Announcement

June 28, 2023

This is the final set of Musings posts -- at least for now.

This set completes 15 years of Musings, with 2,852 posts. (As discussed before, those numbers are not as precise as they sound. But they give an idea.)

I will continue to do light maintenance, at least for a while. So do let me know of problems. That includes text errors, things that are not clear, and science issues. If there is a new development that might change the perspective, let me know. That includes retractions. It is fundamental that science is always "in progress".

I will likely add occasional updates to some posts, with new findings that are interesting. I will provide a list of such updates at the top of this page, but plan no routine notifications of them.

The future? Probably none, but I will think about it, perhaps after a year.

Thank you to all!

And now, the parrots get the last word...

Beethoven's genome

June 26, 2023

A team of scientists -- with 28 author affiliations from three continents -- has reported the genome sequence for Ludwig van Beethoven. Actual conclusions are soft, but what they did is a fun story.

The scientists worked through several possible DNA sources, trying to evaluate the authenticity of each. They ended up with five hair samples with (largely) independent histories that they were sure were from Beethoven. When analyzed, all contained the same genome, showing that they are from the same person. That is, the identification of the genome as Beethoven's builds on multiple, substantially independent, lines of evidence. The discussion of the history of the samples is an interesting aspect of the article.

Beethoven had multiple health problems, and expressed the desire that history might figure them out. Perhaps the best known problem was his hearing loss. The analysis of his genome reported here offers no clues about the hearing loss. However, it does uncover mutations that likely promoted liver disease. The scientists also found sequences of hepatitis B virus in one hair sample. Historical records are inconsistent in describing the level of Beethoven's alcohol consumption. But the genetic factors, along with a liver virus and possible excessive alcohol, might all have contributed to the liver disease that was the likely cause of his death.

Although the primary story in the article is using Beethoven's genome to address his health issues, a couple of other points worth noting came out.

The work on authenticating the hair samples yielded another piece of information -- based on a negative finding. Previous work had suggested lead exposure, based on a hair sample. The current work, establishing the clear history of each sample, showed that the hair sample in question was not from Beethoven. Thus there is no evidence that lead poisoning was relevant, for his hearing loss or any other issues.

The genome analysis also uncovered another little story... Beethoven's ancestry is well-recorded back to Aert van Beethoven (1535-1609), his great-great-great-great-great grandfather. Other descendants of Aert are known, with documented details of ancestry. Five such males were also analyzed here. Interestingly, the Y chromosomes, signature of the male lineage, do not match. The best guess from all the available data is that there was what they call an extra-pair-paternity (EPP) event somewhere between Aert and Ludwig.

The article is an interesting application of modern DNA sequencing technology to an aspect of history.

News stories:
* DNA From Beethoven's Hair Reveals Clues About His Death -- The composer was predisposed to liver disease and had hepatitis B at the end of his life, a new study finds. (Will Sullivan, Smithsonian, March 23, 2023.)
* Beethoven's DNA -- Scientists have sequenced Beethoven's genome from locks of his hair, revealing clues to the composer's health and family history. (Tom Almeroth-Williams, University of Cambridge, March 22, 2023.) Excellent overview; lots of good pictures.

The article, which is open access: Genomic analyses of hair from Ludwig van Beethoven. (Tristan James Alexander Begg et al, Current Biology 33:1431, April 24, 2023.) (The author list contains a famous distinctive family name. The current author is the son of the 97-year-old naturalist so familiar from television.)

Thanks to Greg for sending the article, along with some comments that got us started on the post.

My page Internet resources: Miscellaneous includes a section on Art & Music. There is a list of related Musings posts; it includes two other posts noting Beethoven in the title.

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

Update added September 25, 2023.
Another news story about this -- especially interesting because Beethoven made the cover of a scientific journal.
* News story: About the Cover: B for Beethoven. (Terence Chorba, Emerging Infectious Diseases 29:1948, September 2023.) The original article of this post, above, is reference 2 of this news story.

Update added August 18, 2023.
A piece of skull, allegedly from Beethoven, has been donated to the Medical University of Austria, where it will be displayed -- and studied. The skull piece has been known for many years, but it has not been public. Its authenticity has been unclear. The first step will likely be to try to establish its authenticity, using the genome information discussed above.
* News story: Skull Fragments Thought to Be Beethoven's Return to Vienna. (Teresa Nowakowski, Smithsonian Magazine, July 28, 2023.)
* Thanks to Greg for sending this update.

