA traces were enough to determine the sex and likely ancestry of the people who shed them, raising ethical alarms. …enough [DNA] is present, according to an analysis published today in Nature Microbiology, to potentially identify the donor’s sex, likely ancestry, certain disease risks, and, when linked to other databases, even their full identity…. See also New York Times article, Your DNA Can Now Be Pulled From Thin Air. Privacy Experts Are Worried. [https://www.nytimes.com/2023/05/15/science/environmental-dna-ethics-privacy.html]

023-03-14. Geneticists should rethink how they use race and ethnicity, panel urges. [https://www.science.org/content/article/geneticists-should-rethink-how-they-use-race-and-ethnicity-panel-urges] By Jocelyn Kaiser, Science. Excerpt: The once widely held notion that humans fall into discrete races has led to geneticists drawing erroneous conclusions about the role of genes in shaping health and traits, and in some cases, to harmful discrimination against some groups. An expert committee is now urging an overhaul of this practice. Most notably, the committee’s report calls for researchers to scrap the term “race” itself in most studies, use caution with other labels such as ethnicity and geography, and determine ancestry by quantifying how closely a group’s members are related to reference genomes drawn from certain populations. …Many human geneticists have already dropped the term “race” from their studies. But other recommendations in the report will be new to researchers using genomic data and challenging to put into practice, says clinical and molecular geneticist Wendy Chung of Columbia University, a report reviewer….

2022-11-17. Groundbreaking CRISPR treatment for blindness only works for subset of patients. [https://www.science.org/content/article/groundbreaking-crispr-treatment-blindness-only-works-subset-patients] By Jocelyn Kaiser, Science Magazine. Excerpt: After some early but cautious optimism, a company is shelving its pioneering gene-editing treatment for a rare inherited blindness disorder. Editas Medicine announced today the trial trying to use the gene editor CRISPR to treat Leber congenital amaurosis 10 (LCA10) led to “clinically meaningful” vision improvements in only three of 14 patients….

2022-10-20. Rewritten genetic code allows bacteria to fend off viral attacks. [https://www.science.org/content/article/rewritten-genetic-code-allows-bacteria-fend-viral-attacks] By Mitch Leslie, Science Magazine. Excerpt: Call it a genetic firewall. By partially rewriting the genetic code in bacteria, two groups of researchers have found they can thwart invading viruses, which must hijack the microbes’ genetic machinery to replicate. The strategy, described today in Science and in a preprint posted in July, could shield drug-producing bacteria from viral attacks and keep potentially dangerous genes from escaping from genetically modified organisms. …Because organisms share this genetic programming language, they can gain new abilities by acquiring genes from other organisms. The common language also allows researchers to insert human genes into bacteria, coaxing the cells to manufacture drugs such as insulin. But a universal genetic code leaves cells vulnerable to interlopers such as viruses and plasmids, DNA snippets that reproduce inside bacteria and can ferry genes among them. …The paper “shows a way to make any organism resistant to all viruses—and with one step,” Church says.…

2022-10-19. How the Black Death changed our immune systems. [https://www.science.org/content/article/gene-helped-people-survive-black-death-come-haunt] By Ann Gibbons, Science Magazine. Excerpt: Medieval DNA suggests immune gene helped protect against deadly pathogen, but may cause autoimmune problems today. …The survivors were much more likely to carry gene variants that boosted their immune response to Yersinia pestis, the flea-borne bacterium that causes the plague. One variant alone appears to have increased the chance of surviving the plague by 40%, they reported today in Nature. …The findings also indicate the Black Death caused a dramatic jump in the proportion of people carrying the protective variant; it is the strongest surge of natural selection on the human genome documented so far. But the improved immunity came at a cost: Today, the variant is also associated with higher risk of autoimmune diseases.…

2022-09-22. Genes for seeds arose early in plant evolution, ferns reveal. [https://www.science.org/content/article/genes-seeds-arose-early-plant-evolution-ferns-reveal] By Elizabeth Pennisi, Science Magazine. Excerpt: …The emergence of seed-producing plants more than 300 million years ago was an evolutionary watershed, opening new environments to plants and ultimately leading to the flowering plants that brighten our world and supply much of our food. But it was less of a leap than it seems, newly published DNA sequences suggest. The genomes, from three fern species and a cycad, one of the oldest kinds of seed-bearing plants, show genes key to making seeds are the same as those in the spore-producing machinery of ferns, which emerged tens of millions of years earlier. They evidently existed in a common ancestor but were recruited into different reproductive functions as plants diverged. The fern and cycad genomes, published in a series of papers over the past several months “fill the gap of the gene flow during plant evolution,” says Shu-Nong Bai, a plant developmental biologist emeritus at Peking University who helped sequence a member of the maidenhair fern genus. “Evolutionary innovation [can] come from the alternative use of existing genes or networks, not new genes.” The genomes also teach a second striking lesson: that plants acquired some of their genes not through mutation and selection, but straight from fungi or other microbes through a controversial process dubbed horizontal gene transfer.…

2022-09-16. CRISPR infusion eliminates swelling in those with rare genetic disease. [https://www.science.org/content/article/crispr-infusion-eliminates-swelling-those-with-rare-inflammatory-disease] By Jocelyn Kaiser, Science Magazine. Excerpt: In a medical first, an infusion of the CRISPR gene editor into the blood of three people with a rare genetic disease is easing their symptoms, a biotech company reports. The experimental treatment tamped down a liver protein that causes painful and potentially life-threatening bouts of swelling in the throat and limbs. Two people in the company’s trial are doing so well after a single CRISPR injection that they no longer need drugs to control their condition. The data were reported at a meeting today in Berlin on the disease, called hereditary angioedema. The effort marks the second time the company, Intellia Therapeutics, has used in vivo delivery of CRISPR to inactivate a gene directly inside a person’s body. But the latest results reflect the first report of clinical benefits associated with injecting the tool, which can snip out or replace targeted bits of DNA, says John Leonard, Intellia president and CEO. …CRISPR has already been shown to treat blood disorders via an ex vivo strategy in which a patient’s cells are harvested, edited in a lab, and then returned to the body. An in vivo approach for blindness disorders, where the gene editor is injected into the eye, is also showing tentative benefits. But directing CRISPR to specific organs or cells inside the body via an intravenous infusion is harder. Last year in a landmark study, Intellia and partner Regeneron reported that in people with a rare genetic disease called transthyretin (ATTR) amyloidosis, an in vivo CRISPR drug halted the build-up of liver proteins that can cause nerve pain, numbness, and heart problems. Although the knockdown of the protein appears to be long-lasting, the company hasn’t yet revealed whether the patients’ symptoms improved. For the trial in hereditary angioedema, however, the benefits emerged quickly, Intellia reports.…

2022-08-12. Her Discovery Changed the World. How Does She Think We Should Use It? [https://www.nytimes.com/interactive/2022/08/15/magazine/jennifer-doudna-crispr-interview.html] By David Marchese, The New York Times. Excerpt: It’s entirely possible, maybe even likely, that during some slow day at the lab early in her career, Jennifer Doudna, in a moment of private ambition, daydreamed about making a breakthrough that could change the world. But communicating with the world about the ethical ramifications of such a breakthrough? “Definitely not!” says Doudna, who along with Emmanuelle Charpentier won the Nobel Prize in Chemistry in 2020 for their research on CRISPR gene-editing technology. “I’m still on the learning curve with that.” [Read interview.…]

2022-07-22. Supercharged biotech rice yields 40% more grain. [https://www.science.org/content/article/supercharged-biotech-rice-yields-40-more-grain] By Erik Stokstad, Science Magazine. Excerpt: By giving a Chinese rice variety a second copy of one of its own genes, researchers have boosted its yield by up to 40%. The change helps the plant absorb more fertilizer, boosts photosynthesis, and accelerates flowering, all of which could contribute to larger harvests, the group reports today in Science. The yield gain from a single gene coordinating these multiple effects is “really impressive,” says Matthew Paul, a plant geneticist at Rothamsted Research who was not involved in the work. “I don’t think I’ve ever seen anything quite like that before.” The approach could be tried in other crops, too, he adds; the new study reports preliminary findings in wheat.…

2022-06-28. In 10 years, CRISPR transformed medicine. Can it now help us deal with climate change? [https://news.berkeley.edu/2022/06/28/in-10-years-crispr-transformed-medicine-can-it-now-help-us-deal-with-climate-change/] By Robert Sanders, UC Berkeley News. Excerpt: Coming from a long line of Iowa farmers, David Savage always thought he would do research to improve crops. That dream died in college, when it became clear that any genetic tweak to a crop would take at least a year to test; for some perennials and trees, it could take five to 10 years. …But the advent of CRISPR changed all that. Savage is now pivoting to molecular crop breeding, hoping to find ways to improve their carbon uptake and the amount of carbon they return to the soil. …“The advent of CRISPR basically allowed us to create new molecular tools for potentially skipping the slow aspects of plant tissue culture and plant genetic engineering, which are large barriers to doing experiments in plants,” said Savage, associate professor of molecular and cell biology at the University of California, Berkeley, …and member of the Innovative Genomics Institute (IGI), which focuses on the myriad uses of CRISPR-Cas9 genome editing. One of his collaborators, Krishna Niyogi, UC Berkeley professor of plant and microbial biology, estimates that the suboptimal photosynthetic reactions in plants could be improved with CRISPR editing to be between 20% and 50% more efficient. That means more carbon captured from the air, complementing other efforts — in particular, halting the burning of fossil fuels — to reduce greenhouse gases. Agriculture could potentially sequester billions of tons of carbon each year. …Capturing and sequestering carbon from the atmosphere is key to mitigating some of the worst consequences of climate change.… See also New York Times article CRISPR in the Classroom, by Eleanor Lutz.

2022-06-01. Better than CRISPR? Another way to fix gene problems may be safer and more versatile. By Jocelyn Kaiser, Science Magazine. Excerpt: Tools such as CRISPR that snip DNA to alter its sequence are moving tantalizingly close to the clinic as treatment for some genetic diseases. But away from the limelight, researchers are increasingly excited about an alternative that leaves a DNA sequence unchanged. These molecular tools target the epigenome, the chemical tags adorning DNA and its surrounding proteins that govern a gene’s expression and how it ultimately behaves. A flurry of studies in the past few years in mice suggests epigenome editing is a potentially safer, more flexible way to turn genes on or off than editing DNA. In one example described last month at a gene therapy meeting in Washington, D.C., an Italian team dialed down expression of a gene in mice to lower the animals’ cholesterol levels for months. Other groups are exploring epigenome editing to treat everything from cancer to pain to Huntington disease, a fatal brain disorder…. [https://www.science.org/content/article/better-crispr-another-way-fix-gene-problems-may-be-safer-and-more-versatile] 

2022-02-11. The precious genes of the world’s first cloned ferret could save her species. Joel Goldberg, Science Magazine. Excerpt: The National Black-footed Ferret Conservation Center in Fort Collins, Colorado, isn’t Jurassic Park, but new developments there might sound familiar to fans of the sci-fi classic. This year, the center’s sole cloned ferret, a 14-month-old female named Elizabeth Ann, is expected to become the first clone to be bred for the sake of saving her species from extinction. Three other species have been cloned for conservation: a Przewalski’s horse named Kurt, and two types of Southeast Asian cattle under threat, the gaur and the banteng. But Elizabeth Ann is the only clone set to take the next step and breed, an essential step in delivering her unique genes to the shrinking black-footed ferret gene pool.… [https://www.science.org/content/article/precious-genes-world-s-first-cloned-ferret-could-save-her-species]

2022-02-09. Gene-edited wheat resists dreaded fungus without pesticides. By Erik Stokstad, Science Magazine. Excerpt: New strain survives powdery mildew, a costly disease, without side effects… [https://www.science.org/content/article/gene-edited-wheat-resists-dreaded-fungus-without-pesticides]

2022-01-14. Donkeylike creatures may be first known hybrid animal made by humans. By Tess Joosse, Science Magazine. Excerpt: In the third millennium B.C.E., a strange group of donkeylike creatures was buried alongside royals in an ancient city east of what is now Aleppo, Syria. Archaeologists reckoned the animals were “kungas,” a rare type of ass highly prized by Bronze Age Mesopotamian elites. Yet their true biological identity has remained a mystery. …The genetic material in the skeletons was poorly preserved after thousands of years baking in the Syrian desert. …So the team used highly sensitive sequencing methods to analyze nuclear DNA from the remains, while also looking at regions from the animal’s maternal and paternal lineages. They compared the possible kunga DNA to the genomes of other equids, including modern horses, domestic donkeys, and the extinct Syrian wild ass. The bones weren’t from a single species of equid, the researchers report today in Science Advances. Rather, the animal was the first generation offspring of two species, a female domestic donkey and a male Syrian wild ass. …this is the first documented example of a half-wild, half-domesticated animal. The mule (a hybrid of horse and donkey) is possibly the next-earliest such beast, but it didn’t come onto the scene until later. … [https://www.science.org/content/article/donkeylike-creatures-may-be-first-known-hybrid-animal-made-humans]

2021-07-12. [https://www.nytimes.com/2021/07/12/science/gene-editing-crispr-who.html] – W.H.O. Experts Seek Limits on Human Gene-Editing Experiments. Source: By Gina Kolata, The New york Times. Excerpt: The panel also called on countries to ensure that beneficial forms of genetic alteration be shared equitably. …Their recommendations, made after two years of deliberation, aim to head off rogue science experiments with the human genome, and ensure that proper uses of gene-editing techniques are beneficial to the broader public, particularly people in developing countries, and not only the wealthy…. 

