Musings: May-August 2014 (archive)

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Musings: May-August 2014 (archive)

Musings is an informal newsletter mainly highlighting recent science. It is intended as both fun and instructive. Items are posted a few times each week. See the Introduction, listed below, for more information.

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Archive items may be edited, to condense them a bit or to update links. Some links may require a subscription for full access, but I try to provide at least one useful open source for most items.

Please let me know of any broken links you find -- on my Musings pages or any of my regular web pages. Personal reports are often the first way I find out about such a problem.

August 30, 2014

How can the mantis shrimp see so many colors of UV? They use filters.

August 30, 2014

The visual system of the mantis shrimp has long fascinated biologists. Not only does it have a complex eye structure, it has about a dozen types of color receptors -- several times more than we do. Musings noted recent work showing that these animals do not resolve colors very well, despite having so many distinct color receptors [link at the end].

A new article shows that the multiple color receptors for the ultraviolet (UV) range are made in an unusual way.

The usual way to make receptors for various colors is to use different photoreceptor proteins; these are proteins of the opsin family. Each protein is tuned to receive a particular part of the spectrum. Humans have three kinds of color receptors; they have genes for three types of opsin photoreceptor proteins.

Each photoreceptor has two parts: the opsin protein itself plus a small molecule called retinal, related to vitamin A. The retinal is what absorbs the light. Each opsin protein creates a slightly different chemical environment around the retinal, affecting which color it can receive; this is the "tuning" for color discussed above.

The mantis shrimp have six types of photoreceptors in the UV range. However, they have only two opsins for that range. How can that be? The discovery here is that the mantis shrimp uses filters. Five of those six UV receptors use the same opsin protein, but they use at least four different filters in front of it. The filters help determine which part of the spectrum the photoreceptors respond to.

The following figure shows some of what the scientists found about the mantis shrimp visual system for UV.

Let's start with frame B (upper right).

The top half shows the spectral response of the UV visual pigments -- the opsins with their retinal attached. There are only two of these UV receptor pigments -- even though there are six UV receptors. These visual pigments have peaks at 334 nm (left; orange line) and 383 nm (right; red line).

The bottom half of B shows what the filters do. For example, the filter shown with a green line has a peak near 300 nm at the left. That means that this filter absorbs short UV wavelengths, blocking them from getting to the visual pigment.

Frame A shows the anatomy of the six UV receptors. "Rows" 1-6 are six photoreceptors. Imagine light coming from the right side. Near the far end of the row, to the left, is the visual pigment (the opsin-based receptor). You can see that this is either red or orange -- corresponding to the two receptors we saw in frame B. One is red, five are orange.

Then there is another colored region, in the middle, just before the receptor protein. That is the filter region. Rows 2-5 have different filters -- all with the same visual pigment. (Row 6 is about the same as #5. Indeed its spectral response is about the same.)

So, the scientists think that the spectral response of the receptor row is determined by both the receptor protein and the filter. To test this, they make a model: they calculate what they would expect for the various combinations they found. This calculation uses the spectrum of each receptor protein and of each filter, as shown in frame B. They then compare this predicted response with what has actually been measured for each intact photoreceptor.

Frame C shows an example of what the modeling showed. This is for "row 1" from frame A. At the left in C are the spectra for the specific protein and filter in that photoreceptor row. At the right are two curves. One is what they predicted (solid line) and the other is what was measured (dots). The agreement is not bad. (But the agreement is not perfect. Hm, perhaps there is another filter in there that they have not accounted for?)

If you want to imagine how this works... The red curve at the left is what the receptor protein can see. It is good all the way down to 300 nm. But the purple curve shows the filter. It doesn't allow any light through below about 350 nm (the left segment of that curve). So, the pigment actually only sees light from 350 to 400 nm. Overall, the sensitivity of the photoreceptor is tuned by both the receptor protein and the filter in front of it.

The full version of frame C, in the article, includes the modeling for all six photoreceptors. For four of them, the agreement is good. (The other two are discussed in the article; they need further work.)

This is part of Figure 3 from the article, slightly modified. It includes frames A and B and the top row of frame C from the full figure. I have edited the figure to show a partial x-axis scale for frame C. In fact, the labeling for both sides of frame C is the same as for frame B: the wavelength, from 300 nm to 450 nm.

In some ways none of this is new. The chemicals that the mantis shrimp uses to filter UV light in its eyes are well known. Other animals use them as "sunscreens" -- agents that protect the animal against UV exposure. What's unusual here is that the mantis shrimp has incorporated these same pigments into its eyes as filters. The use of such visual filters is not entirely new. Occasional examples have been found before. What's new is the complexity of the system with the mantis shrimp. The visual system of the mantis shrimp continues to amaze us.

News stories:
* With 'biological sunscreen,' mantis shrimp see the reef in a whole different light. (Science Daily, July 3, 2014.)
* Nature's Most Amazing Eyes Just Got A Bit Weirder. (E Yong, Not Exactly Rocket Science (National Geographic blog), July 3, 2014.) Now archived.

* News story from the journal (in a later issue): Vision: Two Plus Four Equals Six. (E R Loew, Current Biology 24:R753, August 18, 2014.)
* The article, which is freely available: Biological Sunscreens Tune Polychromatic Ultraviolet Vision in Mantis Shrimp. (M J Bok et al, Current Biology 24:1636, July 21, 2014.)

Background post about mantis shrimp color vision: Color vision: The advantage of having twelve kinds of photoreceptors? (February 21, 2014). This post notes a web site by Michael Bok, which includes information on various types of mantis shrimp. Bok is the lead author of the current article.

More about the opsins: A better understanding of the basis of color vision (February 1, 2013). This post discusses the production of an artificial set of opsin-type proteins that absorb light over the spectrum of visible light.

More about one of those chemicals used here as a filter: Fish make their own sunscreen (September 29, 2015).

Another example of filters in color vision: Red color vision in dinosaurs? (October 17, 2016).

More about UV filters and sunscreens and such... How do you know if you have been in the sun too long? (August 5, 2016).

More about UV vision: Butterflies and UV vision (June 29, 2010).

More about eyes: What is the proper length for eyelashes -- and why? (March 16, 2015).

Also see a section of my page Internet resources: Biology - Miscellaneous on Medicine: color vision and color blindness.

A test of a stem cell therapy based on iPSC, in monkeys

August 29, 2014

Briefly noted...

Ever since stem cells were discovered, there has been hope of using them therapeutically. Hope and hype. Little has been delivered. That should be no surprise; it typically takes a long time -- much longer than expected -- for a new development to become useful.

Of particular interest are the pluripotent stem cells -- the ones with the capacity to become anything. That does sound like a magic cure, doesn't it?

The new kid on the pluripotent-stem-cell block is the iPSC (induced pluripotent stem cells). They are much easier to make than the first type that was found, the embryonic stem cells. iPSC offer all the potential of stem cells that can do everything. And all the risk. Unfortunately, among the "everything" in their repertory is causing cancer. It almost goes with the territory: cells that have the potential to do everything may do just that. Indeed, testing cells for their ability to form teratomas is one way scientists show that cells are pluripotent. (A teratoma is a type of tumor that contains many types of cells.)

