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Getting to the Root of Plant-soil Interactions: Optical Instrument to Give Clearest 3D Images yet of Rhizosphere

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An interdisciplinary team of researchers from the Georgia Institute of Technology has received a $2 million federal grant to create tools that will provide the clearest three-dimensional images yet of the chemical and biomolecular interactions between plants and the soil in which they grow.

An interdisciplinary team of researchers from the Georgia Institute of Technology has received a $2 million federal grant to create tools that will provide the clearest three-dimensional images yet of the chemical and biomolecular interactions between plants and the soil in which they grow.

At just a few inches underground, the rhizosphere — the thin strip of earth that includes the soil-root interface — has so far been difficult to visualize on site. If scientists can build instruments that capture in real-time clearer images of the physical associations of microbes attached to roots, along with the oxygen-carbon-nitrogen chemical exchanges they mediate, it could help mitigate the effects of climate change and lead to the development of more sustainable fuels and fertilizers.

“From a microbiological perspective, we have catalogued what microbes are in the root zone and how abundant they are,” said Joel Kostka, professor in the School of Biological Sciences and School of Earth and Atmospheric Sciences at Georgia Tech. “But there’s been very little work to understand their dynamics under real soil conditions.”

Kostka, who also serves as associate chair for Research in Biological Sciences, joins Marcus Cicerone, professor in the School of Chemistry and Biochemistry and principal investigator for the new grant from the U.S. Department of Energy’s Office of Biological and Environmental Research. The research team also includes Francisco Robles, assistant professor in the Wallace H. Coulter Department of Biomedical Engineering, and Lily Cheung, assistant professor in the School of Chemical and Biomolecular Engineering in the College of Engineering.

Together, the researchers plan to produce a new optical instrument that will provide 3D images of dynamic metabolic processes with chemical specificity — meaning it will be able to identify carbon sources (sugars, organic acids) exuded by plant roots and nitrogen-rich compounds provided to the root by nitrogen-fixing (diazotrophic) microbes. The instrument will be built with commercially available components, and with an eye towards simplicity so that it can be easily leveraged by Department of Energy (DOE) Bioenergy Research Centers and field sites.

A ‘hotspot for microbes in 3D

Understanding more about the metabolic processes happening in the rhizosphere will help the DOE develop a wider range of sustainable products like new types of biofertilizers and biofuels. The research will also help create practices for better crop management — and will help researchers use plants and soil as more effective carbon traps that sequester greenhouse gases from the atmosphere into the soil.

“The problem is that we don’t know much about the free-living bacteria in the soil, because we can’t get in there and look,” Cicerone said. “The DOE wanted somebody to build an instrument that would allow them to image or gather information about the metabolic processes, the interaction — the metabolic interactions between the microbes and the plants, in real time.”

Kostka adds that the rhizosphere is “a hotspot for microbes.”

“It’s often where the plant is communicating with the outside world,” he explained. “Our goal is to develop an instrument that they (the DOE) can use to better understand those interactions between plants and microbes and how those can be tweaked, say, to optimize plant production, crop production, biofuels and biomass production. And that’s the long-term goal for us.”

How light gets scattered, smothered, and covered in soil

Cicerone says the visibility issue with soil involves how photons — or particles of light — scatter once they hit the soil. He likens it to someone putting a red light up to the back of their thumb.

“You turn your thumb around, your thumb glows red, right? So, the light comes through, but most of it scatters. The unscattered light contains the spatial information, but it is so weak that you can’t detect it by eye, and you lose the spatial information. The same thing happens with the soils. You get a lot of light scattering, and you lose spatial information,” Cicerone said.

Cicerone and Robles will build instrumentation that will focus light into the soil and that is “exquisitely sensitive to the minuscule amount of light that only scatters when it reaches its target.” Evaluating that light will help scientists learn even more about the chemical processes in the rhizosphere.

The visibility enhancements will be implemented in optical techniques with names like coherent Raman scattering and optical coherence tomography, which are commonly used for non-invasive imaging of thin biological material, like the retina of the eye — or the tiniest of plant roots.

“We learn two things from the light coming out of the sample. The amount of light coming out tells you about the refractive index of the material, and the light’s frequency change tells you about the chemical composition of the material,” Cicerone explained.

It’s through imaging and then optimizing those microbe-plant interactions that the DOE aims to design more sustainable products and practices, based on the chemistry to be learned from the team’s new optical instruments.

