Category Archives: public health

How to Engineer Bacteria to Search for Underground Chemical Weapons: DARPA

U.S. military researchers asked in 2019 two companies to develop new kinds of biological sensors that can detect underground disturbances or the presence of buried chemicals or weapons.

Officials of the U.S. Defense Advanced Research Projects Agency (DARPA) in Arlington, Va., are looking to Raytheon BBN Technologies, and Signature Science, for the BioReporters for Subterranean Surveillance program.  This project seeks to use indigenous and engineered organisms to sense changes of interest to military commanders in natural and built environments. Raytheon BBN and Signature Science won separate $1.6 million contracts for the Subterranean Surveillance progam.

The two companies will perform laboratory research and proof-of-concept demonstrations of biological sensing systems in well- controlled field tests that take advantage of recent advances in microbial science and synthetic biology to develop biological sensors, signal transducers, and reporters that can reveal subterranean phenomena at a distance.  Bio Reporters should be able to sense a phenomenon at least one meter below the surface, propagate a signal to the surface within seven days, and be continuously detectable on the surface at a distance of 10 meters over the subsequent seven days.

DARPA researchers want Raytheon BBN and Signature Science experts to take advantage of the extensive biological networks that exist underground to monitor large areas to increase the military’s ability to detect subterranean events without the need for precise coordinates.

Excerpts from John Keller, Researchers eye new biological sensors to to detect underground objects like buried chemicals and weapons, https://www.militaryaerospace.com,  Nov. 6, 2019

In more detail  Signature Science and its partner, the Texas A&M University Center for Phage Technology, aim to leverage modern and synthetic phage biology and the straightforward molecular genetics of the harmless soil bacterium Bacillus subtilis to generate a new platform to recognize and report on specific chemical threats underground. The Spore-Phage Amplified Detection (SPADe) method, potentially extensible to explosives, radiation or physical disturbance sensing, seeks to substantially advance currently used techniques which rely heavily on manual soil testing. 

Scrubbing Sulfur Pollution

From January 2020, the United Nations International Maritime Organization (IMO) will ban ships from using fuels with a sulphur content above 0.5%, compared with 3.5% now.The rules herald the biggest leap in how ships are powered since they switched from burning coal to oil over a century ago, but vessels will still be allowed to use higher-sulphur fuel if fitted with cleaning devices called scrubbers.  Closed-loop scrubbers keep most of the water used for sulphur removal onboard for disposal at port. Open-loop systems, however, remove sulphur coming through a ship’s smokestack with water that can then be pumped overboard.

Years of studies have examined whether open-loop scrubbers introduce into waterways acidic sulphur harmful to marine life, cancer-causing hydrocarbons, nitrates leading to algal blooms and metals that impair organ function and cause birth defects.  The results have largely been inconclusive and the IMO itself has encouraged further study into the environmental impact of scrubbers.

The stated aim of the new IMO measures is to improve human health..  A study in the journal Nature last year found ship emissions with current sulphur levels caused about 400,000 premature deaths from lung cancer and cardiovascular disease as well as around 14 million childhood asthma cases every year.

Singapore and Fujairah in the United Arab Emirates have banned the use of open-loop scrubbers from the start of next year. China is also set to extend a ban on scrubber discharge to more coastal regions. 

Excerpts from Noah Browning, Going overboard? Shipping rules seen shifting pollution from air to sea, Reuters, Oct. 21, 2019

Rivers of Crude Oil: the poisoned land of Iraq

A biological remediation pilot project seeking to enhance nature’s own ability to clear up oil spills in Iraq’s conflict-affected areas has been launched in Kirkuk, Iraq…This UNEP initiative seeks to harness naturally occurring soil bacteria as a powerful natural ally to decontaminate poisoned land.  Over three years ago in summer 2016, the residents of Qayyarah—a small town of around 25,000 people, some 60 km south of Mosul—were caught in the line of fire as so-called Islamic State fighters torched nineteen nearby oil wells. So thick were the clouds of smoke, that people could not distinguish day from night for weeks in what infamously came to be known as the “Daesh winter”.  Rivers of crude oil flowed through Qayyarah’s streets and into seasonal wadis as oil wells spewed tens of thousands of barrels of oil relentlessly for months. The specter of an even worse environmental catastrophe was heightened as the oil slick migrated to less than three kilometers from the Tigris River, Iraq’s water lifeline.

