Look deep into nature, and then you will understand everything. Albert Einstein

AGRICULTURE

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In 2001, the U.S. Environmental Protection Agency banned residential use of chlorpyrifos because of the harm to children exposed in the home. Chlorpyrifos continues to be heavily used on fruit and nut orchards, soybeans, and corn, with an estimated 5 million pounds applied in the U.S. annually. This widespread agricultural use means that people continue to be exposed through contaminated foods, drinking water, and pesticide blowing off of farmland and into neighboring areas.

Source: Chlorpyrifos Pesticide Challenge | Earthjustice

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To grow food without poisonous chemicals, you need to buck the system.

While Earthjustice has been fighting to ban a widely-used, brain-damaging pesticide called chlorpyrifos, some farmers are already finding ways to do without it—and not just chlorpyrifos, but even the next toxic chemical that springs up to replace it. As farmers rediscover natural ways to control pests, and environmental advocates continue to drive down the use of the most harmful chemicals, the two movements could bring about a fundamental change in how we feed our families.

Chlorpyrifos is one of the most widely used pesticides in America. It also causes irreversible brain damage in children, one of several reasons this dangerous chemicalmay soon be pulled off the market. If the EPA does its job and chlorpyrifos is indeed on the way out, that’s great news. But all too often, one toxic pesticide simply gets replaced with another. That’s how our industrial agricultural system works. Widespread, intensive use of toxic chemicals is the default setting for food production. To grow food without poisons like chlorpyrifos, you need to buck the system.

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The biggest source of water pollution in the United States remains largely outside the law. (Spanish language version available.)

A headline in the Des Moines Register recently attempted to reassure readers that “Iowa’s Water Rarely Exceeds Lead Limits.” This statement isn’t the confidence-booster it’s meant to be. For one thing, federal limits on lead in drinking water aren’t protective enough, especially for those most vulnerable to lead poisoning: pregnant women and bottle-fed infants. And the foremost water issue for many in Des Moines isn’t lead (although it may well be a concern). It’s pollution from the farms that surround the city, which is infiltrating the city’s drinking water supply.

Source: Concerns About Drinking Water Go Beyond Lead | Earthjustice

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EthBr

 

 

 

 

 

Derek Lowe’s commentary on drug discovery and the pharma industry. An editorially independent blog from the publishers of Science Translational Medicine.

By Derek LoweApril 18, 2016
Ethidium bromide is found in pretty much every molecular biology lab around. Ask most biologists about handling it, and you’re get a fearful expression and advice to use gloves, etc. That’s because the compound is used to make DNA fluoresce when running gels, and it does that by slipping neatly between the base pairs (intercalation), like sliding a card into a deck. That is not something you want to have happen to your own DNA, naturally, so EthBr is widely believed to be a human mutagen that should be dealt with cautiously. Laboratory suppliers certainly think so: a search for “ethidium bromide alternative” will bring up a whole list of “non-toxic, non-mutagenic” substitutes on offer.

EthBr

There’s only one problem with all this: ethidium bromide, as far as can be told from the data, is not a human mutagen. It’s not a mouse mutagen or rat mutagen either. Nor apparently a mutagen in cows and other farm animals, where it’s used in veterinary medicine at concentrations one thousand times higher than the red solutions that are so feared in biology labs, seemingly with no bad effects. It’s not even Ames-positive by itself, but only after it’s been exposed to metabolizing enzymes, which tells you that some derivative of it has mutagenic potential, should you ingest it and send it through your liver, but apparently not the parent compound. (Note the 2002 “In the Pipeline” link – I’ve been doing this for a while, haven’t I?)