Briefly noted... Human origins -- more complexity

June 21, 2023

Humans arose in Africa. It has been assumed that there was a single ancestral population in Africa -- for lack of data to the contrary. A new article provides data to the contrary. The key work is an extensive analysis of genomes from various modern African populations. Large-scale genome analysis is always complex, with conclusions largely from computer modals. But the results suggest that there have long been multiple distinct populations in Africa, with some genetic mixing. The human scene prior to migration out of Africa was more complex than we had thought. As so often, having more data suggests a more complex model -- one that is probably more realistic, but still just a model.
* News stories:
- A new understanding of human origins in Africa. (Phys.org (McGill University), May 17, 2023.)
- Unraveling the origins of humanity: New research challenges single-origin theory. (Bhavana Kunkalikar, News-Medical.net, May 21 2023.) More detailed.
* The article, which is open access: A weakly structured stem for human origins in Africa. (Aaron P Ragsdale et al, Nature 617:755, May 25, 2023.)
* An early post on the contribution of genome analysis to understanding the complexity of the human family tree: Contributions of Neandertals and Denisovans to the genomes of modern humans (July 6, 2016).
* There is more about genomes on my page BITN - DNA and the genome. It includes a list of Musings posts.

Plasticosis

June 18, 2023

There is a lot of waste plastic around. There is relatively little good information about its effects.

A recent article provides some good information about the effects of plastic in one species of sea bird in the wild. It may also be a step toward organizing information on the health effects of plastics.

The first figure shows stained tissue slices from the stomachs of three birds...

That grading scale is introduced in this article; it is an important outcome of the work. Tissue slices are analyzed in the lab, and given a score, by an objective scoring system.

Does the score have any significance? The following figure explores that question...

The point is that the observed stomach damage, as reflected in the grade, is related to the amount of plastic in the stomach. (It is not claimed that plastic is the only cause of stomach scarring.)

The scientists not only developed a grading scale, but also a word to describe the condition. The birds with stomach scarring due to plastic are said to have plasticosis.

News stories:
* Plasticosis: A new disease caused by plastic that is affecting seabirds. (Phys.org (James Ashworth, Natural History Museum), March 3, 2023.)
* Seabirds that swallow ocean plastic waste have scarring in their stomachs - scientists have named this disease 'plasticosis'. (Matthew Savoca, The Conversation, March 21, 2023.) General perspective. It refers (and links) to two recent articles from the same lab. The second one, referred to as "newest paper ", is the focus of this post.

The article, which is open access: 'Plasticosis': Characterising macro- and microplastic-associated fibrosis in seabird tissues. (Hayley S Charlton-Howard et al, Journal of Hazardous Materials 450:131090, May 15, 2023.)

A post about plastics in humans: Consumption of microplastics by humans: a report and review from WHO (September 23, 2019). A big caution about the whole field. Plastics are diverse in both chemical and physical properties, including size. These things matter.

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

Briefly noted... Can we make good vaccines and spare the sharks?

June 14, 2023

Squalene is an interesting chemical. It is a terpene, commonly used in vaccines as an adjuvant, to enhance the immune response. The main supply of squalene is shark liver. A recent article offers an alternative. There is a now a process for making a related chemical, called β-farnosene, using yeast. The new article reports making not only squalene but also a variety of related chemicals using that microbial β-farnosene. Testing suggests that some of the new chemicals may even be better than squalene. It's all early, but the article offers the possibility of better vaccines as well as eliminating one need to harvest endangered sharks.
* News stories:
- Synthesizing squalene to reduce need for shark liver oil. (Bob Yirka, Medical Xpress, February 23, 2023.) Good overview of the current work.
- Shark-Sourced Vaccine Ingredient May Be on Its Way Out. (Molly Campbell, Technology Networks, April 4, 2023.) Includes more of the background.
* The article, which is open access: Semi-synthetic terpenoids with differential adjuvant properties as sustainable replacements for shark squalene in vaccine emulsions. (Karl J Fisher et al, npj Vaccines 8:14, February 16, 2023.)
* This post is listed on my page Biotechnology in the News (BITN) -- Other topics in the section Vaccines (general).

