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Musings: January - April 2023 (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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   Introduction (separate page).
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2023 (January - April)
   April 26    April 19    April 12    April 5    March 29    March 22    March 15    March 8    March 1    February 22    February 15    February 8    February 1    January 25    January 18    January 11

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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 web pages. Personal reports are often the first way I find out about such a problem.

April 26, 2023

Briefly noted... Novel Fe-O compounds in the Earth's inner core?

April 26, 2023

The solid inner core of the Earth remains quite mysterious -- and inaccessible. It is at extremely high temperature and pressure. It is, we think, composed mainly of iron, with miscellaneous things dissolved in it. Oxygen is generally thought to be uncommon. New work, using lab-scale high pressure systems, suggests that novel arrangements of Fe and O may be stable under inner-core conditions. These involve layers of Fe atoms and layers of O atoms. The familiar iron oxides are all at least 50% oxygen by atom count; the novel high-pressure structures reported here are iron-rich, more like Fe₂O. The relevance to the actual inner core is open for now, but there may be more oxygen down there than we thought. In any case, the work is another example of the novelty of chemistry at ultra-high pressures.
* Earth's inner core may be oxygen-rich. (Phys.org (Center for High Pressure Science & Technology Advanced Research), December 13, 2022.)
* The article, which is open access: Iron-rich Fe-O compounds at Earth's core pressures. (Jin Liu et al, The Innovation 4:100354, January 30, 2023.)
* Added May 31, 2023. More about the inner core: Briefly noted... Rotation of Earth's inner core (May 31, 2023).
* An earlier example of high-pressure chemistry: Novel forms of sodium chloride, such as NaCl₃ (January 17, 2014).

Features of Alzheimer's disease in dolphins?

April 24, 2023

The following figure shows a brain sample tested with an antibody to amyloid-beta (Aβ), as reported in a new article...

It is quite positive. The brain sample is from a dolphin, Globicephala melas, commonly known as the long-finned pilot whale. The animal tested here was found dead, stranded on a beach. It was an old animal, though the exact age is not known.    This is Figure 1b from the article.

In humans, such deposits of Aβ are a hallmark of Alzheimer's disease (AD). Inevitably, we must ask: Did this dolphin have AD?

We don't know. AD is a type of dementia. We have no evidence about the mental state of this animal, much less any changes in it. The first encounter with it was after it died.

We can add a little more about what was reported here...

The work dealt entirely with dolphins found dead on beaches.

Several of the animals were found to have Aβ deposits in the brain.

Animals testing positive for Aβ were from three species of dolphin.

Further testing showed additional signs that are commonly associated with AD. They include signs of tau pathology.

Older animals were more likely to have Aβ deposits and other AD features than younger animals. This suggests development of AD features with age. Caution, the numbers are small.

The authors also note...

For all three dolphin species showing positive results for Aβ deposits, the amino acid sequence of their Aβ peptide is the same as for humans.

There is one major colony of captive dolphins; it is maintained by the United States Navy. The authors suggest that we consider monitoring that colony for AD.

It is tempting to speculate about whether AD might have contributed to the stranding of the dolphins, perhaps with younger animals following the lead of an afflicted elder.

It is an intriguing article. Be careful about over-interpreting it.

News stories:
* Dolphins show hallmarks of Alzheimer's disease, new study suggests. (Hafsa Khalil, CNN, December 21, 2022.)
* Dolphins may suffer from Alzheimer's disease, say researchers in Scotland -- Bottlenose dolphin, a long-finned pilot whale and a third species found to have markers of the degenerative disease. (Patrick Barkham, Guardian, December 19, 2022.)
* Stranded dolphins' brains show common signs of Alzheimer's disease. (Medical Xpress (University of Glasgow), December 19, 2022.)

* Commentary accompanying the article; it is open access: Of dolphins, humans, other long-lived animals and Alzheimer's disease (Commentary on Vacher et al.). (Guadalupe Pereyra & Paola Bovolenta, European Journal of Neuroscience 57:1180, April 2023.) A broad perspective on AD markers in animals other than humans. Recommended.
* The article, which is open access: Alzheimer's disease-like neuropathology in three species of oceanic dolphin. (Marissa C Vacher et al, European Journal of Neuroscience 57:1161, April 2023.)

The only previous post on AD in an animal other than humans: Do chimpanzees get Alzheimer's disease? (October 17, 2017).

My page for Biotechnology in the News (BITN) -- Other topics has a section on Alzheimer's disease. It includes a list of related Musings posts.

Posts about dolphins include: Do dolphins talk to each other? (November 19, 2016)

Graphene-based sensors for capturing your brain waves

April 22, 2023

If we could capture your brain waves, we could make use of them. Musings has noted work in this field [link at the end]. The field is described by terms such as brain-computer interface (BCI).

The best place to get the brain waves is in the brain. Indeed, some people have had electrodes implanted in the brain during surgery that was otherwise planned.

If we could capture brain waves from outside the head, the method would have wider applicability. However, it is difficult; the signal is much degraded.

A new article offers new developments in capturing brain waves outside the head.

The first figure shows two views of the new system...

Start with part d (bottom). The person is wearing a headband, with sensors inside the headband. At this level, this is not particularly novel. The sensors are positioned over the occipital region of the brain; the intent is to get signals based on the user's vision. Part b (top) shows a set of sensor devices. The device is largely made of silicon, with multiple contact points. Each contact is a pillar with electrically conductive graphene at the tip. The overall device is about one centimeter across. The person has about five millimeter-long hair at the region of the sensors. Hair is an issue in establishing good contact.    This is part of Figure 4 from the article.

Much of the article is about developing those graphene-tipped pillars. Current sensors typically use liquid contacts. Dry contacts would seem to have advantages, but establishing good contact, especially in scalp areas of complex curvature or in the presence of hair, is challenging.

The following table shows some data on their performance...

The test measured the sensitivity of the devices, expressed as signal-to-noise ratio (S/N). Eight individual dry-contact sensors were compared to eight traditional liquid-contact electrodes. The traditional electrodes all gave a 30 decibel S/N ratio. The new dry-contact sensors gave results from 5 dB to 25 dB.    This is Table 2 from the article.

The authors are encouraged that their best results are close to the benchmark. They think that the variation is due to differences in the specific contacts. They hope that they can develop their system further, to get consistent good results using dry-contact sensors.

Part of the story here is using the person's brain waves to control a robot. Indeed there are some results in the article. Apparently, the robot understood the instructions correctly about 94% of the time. The robot part is fun, but the science here is learning how to get good brain waves from humans.

News stories:
* Researchers Develop Non-Invasive Graphene Sensors for Brain-Machine Interfaces. (Sci.News, March 21, 2023.)
* A graphene sensor to wirelessly control robots using only brain waves. (Nanowerk News (ACS), April 3, 2023.)

The article, which is open access: Noninvasive Sensors for Brain-Machine Interfaces Based on Micropatterned Epitaxial Graphene. (Shaikh Nayeem Faisal et al, ACS Applied Nano Materials 6:5440, April 14, 2023.)

A background post on BCI: Brain-computer interface -- without invasive electrodes (December 28, 2016). Links to more.

More about brains is on my page Biotechnology in the News (BITN) -- Other topics under Brain. It includes a list of related Musings posts.

Posts about graphene and such are listed on my page Introduction to Organic and Biochemistry -- Internet resources in the section on Aromatic compounds.

April 19, 2023

Briefly noted... Soda tax: effect on obesity rate

April 19, 2023

The idea of a "soda tax" is to reduce the consumption of sugar by raising the price of popular sugar sources that people tend to over-consume. Of course, the real goal is to improve health, e.g., by reducing obesity. Musings previously noted results following a local soda tax; the article reported a small reduction in consumption. We now have an article addressing changes in the incidence of obesity in children in the UK following such a tax. The headline conclusion is that there is a small reduction is obesity in 10-year-old girls; the reduction is most pronounced in lower income areas. No effect was seen in boys. As usual, the full story is more complicated. It is perhaps best to think of this article, too, as an early step in addressing the question.
* News stories:
- UK soft drink taxes associated with decreased obesity in girls -- Study tracking childhood obesity in England from 2014-2020 found 8% reduction in obesity among 10-11 year old girls coinciding with 2018 soft drinks industry levy. (EurekAlert! (PLOS), January 26, 2023.)
- Expert reaction to study looking at the UK sugary drinks tax and obesity in children. (Science Media Centre, January 26, 2023.) Diverse views, including some skepticism.
* The article, which is open access: Associations between trajectories of obesity prevalence in English primary school children and the UK soft drinks industry levy: An interrupted time series analysis of surveillance data. (Nina T Rogers et al, PLoS Medicine 20:e1004160, January 26, 2023.)
* Background post: The Berkeley soda tax: does a "fat tax" work? (August 30, 2016).

Unequal allele expression

April 18, 2023

We have two copies of most genes, one from each parent. (The exceptions don't matter here.) One might expect that those two copies function equally -- and thus contribute equally to our phenotype.

It need not be so. The following figure, from a recent article, is a cartoon guide to some possibilities.

Caution... The article discussed here is complicated and even confusing. It is about an odd -- and confusing -- phenomenon. The main goal here is to raise the idea that the two alleles of a gene may be expressed unequally, for reasons beyond our usual views of how genes function.

Start with part C -- the expected case. There are two alleles, and they function equally. (Note the equal arrows on the two gene lines at the left.) Biallelic balanced. Look at the wavy lines to the right. Five sets of them, reflecting five different sources (tissues) in the body. Each wavy line is for one RNA transcript. For each source, there are (approximately) equal numbers of red and green lines, indicating that the two alleles are transcribed equally. (The pictures labeled "cell sample" show this another way.) The little graph at the far right illustrates this with a probability distribution. It is centered on 0.5 (for the fraction of transcripts for one allele). However, there are other possible results, shown in the other parts. Part B shows the case of a gene that has been imprinted. One allele functions, one does not. All the transcripts are "red", and the probability distribution is an extreme 100% on one side. Part D shows a case of a less complete bias, but always in the same direction. For each source, there are more green transcripts than red. The probability distribution is distinctly off to one side. Part E shows a case where there is a variable bias. More green transcripts from some sources, more red transcripts from others.    This is part of Figure 1 from the article. For part B, there is more in the full figure; I have added the label B to the portion kept here.

The article is about that last case (E), where the expression of the two alleles is unequal, and the preferred allele varies. The authors call the phenomenon random allelic expression, or RAE.

The term "random" there reflects the current state of observation. The preference for one allele functioning varies, and it seems random to us at this point. It is probably best to not interpret the term further; it is quite possible that there is a good explanation for what happens, and it is not random once understood mechanistically. I prefer the term "unequal".

The random inactivation of one X-chromosome (X-chromosome inactivation = XCI) is one way to get this result. But what about genes on the other chromosomes (the autosomes)? The current article is an extensive analysis to see what happens for other genes. The main result is that about 2,000 genes show this behavior. That is about 10% of our genes.

We might say that the current article is about RAE beyond XCI. "aRME" in the figure means autosomal random monoallelic expression.

Why does that happen? The authors suggest that one way is for genes on opposite strands to interfere with each other. The interference may vary, depending, for example, on the tissue; the variable interference could lead to variable -- and seemingly random -- expression of an allele. The following figure illustrious this, and has some data...

Part A (top) shows the idea. Two genes, coded by opposite strands of the DNA, overlap. It may be that transcription of the two genes affects each other -- and we do not understand that. (In other cases, the two genes may be very close to each other, still with some effect.) Part B (bottom) shows some data. Caution, it is a confusing figure, but we'll try to highlight the key point. The top data set is for "all tissue". There are four bars. However, one is almost invisible; there is a faint (light tan?) bar in the top row, pointing to the right.

