New Food Safety Test Can Detect Bacteria in Half the Time

<section class="entry-content instapaper_body clearfix" itemprop="articleBody">
<div class="add-container clearfix" id="add-block-placer">
</div>

 A new method for detecting disease-causing bacteria in food could eventually help keep tainted products from landing on diners’ plates.
 

 The new test was able to detect much lower levels of
 
 Salmonella
 
 bacteria in beef and poultry than two commonly used methods. It also proved equally accurate at identifying disease-causing strains of the organism while ignoring benign ones that may have been present. The research was published in a recent issue of the
 
 Journal of Food Safety
 
 .
 

 “People think that nowadays pathogen testing has reached its limit or it’s already pretty much saturated, but there are still many things we could do to improve this technology,” said Dr. Soohyoun Ahn, an assistant professor of food science at the University of Florida and the study’s senior author.
 
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/frozen-pizza.width-990_UGhmTOk.jpg"/>
<figcaption>A new test could prevent contaminated food from landing on store shelves.
 
 </figcaption>
</figure>

 Bacteria and other microbes in food cause an estimated 48 million illnesses in the United States each year, according to a 2011 report from the U.S. Centers for Disease Control. Ten percent of the infections with a known cause were due to
 
 Salmonella
 
 , leading to roughly 19,000 hospitalizations and 378 deaths, more than any other food-borne contagion. Those with weakened immune systems, such as the elderly and children under age five, are particularly likely to require medical intervention.
 

 Ahn’s method adds two more steps to a standard test called an ELISA that is used to detect substances such as bacterial cells in laboratory samples. Ahn first added a process already employed in food testing that uses a magnet to bring together magnetic beads that have picked up bacteria from the sample. This technique, known as immunomagnetic separation (IMS), concentrates the bacteria and allows the test to detect smaller populations. Her method also utilizes another sensitivity-boosting procedure called tyramide signal amplification that is not currently used for testing food products.
 

 “Tyramide signal amplification is a very robust detection method, and I am not surprised that it was demonstrated to be more sensitive than prior methodologies,” said Dr. Kevin Roth, head pathologist at the Columbia University Medical Center and editor-in-chief of the
 
 American Journal of Pathology
 
 . Roth, who was not involved in the study, added that it is “capable of enhancing signals by orders of magnitude over conventional detection methods.”
 

 Ahn first detailed her procedure in a 2014 paper in the
 
 Journal of Food Protection
 
 , which showed that it could detect much lower levels of
 
 E. coli
 
 bacteria in beef and milk compared to the standard assay with IMS but no signal amplification.
 

 The new study focused on reducing the amount of time that
 
 Salmonella­­­
 
 bacteria from food samples need to grow before Ahn’s test can detect them with high accuracy. Bacterial samples taken from food are usually allowed to grow before tests are run, a process known as enrichment. A more responsive method that can detect smaller amounts of bacteria would require less enrichment time, and her test was able to achieve the same sensitivity with just 12 hours of enrichment as ELISA did with 24 hours.
 

 Because properly cooking food kills bacteria, detecting
 
 Salmonella
 
 in raw meat is not necessarily a cause for concern. But manufacturers of ready-to-eat meals containing meat have to be more vigilant, and while they test their products before shipping them, no test is perfect. A more sensitive method like Ahn’s could identify food containing lower levels of all sorts of bacteria, thereby catching more contaminated products before they reach grocery stores.
 

 New methods of testing require extensive validation, so if Ahn’s technique is eventually adopted, it will not happen anytime soon. If it is one day approved, it would be added to the arsenal of testing methods used by food manufacturers and the government.
 

 “Pathogen detection is a really sensitive issue,” Ahn said. “We are talking about public health.”
 
</section>

 Photo credit:
 <a href="https://www.flickr.com/photos/ais3n/11296254013/">
 ais3n/Flickr (CC BY-NC)
 </a>

Magnetosensitive Deep-Sea Bacteria Could Deliver Chemo to the Hearts of Tumors

<section class="entry-content instapaper_body clearfix" itemprop="articleBody">
<div class="add-container clearfix" id="add-block-placer">
</div>

 An obscure ocean-dwelling bacterium could be just the weapon doctors need to strike directly at the heart of a tumor, according to
 <a href="http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2016.137.html">
 a new study
 </a>
 by a Canadian research team.
 