An antidote to the mushroom toxin α-amanitin

June 12, 2023

Amanita phalloides, the death cap mushroom, is deadly. The major toxic ingredient is α-amanitin (AMA), a liver and kidney toxin. The drug treatments available so far are limited and poorly understood.

A new article reports an antidote to AMA. Further, it is an interesting story how the scientists found it.

Let's start with the bottom line...

The following figure shows that the benefit of the antidote can be seen in a simpler system...

How did they get the antidote? They started with the basics... how does the toxin work? They used CRISPR to knock out individual genes. From that screen, they identified pathways and genes that were needed for AMA toxicity.

One gene, STT3B, seemed of particular interest. (It codes for an enzyme involved in N-glycan synthesis, modifying proteins by adding sugar chains.)

They then screened for inhibitors of the STT3B enzyme -- starting with a collection of FDA-approved small molecules. The first stage of this screening was done "in silico", looking for binding of candidate drugs to the candidate target using computer modeling of the structures. ICG popped out. An inhibitor of a key enzyme needed by AMA. They found something that is promising, and it is already approved by the FDA. The two experiments discussed above were part of the drug characterization that followed its identification as a candidate.

Overall, the work here not only offers a promising lead, but provides some basic background for further drug development.

FDA = US Food and Drug Administration.

What does it mean that the chemical is already approved by the FDA? It has nothing to do with the current proposed use. It just means that, for some reason (use in diagnostics, in this case), the chemical has already been considered by the FDA. There is presumably much known about its pharmacology -- and safety. That prior knowledge can make it easier to get an agent approved for a new specific use. Full data on its effectiveness, and its safety in this context, is still needed.

Just to be explicit... The drug has not yet been tested in humans for the use discussed here. That is perhaps the next step. Direct translation from model organisms to humans is not to be taken for granted. Further, there are plenty of hints that the full situation may be more complex than discussed here. Finding and treating one important step is progress.

News stories:
* Scientists find possible antidote for death cap mushroom poisoning -- Indocyanine green identified using genome-wide CRISPR study and virtual drug screening. (Bethany Halford, C&EN News, May 16, 2023.)
* Possible antidote discovered for deadliest mushroom: study. (Daniel Lawler, Phys.org, May 16, 2023.)

The article, which is open access: Identification of indocyanine green as a STT3B inhibitor against mushroom α-amanitin cytotoxicity. (Bei Wang et al, Nature Communications 14:2241, May 16, 2023.)

More mushrooms and such:
* Are yeasts important partners in lichens? (September 12, 2016)
* Quiz: What is it? (September 23, 2014). Well, this animal looks something like a mushroom.
* SquarePants on Borneo (September 24, 2011)
* Lux aeterna: Mushrooms; Mozart (December 7, 2009)

Briefly noted... Might the doctor's politics affect how they treat COVID?

June 7, 2023

You may have noticed during the COVID pandemic... politics and science/medicine can get intertwined. A recent article addresses the issue with scientific data. As an example, American doctors who identify as politically conservative were more likely to suggest use of the drug hydroxychloroquine to treat COVID-19 than were liberal doctors. This is based on scientific polling, not on data from actual medical records. The broad issue has implications beyond COVID, of course. It's an intriguing article. As always, be careful with interpreting a single article.
* News stories. Note that one of these is the press release from the lead institution; the other is from an independent source that specializes in infectious diseases.
- Political leaning influences doctors' beliefs about COVID treatments, study finds. (Mary Van Beusekom, CIDRAP, February 7, 2023.)
- Political Leaning Shapes Physicians' and Laypeople's Beliefs About COVID-19 Treatments. (University of Pittsburgh, February 6, 2023.)
* The article, which is open access: The political polarization of COVID-19 treatments among physicians and laypeople in the United States. (Joel M Levin et al, PNAS 120:e2216179120, February 8, 2023.)
* Some background on hydroxychloroquine: Does post-exposure administration of hydroxychloroquine prevent Covid-19? A clinical trial (June 16, 2020).
* There is a BITN section for SARS, MERS (coronaviruses). It includes a list of Musings posts in the field.

The nanobacteria of Omnitrophota

June 5, 2023

You may not be familiar with Omnitrophota. It is a phylum of bacteria; rather, it would be if it gets officially recognized. So far, no member of the Omnitrophota has been grown in pure culture in the lab; most have not even been seen directly.

