Tag: Biochemistry

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changing leaves by Nancie Zivetz-Gertler

mix in some sugar
and the red only deepens
the leaves are changing

by Nancie Zivetz-Gertler

A poet with no background in the actual science of trees , writing haiku often leads me to learn unexpected things!

I was working with the kigo “changing leaves” and wondered why the reds are so red, why so breathtaking….

Then I discovered anthocyanins!

Extract from ‘Why do leaves change color in the fall?’:

“Most of the year, these leaves are green because of the chlorophyll they use to absorb energy from sunlight during photosynthesis. The leaves convert the energy into sugars to feed the tree.

As the season changes, temperatures drop and days get shorter. Trees get less direct sunlight, and the chlorophyll in the leaves breaks down.

The lack of chlorophyll reveals yellow and orange pigments that were already in the leaves but masked during the warmer months. Darker red leaves are the result of a chemical change: Sugars that can get trapped in the leaves produce new pigments (called anthocyanins) that weren’t part of the leaf in the growing season. Some trees, like oaks and dogwoods, are likely to produce red leaves.

How much and how fast leaves transform varies by location on the globe. The best colors are produced when the weather is dry, sunny and cool. Places that are cloudy, damp or warm won’t see the same degree of changing color.”

Further reading:

‘Why do leaves change color in the fall?’, 2021, Smithsonian Story, available: https://www.si.edu/stories/why-do-leaves-change-color-fall

‘Autumn splendor: Why do leaves change color in the fall?’, 2017, STEMvisions Blog, Smithsonian Science Education Centre, available: https://ssec.si.edu/stemvisions-blog/autumn-splendor-why-do-leaves-change-color-fall

‘Autumn Views: Art That Captures the Mood, Color, and Light of the Fall Season’, autumnal art from across the Smithsonian, available: https://www.si.edu/spotlight/autumn

Author bio:

Nancie Zivetz-Gertler, a poet and visual artist, studies Haiku in a community of poets with Clark Strand. Her work has been published in Haiku Pause, Tricycle Haiku Challenge, Asahi Haikuist Network, Folk ku, Haiku Avenue and Cold Moon Journal. A recently retired psychotherapist, she lives in Bend. Oregon.

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Matriarch by James Penha

when earth spun faster
Luca settled in the sea
and begat us all

by James Penha

Last July, researchers at Bristol University concluded that Luca (last universal common ancestor from which all life on Earth stems) lived 4.2 billion years ago—early enough in the planet’s existence to suggest that life might be an inevitability rather than an accident.

Further reading:

‘Luca is the progenitor of all life on Earth. But its genesis has implications far beyond our planet’, 2025, Ball, P., The Observer, available: https://www.theguardian.com/science/2025/jan/19/luca-is-the-progenitor-of-all-life-on-earth-but-its-genesis-has-implications-far-beyond-our-planet

‘The nature of the last universal common ancestor and its impact on the early Earth system’, 2024, Moody, E.R.R., et al., Nature Ecology & Evolution, available: https://doi.org/10.1038/s41559-024-02461-1

Author bio:

Expat New Yorker James Penha (he/him ?) has lived for the past three decades in Indonesia. Nominated for Pushcart Prizes in fiction and poetry, his work is widely published in journals and anthologies. His newest chapbook of poems, American Daguerreotypes, is available for Kindle. Penha edits TheNewVerse.News, an online journal of current-events poetry. You can find out more about James’ poetry on his website https://jamespenha.com and catch up with him on BlueSky @jamespenha.bsky.social

Read more of James’ sciku here.

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Jellyfish by Mike Fainzilber

fifteen elephants
carefully balanced
on columns of fat

by Mike Fainzilber

Believe it or not, this is a haiku about jellyfish – specifically deep-sea jellyfish that live at depths where the water pressure is equivalent to that that would be applied by 15 African elephants piled up on the palm of the reader’s hand. When such jellyfish are brought to the water surface they literally vanish, melting into their surroundings.

