Aurelia Butler

Commercially viable biofuel crops are vital to reducing greenhouse gas emissions, and a new tool developed by the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) should accelerate their development — as well as genetic editing advances overall.
The genomes of crops are tailored by generations of breeding to optimize specific traits, and until recently breeders were limited to selection on naturally occurring diversity. CRISPR/Cas9 gene-editing technology can change this, but the software tools necessary for designing and evaluating CRISPR experiments have so far been based on the needs of editing in mammalian genomes, which don’t share the same characteristics as complex crop genomes.
Enter CROPSR, the first open-source software tool for genome-wide design and evaluation of guide RNA (gRNA) sequences for CRISPR experiments, created by scientists at CABBI, a Department of Energy-funded Bioenergy Research Center (BRC). The genome-wide approach significantly shortens the time required to design a CRISPR experiment, reducing the challenge of working with crops and accelerating gRNA sequence design, evaluation, and validation, according to the study published in BMC Bioinformatics.
“CROPSR provides the scientific community with new methods and a new workflow for performing CRISPR/Cas9 knockout experiments,” said CROPSR developer Hans Müller Paul, a molecular biologist and Ph.D. student with co-author Matthew Hudson, Professor of Crop Sciences at the University of Illinois Urbana-Champaign. “We hope that the new software will accelerate discovery and reduce the number of failed experiments.”
To better meet the needs of crop geneticists, the team built software that lifts restrictions imposed by other packages on design and evaluation of gRNA sequences, the guides used to locate targeted genetic material. Team members also developed a new machine learning model that would not avoid guides for repetitive genomic regions often found in plants, a problem with existing tools. The CROPSR scoring model provided much more accurate predictions, even in non-crop genomes, the authors said.
“The goal was to incorporate features to make life easier for the scientist,” Müller Paul said. More

Understanding the nitty gritty of how molecules interact with each other in the real, messy, dynamic environment of a living body is a challenge that must be overcome in order to understand a host of diseases, such as Alzheimer’s.
Until now, researchers could capture the motion of a single molecule, and they could capture its rotation — how it tumbles as it bumps into surrounding molecules — but only by compromising 3D resolution.
Now, the lab of Matthew Lew, assistant professor of electrical and systems engineering at the McKelvey School of Engineering at Washington University in St. Louis, has developed an imaging method that provides an unprecedented look at a molecule as it spins and rolls through liquid, providing the most comprehensive picture yet of molecular dynamics collected using optical microscopes.
The research was published in a special issue of the Journal of Physical Chemistry B. The Feb. 17, 2022, Festschrift is dedicated to Nobel laureate William E. (W.E.) Moerner, an imaging pioneer, Washington University alumnus and mentor to more than 100 students over the years, including Lew.
Moerner was the first person to observe optical signatures of a single molecule; previously, researchers weren’t sure it was even possible to measure such signals.
Now Lew’s lab is the first to be able to visualize the orientation and direction of a molecule’s rotational movement — how it spins and wobbles — while it’s in a liquid system. More

You won’t see them move no matter how closely you watch.
You won’t hear their vibrations, even with your ear pressed to the cool sandstone.
But new research shows that the red rock towers found in Southern Utah and throughout the Colorado Plateau are in constant motion, vibrating with their own signature rhythms as unique as their dramatic profiles against the depth of the blue desert sky.
University of Utah researchers know well how rock towers and arches shimmy, twist and sway in response to far-off earthquakes, wind and even ocean waves. Their latest research compiles a first-of-its-kind dataset to show that the dynamic properties, i.e. the frequencies at which the rocks vibrate and the ways they deform during that vibration, can be largely predicted using the same mathematics that describe how beams in built structures resonate.
Knowing these properties is crucial to understanding the seismic stability of a rock tower and its susceptibility to hazardous vibrations. But it’s tough to get the needed data, partly because getting to the base of the towers often requires traveling through treacherous terrain — and then someone has to climb them to place a seismometer at the top.
With the help of experienced climbers, though, University of Utah researchers have now measured the dynamic properties of 14 rock towers and fins in Utah, creating a unique dataset with a variety of heights and tower shapes. More

Engineers at Caltech have developed an approach for quantum storage could help pave the way for the development of large-scale optical quantum networks.
The new system relies on nuclear spins — the angular momentum of an atom’s nucleus — oscillating collectively as a spin wave. This collective oscillation effectively chains up several atoms to store information.
The work, which is described in a paper published on February 16 in the journal Nature, utilizes a quantum bit (or qubit) made from an ion of ytterbium (Yb), a rare earth element also used in lasers. The team, led by Andrei Faraon (BS ’04), professor of applied physics and electrical engineering, embedded the ion in a transparent crystal of yttrium orthovanadate (YVO4) and manipulated its quantum states via a combination of optical and microwave fields. The team then used the Yb qubit to control the nuclear spin states of multiple surrounding vanadium atoms in the crystal.
“Based on our previous work, single ytterbium ions were known to be excellent candidates for optical quantum networks, but we needed to link them with additional atoms. We demonstrate that in this work,” says Faraon, the co-corresponding author of the Nature paper.
The device was fabricated at the Kavli Nanoscience Institute at Caltech, and then tested at very low temperatures in Faraon’s lab.
A new technique to utilize entangled nuclear spins as a quantum memory was inspired by methods used in nuclear magnetic resonance (NMR). More

