26 Nov 2021

Vacuuming up eDNA

 by Yolanda Ridge

In crime shows the first thing detectives look for is fingerprints. I’m sure you know why —because every person has a unique pattern on the tips of their fingers. This means anything touched by the criminal could help to identify them.

 

Smart criminals wear gloves for exactly this reason. To stay one step ahead, detectives and scientists figured out how to look for something else that’s unique — DNA fingerprints.

What is DNA? It’s the alphabet used to write the instruction manual on how all living things develop, grow and function. A copy of this instruction manual is contained in every single cell of our body. Which means that if a criminal leaves a piece of hair of a speck of spit at the scene of the crime, scientists can examine the DNA within the cells to try and identify a suspect.

DNA fingerprinting has been available for a while but now there’s something new on the scene — environmental DNA. Better known as eDNA, environmental DNA is DNA that’s been shed by an organism into the environment. And it’s found almost everywhere — water, soil, ice and even air.

 

 

Environmental DNA is not being used to fight crime — at least not yet. But over the past ten years it’s been used to do some cool stuff including:

  • verify a new whale species in Mexico

  • monitor endangered fish species like the dwarf Galactus in Australia

  • determine whether there’s enough food for tigers in Bhutan

  • research biodiversity and native species in areas like Columbia

  • track polar bear populations and movement in the arctic

  • detect invasive species such as Asian carp, American bullfrogs and New Zealand mudsnails

  • detect microbes dangerous to plant, animal and human health in waterways around the world


More recently, scientists showed they could vacuum eDNA directly from the sky. To prove it, two different research groups identified DNA from animals at a nearby zoo in samples of the air.

 


To find out more about eDNA, check out these YouTube videos:


  1. EnviroDNA (Australia): https://www.youtube.com/watch?v=TQdTV1rAlWY

  2. From the World Wildlife Fund: https://www.youtube.com/watch?v=4YXfZvEvUgc


And keep following science blogs like this to learn more about how eDNA gets used in the future. It’s coming soon to a crime scene near you (but hopefully not too near you!).



Yolanda Ridge is a middle grade author, science writer and knowledge translation co-ordinator from Rossland, BC. Visit her website at www.yolandaridge.com to find out more.


Photo credits:

Fingerprint image by Stux from pixabay.com

DNA by Jerome Walker from Wikimedia Commons

eDNA image from Biological Conservation via ScienceDirect

Cloud DNA by Andrew Brumagen via Freethink


References:

https://doi.org/10.1016/j.biocon.2014.11.019

https://www.freethink.com/environment/environmental-dna-whale

https://www.science.org/content/article/dna-pulled-thin-air-identifies-nearby-animals

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwiz6Ob40Kr0AhUBHzQIHR5lDP8QFnoECAMQAw&url=https%3A%2F%2Fwww.usbr.gov%2Fresearch%2Fprojects%2Fdownload_product.cfm%3Fid%3D2513&usg=AOvVaw07mx_aLfvVMelg5lPygWdF

 

17 Nov 2021

What Happens When Scientists Give Their Discoveries Away?

The work that scientists do is real work. It takes time, careful effort, training, and applied knowledge. Sometimes there are hours of tiring or boring work. There can even be heavy lifting or danger! And always, the work of a scientist must be recorded accurately and shared among other scholars. 

So, what is the work of a scientist worth? There are lots of ways to answer that question, from the wages of a researcher working for a corporation or the complex roles of tenured professors and their colleagues at universities. What about their discoveries  -- what are those worth?

There's one example well worth remembering. A hundred years ago, when Frederick Banting, Charles Best, and James Collip discovered how to make insulin, a treatment for diabetes, they patented their discovery, and then sold the rights to the University of Toronto for a dollar each. Banting felt it was unethical for a doctor to profit personally from a lifesaving discovery. Best and Collip wanted to be sure that those who needed insulin would be able to afford it.

Here's another example from an article published this autumn, by Luke D. Lavis. He and his research team developed a new fluorescent dye. It's particularly useful for biologists studying cells. As Lavis wrote in his article, his team agreed to give samples of the dye to any researcher who asked. Over the next four years, they gave thousands of sample of over 50 kinds of dyes. The result has been great for researchers using the dyes, who have done complicated work with living cells stained to show tiny details. The result has also been great for the institute where Lavis and the team work. Read all about it at this link.