2021-06-04. [https://www.sciencemag.org/news/2021/06/scientists-evolve-fungus-battle-deadly-honey-bee-parasite] – Scientists evolve a fungus to battle deadly honey bee parasite. By Erik Stokstad, Science Magazine. Excerpt: The biggest scourge to bees is tiny—a mite the size of a pinhead that feeds on them and spreads deadly viruses. Getting rid of the parasite, Varroa destructor, is tough: Chemicals can kill it, but the mite has started to evolve resistance to the usual pesticides; moreover, these and other treatments can harm the bees themselves. Now, researchers have toughened up a mite-killing fungus so it can slay the bee slayers inside a hot beehive. If the new strain passes further tests, it could help honey bees around the world avoid a gruesome fate, and reduce the use of chemical pesticides. …One biopesticide, the common soil fungus Metarhizium acridum, has been used against locusts in recent years. Some 2 decades ago, researchers at the U.S. Department of Agriculture and elsewhere began to study related species that can kill the varroa mite. …When spores of M. anisopliae, for example, land on a varroa mite, they germinate and grow tiny tubes that drill through the exoskeleton and grow throughout the insect, killing it…. …The fungus might have been a great biopesticide, but for one catch: It wouldn’t grow well inside the warmth of the hives, which can reach temperatures of 35°C. …So Han and colleagues set out to create a heat-tolerant strain of the related M. brunneum. First, they stressed the fungus by starving spores or adding hydrogen peroxide to its growing medium. This sped up the rate of mutations. Then, the researchers put spores from the stressed fungus in an incubator and gradually raised the temperature. Most of the spores died, but the survivors seeded the next generation. After seven rounds of this unnatural selection, the percentage of spores that germinated at 35°C—a crucial step for infecting the mites—increased from 44% to 70%…. 

2021-02-18. Meet Elizabeth Ann, the First Cloned Black-Footed Ferret. By Sabrina Imbler, The New York Times. Excerpt: Her birth represents the first cloning of an endangered species native to North America, and may bring needed genetic diversity to the species… [https://www.nytimes.com/2021/02/18/science/black-footed-ferret-clone.html] 

2021-02-10. Fish had the genes to adapt to life on land—while they were still swimming the seas. By Elizabeth Pennisi, Science Magazine. Excerpt: Almost 700 years ago, Jacob van Maerlant, a Dutch poet, envisioned a fish all set for life on land: It had sprouted arms to hoist itself ashore. Now, three genetic studies make his fantasy look remarkably prescient. Together, the studies suggest that in terms of genes, the aquatic precursors of four-limbed land animals, or tetrapods, were as well-prepared as the Dutch fantasy fish. They were pre-equipped with genes that could be turned to making limbs, efficient air-breathing lungs, and nervous systems tuned to the challenges of life on land. …In the trio of studies published last week in Cell, genes in living fish took the place of fossils as a way to peer back in time. One set of clues came from studies of mutagenized zebrafish, a favorite model for studying development. M. Brent Hawkins, then a Harvard University graduate student and now a postdoc, was shocked to discover zebrafish mutants with two bones resembling the forelimb bones of land animals in their front fins, complete with muscles, joints, and blood vessels…. [https://www.sciencemag.org/news/2021/02/fish-had-genes-adapt-life-land-while-they-were-still-swimming-seas]

2021-01-29. VIDEO – How do the leading COVID-19 vaccines work? Science explains. By ScienceSenior Correspondent Jon Cohen, Science Magazine. Excerpt: As countries like the United States and United Kingdom inoculate their residents with never-before-used vaccine technology, others, including Russia, China, and India, are investing in more traditional approaches, like inactivated coronavirus vaccines. But no matter the technique, together they have the potential to create multiple lines of defense against SARS-CoV-2. ScienceSenior Correspondent Jon Cohen explains how each of these vaccines can protect us from severe illness—and what understanding the details of our immune responses could mean for the future of human trials…. [https://www.sciencemag.org/news/2021/01/how-leading-covid-19-vaccines-work]  See also “Proud of vaccine success, Warp Speed’s ex–science head talks politics, presidents, and future pandemics” by Jon Cohen.

2020-11-03. ‘Landmark’ study resolves a major mystery of how genes govern human height. By Jocelyn Kaiser, Science Magazine. Excerpt: …Studies of identical and fraternal twins suggest up to 80% of variation in height is genetic. But the genes responsible have largely eluded researchers. Now, by amassing genome data for 4 million people—the largest such study ever—geneticists have accounted for a major share of this “missing heritability,” at least for people of European ancestry. In this group, they’ve identified nearly 10,000 DNA markers that appear to fully explain the influence of common genetic variants over height. …If the missing genetic contributors to other traits and diseases can be identified, and extended to other ancestries, the results could “inform new biology and contribute to personalized medicine,” suggests Loïc Yengo of the University of Queensland in St. Lucia, Australia, whose team presented the work online this week at the annual meeting of the American Society of Human Genetics…. [https://www.sciencemag.org/news/2020/11/landmark-study-resolves-major-mystery-how-genes-govern-human-height] 

2020-07-22. How bats have outsmarted viruses—including coronaviruses—for 65 million years. By Elizabeth Pennisi, Science Magazine. Excerpt: Although the SARS-CoV-2 virus has sickened more than 14 million people, bats contract similar viruses all the time without experiencing any known symptoms. Now, the newly sequenced genomes of six species spanning the bat family tree reveal how they’ve been outsmarting viruses for 65 million years. The findings are an “excellent starting point for understanding the superstar immune systems of bats,” says Laurel Yohe, a postdoc at Yale University who studies bat evolution and was not involved with the work. With more than 1400 species, bats are the second most diverse group of mammals on Earth. They live on every continent except Antarctica, and range in size from two to more than 1000 grams. They fly, they echolocate, and some live up to 41 years—a long time for animals of their size. They are also known to carry many different kinds of viruses, including coronaviruses, with no ill effects. …an international consortium launched the Bat1k project, which stands for bat 1000, in 2017 to sequence the genomes of all bat species. Six of those genomes are now complete, the consortium reports today in Nature [https://www.nature.com/articles/s41586-020-2486-3]. …analysis revealed bats have disabled at least 10 genes that other mammals use to mount inflammatory responses against infection. But they also have extra copies and modifications of antiviral genes that may explain their high tolerance for disease. Finally, their genome is littered with DNA pieces derived from past viral infections that got incorporated when the viral genomes were replicated. “These nonbat genes leave a kind of medical record … a diary of previous infections,” Yohe says. That diary reveals that bats have probably had more viral infections than all other mammals over time and have even been infected by viruses thought only to attack birds, the team reports. “The findings highlight bats’ ability to tolerate and survive viral infections more efficiently than other mammals,” says Sharlene Santana, an evolutionary biologist at the University of Washington, Seattle…. [https://www.sciencemag.org/news/2020/07/how-bats-have-outsmarted-viruses-including-coronaviruses-65-million-years]  

2020-07-08. New method to edit cell’s ‘powerhouse’ DNA could help study variety of genetic diseases. By Jon Cohen, Science Magazine. Excerpt: In a biological beating of swords into plowshares, researchers have converted a bacterial toxin into a genome editing tool that, for the first time, can make precise changes to DNA in mitochondria, the cell’s power plants. The tool, which worked in lab experiments with human cells, could open the door to new studies of—and one day therapies for—dozens of hard-to-treat diseases caused by mutations in mitochondrial DNA (mtDNA). These rare conditions, which include Leber hereditary optic neuropathy and lethal infantile cardiomyopathy, collectively affect about one in 4000 people. Until now, research on these illnesses has been stymied in part because there was no way of reproducing the mutations in strains of mice. …To create the new tool, which combines features of CRISPR and an older technology called transcription activator-like effectors (TALEs), three teams joined forces. “Part of what made the project so fun to work on, and ultimately successful, is the fact that three labs came together organically because the science led us to each other,” says David Liu, a chemist at the Broad Institute and the last author of a paper that describes the work in Nature today…. [https://www.sciencemag.org/news/2020/07/new-method-edit-cell-s-powerhouse-dna-could-help-study-variety-genetic-diseases] 

2020-05-14. How Venus flytraps evolved their taste for meat. By Elizabeth Pennisi, Science Magazine. Excerpt: How does a plant develop a taste for flesh? In the play Little Shop of Horrors, all it takes is a drop of human blood. But in real life, it takes much more. Now, a study of three closely related carnivorous plants suggests dextrous genetic shuffling helped them evolve the ability to catch and digest protein-rich meals. Carnivorous plants have developed many devious ways to snare prey. Pitcher plants, for example, use “pitfall traps” that contain enzymes for digesting stray insects. Others—including the closely related Venus flytrap (Dionaea muscipula), the aquatic waterwheel plant (Aldrovanda vesiculosa), and the sundew (Drosera spatulata)—use moving traps. The sundew rolls up its sticky landing pad when mosquitoes get caught. And the Venus flytrap uses modified leaves, or pads, that snap shut when an insect lands—but only after the pads sense multiple touches on their trigger hairs. To find out how these traps evolved, researchers led by computational evolutionary biologist Jörg Schultz and plant biologist Rainer Hedrich, both of the University of Würzburg, sequenced the genomes of the sundew, the aquatic waterwheel, and the Venus flytrap, which are all closely related. They then compared their genomes with those of nine other plants, including a carnivorous pitcher plant and noncarnivorous beetroot and papaya plants. They found that the key to the evolution of meat eating in this part of the plant kingdom was the duplication of the entire genome in a common ancestor that lived about 60 million years ago, the team reports today in Current Biology [https://www.cell.com/current-biology/fulltext/S0960-9822(20)30567-4]. That duplication freed up copies of genes once used in roots, leaves, and sensory systems to detect and digest prey. For example, carnivorous plants repurposed copies of genes that help roots absorb nutrients, to absorb the nutrients in digested prey. “That root genes are being expressed in the leaves of carnivores is absolutely fascinating,” says Kenneth Cameron, a botanist at the University of Wisconsin, Madison…. [https://www.sciencemag.org/news/2020/05/how-venus-flytraps-evolved-their-taste-meat]  

2020-04-09. How a gene from a grass-living fungus could save wheat crops worldwide. By Erik Stokstad, Science Magazine. Excerpt: Wheat scab hits farmers with a double punch. The fungal disease, also known as Fusarium head blight, shrivels grain and can significantly dent harvests of wheat and barley. Worse, the toxins released by the fungus Fusarium graminearum, a growing problem in the breadbaskets of Europe, North America, and China, remain in grain intended for food. Above legal limits, they can harm people and animals. …Fungicides are no panacea, in part because the pathogen infects during wet weather, when the chemicals wash away. But researchers have now found a protective gene in a wild relative called wheatgrass. Called Fhb7, it encodes a toxin-destroying enzyme, the team reports online today in Science. “The gene could have a very large impact in breeding for Fusarium resistance in wheat,” says James Anderson, a wheat breeder at the University of Minnesota, Twin Cities…. [https://www.sciencemag.org/news/2020/04/how-gene-grass-living-fungus-could-save-wheat-crops-worldwide] 

