New Study Deepens Understanding of How Animals See, and What Colors

 Researchers determined that animals adapted to land see more colors than animals adapted to water. Animals adapted to open terrestrial habitats see a wider range of colors than animals adapted to forests.
 Credit: Artwork by Matt Murphy

Gathering vision data for hundreds of vertebrates and invertebrates, U of A biologists have deepened scientists’ understanding of animal vision, including the colors they see.

Researchers have determined that animals adapted to land are able to see more colors than animals adapted to water. Animals adapted to open terrestrial habitats see a wider range of colors than animals adapted to forests.

However, evolutionary history — primarily the difference between vertebrates and invertebrates — significantly influences which colors a species sees. Invertebrates see shorter wavelengths of light, compared to vertebrates.

Biological sciences doctoral student Matt Murphy and assistant professor Erica Westerman recently published these findings in Proceedings of the Royal Society B, a top British scientific journal. Their article, “Evolutionary history limits species’ ability to match color sensitivity to available habitat light,” explains how environment, evolution and, to some extent, genetic composition influence how and what colors animals see.

Copper makes seed pods explode

A stiff polymer called lignin (stained red) is deposited in a precise pattern in the cell walls of exploding seed pods. Researchers identified three laccase enzymes required to form this lignin. No lignin forms in the cell wall (stained blue) when all three genes are knocked out by CRISPR/Cas9 gene editing. 
Credit: Miguel Pérez Antón

Plants have evolved numerous strategies to spread their seeds widely. Some scatter their seeds to the wind, while others tempt animals and birds to eat their seed-filled fruits. And a few rare plants – such as the popping cress Cardamine hirsuta – have evolved exploding seed pods that propel their seeds in all directions. In their new study published in PNAS, Angela Hay and colleagues – from the Max Planck Institute for Plant Breeding Research in Cologne, Germany – investigate what genes control the mechanical structure of these exploding seed pods. Their findings show that a key micronutrient – copper – is essential for laying down a precise pattern of lignin in the seed pods. Lignin is an abundant plant polymer found in lignocellulose, the main structural material in plants. It is present in plant cells walls and is responsible for making wood stiff.

C. hirsuta seed pods consist of two, long valves. When the seeds are ready for dispersal, these valves rapidly separate and coil back, firing seeds out across a large area. The secret to these pods explosive nature is their unique mechanical design, which features three stiff rods of lignin connected by hinges. These hinges are crucial for the explosive release of potential energy stored in the pod. To create these hinged structures, lignin is deposited in a precise pattern in a single layer of seed pod cells, called endocarpb.

How animals reach their correct size

The development of hundreds of C. elegans individuals growing in micro-chambers was recorded with time-lapse microscopy.
Credit: Towbin Lab

Adults of the same species usually differ very little in their size. A team from the University of Bern and the Friedrich Miescher Institute for Biomedical Research (FMI) in Basel has now discovered a mechanism that ensures such size uniformity. The research using nematodes showed that the speed of growth determines the speed of a genetic clock that times development. Thereby, individuals that grow slowly are given more time to grow and can reach the same adult body size.

By and large, individuals of the same species grow to the same size. This uniformity in size is astounding, since intrinsic randomness in developmental processes and in environmental conditions produce substantial differences in how fast individuals grow. Moreover, because animal growth is often exponential, even small differences in growth can amplify to large differences in size. How do animals nevertheless make sure to reach the correct size?

Lab Earthquakes Show How Grains at Fault Boundaries Lead to Major Quakes

A three-dimensional visualization shows how rock gouge can arrest a rupture (in red) but, with a combination of dynamic stressing and dynamic weakening, will ultimately re-nucleate the rupture shortly thereafter (in blue).
Credit: Vito Rubino / California Institute of Technology

By simulating earthquakes in a lab, Caltech engineers have provided strong experimental support for a form of earthquake propagation now thought responsible for the magnitude-9.0 earthquake that devastated the coast of Japan in 2011.

Along some fault lines, which are the boundaries of tectonic plates, a fine-grained gravel is formed as the plates grind against one another. The influence of this gravel on earthquakes has long been the subject of scientific speculation. In a new paper appearing in the journal Nature the Caltech researchers show that the fine gravel, known as rock gouge, first halts earthquake propagation, but then triggers the rebirth of earthquakes to generate powerful ruptures.