5 Nov 2021

Soaking Up Storms

 by Megan Clendenan

Where I live, in the Pacific Northwest, autumn means rain and plenty of it. The rain pours down and flies sideways, soaking your cuffs and everything else if you’ve forgotten an umbrella.


If you’re out walking during a storm in a city, you might notice rainwater soaking the streets, skidding across parking lots and sidewalks and then pouring into drains – if they aren’t clogged by soggy leaves or other debris. All that storm water draining into the sewer mixes with oils, heavy metals, pesticides and other pollutants that are on our roadways. In cities, where impermeable surfaces such as concrete sidewalks, roads and parking lots are common, a significant portion of rainfall ends up in the sewer system alongside whatever chemicals it has picked up along the way. Then, depending on the city’s location, it runs into nearby waterways, lakes or oceans.
 

With rising global temperatures and changing weather patterns, more than 50% of the world’s population now reside in cities, on the front line of climate change. How can cities cope? One strategy is to learn from nature, and adapt urban buildings, infrastructure, and surfaces to work with the surrounding ecosystem.
 

Take Seattle, Washington, a city with significant annual rainfall. In 2017, a nonprofit group called Urban Greenprint teamed up with engineers, biologists, and city planners to study how they could design buildings and infrastructure to help mimic the evaporation rate of the Pacific Northwest forest to help reduce flooding as well as reduce polluted runoff from washing into the nearby Pacific Ocean.

 

Can you count all the layers? Photo by Megan Clendenan

The forest consists of thousands of layers, which work together to slow the rain and retain moisture before it reaches the ground. Moss and tree bark can hold water like a sponge. Douglas fir trees, common to the area, have needles that spear raindrops, breaking them into smaller parts, increasing the amount of evaporation and decreasing soil erosion.
 

With thoughtful design, urban buildings and other infrastructure can mimic layers found in the forest. Living walls can slow rainfall as it moves from the roof, through the textured green wall, absorbing moisture during each stage of the process. Canopies, awnings, screens and wire sculptures can mimic the ability of pine needles to split raindrops and increase evaporation. Green rooftops and ‘rain gardens’ planted next to sidewalks can soak up water like sponges.


A rain garden next to a sidewalk also shields pedestrians
from the cars. Photo by Megan Clendenan

So next time I’m out during a big rainfall, I’m going to keep my eyes open for places where my city is soaking up the storm – and where adaptations could be made.

Design Concepts Learned from Pacific Northwest Forests, Urban Greenprint, Seattle
https://issuu.com/urbangreenprint/docs/urban_greenprint_seedkit_v1
https://www.asla.org/climatemitigation.aspx
https://www.nrdc.org/stories/green-infrastructure-how-manage-water-sustainable-way 


29 Oct 2021

Climbing Volcanoes

Climbing Volcanoes

By Elaine Kachala

I waited…and waited. One by one, people descended the mountain. They looked sweaty, red-faced, and they were breathing heavily. But where were my husband and daughter? They’d woke early to hit the trailhead at 6 am. But it was going on twelve hours since they’d left our campsite to hike Mount St. Helens—an active volcano in Washington State. 

The mountain stands at 8,363 (f) (2,549 m). The hike is 10 miles (16 km) with an elevation gain of 4500 ft (1,372 m). At first, the hike seems innocent enough with a gradual 1000 ft (305 m) climb. But it’s no ordinary hike! After the first two miles through forest and open meadows, the challenge to the summit begins. The next 2500 ft. (762 m) is a climb through mega boulder fields dusted with ash and pumice that can shred your skin. Did they remember to take gloves? The last 1000 ft. (305 m) climb to the crater rim is through ash and small rocks. Did they pack enough water and snacks?  At the summit is a cornice—an overhanging ledge caused by layers of wind-blowing snow. If you step on it, it could collapse with any weight. Even standing on rock or dirt near the cornice is risky. How close to the edge did they step for the perfect view? When Mount St. Helens erupted in 1980 it was one of the most destructive volcanoes in US history. It erupted again in 2008, and it’s still active. When will it erupt again? Scientists are monitoring it carefullyA lot of questions ran through my mind as I waited.