 The new treatment method uses chemotherapy-carrying bacteria to deliver drugs directly to the low-oxygen regions of tumors, where cancer-promoting activity is thought to be particularly prevalent. Conventional approaches often fail to attack these “hypoxic” areas because they lack the blood vessels that drugs need to reach them and the oxygen required for radiation to be effective. Using chemo-laden bacteria dramatically increased the amount of drug that reached these portions of tumors in mice, although the study did not examine whether this successfully reduced the size of the cancerous masses. The study was published online in August in Nature Nanotechnology.
 
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/nanorobotics-lab_1024x576.width-990_pHIDtSZ.jpg"/>
<figcaption>By strapping chemo to ocean-dwelling bacteria, a team of scientists has figured out how to deliver drugs to vulnerable, low-oxygen regions of tumors.
 
 </figcaption>
</figure>

 Modern chemotherapy is like carpet bombing because it is toxic to both cancerous and healthy tissue, said Sylvain Martel, head of the NanoRobotics Laboratory at Polytechnique Montreal and the study’s senior author. “But what we do is we reduce the dose and we put it on a cruise missile and design the GPS system and the sensors to be able to deliver the therapy to a specific location,” Martel said. “We create less collateral damage and a more efficient treatment for the amount of drug that we deliver.”
 

 Martel’s method relies on a species of bacteria called
 
 Magnetococcus marinus
 
 , which lives in deep-sea waters where oxygen is scarce. The bacteria have the ability to navigate using Earth’s magnetic field, which scientists call magnetotaxis, and they are also able to sense oxygen concentrations. In the wild, these two systems help them find areas of the ocean where they can thrive, but the researchers coopted those abilities to deliver drugs directly to tumors.
 

 First, they attached numerous tiny, chemotherapy-filled sacs called nanocarriers to the bacteria. Then they injected the bacteria into mice and used a magnetic field to guide them to the location of cancer cells that were implanted in the animals. Upon arrival, the microbes’ preference for low oxygen concentrations led them to bury into the masses’ hypoxic zones to deliver their cancer-killing payload.
 

 While nanocarriers have the advantage of shielding healthy cells from their toxic contents, very few of them will reach a tumor without help because they rely on the blood stream to get around. “You inject [them] into the systemic blood circulatory system, which is close to 100,000 kilometers, two-and-a-half times the circumference of the Earth at the equator,” Martel said. “They circulate everywhere, so you need to inject a huge quantity.” And even those that make it to a tumor often cannot access its hypoxic areas. Without guidance, nanocarriers deliver as little as two percent of the chemotherapy dose to tumors, but in Martel’s experiments slightly more than half of the injected bacteria successfully penetrated their targets. This could allow clinicians to use lower doses of chemotherapy.
 

 Prior attempts to target the hypoxic regions of tumors have not had much success because the oxygen concentrations in tumors fluctuate over time, differ in different parts of the tumor, and vary between tumor types, according to Michael P. Hay, an associate professor at the Auckland Cancer Society Research Centre at New Zealand’s University of Auckland. “Hypoxia is definitely of interest but is a hard nut to crack,” Hay said. In addition to overlooking the question of how the treatment affected the tumors, the study also suffers from other limitations. According to Johns Hopkins University oncologist Shibin Zhou, therapies must target parts of tumors with both low and normal oxygen concentrations in order to completely destroy them. Moreover, because the approach was only tested in mice with weakened immune systems, it is unclear if a healthy human body will attack the bacteria, which could set off a life-threatening systemic reaction known as sepsis, said Richard Frankel, an expert in magnetotactic bacteria at California Polytechnic State University.
 

 However, according to Martel, forthcoming research shows that the bodies of mice with normal immune systems do not attack the bacteria, implying the treatment would be similarly safe in humans because the bacteria cannot survive in human hosts. Martel is also confident that it will be more effective than approaches that fail to bring drugs directly to the hypoxic areas of tumors.
 

