Rice researchers set up aMicrosoft HoloLens as a mixed-reality sensor to feed VegSense, their application to measure understory vegetation, plant life that grows between the forest canopy and floor.

A proof-of-concept study by graduate student Daniel Gorczynski and bioscientistLydia Beaudrot shows VegSense could be a suitable alternative to traditional classical field measurements at a low cost.

Their study in Methods in Ecology and Evolution shows the hardware-software combination excels at quantifying relatively mature trees in the wild, which is one measure of a forest’s overall health.

Gorczynski came up with the idea to try HoloLens, commonly marketed as a productivity tool for manufacturing, health care and education. He developed the open-source software for the device and noted that while the combination is less effective at picking up saplings and small branches, there’s ample room for improvement.

Gorczynski said he was introduced to mixed-reality sensing while an undergraduate at Vanderbilt University and recognized its potential for biological studies. “It seemed sort of like a natural fit,” he said. Gorczynski brought the idea to Beaudrot in 2019 shortly after his arrival at Rice.

The combination of stock hardware and custom software cost far less than systems based onlidar (for “light detection and ranging”) most often used in three-dimensional field studies, said Gorczynski, who developed VegSense on a platform geared more toward 3D games and interactive experiences than hard science.

Field tests at Houston’s Memorial Park showed that at least for mature trees, the smaller solution is just as good. In their case study, VegSense easily detected 48 of 50 such trees in the target area, a circle about 30 feet in diameter that Gorczynski walked, looking up, down and around to build the 3D database. (“Imagine an asterisk with a circle around it,” he said, describing the data-capture pattern.)

“For this study, we wanted to be really deliberate in trying to replicate more traditional understory vegetation structure measurements,” Gorczynski said. “We tried to get that level of detail.”

What he sees as he scans the environment is a holograph-like grid pattern that tracks the surfaces of vegetation. “What’s really cool about that is you can see what the scanner is picking up, but also the spots you missed,” Gorczynski said. “The idea is to get the mesh to cover as much of the vegetation as possible because that’s what gets you the best scan.”

“The results were so nice that Dan quickly wrote it up for publication,” Beaudrot said, noting that Gorczynski expanded his validation of the gear during a subsequent field trip to Tanzania, the focus of one of 15 tropical forests in a recent rainforest study by the Rice group.

“This device can facilitate a lot of great ecological research, particularly because it’s so cost-effective,” she said. “Collecting vegetation information on the forest floor right now is really hard to do without a lot of manual labor, or a really expensive lidar system.”

“So this is a groundbreaking, cost-effective device,” Beaudrot said. “It’s not going to give you the same resolution data that lidar will, but this is just the first application. We hope making VegSense open-source to the ecological research community will spur all the potential ways it can be developed.”

Northrop Grumman, Conservation International and Rice supported the research.

Video: https://youtu.be/dBHfxvhMChU

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Materials provided by Rice University. Original written by Mike Williams. Note: Content may be edited for style and length.

The discovery involves a once maligned collection of molecules called reactive oxygen species (ROS), which are produced by anything that uses oxygen, like animals, people and plants. But Ron Mittler at MU has uncovered a redeeming quality of ROS — their role as a communication signal that can indicate whether plants are stressed out.

“When stressors from heat and drought are added together, plants don’t have ground water to draw from, so they close the stomata [leaf pores], and this makes the leaves become really hot,” said Mittler, whose appointment is in the College of Agriculture, Food and Natural Resources. “This is why the combination of drought and heat is really dangerous, because the leaf temperature is much higher than with a plant subjected to just heat. The change can be anywhere between two and four degrees, and that can make the difference between life and death.”

Plant stress is also tied to crop loss, but existing analytical research on the subject has typically focused on how crops react to just one stressor. However, Mittler said a plant’s survival rate will dramatically decrease as the number of stressors continues to increase to three to six different stressors. The key, he said, is to keep ROS levels in check. Either too much or too little can be damaging, but an optimum level of ROS can be considered safe for life.