 

Photo by Dylan Klinesteker and Mount St Helens Institute

Alas! Twelve hours and 33 minutes later, they emerged, exhausted but satisfied. At first, they were quiet. I guess they were still processing the experience. They’d climbed a phenomenal beast of a mountain. And, they’d endured the most intense physical test of their lifetime. Back at the campsite, there was an eruption of a different sort: words and photos. 

I heard about their agonizing climb over the boulders and the endless trudge through deep ash. But at the summit, spectacular views were the reward, as Mount. Rainier appeared in the distance.

 

Photo by Dylan Klinesteker and Mount St Helens Institute

Mount St. Helens and Mount Rainier are part of the Cascade Range, also known as the Cascade Volcanic Arc. It’s a 1,200-mile (1,931 km) line of volcanoes from British Columbia to northern California.

Washington State has five volcanoes that are part of the Cascade Range, and that have a high or very high potential of blowing. They are Mount St. Helens, Mount Rainier, Mount Adams, Mount Baker, and Glacier Peak. Mount St. Helens is the youngest and most active.  

Will my husband and daughter venture to climb other volcanoes? Yes, actually. They attempted Mount. Adams (12,277 (f) 3,742 m)…but that’s another story!   

Are you ready for an epic volcano climb? If so, don’t wait too long! Strap on your boots, fill your water bottle, and expect the adventure of your life! Even if you’re not ready to climb to the summit, you can still experience these fascinating volcanic monuments with hikes around the mountains.


More about Mount St. Helens:

  • It began growing before the end of the Ice Age.

  • Captain George Vancouver of the British Royal Navy named the mountain in 1792 in honor of his friend, Alleyne Fitzherbert, a British diplomat.

  • Researchers call it a “living laboratory.” For three decades, scientists have been studying how land and life return after eruptions, and how to forecast future hazards. 


References

History. https://www.history.com/topics/natural-disasters-and-environment/mount-st-helens

Mount St. Helens Institute https://www.mshinstitute.org/about_us/

NASA Science. https://spaceplace.nasa.gov/volcanoes2/en/

Smithsonian https://volcano.si.edu/

USGS. Science for a changing world. https://www.usgs.gov/

Washington State Department of Natural Resources. https://www.dnr.wa.gov/

Washington Trails Association https://www.wta.org/go-hiking/hikes/mount-st-helens-monitor-ridge#trailhead-map

22 Oct 2021

Where Does The Green Go?

 by Kim Woolcock


It’s autumn where I am, and the leaves are turning. They look like they’re setting themselves on fire before they fall, going out in a blaze of glory. Crispy husks carpet the forest floor, ready to be turned into next year’s nutrients. 

 

Leaves of Acer palmatum subsp. matsumurae (Koidz) Ogata

Photo credit: 松岡明芳


I love it, but it also seems extravagant. Why don’t leaves just stay green until they fall?

It turns out the trees are being thrifty. The leaves are full of chloroplasts, which contain lots of chlorophyll, the green light-harvesting pigment that lets plants spin sunlight into sugar. Chlorophyll is expensive, nutrient-wise. It’s loaded with nitrogen, and so trees tuck it away for winter. They break down the chloroplasts, pack the nutrients for transport, and send them to the trunk and roots. When they’re done collecting what they need, they build a waxy wall between the branch and the leaf and then let the leaf drop.

Packing up the green pigment lets the yellow and orange pigments, carotenoids, shine through. They were there all along, helping the leaves capture light of different wavelengths, but they were masked by the green. As the chlorophyll is removed, the carotenoids pick up some of the slack, making as much energy as they can with the last rays of autumn.

Not all leaves turn yellow or orange—some turn flaming red, thanks to anthocyanins. These pigments aren’t there in the summer, but are made specially in the fall. They act as sunscreen, protecting other leaf molecules from sun damage after the chlorophyll’s gone. That’s why they’re brightest in areas where fall days are sunny. They’re also made from leftovers. As the days get shorter, leaves keep producing sugar and sending it to the roots. But when nights get too cold, sugar transport is slowed, and some sugar gets stuck in the leaves, where it’s made into anthocyanins instead.