The first two bars are marked with an x, for "no gene overlap". The top bar (nearly invisible) goes to the right, showing that genes with normal bilallelic expression are enriched in the no-overlap set of genes. In contrast, the next bar shows that genes with RAE are depleted in the no-overlap set. The next two bars (for all tissue) have a check mark, for "gene overlap". The results are just the opposite. For example, the lower, RAE, bar goes to the right, showing enrichment. That is, genes that overlap are more likely to show RAE. The other two data sets here separate the "all tissue" data into "body" and "brain". The qualitative pattern is similar. (There are some quantitative differences.)    This is part of Figure 5 from the article.

The figure is confusing, but the point is that it begins to show that there may be identifiable explanations for why some genes are expressed more from one allele than the other.

There seems to be some controversy about some of this work. It is difficult work. But the disagreement is probably more about details than the big idea: there are genes, perhaps many genes, whose expression from the two alleles is different. That can have implications for disease and treatment. Further attention will likely focus on improving the understanding of individual cases.

News story: Random Allelic Expression of Genes Could Complicate Disease, Diagnosis. (University of Utah, February 13, 2023.)

The article, which is open access: Random allelic expression in the adult human body. (Stephanie N Kravitz et al, Cell Reports 42:111945, January 31, 2023.)

A recent post about X-chromosome inactivation: X-chromosome inactivation in males -- in cancer (February 6, 2023).

A post about imprinting of chromosomes to indicate which parent they came from... Children with two fathers (January 3, 2011).

Can we distinguish monkey tools and human tools?

April 17, 2023

Look at the rock flakes in the following set of photos, from a new article...

The flakes on the right (part N) are artifacts found with ancient hominin fossils. They are usually taken as evidence for intentional tool production by the ancients of our human lineage, dating as far back as 3.3 million years.

The flakes on the left (L & M) were made by macaque monkeys using stones to break open food sources (e.g., nuts, shellfish). The flakes formed during the stone use. The scientists observed the whole process, and also collected flakes that had accumulated in the surrounding environment.

The monkey-flakes are clearly unintentional. Doesn't that undermine the interpretation that the flakes associated with human (hominin) fossil remains reflect intentional tool production?

Be careful to distinguish tool use and tool production. The monkeys are using stone tools -- intentionally. But tool production is presumed to be more sophisticated, and to require a higher level of brain development.

That's the essence of the article. It weakens one kind of evidence for tool production by ancient humans.

There are some subtle differences between flakes from the two sources. Further work may show whether it is possible to distinguish flakes made intentionally vs unintentionally.

News stories:
* Macaques challenge the origin of tool invention. (Sukanya Charuchandra, Advanced Science News, April 4, 2023.)
* Surprising similarities in stone tools of early humans and monkeys. (Phys.org (Max Planck Society), March 10, 2023.)

Movies. There are seven movie files posted along with the article as Supplementary Material. They are provided together as a single zip file. Movie #1 shows the monkeys using stones to break open nuts (one minute; no narration, but well-labeled). The others show flakes, in various detail.

The article, which is open access: Wild macaques challenge the origin of intentional tool production. (Tomos Proffitt et al, Science Advances 9:eade8159, March 10, 2023.)

More stones:
* Do monkeys make stone tools? (December 18, 2016). Links to more.
* Sliced meat: implications for size of human mouth and brain? (March 23, 2016).

The importance of choline as a dietary nutrient

April 15, 2023

Choline is an essential nutrient. It is used to make the neurotransmitter acetylcholine; it is also a component of biological membranes. Humans can make choline, but not at sufficient levels. Choline is common in foods; perhaps as a result, we usually don't pay much attention to it.

A recent article focuses on what happens in choline deficiency. The main tool is a pair of mouse diets, one with a normal level of choline and one lacking choline. Some tests are done using ordinary mice, but some are done with a mouse strain considered a model for Alzheimer's disease (AD).

The following figure shows the growth of the two kinds of mice with and without choline...

The two black curves are for ordinary mice ("NonTg") with and without choline: solid line (ChN) and dotted line (Ch-), respectively. The two red curves are for the AD-model mice, labeled "3x Tg-AD". (Tg-AD means transgenic for AD.) With and without choline, as above. For each type of mouse, the mice are bigger with the choline deficiency (dotted line). For the Tg-AD mice, much bigger. The solid black line (normal mice, normal diet) is taken as normal; choline deficiency leads to obesity.    This is Figure 2a from the article.

The next figure shows the results of a test for physical agility (motor function).

The y-axis is labeled "latency to fall". In plain English, how long can a mouse hold on (to a spinning rod) before falling? High numbers are good. The two bars at the left are for the normal mice (nonTg), with and without choline. By any measure, the mice with normal choline (ChN) did better. (Look at the medians, the boxes, or the high tails.) The two bars at the right are for the AD-model mice. The pattern is about the same; the overall results are a bit worse than for the normal mice.    This is Figure 1d from the article.

There is much more in the article. The big picture is that choline deficiency can have diverse and serious consequences. Aside from the consequences for normal mice, it can also make Alzheimer's disease worse. (A reminder... the AD-mice are a disease model, and sometimes not a very good one.)

This is not entirely new information. However, the importance of choline is often neglected, since it is widely found in food. Of course, that varies. The article serves to bring choline to our attention. Its relevance to AD is particularly important.

The authors note that 90% of Americans do not consume the recommended levels of choline. We also note that there is little basis for those current recommendations. And as a little bonus, excess choline may be bad for you. The choline story is quite incomplete.

News stories:
* The essential nutrient that nobody has heard of -- If you lack the nutrient choline, you may get liver disease. And your risk of getting Alzheimer's or cardiovascular diseases may increase. (Ingrid Spilde, Science Norway, January 25, 2023.) General; it notes the current article. Includes the chemical structure of choline at the top.
* Study explores effects of dietary choline deficiency on neurologic and system-wide health -- Reaching adequate dietary choline intake is critical to offset organ pathologies and may help protect the brain against Alzheimer's disease. (EurekAlert! (Arizona State University), January 17, 2023.)

The article, which is open access: Dietary choline intake is necessary to prevent systems-wide organ pathology and reduce Alzheimer's disease hallmarks. (Nikhil Dave et al, Aging Cell 22:e13775, February 2023.)

A post about one of the best known forms of choline... A bio-marker for SIDS? (June 27, 2022).

An earlier post about TMA and TMAO: Red meat and heart disease: carnitine, your gut bacteria, and TMAO (May 21, 2013). These products can arise from choline, and also from carnitine, as discussed in this earlier post. (They may be the reasons why excess choline is bad for you.)

My page Internet resources: Biology - Miscellaneous contains a section on Nutrition; food and drug safety. It includes a list of related Musings posts.

My page for Biotechnology in the News (BITN) -- Other topics has a section on Alzheimer's disease. It includes a list of related Musings posts.

April 12, 2023

Briefly noted... Neurons at play

April 12, 2023

Remember Pong? A recent article reports that lab cultures of neurons can learn to play Pong, in minutes. Both mouse and human cells can do it (though the human neurons do better). It is a fascinating and complex story. The authors provocatively suggest that the cultures are sentient (see the title of the article); they go on to explain what they mean by that. Regardless of the hype, the work introduces an experimental system, DishBrain, that is likely to be useful. The key point is that an isolated system of neurons does things, gets feedback, and adapts (learns?).
* News stories:
- Watch Live Human Brain Cells in a Dish Learn To Play Pong. (SciTechDaily (Cortical Labs), October 12, 2022.)
- Human brain cells in a dish learn to play Pong in real time. (Science Daily (Cell Press), October 12, 2022.)
- Human Brain Cells in a Dish Learn to Play "Pong". (GEN, October 13, 2022.)
* The article, which is open access: In vitro neurons learn and exhibit sentience when embodied in a simulated game-world. (Brett J Kagan et al, Neuron 110:3952, December 7, 2022.) The lead institution is Cortical Labs (Melbourne, Australia).
* My page for Biotechnology in the News (BITN) -- Other topics includes a section on Brain. It includes a list of brain-related posts.

The sounds that plants make

April 10, 2023

A new article reports that plants make sounds when stressed.

How do you know a plant has made a sound? Just listen. Put your ear by the plant. Or use a microphone.

The basic apparatus used by the scientists in the new article. (They were also able to record sounds in an ordinary greenhouse, with ambient noise.)    This is Figure 1A from the article.

Actually, using a microphone is important. The following figure shows the frequency spectrum of sounds from two kinds of plants with two kinds of stresses...

In each case, the peak sound is at 40,000 to 60,000 Hertz (Hz). (The highest frequency people can hear is usually taken as about 20,000 Hz. Human ears won't work well here.)    This is Figure 1D from the article.

What's the connection to stress? The plants only make the sounds when stressed. Cutting stems or stopping normal watering were the two stresses studied. They are the two stresses used in the previous figure. (There is no unstressed control shown in this figure.)

The following figure shows an example of the response to stress...

The figure shows number of sounds made per day (y-axis) vs days without water (x-axis). The sounds increased steadily as water was withheld, at least for the first few days.    This is Figure 3A from the article.

Are these just random sounds?

Look...

The graph shows the frequency of sounds during the course of four days without water (tomato plants). That's the black curve (y-axis at left). The red curve shows the transpiration rate (y-axis at right). Looks like there is some connection between the timing of the two activities, but it is not simple.    This is Figure 4A from the article.

Is anyone listening? A few scientists have started listening, and they are intrigued. Beyond that, this is an open question for now.

In addition to studying the natural role of plant sounds, we might also wonder about how we might make use of those sounds. For example, perhaps a farmer could improve crop watering by waiting until the plants ask for water.

It is an intriguing article, even provocative. As so often, time will tell.

News story: Stressed plants emit airborne sounds that can be detected from more than a meter away. (Phys.org (Cell Press), March 30, 2023.)

The article, which is open access: Sounds emitted by plants under stress are airborne and informative. (Itzhak Khait et al, Cell 186:1328, March 30, 2023.)

Also see:
* Electronic monitoring of plant health; it might even allow an injured plant to call a doctor (June 21, 2020).
* What should a plant do if it hears bees coming? (December 10, 2019). From the same lab.
* Inter-plant communication via the Cuscuta parasite (September 15, 2017).
* Can a plant learn to associate a cue and a reward? (March 3, 2017).

Is erythritol a toxic sweetener?

April 8, 2023

Erythritol is used as a sweetener in some food products. A new article suggests its safety should be examined more carefully.

The following figure shows the first set of evidence that got the scientists' attention. It involved looking at the medical records of a group of people already at risk of heart disease. (That is, it is not a random sample of the population. Further. the work is not a controlled trial.)

The next figure explores the effect of erythritol on blood...

The first figure suggests a connection between high erythritol levels and heart disease. The second figure suggests a possible mechanism.

It is important to stress that the work here is suggestive but does not offer proof. The first figure shows a correlation, but is not a controlled trial. Although adjustment was made for some variables thought to be relevant, there is no assurance that proper adjustment is complete. The second figure shows what the chemical might do, but does not actually link it to disease.

What an article such as this does is to focus attention on this chemical, so that further, more definitive work can be done.

News stories:
* Zero-calorie sweetener linked to heart attack and stroke, study finds. (Sandee LaMotte, CNN, February 27, 2023.)
* Cleveland Clinic Study Finds Common Artificial Sweetener Linked to Higher Rates of Heart Attack and Stroke Research showcases the need for further safety studies. (Cleveland Clinic, February 27, 2023.)