I write this as an organic chemist who handles worse stuff than EthBr all the time, and as someone who’d long been unable to grasp the molecular biology attitude towards the compound. You will see reference after reference to it as “highly toxic”, “notoriously unsafe“, and a “potent mutagen”, when it’s really none of those. These statements are bizarre, based on the amount of evidence behind them. Here’s Rosie Redfield on the issue – she’s also baffled by the attitude towards the compound, and has some questions about the safety profile of the alternatives that are being touted by other vendors and the over-the-top means used to deal with the compound itself:

Excessive concern about mutagenicity can make us overlook short-term toxic effects, and here EthBr is the safer dye. The reference above found that the SYBRsafe alternative was actually much more toxic than EthBr to the bacterial cells used in the mutagenicity tests. SYBRsafe was toxic at concentrations as low as 1 microgram/ml, whereas EthBr toxicity was not observed until 250micrograms/ml. The authors suggest that this is because living cells are much more permeable to SYBR green than to EthBr. But a MSDS for SYBR safe reports a LD50 for rats of >5g/kg, which is higher than that of EthBr (1.5g/kg). As both these LD50s are many orders of magnitude higher than the concentrations used in molecular biology, toxicity of gel staining solutions is trivial compared to the risks of of burns from melted agarose or slipping on spilled gel buffer.

Perhaps the largest real hazards associated with use of EthBr in molecular biology are the methods used to inactivate it. Some labs now incinerate all waste containing even a trace of EthBr, and others absorb it onto activated charcoal. Harsher methods involve use of bleach and sodium hydroxide, or hydrophosphorous acid and sodium nitrite, all much more dangerous than EthBr.
Yep, some of the “safe” alternatives actually light up the Ames test more than ethidium bromide itself. I’m not saying to bathe in the stuff, or use it to dye your hair. But it can be handled with normal care appropriate to a laboratory chemical, and not as the Mutagen From Mars.I can see where some of the fear comes from – after all, you can see this stuff react with DNA right in front of you, and assuming that it’s a mutagen is not silly. But we don’t have to assume things in toxicology when the experiments have already been done. Have a look at the evidence – knowledge will protect you far more than fear ever can.

Source: The Myth of Ethidium Bromide | In the Pipeline

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In the complex architecture that ferries fluids in plants and brains, scientists are finding a model of resilience.

Examine the delicate branching patterns on a leaf or a dragonfly’s wing and you’ll see a complex network of nested loops. This pattern can be found scattered throughout nature and structural engineering: in the brain’s cerebral vasculature, arrays of fungi living underground, the convoluted shape of a foraging slime mold and the metal bracings of the Eiffel Tower.

Source: In Natural Networks, Strength In Loops | Quanta Magazine

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Another group in China has modified genomes of unviable embryos to prevent disease

Source: CRISPR debate fueled by publication of second human embryo–editing paper | Science | AAAS

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Physicists find a way to probe the quantum realm without wrecking everything

In 1930, German theoretical physicist Werner Heisenberg came up with a thought experiment, now known as Heisenberg’s microscope, to try to show why it’s impossible to measure an atom’s location with unlimited precision. He imagined trying to measure the position of something like an atom by shooting light at it.

Light travels as a wave, and Heisenberg knew that different wavelengths could give you different degrees of confidence when used to measure where something is in space. Short wavelengths can give a more precise measurement than long ones, so you’d want to use light with a tiny wavelength to measure where an atom is, since atoms are really small. But there’s a problem: light also carries momentum, and short wavelengths carry more momentum than long ones

Source: Physicists find a way to probe the quantum realm without wrecking everything – ScienceAlert

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In the last decade there has been a great deal of activity in the development of renewable feedstocks for a variety of chemical processes.  Compared to conventional petroleum-derived feedstocks, these new materials offer lower greenhouse gas emissions and reduced toxicity.  More importantly to the companies that use chemicals in their industrial processes, they offer significantly lower costs.  In contrast to the consumer market, where choosing green products usually entails paying a premium, greener is cheaper in industry.  Most renewable feedstocks are produced through biological processes or thermal and chemical processes applied to cellulosic materials, such as wood, agricultural waste, or non-food plants like switchgrass – all of which are less costly than the purchase of petroleum products.

According to a recent report from Pike Research, the use of green chemistry in a range of industrial activities will grow rapidly in the coming decade, offering significant direct cost savings as well as indirect savings in the form of avoiding liability for environmental and social impacts.  The total amount saved, the cleantech market intelligence firm forecasts, will reach $65.5 billion by 2020.