Following an epic battle to control the oil fires that took nearly a year, North Oil Company, which manages the oil fields of northern Iraq, is currently collecting an estimated 20,000 tonnes of remaining oil waste in Qayyarah into around a dozen large pits.  Progress, however, has been slow and pools of heavy viscous oil remain on the doorsteps of entire neighborhoods and households, who complain about the impacts of noxious fumes on their children’s health.

“In some places, the layer of heavy oil is two to three meters thick, and long stretches of wadi channels are now effectively tarmac roads on which cars can be driven,” observed Mohammed Dawood, head of Qayarrah oil refinery’s environmental unit. Furthermore, Environment Ministry officials expressed concern that exceptionally heavy rains and flash floods of the 2018/19 winter season washed out oil from the holding pits into the Tigris River.

While oil production restarted in Qayyarah immediately after the conflict ended in June 2017, reaching currently an estimated 40,000 barrels per day, little has been done to clean up the conflict’s toxic aftermath… The UN Environment Programme in collaboration with the UN Assistance Mission in Iraq delivered a four-day hands-on training workshop on remediation of oil spills by the use of bacteria  in September 2019. “By adding nutrients from manure, bulking agents like wood chips and water, we are simply creating the ideal conditions for bacteria to thrive and speeding up the natural process of breaking down the oil,”

Excerpts from  Microbes offer hope of cleaning up Iraq conflict’s pollution legacy, UNEP Press Release, Oct. 23, 2019

The Impact of Oil Spills on the Deep Sea: the Deepwater Horizon Oil Spill

The Louisiana University Marine Consortium (LUMCON) published in September 2019 a study on the Deepwater Horizon Oil Spill in Royal Society Open Science.  The BP’s Deepwater Horizon oil rig exploded in April 2010, killing 11 workers.  The subsequent cleanup and restoration had cost nearly $65 billion..but while while we can burn off and disperse oil on the surface, but we don’t have the technology to get rid of oil on the seafloor. So approximately 10 million gallons of it settled there….In 2017 , the The LUMCON surveyed the site surrounding the wreck of the rig, and another one 1,640 feet north. There were no giant isopods, glass sponges, or whip corals that would have jumped (metaphorically) at the chance to colonize the hard substrate of the rig, such as discarded sections of pipe…..But]  crabs were just about everywhere. The researchers were shocked by the sheer number of crustaceans and other arthropods that had colonized the spill site. According to rough estimates, Atlantic deep sea red crabs, red shrimp, and white caridean shrimp were nearly eight times more populous at the Deepwater site than at other spots in the Gulf. “Everywhere there were crabs just kicking up black plumes of mud, laden with oil,” Nunnally says. But abundance does not mean the site was recovering, or even friendly to life. Particularly eerie was the crab’s achingly slow movement. “Normally, they scatter when they see the ROV lights,” he says. But these crabs seemed unbothered, or unaware of the robot’s presence.

Crabs on the seabed of the Deepwater Horizon oil spill

The researchers hypothesize that degrading hydrocarbons are what’s luring unwitting crabs from the surrounding seafloor to the deep-sea equivalent of a toxic dump. “The chemical makeup of oil is similar to the oils naturally present on crustaceans,” Nunnally says. “They’re attracted to the oil site, but everything goes downhill for them once they’re in the area.” A similar kind of chemical confusion occurred at an oil spill in Buzzards Bay in New England in 2003, which attracted hordes of American lobsters. The researchers liken the death trap to the La Brea Tar Pits: Once lured in, the crabs lose their ability to leave. With no other species able to thrive in the area, the crabs have no food source—except each other. And as one might imagine, consuming the flesh of a toxin-riddled crab or starving to death in a deep-sea tar pit is sort of a lose/lose situation.

The crabs also looked anything but normal: some claws shrunken, some swollen, shriveled legs, a dusting of parasites. “There were deformities, but mostly things were missing,” Nunnally says. “You come in with eight legs and try to get away on four or five.” The researchers have yet to ascertain what specific toxins led to these maladies. The shrimp looked just as awful as the crabs. “They didn’t look like shrimp from other sites,” Nunnally says, adding that many of the small crustaceans had humps in their backs—tumors, perhaps.