* News story accompanying the article: Cardiovascular diseases: Non-nutritional sweeteners and cardiovascular risk -- The widely used artificial sweetener erythritol affects platelet function and is associated with major cardiovascular events - fuelling calls for a re-evaluation of the use and regulation of non-nutritive sweeteners. (Konstantinos D Rizas et al, Nature Medicine 29:539, March 2023.)
* The article: The artificial sweetener erythritol and cardiovascular event risk. (Marco Witkowski et al, Nature Medicine 29:710, March 2023.)

Previous posts on erythritol: none.

Among posts about added sweeteners:
* What should a plant do if it hears bees coming? (December 10, 2019).
* Artificial sweeteners: Saccharin and high blood sugar levels (December 7, 2014). Links to more.

Added May 9, 2023. More on blood clotting... Why bears don't get blood clots during hibernation (May 9, 2023).

April 5, 2023

Briefly noted... The Jerry Brown beetle

April 5, 2023

Bembidion brownorum (male). This is reduced from Figure 1 of the article; the figure there is a full page. Actual length of the animal is about 5 millimeters. Musings has noted organisms named after US Presidents. We now have one named after our former California Governor Jerry Brown. The connection between the beetle and the Governor? The re-discovery of the beetle occurred on the Governor's ranch.

* News story: Rare beetle, rediscovered after 55 years, named in honor of Jerry Brown. (Kara Manke, University of California - Berkeley, March 27, 2023.) * The article, which is open access: Re-collected after 55 years: a new species of Bembidion (Coleoptera, Carabidae) from California. (David R Maddison et al, ZooKeys 1156:87, March 27, 2023.) * Also see: Briefly noted... The Biden octopus (March 22, 2022).

Capturing CO₂ in concrete

April 4, 2023

The production of concrete is a significant contributor to CO₂ emissions.

A new article explores one approach to storing CO₂ in concrete. If some such process could be shown to work, it would help to mitigate the CO₂ emissions associated with making it.

Here are some results, from lab-scale work on making concrete with variations intended to promote incorporation of CO₂...

The figure shows two measures of the strength of the concrete, as it develops ("cures") over time (x-axis). The strength measures are shown on the y-axis, one per graph. The test involves using various amounts of an additive. Start with the top graph. The black line is for the control, with no additive. At early times, the additive actually leads to stronger concrete. By the end, the control concrete is the strongest -- but not by much. The results are similar for the second graph.    This is Figure 1A from the article.

That's the main point. The scientists have a way to make good concrete with a much reduced greenhouse gas contribution, by incorporating CO₂ into it. We can quibble about the details, but if we take this as step 1, it is encouraging. The authors consider the work here a model system.

What did they do? The additive was sodium bicarbonate, a solid form of CO₂. In the alkaline conditions of newly formed concrete, CaCO₃ forms.

A key point is adding the CO₂ (here, as bicarbonate) early; previous work had shown that adding such things to concrete that had largely cured led to loss of strength. But adding it early seems to work reasonably well. Curing is actually accelerated a bit; importantly, the quality of the final concrete is very similar to current concrete, based on the measurements so far. The article includes characterization of how the added CO₂ is incorporated. The system can be developed further.

The authors refer to the process as forced carbonation. This refers to the CO₂ (or bicarbonate) being added, rather than simply absorbed from, say, the air.

You'll encounter some unusual abbreviations in the article. The C-S-H in the article title means calcium-silicate-hydrate. A key ingredient is described as C₃S; that is alite: (CaO)₃SiO₂.

News stories:
* MIT Researchers Develop New Additives For "Green" Concrete -- Researchers at MIT are discovering new ways of making concrete that will release less carbon dioxide in the atmosphere. (Steve Hanley, CleanTechnica, March 29, 2023.) This story is largely based on the MIT press release (below), but also includes some notes about ancient Roman concrete.
* New additives could turn concrete into an effective carbon sink -- MIT engineers discover new carbonation pathways for creating more environmentally friendly concrete. (David L Chandler, MIT, March 28, 2023.)

The article, which is open access: Cementing CO₂ into C-S-H: A step toward concrete carbon neutrality. (Damian Stefaniuk et al, PNAS Nexus 2:pgad052, March 2023.)

A post that alludes to the environmental costs of concrete: Building with wood: might it replace steel and concrete? (June 14, 2017)

Among other posts about concrete: Using the walls of a building as a rechargeable battery? (May 24, 2021).

Briefly noted... Extracting rare earth elements from coal fly ash: use of various supercritical solvents

April 1, 2023

Coal ashes contain lots of metals, including low levels of the rare earth elements (REE). A new article reports studies of extraction of the REE, using supercritical fluids instead of organic solvents. In one test, the scientists started with coal fly ash that contained 0.0234% total REE, and obtained a product with 6.47% REE. That is a 276-fold enrichment -- with a product that is amenable to traditional chemistry. The authors tried supercritical nitrogen and air, as well as the more common CO₂; the alternatives aren't quite as good, but they do have process advantages, and may be worth exploring further.
* News story: Novel process extracts rare earth elements from waste. (Tech Xplore (Beth Miller, Washington University in St Louis), March 24, 2023.)
* The article, which is open access: Supercritical carbon dioxide/nitrogen/air extraction with multistage stripping enables selective recovery of rare earth elements from coal fly ashes. (Yaguang Zhu et al, RSC Sustainability 1:251, March 2023.)
* Background post: Coal: a new source of rare earth elements? (April 6, 2016).
* Fly ash? It is the unburned solid material that would exit with the exhaust gases. It is now collected. See Wikipedia: Fly ash.
* Added February 26, 2024. This post is listed on my page Introductory Chemistry Internet resources in the section Lanthanoids and actinoids.

March 29, 2023

Recycling poly(vinyl chloride)

March 28, 2023

PVC [poly(vinyl chloride)] is a major type of plastic. It is probably the least recycled of any major plastic. (Recycling of PVC in the US is usually taken as zero.)

Why is PVC not recycled? For one thing, it tends to give off HCl during many kinds of processing.

A recent article takes a fresh look at the PVC problem. The scientists start by trying to make use of that HCl.

The following figure tells much of the story...

Overall, the article shows that the Cl in PVC can be put to good use. The additive in the PVC is useful, too, in making the reaction work. (There are complications on that point.) And what's left after using the Cl is closer to being a simple hydrocarbon polymer, which is easier to deal with.

The authors do not claim that they have a practical process here. What they claim is a novel way of looking at the problem, with some promising results.

News story: U-M team recycles previously unrecyclable plastic. (Morgan Sherburne, University of Michigan, November 30, 2022.)

The article: Using waste poly(vinyl chloride) to synthesize chloroarenes by plasticizer-mediated electro(de)chlorination. (Danielle E Fagnani et al, Nature Chemistry 15:222, February 2023.)

Previous posts about PVC: none.

A general post on plastics, with links to much more: History of plastic -- by the numbers (October 23, 2017).

Using microneedles for drug delivery

March 25, 2023

Microneedle patches allow the delivery of materials (e.g., drugs, vaccines, nutrients) through a surface. Musings has noted developments in this field [link at the end].

A recent article reports a new type of application. The following figure shows some results...

The general conclusion is that the microneedle patch gave good results. All variations of the treatment, including the simplest, gave similar results.

What about side effects? It is well known that plants respond to wounding with a damage-control response. The following figure gives an idea what happened in this case...

Caution... This graph is not very clear. We show it mainly to give an idea how the scientists looked at the issue. The graph shows a measure of the wounding response (y-axis) for several cases. What is measured is the level of gene expression for a group of genes known to be involved in the wounding response. That is expressed as a ratio compared to untreated. Since the ratio is shown on a log scale, the "ideal" value is zero.

Observations... * The first two data sets are for the needle-patch treatment, at 3 and 24 hours. There is some effect, but it is significantly reduced by 24 hours. * The third set is for the mock treatment (needles, no hormone) at 24 hours. The response is similar to the treated plants at 3 hr. That might suggest that the hormone is in fact mitigating damage.    This is Figure 2c from the article.

The general conclusion of the authors from experiments such as this is that damage due to the microneedle treatment is not a big concern.

The general point of the article is to open the door to the use of microneedle patches in agriculture. Among the features of the approach is that the payload is delivered directly into the plant, minimizing the wastage that typically accompanies other modes of application.

The article includes some testing with a variety of crop plants, including both monocots and dicots. The method seems to be widely applicable.

News stories:
* Researchers unveil "world's first microneedle" plant drug delivery system to tackle crop disease. (Food Ingredients First, March 14, 2023.)
* [Press Release] SMART researchers develop the world's first microneedle-based drug delivery technique for plants. (EurekAlert! (SMART = Singapore-MIT Alliance for Research and Technology), March 14, 2023.)

The article, which is open access: Drug Delivery in Plants Using Silk Microneedles. (Yunteng Cao et al, Advanced Materials 35:2205794, January 12, 2023.)

Background post about the use of microneedles: Treating a heart attack using a microneedle patch (January 11, 2019). Links to more.

Among posts about using Arabidopsis... Cauliflower math (July 26, 2021). Links to more.

March 22, 2023

Superconductivity near room temperature: let's try again, now using lutetium

March 21, 2023

In 2020 Musings noted the announcement that scientists had finally achieved the long-sought goal of superconductivity near room temperature (T). Two years later the article behind that post was retracted. The inability of others to reproduce the key findings was central to the journal making the retraction, over the objections of the authors.

We now have two new developments. Both follow the trend of studying high T superconductivity using hydrides.

First, there is a new article reporting superconductivity at room T in a new chemical. The previous report was with hydrides of sulfur, with some carbon. The current work, from the same team, is with hydrides of lutetium, doped with nitrogen. The results are actually better than in the previous work: superconductivity occurs at higher temperature than before, and also at a lower pressure.

Further, as we write this, we also learn that an updated article on the topic of the retracted article has been submitted, and is currently under review. More data, including some from other labs. (The preprint, not yet peer reviewed, is posted at ArXiv. There is a link below, with the background post.)

We included some data last time. Now, let's just enjoy the saga. This is a story of science in progress, in a very difficult field. We are already hearing caution from those in the field. Scientific stories develop over time, as people repeat and extend what has already been reported. Recognizing what the key breakthroughs were may only be clear in hindsight.

What we can say is that we have two new reports extending the story of superconductivity near room temperature. Our previous post on the topic turned out to be premature. We'll see how the new reports (including one that has not yet been peer-reviewed) turn out.

News stories:
* Evidence for 'near-ambient' superconductivity found in lutetium hydride. (Michael Banks, Physics World, March 8, 2023.)
* Muted Response to New Claim of a Room-Temperature Superconductor -- A research team says that they have made a material that conducts electricity without resistance at near-ambient conditions. The community has heard it before. (Sophia Chen, Physics 16:39, March 9, 2023.)

The two news stories listed above are from highly respected sources specializing in physics.

As always, you can find more news stories by using the article title (below) as a search term. In this case, I found that stories from generally reasonable sources had significant errors, perhaps propagating misunderstandings. Looking at a range of stories can be good, providing different perspectives. Just be careful -- as always.

* News story accompanying the article: Condensed-matter physics: Hopes raised for ambient superconductors -- A hydrogen-rich compound has taken the lead in the race for a material that can conduct electricity with zero resistance at room temperature and ambient pressure - the conditions required for many technological applications. (ChangQing Jin & David Ceperley, Nature 615:221, March 9, 2023.)
* The article: Evidence of near-ambient superconductivity in a N-doped lutetium hydride. (Nathan Dasenbrock-Gammon et al, Nature 615:244, March 9, 2023.)

Background post about superconductivity at room temperature: Superconductivity at room temperature -- at last (October 18, 2020). As noted there (and above), the article behind that post has been retracted. A new version of the article has been submitted, and is currently freely available as a preprint (prior to peer review): Observation of Conventional Near Room Temperature Superconductivity in Carbonaceous Sulfur Hydride. (Hiranya Pasan et al, ArXiv, February 22, 2023.) I have added this new article (preprint) to the original post.