"Our novel experimental approach has enabled us to look into the earthquake process up close, and to uncover key features of rupture propagation and friction evolution in rock gouge," says Vito Rubino, research scientist and lead author of the Nature paper. "One of the main findings of our study is that fault sections previously thought to act as barriers against dynamic rupture may in fact host earthquakes, as a result of the activation of co-seismic friction weakening mechanisms."

Hallucinating to better text translation

Source/Credit: MIT

As babies, we babble and imitate our way to learning languages. We don’t start off reading raw text, which requires fundamental knowledge and understanding about the world, as well as the advanced ability to interpret and infer descriptions and relationships. Rather, humans begin our language journey slowly, by pointing and interacting with our environment, basing our words and perceiving their meaning through the context of the physical and social world. Eventually, we can craft full sentences to communicate complex ideas.

Similarly, when humans begin learning and translating into another language, the incorporation of other sensory information, like multimedia, paired with the new and unfamiliar words, like flashcards with images, improves language acquisition and retention. Then, with enough practice, humans can accurately translate new, unseen sentences in context without the accompanying media; however, imagining a picture based on the original text helps.

This is the basis of a new machine learning model, called VALHALLA, by researchers from MIT, IBM, and the University of California at San Diego, in which a trained neural network sees a source sentence in one language, hallucinates an image of what it looks like, and then uses both to translate into a target language. The team found that their method demonstrates improved accuracy of machine translation over text-only translation. Further, it provided an additional boost for cases with long sentences, under-resourced languages, and instances where part of the source sentence is inaccessible to the machine translator.

Bumps could smooth quantum investigations

Stamping or growing 2D materials onto a patterned surface could create models for 1D systems suitable for the exploration of quantum effects, according to a new theory by Rice University engineers. The “bumps” would manipulate the flow of electrons into bands that mimic 1D semiconductors.
Credit: Yakobson Research Group/Rice University

Atoms do weird things when forced out of their comfort zones. Rice University engineers have thought up a new way to give them a nudge.

Materials theorist Boris Yakobson and his team at Rice’s George R. Brown School of Engineering have a theory that changing the contour of a layer of 2D material, thus changing the relationships between its atoms, might be simpler to do than previously thought.

While others twist 2D bilayers -- two layers stacked together -- of graphene and the like to change their topology, the Rice researchers suggest through computational models that growing or stamping single-layer 2D materials on a carefully designed undulating surface would achieve “an unprecedented level of control” over their magnetic and electronic properties.

They say the discovery opens a path to explore many-body effects, the interactions between multiple microscopic particles, including quantum systems.

The paper by Yakobson and two alumni, co-lead author Sunny Gupta and Henry Yu, of his lab appears in Nature Communications.

Breakthrough paves way for photonic sensing at the ultimate quantum limit

Photonic chip with a microring resonator nanofabricated in a commercial foundry.
Photo credit: Joel Tasker, QET Labs

A Bristol-led team of physicists has found a way to operate mass manufacturable photonic sensors at the quantum limit. This breakthrough paves the way for practical applications such as monitoring greenhouse gases and cancer detection.

Sensors are a constant feature of our everyday lives. Although they often go unperceived, sensors provide critical information essential to modern healthcare, security, and environmental monitoring. Modern cars alone contain over 100 sensors and this number will only increase.

Quantum sensing is poised to revolutionize today's sensors, significantly boosting the performance they can achieve. More precise, faster, and reliable measurements of physical quantities can have a transformative effect on every area of science and technology, including our daily lives.

However, the majority of quantum sensing schemes rely on special entangled or squeezed states of light or matter that are hard to generate and detect. This is a major obstacle to harnessing the full power of quantum-limited sensors and deploying them in real-world scenarios.

New nanoparticles aid sepsis treatment in mice

Shaoqin “Sarah” Gong
Source: University of Wisconsin–Madison

Sepsis, the body’s overreaction to an infection, affects more than 1.5 million people and kills at least 270,000 every year in the U.S. alone. The standard treatment of antibiotics and fluids is not effective for many patients, and those who survive face a higher risk of death.

