Thursday, September 23, 2021

Olfacotry Camouflage

Scientists used 'fake news' to stop predators from killing endangered birds—and the result was remarkable
Mar 2021,

Amazing; you just don't hear about olfactory camouflage much:

Odors emanating from the shorebirds' feathers and eggs attract these scent-hunting mammals, which easily find the nests.

Five weeks before the shorebirds arrived for their breeding season in 2016, we mixed the odors with Vaseline and smeared the concoction on hundreds of rocks over two 1,000-hectare study sites. We did this every three days, for three months.

The predators were initially attracted to the odors. But within days, after realizing the scent would not lead to food, they lost interest and stopped visiting the site.

via: Grant L. Norbury et al. Misinformation tactics protect rare birds from problem predators, Science Advances (2021). DOI: 10.1126/sciadv.abe4164

Image credit: Lord of the Rings, scene where the Black Rider sniffs and misses.

Friday, September 10, 2021

Olfactory Training for Olfactory Dysfunction

Parking this here for future reference, and for anyone still having trouble getting their sense of smell back:

Hura N, Xie DX, Choby GW, Schlosser RJ, Orlov CP, Seal SM, Rowan NR. Treatment of post-viral olfactory dysfunction: an evidence-based review with recommendations. Int Forum Allergy Rhinol. 2020 Sep;10(9):1065-1086. doi: 10.1002/alr.22624. Epub 2020 Jun 25. PMID: 32567798; PMCID: PMC7361320.

Background: Post-viral olfactory dysfunction (PVOD) is one of the most common causes of olfactory loss. Despite its prevalence, optimal treatment strategies remain unclear. This article provides a comprehensive review of PVOD treatment options and provides evidence-based recommendations for their use.

Methods: A systematic review of the Medline, Embase, Cochrane, Web of Science, Scopus, and Google Scholar databases was completed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Studies with defined olfactory outcomes of patients treated for PVOD following medical, surgical, acupuncture, or olfactory training interventions were included. The Clinical Practice Guideline Development Manual and Conference on Guideline Standardization (COGS) instrument recommendations were followed in accordance with a previously described, rigorous, iterative process to create an evidence-based review with recommendations.

Results: From 552 initial candidate articles, 36 studies with data for 2183 patients with PVOD were ultimately included. The most common method to assess olfactory outcomes was Sniffin' Sticks. Broad treatment categories included: olfactory training, systemic steroids, topical therapies, a variety of heterogeneous non-steroidal oral medications, and acupuncture.

Conclusion: Based on the available evidence, olfactory training is a recommendation for the treatment of PVOD. The use of short-term systemic and/or topical steroids is an option in select patients after careful consideration of potential risks of oral steroids. Though some pharmacological investigations offer promising preliminary results for systemic and topical medications alike, a paucity of high-quality studies limits the ability to make meaningful evidence-based recommendations for the use of these therapies for the treatment of PVOD.

And don't forget:
Monell Center Scientists Find that Insulin is Necessary for Repairing Olfactory Neurons: Findings Point to Possible Treatment for Smell Loss
May 2021 - Monell Center

Thursday, September 9, 2021

Dark Taxa AKA Creating Taxonomies From Scratch

New norms needed to name never-seen fungi
May 2021,

There's 150,000 species of fungi known, yet a projected 2.2 to 3.8 million still waiting to be discovered (these are called dark taxa). But because of advances in DNA sequencing and microscopy, we're learning so fast that we need a new way to organize it all. 

This comes up in the context of biosecurity, where it can only work if "organisms detected can be reliably identified and have accurate names." For fungi, that's not really possible, because believe it or not, we don't have a good catalog of fungi. 
-via: Robert Lücking et al. Fungal taxonomy and sequence-based nomenclature, Nature Microbiology (2021). DOI: 10.1038/s41564-021-00888-x

We also don't have a good way to organize the words we use to describe everyday smells, and we don't have something like a "smell taxonomy." There are plenty of sub-domains that organize their relevant smells, found in subjects like coffee, wine, perfume, and culinary arts. They always seem to take the form of a wheel (not the most complex form). You can get a good start with everyday smells at the South Coast Air Quality Management District, who created a "Characterization of Odor Nuisance" odor wheel, with the help of environmental scientist Jane Curren at UCLA circa 2016. It was based on a bunch of phone calls made to the District where people were complaining about odors in their neighborhood. She took all the words they used and organized them. 

You could also look into Ann-Sophie Barwich who is a cognitive scientist who did her dissertion on olfactory categorization, and then wrote a book called Smellosophy. Probably one of the most interesting academics you will ever hear of. I mean, her master's thesis was about the relevance of  Leibniz causality on biological classification.