Previous posts about lutetium: none.

Added February 26, 2024. This post is listed on my page Introductory Chemistry Internet resources in the section Lanthanoids and actinoids.

Graphullerene

March 20, 2023

Another new form of carbon. Graphullerene, reported in a recent article. The name is a combination of graphene and fullerene.

Look...

The three structures are: fullerene (a), graphene (b), and graphullerene (c). (The structures show the arrangement of the atoms, but omit double bonds.) Fullerene is a ball-shaped molecule ("bucky-ball"). Graphene is a two-dimensional (2D) sheet of carbon atoms. You can think of graphullerene as a 2D sheet of fullerenes. Note that there are two kinds of bonding between the fullerene units. The horizontal and vertical connections between fullerenes are different. (You can see this best by looking at the middle fullerene, which is fully surrounded (in 2D) by fullerenes.)    This is Figure 1 from the article.

That's a new chemical structure.

What did the scientists make it from? This stuff...

The left-hand view looks much like the graphullerene -- except for the green dots. Those green dots are magnesium (Mg) atoms. The right-hand view shows that this chemical occurs as a stack of such layers. The authors give the formula as (Mg4C60)∞. (Yes, they write the formula with an infinity sign.)    This is Figure 2c from the article.

Take that, dissolve away the Mg with a little acid, and you get graphullerene.

To fill out that story a little... The product is a multi-layer structure, which they call graphullerite, by analogy to graphite. They can mechanically pull off thinner samples, just as graphene is made from graphite by exfoliation. They have made material as thin as bilayer.

Properties? Here is an example...

Caution... This is a complex figure. However, there is one key point, which is quite simple. The graph shows the thermal conductivity of materials (y-axis; log scale) vs temperature (x-axis). Look at 300 K. Two isolated points (not part of any line) with open triangle symbols. The upper one is for graphullerene (more precisely, graphullerite), (C60)∞; the lower one is for fullerene, C60. The thermal conductivity of fullerene is increased by about a factor of 10 by joining the balls together to make graphullerene. That's interesting. Those two points are the only experimental data on the graph.

What about the sets of points (lines)? They show predictions of the thermal conductivity of graphullerene. Why three lines? For the three directions across the structure. Lines b and c are for the two different directions in the plane of the graphullerene structure; these give the two lines with predicted high thermal conductivity, at the top. Line a is for the direction through a small stack of such planes (graphullerite). The single measured value is in the range of the predictions.    This is Figure 5b from the article.

Another form of elemental carbon. And at least a hint of interesting properties.

This could be the first in a new class of chemicals. There are various kinds of fullerenes, and various ways one might connect them. Further, one can make modified fullerenes, and thus get modified graphullerenes. They would not be forms of elemental C, but they would be novel chemicals.

News stories:
* Graphene-Like Sheet Made from Fullerenes. (Chemistry Views, January 12, 2023.) The top picture gives a good idea of the structure of one layer of graphullerene. Note the different horizontal and vertical layouts.
* Newly discovered form of carbon is graphene's 'superatomic' cousin. (Phys.org (Ellen Neff, Columbia University), January 5, 2023.) Includes a cute picture; note the name on the shirt.

The article: A few-layer covalent network of fullerenes. (Elena Meirzadeh et al, Nature 613:71, January 5, 2023.)

A recent post about carbon: A new form of carbon -- hard enough to scratch diamond (March 1, 2022). Links to more.

Posts about fullerenes include: Y-Y: the first (May 5, 2019).

Posts about graphene and such are listed on my page Introduction to Organic and Biochemistry -- Internet resources in the section on Aromatic compounds.

Briefly noted... A pathway to renewable acrylate

March 18, 2023

Acrylates are an important type of plastic -- derived from petroleum. Would it be possible to make them from biomass? In fact, the basic monomer unit, acrylic acid, is just a single step from the common biochemical lactic acid. On paper. It's hard to do, because of competing reactions. A recent article reports progress on making acrylic acid from lactic acid (or the simple derivative methyl lactate). Catalyst development is a key part of the work.
* News stories:
- Chemical researchers discover catalyst to make renewable paints, coatings, and diapers. (Nanowerk News (University of Minnesota), January 9, 2023.)
- Can We Sustainably Manufacture Acrylic Acid? (Samudrapom Dam, AZo Materials, January 25, 2023.) Among the "Related Stories" listed there is one with the title "Catalyzing the Sustainable Production of Acrylic Acid ..."; it is an interview with one of the authors of the article.
* The article, which is open access: Multifunctional Amine Modifiers for Selective Dehydration of Methyl Lactate to Acrylates. (Yutong Pang et al, JACS Au 3:368, February 27, 2023.)
* Related: A "greener" way to make acrylonitrile? (January 6, 2018).

March 15, 2023

Ultra-fast PCR

March 14, 2023

Here are some results from a PCR (polymerase chain reaction) run, as reported in a recent article...

The big idea here is that the scientists have developed a version of PCR that is about 10 times faster than conventional PCR. All the PCR logic is the same, and the quality of results seems similar. It is just faster.

How did they do this? By heating with a laser, using materials that absorb light and give off heat. The idea is not new; making it practical in this context is.

The photothermal material here is based on graphene, and allows heating and cooling at rates above 20 °C per second. The PCR reaction materials are embedded in a hydrogel matrix, with a reaction volume of about 100 nanoliters (0.1 microliters). Multiple PCR tests can be run together.

Is this ready to go? Apparently not quite. The authors say they need another year or so of development work to make a convenient commercial version of ultra-fast PCR.

News story: This PCR Covid-19 test takes only 5 minutes: KIST. (Lee Han-soo, Korea Biomedical Review, January 6, 2023.) There is actually nothing in the current article about Covid; otherwise, the story itself here is fine.

The article, which is open access: Ultrafast Real-Time PCR in Photothermal Microparticles. (Bong Kyun Kim et al, ACS Nano 16:20533, December 27, 2022.)

Posts that mention PCR include...
* Targeted degradation of the viral genome as a treatment for COVID? (March 13, 2022). A post about an article that includes a conventional use of PCR to measure the level of a viral genome.
* An easier way to tell if a mosquito carries Zika virus? (June 2, 2018). A post about an article that claims an assay 20 times faster than PCR -- but that assay is unrelated to PCR.
* Science: breakthrough of the year (January 4, 2010). History; see the note at the end.

A perspective on POC... POCDx -- What's the barrier? (January 29, 2013). POC stands for point-of-care. Dx, in the title, stands for diagnostics. The current article can be thought of as moving PCR toward POC use.

Posts about graphene and such are listed on my page Introduction to Organic and Biochemistry -- Internet resources in the section on Aromatic compounds.

The whitest feathers

March 11, 2023

We have talked about white paint before [link at the end]. Now, white feathers.

The following figure tells the story...

The birds may communicate their presence by the white feather tips. These birds are most active at times of dim light (dawn and dusk). The highly reflective feather tips may well be an adaptation to promote communication in dim light. The location and limited scope of the white regions also allow the birds to remain concealed as they sleep during the day. However, there is little actual information on the matter. (The two birds shown above are a female on the ground and a male in the air.)

How is such high reflectance achieved? The authors went on to explore that, largely through electron microscopy analysis of the feather structure. The feather tips are interesting structures, with these very bright tips, yet consistent with the generally camouflaged nature of the bird.

News stories:
* The Whitest Feathers of Any Bird Have Been Found, And They're Dazzling. (Felicity Nelson, Science Alert, March 7, 2023.)
* European woodcocks have the brightest feathers known to exist. (Josh Davis, Natural History Museum (London), March 1, 2023.) The Museum was one of the institutions involved in the work.
* Woodcocks have the brightest white feathers ever measured. (EurekAlert! (Imperial College London), March 1, 2023.)

The article, which is open access: How woodcocks produce the most brilliant white plumage patches among the birds. (Jamie Dunning et al, Journal of The Royal Society Interface 20:20220920, March 2023.)

Background post about white paint: A lightweight white paint (January 23, 2023). Links to more.

Previous post about feathers -- and their color... Are birds adapting to the radiation at Chernobyl? (August 3, 2014).

March 8, 2023

How to make yourself more transparent while you sleep

March 7, 2023

Here is the phenomenon...

Start at the bottom. The bottom leaf has a little frog on it. An ordinary frog. The first two pictures also have frogs on them, about the same size, but a different (but closely related) kind. The (two) frogs in the top picture are sleeping; the frog in the second picture is active ("exercised"). It is much easier to see the active frog. That is, when sleeping, this kind of frog is hard to see; it is largely transparent. Such frogs are known as glassfrogs. (Yes, that is one word.) How they execute this camouflage has long been of interest. It clearly involves multiple steps. The glassfrogs here are Hyalinobatrachium fleischmanni. The frogs can be as small as 2 cm long.    This is part of Figure 1A from the article.

A recent article reveals one step in how glassfrogs become transparent. They hide their blood cells -- in the liver.

The following pair of images provides some of the evidence...

There are more tests reported in the article to reinforce that interpretation.

From the top figure, it is reasonable that becoming transparent is a survival tactic, a type of camouflage. The current work reveals part of how it works.

Making such measurements is not easy. The whole point is that the measurements must be made on undisturbed sleeping frogs. The work uses an unusual imaging technique, called photoacoustic microscopy (PAM). In this technique, a light signal is converted to sound by the analyte.

In vertebrates, high concentrations of blood cells can have serious consequences. How do the frogs avoid that? An interesting question, with possible implications for human cardiovascular health.

News stories:
* Study: Glassfrogs Hide Red Blood Cells in Their Liver to Achieve Transparency. (Sci.News, December 28, 2022.)
* Glassfrogs Hide Red Blood Cells in Their Liver to Become Transparent -- Researchers finally decipher how a species of frog becomes a master of camouflage with the help of modern biomedical imaging techniques. (Michaela Kane, Duke University, December 27, 2022.)

The article: Glassfrogs conceal blood in their liver to maintain transparency. (Carlos Taboada et al, Science 378:1315, December 23, 2022.)

There are five movie files posted with the article. (Available there as a single zip file.) The first two are perhaps the best, with good pictures and some good action. (About one minute each; no sound, but reasonably labeled.)

Among other posts about frogs...
* Does the frog population affect the incidence of malaria? (October 17, 2022)
* Designing reconfigurable organisms (January 19, 2020).
* The smallest frog (January 31, 2012).

A recent post about transparency in an animal: Evidence for a REM stage of "sleep" in spiders? (October 11, 2022).

Among other posts about transparency...
* Transparent wood (March 6, 2021).
* Transparency of clinical trials -- Is the flu drug Tamiflu worthless? (May 4, 2014).
* Transparent soil (October 13, 2012).

Keanu Reeves and a broad-spectrum fungicide

March 6, 2023

Yes, there is a joke in there. But there is a good science story, too, and that will be our main focus.

The following figure shows some results for a fungal infection, as reported in a recent article...

Three leaves were infected with small blocks of fungus (Botrytis cinerea) at day 0; the light circles show the infection sites. Two leaves were then treated with a solution of a new anti-fungal agent. A "control" leaf was not treated. The leaves were examined at days 3 and 5 dpi (days post infection). The dark area around the fungal inoculum shows the damage caused by the infection. See the control (at the left). Both treatment solutions reduced the damage; "Sup 2" (at the right) did so almost completely.    This is Figure 4A from the article.

What is this new anti-fungal agent? It is keanumycin A, one of a group of closely related chemicals reported in the new article.

Here is keanumycin C...