A recent article offers progress in showing that iPSC may be useful therapeutically. The scientists use iPSC to stimulate bone formation in monkeys. The stem cells themselves are derived from the animal that gets the treatment; this is important in avoiding an immune response, and is one of the advantages of using iPSC. If the scientists give the monkeys iPSC, they get bone formation, but also a significant frequency of tumors. However, if they induce bone formation in the lab before giving the cells to the monkeys, they get bone formation with no tumors.

This result is not too surprising. You can make use of pluripotent cells, but get them started on the right path before putting them into animals. This had been shown with rodents; the new work extends it to primates. It's encouraging.

News story: First test of pluripotent stem cell therapy in monkeys is a success. (Phys.org, May 15, 2014.) Good overview.

The article, which is freely available: Path to the Clinic: Assessment of iPSC-Based Cell Therapies In Vivo in a Nonhuman Primate Model. (S G Hong et al, Cell Reports 7:1298, May 22, 2014.)

A recent post on making iPSC: Improving the efficiency of making induced pluripotent stem cells (iPSC) (February 1, 2014).

A post on a clinical trial, in humans, of cells derived from embryonic stem cells: Therapy based on embryonic stem cells: the first clinical trial (October 23, 2010). The Geron trial. Links to follow-up posts.

More about bone formation... Need a new bone? Just print it out (November 13, 2016).

Also see my Biotechnology in the News (BITN) page for Cloning and stem cells. It includes an extensive list of Musings posts in the fields of stem cells and regeneration -- and, more broadly, replacement body parts, including prosthetics. Despite the slow progress in developing therapeutic use of iPSC, they are proving very useful in research.

August 27, 2014

Our microbiome: a caution

August 26, 2014

A hot topic of recent years has been work on the human microbiome, the microbes that live as part of the human body. The explosion of work in this field has been made possible by developments in nucleic acid technologies, including the dramatic reduction in cost of genome sequencing. We are now flooded with information about who lives within us, both in health and disease, and how they get there.

The problem is that information is coming in faster than we can digest it. The flood of information leads to hypotheses about what it all means. It's all too easy to forget that these hypotheses need testing.

A recent "Comment" story in Nature reminds us to be cautious. It's short and good. Look it over. Nothing here is meant to minimize the importance of developments in the field. It's merely to remind us to distinguish what is suspected from what is known. At this early stage, there is much more of the former than the latter.

"Comment" article, which is freely available: Microbiology: Microbiome science needs a healthy dose of scepticism -- To guard against hype, those interpreting research on the body's microscopic communities should ask five questions. (W P Hanage, Nature 512:247 (August 21, 2014.)

Posts on the microbiome include...
* Glyphosate and the gut microbiome of bees (October 16, 2018).
* Possible role of gut bacteria in Parkinson's disease? (March 17, 2017).
* Artificial sweeteners: Saccharin and high blood sugar levels (December 7, 2014).
* Could we treat obesity with probiotic bacteria? (August 5, 2014).
* Malnutrition: is more (or better) food the answer? (March 8, 2013).

Book. The following book is listed on my page of Books: Suggestions for general science reading. Blaser, Missing Microbes -- How the overuse of antibiotics is fueling our modern plagues (2014). The theme of Blaser's book is that we have changed our microbiota by our use of antibiotics, and that is causing problems. The current article is something of a response to Blaser. (In my opinion, Blaser himself is rather bold in proposing things, but cautious about reaching conclusions. Others are not always so cautious; the book is more in response to them. In any case, this book is highly recommended. And the listing on my Books page includes links to more Musings posts.)

If it quacks like a whale...

August 25, 2014

An odd story, with an article that is not very clear. However, it does seem to solve a mystery -- and it may even be useful.

For a half century observers have noted an unusual sound in the oceans near Antarctica. It's commonly characterized as a quack. The source has been unknown; people simply attributed it to an unidentified "bio-duck" -- a strange term in itself. Some people weren't even sure it was a biological sound at all.

Now a team of scientists report that the bio-duck is a whale -- an Antarctic minke whale.

How did they figure this out? They had tagged two Antarctic minke whales with microphones, and were recording them. They found the bio-duck sound, along with the better-known downsweep sound of the whales. Examination of the records showed that no other animals were around. The simplest conclusion? The whales quack.

Useful? The sound is common, and the Antarctic minke whales are hard to study. Following the quacks may be a new tool for following these creatures. Of course, attempts to do so will provide a chance to confirm the identification of the sound source.

News stories:
* Mystery of 'ocean quack sound' solved. (BBC, April 22, 2014.)
* What's Making Duck Sounds in the Ocean? Mystery Solved. (National Geographic, April 23, 2014.)

The sounds. (Sound track; no meaningful video; 4 minutes.) The file contains four segments. All but the first are labeled. The first two are perhaps most useful. (This composite file is based on some sound tracks posted as supplemental data at the article's web site. )

The article, which is freely available: Mysterious bio-duck sound attributed to the Antarctic minke whale (Balaenoptera bonaerensis). (D Risch et al, Biology Letters 10:20140175, April 2014.)

More about whales and the sounds they make... Tracking new songs as they cross the Pacific (June 21, 2011).

* A recent post about whales: Whales in the Chilean desert -- the oldest known case of a toxic algal bloom? (April 13, 2014).
* Next: The advantage of menopause: grandma knows where dinner is (June 15, 2015).

* A recent post about the Antarctic: IceCube finds 28 neutrinos -- from beyond the solar system (June 8, 2014).
* Next: What if your compass pointed south? (October 24, 2014).

Were dinosaurs cold-blooded or warm-blooded?

August 23, 2014

Maybe not -- according to a recent article.

Warm- vs cold-bloodedness relates to more than body temperature. It reflects basic patterns of energy use.

In the new article, the scientists collect data on the metabolic rates and growth rates of a wide range of vertebrates. (Vertebrates are animals with backbones. Loosely, that means fish and "up".)

The figure summarizes, in a very compact form, what they found. It shows the growth rate (y-axis) vs metabolic rate (x-axis) for a wide range of vertebrates.

Both of these are "scaled", to take into account that the figure includes animals of very different sizes. The x-axis is labeled mass-independent metabolic rate to reflect this scaling; the y-axis is scaled similarly. (More about this scaling as we go on; don't worry much about it for now.)

There is a big diagonal line. It shows that there is a general trend: animals that have a higher metabolic rate grow faster. That should seem reasonable enough. The line is labeled -- showing that endotherms (warm-blooded animals) are near one end of the curve, and ectotherms (cold-blooded animals) are near the other end. That should also seem reasonable; we think of warm-blooded animals as being more metabolically active. (Remember, this is scaled for size. The line does not mean that bigger animals are more likely to be warm-blooded. It means that, at a given size, the warm-blooded ones are likely to be more active.)

In the middle is a region marked mesotherms. This may be a new term. What does it mean? It refers to animals that are intermediate between warm- and cold-blooded. They raise their body temperature (T) above the ambient T -- as warm-blooded animals do -- but they do not control it to any particular body T. The tuna is an example of a mesotherm. A few other examples are known. (Any echidna fans out there?)

Then there are some points shown as open squares. These are for dinosaurs. Of course, these are not measured directly, but have been estimated from measurements of dinosaur growth. Musings has discussed some of those estimates [links at the end]. Interestingly, the estimates for the dinosaurs put them in the middle region of this graph -- along with known mesotherms.