The Omnitrophota show up in metagenomic analyses, where one simply analyzes the DNA found somewhere, and infers what chromosomes -- hence organisms -- must be present. There are hints that these are tiny bacteria, which eat "everything", as the phylum name might suggest (omni-troph). They are related, and grouped into a candidate phylum, by their characteristic ribosomal RNA sequences.

A recent article presents the most thorough analysis of the Omnitrophota so far.

The first figure shows the genome sizes...

The next figure provides some information on cell size...

The genome sequences reveal not only the genome sizes, as shown above, but also the metabolic capabilities. Most of the genomes are streamlined, but they generally seem to have core metabolic genes. Interestingly, genes associated with symbiotic bacteria are common in the Omnitrophota. The scientists suspect that these bacteria live in close association with other bacteria. Perhaps they are unable to grow free-living, or at least to do so well. However, they appear to be very active organisms, just requiring a partner. Of course, that would explain why none of the Omnitrophota have been grown in pure culture in the lab.

The Omnitrophota are quite diverse. We saw diversity with the genome sizes; the specifics of the gene collections suggest diversity of metabolic capability.

The Omnitrophota would seem to warrant much further work. We consider them a group of relatives, based on the similarities of their ribosomal RNA, but beyond that they are very different. However, they will remain hard to study until we learn how to study them along with their hosts.

It is often said that most microbes have not yet been isolated or even identified. The work with bacteria of the not-yet-official phylum Omnitrophota illustrates the problem, and reinforces the importance of solving it.

News stories:
* Study Shines New Light On Ancient Microbial Dark Matter. (Astrobiology (Keith Cowing, University of Nevada, Las Vegas), March 17, 2023.) Don't worry about the complex figure at the top.
* Integrating genomes and qSIP to probe the activity of Omnitrophota -- Weaving between different data types allowed us to integrate otherwise discrete observations and build an incisive and testable picture of this enigmatic phylum. (Cale Seymour, Nature Portfolio Microbiology Community, March 20, 2023. Now archived.) From the lead author of the article. Good for background.

The article, which is open access: Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. (Cale O Seymour et al, Nature Microbiology 8:727, April 2023.)

A previous post involving metagenomics: The Asgard superphylum: More progress toward understanding the origin of the eukaryotic cell (February 6, 2017). A follow-up post is about the first lab culture of a member of the group, previously known only by metagenomics. Links to more.

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

Briefly noted... Rotation of Earth's inner core

May 31, 2023

The solid inner core of Earth does not rotate exactly as the rest of Earth does. It may rotate a bit faster or a bit slower; it varies. Slower rotation leads to it seeming to rotate backwards -- with respect to the mantle or surface. Reasons for the varying rotation of the inner core are not well understood, but may include magnetic and gravitational effects. Remember, that solid inner core is within a liquid region, so it is not tightly coupled to the upper layers. How do we know how the inner core rotates? Seismic waves provide information on what is inside Earth -- and the reflection patterns seem to be changing. A recent article explores this, with additional data from the archives. It's an interesting story, but a caution... The question and the tools may be of most interest at this point. The answers and explanations are murky.
* News stories:
- Study: Changes in Rotation of Earth's Inner Core Occur on Decadal Scale. (Sci.news, January 24, 2023.) Good overview of the work; includes a diagram of Earth's inner layers.
- Earth's inner core rotating slower than surface, study suggests (Update). (Daniel Lawler, Phys.org, January 24, 2023.) Includes more of the debate about what it all means.
* The article: Multidecadal variation of the Earth's inner-core rotation. (Yi Yang & Xiaodong Song, Nature Geoscience 16:182, February 2023.)
* More about the inner core: Briefly noted... Novel Fe-O compounds in the Earth's inner core? (April 26, 2023).

Can ticks transmit CWD prions?

May 28, 2023

CWD = chromic wasting disease, a prion disease of deer and related animals (cervids).

Deer carry ticks, and transmission of ticks between deer is likely, e.g. during grooming. Is it possible that the ticks can transmit CWD -- thus spreading the disease through a herd?

A new article offers some evidence suggesting that they can. Prion diseases are difficult experimental systems, and it is common that actual transmissions are hard to document, but the article makes tick transmission a possibility that should be considered.

The following figure shows one key result...

That result suggests that ticks could acquire prions from the deer they feed on.