2020-02-20. High-altitude genes could turn Himalayan wolves into a new species. By Virginia Morell, Science. Excerpt: In the high grasslands of Earth’s tallest mountains lives a group of wolves known for their long snouts, pale woolly pelts, and low-pitched calls. …A new study suggests these wolves—which range across northern India, China, and Nepal—are genetically distinct from the gray wolves that live nearby, thanks to genes that help them cope with the thin air above 4000 meters. …The finding supports previous calls for it to be recognized as a separate species, and it also suggests the wolf’s range is twice as large as was thought. …samples of wolf feces collected across the Tibetan Plateau of China, Tajikistan, and Kyrgyzstan provide genetic evidence that it is a different breed. …The widespread presence of scat from Himalayan wolves also suggests they are not restricted to the Himalayas, but roam the entire Tibetan Plateau at elevations above 4000 meters. Together, these findings suggest the high-living wolf should be considered a distinct species—or at least as an “evolutionary significant unit,” the researchers write. And they support previous research suggesting these little-studied canids are the oldest lineage of modern wolves, having diverged from other wolves between 630,000 to 800,000 years ago…. [https://www.sciencemag.org/news/2020/02/high-altitude-genes-could-turn-himalayan-wolves-new-species] 

2020-02-10. Pangolins Are Suspected as a Potential Coronavirus Host. By James Gorman, The New York Times. Excerpt: In the search for the animal source or sources of the coronavirus epidemic in China, the latest candidate is the pangolin, an endangered, scaly, ant-eating mammal that is imported in huge numbers to Chinese markets for food and medicine. The market in pangolins is so large that they are said to be the most trafficked mammals on the planet. All four Asian species are critically endangered, and it is far from clear whether being identified as a viral host would be good or bad for pangolins. …It is also far from clear whether the pangolin is the animal that passed the new virus to humans. Bats are still thought to be the original host of the virus. …Chinese researchers published a report in October that documented that pangolins can host a variety of coronaviruses. They released the genetic sequences from their analysis to public databases where they could be analyzed. Then, on Friday, the Xinhua News Agency reported that researchers at South China Agricultural University had found a virus in pangolins that had a 99 percent match to the novel coronavirus that has now sickened 40,000 people and killed more than 900. That would be the closest match so far. …Public databases enable any lab, anywhere, to investigate and analyze genetic sequences published for bat and pangolin coronaviruses, and hypothesize what may have happened…. [https://www.nytimes.com/2020/02/10/science/pangolin-coronavirus.html] 

2019-07-31. China’s CRISPR push in animals promises better meat, novel therapies, and pig organs for people. By Jon Cohen, Science Magazine. [https://www.sciencemag.org/news/2019/07/china-s-crispr-push-animals-promises-better-meat-novel-therapies-and-pig-organs-people] Excerpt: … Through a combination of patience, ingenuity, and enormous animal resources, the team has already used CRISPR to create an astonishing range of genome-edited monkeys to serve as models for studying human diseases. …They’ve built on that success, exploiting CRISPR’s speed and precision to create monkey models of muscular dystrophy, autism, and cancer. …Almost 2 years ago, in a proof of principle for He’s infamous experiment, they knocked out in monkey embryos the gene for the immune cell protein CCR5, a mutation that makes humans resistant to infection with the most commonly transmitted variant of HIV. That work leaves them uneasy today. “We had no idea he was going to do this in a human being,” Niu says, stressing that their study had yet to evaluate how the editing affected the monkeys when news of the edited babies broke. “It’s unbelievable.” China now has at least four groups of CRISPR researchers doing gene editing with large colonies of monkeys. …says reproductive biologist Jon Hennebold at the Oregon National Primate Research Center in Hillsboro “The level of animal support they have to do those experiments is really astounding.” It’s not just monkeys. China’s researchers have racked up a long list of CRISPR firsts in dogs, mice, rats, pigs, and rabbits. That research promises higher quality meats, disease-resistant livestock, and new medical treatments and organs for human transplantation…. See also To feed its 1.4 billion, China bets big on genome editing of crops [https://www.sciencemag.org/news/2019/07/feed-its-14-billion-china-bets-big-genome-editing-crops ] 

2019-06-06. $180 million DNA ‘barcode’ project aims to discover 2 million new species. By Elizabeth Pennisi, Science Magazine. [https://www.sciencemag.org/news/2019/06/180-million-dna-barcode-project-aims-discover-2-million-new-species] For GSS Losing Biodiversity chapter 4. Excerpt: For centuries biologists have identified new species at a painstakingly slow pace, describing specimens’ physical features and other defining traits, and often trying to fit a species into the tree of life before naming and publishing it. Now, they have begun to determine whether a specimen is likely a novel species in hours—and will soon do so at a cost of pennies. It’s a revolution driven by short stretches of DNA—dubbed barcodes in a nod to the familiar product identifiers—that vary just enough to provide species-distinguishing markers, combined with fast, cheap DNA sequencers. …Biodiversity experts estimate that Earth has between 8.7 million and 20 million kinds of plants, animals, and fungi, but to date only 1.8 million of them have received formal descriptions. Insects, in particular, are a vast realm of undiscovered species. “Yet collectively, they may contribute more biomass in terrestrial habitats than all wild vertebrates combined,” says Rudolf Meier, a biologist from the National University of Singapore who has been developing barcoding approaches with a small DNA sequencer….

2019-02-07. This spud’s for you: A breeding revolution could unleash the potential of potato. By Erik Stokstad, Science Magazine.  Excerpt: THE SACRED VALLEY OF THE INCAS IN PERU—On a bleak, brown hill here, David Ellis examines a test plot of potato plants and shakes his head. “They’re dead, dead, dead,” he says. Pests and lack of rain have laid waste to all 17 varieties that researchers had planted. It is a worrying sign for Ellis, the now-retired director of the gene bank at the International Potato Center (CIP) in Lima. People have grown potatoes in this rugged stretch of the Andes for thousands of years. In recent years, that task has gotten tougher, in part because of climate change. Drought and frost are striking more often. The rains come later, shortening the growing season. And warmer temperatures have allowed moths and weevils to encroach from lower elevations. To find potatoes that can cope with those challenges, researchers and Peruvian farmers are testing dozens of the 4350 locally cultivated varieties, or landraces, kept in CIP’s refrigerated storage. The plants in this plot fell short. “Native landraces evolved over time,” Ellis says. But, he says, climate change is happening “too fast for these varieties to adapt.”… [https://www.sciencemag.org/news/2019/02/spud-s-you-breeding-revolution-could-unleash-potential-potato]

2019-01-29. Seeking Superpowers in the Axolotl Genome. By Steph Yin, The New York Times.  [https://www.nytimes.com/2019/01/29/science/axolotl-dna-genome-sequence.html] Excerpt: The smiling salamanders can regrow most of their body parts, so researchers are building improved maps of their DNA. …Threatened by habitat degradation and imported fish, they can only be found in the canals of Lake Xochimilco, in the far south of Mexico City. Captive axolotls, however, are thriving in labs around the world. In a paper published Thursday in Genome Research, a team of researchers has reported the most complete assembly of DNA yet for the striking amphibians. Their work paves the way for advances in human regenerative medicine….  

2019-01-07. Monogamy may have a telltale signature of gene activity. By Kelly Servick, Science Magazine. [https://www.sciencemag.org/news/2019/01/monogamy-may-have-telltale-signature-gene-activity] Excerpt: In the animal world, monogamy has some clear perks. Living in pairs can give animals some stability and certainty in the constant struggle to reproduce and protect their young—which may be why it has evolved independently in various species. Now, an analysis of gene activity within the brains of frogs, rodents, fish, and birds suggests there may be a pattern common to monogamous creatures. Despite very different brain structures and evolutionary histories, these animals all seem to have developed monogamy by turning on and off some of the same sets of genes. …Neuroscientist Hans Hofmann and evolutionary biologist Rebecca Young at the University of Texas in Austin…wanted to hunt down a gene activity signature associated with monogamy in males across a wide variety of species—frogs, mice, voles, birds, and fish. So in each of these groups, they selected two species, one monogamous and one nonmonogamous. Rounding up the brains of those animals took an international team and years of effort. …Back the lab, the researchers then grouped roughly comparable genes across all 10 species based on similarities in their sequences. For each of these cross-species gene groups, they measured activity based on how much the cells in the brain transcribed the DNA’s proteinmaking instructions into strands of RNA. Among the monogamous animals, a pattern emerged. The researchers found certain sets of genes were more likely to be “turned up” or “turned down” in those creatures than in the nonmonogamous species….  

2019-01-07. Dog breeds really do have distinct personalities—and they’re rooted in DNA. By Elizabeth Pennisi, Science Magazine. [https://www.sciencemag.org/news/2019/01/dog-breeds-really-do-have-distinct-personalities-and-they-re-rooted-dna 0] Excerpt: American Kennel Club descriptions of dog breeds can read like online dating profiles: The border collie is a workaholic; the German shepherd will put its life on the line for loved ones. Now, in the most comprehensive study of its kind to date, scientists have shown that such distinct breed traits are actually rooted in a dog’s genes. The findings may shed light on human behaviors as well. …When the dog genome was sequenced in 2005, scientists thought they would quickly be able to pin down the genes that give every breed its hallmark personality. But they found so much variation even within a breed that they could never study enough dogs to get meaningful results. So in the new study, Evan MacLean, a comparative psychologist at the University of Arizona in Tucson, Noah Snyder-Mackler at the University of Washington in Seattle, and colleagues began by looking at behavioral data for about 14,000 dogs from 101 breeds. The analyses come from the Canine Behavioral Assessment & Research Questionnaire (C-BARQ; https://vetapps.vet.upenn.edu/cbarq/), …C-BARQ asks questions like, “What does your dog do when a stranger comes to the door?” to allow owners to objectively characterize 14 aspects of their pet’s personalities, including trainability, attachment, and aggression. Since the survey was developed in 2003, more than 50,000 owners have participated….  

2019-01-03. Genetic data on half a million Brits reveal ongoing evolution and Neanderthal legacy. By Ann Gibbons, Science Magazine. [https://www.sciencemag.org/news/2019/01/genetic-data-half-million-brits-reveal-ongoing-evolution-and-neanderthal-legacy] Excerpt: Neanderthals are still among us, Janet Kelso realized 8 years ago. She had helped make the momentous discovery that Neanderthals repeatedly mated with the ancestors of modern humans—a finding that implies people outside of Africa still carry Neanderthal DNA today. Ever since then, Kelso has wondered exactly what modern humans got from those prehistoric liaisons—beyond babies. How do traces of the Neanderthal within shape the appearance, health, or personalities of living people? …a few years ago, Kelso and her colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, turned to a new tool—the UK Biobank (UKB), a large database that holds genetic and health records for half a million British volunteers. The researchers analyzed data from 112,338 of those Britons—enough that “we could actually look and say: ‘We see a Neanderthal version of the gene and we can measure its effect on phenotype in many people—how often they get sunburned, what color their hair is, and what color their eyes are,’” Kelso says. They found Neanderthal variants that boost the odds that a person smokes, is an evening person rather than a morning person, and is prone to sunburn and depression. …When it comes to natural selection in humans, most studies have only been able to detect dramatic cases thousands or millions of years ago in genes of known function. Now, Pickrell and Przeworski wondered whether they could detect genetic variants that affect survival today—and whether natural selection in recent generations has been weeding out harmful ones or favoring beneficial ones….