This is Figure 2B from the article.

The conclusion from this study, then, is that the dinosaurs may be intermediate. A key part of this is recognizing that being intermediate is "allowed". Dividing animals into two distinct categories, warm-and cold-blooded, is a simplification. We know of modern animals that are intermediate; the data for dinosaurs, such as it is, are consistent with the dinosaurs being intermediate, too.

This article won't resolve the question of whether dinosaurs are cold-blooded or warm-blooded. After all, the measurements are difficult, and people will continue to try to make better ones. But we now have a broader perspective. Maybe dinosaurs are intermediate; maybe they vary. Maybe it makes sense that dinosaurs, a group of organisms intermediate between the cold-blooded reptiles and the warm-blooded birds, have intermediate characteristics.

More about the scaling used in the figure above... As noted, the scaling allows the authors to condense a large amount of data into a single curve. The scaling takes size into account -- but it also hides size. The article itself has graphs showing unscaled data. For example, Figure 1 shows growth rate vs size; you can see that data for ectotherms, mesotherms, and endotherms seem to give different lines. There is more than one way to look at the data; the scaled graph is compact, and good as an overview.

News stories:
* Not too fast, not too slow: Researchers untangle energetics of extinct dinosaurs. (Phys.org, June 12, 2014.)
* Why Dinosaurs Were Like Tuna, Great Whites, and Echidnas. (E Yong, Not Exactly Rocket Science (National Geographic blog), June 12, 2014. Now archived.) Excellent.

* News story accompanying the article: Paleontology: Dinosaur metabolism neither hot nor cold, but just right -- Growth rates suggest answer to long debate: Dinosaurs were "mesothermic," like today's tuna and echidna. (M Balter, Science 344:1216, June 13, 2014.)
* The article: Evidence for mesothermy in dinosaurs. (J M Grady et al, Science 344:1268, June 13, 2014.)

Background posts on dinosaur growth:
* The oldest dinosaur embryos, with evidence for rapid growth (May 7, 2013).
* Do animal bones have something like annual growth rings? (August 7, 2012).

Also see...
* T rex census (May 25, 2021).
* Facultative endothermy: a lizard that is warm-blooded in October (February 1, 2016).
* The opah: a big comical fish with a warm heart (July 13, 2015).
* Underground hibernation in primates? (October 6, 2013).

Why male scientists may have trouble doing good science: the mice don't like how they smell

August 22, 2014

It's something people joke about. Sometimes there are anecdotal reports. Now a team of scientists has done the test... It really does matter who does the experiment. More specifically, male and female experimenters may well get different results in experiments with mice. Why? Because the mice respond to the odors -- and they don't like having males around.

Some data from the recent article...

The figure summarizes results from one experiment.

The y-axis is a measure of the pain "reported" by the mice. In this test, the mice are injected with an inflammatory agent; their level of pain is judged by their grimace. MGS on the y-axis label means Mouse grimace scale. It is a standard test.

The x-axis shows the humans who were present; the labeling may be confusing.

The first bar (left) is the control, with no human present. It is labeled "none". None? The humans here were "observers", not experimenters. This was done during a phase of the test that did not require presence of a human.

Then there are five blue bars for males, and five pink bars for females. Caution... The scientists tested four people of each sex; the first four bars of each set are labeled with the person's initials. The fifth bar of each set is the average for those four; it is labeled M or F, and is darker than the other bars. (The number at the bottom of each bar is the number of trials; the number for the fifth bar is the sum of the numbers for the four individuals of the first four bars.)

That makes it easy now... Just look at the right bar of each set, the bar for the averages for M and F. Compare them to "none". You can see that the F average bar is close to that of the control, but the M average bar is considerably lower.

Their statistical testing confirms that, but they create further confusion in how they label the bars. They use two different symbols, asterisks and dots; they mean different things. The asterisks indicate that the result is significantly different from the "none" control. You can see that the male average (and three of the individual males) have three *** -- showing the highest level of significance (p < 0.001). None of the female data has any asterisks; none is significantly different from the control.

The bar for the female average has three dots. That means it is (highly) significantly different from the corresponding bar for the males -- the male average. (That test is applied only to the average.)

This is Figure 1a from the article.

In summary, the experiment described above shows that the presence of males vs females has a different effect on the results. In the particular case, males dampen the pain response of mice.

In further testing, they elaborate. The same result is obtained by using T-shirts that have been worn by the individuals; the presence of the person is not needed. In fact, the result can be obtained by the use of certain chemicals known to be part of the male odor. Further, they test bedding materials from several mammals. The response is general: samples from males block the pain response of the mice. The samples don't have be from humans: any "reproductively intact" male mammal will do.

The story here makes sense in terms of the biology of mice and the type of test. It's an interesting experiment. And it has real implications. People do tests like this, and it is typically not even reported who was in the room with the mice. It matters.

News stories:
* Men Trigger Mouse Stress -- Mice become stressed in the presence of male, but not female, experimenters, triggering a physiological response that dampens pain. (The Scientist, April 28, 2014.)
* Male Experimenters Attenuate Pain Responses in Mice. (Pain Research Forum, May 2, 2014. Now archived.)

The article: Olfactory exposure to males, including men, causes stress and related analgesia in rodents. (R E Sorge et al, Nature Methods 11:629, June 2014.) Check Google Scholar and you may find a pdf of a preprint.

Among posts about mouse behavior:
* Male mice are stressed by the odor of bananas or pregnant females (June 14, 2022).
* Would wild mice use an exercise wheel? (July 11, 2014).

For more about M-F biochemical differences: Post-traumatic stress disorder (PTSD): a clue to its biochemistry (April 15, 2011).

Another post about the effects of humans on other animals: Do elephants suffer long term harm if their social groups are disrupted by human intervention? (April 27, 2014).

More about pain:
* I feel your pain -- how does that work? (March 4, 2017).
* Alcohol consumption, an "ethnic" mutation, and a possible new drug (October 28, 2014).
* Would a placebo work even if you knew? (January 31, 2014).

August 20, 2014

The new Ebola virus

August 19, 2014

We are experiencing the largest outbreak of Ebola virus ever recorded, and the outbreak is not under control. Ebola is a frightening disease: there is no established treatment, and half or more of those known to be infected may die. It is also quite rare: the virus was discovered only in 1976, and the total number of recorded cases -- prior to this outbreak -- is fewer than 3,000.

One issue of interest is the identification of the virus, and determining its relationship to other Ebola virus strains that are known. A new article studies the virus from 15 cases, with full genome sequencing for three of the viral isolates. The work makes clear that the patients do indeed have Ebola virus. The complete sequencing shows that it is closely related to what is known as the Zaire strain, but that it is distinct from previously known strains.

The figure shows the focus of the current outbreak.

This is Figure 1 from the article. Their figure legend is included.

A couple of notes...
* You can see where Guinea, the country where the outbreak started -- in the red region (lower right), is in relation to Sierra Leone and Liberia; those three countries are the heart of the current event.
* The map here is based on the findings in March 2014.

What do we conclude from identification and characterization of the current Ebola virus?

First, the fact that the virus is distinct suggests that the current outbreak is not due to simple transmission from the Zaire area to the Guinea area. (Zaire is now called the Democratic Republic of the Congo.) It is more likely that the Guinea outbreak began with a separate and recent transmission event from non-human hosts to humans in that area.