The scientists also showed that some of the ticks found on deer in an infected herd do carry prions. That is, what they found in nature agrees with what they found in the lab.

There is no reason to think the prions can replicate in the ticks. Arthropods do not carry a mammalian prion gene, needed for prion "replication". (Remember, ticks are 8-legged; they are arachnids, along with the spiders, not insects.)

There is also no evidence for effective disease transmission from ticks to deer in a natural setting. That would be a very difficult experiment to do. But such disease transmission now seems quite possible -- and that is the point of the article.

News stories:
* Ticks Carry Chronic Wasting Disease and They Could Be Transmitting It to Wild Deer -- New research has found that ticks can ingest "transmission-relevant amounts" of CWD prions and may pose a risk to cervids. (Katie Hill, Outdoor Life, May 22, 2023.)
* Ticks may be able to indirectly spread chronic wasting disease. (Mary Van Beusekom, CIDRAP, May 22, 2023.)
* Ticks found to harbor and release prions of chronic wasting disease. (Pooja Toshniwal Paharia, News-Medical.net, May 17 2023.) Very detailed.

The article, which is open access: Ticks harbor and excrete chronic wasting disease prions. (H N Inzalaco et al, Scientific Reports 13:7838, May 15, 2023.)

Previous post: about CWD: Unusual nature of CWD; implications for transmission to humans (September 24, 2022).

For more about prions, see my page Biotechnology in the News (BITN) - Prions (BSE, CJD, etc). It includes a list of related Musings posts.

Among posts about ticks: An anti-freeze story: Why a tick carries a human pathogen (October 29, 2010).

Update added March 13, 2024.
Can plants serve as carrier in the transmission of prion diseases? A recent article shows that plants can take up prions via their roots, with resulting prion accumulation in the parts of the plant above ground. Mice fed such plants can acquire prion disease. As so often with prion work, the real-world implications are not clear, but this is another example of how hardy prions might spread through the environment. (The work here was done with two lab-adapted prion strains, from transmissible mink encephalopathy and scrapie.)
* News story: Plants can take up CWD-causing prions from soil in the lab. What happens if they are eaten? (Mary Van Beusekom, CIDRAP, February 22, 2024.)
* The article, which is open access: Plants as vectors for environmental prion transmission. (Christina M Carlson et al, iScience 26:108428, December 15, 2023.)

A new ice, with the density of liquid water

May 23, 2023

If you break a big object into smaller pieces, what is the density of the pieces? Imagine hitting a piece of glass or ice with a hammer. The individual pieces will have the same density as the original big block. Density is a property of the (type of ) material, and does not depend on size.

If someone did such a test and found that the density did not change, it probably would not be worthy of a scientific article. So, beware, we're up to something.

The work starts with ordinary ice, which is treated to break it into small pieces. Look at what happens...

It is not entirely clear what is happening. There is more data, and some computer modeling. The sense is that the thin layers of ice released by ball milling are re-arranging into a denser form -- an amorphous (non-crystalline) ice about the same density as liquid water. The authors think its structure is very much like liquid water -- just now frozen in place. (But note, that is not how it is made; it is made from common crystalline ice, of low density.) They think it might be considered a glassy form of water.

Many kinds of ice are recognized, including at least two forms of amorphous ice. The authors refer to their new material as MDA ice, for medium-density amorphous ice. If nothing else, MDA ice fills a gap between the previously known amorphous ices of low and high density.

The density of MDA ice is a bit more complicated than the graph above suggests. The material tested there is a mixture. From the measured density and percent of MDA, the authors calculate that the density of MDA ice is 1.06 +/- 0.06 g/cm³.

The list of water-ices gets longer. And it continues to raise questions about the nature of water. Amorphous ices, perhaps including MDA, are likely to be geologically important, especially in ultra-cold environments beyond Earth.

Movies: There are two movie files posted with the article, as Supplementary Materials. The first shows much of the process of making MDA ice in the lab, and may be worth a look (9 minutes; narrated, by the lead author). Movie 2 outlines the computational modeling (2 minutes; music, but no narration).

News stories:
* Scientists discover a new type of ice that behaves like liquid water -- It's been described as "stop-motion water". (Tibi Puiu, ZME Science, February 3, 2023.)
* Discovery of new ice may change understanding of water. (Nanowerk News (University College London), February 4, 2023.)