“The worldwide chemical industry is valued at around $4 trillion, so even small improvements in efficiency can have very large impacts,” says senior analyst Mackinnon Lawrence.  “Just by bringing laggard companies up to the baseline standard of the industry as a whole, it’s possible to capture more than $40 billion in cost savings and avoided liabilities.”

Originally developed in the 1990s, partly as a result of the passage in the United States of the Pollution Prevention Act of 1990, green chemistry is less a description of a distinct industrial segment than a way of carrying out industrial activities from design to manufacturing.  The primary pathways for green chemistry, in Pike Research’s view, include waste minimization in the chemical production process, replacement of existing products with less toxic alternatives, and the shift to renewable, non-petroleum-based feedstocks.  The evolution of these practices is being driven by a combination of technical, regulatory, consumer preference, and economic factors. Most notably, rapid advances in biotechnology have created powerful new toolkits for the manipulation of organisms (bacteria, yeasts, and algae) to produce industrially useful compounds with great efficiency and minimal waste. At the same time, the rising price of petroleum – critical both as a source of process energy and as a feedstock for many chemical processes – has fueled interest and investment in finding alternative, renewable feedstocks.

Overall, green chemistry represents a market opportunity that will grow from $2.8 billion in 2011 to $98.5 billion by 2020.

Pike Research’s report, “Green Chemistry”, examines the three major segments of the green chemical market:  waste minimization in conventional synthetic chemical processes, green replacements for conventional chemical products, and the use of renewable feedstocks to produce chemicals and materials with smaller environmental footprints than those produced by current processes.  Representative companies from each segment are profiled and global forecasts, segmented by world region, extend through 2020.  An Executive Summary of the report is available for free download on the firm’s website.

Pike Research is a market research and consulting firm that provides in-depth analysis of global clean technology markets.  The company’s research methodology combines supply-side industry analysis, end-user primary research and demand assessment, and deep examination of technology trends to provide a comprehensive view of the Smart Energy, Smart Grid, Smart Transportation, Smart Industry, and Smart Buildings sectors.  For more information, visit www.navigantresearch.com or call +1.303.997.7609.

Source: » Green Chemicals Will Save Industry $65.5 Billion by 2020 Navigant Research

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Nitrogen fertilizer applied to farmers’ fields has been contaminating rivers and lakes and leaching into drinking water wells for more than 80 years. Now, a new University of Waterloo study shows that fertilizer applied today will continue to pollute water for decades because it’s building up in the soil.

The findings are significant because agricultural runoff that leaches into drinking water wells can cause newborns to develop something called “blue baby syndrome,” a potentially fatal condition that reduces oxygen-flow in the blood. There are also serious environmental concerns because excess nitrogen, flowing into rivers and oceans, creates “dead zones” for fish and other marine life.

he study, published this week in a special issue of the journal Environmental Research Letters by University of Waterloo Professor Nandita Basu and doctoral student Kim Van Meter, presents the first direct evidence of a large-scale nitrogen legacy across the United States’ Mississippi River Basin.

“A large portion of the nitrogen applied as fertilizer has remained unaccounted for the last several decades,” said Basu, a professor jointly appointed to the Faculties of Science and Engineering. “The fact that nitrogen is being stored in the soil means it can still be a source of elevated nitrate levels long after fertilizers are no longer being applied.”

Similar to phosphorus, nitrogen is a nutrient for plants and when applied as fertilizer helps increase crop yields. But to maximize these yields, an excess of fertilizer is often applied, leaving large amounts of nitrogen remaining in soil.

This nitrogen is easily converted to nitrate, a highly soluble, inorganic compound that has become the most common drinking water pollutant in the U.S. The issue has been controversial in Iowa, where, in an unprecedented, bold move, Iowa’s largest drinking water utility – the Des Moines Water Works – filed a lawsuit against three upstream rural counties for failing to address harmful surface-water nitrate levels that are more than twice the US federal drinking water standard.

The utility has been forced to invest millions in order to treat a drinking water supply that continues to receive unsafe, ever-increasing levels of nitrate.

Where does all the fertilizer go?

Since the 1970s, farmers and policymakers alike have worked hard to reduce the amount of fertilizer leaching from agricultural fields to groundwater and nearby lakes and streams. Yet in some rural areas, nitrate levels in groundwater have been found to be more than ten times the drinking water standard.