Image credit: Penicillin, Kew Royal Botanical Gardens for BBC

State of the World's Fungi, by the Kew Royal Botanical Gardens (2018), is the first ever State of the World's Fungi report revealing how important fungi are to all life on Earth. [pdf]
[State of the World's Fungi]

International Commission on the Taxonomy of Fungi (ICTF)

MycoBank is the on-line repository and nomenclatural registry provided in collaboration between the International Mycological Association and the Westerdijk Fungal Biodiversity Institute. It provides a free service to the mycological and scientific society by databasing mycological nomenclatural novelties (new names and combinations) and associated data, such as descriptions, illustrations and DNA barcodes. Nomenclatural novelties are each allocated a unique MycoBank number to be cited in the publication where the nomenclatural novelty is introduced, to conform with the requirements of the International Code of Nomenclature for algae, fungi and plants.

Identification and quantification of nuisance odors at a trash transfer station. Jane Curren, et al.  PubMed, Waste Manag. 2016 Dec;58:52-61. doi: 10.1016/j.wasman.2016.09.021. Epub 2016 Sep 28.

Post Script:
I'm looking at a popular science article about fungi. The first two "interesting" points, when looked at together, remind me of why I always have the feeling like fungi are from outerspace:
  • Fungi are in a kingdom of their own but are closer to animals than plants
  • They have chemicals in their cell walls shared with lobsters and crabs (you do know we're all becoming crabs, right?)

Monday, August 30, 2021

Promiscuous Pattern Recognition

Study reveals how smell receptors work
Aug 2021,

Big smell news - for the first time ever, using cryo-electron microscopy, we can see an olfactory receptor in action. And as expected, it doesn't work like any other receptor.

Odorant receptors are known for their 'promiscuous chemical sensitivity;' that's a scientific term, by the way. It means that any one receptor might be sensitive to hundreds of molecules, so it's been really hard  to figure out what makes any particular molecule match with a receptor.

They looked at the jumping bristletail (surprise - not the fruit fly) because it has only five types of receptors, and because one of those receptors (OR5) is really broad, responding to 60% of the smell molecules they presented to it (promiscuous).

So they look at this receptor in its default state, and then again as they expose it to smell molecules (either eugenol or DEET).

And? Its ion channel pore dilates. That's it. Both of the competing theories about how smells work were wrong. It turns out they work via nonspecific chemical interactions -- they are not recognizing a specific chemical characteristic, but something more general about the molecule itself.

And there you have it! Olfaction is still one of the strangest senses we have.

Don't forget to thank cryo-electron microscopy, and the hundreds of scientists who have been trying to figure this out over the past hundred years.

via Rockefeller University: del Mármol, J., Yedlin, M.A. & Ruta, V. The structural basis of odorant recognition in insect olfactory receptors. Nature (2021).

Tuesday, August 24, 2021

Amoore' Anosmias Get a Tune-Up

Back in the 1960's, a scientist named John Amoore tried to get a number on how much our sense of smell varies from person to person. In his study (limited mostly to Europeans), he found that half are anosmic to something. That was long before we sequenced the human genome. This study goes a bit further:

There's a gene for detecting that fishy smell, olfactory GWAS shows
Oct 2020,
9,000 people in Iceland showed that not only do they smell licorice and cinnamon differently, but there's a mutation that makes rotten fish smell a little less fishy. (The odors they used weren't limited to these three, there were also lemon, peppermint, and banana.)

One of the genes is called a "non-canonical olfactory receptor gene" or a trace amine receptor, TAAR 5 in this case. People with a particular variant of this gene were more likely to not smell anything when presented with the fish odor or to use descriptors for it that were neutral or positive and not seafood related, such as "potatoes," "caramel," and "rose."

"Carriers of the variant find the fish odor less intense, less unpleasant, and are less likely to name it accurately," Gisladottir said. 

"We discovered a common variant in a cluster of olfactory receptors which is associated with increased sensitivity to trans-anethole, found in black licorice products but also in spices and plants such as anise seed, star anise, and fennel," Gisladottir said. "Carriers of the variant find the licorice odor more intense, more pleasant, and can name it more accurately. Interestingly, the variant is much more common in East Asia than in Europe."

The cinnamon variant influenced the perception of trans-cinnamaldehyde, the major ingredient in both Chinese and Ceylon cinnamon. Carriers of the variant can name the cinnamon odor more accurately, they report. They also find it more intense.

via deCODE Genetics in Reykjavik, Iceland: Current Biology, Gisladottir et al.: "Sequence variants in TAAR5 and other loci affect human odor perception and naming. DOI: 10.1016/j.cub.2020.09.012

Post Script:
Here's another way to measure the difference in how we smell things -- we have a 30% variation from person to person:
378-dimensional individual olfactory receptor subtype genome:
Individual olfactory perception reveals meaningful nonolfactory genetic information.
Secundo L, Snitz K, Weissler K, Pinchover L, Shoenfeld Y, Loewenthal R, Agmon-Levin N, Frumin I, Bar-Zvi D, Shushan S, Sobel N. Proc Natl Acad Sci U S A. 2015 Jul 14; 112(28):8750-5.

