Category Archives: Academia

For infants, cleanliness leads to unhealthiness


Years ago, our maternal grandmother once declared, “Mothers worry too much about keeping their kinds clean these days. It’s downright unhealthy.”

Turns out she was right.

At least that’s what the latest researcher about the development of children’s immune systems seems to prove.

From Finland’s Aalto University:

Exposure to pathogens early in life is beneficial to the education and development of the human immune system.

Over the past few decades, the healthcare community has observed an intriguing phenomenon: diseases related to the immune system – type 1 diabetes, and other autoimmune diseases, allergies, and the like – have taken hold in countries that have thriving, modern economies, while barely making a mark in the developing world. One of the best-supported theories to explain this peculiar public health pattern has been dubbed the hygiene hypothesis. The theory is based on the premise that exposure to pathogens early in life is actually beneficial to the education and development of the human immune system.

  • Exposure to bacteria may play a pivotal role in the immune system, and that we might be able to understand what that role is by studying the human microbiome, says Aleksandar Kostic, a postdoctoral fellow in the lab of Ramnik Xavier at the Broad Institute of MIT and Harvard.

The work is the product of an extensive collaboration involving researchers at Aalto University, Broad Institute, University of Helsinki, the Novartis Institute of Biomedical Research, and other organizations across the globe working together as part of the DIABIMMUNE Study Group. By looking at the gut microbiomes of infants from three different countries, the team uncovered evidence that not only supports the hygiene hypothesis, but also points to interactions among bacterial species that may account, at least in part, for the spike in immune disorders seen in western societies.

Silent microbiomes

The DIABIMMUNE Study Group recruited and began collecting monthly stool samples from infants in each of the three countries: Finland, Estonia and Russian Karelia. Along with the samples, from which they would identify and quantify the bacteria that made up the infants’ gut microbiomes, they also collected lab tests and questionnaires about such topics as breastfeeding, diet, allergies, infections, and family history. They evaluated all of this data, which was collected from birth to age three from over 200 infants, to see whether connections might exist between disease incidence and what they found in the microbiome.

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Headline of the day II: UC Follies show continues


From ProPublica, the University of California administration never fails to not disappoint:

University of California Regent Violated Ethics Rules, Review Finds

A secret 2015 report found that a doctor on the UC board of regents tried to negotiate a deal between his eye clinics and UCLA, and engaged in discussions in which he had a financial interest. He denied wrongdoing but resigned as chair of the regents’ health committee.

UC Davis chancellor investigated, sent on leave


University of California, Davis Chancellor Linda Katehi [previously], formerly known as the boss of the Pepper-Spraying Cop and the beneficiary of large chunks of cash from corporations publishing textbooks used by her students and operating a for-profit university, is out, at least for now.

The move comes two weeks after the University of California Students Association formally called for her ouster.

From the Los Angeles Times:

Suddenly, however, Katehi was gone — abruptly placed on administrative leave late Wednesday by UC President Janet Napolitano.

Napolitano ordered an outside investigation into “serious questions” over Katehi’s involvement in jobs for family members, possible misuse of student funds and “material misstatements” about her role in the hiring of social media firms to bury negative publicity about a campus police pepper-spraying of peaceful student protesters in 2011. If proven, Napolitano said, the actions may violate university policies on conflicts-of-interest, ethical conduct and use of student fees.

Katehi’s attorney has called the allegations “entirely unjustified,” while the chancellor told faculty members on Wednesday morning that she was “100% committed” to staying at Davis.

On Thursday, the campus was abuzz with a central, perplexing question: How could such a brilliant woman stumble so badly with a string of such questionable decisions?

The latest issues raised follow weeks of controversy over Katehi’s decision to take two paid board positions — one with a textbook publisher, the other with a for-profit firm, DeVry Education Group, which is being investigated by state and local authorities for allegedly deceiving students over job and income prospects.

In addition to her personal profiteering Katehi came to the university with a express agenda: Pull research away from the big questions of general science and refocus on work that could lead to profitable patents.

From Ars gratia artis to Ars gratia emolimentum.

There’s a certain hypocrisy in Napolitano’s action, given that the university system actively hypes its celebrity academics who reap millions from startup companies they found based on work they did on the public payroll.

Retweet something important? Fuggedaboudit


While everyone hypes the importance of social media as critical tools for keeping us informed about the world around us, the medium poses at least one significant problems.

If we think something in a Tweet we’ve received is important enough to pass along to friends and others in a retweet, chances are, the very act of passing it on makes us less likely to recall it later.