It is a lipopeptide. It has a hydrophobic tail at the upper left. The rest is basically a small peptide -- a nonribosomal peptide, made by a series of enzymes that add specific amino acids. Such enzyme-directed synthesis (rather than mRNA-directed on ribosomes) allows for unusual subunits. In fact, both the lipid and amino acid parts of the keanumycins include some unusual features. The red shows distinctive features of keanumycin C. I chose to show keanumycin C here, because it is the clearest structure shown in the article.    This is part of Figure 1A from the article.

The test shown in the top figure is with a fungus that is a serious plant pathogen of economic importance. Further testing showed that the keanumycins are active against a wide range of fungi, including some important human pathogens. There is some evidence suggesting they are of low toxicity. There is enough here to warrant further study of the keanumycins.

How did the scientists find these novel agents? It's a complex and clever story. The authors were working with Pseudomonas bacteria, and found that they killed amoebae. This finding led them to explore the bacterial genome, where they found genes that could lead to the type of product discussed here. Getting from amoebae to fungi, with low toxicity to plants and animals, is not a simple jump, but that is what the data suggest at this point. We'll see.

How do these agents act? Probably at the level of the membrane. That leaves open why they affect diverse fungi, but not all, and why they seem to have little effect on other organisms.

Why did they name these new broad-spectrum anti-fungal agents after Keanu Reeves? I'll let you discover that for yourself. It is the last sentence of the Introduction in the article. (It is also noted in the news story, but better to get the story from the scientific article.)

News story: Keanu Reeves, the molecule: New active ingredient from bacteria could protect plants. (Phys.org (Ronja Münch, Leibniz Institute for Natural Product Research and Infection Biology), February 6, 2023.)

The article, which is open access: Ecological Niche-Inspired Genome Mining Leads to the Discovery of Crop-Protecting Nonribosomal Lipopeptides Featuring a Transient Amino Acid Building Block. (Sebastian Götze et al, Journal of the American Chemical Society 145:2342, February 1, 2023.)

Posts about fungicides include:
* What do we learn from the sulfur isotopes in the California vineyards? (June 28, 2022).
* Largest field trials yet... Neonicotinoid pesticides may harm bees -- except in Germany; role of fungicide (August 20, 2017).

A perennial rice

March 4, 2023

Rice is an "annual" crop; it must be planted anew for each season. Scientists have now developed a perennial rice, which will re-grow after harvest. Trials of the perennial rice are reported in a new article.

The following figure shows the harvests from traditional annual rice and the new perennial rice over a five year period...

The harvests are shown in Mg/ha (megagrams per hectare). The x-axis time scale shows two harvests per year; F and S refer to first and second harvest of the year. (The second season is cooler, and gives lower yields.) Each point is for one test site. Big picture... - For the perennial rice (red), yields are similar over most of the time shown. There was only a single planting for each site, with twice-yearly harvest. - Yields are mostly similar for the perennial rice and annual rice.

Some caution is needed in making those statements based on that graph. However, they both seem reasonable after checking the more complete data shown in the article. Extended Data Figure 4 shows the results by site, which makes things clearer. The authors suggest that the PR strain tested here is good for four years, with eight harvests.    This is Figure 2d from the article.

If the yields are about the same, what is the point of using perennial rice? Planting is expensive. Using perennial rice would be simpler and cheaper than having to plant for each crop.

The following figure shows some of the economic analysis offered in the article...

From the two figures above, we see that the new perennial rice gives a similar crop yield, but with reduced costs. The article also notes improvements in soil quality associated with the perennial rice.

How did the scientists get this PR? Traditional plant breeding, crossing strains of rice with different properties. Rice strains vary in how well they re-grow. Commonly used crop strains re-grow some, but poorly. That is, at least some of the properties needed for regrowth are present. (It is thought that perennial is the original trait for rice.) A common crop strain was crossed with a poor-yield strain with good regrowth. Over multiple generations, the scientists got strains with good yields and good regrowth.

The strain tested above has now been grown for multiple seasons in various countries in Asia and Africa, with encouraging results. It is available commercially in some countries. (Further breeding work has given a couple of strains better than the one tested above.)

News stories:
* Productivity and agronomic potential of perennial rice. (Mary Williams, Plantae (American Society of Plant Biologists ), November 18, 2022.)
* Farmers in China, Uganda move to high-yielding, cost-saving perennial rice. (Lauren Quinn, University of Illinois, November 7, 2022.)

* News story accompanying the article: Perennial cropping: Newer roots for agriculture -- Annual grains, domesticated from wild species, have dominated agriculture since the Neolithic. A new study reports how turning to high-yield perennial rice crops could maintain key ecosystem functions while supporting livelihoods. (Jerry Glover, Nature Sustainability 6:5, January 2023.)
* The article, which is open access: Sustained productivity and agronomic potential of perennial rice. (Shilai Zhang et al, Nature Sustainability 6:28, January 2023.)

Among posts about rice...
* Wheat, rice, and Starbucks (August 3, 2018).
* How rice leads to global warming, and what we might do about it (September 2, 2015).
* How rice recognizes a Xoo infection (August 28, 2015).
* DEEPER ROOTING leads to deeper rooting -- and to drought tolerance (August 16, 2013).
* Golden rice as a source of vitamin A: a clinical trial and a controversy (November 2, 2012).
* The rice-arsenic issue: Consumer Reports and the FDA weigh in (September 25, 2012).

March 1, 2023

Briefly noted... The mosquito microbiome - inside and out

February 28, 2023

We know that mosquitoes transmit disease by injecting material into the blood. We also know that flies transmit disease simply by carrying microbes on their feet. Do mosquitoes do that, too? Do they carry pathogens on their surfaces? A new article offers a first step in exploring the matter. The scientists isolated bacteria from both the surface and internal parts of Anopheles mosquitoes found in various houses. There are no clear implications, but there are some interesting findings. One finding of possible concern is that Rickettsia were found in the mosquitoes; some Rickettsia are human pathogens. The scientists also found that the surface bacteria varied a lot from house to house, whereas the internal ones were more characteristic of the species and its outside environment. Not a surprising finding, but showing it is a step toward understanding the mosquito microbiome.
* News story: Study Examines Bacteria Living In and On Mosquitoes. (Mick Kulikowski, North Carolina State University, December 16, 2022.)
* The article, which is open access: Internal and external microbiota of home-caught Anopheles coluzzii (Diptera: Culicidae) from Côte d'Ivoire, Africa: Mosquitoes are filthy. (Kaiying Chen et al, PLoS ONE 17:e0278912, December 15, 2022.) As so often, browsing the Introduction may be good.
* Previous post about a microbiome: A drug to treat the gut microbiome (February 25, 2023). Three days ago.
* This item is listed on my BITN-Other topics page under Malaria. Anopheles mosquitoes transmit malaria; this section also includes some general items about mosquitoes.

Update added March 20, 2024.
Oldest mosquito fossils: bloodsucking males. A recent article uncovers some old mosquitoes, preserved in amber. They are of interest for two reasons. First, they are the oldest mosquitoes we have seen. Second, they are males with mouth parts that suggest they drank blood. In modern mosquitoes, only the females suck blood.
* News story: Oldest mosquito fossil shows males were once bloodsuckers too -- Oldest fossil mosquito found in Lebanese amber suggests ancient males also fed on blood, revising our knowledge of mosquito evolution. (Tibi Puiu, ZME Science, December 4, 2023.)
* The article: The earliest fossil mosquito. (Dany Azar et al, Current Biology 33:5240, December 4, 2023.)
* There are many posts about mosquitoes on the BITN page linked above. Just search the page for mosquito.

Electric insects

February 27, 2023

The following figure shows the electric field in the air as a swarm of bees flies by...

	The black curve shows the electric field (left-hand y-axis) vs time (x-axis). The green curve is a measure of the bee density (right-hand y-axis; the figure legend says "pixel density", from photos of the scene). You can see that the electric field closely follows the bee density.
The inset shows two electric field profiles over time. One is at a place where a swarm of bees went by; the other had no bees. Part F of the full figure shows a similar graph for another bee-swarm event, with potential gradients ten-fold higher.    This is Figure 1C from the article.

The next figure provides some context, comparing the electric fields from swarming insects to those from other atmospheric phenomena...

The top two bars are for swarms of bees and locusts. The bottom two bars are for thunderstorm clouds and electrified dust storms. You can see that those two insect sources and those two non-biological sources give substantial electrical effects. In this analysis, the bees give the extreme range of values. The middle two bars are for some insects that usually do not swarm at high density and fair-weather air.

The atmospheric electricity is shown here as charge density. The values shown here for the insects are based on modeling, using the known charge per individual for each type of insect and estimated swarm densities. For the bees, the measurements and modeling have been shown to agree well. (For locusts, the measured charge per individual is about 800 picocoulombs.)    This is Figure 2C from the article.

The authors say this is the first article on how insects make a substantial contribution to atmospheric electricity. It is likely that insects can change the atmosphere enough to affect aggregation of dust, and thus its transport over long distances.

News stories:
* Insects affect electric fields in the atmosphere, researchers find. (University of Bristol, October 24, 2022.)
* Insects Can Produce As Much Atmospheric Electric Charge as a Thunderstorm Cloud. (SciTechDaily (Cell Press), October 26, 2022.)
* Insect swarms might electrify the air as much as storm clouds do -- The role insects play in creating electricity in the atmosphere may be unappreciated. (Darren Incorvaia, Science News Explores, November 22, 2022.)

The article, which is open access: Observed electric charge of insect swarms and their contribution to atmospheric electricity. (Ellard R Hunting et al, iScience 25:105241, November 18, 2022.) A short readable article. If you haven't thought much about electricity in the calm atmosphere, you might browse the Introduction here.

More about insects and electricity...
* How bumblebees detect the electric field (October 22, 2016).
* Bees and flowers: A 30-volt story (June 21, 2013).

A drug to treat the gut microbiome

February 25, 2023

Recurrent infection with Clostridioides difficile ("C diff") can be a serious problem. Underlying C diff infection is often a disruption of the normal gut microbiome. Restoration of the microbiome can be useful; fecal transplantation has shown some success in treating C diff. See background posts [links at the end]. (Prior to 2016, the organism was classified in the genus Clostridium.)

An alternative to fecal transplantation might be to inoculate with a known microbial mixture. In fact, the drug SER-109 is just that, and it is in clinical trial as a treatment for recurrent C diff infection.

A new article reports one part of the analysis, focusing not on the infection per se, but on measures of quality of life (QOL). In this trial, the C diff was treated with antibiotics, then the drug (or placebo) was given for three days. The drug provided microbes, intended to restore a healthy microbiome.

Here is a summary of some of the QOL analysis...

The trial also recorded whether patients had recurrent infections; that part of the trial had been reported previously. In the current analysis, it was found that QOL improvements in the placebo group correlated with not getting recurrent C diff infection. However, in the treatment group, QOL improvements were seen both with and without recurrent infections. That is a particularly good result; improving the gut microbiome benefits the QOL even if it does not eliminate the pathogen.

The big picture is that the new microbe-drug leads to improvement in quality of life for people with C diff. That is encouraging. Benefit is seen even if the infection recurs. A three-day treatment leads to a QOL improvement at least through eight weeks.

News stories:
* Microbiome drug for recurrent C diff linked to improved quality of life. (Chris Dall, CIDRAP, February 2, 2023.) First item on the page.
* Microbiome therapeutic linked to quality of life improvement in patients with recurrent C. diff infection. (News-Medical.net (University of Houston), February 1, 2023.)

The article, which is open access: Assessment of Quality of LifeAmong Patients With Recurrent Clostridioides difficile Infection Treated with Investigational Oral Microbiome Therapeutic SER-109 Secondary Analysis of a Randomized Clinical Trial. (Kevin W Garey et al, JAMA Network Open 6:e2253570, January 30, 2023.)