In new research published in the journal Nature Nanotechnology today, the lab of Shaoqin “Sarah” Gong, a professor with the Wisconsin Institute for Discovery at the University of Wisconsin–Madison, reported a new nanoparticle-based treatment that delivers anti-inflammatory molecules and antibiotics.

The new system saved the lives of mice with an induced version of sepsis meant to serve as a model for human infections, and is a promising proof-of-concept for a potential new therapy, pending additional research.

The new nanoparticles delivered the chemical NAD+ or its reduced form NAD(H), a molecule that has an essential role in the biological processes that generate energy, preserve genetic material and help cells adapt to and overcome stress. While NAD(H) is well known for its anti-inflammatory function, clinical application has been hindered because NAD(H) cannot be taken up by cells directly.

“To enable clinical translation, we need to find a way to efficiently deliver NAD(H) to the targeted organs or cells. To achieve this goal, we designed a couple of nanoparticles that can directly transport and release NAD(H) into the cell, while preventing premature drug release and degradation in the bloodstream,” says Gong, who also holds appointments in the Department of Biomedical Engineering and the UW School of Medicine and Public Health’s Department of Ophthalmology and Visual Sciences.

The interdisciplinary work was led by Gong along with Mingzhou Ye and Yi Zhao, two postdoctoral fellows in the Gong lab. John-Demian Sauer, a professor in the Department of Medical Microbiology and Immunology, also collaborated on the project.

An edible QR code takes a shot at fake whiskey

The days of fake whiskey could be numbered, thanks to a team of biomedical engineers from Purdue University and South Korea. The team, led by Young Kim, associate head for research and an associate professor in Purdue’s Weldon School of Biomedical Engineering, has developed an QR code on an edible silk tag that manufacturers can place in bottles of whiskey. Consumers can use a smartphone app to confirm the whiskey’s authenticity. 
Credit: Purdue University photo/John Underwood

In the future, when you order a shot of whiskey, you might ask the bartender to hold an edible fluorescent silk tag that could be found floating inside – even though it is safe to consume.

This little silk tag with a QR code is a security measure that could reveal if the whiskey you’re wanting to buy is fake. Simply using a smartphone to scan the tag, which was developed by biomedical engineers from Purdue University and the National Institute of Agricultural Sciences in South Korea, could confirm the drink’s authenticity.

There are, of course, no tags currently placed in bottles of whiskey. But this new anticounterfeiting technology, published in the journal ACS Central Science, could be a step toward not only finding a solution for the alcohol industry but also addressing fake medications.

“Some liquid medicines contain alcohol. We wanted to test this first in whiskey because of whiskey’s higher alcohol content,” said Young Kim, associate head for research and an associate professor in Purdue’s Weldon School of Biomedical Engineering. “Researchers apply alcohol to silk proteins to make them more durable. Because they tolerate alcohol, the shape of the tag can be maintained for a long time.”

Analysis of huntsman spiders reveals patterns of social behavior

 The Australian huntsman (Delena gloriosa) and her plastered egg sac.
Credit: Linda S. Rayor

A new study of huntsman spiders links evolutionary lineages with life history traits, providing patterns for predicting social behaviors in other less-studied species. Sociality is very rare in spiders – only five out of close to 1,300 huntsman species are known to exhibit social behaviors.

The study, “Huntsman Spider Phylogeny Informs Evolution of Life History, Egg Sacs and Morphology,” published in the journal Molecular Phylogenetics and Evolution, was part of the undergraduate thesis of lead author Jacob Gorneau ’20.

It represents the broadest and most in-depth phylogeny of huntsman spiders – a tree-like diagram showing evolutionary relatedness among groups of organisms – while incorporating extensive biology and life history data for each species. Compared with solitary species, the findings reveal, the social species live in larger permanent family group retreats until the offspring are up to a year old, have egg sacs plastered to surfaces so they can’t be moved and begin foraging later in their development.

“The social species are doing something different than all the other solitary species,” said Linda Rayor, the paper’s senior author and a senior research associate in the Department of Entomology in the College of Agriculture and Life Sciences (CALS).