From Cornell University:

In a digital world where information is at your fingertips, be prepared to hold on tight before it slips right through them. Research at Cornell and Beijing University finds retweeting or otherwise sharing information creates a “cognitive overload” that interferes with learning and retaining what you’ve just seen.

Worse yet, that overload can spill over and diminish performance in the real world.

“Most people don’t post original ideas any more. You just share what you read with your friends,” said Qi Wang, professor of human development in the College of Human Ecology. “But they don’t realize that sharing has a downside. It may interfere with other things we do.”

Wang and colleagues in China conducted experiments showing that “retweeting” interfered with learning and memory, both online and off. The experiments are described in Issue 59 [$19.95 for a look at the article — esnl] of the journal Computers in Human Behavior.

The experiments were conducted at Beijing University, with a group of Chinese college students as subjects. At computers in a laboratory setting, two groups were presented with a series of messages from Weibo, the Chinese equivalent of Twitter. After reading each message, members of one group had options either to repost or go on to the next message. The other group was given only the “next” option.

After finishing a series of messages, the students were given an online test on the content of those messages. Those in the repost group offered almost twice as many wrong answers and often demonstrated poor comprehension. What they did remember they often remembered poorly, Wang reported. “For things that they reposted, they remembered especially worse,” she added.

There’s more, after the jump. . .

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New studies reveal fracking environmental costs


Two new reports focus on the growing evidence of the dangers of fracking to environments both far and near.

First up, from NASA’s Earth Observatory, a report on the danger that fracking in the lower 48 and elsewhere poses to the Arctic:

BLOG Frack gas

Researchers have suspected for several years that the flaring of waste natural gas from industrial oil and gas fields in the Northern Hemisphere could be a significant source of nitrogen dioxide and black carbon pollution in the Arctic. Research from a NASA-sponsored study lends new weight to that hypothesis.

Nitrogen dioxide is a well-known air pollutant that is central to the production of ground-level smog and ozone. It is closely associated with black carbon (also known as soot), which is an agent of global warming, particularly in the Arctic. In addition to absorbing sunlight while aloft, black carbon darkens snow when it settles on the surface. Both processes lead to heating of the air and the land surface, accelerating the melting of snow and ice.

The amount of black carbon that reaches the Arctic is poorly estimated, but scientists know that any soot could have a significant impact. “The Arctic starts from a very clean state, as there are no significant local sources of dust or smoke pollution,” said Nickolay Krotkov, an atmospheric scientist at NASA’s Goddard Space Flight Center and a member of a team examining the origins of Arctic black carbon. “In this kind of pristine environment, even small anthropogenic sources make a big difference.”

Previous research has suggested that gas flares from oil and natural gas extraction near the Arctic could be a key source of black carbon. But since international inventories of industrial emissions have gaps in observations and in reporting, they often over- or underestimate the amount of pollutants.

Gas flares are an often-overlooked subset in that already messy data set. Regional estimates from Russia, for example, suggest that gas flaring may account for 30 percent of all black carbon emissions. But with few monitoring stations near flaring sites, the scientific community has had great difficulty getting accurate estimates of emissions.

Can Li and other researchers at NASA Goddard were recently asked by atmospheric modelers to see if they could provide flaring estimates based on satellite data. Black carbon levels in the atmosphere cannot be directly measured by satellites, but they can be derived indirectly. Black carbon is associated with nitrogen dioxide and with the total concentration of aerosol particles in the atmosphere. Nitrogen dioxide and black carbon particles are often produced at the same time when fossil fuels are burned.

The modelers were simulating the trajectories of pollution through the atmosphere based on existing, flawed emission inventories. And their results generally underestimated the amount of black carbon reaching the Arctic compared to what scientists in the field were measuring directly.

The first step for Li, Krotkov, and colleagues was to find gas flares. They compiled “night lights” data from the Visible Infrared Imaging Radiometer Suite on the Suomi NPP satellite. They examined four known fossil fuel extraction sites: Bakken, North Dakota (shown above); Athabasca Oil Sands in Alberta, Canada; the North Sea near Great Britain and Norway; and western Siberia, Russia. The researchers pinpointed gas flares by excluding electric light from nearby towns and roads.

For each study site, Li and Krotkov analyzed nitrogen dioxide data from the Ozone Monitoring Instrument aboard the Aura spacecraft. A sample is shown at the top of this page. Fellow NASA researchers Andrew Sayer and Christina Hsu retrieved aerosol concentration data from the Moderate Resolution Imaging Spectroradiometer aboard NASA’s Aqua satellite.