“This is a three-year funded project, and we hope at the end of the three years to have an experimental system, where we can do something that nobody else can do,” Cicerone added. “And that is that we can follow the biochemistry under the soil, in situ, in real time, to clearly see what’s going on there and find out what the microbes really are doing in natural conditions. At that point, we can start manipulating the biology, start doing the experiments that the DOE is primarily interested in.”

Award Number: DE-SC0022121
Title: Deep Chemical Imaging of the Rhizosphere
Institution: Georgia Tech Research Corporation, Atlanta, GA
Principal Investigator: Cicerone, Marcus

About Georgia Institute of Technology

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 40,000 students representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

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Are Researchers One Step Closer to Developing the Theory of Impulse Circuits?

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Computers play an important role in many aspects of life today. Digital computers are the most widely used, while quantum computers are well known. However, the least known computers are the so-called Stochastic Pulse Computers. Their work is based on highly parallel logical operations between trains of electrical pulses, where the pulses occur at random times, as in neurons, the nerve cells in the brains of humans and mammals.

Computers play an important role in many aspects of life today. Digital computers are the most widely used, while quantum computers are well known. However, the least known computers are the so-called Stochastic Pulse Computers. Their work is based on highly parallel logical operations between trains of electrical pulses, where the pulses occur at random times, as in neurons, the nerve cells in the brains of humans and mammals.

The main motivation for the growing interest in research on RPC computers over the past decade is the hope that they could solve faster and with less energy consumption tasks that are normally easy for living beings, but difficult for digital computers, such as instantaneous responses to stimuli, pattern recognition, robustness to errors and damage in the system, learning, and autonomy.

In a recent study published in Scientific Reports, researchers from the Croatian Centre of Excellence for Advanced Materials and Sensors, Dr Mario Stipčević of the Ruđer Bošković Institute (RBI) and Mateja Batelić, a student at the Faculty of Science at the University of Zagreb (FS), Croatia, describe new or improved versions of RPC circuits that use quantum randomness for the first time, but also go a significant step further and lay the first foundation for RPC circuit theory.

Namely, while circuits for processing information in a digital computer can be assembled from logic circuits as building blocks based on the well-known Boolean theory, a similar theory for RPC circuits does not yet exist. Therefore, the synthesis of circuits for an RPC is limited to trial and error through experimentation or simulation.

‘’The central part of our paper is the formulation and proof of the so-called entropy budget theorem, which can be used to easily verify whether a given mathematical (or logical) operation can be performed or “calculated” by any physical circuit, and if so, how much excess entropy must be available to a circuit in order to perform the given operation.

In this paper, we demonstrate the theorem using several examples of mathematical operations. Perhaps the most interesting proof is the existence of a deterministic half-sum circuit (a + b) / 2. However, this circuit is not yet known, and finding it is a challenge for further research,” says Mario Stipčević, head of the Laboratory of Photonics and Quantum Optics at the Ruđer Bošković Institute.

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PSMA PET Validates EAU Classification System to Determine Risk of Prostate Cancer Recurrence

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Reston, VA (January 20, 2022)—New research has confirmed the accuracy of the novel European Association of Urology (EAU) risk classification system that groups prostate cancer patients based on their risk of recurrence. Prostate-specific membrane antigen (PSMA) PET imaging of men with prostate cancer validated the EAU groupings and provided insights that could further refine risk assessment for patients. This study was published in the January issue of The Journal of Nuclear Medicine.

Credit: Justin Ferdinandus, Wolfgang P. Fendler, Andrea Farolfi, et al.

Reston, VA (January 20, 2022)—New research has confirmed the accuracy of the novel European Association of Urology (EAU) risk classification system that groups prostate cancer patients based on their risk of recurrence. Prostate-specific membrane antigen (PSMA) PET imaging of men with prostate cancer validated the EAU groupings and provided insights that could further refine risk assessment for patients. This study was published in the January issue of The Journal of Nuclear Medicine.

The diagnostic workup of prostate cancer has changed rapidly over the past few years. Recently, the EAU introduced a clinical system separating patients with rising PSA values after first-line therapy (prostate surgery or radiation) into groups of those with high risk and those with low risk for development of metastases. Shortly after this, the U.S. Food and Drug Administration approved 68Ga-PSMA-11 as the first PET drug to target the PSMA for men with prostate cancer.

“Given the growing availability of PSMA-directed PET imaging, our study sought to assess disease in patients based on the EAU classifications while using PSMA PET to identify subgroups of patients, such as those with undetectable, locoregional or distant metastatic disease,” said Justin Ferdinandus, MD, nuclear medicine physician at University Hospital in Essen, Germany.