Second, it raises a question: how similar is the biology of this virus to that of other Ebola viruses? For example... Is it possible that the difficulty of dealing with this outbreak is, in part, due to it being a different virus? Is it possible that the virus transmission is different for this virus? We don't know, but can only ask. Strains of Ebola vary in their behavior. For example, the Reston strain does not seem to cause disease in humans at all. The current outbreak may have a lower frequency of the hemorrhaging that used to be considered a key feature of Ebola. Is this a reflection of a different virus, or of some environmental influence?

News story: Researchers identify a new variant of Ebola virus in Guinea. (Science Daily, April 22, 2014.)

The article, which is freely available: Emergence of Zaire Ebola Virus Disease in Guinea -- Preliminary Report. (S Baize et al, New England Journal of Medicine 371:1418, October 9, 2014.) The article includes a reconstruction of the likely transmission of the virus for the earliest cases, from December 2013 through March 2014 (Figure 2).

The following page is the source of the number I gave for previous Ebola outbreaks: Ebola virus disease. (WHO Fact sheet #103, updated April 2014.) The page also shows that the total number of reported Ebola cases in the previous five years (2009-2013) is fewer than 100 -- almost entirely in 2012. Remember that reported counts for any disease are likely to be low.

A news page from CIDRAP on Ebola -- from last Friday: West Africa Ebola outbreak tops 2,000 infections. (CIDRAP, August 15, 2014.)

* * * * *

More on the nature of the Ebola virus: Ebola virus: ancient origins? (November 4, 2014).

There is more about Ebola on my page Biotechnology in the News (BITN) -- Other topics in the section Ebola and Marburg. That section includes links to good sources of information and news.

More about emerging diseases in general is on that same BITN page in the section Emerging diseases. It includes links to some Musings posts on various emerging diseases.

There is more about genomes on my page Biotechnology in the News (BITN) - DNA and the genome. It includes an extensive list of Musings posts on sequencing and genomes.

Quality of oil and gas wells -- fracking and conventional

August 18, 2014

Hydraulic fracturing, or "fracking", is a new way to release gas (or oil) from rocks. It is controversial, partly because it is new and any new process has growing pains and partly for political reasons. I don't want to deal much with the political aspects, but they are there and color the debate; they can make it hard to deal with the substantive issues.

A new article reports on problems with gas wells in Pennsylvania -- fracking wells as well as conventional wells. (The study includes both oil and gas wells. We won't try to separate those in this post.) These are problems with the physical integrity of the well, which can lead to release of methane. Release of methane is bad, since it is a potent greenhouse gas.

What did the scientists do in this new article? They looked at the official state records for well inspections, and noted the frequency of problems. Doing that is more complex than it sounds, but let's accept the general intent. The data are quite objective; what they mean is open to interpretation.

The following table summarizes the findings. Each result is the percentage of wells with structural defects, as recorded by the state inspection.

There are three variables: well date, location, and type of well. Let's look at some specifics...

The first variable is the well date -- the age of the well. It's shown in the left-hand column, "Wells spudded"; the spud date is the date drilling of the well started. Old wells (pre-2009) vs new wells (post-2009). The two halves of the table are for two geographic regions: NE counties (northeast part of Pennsylvania) at the right, and non-NE counties at the left. Why this distinction? The "NE counties" is the area of the state where there has been a recent boom in drilling, especially unconventional (fracking) wells.

So let's start with the non-NE data, at the left. Conventional vs unconventional wells, old vs new. All the data show about 1-2% of problems. The biggest effect is that new wells show more problems than old wells. Read that carefully. If you think you might expect old wells to show more problems, because they are old -- it's the other way around. Unconventional wells are worse among old wells, a bit better among new wells.

Now look at the right-hand set of data, for the NE counties. Everything is worse. Much worse, for the most part. Unconventional (fracking) wells have problem rates near 10%.

This is Table 1 from the article.

There are the data. Now what?

Various interpretations are possible. For example, it is possible that the data mean exactly what they say -- that unconventional wells in the NE counties have a 10% rate of problems, and that this is worse than for the other categories. It is also possible that there is sampling bias. Maybe wells are being inspected more carefully now than before. Or maybe they are inspected more carefully in the more active NE region, given the news coverage and controversy. And so forth.

Those with political bias favor one interpretation or another -- with little evidence. I don't want to resolve that here. Whatever the interpretation, there seems to be a problem with quality of wells. That means there is a potential for leakage. We can quibble over the numbers and who is worse, but the problem seems worthy of attention. Maybe we should just say that the results suggest there are problems with the quality of wells, and it needs further investigation -- with the goal of reducing methane leakage.

Since it is a political issue, one may wonder whether the authors have a political view. Indeed, the lead author, a professor at Cornell University, is head of an environmental group that opposes fracking; his university research is focused on showing technical problems with the process. His affiliation with the environmental group is quite open; the group is listed in the article as an author affiliation. (Another author also lists both a university affiliation, Berkeley, as well as the environmental group.) That is, they have what would easily be recognized as a "conflict of interest"; they are advocates for one side in a controversy. Does that mean we reject their work? No, it means we look at the quality of the work, just as we do with any science. And we are aware of what their bias is. Most people have bias; the current authors are quite open about theirs. Their study suggests that quality of wells needs attention.

Interestingly, the article records formally that "The authors declare no conflict of interest" (footnote on first page). That formal statement refers to hidden issues such as funding. Since the authors have declared their affiliation with the environmental group, which apparently funded the work, this is probably a proper statement. "Conflict of interest" means various things. People have biases and opinions; the purpose of the formal conflict of interest statement is typically more to disclose any financial conflicts that might otherwise be hidden.

News story: Fracking study finds new gas wells leak more. (Phys.org, June 30, 2014.)

* "Commentary" accompanying the article: The integrity of oil and gas wells. (R B Jackson et al, PNAS 111:10902, July 29, 2014.) Check Google Scholar for a preprint. If you can get hold of this item, it is quite worth reading.
* The article, which is freely available: Assessment and risk analysis of casing and cement impairment in oil and gas wells in Pennsylvania, 2000-2012. (A R Ingraffea et al, PNAS 111:10955, July 29, 2014.)

More about fracking:
* Fracking: the earthquake connection (June 19, 2015).
* Fracking: Implications for energy usage and for greenhouse gases (October 26, 2014).
* Shale gas recovery using hydraulic fracturing (fracking) (October 7, 2013). Useful overview of fracking.

More about methane leakage:
* Boston is leaking (February 13, 2015).
* Space-based observation of atmospheric methane -- and the Four Corners methane hotspot (December 29, 2014).
* Methane leaks -- relevance to use of natural gas as a fuel (April 7, 2014).

There is more about energy issues on my page Internet Resources for Organic and Biochemistry under Energy resources. It includes a list of some related Musings posts.

August 13, 2014

A better mouse -- it has a humanized liver

August 12, 2014

A recent article offers an intriguing development, which focuses our attention on the problem of how we test whether drugs are safe.

In our modern world, drugs are tested in various kinds of cells and then a variety of animals before they are given to humans. Despite that, some drugs go to testing in humans and turn out to be toxic. I'm not talking here about subtle or rare problems that would take years to detect, but major toxicities. In the case that is the focus of the current work, the drug fialuridine was being tested as a treatment for hepatitis B virus. The drug passed animal testing; it even passed preliminary short-term testing in humans. Then, 15 humans were given the drug: 7 suffered serious liver problems within a few weeks; 5 of them died.