“We found a pretty good match-up between the gas flare signals from the night lights and the nitrogen dioxide retrievals for two regions—Bakken and the Canadian oil sands,” said Li. Every year from 2005 to 2015, the levels of atmospheric NO2 rose about 1.5 percent per year at Bakken and about 2 percent per year at Athabasca. This means the concentration of black carbon produced by those flares was also likely on the rise.

The team saw a smaller rise in nitrogen dioxide in western Siberia, and no discernable flaring signal from well-established oil rigs in the North Sea. According to Li, the North Sea signal was likely obscured by the abundance of nitrogen dioxide pollution in Europe.

Aerosol data were less conclusive. Aerosols tend to linger in the atmosphere longer than nitrogen dioxide, making it more difficult to establish whether there was an increase due to oil field activities, as opposed to general background levels, Sayer said.

The new observational results fit well with modeling done by Joshua Fu, an atmospheric modeler at the University of Tennessee at Knoxville and a collaborator on the paper. When Fu and colleagues added the gas flare locations and estimated emissions into a model of chemical transport in the atmosphere, they were able to reproduce the amount of black carbon observed in the Arctic by ground stations and aircraft.

Fracking waste spills pollute soil, water

Next, from Duke University, a report revealing that far from being exceptional, soil- and water-polluting spills of contaminated fracking waste water, filled with chemicals fracking companies aren’t even required to report to the concenred public, are all-too-common occurrences:

Accidental wastewater spills from unconventional oil production in North Dakota have caused widespread water and soil contamination, a new Duke University study finds.

Researchers found high levels of ammonium, selenium, lead and other toxic contaminants as well as high salts in the brine-laden wastewater, which primarily comes from hydraulically fractured oil wells in the Bakken region of western North Dakota.

Streams polluted by the wastewater contained levels of contaminants that often exceeded federal guidelines for safe drinking water or aquatic health.

Soil at the spill sites was contaminated with radium, a naturally occurring radioactive element found in brines, which chemically attached to the soil after the spill water was released.

At one site, the researchers were still able to detect high levels of contaminants in spill water four years after the spill occurred.

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Old growth forest buffer against climate change


To listen to corporate mouthpieces for Big Timber, a forest is a forest is a forest.

To them it doesn’t matter if the forest is an ancient and constantly evolving ecosystem or a tree farm planted by machines and harvested [also by machines] just like any other crop.

And those pesky tree-hugging environmentalists who say otherwise are just a bunch of airheads, right?

Well, no.

And, as it now it turns, those magnificent old growth forest are farm more than simply glorious sights for human eyes. They are also havens capable of protecting otherwise threatened species from some of the worst impacts of climate change

Differences in microclimate conditions across a gradient in forest structure. (A) Principal components analysis (PCA) showing how vegetation structure metrics differ between mature/old-growth forest sites and plantations. The ellipses represent 68% of the data assuming a normal distribution in each category (plantation and mature/old growth). (B) Three-dimensional LiDAR-generated images of plantation forests [(i) side view; (ii) overhead view] and old-growth forests [(iii) side view; (iv) overhead view] at the Andrews Forest. (C and D) Results from generalized linear mixed models show the modeled relationship between forest structure [PC1, the first component of a PCA on forest structure variables (A)] and the residuals from an elevation-only model of mean monthly maximum during April to June (C) and mean monthly minimum during April to June (D) after accounting for the effects of elevation. Closed circles represent 2012 and open circles represent 2013. Maximum monthly temperatures (C) decreased by 2.5°C (95% confidence interval, 1.7° to 3.2°C) and observed minimum temperatures (D) increased by 0.7°C (0.3° to 1.1°C) across the observed structure gradient from plantation to old-growth forest.

Differences in microclimate conditions across a gradient in forest structure.
(A) Principal components analysis (PCA) showing how vegetation structure metrics differ between mature/old-growth forest sites and plantations. The ellipses represent 68% of the data assuming a normal distribution in each category (plantation and mature/old growth). (B) Three-dimensional LiDAR-generated images of plantation forests [(i) side view; (ii) overhead view] and old-growth forests [(iii) side view; (iv) overhead view] at the Andrews Forest. (C and D) Results from generalized linear mixed models show the modeled relationship between forest structure [PC1, the first component of a PCA on forest structure variables (A)] and the residuals from an elevation-only model of mean monthly maximum during April to June (C) and mean monthly minimum during April to June (D) after accounting for the effects of elevation. Closed circles represent 2012 and open circles represent 2013. Maximum monthly temperatures (C) decreased by 2.5°C (95% confidence interval, 1.7° to 3.2°C) and observed minimum temperatures (D) increased by 0.7°C (0.3° to 1.1°C) across the observed structure gradient from plantation to old-growth forest.