The multicenter, international study analyzed PSMA PET scans of nearly 2,000 patients with prostate cancer and rising PSA levels. Patterns of disease spread on PSMA PET imaging were used to classify prostate cancer patients into both low- and high-risk groups. High-risk groups were found to have higher rates of metastatic disease on PSMA PET compared to low-risk groups. However, PSMA PET also found metastatic disease in low-risk and no disease in high-risk patients.

“Our study underscores the utility of the EAU risk groups to determine risk of metastasis in biochemically recurrent prostate cancer. But not every high-risk patient has metastases and not every low-risk patient has locoregional or no disease,” said Wolfgang Fendler, MD, nuclear medicine physician at University Hospital in Essen.

He continued, “The ultimate aim of imaging is to provide the right treatment for each patient. As evidenced in this research, the accuracy of PSMA PET is essential to improve stratification and potentially outcomes both in low-risk and high-risk settings.” 

The authors of “PSMA PET validates higher rates of metastatic disease for European Association of Urology Biochemical Recurrence Risk Groups: an international multicenter study” include Justin Ferdinandus, Department of Nuclear Medicine, University of Duisburg-Essen and German Cancer Consortium (DKTK)-University Hospital Essen, Essen, Germany; Wolfgang P. Fendler and Ken Hermann, Department of Nuclear Medicine, University of Duisburg-Essen and German Cancer Consortium (DKTK)-University Hospital Essen, Essen, Germany, and Ahmanson Translational Imaging Division, Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California; Andrea Farolfi, Department of Nuclear Medicine, University of Duisburg-Essen and German Cancer Consortium (DKTK)-University Hospital Essen, Essen, Germany, and Division of Nuclear Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Samuel Washington, Department of Urology, University of California San Francisco, San Francisco, California, and Department of Epidemiology and Statistics, University of California San Francisco, San Francisco, California; Osama Mohamad, Department of Radiation Oncology, University of California San Francisco, San Francisco, California; Miguel H. Pampaloni and Thomas A. Hope, Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California; Peter J.H. Scott, Melissa Rodnick, Benjamin L. Viglianti and Morand Piert, Department of Radiology, University of Michigan, Ann Arbor, Michigan; Matthias Eiber, Department of Nuclear Medicine, Klinikum rechts der Isar, Technical University Munich, Munich, Germany; and Johannes Czernin, Wesley R. Armstrong and Jeremie Calais, Ahmanson Translational Imaging Division, Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California.

Visit JNM’s new website for the latest research, and follow our new Twitter and Facebook pages @JournalofNucMed.

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Please visit the SNMMI Media Center for more information about molecular imaging and precision imaging. To schedule an interview with the researchers, please contact Rebecca Maxey at (703) 652-6772 or [email protected].
 

About JNM and the Society of Nuclear Medicine and Molecular Imaging
The Journal of Nuclear Medicine (JNM) is the world’s leading nuclear medicine, molecular imaging and theranostics journal, accessed more than 13 million times each year by practitioners around the globe, providing them with the information they need to advance this rapidly expanding field. Current and past issues of The Journal of Nuclear Medicine can be found online at http://jnm.snmjournals.org.

JNM is published by the Society of Nuclear Medicine and Molecular Imaging (SNMMI), an international scientific and medical organization dedicated to advancing nuclear medicine and molecular imaging—precision medicine that allows diagnosis and treatment to be tailored to individual patients in order to achieve the best possible outcomes. For more information, visit www.snmmi.org.

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UCLA Researchers Develop Novel Microscopic Picoshell Particles

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Production of high-energy fats by microalgae may provide a sustainable, renewable energy source that can help tackle climate change. However, microalgae engineered to produce lipids rapidly usually grow slowly themselves, making it difficult to increase overall yields. 

Production of high-energy fats by microalgae may provide a sustainable, renewable energy source that can help tackle climate change. However, microalgae engineered to produce lipids rapidly usually grow slowly themselves, making it difficult to increase overall yields. 

UCLA bioengineers have created a new type of petri dish in the form of microscopic, permeable particles that can dramatically speed up research and development (R&D) timelines of biological products, such as fatty acids for biofuels. Dubbed PicoShells, the picoliter (trillionth of a liter), porous, hydrogel particles can enable more than one million individual cells to be compartmentalized, cultured in production-relevant environments, and selected based on growth and biomass accumulation traits using standard cell-processing equipment. 

Proceedings of the National Academy of Sciences recently published a study detailing how PicoShells work and their potential applications.