 

The green is almost gone. Image credit: Sander van der Wel


It’s a big job, getting ready for winter. Consider a single aspen tree (Populus tremula). Researchers made a detailed calendar of fall events for this tree, tracking components such as pigments, metabolites, nutrients, and photosynthesis rate. The tree has several million leaves, each of which contains ~30 million cells. Each cell contains ~40 chloroplasts. So every autumn, the tree has to synchronize the dismantling and transport of 1015 chloroplasts (one quadrillion, or the total number of ants on earth, just for scale), all in about a month. That’s just one tree. No wonder they look like they’re on fire.

So that’s where the green goes. It’s stashed away in trunks and roots for the winter, waiting to be remobilized in spring. Winter has always seemed drab compared to fall, to me. But knowing this makes me look at winter tree trunks differently – they are actually full of secret green. 

 

Kim Ryall Woolcock is the co-author of Design Like Nature: Biomimicry for a Healthy Planet (Orca, 2021) with Megan Clendenan. Her next book Tough to be Tiny is coming out from Flying Eye Books in July 2022. You can find out more at www.kimwoolcock.com
 

Resources:

John King. 2011. “Reaching for the Sun: How Plants Work, second edition.” Cambridge University Press, Cambridge. 298 pp.

Johanna Keskitalo et al. 2005. “A Cellular Timetable of Autumn Senescence.” Plant Physiology, 139:4, 1635–1648. https://doi.org/10.1104/pp.105.066845

https://www.sciencedaily.com/releases/1997/10/971005050137.htm

 

 

15 Oct 2021

The Wild Side of Everyday Food

 by Anne Munier

Thousands of years ago, in what is now Mexico, people chewed a wild grass called teosinte, enjoying the sweet juice from the stalks. The plant was short and bushy-looking, with lots of stems going every which way. People didn’t bother much with the seeds, because they were covered by a hard, protective case.

But every once in a while a mutation -- or unexpected slipup in the plant’s genetic structure -- came along, and suddenly some plants appeared without seed casings. This wasn’t great news for the plant -- animals could eat and digest these unprotected seeds, so the plant was less likely to reproduce. It was pretty good news for people though, who got to finally taste the seeds!

Teosinte seed head. Photo credit: Two Row Times

In truth, even the “naked seeds” weren’t anything to get too excited about -- there were only a few per seed head, which were dry and potatoey-tasting. But they were good enough for people to eat, and even to plant a few (perhaps inadvertently at first, when seeds accidentally fell into the soil near people’s home). 

Hard little teosinte seeds. Photo Credit: Two Row Times

These seeds produced more naked-seeded teosinte. Over time, people learned that when they planted the seeds from their favourite plants -- say those with the biggest, juiciest, or sweetest seeds; or those easiest to grind into flour; or those less vulnerable to pest attacks -- many of the next generation’s plants would have these same characteristics. 
Over hundreds, perhaps thousands of years, farmers changed the plant from a bushy wild grass with lots of tiny seed heads, into a tall, straight plant with a few large cobs, each containing hundreds of big seeds. Not only did the plant provide more food, but it was easier to harvest, easier to eat, and, well, it just plain tasted better. In short, about 9000 years ago, these Mexican farmers turned the wild grass teosinte into maize (also called corn), now one of the most important food crops in the world! 

Lots of changes on the journey from teosinte to corn! Check out how large the cob is compared to a coin. Photo credit: Nicole Roger Fuller, National Science Foundation

The process of changing wild plants (and animals!) into domestic ones by choosing the favourite ones to reproduce is called selective breeding. It’s the basis of agriculture! While corn was being domesticated in Mexico, the same process was happening with wheat in the Middle East, bananas in New Guinea, rice in China, and millet in Africa (among so many others). 

Wild relatives of modern potatoes. Photo by L. Salazar

 
A commercially-sold banana beside a wild relative. Photo by A. D'Hont

Carrots still look much like wild carrots, though larger and juicy!

It’s Thanksgiving as I write this, one of many harvest festivals celebrated around the world. As we honour food, family and friends, I think of the special debt of gratitude we owe Indigenous People in all parts of the world who -- over millennia and still today -- learned and shared so much about the local environment, and how we can sustain communities with the gifts of nature.

(Traditional knowledge has many stories for the origin of corn/maize, taro, camas, and other important foods. Some of these stories are shared in books and online resources. Indigenous people keep this traditional knowledge as part of culture, history, and how the world is understood.)