2018-12-08. Seeking Clues to Longevity in Lonesome George’s Genes. By Steph Yin, The New York Times. [https://www.nytimes.com/2018/12/08/science/lonesome-george-tortoise.html] Excerpt: The giant tortoise lived for more than a century, carrying genes linked to a robust immune system, efficient DNA repair and resistance to cancer. When Lonesome George, the only survivor of the Pinta Island tortoises of the Galápagos, died in 2012, the news landed with a blow. Rationally, people had time to prepare for the reality that George would one day fade away, and with him, an entire lineage. He had lived for a century or more, a common life expectancy for giant tortoises, and all attempts to mate him during his last few decades were unsuccessful. But emotionally, it’s hard to brace oneself for the realization that something that was once there is finally, completely gone. It’s the kind of stuff that makes you ponder life, our fleeting stint in the universe and the unrelenting, forward march of time.m Similar feelings drive longevity research. Recently, a team of scientists turned to George for help in this search, mining his genetic code for clues to his long life span. In a paper published Monday in Nature Ecology & Evolution, the researchers reported preliminary findings of gene variants in George linked with a robust immune system, efficient DNA repair and resistance to cancer. The study also sets the stage for understanding giant tortoises’ evolutionary past, which might help to conserve them in the future….

2018-11-26. CRISPR bombshell: Chinese researcher claims to have created gene-edited twins. By Dennis Normile, Science Magazine. [https://www.sciencemag.org/news/2018/11/crispr-bombshell-chinese-researcher-claims-have-created-gene-edited-twins] Excerpt: HONG KONG, CHINA—On the eve of an international summit here on genome editing, a Chinese researcher has shocked many by claiming to have altered the genomes of twin baby girls born this month in a way that will pass the modification on to future generations. The alteration is intended to make the children’s cells resistant to infection by HIV, says the scientist, He Jiankui of the Southern University of Science and Technology in Shenzhen, China. The claim—yet to be reported in a scientific paper—initiated a firestorm of criticism today, with some scientists and bioethicists calling the work “premature,” “ethically problematic,” and even “monstrous.” The Chinese Society for Cell Biology issued a statement calling the research “a serious violation of the Chinese government’s laws and regulations and the consensus of the Chinese scientific community.” And He’s university issued a statement saying it has launched an investigation into the research, which it says may “seriously violate academic ethics and academic norms.” Other scientists, meanwhile, asked to see details of the experiment and its justification before passing judgment….  See related Science Magazine articles: Researcher who created CRISPR twins defends his work but leaves many questions unanswered [https://www.sciencemag.org/news/2018/11/researcher-who-created-crispr-twins-defends-his-work-leaves-many-questions-unanswered]; Ethics aside, does the CRISPR baby experiment make scientific sense? [https://www.sciencemag.org/news/2018/11/ethics-aside-does-crispr-baby-experiment-make-scientific-sense]; ‘I feel an obligation to be balanced.’ Noted biologist comes to defense of gene editing babies [https://www.sciencemag.org/news/2018/11/i-feel-obligation-be-balanced-noted-biologist-comes-defense-gene-editing-babies]; Organizers of gene-editing meeting blast Chinese study but call for ‘pathway’ to human trials [https://www.sciencemag.org/news/2018/11/organizers-gene-editing-meeting-blast-chinese-study-call-pathway-human-trials]; An ‘epic scientific misadventure’: NIH head Francis Collins ponders fallout from CRISPR baby study [https://www.sciencemag.org/news/2018/11/epic-scientific-misadventure-nih-head-francis-collins-ponders-fallout-crispr-baby-study]

2018-09-07. The secret sex life of strawberries. By Carol Cruzan Morton, Science Magazine. [http://www.sciencemag.org/news/2018/09/secret-sex-life-strawberries] Excerpt: …scientists have figured out how strawberries, which have the youngest known sex chromosomes of any plant or animal, made their recent transition to male and female. The unusual “jumping” genes responsible could mean sex differences can change faster in plants than anyone realized. “For the first time, we now have a view of sex chromosome evolution over space and time,” says Alex Harkess, an evolutionary biologist at Donald Danforth Plant Science Center in St. Louis, Missouri, who was not involved in the study. “It’s not just about the establishment of sex chromosomes, it’s how the sex-determining regions continue to evolve.”…

2018-06-21. How the snowshoe hare is losing its white winter coat. By Elizabeth Pennisi, Science Magazine.  Excerpt: Like the iconic arctic fox, the snowshoe hare dons white fur for the winter—a good camouflage in the snow. But as the climate warms, the hares are increasingly ditching their winter wardrobes and keeping the brown fur they sport during the rest of the year. Now, a new study shows how: by borrowing a gene from a jackrabbit, one of their long-eared cousins. To find out how snowshoe hares (Lepus americanus) maintain their summertime pelage, scientists sequenced the genomes of “winter white” and “winter brown” hares and compared them with the genomes of several relatives, including the black-tailed jackrabbit (L. californicus). They quickly realized that the black-tailed jackrabbit, which doesn’t undergo a winter wardrobe switch, must have mated multiple times with the winter browns. One key souvenir from that mating: a jackrabbit version of agouti, the gene that normally revs up its activity and turns snowshoe fur white in the winter, the researchers report today in Science. Hares carrying this borrowed gene are unable to turn white…. http://www.sciencemag.org/news/2018/06/how-snowshoe-hare-losing-its-white-winter-coat

2017-10-12. Genes for Skin Color Rebut Dated Notions of Race, Researchers Say. By Carl Zimmer, The New York Times. Excerpt: For centuries, skin color has held powerful social meaning — a defining characteristic of race, and a starting point for racism. “If you ask somebody on the street, ‘What are the main differences between races?,’ they’re going to say skin color,” said Sarah A. Tishkoff, a geneticist at the University of Pennsylvania. On Thursday, Dr. Tishkoff and her colleagues showed this to be a profound error. In the journal Science, the researchers published the first large-scale study of the genetics of skin color in Africans. The researchers pinpointed eight genetic variants in four narrow regions of the human genome that strongly influence pigmentation — some making skin darker, and others making it lighter. These genes are shared across the globe, it turns out; one of them, for example, lightens skin in both Europeans and hunter-gatherers in Botswana. The gene variants were present in humanity’s distant ancestors, even before our species evolved in Africa 300,000 years ago. The widespread distribution of these genes and their persistence over millenniums show that the old color lines are essentially meaningless, the scientists said. The research “dispels a biological concept of race,” Dr. Tishkoff said…. https://www.nytimes.com/2017/10/12/science/skin-color-race.html

2017-05-19. Genetic Tidying Up Made Humped Bladderworts Into Carnivorous Plants. By Joanna Klein, The New York Times. Excerpt: …the humped bladderwort …grows pretty, yellow flowers, and it has no roots to hold it down. To get the nutrients it needs, it spends its time floating in lakes and waterways eating miniature crustaceans, called water fleas, and other things. It operates sort of like an aquatic Venus flytrap, but a hundred times faster. It feeds by dangling tiny vacuous sacs from its stems into the water. These bladders, just a few millimeters big (with walls only two cells thick), are normally filled with water. But when the trap is set, the plant pumps the water out, creating a vacuum and a mouth, which is covered in tiny hairs. “When a prey animal stimulates those trigger hairs — whoosh,” said Victor Albert, an evolutionary plant biologist at the State University of New York, University at Buffalo. The bladderwort can trap dinner in less than a millisecond. More than just a remarkable carnivorous plant, in genetic terms, it is a minimalist. It has the smallest reliably sequenced genome of any flowering plant. Inside that genome, it carries only the stuff it needs to function as a plant and uphold its strange identity. But its envious life took millions of years of evolutionary refinement, according to a study published by Dr. Albert and his colleagues on Monday in Proceedings of the National Academy of Sciences. With new tools that allowed researchers to observe the plant’s genome more closely than ever before, they were able to see just what type of genetic changes created this flesh-eating plant….  https://www.nytimes.com/2017/05/19/science/humped-bladderwort-carnivorous-plant-genome.html

2017-03-02. The Woolly Mammoth’s Last Stand. By Nicholas Wade, The New York Times. Excerpt: In a remote, mist-wrapped island north of the eastern tip of Siberia, a small group of woolly mammoths became the last survivors of their once thriving species. They fell extinct 4,000 years ago, having endured for some 6,000 years after the mammoths of the mainland had died off. From a message left in the tooth of a male mammoth, geneticists have now deciphered the probable reason for the population’s demise. The story is relevant to living populations of endangered species, because it supports the idea that as a population dwindles, natural selection becomes less efficient at purging bad mutations, leading to loss of genes and a slow meltdown of the genome. The implication is that once numbers fall below a certain level, genetic decline is irreversible….  https://www.nytimes.com/2017/03/02/science/woolly-mammoth-extinct-genetics.html

See also: UC Berkeley News article  – Woolly mammoths experienced a genomic meltdown just before extinction.

2016-12-09. Rapid Evolution Saved This Fish From Pollution, Study Says. By Joanna Klein, The New York Times. Excerpt: The State of New Jersey says you can’t eat the fish or shellfish from the Lower Passaic River and Newark Bay. That’s because they’re living in the Diamond Alkali Superfund Site, where toxic leftovers from the manufacture of chemicals like DDT and the infamous Agent Orange oozed into surrounding waterways to be taken up by the animals that inhabited them. It’s an evolutionary miracle some of these animals are even alive. …A fish that adapted to survive in this water shows evolution at its finest, according to a study published Thursday in Science. The Atlantic killifish is a slippery sliver of silver about the size of a fat finger and as common as the minnow. Starting in the late 1990s, researchers became aware that the fish was tolerant of the toxic waters at the Lower Passaic Superfund site and at least three other highly polluted areas along the Atlantic coastline. The new study found that over just a few decades, distinct populations of killifish independently developed similar genetic adaptations that make life possible in the most unlikely environments. The findings show that evolution doesn’t have to start in one place to be repeated. …Normally, toxic chemicals like dioxins and polychlorinated biphenyls, or PCBs, set off a number of changes inside sensitive fish that interfere not just with the survival of adults, but also with the development of their embryos. But in the tolerant fish, the trigger for those changes is turned off, allowing some fish to survive levels of PCBs thousands of times higher than the levels affecting sensitive fish….  http://www.nytimes.com/2016/12/09/science/atlantic-killifish-evolution-pollution.html

2016-11-15. European diseases left a genetic mark on Native Americans. By Michael Price, Science. Excerpt: When the indigenous peoples of the Americas encountered European settlers in the 15th century, they faced people with wildly different religions, customs, and—tragically—diseases; the encounters wiped out large swaths of indigenous populations within decades. Now, researchers have found that these diseases have also left their mark on modern-day populations: A new study suggests that infectious diseases brought by Europeans, from smallpox to measles, have molded the immune systems of today’s indigenous Americans, down to the genetic level….  http://www.sciencemag.org/news/2016/11/european-diseases-left-genetic-mark-native-americans

2016-10-29. Doubts About the Promised Bounty of Genetically Modified Crops. By Danny Hakim, The New York Times. Excerpt: LONDON — The controversy over genetically modified crops has long focused on largely unsubstantiated fears that they are unsafe to eat. But an extensive examination by The New York Times indicates that the debate has missed a more basic problem — genetic modification in the United States and Canada has not accelerated increases in crop yields or led to an overall reduction in the use of chemical pesticides. The promise of genetic modification was twofold: By making crops immune to the effects of weedkillers and inherently resistant to many pests, they would grow so robustly that they would become indispensable to feeding the world’s growing population, while also requiring fewer applications of sprayed pesticides. …An analysis by The Times using United Nations data showed that the United States and Canada have gained no discernible advantage in yields — food per acre — when measured against Western Europe, a region with comparably modernized agricultural producers like France and Germany. Also, a recent National Academy of Sciences report found that “there was little evidence” that the introduction of genetically modified crops in the United States had led to yield gains beyond those seen in conventional crops….  http://www.nytimes.com/2016/10/30/business/gmo-promise-falls-short.html

2016-05-17. Humans are still evolving—and we can watch it happen. By Elizabeth Pennisi, Science. Excerpt: Many people think evolution requires thousands or millions of years, but biologists know it can happen fast. Now, thanks to the genomic revolution, researchers can actually track the population-level genetic shifts that mark evolution in action—and they’re doing this in humans. Two studies presented at the Biology of Genomes meeting here last week show how our genomes have changed over centuries or decades, charting how since Roman times the British have evolved to be taller and fairer, and how just in the last generation the effect of a gene that favors cigarette smoking has dwindled in some groups….  http://www.sciencemag.org/news/2016/05/humans-are-still-evolving-and-we-can-watch-it-happen