Excerpts from SABRINA IMBLERS, A Decade Later, the Deepwater Horizon Oil Spill Has Left an Abyssal Wasteland, Atlas Obscura, Sept. 18, 2019

The Fight Against Toxic Algae

Signs posted around the Grand Lake, Ohio read: “Danger: Avoid all contact with the water.”  When dangerously high levels of toxins from blue-green algae in Grand Lake, Ohiio were publicized in 2009, many residents and tourists stopped using the 13,000-acre lake in northwest Ohio. Hotel revenue and home values sank for several years as algae bloomed in the state’s largest inland lake.

Greenish water still laps at Grand Lake’s shores, but recent water samples show that the amount of algae-feeding nutrients entering the lake is down significantly. State, federal and private donations covered more than $10 million in projects aimed at improving water quality. More people are boating on the lake again. Grand Lake could now serve as an example for communities with algae problems across the nation, experts say.

Algal blooms are on the rise, from Lake Erie to the Florida Everglades. In August 2019, the Environmental Protection Agency listed algae-related beach closures or health advisories in 23 states, and it said other blooms may not have been reported. In 2010, the EPA found that 20% of 50,000 lakes surveyed had been affected by phosphorous and nitrogen pollution, which feeds algae.e  Cleaning up bodies of water choked with toxic algae has proved difficult. The project to repair Grand Lake, once one of the most polluted by algae in the nation, is one of the clearest successes. It shows cleanup is possible, but also expensive and time-consuming.

“It’s not restored yet, but it’s on the road to recovery,” said Stephen Jacquemin, an associate professor of biology at Wright State University-Lake Campus in Celina.  Beginning in 2012, wetlands areas were built around the lake, which was hand dug in the 1830s. The thick stands of bulrushes and other plants have reduced phosphorous and nitrogen levels in water entering the wetlands before reaching the lake by as much as 90%, Dr. Jacquemin said.  Three wetland areas, which cost a total of about $6 million to build, are constructed as a series of interconnected pools that allow particulates to settle out and plants and microbes to remove nutrients.

Areal View of Artificial Wetlands, Great Lake Ohio

 The state’s Department of Natural Resources has also dredged the lake bottom to remove nutrient-loaded sediment, and tried to clean up one of Grand Lake’s beaches near St. Marys by building a rock jetty and installing aerators and a curtain to filter water. Recent water tests there showed levels below 6 parts per billion of the toxin microcystin, under Ohio’s threshold of 20 parts per billion for avoiding contact with water.

As Green Algae Forces Beaches to Close, Ohio Lake Offers Hope, WSJ, Sept. 18, 2019

The Truth About Forest Fires

BBC has used satellite data to assess the severity of fires in Brazil, Indonesia, Siberia and Central Africa.  It has concluded that although fires in 2019 have wrought significant damage to the environment, they have been worse in the past.   More than 35,000 fires have been detected so far in 2019 in East Asia  spreading smoky haze to Malaysia, Singapore, the south of Thailand and the Philippines, causing a significant deterioration in air quality.  But this is substantially fewer than many other years including those, such as 2015, exacerbated by the El Nino effect which brought unusually dry weather.

Haze Pollution

In Indonesia, peatland is set alight by corporations and small-scale farmers to clear land for palm oil, pulp and paper plantations, and can spread into protected forested areas.  The problem has accelerated in recent years as more land has been cleared for expanding plantations for the lucrative palm oil trade.  Old palm trees on plantations that no longer bear fruit are often set on fire to be replaced by younger ones.

The number of recorded fires in Brazil rose significantly in 2019, but there were more in most years in the period 2002 to 2010.  There is a similar pattern for other areas of Brazilian forestry that are not part of the Amazon basin.  For 2019, we have data up to the end of August, and the overall area burnt for those eight months is 45,000 sq km. This has already surpassed all the area burnt in 2018, but appears unlikely to reach the peaks seen in the previous decade… “Fire signals an end of the deforestation process,” says Dr Michelle Kalamandeen, a tropical ecologist on the Amazon rainforest.  “Those large giant rainforest trees that we often associate with the Amazon are chopped down, left to dry and then fire is used as a tool for clearing the land to prepare for pasture, crops or even illegal mining.”

The environmental campaign group Greenpeace has called the fires that have engulfed the Russian region of Siberia this year one of the worst outbreaks this century.  The cloud of smoke generated was reported to have been the size of all the European Union countries combined.  Forest fires in Siberia are common in the summer, but record-breaking temperatures and strong winds have made the situation particularly bad.  Russia’s Federal Forestry Agency says more than 10 million hectares (100,000 sq km) have been affected since the start of 2019, already exceeding the total of 8.6 million for the whole of 2018…. Drawing on data for the number of fires, it is clear that there have been other bad years, notably in 2003.

