Every year, an estimated 48 million Americans get sick from foodborne illnesses, resulting in some 128,000 hospitalizations and 3,000 deaths, according to the U.S. Centers for Disease Control and Prevention. This public health problem is compounded by billions in economic damage from product recalls, highlighting the need to rapidly and accurately determine the sources of foodborne illnesses.With the increasing complexity of global supply chains for the myriad foods available to consumers, however, the task of tracing the exact origin of contaminated items can be difficult.In a novel solution that can help determine the origin of agricultural products and other goods, Harvard Medical School (HMS) scientists have developed a DNA-barcoded microbial system that can be used to label objects in an inexpensive, scalable and reliable manner.A flask of DNA-barcoded spores. Photos courtesy of Jason QianReporting in Science on June 4, the research team describes how synthetic microbial spores can be safely introduced onto objects and surfaces at a point of origin, such as a field or manufacturing plant, and be detected and identified months later.The spores are derived from baker’s yeast and a common bacterial strain used in a wide variety of applications, such as probiotic dietary supplements, and designed to be incapable of growing in the wild to prevent adverse ecological effects.“Spores are in many ways an old-school solution and have been safely sprayed onto agricultural goods as soil inoculants or biological pesticides for decades. We just added a small DNA sequence we can amplify and detect,” said study corresponding author Michael Springer, associate professor of systems biology in the Blavatnik Institute at HMS.“We also worked hard to make sure this system is safe, using commonplace microbial strains and building in multiple levels of control,” Springer added. “We hope it can be used to help solve problems that have enormous public health and economic implications.”In recent years, scientists have learned a great deal about the interactions between microbes and their environments. Studies show that microbial communities in homes, on cell phones, on human bodies and more have unique compositions, similar to fingerprints. Attempts to use microbial fingerprints to identify provenance can be time consuming and are not easily scaled, however.The use of custom-synthesized DNA sequences as barcodes has been shown in principle to be effective for labeling food and other items. To be widely useful, DNA barcodes must be produced cheaply in large volumes, persist on objects in highly variable environments, and able to be reliably and rapidly decoded — hurdles that have thus far not been overcome because DNA is fragile.Heavy-duty packagingIn their study, Springer and colleagues set out to determine if DNA barcodes packaged within microbial spores, which can be sprayed onto crops and identified months later, could help solve these challenges.Many microorganisms, including bacteria, yeasts and algae, form spores in response to harsh environmental conditions. Analogous to seeds, spores allow microorganisms to remain dormant for extraordinarily long periods and survive extreme conditions such as high temperatures, drought and UV radiation.The research team created custom-made DNA sequences that they integrated into the genomes of the spores of two microorganisms — Saccharomyces cerevisiae, also known as baker’s yeast, and Bacillus subtilis, a common bacterium that has numerous commercial uses, including as a dietary probiotic, a soil inoculant and a fermenting agent in certain foods. These spores can be cheaply grown in the lab in large numbers.The synthetic DNA sequences are short and do not code for any protein product and are thus biologically inert. Inserted into the genome in tandem, the sequences are designed so that billions of unique barcodes can be created.The team also ensured that DNA-barcoded spores could not multiply, grow and spread in the wild. They did so by using microbial strains that require specific nutritional supplementation and by deleting genes required for the spores to germinate and grow. Experiments involving from hundreds of millions to more than a trillion of the modified spores confirmed that they are unable to form colonies.To read the DNA barcodes, the researchers used an inexpensive CRISPR-based tool that can detect the presence of a genetic target rapidly and with high sensitivity. The technology, called SHERLOCK, was developed at the Broad Institute of MIT and Harvard, in a collaboration led by institute members James Collins and Feng Zhang.“Spores can survive in the wild for an extremely long time and are a great medium for us to incorporate DNA barcodes into,” said study co-first author Jason Qian, a graduate student in systems biology at HMS. “Identifying the barcodes is straightforward, using a blue light source, an orange plastic filter and a cell phone camera. We don’t envision any challenges for field deployability.” Real worldThe team examined the efficacy of their barcoded microbial spore system through a variety of experiments.They grew plants in the laboratory and sprayed each plant with different barcoded spores. A week after inoculation, a leaf and a soil sample from each pot were harvested. The spores were readily detected, and even when the leaves were mixed together, the team could identify which pot each leaf came from.When sprayed onto grass outside and exposed to natural weather for several months, spores remained detectable, with minimal spread outside the inoculated region. On environments such as sand, soil, carpet and wood, the spores survived for months with no loss over time, and they were identified after disturbances such as vacuuming, sweeping and simulated wind and rain.Researchers built a sandpit to test the barcoded microbial spore system in simulated real-world environments.Spores are very likely to persist through the conditions of a real-world supply chain, according to the researchers. As a proof-of-principle, they tested dozens of store-bought produce items for the presence of spores of Bacillus thuringiensis (Bt), a bacterial species that is widely used as a pesticide. They correctly identified all Bt-positive and Bt-negative plants.In additional experiments, the team built a 100-square-meter (~1,000 square feet) indoor sandpit and found that the spread of spores was minimal after months of simulated wind, rain and physical disturbances.They also confirmed that spores can be transferred onto objects from the environment. Spores were readily identified on the shoes of people who walked through the sandpit, even after walking for several hours on surfaces that were never exposed to the spores. However, the spores could not be detected on these surfaces, suggesting that objects retain the spores without significant spread.This characteristic, the team noted, could allow spores to be used to determine whether an object has passed through an inoculated area. They tested this by dividing the sandpit into grids, each labeled with up to four different barcoded spores. Individuals and a remote-control car then navigated the sandpit.They found that they could identify the specific grids that the objects passed through with minimal false positives or negatives, suggesting a possible application as a complementary tool for forensics or law enforcement.The team also considered potential privacy implications, noting that existing technologies such as UV dyes, cell phone tracking and facial recognition are already widely used but remain controversial.“As scientists, our charge is to solve scientific challenges, but at the same time we want to make sure that we acknowledge broader societal implications,” Springer said. “We believe the barcoded spores are best suited for farming and industrial applications and would be ineffective for human surveillance.”Regardless, the use and adoption of this technology should be done with a consideration of ethics and privacy concerns, the study authors said.The researchers are now exploring ways to improve the system, including engineering potential kill-switch mechanisms into the spores, finding ways to limit propagation and examining if the spores can be used to provide temporal information about location history.“Outbreaks of harmful foodborne pathogens such as listeria, salmonella and E. coli occur naturally and frequently,” Springer said. “Simple, safe synthetic biology tools and knowledge of basic biology allow us to create things that have a lot of potential in solving real world safety issues.”Study co-first authors include Zhi-xiang Lu, Christopher Mancuso, Han-Ying Jhuang,Rocío del Carmen Barajas-Ornelas, and Sarah Boswell.Additional authors include Fernando Ramírez-Guadiana, Victoria Jones, Akhila Sonti, Kole Sedlack, Lior Artzi, Giyoung Jung, Mohammad Arammash, Mary Pettit, Michael Melfi, Lorena Lyon, Siân Owen, Michael Baym, Ahmad Khalil, Pamela Silver, and David Rudner.This work was supported by DARPA Biological Robustness in Complex Settings (grant HR001117S0029).