8 Oct 2021

Rotifers!

 How the Bdelloid Rotifer Lived for Millennia—Without Sex

by Nina Munteanu 

 

As a child, I always wanted a microscope.

I would have collected slimy waters from the scum ponds and murky puddles near my house. I would have brought them home and exposed them to the light of my microscope. I would then have peered deep into a secret world, where shady characters and alien forms lurked and traded.

It would be many years, when I was in college, before I finally witnessed this world—so alien, it might have inspired the science fiction books I wrote later as an adult. As it turned out, I was led to pursue a Masters of Science degree, studying periphyton (microscopic aquatic communities attached and associated with surfaces like rocks and plants) in local streams in the Eastern Townships of Quebec.

While my work focused on how diatoms (glass-walled algae) colonized surfaces, micro-invertebrates kept vying for my attention. Water fleas (cladocerans), copepods, rotifers, seed shrimps (ostracods) and water bears sang across my field of vision. They flitted, lumbered, wheeled and meandered their way like tourists lost in Paris. But this wasn’t Paris; I’d taken the blue pill and entered the rabbit hole into another world...


 

The Secret—and Dangerous—World of Micro-Organisms

Small freshwater habitats are home to a highly productive and diverse collection of micro-invertebrates—multicellular animals that can barely be seen with the naked eye. Many average from 0.5 to 1 mm in size and resemble little white blobs; however, a scholar can distinguish each invertebrate by its unique movement. For instance, when presented with a jar of pond water, I can usually distinguish among the wheel-like wandering of a gastrotrich, dirigible-like gliding of an ostracod (seed shrimp), the vertical goldfinch-style “hopping” of the cladoceran (water flea) as it beats its antennae, or the halting-jerking movements of copepods (oar-feet) as their antennae drive them along like a dingy propelled by an amateur oarsman.


Alas, puddles, ephemeral ponds and vernal pools pose sketchy habitats, given their tendency to appear and disappear. These environments are ever-changing, unstable, chaotic and unpredictable. Yet, anyone who has studied these ecosystems understands that they team with life.


When a puddle or ephemeral pond dries up then reappears with rain, how can these communities thrive? Do they all die off and then somehow recruit when the pond reappears? Many of these invertebrates have evolved creative ways to survive in very unstable environments. Some form a resting stage—a spore, resting egg or ‘tun’—that goes dormant and rides out the bad weather.


Animalcules & Sleeping Rotifers

Rotifers are cosmopolitan detrivores (they eat detritus) and contribute to the decomposition of organic matter. Rotifers create a vortex with ciliated tufts on their heads that resemble spinning wheels, sweeping food into their mouths. They often anchor to larger debris while they feed or inch, worm-like, along substrates. Some are sessile (attached), living inside tubes or gelatinous holdfasts and may even be colonial. Others move about and may temporarily anchor themselves as they feed. Rotifers include species that alternate sexual reproduction with asexual reproduction, depending on environmental conditions.

Bdelloid Rotifer as photographed by Bob Blaylock

In 1701, Antonie van Leeuwenhoek observed that “animalcules” (likely the bdelloid rotifer Philodina roseaola) survived drying up and were “resurrected” when water was added to them. He’d discovered a highly resistant dormant state of an aquatic invertebrate to desiccation.


Dormancy is a common strategy of organisms that live in harsh and unstable environments and has been documented in crustaceans, rotifers, tardigrades, phytoplankton and ciliates. “Dormant forms of some planktonic invertebrates are among the most highly resistant … stages in the whole animal kingdom,” writes Jacek Radzikowski in a 2013 review in the Journal of Plankton Research. Radzikowski describes two states of dormancy: diapause and quiescence.


Diapausing results in the production of a dormant egg or cyst whose thick envelope or shell protects it from drying, freezing, mechanical damage, microbial invasion and predation, UV radiation and harmful chemicals. Many survive being eaten and can resist vertebrate digestive enzymes, helping them disperse and colonize isolated water bodies. Diapause is controlled by an internal mechanism that is initiated by various cues, such as temperature or photoperiod. In short-lived organisms, it is typically initiated only in a single ontogenetic stage. “Breaking of diapause requires specific cues, and not necessarily the return of favorable conditions,” writes Radzikowski.