How can that happen? How can major toxicity escape detection? The simple answer, stated somewhat flippantly, is that humans aren't mice. The toxicity of a drug depends on many things, including how it is metabolized and the nature of its targets. After all, we test drugs in several animals because we know animals vary in drug effects. There is no assurance that humans are like any of the animals used for drug testing -- as the fialuridine trial showed.

What are we to do? One answer is that we have learned to be quite cautious in trying a new drug in humans, regardless of the data in other animals.

A new article offers a little trick, which may also help. The drug at hand was active in the liver, where its purpose was to treat the liver virus hepatitis B. The toxicity that was found was liver toxicity. Further, the liver is often important in drug metabolism. What if we tested the drug in some other animal with a human liver?

What the new work does is to use a mouse strain with a "human liver". Indeed this chimeric mouse does reveal the toxicity.

We will look at how they made this mouse strain later, but first let's look at some results...

The graph shows the blood level of the enzyme ALT, which reflects liver damage. Results are shown for five conditions; each point shows the enzyme level found in one mouse.

Let's jump in and look at the two key conditions: the first and last sets of points. In both of these, the mice were given the drug ("FIAU") for four days; see the rows labeled drug and day. The difference? At the left, the mouse was a control ("Cont" in the row labeled mouse), and at the right the mouse had a humanized liver ("Hu").

You can see that the levels of the ALT enzyme, reflecting liver damage, were much higher in the Hu mice (at the right) than in the Cont mice (left). That is, the drug caused liver damage in the mice with the humanized liver, but not in control mice.

The other data sets are for various controls, and all showed low enzyme levels. The second condition is the control mice at a longer time; even at 14 days, there is no evidence of liver toxicity. The next two conditions were with Hu mice -- the mice with the humanized liver. These conditions lacked the drug; one used the "vehicle" the drug was delivered in. Neither of these showed an effect. The effect on mice with the humanized liver occurred only when the drug was delivered.

This is Figure 1A from the article.

The general conclusion from that experiment is that the mice with the humanized liver showed toxicity of the drug. That is, the test here with these humanized mice properly predicted what was found when the drug was tested in humans.

How does one make a mouse with a human liver? Logically, it's fairly straightforward. You inject human liver cells into the mouse. Well, that won't quite work, because the mouse immune system would reject them. So you knock out the mouse immune system. That's really it, in terms of basic logic: knock out the mouse immune system and give them human liver cells. It works. Immune-deficient mice are a staple of mouse research, and they are often given various kinds of human cells. In fact, this strain of mice with a humanized liver had been made a few years ago. What's new here is putting it to use for drug testing.

The authors suggest that it might be good to routinely test new drugs with a mouse strain such as this. It will be interesting to watch how this suggestion is received.

News stories:
* Mouse model would have predicted toxicity of drug that killed 5 in 1993 clinical trial. (Science Daily, April 15, 2014.)
* Mice with human livers would have saved lives if used in toxicology testing, study shows. (Stanford University School of Medicine, April 15, 2014.)

The article, which is freely available: Fialuridine Induces Acute Liver Failure in Chimeric TK-NOG Mice: A Model for Detecting Hepatic Drug Toxicity Prior to Human Testing. (D Xu et al, PLoS Med 11(4):e1001628, April 15, 2014.) There is a one page "Editors' Summary" at the end that serves as a news story from the journal. It is very good at summarizing the main points in something close to plain English.

A post that noted the monitoring of liver toxicity by measuring the ALT enzyme: Gene therapy: Could we now treat Queen Victoria's sons? The FIX Fix. (January 6, 2012).

Another example of a clinical trial that went bad because the animal testing did not reveal an important toxicity is noted on my page Biotechnology in the News (BITN) -- Other topics in the section TGN1412: The clinical trial disaster. That example is quite different from this one, and the test discussed here would not have helped.

Another example of studying mice that have been partly humanized, in this case with a particular gene: Mouse with human gene for language: is it smarter? (November 15, 2014).

More about toxicity testing: Predicting the toxicity of chemicals (September 11, 2018).

Also see: Using lab-grown organoids in medical treatment (May 3, 2021).

Another FDA approval: exoskeleton

August 11, 2014

The US Food and Drug Administration (FDA) recently approved a high-tech prosthetic arm. We now have FDA approval of an exoskeleton to help those with loss of lower limb function stand -- and walk. Musings posts have noted some of the background work behind these developments, as well as the arm approval [links at the end].

As the news stories make clear, these developments do not mean that the problems have been solved. The new devices are complex and expensive. But they are milestones; what used to be intractable problems now have solutions worth officially recognizing. Improvements will continue.

Musings presents scientific work at various stages of development. Some is very preliminary, sometimes so preliminary that the ideas are hard to accept; in fact, some turn out to be wrong. But some things progress to useful products or to accepted knowledge. Individual articles are steps along those pathways -- steps whose real value is not clear when they are published. The two posts about FDA approvals of prosthetic devices are examples of success stories.

News stories:
* FDA approves first ever personal exoskeleton. (ExtremeTech, July 3, 2014.)
* FDA Approves First Exoskeleton for the Disabled. But Who Will Pay for It? (Slate, July 2, 2014.)

FDA announcement: FDA allows marketing of first wearable, motorized device that helps people with certain spinal cord injuries to walk. (FDA, June 26, 2014. Now archived.) Also available in Spanish. Very informative.

Background posts...
* Recent FDA approval of a prosthetic device: FDA to fast-track prosthetic arm -- Follow-up #2: approval (June 9, 2014).
* Musings has posted on another exoskeleton product that is under development: Berkeley Bionics: From HULC to eLEGS (October 22, 2010). Berkeley Bionics is now called Ekso Bionics; it is referred to in some of the news stories.

More... Personal optimization of an exoskeleton (September 22, 2017).

Also see my Biotechnology in the News (BITN) page for Cloning and stem cells. It includes an extensive list of Musings posts in the fields of stem cells and regeneration -- and, more broadly, replacement body parts, including prosthetics.

Effect of radiation near Fukushima on local monkeys

August 10, 2014

A recent post was about birds in the region of the Chernobyl nuclear disaster; the message was that the birds are showing signs of adapting to the radiation [link at the end]. Now we have an article about monkeys in the region of the Fukushima nuclear disaster; the message is that the monkeys are showing signs of harm from the radiation. We'll come back to the "big picture" at the end, but first let's look at what the new article found.

In this new work, the scientists studied three populations of monkeys: two live near the Fukushima site (about 70 kilometers from the power plants), and the third lives further away (about 400 km away). The scientists collected blood samples, and measured many properties, such as the amount of hemoglobin and the number of white blood cells.

What did they find? For some properties, the monkeys that lived near Fukushima showed effects that were statistically significant. All the significant effects they found were in the direction that one might judge the monkeys near Fukushima to be below normal.

The following figure shows what may be the most important effect they found...

This graph shows the white blood cell counts (WBC; y-axis) for juvenile monkeys as a function of their level of radioactive cesium (x-axis).

There is lots of scatter, but there is also some trend: monkeys with the highest levels of radioactive cesium tend to have the lowest WBC.