2015-12-04. Inside the summit on human gene editing: A reporter’s notebook. By John Travis, The New York Times. Excerpt: …The conference ended with the organizing committee, a mix of 12 biologists, physicians, and bioethicists, strongly endorsing the use of CRISPR and similar methods for basic research that involves altering the DNA sequences of human eggs, sperm, or embryos—work that is at the moment ineligible for federal funding in the United States and that in Germany could even get a scientist imprisoned. But the summit’s organizers concluded that actually trying to produce a human pregnancy from such modified germ cells or embryos, either through in vitro fertilization (IVF) with the sperm or eggs or the implantation of an embryo, is currently “irresponsible” because of ongoing safety concerns and a lack of societal consensus. The group’s statement, however, did not permanently rule out such gene editing of the germline, presumably to prevent the transmission of genetic disease from a parent to child. (Introducing permanent “enhancements” into the human genome was largely deemed off-limits, although a few attendees rejected that general consensus.) In fact, the missive called for revisiting the issue on a “regular basis.” “Over the years, the unthinkable has become conceivable. We’re on the cusp of a new era in human history,” Massachusetts Institute of Technology (MIT) in Cambridge biologist David Baltimore, chair of the summit organizing committee, told the audience….  http://news.sciencemag.org/scientific-community/2015/12/inside-summit-human-gene-editing-reporter-s-notebook 0

2015-11-26. Open Season Is Seen in Gene Editing of Animals. By Amy Harmon, The New York Times. Excerpt: SIOUX CENTER, Iowa — Other than the few small luxuries afforded them, like private access to a large patch of grass, there was nothing to mark the two hornless dairy calves born last spring at a breeding facility here as early specimens in a new era of humanity’s dominion over nature. But unlike a vast majority of their dairy brethren, these calves, both bulls, will never sprout horns. That means they will not need to undergo dehorning, routinely performed by farmers to prevent injuries and a procedure that the American Veterinary Medical Association says is “considered to be quite painful.” Instead, when the calves were both just a single cell in a petri dish, scientists at a start-up company called Recombinetics used the headline-grabbing new tools of gene editing to swap out the smidgen o f genetic code that makes dairy cattle have horns for the one that makes Angus beef cattle have none. …The uproar over the new ease and precision with which scientists can manipulate the DNA of living things has centered largely on the complicated prospect of editing human embryos. But with the federal government’s approval last week of a fast-growing salmon as the first genetically altered animal Americans can eat, a menagerie of gene-edited animals is already being raised on farms and in laboratories around the world — some designed for food, some to fight disease, some, perhaps, as pets….  http://www.nytimes.com/2015/11/27/us/2015-11-27-us-animal-gene-editing.html

2015-11-19. FDA approves AquaBounty Technologies’ application to sell the genetically modified salmon to U.S. consumers. Wikipedia. Excerpt: …The decision marks the first time a genetically modified animal has been approved to enter the United States food supply. The decision came nearly twenty years after the company first submitted data to the FDA, and after they had raised ten generations of the animals. The announcement released by the FDA states: “AquAdvantage salmon is as safe to eat as any non-genetically engineered (GE) Atlantic salmon, and also as nutritious.”  …a release of GM fish from a salmon farm into the wild, the GM salmon could initially outcompete wild-type salmon for food. This success would allow the GM salmon’s greater survival.  …Whole Foods, Trader Joe’s, Aldi, and other grocery stores throughout the United States have announced that they would not offer AquAdvantage.  …the application for FDA approval of AquAdvantage salmon specified land-based tank cultivation with no ocean involvement. …AquaBounty addresses these concerns by cultivating reproductively incapable females. Most escapees cannot reproduce either natively or by interbreeding with wild stocks, because treatments of eggs have been found to render 98.9% of them triploid; batches with more than 5% diploid individuals will be destroyed. The company plans to provide farmers with fish rather than eggs,^[1] and has proposed that AquAdvantage fish only be raised in land-based facilities….  https://en.wikipedia.org/wiki/AquAdvantage_salmon

2015-06-19. The Sequencer is Mightier than the Sword. By Brian Palmer, onEarth, Natural Resources Defense Council.  Excerpt: The U.S. Fish & Wildlife Service brought a ton of ivory to Times Square this morning—and crushed it into tiny pieces. The service hopes to send a message to poachers and traders that the United States is committed to protecting elephants and curtailing the ivory business. …New York City is one of the country’s biggest hubs for the illegal ivory trade. …Elephants range more than one million square miles of Africa. Policing an area that size is nearly impossible. …study released yesterday in the journal Science …University of Washington biologist and elephant ivory expert Samuel Wasser analyzed 28 major ivory seizures between 1996 and 2014. Comparing the confiscated ivory’s DNA with DNA collected from elephant dung of known origin, Wasser found that poachers have narrowed their hunting grounds substantially over the past decade. Almost all the forest elephant ivory in Wasser’s sample came from a single protected ecosystem…. The ivory from elephants living on savannahs also came from a limited area, located mostly in Tanzania but spilling into northern Mozambique. This research is a gift to the anti-poaching effort. …According to United Nations data, the illegal wildlife trade is now worth $20 billion per year, making it one of the world’s largest forms of organized crime. The Convention on International Trade in Endangered Species of Wild Fauna and Flora announced that elephant poaching rates remained unchanged between 2013 and 2014, at a level that exceeds the species’ natural growth rate. Some estimates put elephant-poaching deaths at 96 each day, putting the animal on a steady decline into extinction. Rebel groups and poachers attack, torture, and murder anti-poaching police with alarming regularity. One watchdog group claims that at least two park rangers are killed every week…. http://www.onearth.org/earthwire/ivory-dna-study-elephant-poachers

2014-10-13. A Threat Is Seen in Pumas’ Isolation. By Douglas QuenQua, The New York Times. Excerpt: The isolating effects of human development are causing a sharp decline in genetic diversity among mountain lions in Southern California, a new study says. Researchers from the University of California, Davis, collected DNA samples from more than 350 mountain lions throughout California and found that animals separated by little more than a highway have far less genetic material in common than they did just 80 years ago, suggesting that there is far less interbreeding among populations. Pumas in the Santa Ana Mountains — effectively fenced in by Interstate 15 to the east, the Pacific Ocean to the west and Los Angeles to the north — displayed lower genetic diversity  …So severe is their isolation that the Santa Ana pumas have more in common genetically with lions 400 miles to the north than their neighbors in the Santa Monica Mountains. … “Genetically diverse populations are better able to handle whatever nature or humans throw at them, like climate change or disease,” said Dr. Ernest, a geneticist now at the University of Wyoming. “If mountain lions lose that genetic diversity, they lose that resilience.”…. By Douglas Quenqua, The New York Times. http://www.nytimes.com/2014/10/14/science/a-threat-is-seen-in-pumas-isolation.html?ref=science.

2014-06-16. A Faster Way to Find the Origin of Malaria. Excerpt: By using a DNA “bar code” of 23 short snips from the genes of parasites that cause malaria, scientists can now often quickly determine where they originated, British researchers report. The information could be useful in fighting local outbreaks, which may be caused by parasites from other parts of the world. And it should be possible to make a test kit that will get that information from a spot of dried blood in two hours — far less time than is needed to sequence a whole genome. For the study, published on Friday in the journal Nature Communications, researchers from the London School of Hygiene and Tropical Medicine analyzed the DNA of more than 700 malaria-causing parasites from all over the world. For Plasmodium falciparum — the most dangerous species — they found 23 consistent mutations that let them tell, with 92 percent accuracy, whether a strain was from West Africa, East Africa, Southeast Asia, South America or the South Pacific. They still hope to find markers that distinguish strains from Central America, the Caribbean, southern Africa and the Indian subcontinent…. http://www.nytimes.com/2014/06/17/health/a-faster-way-to-find-the-origin-of-malaria.html. By Donald G. McNeil Jr, The New York Times. 

2014-03-27. Custom Chromo: First Yeast Chromosome Built From Scratch. Excerpt: …Using the labor of dozens of undergraduate students, scientists have built a customized yeast chromosome from scratch. It’s a milestone in the rapidly growing field of synthetic biology, where organisms can be tailored for industrial use. In this case, the near-term goal is to understand the genetics of yeast, and eventually the genetics of us. This was quite an undertaking. Yeast have about 6,000 genes packed in 16 tidy bundles called chromosomes. Each chromosome is an enormous molecule of DNA packed in proteins. …[Jef] Boeke and his colleagues put together a class, called Build-A-Genome, and got undergraduates at Hopkins to do the painstaking labor of constructing long strings of DNA. These would eventually become segments of their yeast chromosome. …To make the chromosome useful for research, they’ve deleted some parts of the DNA that they believe are not essential, “and then we add a number of bells and whistles to the chromosome, that we think will make for a more interesting version that we can play evolutionary games with in the laboratory,” Boeke says. …Of course, this deep manipulation of DNA also raises ethical questions — about everything from patenting life-forms, to the potential misuse of biotechnology for weapons or other nefarious purposes. So part of the class involved an ethics discussion, led by Debra Mathews, a bioethicist at Johns Hopkins…. http://www.npr.org/blogs/health/2014/03/27/295260600/custom-chromo-first-yeast-chromosome-built-from-scratch. Richard Harris, NPR. 

2013-12-04. Baffling 400,000-Year-Old Clue to Human Origins.    Excerpt: …In a paper in the journal Nature, scientists reported Wednesday that they had retrieved ancient human DNA from a fossil dating back about 400,000 years, shattering the previous record of 100,000 years. The fossil, a thigh bone found in Spain, had previously seemed to many experts to belong to a forerunner of Neanderthals. But its DNA tells a very different story. It most closely resembles DNA from an enigmatic lineage of humans known as Denisovans. Until now, Denisovans were known only from DNA retrieved from 80,000-year-old remains in Siberia, 4,000 miles east of where the new DNA was found. …“The more we learn from the DNA extracted from these fossils, the more complicated the story becomes,” Dr. Shapiro said. This complicated story has come to light only because of advances over the past 20 years in retrieving ancient DNA. When an organism dies, its DNA breaks down into smaller and smaller fragments, while also becoming contaminated with the DNA of other species like soil bacteria. So piecing the fossil DNA together is a bit like putting together a jigsaw puzzle created by a sadist…. http://www.nytimes.com/2013/12/05/science/at-400000-years-oldest-human-dna-yet-found-raises-new-mysteries.html, Carl Simmer, The New York Times.

2013-07-27.  A Race to Save the Orange by Altering Its DNA. Excerpt: …The disease that sours oranges and leaves them half green, already ravaging citrus crops across the world, had reached .. [Florida’s] groves. …Florida growers who supply most of the nation’s orange juice poured everything they had into fighting the disease they call citrus greening. … “In all of cultivated citrus, there is no evidence of immunity,” the plant pathologist heading a National Research Council task force on the disease said. In all of citrus, but perhaps not in all of nature. …They would have to alter the orange’s DNA — with a gene from a different species.  …the idea of eating plants and animals whose DNA has been manipulated in a laboratory — called genetically modified organisms, or G.M.O.’s — still spooks many people. Critics worry that such crops carry risks not yet detected, and distrust the big agrochemical companies that have produced the few in wide use. …. http://www.nytimes.com/2013/07/28/science/a-race-to-save-the-orange-by-altering-its-dna.html. Richard Perry, The New York Times.