“Public drinking water sources are vulnerable to receiving elevated nitrate,” says Basu. “But an even greater danger is for people in rural areas living on private well sources.”

To quantify the true extent of the nitrogen problem, numerous researchers have attempted to account for all of the nitrogen inputs to and outputs from watersheds around the world. These so-called mass balance studies, however, have consistently come up short. Although we know that nitrate levels have been increasing in our waterways, the fate of much of the nitrogen that is applied to the land as fertilizer has remained a mystery. Many scientists have suggested that this “missing nitrogen” must leave watersheds via denitrification, a reaction facilitated by microorganisms that transforms nitrate into the harmless nitrogen gas that makes up 78 per cent of our atmosphere.

Basu and her group, however, in their analysis of patterns in stream nitrate concentrations, saw evidence that nitrogen legacies could be present within the landscape.

“We began to ask the question, ‘Could nitrogen be accumulating in soils?’” says first author Van Meter, a doctoral student in the Department of Earth and Environmental Sciences in the Faculty of Science.

Scientists suspicions are confirmed

Basu and her group analyzed long-term data from over two thousand soil samples throughout the Mississippi River Basin, and found a systematic accumulation of nitrogen in agricultural soils. In many areas, this accumulation was not apparent in the upper 25 cm, the so-called plow layer. Indeed, these upper layers appeared to be depleted in nitrogen.

From 25 to 100 centimetres beneath the soil surface, however, they found significant accumulation, accounting for as much as 50 per cent of net nitrogen inputs.

“We hypothesize that this accumulation occurred not only because of the increased use of fertilizers, but also increases in soybean cultivation and changes in tillage practices over the past 80 years,” says Van Meter.

Their modeling results suggest that this nitrogen legacy could still be leaching into waterways more than three decades after nitrogen is no longer being applied to fields.

“The presence of this legacy nitrogen means it will take even longer for best management practices to have a measurable benefit,” says Basu, also a member of the Water Institute. “If we’re going to set policy goals, it’s critical we quantify nitrogen legacies and time lags in human impacted landscapes.”

Basu and other researchers at the University of Waterloo are currently exploring nitrogen legacies in the Grand River Watershed in Southern Ontario, as well as across North America and at a global scale.

Source: Fertilizer applied to fields today will pollute water for decades | Waterloo Stories

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Fungicides_600x195

A new UNC School of Medicine study shows how chemicals designed to protect crops can cause gene expression changes in mouse brain cells that look strikingly similar to changes in the brains of people with autism and Alzheimer’s disease.

March 31, 2016

CHAPEL HILL, NC – Scientists at the UNC School of Medicine have found a class of commonly used fungicides that produce gene expression changes similar to those in people with autism and neurodegenerative conditions, including Alzheimer’s disease and Huntington’s disease.

The study, published today in the journal Nature Communications, describes a new way to home in on chemicals that have the potential to affect brain functions.

Mark Zylka, PhD, senior author of the study and associate professor of cell biology and physiology at UNC, and his team exposed mouse neurons to approximately 300 different chemicals. Then the researchers sequenced RNA from these neurons to find out which genes were misregulated when compared to untreated neurons. This work created hundreds of data sets of gene expression; genes give rise to products, including proteins or RNA.

Zylka’s team then used computer programs to deduce which chemicals caused gene expression changes that were similar to each other.

“Based on RNA sequencing, we describe six groups of chemicals,” Zylka said. “We found that chemicals within each group altered expression in a common manner. One of these groups of chemicals altered the levels of many of the same genes that are altered in the brains of people with autism or Alzheimer’s disease.”

Chemicals in this group included the pesticides rotenone, pyridaben, and fenpyroximate, and a new class of fungicides that includes pyraclostrobin, trifloxystrobin, fenamidone, and famoxadone. Azoxystrobin, fluoxastrobin, and kresoxim-methyl are also in this fungicide class.

“We cannot say that these chemicals cause these conditions in people,” Zylka cautioned. “Many additional studies will be needed to determine if any of these chemicals represent real risks to the human brain.”