PicoShells consist of a hollow inner cavity where cells are encapsulated and a porous outer shell that allows for continuous solution exchange with the external environment so that nutrients, cell-communication molecules and cytotoxic cellular byproducts can transport freely in and out of the inner cavity. The shell also keeps the small groups of growing cells penned in, allowing researchers to study and compare their behaviors — what they do, how fast they grow, what they produce — to those of other groups inside various PicoShells. 

This new class of lab tool allows researchers to grow living, single-cell microorganisms — including algae, fungi and bacteria — under the same industrial-production conditions, such as in a bioreactor filled with wastewater or an outdoor cultivation pond. 

“PicoShells are like very tiny mesh balloons. The growing cells inside them are effectively fenced in but not sealed off,” said study leader Dino Di Carlo, UCLA’s Armond and Elena Hairapetian Professor in Engineering and Medicine at the UCLA Samueli School of Engineering. “With this new tool, we can now study the individual behaviors of millions of living cells in the relevant environment. This could shorten R&D-to-commercial production timelines for bioproducts from a few years to a few months. PicoShells could also be a valuable tool for fundamental biology studies.” 

PicoShells’ permeability can bring the lab to the industrial environment, allowing testing at a sectioned-off area of a working facility. Growth can occur more quickly and cell strains that perform well can be identified and selected for further screening. 

According to the researchers, another advantage of this new tool is that the analysis of millions of PicoShells is automated since they are also compatible with standard lab equipment used for high-volume cell processing.

Massive groups of cells, up to 10 million in one day, can be sorted and organized by certain characteristics. Continuous analysis could result in ideal sets of cells — ones that are already performing well in the environment with suitable temperature, nutrient composition and other properties that could be used in mass production — in just a few days rather than the several months it would take using current technologies.

The shells can be engineered to burst when the cells inside have divided and grown beyond their peak volume. Those free cells are still viable and can be recaptured for continued research or further selection. The researchers can also create shells with chemical groups that break down when exposed to biocompatible reagent, enabling a multifaceted approach to release selected cells.

“If we want to zero in on algae that are the best at producing biofuels, we can use PicoShells to organize, grow and process millions of single algal cells,” said lead author Mark van Zee, a bioengineering graduate student at UCLA Samueli. “And we can do that in machines that sort them using fluorescent tags that light up to signify fuel levels.”

Currently, cultivating and comparing such microorganisms are done mostly using traditional lab tools, such as microwell plates — cartons that hold several dozen small test tube-like volumes. However, these methods are slow and it is difficult to quantify their effectiveness because it can take weeks or months to grow large colonies for study. Other approaches, such as water-in-oil droplet emulsions, can be used to analyze cells in smaller volumes, but surrounding oils prevent the free exchange of medium into the water drops. Even cells or microorganisms that perform well in lab conditions may not do as well once they are placed in industrial environments, such as bioreactors or outdoor cultivation farms. As a result, cell strains that are developed in the lab often do not exhibit the same beneficial characteristic behavior when transferred to industrial production. 

Microwell plates also are limited in the number of experiments that can be performed, resulting in a great deal of trial and error in finding cell strains that work sufficiently well for mass production.

The researchers demonstrated the new tool by growing colonies of algae and yeast, comparing their growth and viability against other colonies grown in water-in-oil emulsions. For the algae, the team found that PicoShell colonies accumulated biomass rapidly while algae did not grow at all in water-in-oil emulsions. Similar results were found in their yeast experiments. By selecting the top growing algae in PicoShells, the researchers could increase the production of chlorophyll biomass by 8% after only a single cycle. 

The authors said PicoShells could offer a faster alternative to develop new algae and yeast strains, leading to improved biofuels, plastics, carbon-capture materials and even food products and alcoholic beverages. Further refinements to the technology, such as coating the shells with antibodies, could also lead to developing new types of protein-based medicines.

Di Carlo, van Zee and study co-author Joseph de Rutte Ph.D. ’20, a former member of Di Carlo’s research group, are named inventors on a patent application filed by the UCLA Technology Development Group.

The other UCLA authors on the paper are Rose Rumyan, Cayden Williamson, Trevor Burnes, Andrew Sonico Eugenio, Sara Badih, Dong-Hyun Lee and Maani Archang. Randor Radakovits from Synthetic Genomics of San Diego is also an author.

The study was supported by the Presidential Early Career Award for Scientists and Engineers and a planning award from the California NanoSystems Institute (CNSI) at UCLA.

Di Carlo holds faculty appointments in bioengineering, and mechanical and aerospace engineering at UCLA Samueli. He is a member of CNSI and the Jonsson Comprehensive Cancer Center at UCLA.

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