2012-12-21. Engineered Fish Moves a Step Closer to Approval | Andrew Pollack, The New York Times. Excerpt: Government regulators moved a big step closer on Friday to allowing the first genetically engineered animal — a fast-growing salmon — to enter the nation’s food supply. The Food and Drug Administration said it had concluded that the salmon would have “no significant impact” on the environment. The agency also said the salmon was “as safe as food from conventional Atlantic salmon.” … The AquAdvantage salmon… is an Atlantic salmon that contains a growth hormone gene from the Chinook salmon and a genetic switch from the ocean pout, an eel-like creature. The switch keeps the gene on so that the salmon produces growth hormone year round, rather than only during warm weather. The fish reach market weight in about 18 months instead of three years. … The main concern addressed was whether the genetically engineered salmon could escape and establish themselves in the wild, with detrimental environmental consequences. The larger salmon, for instance, could conceivably outcompete wild Atlantic salmon for food or mates.  The agency said the chance this would happen was “extremely remote.” It said the salmon would be raised in inland tanks with multiple barriers to escape. Even if some fish did escape, the nearby bodies of water would be too hot or salty for their survival. And reproduction would be unlikely because the fish would be sterilized, though the sterilization technique is not foolproof…. Read the full article: http://www.nytimes.com/2012/12/22/business/gene-altered-fish-moves-closer-to-federal-approval.html?nl=todaysheadlines&emc=edit_th_20121222&_r=0

2012 Sept 05. Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role to Health. By Gina Kolata, The NY Times. Excerpt: Among the many mysteries of human biology is why complex diseases like diabetes, high blood pressure and psychiatric disorders are so difficult to predict and, often, to treat. An equally perplexing puzzle is why one individual gets a disease like cancer or depression, while an identical twin remains perfectly healthy. Now scientists have discovered a vital clue to unraveling these riddles. The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave. The discovery, considered a major medical and scientific breakthrough, has enormous implications f or human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches…. 

2012 Aug 27. As Genes Learn Tricks, Animal Lifestyles Evolve. By Sean B. Carroll, The NY Times. Excerpt: Changes in the structure of the TRPA1 receptor, and the evolution of very high levels of expression in their sensory pits, endowed [snakes] with sensitive infrared detectors. The large evolutionary distance between pit vipers and pythons and boas indicates that the two groups of snakes separately evolved infrared sensing. But TRPA1 is not the only means of infrared sensing…blood-feeding bats also has sensory pits around the noses that the animals use to locate the warmest areas on the surface of their furry prey, where blood flow is the greatest…recruit[ing] a different ion channel/ receptor called TRPV1 to become an infrared sensor. What is especially noteworthy about TRPV1 is that it is the very same receptor that detects capsaicins, the active ingredients in chili peppers, in our neurons. It causes the familiar burning sensation when prompted… scientists discovered that the particular form of the receptor expressed in vampire bat trigeminal neurons was much more heat-sensitive (by about 9 degrees Celsius) than either our TRPV1 receptor or the TRPV1 expressed in fruit bat neurons. The vampire bat receptor is thus tuned to detect heat in ways that other bats and mammals cannot. Both the TRPA1 and TRPV1 genes are hundreds of millions of years old, having arisen deep in evolutionary history, while vampire bats, pit vipers, and pythons and boas are much younger species. The histories of these genes and animals, and the repeated invention of infrared sensing, demonstrate how the evolution of new abilities does not necessarily require new genes, but new variations of very old genes and new ways of using them…. 

2012 May 3. Island’s Genetic Quirk: Dark Skin, Blond Hair by SINDYA N. BHANOO, The NY Times. Excerpt: In the Solomon Islands, about 10 percent of the dark-skinned indigenous people have strikingly blond hair. Some islanders theorize that the coloring could be a result of excess sun exposure, or a diet rich in fish. Another explanation is that the blondness was inherited from distant ancestors — European traders and explorers who came to the islands. About 10 percent of indigenous people in the Solomon Islands have a gene variant for blond hair. But that’s not the case… The gene variant responsible for blond hair in the islanders is distinctly different from the gene that causes blond hair in Europeans….

2012 May 7. It’s Not So Lonely at the Top: Ecosystems Thrive High in the Sky by CARL ZIMMER, The NY Times. Excerpt: Looming over the northern edge of the Amazon rain forest are some of the most remarkable mountains on earth. Known as tepuis, or tabletop mountains, they are typically ringed by sheer cliffs that rise thousands of feet from the surrounding lowland jungles….They are like islands in the sky, covered with low forests and shrublands that support a diversity of animals likes frogs and lizards….Even more intriguing than the tepuis’ long isolation is that many species living atop them are found nowhere else. To many biologists, the only explanation that made sense was that the ancestors of those unique animals and plant species have lived on the tepuis for more than 70 million years. In honor of Conan Doyle, they called this notion the “lost world hypothesis.”….

2011 October 17.  From Telomeres to the Origins of Life. By Claudia Dreifus, The NY Times.  [An interview with biochemist and 2009 Nobel Laureate Dr. Jack W. Szostak] Excerpt: 
Q: [What did you and Elizabeth H. Blackburn discover about telomeres together?]
A: …We figured out the underlying biochemistry and showed that lots of different organisms use that biochemistry. We figured out that there was an enzyme, telomerase, that adds DNA to the ends of chromosomes to balance out the DNA that is naturally lost as cells grow.
Afterward, as people in the field began to see how important it was, telomere research just took off. It became clear that the loss of DNA from telomeres might have something to do with aging. Subsequently, it’s turned out that in almost all cancers, telomerase is turned on so those cells grow indefinitely. Of course, it’s very nice that work we did so long ago turned out to be important! ….
Q: …What do you study now?
A: The origins of life. In my lab, we’re interested in the transition from chemistry to early biology on the early earth… The way that we study that is by trying to make it happen in the lab. We take simple chemicals and put them together in the right way. And we’re trying to build a very, very simple cell that might look like something that might have developed spontaneously on the early earth….

2010 September.  Sex and the Single Chromosome. By Kathleen M. Wong, Science Matters @ Berkeley. Excerpt: …Doris Bachtrog, a Berkeley professor of integrative biology, studies how sex chromosomes evolve these differences. Her approach is to compare related species whose sex chromosomes emerged at different times. ….Bachtrog’s comparisons of various fruit fly species demonstrate that Y chromosomes accumulate specific defects over time. 

2010 July 19. Birds Choose Different Path to Manage Their Sexes. By Nicolas Wade, The New York Times. Excerpt: …In a series of experiments over the past 15 years, David Page of the Whitehead Institute has reconstructed many of the steps in the evolution of the human sex chromosomes, which he calls “an infinitely rich experiment of nature.” He has now started to analyze a parallel experiment, the sex chromosomes of birds.
…In humans, men have an X and a Y chromosome, and women two X’s. In reptilian times, the X and the Y were an ordinary pair of chromosomes until the male-determining gene landed on the Y. Thereupon the Y started shedding the genes it held in common with the X and shriveled to a fraction of its former size.
Birds have evolved a similar system with a twist — it’s the male that has two of the same chromosomes. Their sex chromosomes are called the Z and W, with males having two Z’s and females a Z and a W. The Z and W are derived from a different pair of ancestral chromosomes than the X and Y, a team led by Daniel W. Bellott and Dr. Page report in the current issue of Nature. The Z’s evolution has in several ways paralleled that of the X, even though each is associated with a different sex.
…Masculinity in people is attained with a single Y, so why do male birds need two Z’s? The solution was found last year by a group led by Craig A. Smith and Andrew H. Sinclair of the Royal Children’s Hospital in Melbourne, Australia. In humans, the default condition is female and the reproductive organs develop as male in the presence of the male-determining gene’s protein.
In birds, sex is determined by the dose of the sex gene, which the Melbourne team identified as one called DMRT1. Bird embryos exposed to a single dose develop as female; two copies of the gene make a male.
…“I see an endless chain of revelations i n the future that will come from comparing the human X and Y to other sex chromosomes of species at different evolutionary distances,” Dr. Page said. 

2010 May 31. A Family Feud Over Mendel’s Manuscript on the Laws of Heredity. By Nicholas Wade, NY Times. Excerpt: …The manuscript is the account by Gregor Mendel of the pea-breeding experiments from which he deduced the laws of heredity and laid the foundations of modern genetics.
…The priceless manuscript was discarded in 1911 by the Brünn Natural History Society and, luckily, rescued by a local high school teacher who retrieved it from a wastepaper basket in the society’s library… 
…At some point after 1988, Erich Richter, a Mendel descendant who is also an Augustinian monk known as Father Clemens, told other family members that he possessed Mendel’s manuscript. It had been sent to him by a monk in Prague and he wanted to place it legally in the family’s possession. So in 2001, eight senior members of the Mendel family — including Father Clemens — formed a company to preserve the document as a German cultural treasure, and the manuscript was placed in a safe deposit box in a bank in Darmstadt, Germany. 
…Father Clemens began to change his story about the ownership of the manuscript, suggesting it really belonged to the Augustinians, said William Taeusch, Dr. Schmidt’s husband. “He started to say to the family, ‘Aren’t they the rightful owners?’ The family says, ‘What’s going on, for God’s sake? If you were given it and were told it was the Augustinians’ property, why did you keep it for yourself for 11 years and then sign a bogus contract giving it to the family?’ ” 

2010 Mar 11. Disease Cause Is Pinpointed With Genome. By Nicholas Wade, New York Times. Excerpt: Two research teams have independently decoded the entire genome of patients to find the exact genetic cause of their diseases….
In the decade since the first full genetic code of a human was sequenced for some $500 million, less than a dozen genomes had been decoded, all of healthy people.
Geneticists said the new research showed it was now possible to sequence the entire genome of a patient at reasonable cost and with sufficient accuracy to be of practical use to medical researchers….
In one case, Richard A. Gibbs of the Baylor College of Medicine sequenced the whole genome of his colleague Dr. James R. Lupski, a prominent medical geneticist who has a nerve disease, Charcot-Marie-Tooth neuropathy…. 

2010 Feb 17. Scientists Decode Genomes of Five Africans, Including Archbishop Tutu. By Nicholas Wade, NY Times. Excerpt: The complete genomes of five southern Africans have been decoded, almost doubling the number of published human DNA sequences. The Africans include four Bushmen hunter-gatherers, known as !Gubi, G/aq’o, D#kgao and !Ai, the odd symbols representing different clicking sounds in Bushmen languages. The fifth person, a Bantu, is none other than Archbishop Desmond Tutu.
…African genomes are of particular interest for understanding human genetic history because they have more variation in their DNA than other populations. Everyone outside Africa is descended from a small group that left some 50,000 years ago, carrying away only a small sample of the available genetic diversity….
…Geneticists are interested in variations in the human DNA sequence because these underlie human diversity, including susceptibility to disease. The Pennsylvania team found 1.3 million novel DNA variants in its five Africans, and some 13,000 new changes in those parts of the DNA that specify proteins, the working parts of living human cells…. 

2009 March 3. A Call for Resilient Farms in Warming World. By Andrew C. Revkin, The NY Times. Excerpt: In the icy gloom of Norway’s Arctic archipelago, scientists gathered last week to celebrate the first anniversary of the Svalbard Global Seed Vault, an archive of the world’s agricultural genetic diversity carved into the frigid earth. I got a “post card” over the weekend from one participant, Nina Fedoroff, the science and technology adviser to the secretary of state and to administrator of the United States Agency for International Development.
Dr. Fedoroff is a longstanding proponent of probing and exploiting genes to make crops and livestock more productive and less vulnerable to pests and climate extremes. This puts her at odds with some environmentalists and European governments.
Her full dispatch…is focused on the importance of preserving and exploiting genetic diversity as a way to sustain food production in the face of both growing human populations and appetites (prosperity still tends to boost peoples’ appetite for meat) and rising dangers from warming driven by accumulating greenhouse gases….


2009 February 29. A worldwide pollutant may cause gene loss. By Niladri Basu, Environmental Health News. Excerpt: A new study suggests that long term exposure to a common water pollutant reduced the genetic diversity of the midge – a common water insect.
Aquatic insects are the foundation of healthy waterways. Other insects, invertebrates and fish depend on the tiny creatures for food. A loss of their genetics is a loss for ecosystem diversity.
The pollutant, called tributyltin (TBT), is a widely used pesticide. While TBT affected the growth, survival and reproduction of the midge insect, the greatest effects were found in the genes. TBT-exposed insects lost gene diversity two times greater than non-exposed insects.
The study provides direct evidence from the lab that pollution may cause genetic loss in nature….
Genetic diversity is the number of different kinds of genetic characteristics in a species. Genes govern an individual’s characteristics — whether external appearances or internal functions. Diversity ensures that a population has a large number of gene variations spread among individuals.
…Before its recent worldwide ban, TBT was used extensively in marine paints to keep barnacles and other marine creatures from growing on ship hulls. In the environment, TBT does not break down and it builds up in food chains. Because of its longevity and widespread use, it is no surprise that TBT pollutes harbors, waterways and animals all over the world…. 