Zylka, a member of the UNC Neuroscience Center, and his group found that these chemicals reduced the expression of genes involved in synaptic transmission – the connections important for communication between neurons. If these genes are not expressed properly, then our brains cannot function normally. Also, these chemicals caused an elevated expression of genes associated with inflammation in the nervous system. This so-called neuroinflammation is commonly seen in autism and neurodegenerative conditions.

The researchers also found that these chemicals stimulated the production of free radicals – particles that can damage the basic building blocks of cells and that have been implicated in a number of brain diseases. The chemicals also disrupted neuron microtubules.

“Disrupting microtubules affects the function of synapses in mature neurons and can impair the movement of cells as the brain develops,” Zylka said. “We know that deficits in neuron migration can lead to neurodevelopmental abnormalities. We have not yet evaluated whether these chemicals impair brain development in animal models or people.”

Jeannie T. Lee, MD, PhD, professor of genetics at Harvard Medical School and Massachusetts General Hospital, who was not involved in this research, said, “This is a very important study that should serve as a wake-up call to regulatory agencies and the general medical community. The work is timely and has wide-ranging implications not only for diseases like autism, Parkinson’s, and cancer, but also for the health of future generations. I suspect that a number of these chemicals will turn out to have effects on transgenerational inheritance.”

Zylka’s group also analyzed information from the U.S. Geological Survey, which monitors countywide pesticide usage, as well as the Food and Drug Administration and the U.S. Department of Agriculture, which test foodstuffs yearly for pesticide residues.

Of the chemicals Zylka’s team studied, only the usage of pyridaben has decreased since 2000. Rotenone use has remained the same since 2000. However, the use of all the fungicides in this group has increased dramatically over the past decade.

Indeed, a study from the Environmental Protection Agency found that pyraclostrobin is found on foods at levels that could potentially affect human biology, and another study linked pyraclostrobin usage to honeybee colony collapse disorder.

The pesticide rotenone was previously implicated in Parkinson’s disease through replicated animal experiments and through human epidemiological studies. A separate 2015 UNC study found that Parkinson’s disease is much more common in older adults with autism than in older adults without autism.

Previous work has also shown that a single dose of the fungicide trifloxystrobin reduced motor activity for several hours in female rats and for days in male rats. Disrupted motor function is a common symptom of Parkinson’s disease and other neurological disorders. The related fungicide picoxystrobin impaired motor activity in rats at the lowest dose tested.

Zylka added, “The real tough question is: if you eat fruits, vegetables or cereals that contain these chemicals, do they get into your blood stream and at what concentration? That information doesn’t exist.” Also, given their presence on a variety of foodstuffs, might long term exposure to these chemicals – even at low doses – have a cumulative effect on the brain?

Zylka noted that conventionally grown leafy green vegetables such as lettuce, spinach, and kale have the highest levels of these fungicides. But due to each chemical’s effectiveness at reducing fungal blights and rust, crop yields have increased and farmers are expanding their use of these chemicals to include many additional types of food crops.

Zylka’s team hopes their research will encourage other scientists and regulatory agencies to take a closer look at these fungicides and follow up with epidemiological studies.

“Virtually nothing is known about how these chemicals impact the developing or adult brain,” Zylka said. “Yet these chemicals are being used at increasing levels on many of the foods we eat.”

This research was funded by three of the National Institutes of Health: the National Institute of Environmental Health Sciences, the National Institute on Neurological Disorders and Stroke, and the Eunice Kennedy Shriver National Institute of Child Health and Human Development.

Mark Zylka, PhD, is a member of the Carolina Institute for Developmental Disabilities and the UNC Lineberger Comprehensive Cancer Center. He was named director of the UNC Neuroscience Center in January and will take over for current director William Snider, MD, in July. Brandon Pearson, PhD, and Jeremy Simon, PhD, were co-first authors on the study. Additional authors from UNC include Eric McCoy, PhD, Giulia Fragola, PhD, and Gabriela Salazar.

Source: Could a new class of fungicides play a role in autism, neurodegenerative diseases? — News Room – UNC Health Care

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Minimal genome organism reveals how much scientists don’t know about biology.

Source: Scientists build minimum-genome bacterium | Science News

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