Recent research has now shown that this is because the lipids (fat molecules) that make up the membranes of deep-sea jellyfish are specially adapted to form cylindrical structures (required for functional membranes) under extreme pressure. When pressures are reduced, these lipids change shape, causing membranes to curve and disrupt.

These findings are important for our understanding of how life is possible in the deep oceans and perhaps other high-pressure environments. Indeed, the researchers were able to take advantage of the new insights to engineer bacteria for survival under extreme pressures.

Further reading:

‘Homeocurvature adaptation of phospholipids to pressure in deep-sea invertebrates’, 2024, Winnikoff, J.R., et al., Science. Available: https://doi.org/10.1126/science.adm7607

‘How jellyfish survive pressures that would crush you into oblivion’, 2024, Cummings, S., Science. Available: https://www.science.org/doi/10.1126/science.zdvphja

Author bio:

Mike Fainzilber’s day job is a biologist. He began writing haiku and senryu during the pandemic, and this side effect of COVID-19 has not worn off yet. Editors in his two spheres of activity have been known to suggest that he should best restrict his efforts to the other sphere. Find out more about Mike’s research via his lab’s website and connect with him on Bluesky https://bsky.app/profile/mfainzilber.bsky.social .

Read more sciku by Mike here.

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Polypeptide Poem by Gillian Gaynor

Download Gillian Gaynor’s Polypeptide Poem for a closer look here!

a mind adrift
finding meaning in peptides
deciphering life

By Gillian Gaynor

Peptides are composed of chains of amino acids—organic molecules, encoded by a triplet combination of nucleotides in a strand of DNA or RNA (codon), that contain a carboxyl group, amino group and characteristic side chain.

A protein’s primary structure is determined by the specific sequence of amino acids in a polypeptide chain while the secondary, tertiary and quaternary structures are held together by intra- and intermolecular interactions and refer to the spatial arrangement and 3D conformation of the chain(s). The hierarchical nature of polypeptide formation and folding is crucial to its function as it allows proteins to perform specific roles in an organism.

Proteins are essential to nearly every biochemical process, serving as enzymes to catalyze reactions, hormones and neurotransmitters to regulate physiological responses, and structural units that contribute to the integrity of cells, tissues and bones, among many other examples.

Further reading:

‘Biochemistry, Peptide’, 2023, Forbes, J. & Krishnamurthy, K., StarPearls Publishing, available: https://www.ncbi.nlm.nih.gov/books/NBK562260/

Author bio:

Gillian Gaynor, a novice poet from Pittsburgh, received her bachelor’s degree in biochemistry from Notre Dame. Currently applying to medical school, Gillian bridges her scientific roots and budding poetic interests by crafting “polypeptide poems”—abstract haikus that challenge the reader to decode the hidden meaning in chains of amino acids.

You can connect with Gillian on LinkedIn here: https://www.linkedin.com/in/gilliangaynor/

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Tobacco Road by Michael H. Brownstein

tobacco pathways
across North America
ocean to ocean

by Michael H. Brownstein

Like many others, I always thought the native people of North America smoked and/or ingested a number of different plants to expose themselves to different plains of consciousness. This botany research reveals that isn’t the case. Tobacco was the main plant for smoking–perhaps the only one in certain areas–and it is also a study of how tobacco made it across the nation to the State of Washington.

Further reading:

‘An Ancient Residue Metabolomics-Based Method to Distinguish Use of Closely Related Plant Species in Ancient Pipes’, K.J. Brownstein, S. Tushingham, W.J. Damitio, T. Nguyen and D.R. Gang, 2020, https://doi.org/10.3389%2Ffmolb.2020.00133

‘Biomolecular archaeology reveals ancient origins of indigenous tobacco smoking in North American Plateau’, S. Tushingham, C.M. Snyder, K.J. Brownstein and D.R. Gang, 2018, https://doi.org/10.10bioche73/pnas.1813796115

Author bio:

Michael H. Brownstein’s latest volumes of poetry, A Slipknot to Somewhere Else (2018) and How Do We Create Love (2019) were both published by Cholla Needles Press. In addition, he has appeared in Last Stanza, Café Review, American Letters and Commentary, Skidrow Penthouse, Xavier Review, Hotel Amerika, Meridian Anthology of Contemporary Poetry, The Pacific Review, Poetrysuperhighway.com and others. He has nine poetry chapbooks including A Period of Trees (Snark Press, 2004), Firestorm: A Rendering of Torah (Camel Saloon Press, 2012), The Possibility of Sky and Hell: From My Suicide Book (White Knuckle Press, 2013) and The Katy Trail, Mid-Missouri, 100 Degrees Outside and Other Poems (Kind of Hurricane Press, 2013). He is the editor of First Poems from Viet Nam (2011). Michael recommends Project Agent Orange.

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Attachment

muscles need iron
so do mussels it appears
such sticky anchors

Iron is an essential element for almost all living organisms. The majority of iron in mammals is found in red blood cells (haemoglobin) and muscle cells (myoglobin), supporting the transport, storage and release of oxygen. In humans, iron deficiency is the most common nutritional deficiency in the world and can lead to iron-deficiency anaemia, symptoms of which include fatigue, headaches, weakness, angina, breathlessness, complications during pregnancy and delayed growth in infants and children.

Iron is also important for many animals, utilised to help strengthen hard materials such as rodent teeth or the carbonate armour of some gastropods. Yet iron can be found in soft biological materials too, including the sticky anchors that mussels use to attach to rocks and the threads that connect those adhesives to the mussels’ inner tissues.

To investigate the importance of iron in mussel anchors, Hamada et al. (2020) varied seawater iron levels in a controlled environment and examined adhesive thread samples from Blue mussels (Mytilus edulis) which had been living in the water for 3 days. The researchers measured thread strength by securing the entire length of the threads and measuring how much force was required to pull them until the adhesive failed.

Adhesive strength increased as the iron level of the water increased until an optimal amount was reached, after which the adhesive strength declined. Examination of the plaques themselves also revealed differences in morphology, including colour and microstructural features, arising from the different iron levels of the water.

The results confirm that iron is a key component of how mussels anchor themselves to rocks and demonstrate how changing ocean chemistry might affect these molluscs in the future.

Further reading: https://doi.org/10.1021/acs.est.0c02392

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These membrane proteins by Chris Gillen

These membrane proteins

might reclaim salt from urine

or suck it from ponds.

 

Mosquitoes face extraordinary challenges to their salt and water balance during their complex life-cycles. Larva of most species live in freshwater environments in which they lose salt by diffusion and gain water by osmosis. In contrast, adults live in terrestrial environments where water loss is a problem. Finally, female mosquitoes ingest large amounts of salt and water when they take a blood meal.

In vertebrates, the sodium-potassium-chloride cotransporters (NKCCs) participate in both salt secretion and absorption. Whereas secretory roles for this group of transporters are well-described in insects, their roles in salt absorption are less well studied. Piermarini et al (2017) recently identified yellow fever mosquito transport proteins that have sequence similarity to the vertebrate NKCCs. Two of these transporters apparently resulted from gene duplications early in the insect and mosquito lineages, suggesting that they have diverged into roles related to mosquito osmoregulation. The transporters may contribute to salt absorption, because the researchers found them in adult hindgut and larval anal papillae, both tissues that transport salt into the body.

Original research: Piermarini, P. M., Akuma, D. C., Crow, J. C., Jamil, T. L., Kerkhoff, W. G., Viel, K. C. M. F., and Gillen, C. M. (2017) Differential expression of putative sodium-dependent cation-chloride cotransporters in Aedes aegypti. Comp. Biochem. Physiol. A 214, 40-49. https://doi.org/10.1016/j.cbpa.2017.09.007

Chris Gillen teaches animal physiology and science writing at Kenyon College in Gambier, Ohio.  He is author of The Hidden Mechanics of Exercise (Harvard, 2014) and Reading Primary Literature (Pearson, 2007).