This is Figure 2 from the article.

Is this important? It's hard to know. It is biologically reasonable that young monkeys might be more susceptible to the effects of the radiation than older monkeys. On the other hand, the numbers here are very limited. If it weren't for a few monkeys at the lower right, no trend would be evident. The conclusion? Here are the data at hand. This is what we have so far. It may not be good proof of a problem, but it would be reckless to ignore it.

The article has provoked a response -- not completely constructive. Some argue that the claims are exaggerated or unreasonable, given the amounts of radiation reported. We need to look carefully at what the article does and does not claim. Criticizing the article because it might be over-interpreted is unfair. It's a small report. Observations of Nature in the wake of a disaster are not ideal well-controlled studies.

So far I can tell (including some reading of the news coverage), the authors clearly describe what they did, and note its limitations. For example, they use the level of radioactive cesium as a marker; they quite explicitly do not claim it is the cesium that is the cause of the results. (It might be another radioactive material, one that came from the same source and may correlate with the cesium.) They have two study areas near Fukushima, with different levels of radioactive cesium; they explicitly note that they do not see any difference in the monkeys from those two areas. More generally, they make no claim that the monkeys have suffered any particular ill effect. With a small study such as this, the effects seen might or might not be important.

What this article does is to provide one window into what is happening in the wake of the Fukushima release. A good aspect is that it looks at an animal relatively closely related to us. It reports some data. The data suggest there are some things we want to know more about. In fact, it may be good to think about this work as setting a baseline. Measurements on the monkeys over coming years may help to clarify what the significance is. Be careful about saying much more from it.

In general terms, this report and the recent one about the birds at Chernobyl are similar. They both report what is found in Nature. It is interesting that the birds at Chernobyl are showing signs of adaptation; that does not mean the Chernobyl problem is over. The current work points to a possible problem near Fukushima; further work may help us understand how important it is. For now, people are reporting what they find.

News stories:
* Blood Cell Counts Low in Fukushima Monkeys. (The Scientist, July 29, 2014.) A brief overview.
* Japanese monkeys' abnormal blood linked to Fukushima disaster -- study. (Guardian, July 24, 2014.) This story does a reasonable job at presenting a balanced view of the work.

The article, which is freely available: Low blood cell counts in wild Japanese monkeys after the Fukushima Daiichi nuclear disaster. (K Ochiai et al, Scientific Reports 4:5793, July 24, 2014.)

Background post: Are birds adapting to the radiation at Chernobyl? (August 3, 2014).

The Berkeley RadWatch project has been looking at radiation from Fukushima -- across the ocean in California. We have noted some of that work... Berkeley RadWatch: Radiation in the environment (February 24, 2014). It's really important to distinguish that work and the current work. The effects of radiation depend on dose. The monkeys of the current study are tens or hundreds of kilometers from the Fukushima site. In California we are thousands of kilometers away; it is good to do monitoring, but it would be surprising if much Fukushima radiation were found here.

More from Fukushima:
* Did the Fukushima nuclear accident lead to a burst of thyroid cancer? (July 17, 2016).
* Radioactivity released into ocean from Fukushima nuclear accident reaches North America (March 23, 2015).

My page of Introductory Chemistry Internet resources includes a section on Nucleosynthesis; astrochemistry; nuclear energy; radioactivity. That section contains some resources on the effects of radiation. It also includes a list of related Musings posts.

The advantage of washing with formic acid

August 8, 2014

You might start by watching the following video. It has two segments. The first shows an event involving two kinds of ants. The second shows the smaller ants washing up after such an event. It would be good to watch at least part of each segment as an introduction here.

Video (2 minutes; no sound).

What's this all about? The event shown involves two types of ants, the famous fire ant and the crazy ant. Both are native to South America. Fire ants have established themselves in much of the southern United States. They seem to have few enemies, partly because they make a toxin. In general, other ants have learned to just avoid the fire ants. But not the little crazy ants. The crazy ants do well in the competition -- and they seem oblivious to the fire ant toxin. How can that be? Because the crazy ants wash it off after the battle; that's what you see in the second segment of the video.

A recent article documents all this for us; the video noted above accompanies the article. But the authors of this article do more. They show that the key to washing is the use of formic acid. That acid has long been associated with ants; the formal name for the ant family is Formicidae. It used to be that commercial production of formic acid was based on collecting it from ants. The crazy ants make formic acid; it is an offensive weapon for them -- its normal role in ants. But here the ants use it for defense. Go back to the second segment of that video. The crazy ants make formic acid in a gland in the abdomen. You can see that they transfer it from the abdomen to their mouth, and then they wash their legs. The effect is that they are inactivating the fire ant toxin by washing their legs with formic acid.

The following graph shows one of the experiments the scientists did to develop that story...

The graph shows survival curves for the crazy ants (Nylanderia fulva) under three conditions.

Two are controls, and give the same curve, at the top, with near 100% survival. We'll note the control conditions in a moment.

The third curve shows that survival declines substantially when the defense mechanism is blocked. That curve, with open circles, is for ants that have engaged in conflict with the fire ants (Solenopsis invicta), but have had their acidopore -- where their acid defense is secreted -- blocked.

The two controls? One (dark circles) had a sham treatment that did not actually block acid secretion; one (triangles) had their acid secretion blocked, but did not engage in conflict. The second control shows that blocking the acid secretion per se is not harmful.

This is Figure 2 from the article.

That is, there are two variables in the treatment: acidopore sealed or not, conflict with fire ants or not. Sealing the acidopore alone or avoiding conflict alone allows survival. However, if there is a conflict, sealing the acidopore reduces survival. Thus, the results suggest that the acidopore is needed for survival after the fire ant conflict.

As noted above, it's known that the crazy ants make formic acid. Further work in the current article showed that formic acid alone could serve to detoxify the fire ant venom.

This article helps explain a specific example of chemical warfare between two competing insects. In the broader context, this competition happens to be one of great importance.

A crazy ant, washing itself. It is standing on a cricket leg. The cricket was probably the subject of the encounter between this ant and a fire ant.

This is part B of the figure from the news article by Kaspari & Weiser.

News story: Crazy ants dominate fire ants by neutralizing their venom. (Phys.org, February 13, 2014.) Good overview.

Videos. One video was listed near the start of this post. There is also a video with the Phys.org news story. It is similar to the first one, but with some useful narration, from the lead author of the article. This video is also available at Video, YouTube (1.3 minutes; narrated).

* News story accompanying the article: Ecology: Meet the New Boss, Same as the Old Boss. (M Kaspari & M D Weiser, Science 343:974, February 28, 2014.) Don't worry too much about the title.
* The article: Chemical Warfare Among Invaders: A Detoxification Interaction Facilitates an Ant Invasion. (E G LeBrun et al, Science 343:1014, February 28, 2014.)

Other posts on ants include...
* What's the connection: blue cheese, rotten coconuts, and the odorous house ant? (August 24, 2015).
* Ants: nurses, foragers, and cleaners (May 24, 2013).
* Death-grip scars from zombie ants, 48 million years ago (November 9, 2010).

The work discussed here is an example of chemical ecology. A key figure in the development of chemical ecology, especially in insects, was the late Tom Eisner. A delightful book of his is noted on my page of book suggestions: Eisner, For Love of Insects (2003).

