“We’ve shown that by using high quality transcriptomic data we can answer a long-standing question to the best of our current techniques,” said Dr. Konstantin Khalturin, Staff Scientist in OIST’s Marine Genomics Unit and first author of the paper published in Science Advances.

A genome is the full set of genetic information found in every cell. It is subdivided into genes. These genes are made up of DNA base pairs and each gene contains the instructions needed to create a protein, and thus leads to the proper care and maintenance of a cell. For the instructions to be carried out, the DNA must first be transcribed into RNA. A transcriptome is the result of this, like the reflection of a genome but written in RNA base pairs rather than DNA.

This genetic information differs among species. Those who are closely related have very similar genetic information, while a greater evolutionary distance results in more genetic differences. By using this data, researchers have improved our knowledge of animal evolution, but some questions still prove difficult to answer.

As Kamptozoa and Bryozoa are closely related to mollusks, annelids, and nemertea, small mistakes in the dataset, or missing data, can result in an incorrect placement on the evolutionary tree. Furthermore, while collecting these tiny animals, it’s easy to pick up other organisms, such as algae, that contaminate the sample. Dr. Khalturin highlighted that they were careful to avoid contamination and later screened their dataset for RNA of algae and small animals to remove any that might have come from them.

In total, the researchers sequenced the transcriptome of four species of Kamptozoa and two species of Bryozoa, but to a far higher quality level than had previously been achieved. While past datasets had completeness of 20-60%, in this study, the transcriptome completeness was over 96%.

Using these transcriptomes, they predicted proteins and compared them to similar data of 31 other species, some of which were closely related to Kamptozoa and Bryozoa, such as clams and bristleworms, and others which were more distant, such as frogs, starfish, insects, and jellyfish. The high-quality datasets meant that they could compare many different genes and proteins simultaneously. Dr. Khalturin credited the powerful computational capabilities that the researchers could access at OIST.

“Our main finding is that the two phyla belong together,” said Dr. Khalturin. “This result was originally proposed in the 19th century by biologists who were grouping animals based on what they looked like.”

While Dr. Khalturin stated that this question had now been answered to the best ability available, he also highlighted that the dataset could answer other fundamental evolutionary questions — such as the more precise location of mollusks and annelids on the tree of life, and how life diversified.

The paper in the journal Science Advances brought together experts in salmon ecology, watershed science, mining impacts and mining policy to integrate knowledge across research fields that often work independently from one another. Led by UM researchers at the Flathead Lake Biological Station, the team found past and present mining pressures are extensive across the region and often overlap with important populations of salmon, trout and char.

“Our paper highlights the mosaic of more than 3,600 active and abandoned mines sitting amongst some of the most valuable fish habitat in western North America,” said Chris Sergeant, an FLBS research scientist and the paper’s lead author. “The largest of these mines processes around 160,000 metric tons of earth every day.”

Sergeant said not all mines pose the same level of risk, but their review revealed that harm from mining can be severe and long-lasting. The extent of mining pressures on these watersheds underscores the importance of accurately assessing risk to water, fish and communities.

The study reviewed the ecological complexity of rivers and how mines can impact culturally and economically important fish species such as salmon by contaminating waters with heavy metals, burying stream habitat and diverting water for processing ore. When not managed properly, these cumulative impacts can be impossible to reverse and degrade landscapes for decades to centuries.

“Unfortunately, in some cases, we are learning the hard way that mines can have profound impacts on aquatic ecosystems, leaching far down the watershed from the actual mine site, at scales that were not anticipated in the original impact assessment,” said Erin Sexton, a paper co-author and FLBS senior scientist. “For example, impacts from the Elk Valley coal mining complex in southeast British Columbia have been documented over 155 miles downstream of the mines, crossing the U.S.-Canada international boundary.”

The authors emphasize that up-to-date and transparent science has an important role to play in managing the potential impacts of mines. Emerging science on salmonid ecology, cumulative effects and how climate change is altering these landscapes can improve risk assessment of mines.

The authors highlighted four key issues that will be foundational to modern, science-based risk assessment and mitigation: understanding stressor complexity and uncertainty, accounting for cumulative effects of mining activities across a mine’s life cycle, developing realistic mitigation strategies and recognizing the potential for climate change to magnify risk.

“Emerging science is revealing the complex realities of how salmon watersheds work in this era of climate change and also the many different risk pathways posed by mines,” said co-author Jonathan Moore of Simon Fraser University in British Columbia. “Informed decision-making will need risk assessments that embrace these challenging topics, ranging from cumulative effects to climate change.”

While a low-carbon future will depend to some extent on mined minerals, it is important to consider whether current and future mining projects are operated in such a way that protects fish, water and well-functioning watersheds.