Nasa satellites have identified thousands of fires in Angola, Zambia and DR Congo.However, these have not reached record levels.  “I don’t think there’s any evidence that the fires we’re seeing in Africa are worse than we’ve seen in recent years,” Denis McClean, of the UN Disaster Risk Reduction agency, told the BBC.  According to data analysed by Global Forest Watch, fires in DR Congo and Zambia are just above average for the season but have been higher in past years.  In Angola, however, fires have been reported at close to record levels this year.

Some have drawn comparisons with the situation in the Amazon, but the fires in sub-Saharan Africa are different.  Take DR Congo – most fires are being recorded in settled parts of the country’s southern, drier forest and savannah areas, and so far not in tropical rainforest.  Experts say it is difficult to know what is causing these fires, which are seasonal. Many are likely to be on grassland, woodland or savannah in poor farming communities.  “Fires are very important landscape management tools and are used to clear land for planting crops,” says Lauren Williams, a specialist in Central and West African forests at the World Resources Institute.

Excerpts from Jack Goodman & Olga RobinsonIndonesia haze: Are forest fires as bad as they seem?, BBC, Sept. 19, 2019. For more details and data see BBC

Modernize or Die: Bio-Engineered Food

China is betting that CRISP technology*can transform the country’s food supply.  China also expanded its efforts beyond its borders in 2017, when the state-owned company ChemChina bought Switzerland-based Syngenta—one of the world’s four largest agribusinesses, which has a large R&D team working with CRISPR—for $43 billion. That was the most China has ever spent on acquiring a foreign company, and it created an intimate relationship between government, industry, and academia—a “sort of a ménage à trois” that ultimately could funnel intellectual property from university labs into the company, says plant geneticist Zachary Lippman of Cold Spring Harbor Laboratory in New York.

Chinese leaders “want to strategically invest in genome editing, and [by that] I mean, catch up,” says Zhang Bei, who heads a team of 50 scientists at the Syngenta Beijing Innovation Center…China may one day need CRISPR-modified plants to provide enough food for its massive population….    China needs to resolve how it will regulate CRISPR-engineered crops—a divisive issue in many countries. In a 2018 decision that rocked big agriculture, a European court ruled that such crops are genetically modified organisms (GMOs) that need strict regulation. In contrast, the U.S. Department of Agriculture (USDA) exempts genome-edited plants from regulations covering GMOs as long as they were produced not by transferring DNA from other species, but by inducing mutations that could have occurred naturally or through conventional breeding.  Chinese consumers are wary of GM food. The country strictly limits the import of GM crops, and the only GM food it grows are papayas for domestic consumption. But for CRISPR, many plant researchers around assume China will follow in the United States’s footsteps…

For Corteva, Syngenta, and the other two big ag companies—BASF and Bayer (which acquired Monsanto last year)—the long game is to use CRISPR to develop better versions of their serious moneymakers, the “elite” varieties of a wide range of crops that have big commercial markets. They sell dozens of kinds of elite corn seeds—for example, inbred strains that consistently have high yields or reliable resistance to herbicides. Creating the genetic purity needed for an elite variety typically takes traditional breeding of many generations of plants, and CRISPR is seen as the cleanest way to improve them quickly. The earlier methods of engineering a plant can lead to unwanted genomic changes that must be laboriously culled…

Syngenta sees CRISPR-modified corn as a big opportunity in China, which grows more hectares of corn than any other crop. Yields per hectare are only 60% of those in the United States because corn ear worms often weaken Chinese crops. A fungus thrives in the weakened plants, producing a toxin that makes the resultant ears unfit for animal feed. As a result, China must import a great deal of corn. (According to USDA, 82% of U.S.-grown corn has been engineered to have a bacterial gene that makes it resistant to ear worms.)…“Syngenta is putting a lot of emphasis to grow in China to become the leading seed company. The China market as a whole, if it modernizes as the U.S. has modernized, can be as big as the U.S. market.”

Jon Cohen, To feed its 1.4 billion, China bets big on genome editing of crops, Science Magazine, Aug. 2, 2019

* Genome editing (also called gene editing) is a group of technologies that give scientists the ability to change an organism’s DNA. These technologies allow genetic material to be added, removed, or altered at particular locations in the genome. Several approaches to genome editing have been developed. A recent one is known as CRISPR-Cas9.