Hooked on science

Born and raised in Israel, Mittler wanted to be a veterinarian while growing up. But, after enrolling at the Hebrew University of Jerusalem, he recalls spending a summer in the late 1980s as an undergraduate student working in an agriculture lab, where he got “hooked” on science — particularly the role of ROS in plants. Mittler has been studying ROS ever since.

“At the time, we were trying to identify why certain cell lines were more resistant to salinity than others,” he said. “That was my first-ever scientific research problem. But then I started to work on desert plants, and from there on reactive oxygen species and blue green algae.”

“Reactive oxygen species signaling in plant stress responses,” was published in Nature Reviews Molecular Cell Biology, a journal of Nature. Other authors include Sara Zandalinas and Yosef Fichman at MU; and Frank Van Breusegem at Ghent University in Belgium.

This study was supported by funding from the National Science Foundation (IOS-2110017, IOS-1353886, MCB-1936590 and IOS-1932639), the National Institutes of Health, the University of Missouri Interdisciplinary Plant Group, University of Missouri, Research Foundation — Founders (project G0D7914N) and the Excellence of Science Research (project 30829584). The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies.

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This shell (carapace), it’s been proposed, didn’t evolve from any similar structure in the crustacean ancestor, but appeared de novo (or out of the blue) through somewhat random co-option of the genes that also specify insect wings.

However, in a new study from the Marine Biological Laboratory (MBL), Research Associate Heather Bruce and Director Nipam Patel provide evidence for an alternate view: The carapace, along with other plate-like structures in arthropods (crustaceans, insects, arachnids, and myriapods) all evolved from a lateral leg lobe in a common ancestor.

This evidence buttresses their proposal for a new concept of how novel structures evolve — one which suggests that they aren’t so novel, after all. The study, on the carapace of the crustacean Daphnia, appears online in Current Biology.

“How novel structures arise is a central question in evolution,” Bruce says. “The prevailing idea, called gene co-option, is that genes that are functioning in one context, say to make insect wings, end up in an unrelated context, where they make, say, a carapace,” says Bruce. “But here we show that the Daphnia carapace didn’t just pop out of nowhere.”

Rather, they propose the ancestral, plate-like leg lobe that evolved into both the wing and the carapace was likely present in the ancestor of all living arthropods. But because the wing and carapace look so different from this ancestral plate, and from other plates in neighboring arthropod lineages, no one realized that they were all the same thing.

“We are starting to realize that structures that don’t look anything alike — wings, carapaces, tergal plates — are actually homologous,” Bruce says. “That suggests they have a single origin that is way more ancient than anyone would have thought, way back in the Cambrian period, [500 million] years ago.”

It was there all along (cryptic persistence)

Bruce calls her model for how novel structures emerge “cryptic persistence of serial homologs.”

“Serial homologs are things like hands and feet, or the vertebrae of our spine, or the many legs repeating down a centipede’s body,” she says. “The [repeats] can look really different, but you can see similarities, and they are all built using the same initial genetic pathways. In some cases, the full structure doesn’t grow out — you may get a truncated centipede leg, or it’s really subtle and tiny. While the cells have been programmed to form the leg, they aren’t actually growing out the leg.”

In Bruce’s view, these dormant rudiments — legs, plates, etc — can persist over millions of years, as long as another repeat of the structure is still present somewhere else in the animal. And when the time is right, the structure may grow out again and take different forms in different species — a wing in an insect, say, or a carapace in a crustacean.

“If an ancestral structure is no longer needed, nature probably just truncates or reduces that tissue rather than deleting it completely. But the tissue is still there and can be elaborated again in later lineages, and appear to us to be novel,” Bruce says.

“This kind of truncation is probably common in evolution because genetic networks are so interdependent, “Bruce explains. “if a genetic pathway or tissue were to be deleted, some other pathway or tissue would be affected.”

“I think cryptic persistence can be an explanation for a lot of ‘novel’ structures,” Bruce says.

The authors drew their conclusions by analyzing gene expression patterns in several arthropod species, and by eliminating other hypotheses of how the carapace may have evolved.

“The ancient, common origin of all these plate-like structures [in arthropods] suggests the gene networks that pattern these structures are very evolvable and plastic. They are capable of generating an awesome amount of diversity,” Bruce says.