Background posts about treatment of C diff include...
* Fecal transplantation as a treatment for Clostridium difficile: progress towards a biochemical explanation (February 8, 2015).
* A bacterial cocktail to fight Clostridium difficile (January 19, 2013). In mice.

Next microbiome post: Briefly noted... The mosquito microbiome - inside and out (February 28, 2023).

February 22, 2023

Emissions from gas stoves, even when 'off' -- air pollution implications

February 21, 2023

A new article reports that gas stoves (the kind used for cooking in ordinary homes) can make a significant contribution to air pollution -- when they are off.

Caution... This is an interesting story, but also complicated. There is now a movement to phase out gas appliances, and this article has become part of the argument. As usual here, this is a single article; be careful about reaching big conclusions from it.

Previous work has shown that gas stoves (and such) leak even when off. The current work builds on that.

The first figure shows the top 10 pollutants found in the unburned gas from gas stoves...

The numbers along the right side are the percent of samples with each pollutant. These numbers were used to choose the top 10, and to rank them in this figure. (The numbers are hard to read. Briefly, the top six were found in at least 98% of the samples. The bottom four were found in 7-30% of the samples.) The x-axis shows the concentration found (in ppmv, parts per million by volume). Most of the scale is logarithmic; the authors note that it "smoothly transitions" to linear at the low end.

There is a general trend that pollutants found in more samples (right-hand number) were found at higher levels (x-axis). The first three pollutants listed are saturated hydrocarbons (name ends in -ane). The others are aromatic hydrocarbons (benzene and derivatives; name ends in -ene). I have marked benzene with *** at the left to highlight it. Benzene gets special attention in the article because it is a known carcinogen.    This is Figure 2 from the article. I added *** to the left of 'benzene'.

The next figure shows the results for benzene by geographical region (all within California)...

The striking result is that the benzene level varies by location -- a lot. The last two bars make the point clearly. The three colors are for the three major gas companies in the state. (We don't need to identify them here, but they are well known locally -- and are named in the article.) It's interesting that the three red sets show major differences in benzene levels in three areas served by the same company. NSFV/SCV stands for North San Fernando Valley and Santa Clarita Valley. The authors split off this geographical area from the adjacent "Greater Los Angeles" when they realized it was giving a distinct result. SF = San Francisco.    This is Figure 3C from the article.

The next figure presents modeling results to explore the possible importance of the benzene in unburned natural gas entering homes. This uses the benzene levels measured in the gas, as reported in the figures above, along with estimates of leakage rates, from previous work.

A brief summary of the key points...
- Gas stoves, when off, emit various hydrocarbons. Of particular interest is benzene, a known carcinogen.
- Emissions vary by location -- a lot.
- The higher levels of emissions are high enough to be of concern.

The work raises several questions. For example...
- Why are there emissions when the stoves are off? (Could we do something about it?)
- Why is there such geographical variation in the emissions? (Could we do something about it?)
- Are the concerns that seem to be raised by the third graph proper? (How much are people really exposed?)

I don't have answers for those questions, but it should be understood that the article offers some observations, and is not the last word. The authors note limitations of the work in their own final section (see "Future Research Directions", p 8 of the pdf) .

The big message of the work is that leakage of unburned gas can make a significant contribution to air pollution, and is a source not usually considered. It should be considered.

News stories:
* Gas stoves can spew lots of pollution, even when they're turned off -- Some shed high levels of cancer-causing benzene into a home's air, a new study shows. (Laura Allen, Science News Explores, January 30, 2023.)
* Leaks from gas stoves can create potentially hazardous indoor benzene concentrations -- Scientists find natural gas throughout California contains numerous hazardous air pollutants that can impact air quality and public health. (EurekAlert! (PSE Healthy Energy), October 20, 2022.) This is based on a press release from the main organization doing the work.

The article, which is open access: Composition, Emissions, and Air Quality Impacts of Hazardous Air Pollutants in Unburned Natural Gas from Residential Stoves in California. (Eric D Lebel et al, Environmental Science & Technology 56:15828, November 15, 2022.) The article is from an organization doing energy-related research. Interestingly, the article does not declare any conflict of interest, although the organization clearly benefits from such an article.

A previous post about natural gas leakage: Methane leaks -- relevance to use of natural gas as a fuel (April 7, 2014). This is a general discussion of methane leakage; the post also links to some posts about specific leak issues.

Among those leak posts: Los Angeles leaked -- big time! (April 29, 2016). This is actually from the area identified in the current work as San Fernando Valley. The Aliso Canyon site of this earlier event is mentioned in the current article. It is not obvious that there should be any connection between this leak event and the current work.

Liquid-filled smart windows, inspired by squid

February 17, 2023

Smart windows are windows with properties that vary -- as needed. For example, in the mid-day sun, a smart window would let light in, but not heat. The idea of smart windows is not new; see the background post for an example [link at the end].

What's new in a recent article in how the smartness is implemented. In this case, one puts various liquids into the inside of the window -- liquids with various properties. Further, their smart windows have multiple independent liquid chambers, allowing for independent use of multiple liquids with different effects.

Here is an example of what can be achieved, as judged by a lab-scale test...

It worked. Changing a liquid in the window provided control over the IR (heat) with minimal effect on visible light.

The authors argue that their type of smart window is better than others that have been proposed. The use of multiple liquid layers allows independent control of multiple factors, such as amount of visible and IR light, as well as directional control of the light. There is less use of exotic materials, so it is cheaper. They estimate a cost savings of nearly half, and that the device would pay for itself in two years (for a specific scenario, of coarse).

What about the squid, noted in the title? The authors say that their idea was inspired by the way squid change their properties, such as for camouflage, using multiple cell layers with different roles. They illustrate this in the figure at the right.    This is Figure 1B from the article.

News stories:
* Squid-inspired smart windows could slash building energy use -- Liquid-filled panels that dynamically change how they let light through could cut the energy costs of heating, cooling, and lighting buildings by over 40%. (Prachi Patel, Anthropocene, February 2, 2023.)
* 'Liquid windows' inspired by squid skin could help buildings react to changing environments, save on energy costs -- University of Toronto Engineering researchers create bio-inspired system that can optimize the wavelength, intensity and dispersion of light reaching building interiors. (EurekAlert! (University of Toronto), February 1, 2023.)

The article, which is open access: Multilayered optofluidics for sustainable buildings. (Raphael Kay et al, PNAS 120:e2210351120, January 30, 2023.)

Background post: Windows: independent control of light and heat transmission (February 3, 2014).

Among posts about squid: A new brain study (March 3, 2020).

February 15, 2023

Atmospheric aerosols from passive (non-erupting) volcanoes -- a re-evaluation

February 13, 2023

A new article re-examines the question of how much gas volcanoes emit passively (that is, non-erupting). The results have implications for climate change models.

Sulfate aerosols are of particular interest here. They reduce warming. There are two main sources of sulfate aerosols: volcanic and biological.

It's a complex article -- and a complex, but interesting, story. Let's start with something simple -- the basic data...

So, the fraction of sulfate aerosols due to volcanoes is, according to this new analysis, larger than had been thought. Twice as large.

Why? Now the problems begin. The volcanic fraction could be higher than expected because the volcanic emissions were higher than expected, or because the biogenic emissions were lower than expected. There is nothing in the analysis that distinguishes those explanations. (We assume that the ice core reflects both types equally, but we don't know the absolute levels of either.) The authors suggest that the former is more likely. If so, then the amounts of sulfate aerosols in the past was greater than we had thought.

That has implications for climate change modeling. If the aerosol emissions in the last millennium were not what we had thought, that changes the input data into the models. And of course, that changes the predictions from the models.

The authors' preferred interpretation is that climate may be less sensitive to aerosols than we had thought. It is a complex chain of arguments to get to that conclusion.

The article is actually quite interesting and well written. The authors describe the various issues of concern, and make the logical connections. The difficulty is the uncertainties that underlie such work. If you find the topic of interest, I certainly encourage you to read the article. But a caution... Don't try too hard to reach a conclusion from it. The article offers significant new ideas; they need to be followed up.

News story: Ice cores show even dormant volcanoes leak abundant sulfur into the atmosphere. (Science Daily (Hannah Hickey, University of Washington), February 5, 2023.)

The article, which is open access: Underestimated Passive Volcanic Sulfur Degassing Implies Overestimated Anthropogenic Aerosol Forcing. (U A Jongebloed et al, Geophysical Research Letters 50:e2022GL102061, January 16, 2023.)

Among posts about aerosols: Aerosols and clouds and cooling? (August 27, 2017). This one is about the emissions during a volcanic eruption.

The biological source of sulfate aerosols is dimethyl sulfide (DMS). Here is a post about the complexity of what happens to that chemical: The importance of HPMTF in the atmosphere (June 9, 2020).

Making better straws

February 11, 2023

Plastic drinking straws work well. They are not affected by common drinks. They are strong enough that one can stab a potato with them. However, they are not biodegradable. Even plastic straws labeled as biodegradable, made with poly(lactic acid), degrade poorly. Paper straws are biodegradable, but work poorly. For example, they tend to get soggy.

Plastic-coated paper straws offer an approach that could combine the advantages of the two materials. The basic idea is that it is mostly paper, with enough plastic coating to gain the benefits of plastic without the downside. However, currently available plastic-paper straws have deficiencies.

A new article reports an improvement. The focus is on improving the plastic coating, in particular how it is attached to the paper, to provide a uniform effective layer.

The following two figures show some results comparing the new straws with other straws. We'll discuss the details of the straws, and the labeling, later.

Part d (left) shows a fizz test. A poorly coated straw in a carbonated soft drink gives fizzing (top). This is commonly seen with paper straws. The new straw does not (bottom). Part e shows a strength test. A weight is applied to one end of a wet straw. The straw at the top, poorly coated, bends. The new straw does not, even with twice the weight (bottom). (Left and right sides are for zero and 60 seconds, respectively.) From the strength test, one might predict that the new straw could be used to stab and pick up a potato. The results of such a potato-stabbing test are shown in part f. (Read the figure clockwise, from upper left.)    This is part of Figure 5 from the article.

The next figure shows results for a test of biodegradability...

Straws were put into an ocean environment. The top straw is an ordinary plastic straw. The others are paper straws, with variations. The top one is unmodified -- basically a paper straw; the bottom is the new straw. Images are shown after 60 and 120 days of incubation. If the straw was gone, a small black bar is shown.

The plastic straw remained unchanged. The three paper-based straws were visibly degraded by 60 days, and gone by 120 days. The plastic coating slowed the degradation (as judged by visual inspection at day 60), but overall degradation is good. Comment... What happened to the plastic part of the straw? That is not addressed. It is possible that tiny pieces of "microplastic" remain. However, the plastic here is polyester, in short chains. It would not be surprising if the plastic part of these straws was reasonably biodegraded. In fact, it is stated that the plastic used here is biodegradable. However, that is not directly addressed in this article.    This is Figure 6e from the article.

What are these straws? They start as ordinary paper straws. Cellulose nanocrystals (CNC) are added to the surface. CNC is chemically like the paper itself, but the surface particles promote additional modification. A plastic coating is attached to the CNC, via a special linker. The linker is butylene succinate (BS); the coating per se is PBS = poly(butylene succinate). The final product is referred to as PBS/BS-CNC. The BS linker seems to be key to getting a good uniform, but very light, plastic coating onto the paper.

Overall, the article offers an improved straw, combining favorable proprieties of both paper and plastic. The authors note it is easy to manufacture, but do not address costs.