2008 July/August. Tracing Evolution in Genes. By Kathleen M. Wong, ScienceMatters@Berkeley. Excerpt: How do humans differ from chimpanzees? …we’re taller, less hairy, and-a point no one fails to mention-far brainier than our closest primate relatives.
All of these differences and more have emerged over the past five million years, when the common ancestor of both species reached an evolutionary fork in the road. How early hominids came to walk the savannah, while early chimpanzees returned to the forests, has fascinated professional scientists and armchair anthropologists alike.
The best way to answer those questions, according to Rasmus Nielsen, is to study our respective genomes. “Evolutionary biology is an historical science,” says Nielsen, a Berkeley professor of integrative biology. “But in the absence of a time machine, we can’t really go back and show exactly why certain evolutionary events occurred. All we have to work with is what we observe today. So we look at the DNA to see the evidence for past Darwinian selection.”
Nielsen uses the power of statistics and computing to compare the DNA of different species or populations. By identifying which sets of genes have changed, or mutated, he can describe how ancestral populations diverged step by tiny genetic step. His work not only recasts the story of human evolution but promises to uncover the genetic roots of many diseases…


2008 May. Distant Relatives, Common Genes. By Kathleen M. Wong, ScienceMatters@Berkeley. Excerpt: Glance through any family’s photo album, and you’re likely to home in on a few outstanding ancestral traits. The shape of a nose or the arch of an eyebrow can be passed down for generation after generation.
Biologists have long studied commonalities such as these to infer ancestral relationships between animals. But the more distant the relationship, such as between humans and sponges, the trickier it is to establish connections through simple comparisons of anatomy.
Dan Rokhsar, a Berkeley professor of both physics and molecular and cellular biology, and a faculty scientist at the Department of Energy’s Joint Genome Institute, is sidestepping this problem via a different aspect of inheritance: genes. Genes shared by distantly related animals are likely to have originated in their last common ancestor. So by sequencing and comparing the genomes of creatures ranging from sea anemones to sea squirts, limpets to pufferfish, Rokhsar and his research team hope to reconstruct characteristics of the great-great grandparents to all animals.
“We’re interested in that transition from being a unicellular organism to being multicellular-when it happened and how it happened,” Rokhsar says…
Recently, the skyrocketing price of petroleum and the threat of global climate change have turned Rokhsar’s attention toward greener subjects: plants…
“The cellulose and lignin in plant walls is where all of the carbon goes from photosynthesis. That’s the carbon we want to convert to fuel. How do they do it? One way to find an answer is to look at genomes,” Rokhsar says.
He is now working to sequence the genome of switchgrass, a native plant and strong candidate to produce biofuel…
“We need to collapse the 5,000 years it took to breed maize into an edible plant into 10 years for switchgrass, because we don’t have a lot of time to develop renewable fuels,” Rokhsar says. “And we’ll need to do this sustainably and as a solution for the long term.” 

2008 April 22. Expressing Our Individuality, the Way E. Coli Do. By CARL ZIMMER, The NY Times. Excerpt: We humans differ from one another in too many ways to count…Scientists have only a rough understanding of how this diversity arises… We put a far bigger premium on nature than nurture when it comes to our individuality. That’s one reason why reproductive cloning inspires so much horror. If genes equal identity, then a person carrying someone else’s DNA has no distinct self. But there’s a deep flaw in this way of thinking, one that blinds us to how biology — human or otherwise — really works. A good counterexample is E. coli, a species of bacteria that lives harmlessly in every person’s gut by the billions. A typical E. coli contains about 4,000 genes (we have about 20,000). Feeding on sugar, the microbe grows till it is ready to split in two. It makes two copies of its genome, almost always managing to produce perfect copies of the original. The single microbe splits in two, and each new E. coli receives one of the identical genomes. These two bacteria are, in other words, clones…E. coli expresses its individuality in many other ways, as well…These quirks of E. coli’s personality can mean the difference between life and death for the bacteria. In times of stress, some members of a colony respond by building thousands of toxin molecules and then burst open, killing off the unrelated E. coli around them. Their fellow clones survive, though, and thrive without the competition.
The key to understanding E. coli’s fingerprints is to recognize that the bacteria are not simple machines. Unlike wires and transistors, E. coli’s molecules are floppy, twitchy and unpredictable. In an electronic device, like a computer or a radio, electrons stream in a steady flow through the machine’s circuits, but the molecules in E. coli jostle and wander. When E. coli begins using a gene to make a protein, it does not produce a smoothly increasing supply. It spurts out the proteins in fits and starts. One clone may produce half a dozen copies of a protein in an hour, while a clone right next to it produces none.
Other studies suggest that the unpredictable noisiness in E. coli’s cellular machinery is also responsible for persistence, hairy coats, selfless suicide and vulnerability to viruses. The big question for many scientists is why E. coli has evolved so that noise can produce such drastic changes in its biology…
Identical genes can also behave differently in our cells because some of our DNA is capped by carbon and hydrogen atoms called methyl groups. Methyl groups can control whether genes make proteins or remain silent. In humans (as well as in other organisms like E. coli), methyl groups sometimes fall off of DNA or become attached to new spots. Pure chance may be responsible for changing some methyl groups; nutrients and toxins may change others.
…At the very least, E. coli’s individuality should be a warning to those who would put human nature down to any sort of simple genetic determinism. Living things are more than just programs run by genetic software. Even in minuscule microbes, the same genes and the same genetic network can lead to different fates. 

2008 March 4. Gene Map Becomes a Luxury Item. by Amy Harmon. The New York Times. Excerpt: Dan Stoicescu, 56, a biotechnology entrepreneur who retired two years ago after selling his company, became the second person in the world to buy the full sequence of his own genetic code paying $350,000 price tag. Scientists have so far unraveled only a handful of complete human genomes, all financed by governments, foundations and corporations in the name of medical research. 
But while money may buy a full readout of the six billion chemical units in an individual’s genome, biologists say the superrich will have to wait like everyone else to learn how the small variations in their sequence influence appearance, behavior, abilities, disease susceptibility and other traits.
Biologists have mixed feelings about the emergence of the genome as a luxury item. Some worry that what they have dubbed “genomic elitism” could sour the public on genetic research that has long promised better, individualized health care for all. But others see the boutique genome as something like a $20 million tourist voyage to space — a necessary rite of passage for technology that may soon be within the grasp of the rest of us.
Scientists say they need tens of thousands of genome sequences to be made publicly available to begin to make sense of human variation.
Mr. Stoicescu, who wants to create an open database of genomic information seeded with his own sequence, hopes others will soon join him. 

2008 February. Statistical Challenges in Genomics. by Kathleen M. Wong, ScienceMatters@Berkeley …Called a DNA microarray, it is a miniature laboratory on a chip. In a single experiment it can deliver a detailed snapshot of the thousands of genes and proteins interacting in an organism, whether bacterium or human.For biologists, DNA microarrays have been boon and curse alike. Researchers routinely use these assays to monitor gene expression patterns in cells from cancer patients, with the aim of deriving better diagnosis and treatment strategies for the disease. They can now obtain unprecedented insights into the activities o f genes and cells with a minimum of experimental effort. At the same time, they are struggling to make sense of the tidal wave of data that ensues. “Each microarray experiment yields thousands and thousands of measurements for just one person,” says Sandrine Dudoit, a Berkeley professor of Biostatistics and Statistics. “Microarrays and other high-throughput biological assays are raising challenging statistical design and analysis questions and are a driving force for our discipline. The scale and complexity of the data are unprecedented and far greater than traditional methods allow you to handle.” …Dudoit specializes in developing statistical and computational methods to analyze and comprehend the mind-bogglingly large and intricate datasets generated by high-throughput biotechnologies such as DNA microarrays. …She develops statistical methods to uncover relationships among a patient’s entire genome; demographic and environmental variables such as age, sex, ethnicity, and diet; and medical outcomes such as survival prognosis and response to treatment. …With a next generation of DNA sequencing machines entering the scene, we are facing new and even greater statistical and computational challenges,” Dudoit says. “You feel like your work really matters; it’s being applied immediately, with the goal of elucidating fundamental scientific questions and improving public health.” 

2008 February. Gene escapes to weeds from engineered canola. Union of Concerned Scientists newlstter. A recent study found that canola plants in Quebec, Canada, that were genetically engineered for herbicide resistance have interbred with a weed called wild mustard, producing hybrid plants that are resistant to the herbicide glyphosate. The herbicide-resistance gene persisted over five generations and spread from the hybrids into the mustard weeds, in spite of the fact that no herbicide was applied to the area. The event is significant for two reasons. One, it is the first known escape of a gene from a commercialized genetically engineered crop into a weed. Two, because canola is a major crop, covering an estimated two million acres across Canada, it is likely that gene escape has occurred at multiple sites in addition to the few that were monitored. The event echoes the escape of a gene for glyphosate resistance from field trials of bentgrass into wild relatives (see our previous story). Inadequate confinement of engineered crops may harm ecosystems in some circumstances and may hasten the development of herbicide-resistant weeds. Read the abstract describing the study in the scientific journal Molecular Ecology. 

January 2008. The Copy Machine of the Cell
by Kathleen M. Wong. Excerpt: There comes a 
time in many a cell’s life when it feels the need to reproduce. But 
before it can split into two, it must fashion a second set of genetic instructions to pass on to the new cell. When Berkeley professor of biochemistry and molecular biology Mike Botchan first began studying chromosome copying, basic questions about the process remained unknown. He wanted to understand how and where DNA replication began. Over the past three decades, Botchan has been instrumental in piecing together the story of what he calls “the elaborate dance of replication.” Botchan began by studying viruses, the simplest of all life forms. These microbes contain relatively few genes in their chromosome, borrowing much of the machinery needed to duplicate their own DNA from host cells. …To decipher the string of events required to start replication, Botchan mapped the initiation site-a place on a chromosome where replication begins-in a virus. He found that a certain DNA sequence attracts a virus protein involved in replication initiation. Only then can the virus helicase, which unwinds and separates the strands of DNA, bind to the chromosome and start unraveling DNA….
But do more complex organisms, such as insects and humans, copy their DNA in a similar fashion? To find out, Botchan studied a case of unchecked DNA replication in fruit fly embryos. The cells that go on to form the fly’s eggshell duplicate certain sections of their DNA with astonishing rapidity, initiating replication at many sites at 
once. In these cells, Botchan found and characterized a complex of proteins that finds the initiation site and prepares the chromosome so that a core replication machine can be assembled there. The core replication machine includes a six-protein complex used at all DNA replication sites. Several of these proteins form a pinwheel structure that encircles DNA, while another links to the polymerase enzyme that “reads” the sequence. In cells actively copying their 
DNA, all of these proteins are located right on top of one another.
…Botchan’s work, along with research by Berkeley biologists Eva 
Nogales and James Berger, helps prove that DNA replication has 
changed very little across evolution. “All three kingdoms of life 
share a basic core machinery that assembles on DNA and prepares it for unwinding,” Botchan says. Organisms ranging from E. coli to fruit flies, they find, have nearly identical chromosome copying methods, cementing the relationship of all life forms back to that first ancestral cell. 