Friday, August 20, 2021

On Handshakes and Animal Behavior

AKA Olfactory Sampling

Non-human primates Mark Zuckerberg and Pope Francis shaking hands and about to smell each other's chemosignals once they start covertly raising their hands near their face in about 20 seconds from now.

After you shake someone's hand, you smell your own hand. Sometimes the shaking hand, and sometimes the opposite, depending on the gender match. They call it "olfactory sampling," but we call it "smelling your fingers," and despite its being in poor taste while in public view, we do it almost neurotically, albeit covertly -- so covertly that even we don't notice ourselves doing it. 

I'm surprised this didn't resurface at the outset of the pandemic when we were all paying so much attention to how often we touch our face. In fact, the authors set us up thus:
Consistent with previous studies (Nicas and Best, 2008), we observed that humans often bring their hands to their noses. Of 153 subjects, 85 (55.55%) touched their nose with their hand at least once during baseline before the greet. Idle subjects had a hand (either right or left) at the vicinity of their nose for 22.14% of the time. (that's a lot of time!)
But this isn't just about how you can't keep your own hands off yourself:
Whereas facial self-touching has been considered a form of displacement stress response (Troisi, 2002), akin to rodent grooming, the novel framework we propose here for this behavior is that of olfactory sampling.
In this really carefully controlled study, they videotaped  hundreds of people after shaking hands with a greeter at the lab, and even outfitted the subjects tubes near their nose to monitor their sniffing behavior. The results were "unequivocal," and remind us that we are in fact animals, sniffing up a storm:
We found that humans often sniff their own hands*, and selectively increase this behavior after handshake. After handshakes within gender, subjects increased sniffing of their own right shaking hand by more than 100%. In contrast, after handshakes across gender, subjects increased sniffing of their own left non-shaking hand by more than 100%. Tainting participants with unnoticed odors significantly altered the effects, thus verifying their olfactory nature. Thus, handshaking may functionally serve active yet subliminal social chemosignaling, which likely plays a large role in ongoing human behavior.

*For example, by touching their nose when they were in the room on their own; ... Criterion for scoring was any application of a hand to the face, as long as touching was under the eyebrows and above the chin; n=271 down to 153.
And later on in the report, things get even more complicated:
The body odor of some of the experimenters was tainted by perfumes or gender-specific odors. Volunteers who shook hands with these tainted individuals behaved differently; when the experimenter was tainted with perfume the volunteers spent more time sniffing their own hands, but when the experimenter was tainted with a gender-specific odor they spent less time sniffing of their own hands. This shows that different smells influenced the hand sniffing behavior of the volunteers.
Now that you know, you might notice yourself doing it constantly. What would be really interesting now would be to somehow get some anosmics up in the mix, maybe congenitally, maybe some recent long covid anosmics, and see how these numbers change?

Frumin I, et al. [incl Noam Sobel] A social chemosignaling function for human handshaking. eLife. 2015 Mar 03;4.

Tuesday, August 17, 2021

Did Someone Say Cheese?

Those funky cheese smells allow microbes to 'talk' to and feed each other
Oct 2020,

The more you learn, the more complicated it gets. So we know that the funky cheese smell of isovaleric acid is produced by bacteria, and we know that (some) cheese has fungus growing on it. But now we're told that they're all talking to each other, using other odor molecules.

The "cheese microbiome." Cheese doesn't house only one bacteria species, and it doesn't make only one smell, although isovaleric acid is a pretty good representative. There's a whole cheese microbiome, made of bacteria, yeast and fungi. Each one of these organisms secretes goop that digests their food, in this case that's the cheese. Their goop is kind of like making the whole world your stomach, where your digestive juices aid your digesting al fresco. As their external digestion approach does its thing, the target nutrients get broken down, and a by-product of that breakdown are odorous volatile organic compounds. 

What these researchers have discovered is that fungi also release VOCs, but instead of being an important part of the smell of cheese, they communicate to bacteria. Some bacteria accelerate their growth in the presence of the right fungi-gas. Others get real shy and shut down. These fungus VOCs do real-time genetic modification on the bacteria, changing the way they metabolize nutrients. They also eat the VOCs themselves. They eat smells. We can't eat smells. 

Anyway, the cheese microbiome now contains a VOC-ome sub-component, and this study hints that one day we may be looking very carefully at these VOC-omes, especially in the bio-factories of the future. 

via Tufts University: Casey M. Cosetta et al, Fungal volatiles mediate cheese rind microbiome assembly, Environmental Microbiology (2020). DOI: 10.1111/1462-2920.15223