The world premiere of David Grimm’s Tales from Red Vienna has its official opening night off-Broadway March 18. Starring Nina Arianda and Michael Esper, the Manhattan Theatre Club production is playing at MTC at New York City Center — Stage I. View Comments Directed by Kate Whoriskey, Tales From Red Vienna tells the story of Helena (Arianda), a woman who, having lost her husband and financial security in World War I, struggles to maintain her way of life as she becomes a part of an illicit underworld. She manages to separate her secret life from her public persona until she crosses paths with someone who has the power to expose and ruin her. Star Files Nina Arianda The show also features Tina Benko, Michael Goldsmith, Lucas Hall and Kathleen Chalfant. Michael Esper
Published on June 24, 2015 at 12:17 pm Contact Matt: [email protected] | @matt_schneidman Facebook Twitter Google+ Rakeem Christmas and Chris McCullough are both surrounded with questions ahead of Thursday’s NBA Draft, albeit on different ends of the spectrum. McCullough’s decision to come out early and Christmas’ age and experience are viewed in some light as hindrances to their draft stock.Both are viewed as late first- or early second-round picks, but their landing spots could fluctuate based on how teams view the uncertainties surrounding the pair.On Wednesday morning, ESPN analyst Chad Ford held a teleconference to discuss the NBA Draft and provided some insight into the possible professional fortunes of the two former Syracuse forwards.McCullough cognizant of decision, could land in 1st round“He took a gamble but I think one that he knew,” Ford said. “For circumstances that I think have less to do with basketball and more to do with life, he felt that he needed to turn pro.”AdvertisementThis is placeholder textMcCullough, 20, recently became a father, which may have played into his decision to enter his name in the draft. The likelihood is that he would’ve been a lottery pick if he returned to SU for his sophomore season, but he left after one year despite tearing his right ACL on Jan. 11 against Florida State.Until that point, he averaged 9.3 points and 6.9 rebounds in 16 games played and may have shown scouts enough to be taken just inside the first round.“He was a bubble first-rounder when he declared for the draft and he wasn’t going to be able to work out because of the ACL injury,” Ford said. “Will he go in the first round? I mean the good news for him is that he’s got several teams that have multiple picks in the first round like the Lakers and Celtics and you have a team in the Nets that seems to be a bit enamored with him.”That 27-29 range is one that Ford pegged as a target, as Los Angeles, Boston and Brooklyn are all possible destinations for McCullough. The questions will still be asked, but Ford sees any of those teams having a valid reason to jump on someone who hasn’t played a real game in over five months.“If he went 27, 28, 29 and the team just basically said, ‘Look, I think had he gone back to Syracuse he would’ve been a lottery pick next year, so we’re getting a player like that at 29. We can oversee the rehab, we get to make sure that everything’s great, I think he’s a good pick there,’” Ford said. “If he doesn’t go there, he’ll go in the first 5-10 picks in the 30s.”Christmas’ 2-way swordIt’s no secret Christmas took three years to finally blossom into an NBA Draft prospect. And even after turning in an impressive performance at the NBA Draft Combine, he’s still being projected on the cusp of the first round, more so toward the early second.“The skepticism about Christmas is his age,” Ford said of the 23-year-old. “And when you look at players that age, you expect them to be better than players that are in the 18-, 19-, 20-year-old range, right?”Christmas averaged 17.5 points and 9.1 rebounds in a standout senior season that placed him on the Atlantic Coast Conference first team. He was lauded for his improvement on both ends and proved he’s developing a skill set to match his age, as Ford tabbed him the best player at the combine.But the comparisons between some of the more youthful crop are inevitable.“I think there’s still this grain of salt: he’s doing this with two, three years more experience than a lot of the guys that he’s playing against,” Ford said. “So while teams will absolutely acknowledge he’s more physically mature than a lot of players in the draft, that he’s been better coached and has more experience than those other guys, they’re trying to ask what was he like at 18 and 19 compared to some of the other prospects.“I think Christmas could slide into the late first, I think he’s still more likely to be one of those guys that goes into the 30-45 range.” Comments