From Oregon State University:

The soaring canopy and dense understory of an old-growth forest could provide a buffer for plants and animals in a warming world, according to a study from Oregon State University published  in Science Advances [open access].

Comparing temperature regimes under the canopy in old-growth and plantation forests in the Oregon Cascades, researchers found that the characteristics of old growth reduce maximum spring and summer air temperatures as much as 2.5 degrees Celsius (4.5 degrees Fahrenheit), compared to those recorded in younger second-growth forests.

Landowners who include biodiversity as a management goal, the scientists said, could advance their aims by fostering stands with closed canopies, high biomass and complex understory vegetation.

Management practices that create these types of “microclimates” for birds, amphibians, insects and even large mammals could promote conservation for temperature-sensitive species, the authors wrote, if temperatures rise as a result of global warming.

“Though it is well-known that closed-canopy forests tend to be cooler than open areas, little is known about more subtle temperature differences between mature forest types,” said Sarah Frey, postdoctoral scholar in the OSU College of Forestry and lead author on the study. “We found that the subtle but important gradient in structure from forest plantations to old growth can have a marked effect on temperatures in these forests.”

Temperature is also strongly affected by elevation and even small changes in topography, but the way forests are managed was a critical factor in explaining temperature differences. Researchers at Oregon State and Pacific Northwest Research Station of the U.S. Forest Service conducted the study at the H.J. Andrews Experimental Forest east of Eugene.

There’s more, after the jump. . . Continue reading

Fishy toxin harms body’s ability to fight toxins


The toxins in question aren’t produced by the fish. No, it’s something we make, and it finds its way into the oceans, only to be consumed by and concentrated critters at the top of their food chain, and from there into the worlds number one super predator, Homo sapiens.

And the chemicals in question were introduced with much fanfare, hailed as beneficial to all of, sparing us from the ravages of pest and flame.

From the Scripps Institution of Oceanography:

In a new study, environmental pollutants found in fish were shown to obstruct the human body’s natural defense system to expel harmful toxins. The Scripps Institution of Oceanography at UC San Diego-led research team suggests that this information should be used to better assess the human health risks from eating contaminated seafood. The study was published in the April 15 issue of the journal Science Advances [open access].

A protein found in cells of nearly all plants and animals, called P-gp, acts as the cell’s bouncer by expelling foreign chemicals from the body. P-gp is well known for its ability to transport therapeutic drugs out of cancer cells and, in some cases, rendering these cells resistant to multiple drugs at once.

To determine how effective P-gp is at ridding cells of industrial and agricultural pollutants found in seafood, collectively known as persistent organic pollutants (POPs), the Scripps research team conducted a biochemical analysis of P-gp proteins from humans and mice against POPs. The scientists focused on POPs most commonly found in human blood and urine, and also detected in the muscle tissues of wild-caught yellowfin tuna. The pollutants included older “legacy” compounds such as the pesticide DDT as well as newer industrial chemicals, such as flame retardants.

Working with researchers at UC San Diego’s Skaggs School of Pharmacy and Pharmaceutical Science and School of Medicine, the researchers discovered that all 10 pollutants interfered with the ability of P-gp to protect cells. The study was also the first to show how one of the 10 pollutants, PBDE-100, commonly used as a flame retardant in upholstery foam and plastics, binds to the transporter protein. The POP binds to the protein in a similar way as chemotherapeutics and other drugs, but instead of being transported out of the cell, the bound POP ultimately inhibits the protein’s ability to perform its defense function.

Close-up of the flame retardant PBDE-100 (orange-red) bound to mouse P-gp (grey).

Close-up of the flame retardant PBDE-100 (orange-red) bound to mouse P-gp (grey).

“We show that these inhibitors are found in the fish we eat,” said Scripps postdoctoral researcher Sascha Nicklisch, lead author of the study. “The concentrations in the fat of some tuna were high enough to inhibit P-gp in our assays. Therefore, it is important to consider the potential risk of dietary intake of these pollutants.”

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