News stories:
* Finally, an anti-fizzing paper straw that doesn't get soggy. (Bradley van Paridon, Advanced Science News, November 21, 2022.)
* Development of 100% biodegradable paper straws that do not become soggy. (EurekAlert! (National Research Council of Science & Technology), February 1, 2023.)

The article, which is open access: Biodegradable, Water-Resistant, Anti-Fizzing, Polyester Nanocellulose Composite Paper Straws. (Hojung Kwak et al, Advanced Science 10:2205554, January 4, 2023.)

Many posts about plastics are listed with History of plastic -- by the numbers (October 23, 2017).

The only previous post mentioning a drinking straw: Brain-computer interface: Paralyzed patients control robotic arm by their thoughts (June 16, 2012).

February 8, 2023

Briefly noted... Recorded live, on Mars

February 8, 2023

* Listen. (26 seconds. Be patient.)
* Source/news story: NASA's Perseverance Records a Martian Dust Devil. (NASA, December 13, 2022.) The audio link above is from this page. A video link is also available; good to read this page before trying to make sense of the video.
* The article, which is open access: The sound of a Martian dust devil. (N Murdoch et al, Nature Communications 13:7505, December 13, 2022.)
* More from Perseverance: MOXIE: Making oxygen gas on Mars (October 12, 2022).

X-chromosome inactivation in males -- in cancer

February 6, 2023

In mammals, the females have two X chromosomes, whereas the males have only one. There is a dosage compensation mechanism, so that males and females in general make the same amount of products from X. In females, one X is inactivated. In cases of unusual chromosome counts, the "rule" is that all but one X is inactivated.

An RNA molecule called XIST plays a central role in inactivating excess X chromosomes.

A male would not normally have XIST RNA. So the following finding, from a recent article, is at least a curiosity...

What does this mean? Further analysis shows that the male cancer samples with XIST RNA have two X chromosomes. It is common to find aberrant chromosome counts in cancers -- a condition called aneuploid (not euploid = not having the "true" chromosome count). For male cancers to have two X chromosomes might, then, just be another example of aneuploidy in cancer; that leads to XIST by the usual X-inactivation rules. (Caution... The full data on this point are more complex than suggested here.)

The authors consider some other possibilities, even raising the question of whether treating XIST in some way might be useful. That's pretty much speculation at this point.

I think it is best to treat this article as a novel finding, the significance of which is open for now.

News stories. Caution: Some of the news headlines suggest that "the" X in male cancers is inactivated. No, the finding is that excess X copies may be inactivated. This seems to be mainly a headline problem, and is largely absent from the stories themselves.
* The Male X Chromosome Is Silenced in Some Cancer Types. (Technology Networks, November 9, 2022.)
* The X chromosome is silenced in some male cancers. (Science Daily (Cell Press), November 9, 2022.)

The article: Somatic XIST activation and features of X chromosome inactivation in male human cancers. (Ananthan Sadagopan et al, Cell Systems 13:932, November 16, 2022.)

More about X-inactivation and/or XIST:
* Unequal allele expression (April 18, 2023).
* Briefly noted... X-chromosome inactivation -- more complex than it seems. (May 27, 2020).
* Down syndrome: Could we turn off the extra chromosome? (November 15, 2013).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer. It includes a list of relevant Musings posts.

February 1, 2023

Briefly noted... A good role for "senescent cells"?

February 1, 2023

Senescent cells. Markers of aging. Bad guys. Let's eliminate them. Not so fast, according to a recent article, which offers evidence that some populations of "senescent cells" are involved in healing processes. For example, drugs designed to kill senescent cells inhibited tissue repair. The work should be thought of as leading to a refinement of our ideas about senescent cells.
* News story: Scientists Reappraise the Role of 'Zombie' Cells That Anti-aging Medicine Has Sought to Eliminate. (Neuroscience News (UCSF), October 16, 2022.) Excellent overview, for both context and the current work.
* The article: Sentinel p16^INK4a+ cells in the basement membrane form a reparative niche in the lung. (Nabora S Reyes et al, Science 378:192, October 14, 2022.) Check Google Scholar for a freely available copy. (If the search by title fails, delete the plus sign in the title, and try again.)
* A useful background post: A treatment for senescence? (June 4, 2017). Links to more.
* The page for BITN -- Other topics includes a section on Aging.

Does E coli grow in a multicellular form?

January 31, 2023

Look...

An E coli biofilm. The region marked by the dashed rectangle is shown at higher magnification at the right. Note scale bars just above the images. Pretty. More importantly... Two batches of ordinary (wild type) E coli bacteria were grown up. Same kind of cells, grown up the same way. One batch was given a red stain and one a green stain. The two cultures were mixed, and the mixture allowed to form a biofilm under lab conditions. One might expect, most simply, the biofilm to consist of a random mixture of red and green cells. It doesn't. It consists largely of red and green chains. At the left, the main horizontal dashed lines mark the biofilm. The thickness is shown at one point.    This is Figure 3C from the article.

Why?

The authors investigated how the bacteria were growing. The general conclusion is that they grew into multicellular forms. The key structure consisted of four parallel chains of cells. These 4-chain structures then aligned to form the biofilm.

The first step is forming a "rosette" of four cells. Each rosette seems to form by four cells coming together. Once a rosette is formed, each cell divides in the usual way. The result is four parallel chains of cells, with each chain consisting of about 2¹⁰ (~1000) cells. Those chains then come together to form the biofilm, as seen in the figure above. The scientists found genes needed for some steps.

The following figure shows multiple views of one rosette observed over a few minutes...

One rosette of four E coli cells.    This is Figure 1D from the article.

Intriguing observations. They go against our common idea that E coli simply divides in two, producing two separated and independent daughter cells.

There is more to be done to understand the generality and importance of what was found here. Among the questions... Does recognizing this process for developing biofilms lead to new approaches for preventing them?

News story: More to E. coli Than Meets the Eye: BME Lab Discovers Evidence of Multicellularity in Single Cell Organism. (Jerry Grillo, Georgia Tech, January 25, 2023.)

The article, which is open access: Evidence of a possible multicellular life cycle in Escherichia coli. (Devina Puri et al, iScience 26:105795, January 20, 2023.)

Posts on biofilms include...
* Better bacterial conductivity (November 3, 2020).
* Salmonella and food contamination; the biofilm problem (April 28, 2014).

Using abandoned mines to store energy

January 30, 2023

Here's the idea...

The underlying principle here is not new. We do things like this with water. Hydroelectric plants work by the same principle: water flowing downward, by gravity, turns a turbine and generates electricity. A variation of that is to intentionally pump water up to a storage tank, where it can be used to generate electricity later as needed. This is called pumped-storage hydroelectric. The energy cost of pumping the water is spent when energy is cheap; energy is generated when it is expensive. Such a system is about energy storage, not an energy source.

The device proposed here is the same idea, but uses sand rather than water. The authors make the case that abandoned mines could be used for this purpose.

The following table gives some cost estimates, comparing water and sand devices and lithium ion batteries...

An advantage of using abandoned mines is that they already have basic infrastructure, including connection to the power grid. And they have elevators or such to transport materials from the bottom of the mine to the surface.

Are there enough abandoned mines around to make this significant? The authors estimate that there are enough abandoned mines to, roughly, provide all the world's energy. But it would be developed one mine at a time.

The article opens the door to a new way to store energy: as sand in abandoned mines. The method should be thought of as a complement to other methods of energy storage, perhaps best suited for intermediate term storage (multi-day to months).

The article includes some interesting maps. For example, Figure 1 shows the distribution of (active) mines around the world, labeled by what they are for. This is not really needed for the current content, but does make the point that mines are widespread. Figure 10 shows the storage potential of mines by country; caution, red is good (high capacity) and green is bad on this map.

News stories:
* Scientists propose turning abandoned mines into gravity batteries. (Ben Coxworth, New Atlas, January 12, 2023.)
* Storing renewables via regenerative braking in underground mines -- Scientists in Austria have developed a long-term energy storage system that uses regenerative braking to adjust the descent speed of sand in mine shafts and generate electricity. (Emiliano Bellini, pv magazine International, January 24, 2023.)
* Turning abandoned mines into batteries. (Science Daily (International Institute for Applied Systems Analysis), January 12, 2023.)

The article, which is open access: Underground Gravity Energy Storage: A Solution for Long-Term Energy Storage. (Julian David Hunt et al, Energies 16:825, January 11, 2023.)

The following posts seem to be about energy in mines...
* How to light a cave (August 30, 2021).
* Bacteria that make atomic copper (May 8, 2021).

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.

January 25, 2023

Briefly noted... A practical way to make tetrataenite -- and reduce the demand for rare earth elements

January 25, 2023

Permanent magnets made using rare earth elements, such as neodymium, are important in modern technology. However, there are supply issues with these materials. Perhaps we could use meteorite dust instead. In fact, a promising mineral has been found in meteorites. A new article reports a practical way to make it on Earth. The material is an alloy of iron and nickel. The problem is that the alloy can form two different structures, and the more useful one is hard to make. The key development in the new work is to make the desirable form, called tetrataenite. The key step is to include a few percent of phosphorus in the alloy; the P atoms enhance the mobility of the metal atoms as the melt cools, and a large fraction of it ends up in the desired form. The authors think the process can be improved further, and can be developed into a practical process for making high quality magnets using Earth-abundant materials. The findings may also prompt a re-think of how the mineral forms in meteorites.
* News story: A new way to create permanent magnets. (Andrey Feldman, Advanced Science News, November 17, 2022.) From the journal publisher.
* The article, which is open access: Direct Formation of Hard-Magnetic Tetrataenite in Bulk Alloy Castings. (Yurii P Ivanov et al, Advanced Science 10:2204315, January 4, 2023.)
* A recent post about rare earth elements: Extraction of rare-earth metals: a bacterial assist (February 8, 2022). Links to more.
* Added February 26, 2024. This post is listed on my page Introductory Chemistry Internet resources in the section Lanthanoids and actinoids.

A lightweight white paint

January 23, 2023

We have noted advances in white paint before [link at the end]. White paint is reflective, which is good for keeping cool.

A recent article offers a new development in white paint. The following figure summarizes the status of the field.

This is not the first white paint to achieve 98% reflectance, but it does so at half the thickness of the previous material. Not only 1/2 the thickness, but about 1/5 the weight, because the new paint has a lot of air in it; it is nanoporous. That would be an advantage in applications where weight is an issue -- such as airplanes.

The material used here is the white pigment hexagonal boron nitride (hBN), which is already used commercially for other things (such as lubricants). Interestingly, the computer simulations suggested that a flake form, called nanoplatelets, would be more effective than spherical particles. That prediction was confirmed experimentally.

The graph above shows that the agreement between prediction and data is not good for thinner coatings. The disagreement probably relates to the form of the material, and is a caution that the understanding of the material is incomplete.

The new paint reflects much of the energy at wavelengths that allow it to escape the atmosphere. This issue of radiative cooling was discussed in the background post.

News stories:
* Purdue team develops thin-layer lightweight and ultrawhite paints for daytime radiative cooling. (Green Car Congress, October 4, 2022.)
* World's whitest paint now thinner than ever, ideal for vehicles. (Jared Pike, Purdue University, October 3, 2022.)
* Lightweight hBN Nanoporous Paint with Excellent Cooling Abilities. (Hussain Ahmed, AZoNano, October 10, 2022.) Good discussion of several of the technical issues.

The article, which is open access: Thin layer lightweight and ultrawhite hexagonal boron nitride nanoporous paints for daytime radiative cooling. (Andrea Felicelli et al, Cell Reports Physical Science 3:101058, October 19, 2022.)