“Our paper is not for or against mining, but it does describe current environmental challenges and gaps in the application of science to mining governance,” Sergeant said. “We identify a need and opportunity for strong science-based and transparent risk assessment, as well as the integration of goals and values of impacted communities. In the end, it is possible that some specific places might just be too valuable to risk with major mines.”

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UC Santa Barbara Professor Ben Mazin is developing precision optical sensors for telescopes and observatories. In a paper published in Physical Review Letters, he and his team improved the spectra resolution of their superconducting sensor, a major step in their ultimate goal: analyzing the composition of exoplanets.

“We were able to roughly double the spectral resolving power of our detectors,” said first author Nicholas Zobrist, a doctoral student in the Mazin Lab.

“This is the largest energy resolution increase we’ve ever seen,” added Mazin. “It opens up a whole new pathway to science goals that we couldn’t achieve before.”

The Mazin lab works with a type of sensor called an MKID. Most light detectors — like the CMOS sensor in a phone camera — are semiconductors based on silicon. These operate via the photo-electric effect: a photon strikes the sensor, knocking off an electron that can then be detected as a signal suitable for processing by a microprocessor.

An MKID uses a superconductor, in which electricity can flow with no resistance. In addition to zero resistance, these materials have other useful properties. For instance, semiconductors have a gap energy that needs to be overcome to knock the electron out. The related gap energy in a superconductor is about 10,000 times less, so it can detect even faint signals.

What’s more, a single photon can knock many electrons off of a superconductor, as opposed to only one in a semiconductor. By measuring the number of mobile electrons, an MKID can actually determine the energy (or wavelength) of the incoming light. “And the energy of the photon, or its spectra, tells us a lot about the physics of what emitted that photon,” Mazin said.

Leaking energy

The researchers had hit a limit as to how sensitive they could make these MKIDs. After much scrutiny, they discovered that energy was leaking from the superconductor into the sapphire crystal wafer that the device is made on. As a result, the signal appeared weaker than it truly was.

In typical electronics, current is carried by mobile electrons. But these have a tendency to interact with their surroundings, scattering and losing energy in what’s known as resistance. In a superconductor, two electrons will pair up — one spin up and one spin down — and this Cooper pair, as it’s called, is able to move about without resistance.

“It’s like a couple at a club,” Mazin explained. “You’ve got two people who pair up, and then they can move together through the crowd without any resistance. Whereas a single person stops to talk to everybody along the way, slowing them down.”

In a superconductor, all the electrons are paired up. “They’re all dancing together, moving around without interacting with other couples very much because they’re all gazing deeply into each other’s eyes.

“A photon hitting the sensor is like someone coming in and spilling a drink on one of the partners,” he continued. “This breaks the couple up, causing one partner to stumble into other couples and create a disturbance.” This is the cascade of mobile electrons that the MKID measures.

But sometimes this happens at the edge of the dancefloor. The offended party stumbles out of the club without knocking into anyone else. Great for the rest of the dancers, but not for the scientists. If this happens in the MKID, then the light signal will seem weaker than it actually was.

Fencing them in

Mazin, Zobrist and their co-authors discovered that a thin layer of the metal indium — placed between the superconducting sensor and the substrate — drastically reduced the energy leaking out of the sensor. The indium essentially acted like a fence around the dancefloor, keeping the jostled dancers in the room and interacting with the rest of the crowd.

They chose indium because it is also a superconductor at the temperatures at which the MKID will operate, and adjacent superconductors tend to cooperate if they are thin. The metal did present a challenge to the team, though. Indium is softer than lead, so it has a tendency to clump up. That’s not great for making the thin, uniform layer the researchers needed.

But their time and effort paid off. The technique cut down the wavelength measurement uncertainty from 10% to 5%, the study reports. For example, photons with a wavelength of 1,000 nanometers can now be measured to a precision of 50 nm with this system. “This has real implications for the science we can do,” Mazin said, “because we can better resolve the spectra of the objects that we’re looking at.”

Different phenomena emit photons with specific spectra (or wavelengths), and different molecules absorb photons of different wavelengths. Using this light, scientists can use spectroscopy to identify the composition of objects both nearby and across the entire visible universe.

Mazin is particularly interested in applying these detectors to exoplanet science. Right now, scientists can only do spectroscopy for a tiny subset of exoplanets. The planet needs to pass between its star and Earth, and it must have a thick atmosphere so that enough light passes through it for researchers to work with. Still, the signal to noise ratio is abysmal, especially for rocky planets, Mazin said.

With better MKIDs, scientists can use light reflected off the surface of a planet, rather than transmitted through its narrow atmosphere alone. This will soon be possible with the capabilities of the next generation of 30-meter telescopes.

The Mazin group is also experimenting with a completely different approach to the energy-loss issue. Although the results from this paper are impressive, Mazin said he believes the indium technique could be obsolete if his team is successful with this new endeavor. Either way, he added, the scientists are rapidly closing in on their goals.