More insect warfare...
* Bee wars (March 1, 2015).
* Origin of gas warfare (September 11, 2009).

This post is listed on my page Internet Resources for Organic and Biochemistry in the section for Carboxylic acids, etc.

August 6, 2014

Could we treat obesity with probiotic bacteria?

August 5, 2014

A team of scientists has developed a bacterial strain that can be used to combat obesity. They show the effectiveness of this probiotic strain in two test systems in mice.

The following figure shows the effect of their probiotic strain in one of the mouse systems.

This experiment uses a strain of mice that is prone to obesity. It is fed normal mouse chow.

The graph shows the average weight of the mice over time, for three treatment conditions. The treatment is given over the first 11 weeks -- up to the vertical dashed line. Observations continue, labeled "Follow-up".

The red curve is for the mice treated with the probiotic. The other two curves are for two controls (details below).

This is Figure 13 from the article.

The basic observation: mice treated with the probiotic show less weight gain than the two controls (which are similar to each other). The effect continues beyond the treatment time.

What is this probiotic strain? It is based on a strain of the common gut bacterium Escherichia coli. The scientists have added to that strain a gene that leads to the production of certain lipids -- ones known to lead to weight loss. The bacteria were provided to the mice in the drinking water. (This brings us to the controls noted with the graph. One control uses the bacteria but without the added gene; the other control, labeled "vehicle", omits bacteria.)

As noted at the top, they tested two mouse models for obesity. The other system involved normal mice fed a high fat diet. The results there also showed that the probiotic strain reduced weight gain. This part of the study included other measurements; for example, the bacteria improved the insulin resistance of the mice.

What is the significance of this work? It is a "proof of principle" that modifying the bacteria in the gut, the gut microbiota, might usefully reduce obesity. It is not known if the probiotic strain they use is compensating for a problem with the resident microbiota -- or is simply acting on its own. Whether this strain would work in humans is, of course, unknown; the test here is in mice. There are multiple pathways to obesity -- in mice or in humans. It remains to be seen which types of obesity can be usefully treated with this probiotic -- or with improved or distinct probiotics, and how probiotic treatments would compare with other types of treatments.

Since the bacteria used here were designed to deliver a specific chemical, one might ask if we could deliver the chemical directly, say as a drug. That does work; that's why they chose the chemical. However, if the probiotic could get fully established so that it needed to be given only once, then that would be simpler than a drug taken regularly. They do not achieve full establishment in this work.

Bottom line... This work is an interesting step toward possibly treating obesity with bacteria.

News story: Study suggests probiotics could prevent obesity and insulin resistance. (Kurzweil, July 25, 2014.) (If you haven't seen an obese mouse, have a look at this story. But I don't think the mice shown here are the kind used in this study.)

The article, which is freely available: Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity. (Z Chen et al, Journal of Clinical Investigation 124:3391, August 2014.)

More about probiotics:
* A clinical trial of ice cream (June 2, 2015).
* How probiotics work: a clue? (October 11, 2010).

More about obesity:
* Olfaction and obesity? (July 18, 2017).
* YY in the mouth? (April 4, 2014).

More about the gut microbiota...
* Our microbiome: a caution (August 26, 2014). The hype of microbiome research.
* Red meat and heart disease: carnitine, your gut bacteria, and TMAO (May 21, 2013).

More about lipids is in the section of my page Organic/Biochemistry Internet resources on Lipids. That section contains a list of related Musings posts.

Book. The following book is listed on my page of Books: Suggestions for general science reading. Blaser, Missing Microbes -- How the overuse of antibiotics is fueling our modern plagues (2014). Blaser's theme is that we have changed our microbiota and that is causing problems. Whether the specific intervention suggested by the current work fits with Blaser is an open question. In any case, this is an excellent book.

Twins? A ducky? Spacecraft may soon be able to tell.

August 4, 2014

The Rosetta spacecraft, from the European Space Agency (ESA), passed the asteroid Lutetia in 2010. Two Musings posts presented pictures and scientific findings from that encounter [links at the end].

Rosetta kept going, aiming for an encounter with a comet, 67P/Churyumov-Gerasimenko (67P/C-G for short). Rosetta will go into orbit around 67P/C-G. Later, a probe from Rosetta will attempt to land on the comet.

Rosetta is getting close. It recently re-awoke, and started taking some advance pictures of its target. Surprise...

This is a quite irregular comet. Perhaps it is twins -- two comets joined together after a collision. Perhaps, perhaps.

The news story listed below is a good update and summary. It includes a raw picture, and an animation containing a set of processed pictures viewed at various angles; the picture above is one from that set. Beyond that, the story gives an overview of the interpretations. Importantly, the author cautions us to enjoy but not judge. There is too little information to allow a conclusion at this point -- and much more information will be coming.

Coming soon. The Rosetta spacecraft will go into orbit around 67P/C-G on August 6. It will then be able to take close-up pictures. A major task is for scientists to choose a landing site for the probe. Planned landing date: November 11.

Where would you like to land?

News story: The dual personality of comet 67P/C-G. (ESA blog, July 17, 2014. The author, identified as "emily" on the page, is presumably Emily Lakdawalla, a regular and quite expert commentator on planetary science.)

Update, as posted on the day of the rendezvous: Rosetta arrives at comet destination. (ESA, August 6, 2014.) It includes pictures from August 3; spectacular!

Background posts about the Rosetta encounter with Lutetia:
* Lutetia: a primordial planetesimal? (February 13, 2012).
* Rendezvous with Lutetia (August 14, 2010).

Compare the sizes of Rosetta's targets... Lutetia, as noted most explicitly in the 2010 post, is about 100 km across. Comet 67P/C-G is less than 5 km across; see the figure and scale bar above.

More from Rosetta: The universe -- as viewed from comet 67P/Churyumov-Gerasimenko (June 19, 2018).

Another "comet"... What has six tails -- and is beyond Mars? (November 20, 2013).

More about comets:
* Who is perturbing the orbit of Halley's comet? (October 3, 2016).
* A bit of IPD -- found in Antarctica (January 13, 2015).

More about twins:
* Unusual twins: neither monozygotic nor dizygotic, but... (March 11, 2019).
* A DNA test that can distinguish identical twins (July 17, 2015).

Another odd-looking thing out there: Quiz: what is it? (April 5, 2017).

Are birds adapting to the radiation at Chernobyl?

August 3, 2014

A new article reports that birds in the region of the 1986 Chernobyl nuclear disaster are adapting to the levels of radiation now present there. The birds are adapting to levels of radiation that are still considered too high for habitation by animals (including humans). That is, the birds have effectively become resistant to the radiation. In fact, they may now benefit from the radiation.

It's a fascinating (but difficult) paper. So we want to look at what they found and what the explanation is. We also want to note the limitations of the work.

The scientists focused on certain very specific -- and quantifiable -- measures. As a framework...
- Radiation creates oxidative stress, such as reactive oxygen species (ROS).
- ROS can damage cellular molecules, including DNA.
- Cells can counteract oxidative stress by making antioxidants -- chemicals that scavenge the ROS.
- A major such antioxidant is glutathione; it is often abbreviated GSH.
- So, one thing they did was to measure the amount of GSH (in the blood).
- Further, GSH comes in two forms: GSH itself, and the oxidized form GSSG.
- The ratio of GSSG to GSH is a measure of the oxidative stress, and is one more thing they measured.