The article: Medium-density amorphous ice. (Alexander Rosu-Finsen et al, Science 379:474, February 3, 2023.)

More ice:
* Why is ice slippery? (September 9, 2018).
* Ice in your diamond? (April 23, 2018).

More things glassy: Turning metal into glass (September 21, 2014).

Effect of corticosteroids on brain function

May 20, 2023

Corticosteroids (glucocorticoids) are useful drugs (commonly as anti-inflammatory agents). However, they can have significant side effects, including effects on memory. The natural levels of such steroids fluctuate on a regular basis during the day (circadian rhythm), and there has been suspicion that the added steroid drugs interfere with the natural (endogenous) steroids.

A new article offers some clues about how the effect works. The work is in a rat model.

The article is complex; we'll just peek. The following figure shows a couple of pieces of evidence...

Overall, the article offers clues as to how the administered steroid affects the brain. Much of the work focuses on the hippocampus, a brain region associated with memory. (I skipped over details above, but part G of the figure is about gene function in the hippocampus -- affecting the circadian rhythm.) A simple point is to make clear that the memory effects seen with patients can be due to the added drug in healthy animals. Beyond that, understanding a drug better should open up new avenues for drug development.

News story: Long-Term Use of Steroids Could Impair Memory. (Neuroscience News (University of Bristol), April 16, 2023.)

The article, which is open access: Circadian regulation of hippocampal function is disrupted with corticosteroid treatment. (Matthew T Birnie et al, PNAS 120:e2211996120, April 6, 2023.)

A recent post about circadian rhythms: Daylight savings time: night-owls have more difficulty adapting (August 1, 2021). Links to more.

A post about another such steroid drug: Briefly noted... 1. Dexamethasone: first drug shown to reduce mortality due to COVID-19 -- and an important caveat (July 1, 2020).

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

Briefly noted... A hydrogen-powered comet?

May 16, 2023

The comet 'Oumuamua has fascinated astronomers since its discovery in 2017. Its behavior just doesn't fit. A recent article offers a new proposal to explain its unusual orbit. The key points are:
- In interstellar space it was bombarded by cosmic rays, which led to dissociation of water just below the cometary surface. The resulting hydrogen gas was retained within the comet.
- When it got near the Sun, the H₂ heated up and was forced out, effectively serving as a rocket -- changing the orbit.
There is no way to know for sure whether this is correct, but one prediction is that we might observe similar orbital (mis)behavior for Solar System comets, if only we find some of this tiny size.
* News story: Surprisingly simple explanation for alien comet 'Oumuamua's weird orbit. (Robert Sanders, University of California - Berkeley, March 22, 2023.) Excellent overview.
* News story accompanying the article: Astronomy: A compelling explanation for an enigmatic object -- Seemingly contradictory observations of the first known interstellar object are reconciled in a model that presents a simple and physically realistic framework for understanding the object's many peculiarities. (Marco Micheli, Nature 615:591 March 23, 2023.)
* The article: Acceleration of 1I/'Oumuamua from radiolytically produced H₂ in H₂O ice. (Jennifer B Bergner & Darryl Z Seligman, Nature 615:610 March 23, 2023.)
* 1I/'Oumuamua was mentioned in the post Briefly noted... 1. Visitors from beyond the solar system. (December 11, 2019).
* Previous post about hydrogen: Storing hydrogen in magnesium diboride nanosheets (May 15, 2023). Immediately below.

Should bags be made from torrefied paper?

May 14, 2023

Good idea, according to a recent article.

Here's why...

It's an interesting finding, which could lead to improved paper bags -- better able to tolerate getting wet.

What is this torrefaction? It's basically a dry heat treatment, or "roasting", in an inert atmosphere. It serves to bind things together in the paper. The authors had previously shown that it makes lignocellulose more hydrophobic; that led them to ask if it would have a similar effect on paper, which is nearer to pure cellulose.

The torrefaction has a downside. It is harder to digest the torrefied paper, perhaps for the same reason it is stronger. Thus it would be harder to recycle at the end of its useful lifetime. (Imagine that the paper is to be digested to glucose, and converted to biofuel.) The following figure shows that -- and shows a solution.

The work offers leads about making paper bags that can better withstand getting wet, and still serve as a sugar source for making biofuel at the end of their useful life as bags. The authors are clear that they have not done thorough economic analyses.