 “If you have something very efficient and you deliver it to the right location, it’s going to be much more efficient,” Martel said.
 
</section>

 Image credit: Nanorobotics Laboratory/Polytechnique Montreal

From Black Water to Green Energy

<section class="entry-content instapaper_body clearfix" itemprop="articleBody">
<div class="add-container clearfix" id="add-block-placer">
</div>

 Humans have spent the last two centuries largely dependent on environmentally damaging fossil fuels for power, so when Jeff Moeller attended a workshop discussing ways to replace some of this energy with more sustainable fuel made from algae, he was immediately intrigued.
 

 An expert in wastewater systems and the director of water technologies at the non-profit Water Environment &amp; Reuse Foundation (WE&amp;RF), Moeller wondered if the same process could be applied to another wet, carbon-containing material: the sludge produced by wastewater treatment. After one of the workshop’s leaders confirmed his hunch, he wasted little time contacting a firm commercializing a promising technology, a U.S.-based company called Genifuel Corporation.
 

 Now, a public utility called Metro Vancouver now has plans to pilot a system based on the process to convert human sewage into oil and natural gas at its wastewater treatment plant in Annacis Island, British Columbia. Metro Vancouver chose to undertake the project after an independent assessment organized by Moeller and the WE&amp;RF demonstrated the promise of the technology, which was developed by Genifuel in collaboration with the U.S. Department of Energy’s Pacific Northwest National Laboratory (PNNL).
 
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/crude-oil_1024x576.width-990_Q3FBZVl.jpg"/>
<figcaption>Biocrude oil and liquid fuel
 
 </figcaption>
</figure>

 The Genifuel system combines two separate processes to transform wastewater sludge into fuel. The first step produces a type of oil called biocrude, while the second creates methane, the main component of natural gas. The two techniques are specific types of a procedure called hydrothermal processing, which uses high temperatures and pressures to produce useful products from wet materials that contain organic compounds, or substances made up of carbon. While hydrothermal processing has been around since the 1930s, recent improvements have made it potentially cost-competitive for the first time, said Corrine Drennan, who oversees PNNL’s bioenergy technology research.
 

 Many wastewater treatment plants currently feed their sludge into an oxygen-deficient container called an anaerobic digester in which microorganisms turn some of it into biogas that can be burned for electricity and heat. But this only reduces the amount of sludge by about half, so the plant must pay to have the rest shipped to a landfill or incinerator. “In a big utility that can run into substantial money” said Jim Oyler, CEO of Genifuel.
 

 The Genifuel system eliminates much more of the sludge, dramatically reducing the cost of waste disposal while producing potentially carbon-neutral fuel and clean, sterile water as practically the only byproducts. Moreover, while this process may not displace much fossil fuels on its own, PNNL and the National Renewable Energy Laboratory in Colorado are investigating other sources of liquid waste that could be turned into fuel. Oyler estimates that applying hydrothermal processing to easily accessible wet waste products like wastewater sludge, cow manure, and food processing waste could provide more than 15% of the U.S.’s liquid fuel by 2045, and adding in agricultural and wood waste could boost that figure even further. “It’s not going to be just one thing, but this technology could supply a substantial portion of our transportation fuels if fully implemented,” he said.
 

 Oyler started investigating hydrothermal processing after several other successful business ventures, marking a return to the energy industry where he got his start. “Energy is the most fundamental physical process of all, and it is endlessly interesting,” he said. He sold his technology company and started Genifuel in 2006 with the goal of using hydrothermal processing to make biodiesel from algae. Hydrothermal processing’s ability to handle wet materials makes it more economical than other methods of converting organic matter into fuel because there is no need to spend money or energy drying the material first. But while Oyler’s goal proved technically feasible, it was too expensive to be practical.
 