Quiescent dormancy does not involve the production of a dormant egg or cyst; rather it involves a transformation of the organism itself into a dormant state through a process called cryptobiosis. “Quiescence is … induced directly by the occurrence of harsh environmental conditions. A quiescent organism can enter this state in many stages of its life, and remains dormant only until the adverse conditions end,” writes Radzikowski.


The All-Female Bdelloid Rotifer

I recently had a chance to study a pond sample in a Petri dish through a friend’s microscope. Attached to a pile of detritus shivering in the current like trees in a gale, were several microscopic rotifers; they were feeding. Their ciliated disk-like mouths twirled madly, capturing plankton to eat. Watching them reminded me of my early research days at Concordia University in Montreal. Probably Philodina (a bdelloid); I had seen many during my stream research in Quebec.


The bdelloid rotifer has dispensed with sexual reproduction entirely and reproduces exclusively by female parthenogenesis. All-female bdelloid rotifers have thrived for forty million years. They’re everywhere, in temporary ponds, moss, even tree bark. Part of the reason for their incredible success lies in their strategy of quiescent dormancy.


In response to unfavourable conditions like a pond drying up, bdelloid rotifers enter a process called anhydrobiosis, contracting into an inert form and losing most of their body water. The bdelloid withdraws her head and foot and contracts her body into a compact shape called a tun; a dormant state that remains permeable to gases and liquids. In this state, bdelloid rotifers can resist ionizing radiation because they can repair DNA double-strand breaks. Early research noted that dormant animals could withstand freezing and thawing from −40°C to 100°C and storage under vacuum. They also tolerated high doses of UV and X radiation. Later work reported that some rotifers could survive extreme abiotic conditions, such as exposure to liquid nitrogen (−196°C) for several weeks or liquid helium (−269°C) for several hours. Dried up adult bdelloid rotifers apparently survived minus 80°C conditions for more than 6 years.


Dormancy is an elegant technique to ride out harsh conditions. The bdelloids can go dormant quickly in any stage of their life cycle—embryo, juvenile or adult—and they’re capable of remaining dormant for decades. They can recover from their dormancy state within hours when the right conditions return and go on reproducing without the need to find a mate.


Research has shown that bdelloid mothers that go through desiccation produce daughters with increased fitness and longevity. In fact, if desiccation doesn’t occur over several generations, the rotifers lose their fitness. They need the unpredictable environment to keep robust. This is partly because they incorporate genes from their environment during anhydrobiosis. When dormant, they acquire mobile DNA and stitch it into themselves through a process called horizontal gene transfer (HGT).


Bdelloid rotifers carry change inside them, through phenotypic plasticity, physiological stress response mechanisms, or life history adaptations. That’s why the bdelloid rotifers survived for millennia and will continue for many more. They are able to keep up with rapid and catastrophic environmental change, not to mention something as gigantic as climate change. They adapt by counting on change.



References:

Munteanu, Nina. 2020. “A Diary in the Age of Water.” Inanna Publications, Toronto. 300pp.


Munteanu, Nina. 2016. “Water Is…The Meaning of Water.” Pixl Press, Vancouver. 586pp.


O’Leary, Denise. 2015. “Horizontal gene transfer: Sorry, Darwin, it’s not your evolution anymore.” Evolution News, August 13, 2015. Online: https://www.evolutionnews.org/201508/horizontal_gene/


Ricci, C. And D. Fontaneto. 2017. “The importance of being a bdelloid: Ecological and evolutionary consequences of dormancy.” Italian Journal of Zoology, 76:3, 240-249.


Robinson, Kelly and Julie Dunning. 2016. “Bacteria and humans have been swapping DNA for millennia”. The Scientist Magazine, October 1, 2016. Online: https://www.the-scientist.com/?articles.view/articleNo/47125/title/Bacteria-and-Humans-Have-Been-Swapping-DNA-for-Millennia/


Weinhold, Bob. 2006. “Epigenetics: the science of change.” Environmental Health Perspectives, 114(3): A160-A167.


Williams, Sarah. 2015. “Humans may harbour more than 100 genes from other organisms”. Science, March 12, 2015. Online: http://www.sciencemag.org/news/2015/03/humans-may-harbor-more-100-genes-other-organisms