The article also introduces a technique that may well be new to you.

News stories:
* Stronger paper bags could be the answer to throwaway plastic -- A simple technique to make paper bags stronger, even when wet, would make them more reusable - and they can still be used for biofuel at the end. (Prachi Patel, Anthropocene, May 4, 2023.) (The story refers to the glucose content of the paper. What was actually measured was the recovery of glucose from the paper, which is somewhat distinct.)
* Stronger paper bags - reused repeatedly then recycled for biofuel - could be the future. (Tech Xplore (Jeff Mulhollem, Pennsylvania State University), April 19, 2023.)

The article: Torrefied paper as a packaging material and subsequently as a bioethanol substrate: Synergy of torrefaction and alkaline treatment for increased utility. (Jaya Tripathi et al, Resources, Conservation & Recycling 191:106882, April 2023.)

Previous posts about torrefaction: none.

More bags (posts with 'bag' in the title):
* Lamb-in-a-bag (July 14, 2017).
* What if the caterpillars ate through the plastic grocery bag you put them in? (May 26, 2017)
* Possible transmission of norovirus via reusable grocery bag (May 21, 2012).
* How to fold a bag (May 13, 2011).

Why bears don't get blood clots during hibernation

May 9, 2023

If people sit too long, they can get blood clots in their veins. The condition is called deep vein thrombosis. The clots can be fatal. Some people may be at increased risk for forming such clots.

You might wonder, then, do bears that hibernate over the winter get such blood clots? After all, they are nearly motionless for months.

They do not. A new article explores why.

You might wonder, then, if the answer has any relevance to humans. Bear with us for a bit; we'll come back to that.

The main work in the article was to compare active and hibernating bears. Turns out, blood clotting in hibernating bears is different; the blood platelets became the focus of attention.

To get further detail, the scientists looked at protein levels in the platelets of active and hibernating bears. The following figure summarizes the results -- and points to a candidate of interest...

What is this HSP47 protein? HSP means it is a heat-shock protein. But more to the point, it is known to play a role in blood clotting. Thus it appears that bears shut down a gene involved in blood clotting when they hibernate.

The scientists then looked at parts of the story in other mammals, using various tools; HSP47 is involved in blood clotting for all they examined. Pigs, mice, and ...

What about humans? We said that people who sit for extended periods may develop blood clots. However, there are known exceptions. For example, people who are paralyzed, unable to move their limbs, do not develop blood clots.

The following figure looks at the level of HSP47 protein in people with such paralysis...

Results for more people are shown in the article. Results vary, but certainly paralyzed people tend to have lower levels of HSP47.

In a separate study, people kept bedridden (for other reasons) began to show lower levels of HSP47 after about a month of inactivity. This suggests a natural process is at work, though its basis is unknown at this point.

One implication of the work is that inhibiting HSP47 might be a tool in reducing unwanted blood clotting. That is, inhibiting HSP47 may be a target for drug development.

Hibernating bears and paralyzed people share a feature, and that finding could lead to a drug development. It's an interesting article.

News stories:
* Rethinking What it Means to Sleep Like a Bear. (Science in the News (Harvard), May 4, 2023.)
* Humans, and piglets, and bears, oh my! Preventing dangerous blood clots. (Medical Xpress (University of Reading), April 13, 2023.)
* The paradox of thrombosis: Determining how hibernating bears and paraplegics avoid blood clots. (Phys.org (Max Planck Society), April 14, 2023.)

* News story accompanying the article: Medicine: Sleep like a bear -- Reduced expression of a platelet protein protects against thrombosis during chronic immobilization. (Mirta Schattner, Science 380:133, April 14, 2023.)
* The article: Immobility-associated thromboprotection is conserved across mammalian species from bear to human. (Manuela Thienel et al, Science 380:178, April 14, 2023.)

More about hibernating bears: Bears hibernate -- but stay warm (April 30, 2011).

More about blood clotting:
* Is erythritol a toxic sweetener? (April 8, 2023). This post and the current one both deal with the interaction of platelets and collagen, and the role of that interaction in clotting.
* COVID and cardiovascular events (blood clots) (October 3, 2022).
* Mechanism of blood clotting: how the von Willebrand factor works (May 18, 2021). Links to more.