Background post: A better white paint, using BaSO₄; it's cool (August 10, 2021). The article of this earlier post is reference 21 of the current article. It is also the article noted on the figure as Li et al 2021, for the BaSO₄-based paint. The two articles are from the same lab.

Added May 4, 2023. More paint: Paint without pigment (May 4, 2023).

More boron nitride: Nanopore sequencing of DNA using synthetic membranes (May 15, 2021).

Other things white: The whitest feathers (March 11, 2023).

January 18, 2023

Briefly noted... Was a simpler larynx a key to the development of human speech?

January 18, 2023

Human speech is unique -- and complex, involving both the brain and the anatomy of the speech apparatus. A recent article offers a new idea about one aspect of how speech developed. An analysis of the anatomy of the larynx of over forty primate species suggests that the organ is actually simpler in humans. That simpler larynx allows smoother, more stable sound production. Arguably, the simpler human larynx was a key development allowing for speech. The article is quite complex; I suggest starting by browsing it for the big ideas.
* News story: Simplified voice box enriches human speech -- Anatomical simplifications allowed vocal complexity in human speech. (Science Daily (Kyoto University), August 11, 2022.)
* News story accompanying the article: Evolution: When less is more in the evolution of language -- Did loss of vocal fold membranes typical of nonhuman primates enable human speech? (Harold Gouzoules, Science 377:706, August 12, 2022.)
* The article: Evolutionary loss of complexity in human vocal anatomy as an adaptation for speech. (Takeshi Nishimura et al, Science 377:760, August 12, 2022.)

The role of tiny droplets in driving unfavorable reactions -- such as those needed to get life started

January 17, 2023

Much of the story of life chemistry is about the use of energy: how the energy from an external source is used to drive reactions which, on their own, are unfavorable. A special question is how all that got started in the early stages of establishing life systems.

One example of an important unfavorable reaction is the formation of a peptide bond between two amino acids. The reaction releases water, and is unfavorable in the presence of water. In modern biology, the reaction is done using the energy from ATP, in a fairly complex reaction sequence.

A recent article offers one way that unfavorable reaction might have occurred before energy pathways had been developed. The following figure shows some key evidence behind the idea...

The logic of the test is simple: a solution of the amino acid glycine is sprayed into a mass spectrometer (MS), and analyzed there. A small amount of the dipeptide glycylglycine is found. Apparently, it formed in the droplets between the time the spray was created and the time the droplets entered the MS for analysis. To test this idea further, they varied the distance the droplets traveled, hence the time available in the droplets. The results of that test are shown here: amount of the dipeptide formed (y-axis) vs distance (x-axis). At least for a portion of the curve, greater distance (longer time) gave more of the dipeptide.    This is part I of Figure 1 from the article.

The results support the idea that peptide bond formation is occurring in the spray.

How can that happen, if the reaction is unfavorable? The suggestion is that the reaction occurs at the surface of the droplets. What makes the simple reaction unfavorable is the presence of water. But molecules at the surface of the droplets are at an air-water interface. It is reasonable that the interface shifts the energetics, making the reaction more favorable.

Is there any relevance to prebiotic or early-life chemistry? That would be speculation, of course, but perhaps. Tiny droplets occur in nature; ocean spray is an example. The same basic effect would occur in simply drying-up of puddles or such; the droplets provide an extreme case of increasing the air-water interface, especially with tiny droplets.

In the news story, the authors also note that their procedure could be useful in the lab for synthetic chemists, to facilitate reactions that might otherwise be difficult.

News story: The fountain of life: Water droplets hold the secret ingredient for building life -- Chemists discover key to early Earth chemistry, which could unlock ways to speed up chemical synthesis for drug discovery. (EurekAlert! (Purdue University), October 3, 2022.)

* Commentary accompanying the article (actually, in a later issue): Peptide synthesis in aqueous microdroplets. (Veronica Vaida & Alexandra M Deal, PNAS 119:e2216015119, October 20, 2022.)
* The article: Aqueous microdroplets enable abiotic synthesis and chain extension of unique peptide isomers from free amino acids. (Dylan T Holden et al, PNAS 119:e2212642119, October 3, 2022.)

Another article making a similar point appeared recently...
* News story: Drying process could be key step in development of life. (Phys.org (Jason Daley, University of Wisconsin-Madison), December 21, 2022.)
* The article: Glycine to Oligoglycine via Sequential Trimetaphosphate Activation Steps in Drying Environments. (Hayley Boigenzahn & John Yin, Origins of Life and Evolution of Biospheres 52:249, December 2022.) The work in this article differs from that in the main article, above, in also including phosphates in the reaction mix. The role of surfaces remains central.

* * * * *

Another post about droplets affecting reaction rates: Spontaneous formation of hydrogen peroxide from water (October 26, 2019).

Another way to make peptides, though it is not suitable for use on Earth: Making peptides in space: a new pathway (April 15, 2022).

My page Internet Resources for Organic and Biochemistry has a section on Amino acids, proteins, genes. It includes a list of posts about making proteins.

The effect of climate change on rainbows

January 16, 2023

The following figure shows how the frequency of rainbows is expected to change due to climate change, as reported in a recent article...

At one level, this is a fun article. However, rainbows are physical phenomena, and the analysis here is serious physics. As an example of the complexity, clouds are needed to produce rain, but they can obscure the rainbow that follows. The work started by establishing the current distribution of rainbows, something that apparently had never been done. That distribution was then adjusted to 2100 based on the climate change model.

Among the simpler reasons for changing rainbow patterns... Areas where warming leads to more rain instead of snow are likely to get more rainbows. Areas that become drier will get fewer rainbows.

Over 2/3 of Earth's land area will get more rainbows. However, much of the increase will be at high latitudes and high elevations, where few people will see them.

News stories:
* Somewhere over the rainbow... climate impact is visible -- India, 5 African countries may see a lot more rainbow days due to increased precipitation, finds study. (Madhumita Paul, Down To Earth, November 3, 2022.)
* Climate change to produce more rainbows. (Marcie Grabowski, University of Hawaii at Manoa, October 28, 2022.)

The article, which is open access: Global rainbow distribution under current and future climates. (Kimberly M Carlson et al, Global Environmental Change 77:102604, November 2022.)

Previous posts about rainbows: none.

A recent post about climate change: What caused the extinction of the mammoths -- I (January 16, 2022).

SNO and the higher prevalence of Alzheimer's disease in women

January 14, 2023

Alzheimer's disease (AD) is more prevalent in women; it is not known why. A new article offers a clue.

It's about SNO. That's S-nitrosylation, the attachment of a nitrosyl group (-N=O) to the S atom of cysteine in proteins, using nitric oxide. In particular, it's about SNO of a protein called C3, which is part of the complement cascade in the innate immune system.

The following figure summarizes the key data...

The figure shows the amount of SNO in the C3 protein for four groups of people: males and females with and without AD. The results for non-AD people are very low. The results for people with AD are higher -- especially for females. The analyses were done on post-mortem brain samples. The results shown are for nitrosylation at one specific site in C3, Cys-720.    This is part of Figure 5A from the article.

Those results establish a correlation between SNO and AD, but alone do not say anything about why.

One can suggest connections. The modified protein is associated with inflammation in the brain, and that could promote destruction of synapses. That's an incomplete idea, of course, but it can be followed up. One test will be to intervene by promoting loss of the modification, and see if that has beneficial effects.

It is known that females have higher levels of SNO, a result that was verified in the current work. Also, estrogen is associated with lower levels of SNO, so the modification increases after menopause. (Comment... Does this suggest that hormone replacement might be relevant? That is not mentioned.)

News stories:
* Protein Modifications May Explain Why More Women Get Alzheimer's Disease. (Sarah Whelan, Technology Networks, December 14, 2022.)
* Discovery could explain why women are more likely to get Alzheimer's -- Scripps Research and MIT scientists find that a modified immune protein harming brain connections is much more common in the brains of women with Alzheimer's, compared to men. (EurekAlert! (Scripps Research Institute), December 14, 2022.)

The article, which is open access: Mechanistic insight into female predominance in Alzheimer's disease based on aberrant protein S-nitrosylation of C3. (Hongmei Yang et al, Science Advances 8:eade0764, December 14, 2022.)

Recent post on AD: Alzheimer's disease: a blood treatment? (January 9, 2023).

Another case of sex differences in disease susceptibility... Why some viruses may be less virulent in women (March 1, 2017).

Posts that mention nitric oxide:
* The miracle of Methylomirabilis (May 10, 2010).
* Garlic or rotten eggs? (February 8, 2010).

My page for Biotechnology in the News (BITN) -- Other topics has a section on Alzheimer's disease. It includes a list of related Musings posts.

January 11, 2023

Briefly noted... Making male and female stem cells from one person

January 11, 2023

What's the difference between cells of males and females? Well, one has one each X and Y chromosomes and the other has two X chromosomes, in addition to the usual complement of autosomes. But if we try to study male vs female cells, it's not so simple, because they come from different people, so have their genetic differences. A new article reports making both male and female stem cells from the same person. There is a trick -- and nature did the trick. The donor was a person with XXY sex chromosomes (Klinefelter syndrome). And the person was actually mosaic, with cells of various types. What the scientists did was to make induced pluripotent stem cells (iPSC) from the person; they got stem cells of various types, because the person had various cell types. This will allow studies comparing cell lines that are (nominally) identical except for the sex chromosomes.
* News stories:
- Male and Female Stem Cells Derived from One Donor in Scientific First -- Studying otherwise identical XY, XX, X0, and XXY pluripotent stem cells will allow researchers to investigate sex-based differences in greater depth. (Dan Robitzski, The Scientist, December 22, 2022.)
- Hadassah Researchers Are First in World to Derive Male and Female Cells from the Same Person -- Breakthrough opens path to new discoveries in study of sex differences and development of gender medicine. (Hadassah, November 29, 2022.)
* The article, which is open access: Modeling sex differences in humans using isogenic induced pluripotent stem cells. (Ithai Waldhorn et al, Stem Cell Reports 17:2732, December 13, 2022.)
* There is a BITN page for Cloning and stem cells. It includes lists of Musings posts.

Using an enzyme to make quantum dots

January 6, 2023

Quantum dots are useful, but hard to make. A new article reports use of an enzyme to make cadmium sulfide (CdS) quantum dots in a simple and inexpensive way. The enzyme itself is an artificial enzyme, which had been developed for another purpose.

The following figure gives the idea...

What's going on here? One key issue is that the enzyme is releasing sulfide ion, S^2-, from the cysteine, with PLP as a cofactor. This is related to the property originally found for the protein; it served to reduce the toxicity of metal ions to E coli bacteria, perhaps by leading to the precipitation of the metal sulfide. The current work is an application, where the sulfide is used to make CdS quantum dots -- in vitro.

The common stereoisomer of cysteine is L, used in the work described above. A test showed that the D isomer worked equally well.

The system seems to be reproducible, and to allow growth of the quantum dots at a consistent rate. That may be due to the production of sulfide at a controlled, and very slow, rate. (I must say that I wonder whether the protein is also providing a template for the growth of the quantum dots. There is no reason to invoke this, and the article does not mention it.)

The article is of interest at two levels. First, it is an example of an interesting artificial protein. Second, it may be useful in developing a novel process for making quantum dots.

News story: Chemists create quantum dots at room temp with lab-designed protein. (Wendy Plump, Princeton University, December 12, 2022.)

The article: A de novo protein catalyzes the synthesis of semiconductor quantum dots. (Leah C Spangler et al, PNAS 119:e2204050119, December 12, 2022.) The authors have filed for a patent on their process.

Another case of biology-mediated production of quantum dots: Unusual synthesis of cadmium telluride quantum dots (February 15, 2013). The article of this earlier post is reference 24 of the current article.

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