Musicians are helping scientists analyze data, teach protein folding and make new discoveries through sound.
A team of researchers at the University of Illinois Urbana-Champaign is using sonification — the use of sound to convey information — to depict biochemical processes and better understand how they happen.
Music professor and composer Stephen Andrew Taylor; chemistry professor and biophysicist Martin Gruebele; and Illinois music and computer science alumna, composer and software designer Carla Scaletti formed the Biophysics Sonification Group, which has been meeting weekly on Zoom since the beginning of the pandemic. The group has experimented with using sonification in Gruebele’s research into the physical mechanisms of protein folding, and its work recently allowed Gruebele to make a new discovery about the ways a protein can fold.
Taylor’s musical compositions have long been influenced by science, and recent works represent scientific data and biological processes. Gruebele also is a musician who built his own pipe organ that he plays and uses to compose music. The idea of working together on sonification struck a chord with them, and they’ve been collaborating for several years. Through her company, Symbolic Sound Corp., Scaletti develops a digital audio software and hardware sound design system called Kyma that is used by many musicians and researchers, including Taylor.
Scaletti created an animated visualization paired with sound that illustrated a simplified protein-folding process, and Gruebele and Taylor used it to introduce key concepts of the process to students and gauge whether it helped with their understanding. They found that sonification complemented and reinforced the visualizations and that, even for experts, it helped increase intuition for how proteins fold and misfold over time. The Biophysics Sonification Group — which also includes chemistry professor Taras Pogorelov, former chemistry graduate student (now alumna) Meredith Rickard, composer and pipe organist Franz Danksagmüller of the Lübeck Academy of Music in Germany, and Illinois electrical and computer engineering alumnus Kurt Hebel of Symbolic Sound — described using sonification in teaching in the Journal of Chemical Education.
Gruebele and his research team use supercomputers to run simulations of proteins folding into a specific structure, a process that relies on a complex pattern of many interactions. The simulation reveals the multiple pathways the proteins take as they fold, and also shows when they misfold or get stuck in the wrong shape — something thought to be related to a number of diseases such as Alzheimer’s and Parkinson’s. More

A new study describes previously unexpected properties in a complex quantum material known as Ta2NiSe5. Using a novel technique developed at Penn, these findings have implications for developing future quantum devices and applications. This research, published in Science Advances, was conducted by University of Pennsylvania graduate student Harshvardhan Jogand led by professor Ritesh Agarwal in collaboration with professor Eugene Mele and Luminita Harnagea from the Indian Institute of Science Education and Research.
While the field of quantum information science has experienced progress in recent years, the widespread use of quantum computers is still limited. One challenge is the ability to only use a small number of “qubits,” the unit that performs calculations in a quantum computer, because current platforms are not designed to allow multiple qubits to “talk” to one another. In order to address this challenge, materials need to be efficient at quantum entanglement, which occurs when the states of qubits remain linked no matter their distance from one another, as well as coherence, or when a system can maintain this entanglement.
In this study, Jog looked at Ta2NiSe5, a material system that has strong electronic correlation, making it attractive for quantum devices. Strong electronic correlation means that the material’s atomic structure is linked to its electronic properties and the strong interaction that occurs between electrons.
To study Ta2NiSe5, Jog used a modification of a technique developed in the Agarwal lab known as the circular photogalvanic effect, where light is engineered to carry an electric field and is able to probe different material properties. Developed and iterated in the past several years, this technique has revealed insights about materials such as silicon and Weyl semimetals in ways that are not possible with conventional physics and materials science experiments.
But the challenge in this study, says Agarwal, is that this method has only been applied in materials without inversion symmetry, whereas Ta2NiSe5 does haveinversion symmetry, Jog “wanted to see if this technique can be used to study materials which have inversion symmetry which, from a conventional sense, should not be producing this response,” says Agarwal.
After connecting with Harnagea to obtain high-quality samples of Ta2NiSe5, Jog and Agarwal used a modified version of the circular photogalvanic effect and were surprised to see that there was a signal being produced. After conducting additional studies to ensure that this was not an error or an experimental artifact, they worked with Mele to develop a theory that could help explain these unexpected results. More