Paint without pigment

May 4, 2023

The following figure shows two examples of color in biology. The figure is from a recent article, presented there as background.

That illustrates two ways to get color. The first, using "molecular absorption" by pigments to absorb some wavelengths out of the spectrum, is perhaps more familiar. We have learned more and more about the second, sometimes called structural color, in recent years.

Paint is commonly based on pigments -- the first approach. Can we make paint based on structural color? That is exactly what the new article reports.

Look...

The paint is made from aluminum and aluminum oxide. Making new colors just means organizing them differently.

The new paint also reflects infrared light very well. It thus leads to cooling of whatever it coats.

The paint is lightweight. Only about 0.4 g paint is needed to cover a square meter of surface. The authors estimate that it would take about three pounds of their paint to cover a jet airplane (Boeing 747) -- down from about a thousand pounds now. That is enough of a difference to result in meaningful fuel savings. Further, the new paint should be quite long-lived.

So far, the new paint has been made only at lab scale. However, the authors think the process can be developed at industrial scale.

News stories:
* Scientists Create World's Lightest Paint: Just 3 Pounds Covers a Boeing 747. (Fiona MacDonald, Science Alert, March 31, 2023.)
* UCF Researcher Creates World's First Energy-saving Paint - Inspired by Butterflies. Instead of pigment-based colored paint, which requires artificially synthesized molecules, a UCF researcher has developed an alternative way to produce colored paint that is more natural, environmentally friendly and light weight. (Katrina Cabansay, University of Central Florida, March 8, 2023.)

The article, which is open access: Ultralight plasmonic structural color paint. (Pablo Cencillo-Abad et al, Science Advances 9:eadf7207, March 8, 2023.)

A recent post about paint: A lightweight white paint (January 23, 2023).

More about structural color: How to "dye" carbon fiber -- with titanium dioxide (January 20, 2018).

Update added October 27, 2023. Scientists now report a paint that can remove carbon dioxide from the air and produce oxygen. The approach is to include photosynthetic bacteria (cyanobacteria) in the paint. Finding a suitable strain was an interesting and non-trivial task.
* News story: 'Green living paint' produces oxygen and captures carbon dioxide. (Paul McClure, New Atlas, October 18, 2023.)
* The article, which is open access: Oxygen evolution from extremophilic cyanobacteria confined in hard biocoatings. (Simone Krings et al, Microbiology Spectrum 11:01870-23, September 2023.)

Artificial exercise, using a robotic device glued to the muscle

May 2, 2023

Muscles can atrophy (degrade) if not used. Sometimes, a medical condition may preclude ordinary muscle use.

Perhaps we could exercise muscles artificially. Perhaps we could attach a robot to a muscle, to exercise it.

The following figure shows such a system, from a recent article...

Does it work? The following figure shows some data...

If you have concerns about the conclusion or other observations, we will just note that the article contains other results that generally support the point: the treatment with MAGENTA stimulation helped reduce muscle atrophy.

Overall, the work is encouraging. It should lead to further testing and development for specific situations in humans.

News stories:
* Scientists develop mechanically active adhesive that prevents muscle loss -- The device constantly stretches and contracts immobilized muscles to prevent muscle loss. (Tibi Puiu, ZME Science, November 23, 2022.)
* Wasting muscles built back better -- Programmable mechanically active adhesive makes muscles stretch and contract, preventing and enabling recovery from atrophy. (Benjamin Boettner, Wyss Institute (Harvard), November 14, 2022.)

* News story accompanying the article: Tissue regeneration: A bioadhesive robot to activate muscles -- Soft actuators composed of a tough bioadhesive/elastomer shell encapsulating a stimuli-responsive metallic spring provide in situ mechanical stimulation of skeletal muscles to promote muscle tissue rehabilitation and prevent atrophy. (Xuanhe Zhao, Nature Materials 22:149, February 2023.)
* The article: Active tissue adhesive activates mechanosensors and prevents muscle atrophy. (Sungmin Nam et al, Nature Materials 22:249, February 2023.)

Other posts about muscle include... Making better artificial muscles (March 13, 2018). Links to more.

Among posts about exercise...
* Effect of exercise on developing ALS (July 27, 2021).
* How exercise benefits the brain (August 9, 2020).

There is more about regeneration and related topics on my BITN page for Cloning and stem cells. It includes two extensive lists of related Musings posts.