 Oyler then went searching for other substances his company could make fuel from, ultimately settling on wet waste products like wastewater sludge. “The advantage of processing wastes is that you do not incur the cost of growing and harvesting a crop such as algae,” he said. “Even better, some wastes—such as wastewater sludge—have a ‘negative cost,’ because the solids must be disposed of, and the disposal cost can become part of the revenue stream for hydrothermal processing.”
 

 The WE&amp;RF-organized independent assessment of Genifuel’s system was performed by PNNL under the supervision of engineers from technical consulting company Leidos, Inc. “The overarching goal was really to better assess if the technology does what [Genifuel] says it does,” Moeller said. “Can you produce biocrude oil from sludge, and what’s the composition of the different things that come out of there—the biocrude, the biogas, and the clean, sterile water?”
 

 In PNNL’s bench-scale tests, Genifuel’s entire process reduced the amount of solids requiring disposal by up to 99 percent. The oil-generating step alone converted up to 37 percent of the sludge’s organic solids—the portion that could potentially become fuel—into biocrude, while virtually all of the remaining organic material becomes methane and carbon dioxide. The inorganic compounds like phosphorous and nitrogen in the sludge are the only ones a treatment plant might need to dispose of afterwards, although those two chemicals could be another source of income if they could be filtered out and sold as fertilizer, Moeller said. Moreover, if some of the nitrogen were filtered out, environmental regulations may permit the wastewater to be released into the environment without further treatment.
 

 Genifuel’s system also produced natural gas free of certain silicon-based compounds that are a byproduct in anaerobic digesters. These siloxanes can damage engines, which forces utilities to clean the gas before burning it.
 

 Bench-scale tests like those PNNL performed have significant limitations, and Oyler claims that these shortcomings caused the lab to understate the potential of his technology, which he says typically converts nearly half of the organic solids into biocrude instead of only 37 percent. In addition, because PNNL’s equipment was not designed for energy efficiency, it could not verify Genifuel’s claim that the fuel its system creates contains more energy than is required to make it.
 

 Metro Vancouver hopes to answer that question with its industrial scale pilot. The utility’s Annacis Island facility, which treats the wastewater from more than 1 million individuals in 14 municipalities, will divert some of the sludge from its processing pipeline to Genifuel’s system and evaluate the results. Metro Vancouver will install the equipment for the oil-generating portion of the process after securing full funding for the pilot, which will likely occur by mid-2017, said Paul Kadota, Metro Vancouver’s program manager for utility research and innovation. The utility hopes to begin testing that part of the system by the end of 2018. Depending on its findings, it may later consider adding the second, methane-producing step.
 

 Even if Metro Vancouver proves Genifuel’s claims, there are still economic hurdles to clear. Refining the biocrude into traditional fuels like gasoline and diesel could require expensive transportation unless it could be done economically on-site or nearby, said Dr. Timothy Strathmann, a professor and expert on hydrothermal processing at the Colorado School of Mines who is not involved with the Metro Vancouver pilot.
 

 But if utilities are able to profit from hydrothermal processing of their sludge, Strathmann said, the financial and environmental incentives could dramatically alter wastewater treatment elsewhere. Metro Vancouver also sees great promise in technologies like Genifuel’s, according to senior media relations strategist Sarah Lusk. “Within the realm of wastewater treatment,” she said, “hydrothermal processing could be as dramatic as when the steam locomotive displaced the horse and carriage.”
 
</section>

 Photo credit:
 <a href="https://www.flickr.com/photos/siftnz/4170457688">
 Sustainable Initiatives Fund Trust / (CC BY 2.0)
 </a>

Tweaked Baker’s Yeast Could Make More Biofuel From Less Plant Material

<section class="entry-content instapaper_body clearfix" itemprop="articleBody">
<div class="add-container clearfix" id="add-block-placer">
</div>

 For hundreds of years, the yeast species
 
 Saccharomyces cerevisiae
 
 has helped humans bake bread and brew beer. More recently, it has also assisted in the fight against climate change. Researchers from the University of Wisconsin-Madison have created a variety of the microbe that produces the biofuel ethanol in a more eco-friendly and efficient way than past methods. The study was published last month in
 
 PLOS Genetics
 
 .
 