A bit of the chemistry... The SH part of "GSH" indicates that it contains a sulfhydryl group, -SH. It is this group that is sensitive to oxidation. What happens is summarized by the equation: 2 GSH --> GSSG + 2 [H]. That is, two GSH come together; the H of each GSH is removed, and the two S join. This is the oxidation. Removing hydrogen atoms is a common sign that an oxidation has occurred. The H atoms that are removed are shown here as [H] for simplicity; in the case discussed here, they would be reducing the ROS, thus inactivating them as reactive species.

What did the scientists do in this study? They measured the level of GSH in individual birds; they measured both forms, which gave them measures of the amount of antioxidant and of the level of oxidative stress. The birds were captured from various sites in the Chernobyl region; the level of background radiation at each site was measured.

The article has a lot of numbers and complex statistics. Let's just look at a few summary points, with the caution that the data has a lot of variability.

The key finding was a trend: the higher the radiation dose of the bird, the higher its level of the antioxidant GSH, and the lower the ratio of GSSG to GSH. That is, the birds with higher radiation exposure had more protection and a lower level of oxidative stress. Further, additional measurements showed they had a lower level of DNA breaks, a measure of radiation-induced damage. Overall, then, the results suggest that there is some adaptation to the radiation. In fact, the lower levels of DNA damage as well as lower measure of oxidative stress even suggest that some of the birds have turned the radiation into a benefit.

There is a cost. The effects they found were reduced in birds with certain feather pigments. Why? Because those pigments, based on pheomelanin, require GSH for their production. The birds can make pheomelanin pigments or protect their DNA -- but these two processes compete; the birds can't do both at full level. Thus there is a cost to the radiation resistance of the birds.

All of the effects discussed above are perfectly reasonable. They have been found under lab conditions. What's novel here is finding them "in the wild", making use of the aftermath of the Chernobyl disaster as the basis for an experiment in Nature.

Be cautious about interpreting the significance of this article. Let's assume that everything it says is upheld by further work. We don't know the generality. We don't even know the entire picture for these birds; we know the specific points that were measured, but we do not know the overall long term effect on the birds. Further, the work here on birds does not tell us how other organisms respond. What the article does is to provide one window into how animals respond to low doses of radiation.

News story: Chernobyl's birds are adapting to ionising radiation. (Phys.org, April 28, 2014.)

The article: Chronic exposure to low-dose radiation at Chernobyl favours adaptation to oxidative stress in birds. (I Galván et al, Functional Ecology 28:1387, December 2014.) Check Google Scholar, and you may find a preprint.

More about animals at Chernobyl: Chernobyl exclusion zone: mammal populations (October 24, 2015).

More about Chernobyl: Effect of Chernobyl exposure on the rate of new mutations in the next generation (June 1, 2021).

A recent post about radiation: Berkeley RadWatch: Radiation in the environment (February 24, 2014).

More radiation... Effect of radiation near Fukushima on local monkeys (August 10, 2014).

Another example of an oxidation giving off [H]... Photosynthesis that gave off manganese dioxide? (July 21, 2013).

More about glutathione: Huntington's disease: Is it an amino acid deficiency? (October 4, 2014).

More about oxidants, anti-oxidants, and cancer:
* How vitamin C kills cancer (December 15, 2015).
* Anti-oxidants and cancer? (October 18, 2015).

More about stress responses: How to confuse a yeast -- a sensory illusion (January 15, 2016).

A recent post about birds: The relationship between birds and dinosaurs? (July 25, 2014).

More about feathers: The whitest feathers (March 11, 2023).

More about melanin: The story of the peppered moth (July 9, 2012).

Also see: Science myths (February 23, 2016).

My page of Introductory Chemistry Internet resources includes a section on Nucleosynthesis; astrochemistry; nuclear energy; radioactivity. That section contains some resources on the effects of radiation. It also includes a list of related Musings posts.

Acne, grapevines, and Frank Zappa

August 1, 2014

A new article reports that grapevines get infected with a strain of Propionibacterium acnes, the bacterium associated with human acne. Moreover, the scientists provide some evidence that the strain infecting the grapevines is derived from the human strain.

Frank Zappa would be proud -- especially since the scientists have named the new strain Propionibacterium acnes type Zappae.

The figure shows Propionibacterium acnes in the bark of a grapevine.

Detection of P acnes is based on using a probe that is specific for its DNA. The probe is coupled to a dye that fluoresces green. Thus the green spots are evidence for P acnes.

This is Figure 1c from the article.

The scientists found P acnes in the grapevines during a general survey of the plants to see what microbes were present. They suggest that the strain is distinct, and that the bacterium is now growing intimately within the plant, and even has plant-specific adaptations. The report is quite preliminary and the evidence is thin at this point.

There is a lot to wonder about from this work. If it holds up, it would seem to be the first known case of a human pathogen adapting to a plant as its host. There is nothing at all wrong with that; it's just that there must be an interesting story here. The authors compare some gene sequences for the new strain with other known P acnes strains. This comparison, based on molecular clocks, suggests that the transfer from humans to plants was "recent" -- perhaps a few thousand years ago. That might be around the time that mankind began to cultivate grapes. That time estimate is very rough at this point, but it is intriguing.

News story: Scientists honor Frank Zappa, naming human zit-causing bacterium now infecting vineyards. (Science Daily, February 18, 2014.)

The article: Interkingdom Transfer of the Acne-Causing Agent, Propionibacterium acnes, from Human to Grapevine. (A Campisano et al, Molecular Biology and Evolution 31:1059, May 2014.)

More about acne bacteria:
* Propionibacterium acnes bacteria: good strains, bad strains? (April 1, 2013).
* A virus that could treat acne? (October 21, 2012)

More about grapevines:
* What do we learn from the sulfur isotopes in the California vineyards? (June 28, 2022).
* A half-millennium record of climate change, from the grapes of Burgundy (November 9, 2019).

July 30, 2014

Did the First Americans eat gomphothere?

July 29, 2014

A new article adds to our understanding of the large-animal fauna of early America.

The key finding is a bone, found in association with an early North American settlement. Here is the bone...

The figure at the right shows the key bone structure the scientists found.

It's a jaw. It's identified as the jaw of a gomphothere.

This is from the Phys.org news story. It is probably the same as Figure 6 in the article.

What is a gomphothere? Have a look... gomphothere [link opens in new window]. That figure is from the IBT news story; it shows models (statues) of gomphotheres.

A gomphothere is a type of elephant -- about the same size as the modern elephant (and much smaller than the mammoth).

What makes this story of particular interest is that the gomphothere was thought to be extinct in North America before the date of this settlement. That is, this is the most recent North American gomphothere identified. And it is the first example of gomphotheres being associated with North Americans.

The site studied here is in the state of Sonora, in northwestern Mexico. It is dated to about 13,390 years ago. From the dating and the tools found, it is considered a Clovis-type site. The Clovis culture, named after a town in the US state of New Mexico, was a widespread early American culture. From the way the tools were found associated with the bones, the scientists think it is likely that the humans killed the gomphotheres, probably for food.

Archeological work such as this often gets questioned. Datings and associations can both be controversial issues. For now, the finding of a gomphothere in association with a Clovis site represents a step in our