For the first time, researchers have created a metasurface lens that uses a piezoelectric thin film to change focal length when a small voltage is applied. Because it is extremely compact and lightweight, the new lens could be useful for portable medical diagnostic instruments, drone-based 3D mapping and other applications where miniaturization can open new possibilities.
“This type of low-power, ultra-compact varifocal lens could be used in a wide range of sensor and imaging technologies where system size, weight and cost are important,” said research project leader Christopher Dirdal from SINTEF Smart Sensors and Microsystems in Norway. “In addition, introducing precision tunability to metasurfaces opens up completely new ways to manipulate light.”
Dirdal and colleagues describe the new technology in the Optica Publishing Group journal Optics Letters. To change focal length, a voltage is applied over lead zirconate titanate (PZT) membranes causing them to deform. This, in turn, shifts the distance between two metasurface lenses.
“Our novel approach offers a large displacement between the metasurface lenses at high speed and using low voltages,” said Dirdal. “Compared to state-of-the-art devices, we demonstrated twice the out-of-plane displacement at a quarter of the voltage.”
Combining technologies
The researchers made the new lens using metasurfaces — flat surfaces that are patterned with nanostructures to manipulate light. They are particularly interesting because they can integrate several functionalities into a single surface and can also be made in large batches using standard micro- and nanofabrication techniques at potentially low cost. More

From tiny fruit flies to human beings, all animals on Earth maintain their daily rhythms based on their internal circadian clock. The circadian clock enables organisms to undergo rhythmic changes in behavior and physiology based on a 24-hour circadian cycle. For example, our own biological clock tells our brain to release melatonin, a sleep-inducing hormone, at night time.
The discovery of the molecular mechanism of the circadian clock was bestowed The Nobel Prize in Physiology or Medicine 2017. From what we know, no one centralized clock is responsible for our circadian cycles. Instead, it operates in a hierarchical network where there are “master pacemaker” and “slave oscillator.”
The master pacemaker receives various input signals from the environment such as light. The master then drives the slave oscillator that regulates various outputs such as sleep, feeding, and metabolism. Despite the different roles of the pacemaker neurons, they are known to share common molecular mechanisms that are well conserved in all lifeforms. For example, interlocked systems of multiple transcriptional-translational feedback loops (TTFLs) composed of core clock proteins have been deeply studied in fruit flies.
However, there is still much that we need to learn about our own biological clock. The hierarchically-organized nature of master and slave clock neurons leads to a prevailing belief that they share an identical molecular clockwork. At the same time, the different roles they serve in regulating bodily rhythms also raise the question of whether they might function under different molecular clockworks.
Led by Prof. KIM Jae Kyoung and KIM Eun Young, researchers at the Institute for Basic Science (IBS) and Ajou University used a combination of mathematical and experimental approaches using fruit flies to answer this question. The team found that the master clock and the slave clock operate via different molecular mechanisms.
In both master and slave neurons of fruit flies, a circadian rhythm-related protein called PER is produced and degraded at different rates depending on the time of the day. Previously, the team found that the master clock neuron (sLNvs) and the slave clock neuron (DN1ps) have different profiles of PER in wild-type and Clk-Δ mutant Drosophila. This hinted that there might be a potential difference in molecular clockworks between the master and slave clock neurons.
However, due to the complexity of the molecular clockwork, it was challenging to identify the source of such differences. Thus, the team developed a mathematical model describing the molecular clockworks of the master and slave clocks. Then, all possible molecular differences between the master and slave clock neurons were systematically investigated by using computer simulations. The model predicted that PER is more efficiently produced and then rapidly degraded in the master clock compared to the slave clock neurons. This prediction was then confirmed by the follow-up experiments using animal.
Then, why do the master clock neurons have such different molecular properties from the slave clock neurons? To answer this question, the research team again used the combination of mathematical model simulation and experiments. It was found that the faster rate of synthesis of PER in the master clock neurons allows them to generate synchronized rhythms with a high level of amplitude. Generation of such a strong rhythm with high amplitude is critical to delivering clear signals to slave clock neurons.
However, such strong rhythms would typically be unfavorable when it comes to adapting to environmental changes. These include natural causes such as different daylight hours across summer and winter seasons, up to more extreme artificial cases such as jet lag that occurs after international travel. Thanks to the distinct property of the master clock neurons, it is able to undergo phase dispersion when the standard light-dark cycle is disrupted, drastically reducing the level of PER. The master clock neurons can then easily adapt to the new diurnal cycle. Our master pacemaker’s plasticity explains how we can quickly adjust to the new time zones after international flights after just a brief period of jet lag.
It is hoped that the findings of this study can have future clinical implications when it comes to treating various disorders that affect our circadian rhythm. Chief investigator Kim notes, “When the circadian clock loses its robustness and flexibility, the circadian rhythms sleep disorders can occur. As this study identifies the molecular mechanism that generates robustness and flexibility of the circadian clock, it can facilitate the identification of the cause of and treatment strategy for the circadian rhythm sleep disorders.”
Story Source:
Materials provided by Institute for Basic Science. Note: Content may be edited for style and length. More