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/switchgrass-greenhouse.width-990_00oCm7d.jpg"/>
<figcaption>A researcher measures the productivity of switchgrass, a potential biofuel crop.
 
 </figcaption>
</figure>


 S. cerevisiae
 
 , more commonly known as baker’s yeast, gobbles up the sugars in plants and turns them into ethanol, which can then be mixed with gasoline to create a cleaner-burning fuel. In addition to being made from a renewable resource, ethanol could potentially be carbon-neutral if the growing plants absorb as much carbon dioxide as producing and burning the fuel releases, said Eric Young, an assistant professor of chemical engineering at Worcester Polytechnic Institute, who was not involved in the study.
 

 However, while baker’s yeast is a glutton for the sugar molecule glucose, it cannot normally digest xylose, another sugar that composes up to half of some plants. According to a 2012 study from the U.S. Department of Energy’s Argonne National Laboratory, producing and burning ethanol made from glucose-rich corn kernels reduces greenhouse gas emissions by 19–48% compared to traditional gasoline.
 

 But ethanol made from more xylose-heavy crops like switchgrass, which require less energy and other resources to grow, could cut emissions by 90–115%, with the latter figure taking into account other parts of the plants that could be burned instead of fossil fuels to produce electricity.
 

 While scientists have used genetic engineering to turn yeast into xylose eaters, the microbes still didn’t do it nearly as well as other microorganisms. Unfortunately, these less-picky microbes “are often less reliable workers” in industrial settings, said Douglas Tiffany, an assistant extension professor of agribusiness at the University of Minnesota who was not associated with the study. If baker’s yeast were better at processing xylose, turning xylose-heavy crops into ethanol would become more economical. Because facilities that do this are far more expensive to build than their glucose-focused counterparts, creating such yeast is “fundamental and very necessary” to making those factories viable, Tiffany said.
 

 The researchers created xylose-digesting yeast by injecting them with the genes that grant other organisms that capability and adding a procedure called directed evolution. This step relies on the fact that microorganisms like yeast reproduce extremely quickly, so natural selection can change them drastically in a short amount of time.
 

 The team took yeast that had been given xylose-processing genes and then fed them nothing else, making them dependent on xylose for survival. Over time, the few yeast that were able to get enough energy from the sugar multiplied and their children acquired their xylose-digesting genes as well as random genetic changes that are a natural part of reproduction. While many mutations are neutral or harmful, if you wait long enough, a beneficial change is likely to emerge, spurring a sudden increase in growth.
 

 “What that usually means is that one cell got the right combination of mutations that gave it a fitness advantage and allowed it to propagate much more rapidly than its siblings,” said Trey Sato, the study’s first author and an associate scientist at the University of Wisconsin-Madison’s Wisconsin Energy Institute. In this case, that advantage was an improved ability to consume xylose.
 

 Sequencing the genome of this new, xylose-eating yeast and comparing it to the first generation revealed four mutations that play a role in xylose processing, three of which were not previously known to be involved. Putting those four altered genes into the old yeast gave them the same ability, although it remains unclear precisely how. In addition, one of the mutations caused the yeast to be worse at responding to stress, a limitation that could hinder its ability to produce ethanol.
 

 The research could allow other scientists to transfer those mutated genes into the species they study to quickly and easily turn them into xylose eaters. “There’s no guarantee of course because genes act differently in different species,” Sato said.
 

 Tiffany also thinks the research could be applied to creating yeast that can convert other chemicals found in plants into useful industrial materials. “I think there’s value in this research beyond thinking about fuels,” he said.
 
</section>

 Photo credit:
 <a href="https://www.flickr.com/photos/berkeleylab/2825702325/">
 Roy Kaltschmidt/Lawrence Berkeley National Lab (CC BY-NC-ND)
 </a>

Brandon Levy

Articles

New Food Safety Test Can Detect Bacteria in Half the Time

Magnetosensitive Deep-Sea Bacteria Could Deliver Chemo to the Hearts of Tumors

From Black Water to Green Energy

Tweaked Baker’s Yeast Could Make More Biofuel From Less Plant Material

Support Provided By