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Oh ketchup packet!

Oh ketchup packet!

How to get the last sauce out?

Hydrocarbon films!

 

Waste from packaging where food products can’t be completely extracted builds up. Now research by Mukherjee et al (2018) suggests a solution might be at hand. The researchers found that hydrocarbon-based polymer films can be stably impregnated with vegetable oils. The resulting material is slippery and durable, ideal for the inside of packaging to reduce food sticking and waste.

Whilst this sounds high-tech the researchers were actually inspired by the pitcher plant which uses a slippery coating on its leaves to capture visiting insects.

Original research: http://dx.doi.org/10.1038/s41598-018-29823-7

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Patches on Venus

Patches on Venus:

Atmosphere harbouring the

conditions for life?

 

In the hunt for extra-terrestrial life, Venus is rarely considered due to the high surface temperatures (~465 °C) and the intense atmospheric pressure (92 times that on Earth). Yet a new study by Limaye et al (2018) suggests that life off the surface of the planet may be possible since the lower cloud layer harbours conditions suitable for microbial life: water, solutes, ~60 °C and an atmospheric pressure roughly equivalent to Earth.

What’s more, observations of Venus have revealed dark patches in the atmosphere that change shape, size and position over time. These are made up of particles roughly the same size as common Earth bacteria and also absorb light of at a similar spectrum. The changes in patch patterns could therefore be the equivalent of algae blooms.

Venus is thought to have once had water on its surface, potentially for as long as 2 billion years providing enough time for life to evolve. As the surface water evaporated the microorganisms could have been transported to the clouds, in similar ways to how bacteria have been found in the atmosphere of Earth (although on Earth aerial microbes do not appear to remain aloft indefinitely). Life on the second planet from the sun therefore remains a possibility and only further observations and potentially even atmospheric sampling will reveal whether the changing dark patches are indeed patterns of microbial life.

Original research: https://doi.org/10.1089/ast.2017.1783

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Tiny passengers

What will satisfy

these cravings? I should ask my

tiny passengers.

 

Choosing what and how much to eat is crucial as even those nutrients that are normally beneficial can be harmful if consumed excessively. But the mechanism for how animals regulate the amount they eat isn’t always clear.

The common fruit fly develops a strong appetite for amino acid-rich food if fed a diet lacking in certain essential amino acids, and the fly’s reproductive effort will also decrease. However, this change in appetite and reproduction is suppressed if the fly has certain species of gut bacteria. Interestingly, when given the choice fruit flies will eat more food that contains these bacteria than food that doesn’t suggesting an ability of the flies to direct their own gut bacterial microbiome.

How the bacteria influence fruit fly behaviour and physiology is uncertain but results suggest that it is not down to the bacteria producing the missing amino acids for the flies or that the flies are consuming the bacteria themselves. Possible explanations are that the bacteria secrete metabolites that help the flies use their remaining amino acids more effectively or that the bacteria directly modulate the flies own nutrient sensing pathways so that the flies don’t recognise a decrease in amino acids. Leitão-Gonçalves et al, 2017.

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The drink of the gods

The drink of the gods

curbs oxidative stress through

clever conversions

 

The energetic demands of flying causes muscular oxidative damage. Whilst some foods have antioxidants, nectar doesn’t – a potential issue for flying nectar-feeding animals. To get around this issue hawkmoths appear to be able to “generate antioxidant potential by shunting nectar glucose to the pentose phosphate pathway”. Levin et al, 2017.

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Locked-In

Complete locked-in state.

Infra-red plus oxygen:

Communication!

 

Complete locked-in state is a condition where patients are suffering from motor paralysis but retain their mental processing abilities. The inability to control their own body movements has made communication with people suffering from this condition effectively impossible. However, by using functional near-infrared spectroscopy measure changes in frontocentral oxygenation patients were able to answer yes and no questions. Chaudhary et al, 2017.