October 2007 The Mathematician and the Genome. By Kathleen M. Wong, ScienceMatters@Berkeley.
Excerpt: …The completion of the Human Genome Project in 2001 was hailed as a major breakthrough in science. For the first time, humans could look at their DNA and discover traits ranging from their propensity to alcohol addiction to the likelihood that their children will have blue eyes.
…Since then, scientists have added the rat, cow, chicken, dog, and even platypus to the list of creatures whose genes have been read like a biochemical book. Each species has shed new light on the structure and function of our own genetic code.
Lior Pachter has been at the forefront of these new genomic analyses. Officially a UC Berkeley professor of mathematics and computer science, Pachter considers himself a mathematical biologist. He uses the power of mathematical modeling and statistics to evaluate the vast quantities of data in DNA.
…Pachter likens genome studies to recreating plans for an existing building. “Until now, we’ve just been labeling the parts, the doorknobs and windows. Only recently have we started to ask about the function of the parts, and how these functions are related to each other.”
…In addition to sequence data, a profusion of other genetic information is now flooding the field. Measurements of gene expression in different tissues, ways to measure gene variations between individuals, and other information can all help make sense of how our DNA makes us who we are. “Mathematics and statistics provides a good means for synthesizing the data in a reasonable way,” Pachter says.
Just this year, Pachter began collaborating on the Human Microbiome Project. This new initiative from the National Institutes of Health seeks to analyze the microbial flora that lives in and on the human body. Scientists estimate that each person carries around 10 times more bacterial than human cells, species ranging from helpful gut microbes to pathogens like streptococci. The project will generate a jumble of gene fragments from both known and new species. Pachter’s role is to help determine the rough number of creatures represented in the mix.
“It’s fun for me that I can combine both mathematics and biology and participate in these major enterprises,” Pachter says. “The best thing is, I get to do a lot of beautiful math to go along with it.”

26 June 2007. Human DNA, the Ultimate Spot for Secret Messages (Are Some There Now?). The New York Times. ByDennis Overbye. Excerpt: … Using the same code that computer keyboards use, the Japanese group, led by Masaru Tomita of Keio University, wrote four copies of Albert Einstein’s famous formula, E=mc2, along with “1905,” the date that the young Einstein derived it, into the bacterium’s genome, the 4.2-million-long string of A’s, G’s, T’s and C’s that determine everything the little bug is and everything it’s ever going to be. The feat, they said in a paper published in the journal Biotechnology Progress, was a demonstration of DNA as the ultimate information storage material, able to withstand floods, terrorism, time and the changing fashions in technology, not to mention the ability to be imprinted with little unobtrusive trademark labels — little “Made by Monsanto” tags, say. In so doing they have accomplished at least a part of the dream that Jaron Lanier, a computer scientist and musician, and David Sulzer, a biologist at Columbia, enunciated in 1999. To create the ultimate time capsule as part of the millennium festivities at this newspaper, they proposed to encode a year’s worth of the New York Times magazine into the junk DNA of a cockroach. “The archival cockroach will be a robust repository,” Mr. Lanier wrote, “able to survive almost all conceivable scenarios.” …

June 2007. Looking Deep, Deep Into Your Genes. OnEarth, NRDC. by Laura Wright. Excerpt: Discoveries about the impact of the environment on our DNA could revolutionize our concept of illness. …Although some diseases are inherited through a single genetic mutation — cystic fibrosis and sickle cell anemia are examples — the classic “one gene, one disease” model doesn’t adequately explain the complex interplay between an individual’s unique genetic code and his or her personal history of environmental exposures. That fragile web of interactions, when pulled out of alignment, is probably what causes many chronic diseases: cancer, obesity, asthma, heart disease, autism, and Alzheimer’s, to name just a few….
…The completion of the Human Genome Project in 2003 armed scientists with a basic road map of every gene in the human body, allowing them to probe more deeply into the ways our DNA controls who we are and why we get sick, in part by broadening our understanding of how genes respond to external factors.
…In 2001, Jennifer Sass, a neurotoxicologist and senior scientist at the Natural Resources Defense Council (NRDC), who was then a postdoctoral researcher at the University of Maryland, designed an experiment that included the use of microarrays and other molecular tools to figure out how, exactly, mercury was interfering with both our nervous and immune systems. …The findings of Sass, Silbergeld, and others indicate that mercury might play a role in the development of diseases involving immune system dysfunction. These diseases perhaps include autism … but also the spate of autoimmune disorders that we can’t fully explain, from Graves’ disease and rheumatoid arthritis to multiple sclerosis and lupus.
“Do we need to reevaluate our fish advisories?” Silbergeld asks. “Are our regulations actually protecting the most sensitive people?” We target pregnant women and children because we’ve presumed that mercury’s neurotoxic effects are most damaging to those whose brains are still developing. Sass and Silbergeld’s findings don’t contradict that assumption, but they do suggest that there might be other adults who are far more vulnerable than we’d realized — who simply can’t tolerate the more subtle effect the metal has on their immune system because of a peculiarity in their genetic makeup. Designing fish advisories for those people, whose sensitivities are coded in their DNA, is a challenge we’ve never tackled before….

23 May 2007. Study: Climate Change Could Harm CropsBy THE ASSOCIATED PRESS. Excerpt: ROME (AP) — …During the next 50 years, more than 60 percent of 51 wild peanut species analyzed and 12 percent of 108 wild potato species analyzed could become extinct because of climate change, according to a study released Tuesday by the Consultative Group on International Agricultural Research. Surviving species would be confined to much smaller areas, further eroding their capacity to survive, the report said. The study looked at the distribution of various species and predicted their ability to survive based on current and projected climate data for 2055. Farmers and researchers often depend on wild plants to breed new varieties of crops that contain genes for traits such as pest resistance or drought tolerance, and that reliance is expected to increase as climate changes strain the ability of crops to continue to have the same yields as now, the group said in a statement. In recent years, genes found in wild relatives have helped develop new types of domesticated potatoes that can fight devastating potato blight and new varieties of wheat more likely to survive droughts, the statement said. ”There is an urgent need to collect and store the seeds of wild relatives in crop diversity collections before they disappear,” said Andy Jarvis, an agricultural geographer who led the study. ”At the moment, existing collections are conserving only a fraction of the diversity of wild species that are out there.” ….Consultative Group on International Agricultural Research: http://www.cgiar.org

5 September 2006. This Can’t Be Love. By CARL ZIMMER. NY Times. Across the eastern United States, a gruesome ritual is in full swing. The praying mantis and its relative, the Chinese mantis, are in their courtship season. A male mantis approaches a female, flapping his wings and swaying his abdomen. Leaping on her back, he begins to mate. And quite often, she tears off his head. The female mantis devours the head of the still-mating male and then moves on to the rest of his body. …Sexual cannibalism has fascinated biologists ever since Darwin. It is not limited to mantises, but is also found in other invertebrates, including spiders, midges and perhaps horned nudibranchs. Biologists have debated how this behavior has evolved in these species. Some have suggested that sexual cannibalism is just a result of a voracious female appetite. But experiments have also suggested that it is a strategy that females use to select the best fathers for their offspring….

11 October 2005. In the Classification Kingdom, Only the Fittest Survive. By CAROL KAESUK YOON. NY Times. Carolus Linnaeus, the 18th-century botanist and father of scientific naming, enjoyed the unusual status of international scientific hero. Celebrated as the creator of a classification system that … uses kingdoms of life and two-part Latin names for species, was so complete that it seemed he had forever solved the problem of cataloging the world’s living things. So Linnaeus would most likely be shocked – after guessing there were fewer than 15,000 species of animals and plants on earth – to learn that more than 200 years later, scientists are far from finishing the naming of living things and are once again being overwhelmed by an explosion of new species and names. Between 1.5 million and 2 million species have been named, and a deluge of what could be millions more appears imminent. As a result, scientists have once again been seized by 18th-century paroxysms of fear that the field of classification could descend into chaos with precious information lost. For while the Linnaean method for organizing life is still followed and has held up well, no one oversees what has become the rapid and sometimes haphazard proliferation of species names. 

19 March 2005. Latest research into the X chromosome brings startling discoveries. The Scotsman. by ROBERT LEE HOTZ. SCIENTISTS have found genetic evidence for what some men have long suspected: it is dangerous to make assumptions about women. The key is the X chromosome, the “female” sex chromosome that all men and women have in common. In a study published this week in the journal Nature, scientists said they had found an unexpectedly large genetic variation in the way parts of women’s two X chromosomes are distributed among them. The findings were published in conjunction with the first comprehensive decoding of the chromosome. Females can differ from each other almost as much as they do from males in the way many genes at the heart of sexual identity behave, researchers say. “Literally every one of the females we looked at had a different genetic story,” says Duke University genetics expert Huntington Willard, who co-wrote the study. “It is not just a little bit of variation.” …The newly discovered genetic variation between women might help account for differing gender reactions to prescription drugs and the heightened vulnerability of women to some diseases, experts say. …All told, men and women may differ by as much as 2 per cent of their entire genetic inheritance, greater than the hereditary gap between humankind and its closest relative, the chimpanzee. “In essence,” Willard says, “there is not one human genome, but two: male and female.” …The X chromosome contains a larger share of genes linked to disease than any other chromosome. It is implicated in 300 hereditary disorders, including colour blindness, haemophilia and Duchenne muscular dystrophy. Nearly 10 per cent of the genes may belong to a group known to be more active in testicular cancers, melanomas and other cancers, the team reports.

3 May 2005. NASA RELEASE: 05-115. NASA and EPA Team to Improve Crop Management. Can you see the difference between traditional corn and bio-engineered corn? NASA technology is beginning to provide the answer in a snapshot. The technology is called hyperspectral imaging. It uses a special camera to cut one snapshot into 120 color-specific images. Hyperspectral means getting many more images within the spectrum of just one picture. Each image shows a unique characteristic not visible to the human eye. …The Environmental Protection Agency (EPA) teamed with NASA to use the technology to ensure appropriate management practices are used to avoid the development of resistance in corn pest populations. Pest resistance could severely limit the continued use of these new varieties of corn. With more than 25 million acres of corn planted this year, it is physically and economically infeasible to sample each one. This new technology seeks to provide an active monitoring capability to inform the grower of pest resistance development. Early use of hyperspectral imaging provides the ability to distinguish between the two types of corn and identify pest infestation conditions. Bio-engineered corn has inserted genes to make the plant resistant to insects. …”This effort will enhance NASA’s understanding of image processing techniques to extract knowledge from hyperspectral data sets,” said Brian Mitchell of NASA’s Space Partnership Development Program at Marshall. “The research being conducted with genetically modified plants and plant growth has the potential to contribute significantly in our ability to grow sustainable and nutritional crops in space. This could prove vital for long duration exploration missions.” …Hyperspectral imaging may be used to treat crew injuries in space. The Institute is working on a portable, handheld camera to take images of a wound site. Using that image to identify wound severity and healing progress will allow doctors to decide the best treatment. The imaging could save precious diagnostic time, which would also improve healing by ensuring timely and proper treatment. Hyperspectral imaging will also detect mold and toxins in spacecraft, a needed tool during long-duration missions to ensure crews have a clean, healthy environment. For info…, visit:
http://www.nasa.gov/home/index.html. For related material on crops and bioengineering, see the Union of Concerned Scientists web page on “Food and Environment“

Summer 2004. Prescription Rice: The Brave New World of Pharma Foods, by Melissa Pamer. Terrain magazine, pp. 10-13. Excerpt: … Farmers in California’s flat, hazy rice fields have worked for years…to please the demanding Japanese palate and gain a toehold in its lucrative market. And it’s beginning to work: roughly 40 percent of the rice grown in California goes to Japan. … Just in the past few years California’s rice has finally earned some respect in Japan and other finicky Asian markets, and last year’s crop could achieve the best return for farmers in the state’s history. But now California farmers worry that the purity of their rice, its hard-won status, and their own livelihood may become casualties of the global debate on genetic modification. At issue is a new kind of rice-a new kind of farm crop, in fact-that is genetically engineered to produce pharmaceuticals. Using the same recombinant DNA techniques that have created GE foods, biotechnology companies are now making plants like rice, corn, and tobacco into “factories” for producing medically useful compounds….Over the past few months, a small Sacramento-based biotechnology company’s aim to expand its experimental crop of pharmaceutical rice has caused a shake-up in the normally hermetic California rice industry. In October of last year, Ventria BioScience petitioned the California Rice Commission (CRC) for permission to grow 120 acres of two varieties of rice engineered to produce artificial versions of two human proteins-lysozyme and lactoferrin-which occur naturally in breast milk and tears. …Ventria’s petition set off a review process. …”One little slip. One slip, that’s all it’s gonna take. If there’s a mistake, the farmer is going to pay-big time,” rice farmer Joe Carrancho told the CRC advisory board as it prepared to vote on Ventria’s protocol in late March. In work boots and dusty blue overalls, Carrancho held up a chart showing 100 percent opposition to GMO wheat from Japanese consumers. “We are fearful,” he said.