This study creates a roadmap for understanding the many different ways that viruses could modify the effects of warming on communities of microbes. Viruses likely have strong effects on processes with microbes and the ways ecosystems function. Incorporating these previously ignored effects into ecosystem models will help scientists improve their predictions of how ecosystems could respond to climate change.

Microorganisms play integral roles in ecosystems by controlling the flow of energy and matter through processes like photosynthesis (carbon uptake), respiration (carbon release), and decomposition (carbon recycling). Climate change is currently altering how ecosystems function by changing how organisms operate within microbial food webs. Scientists know that viruses can have strong impacts on microbial processes, but they have less knowledge of how these impacts will change with future warming.

In this study, scientists from Duke University, the University of Tennessee Knoxville, the Netherlands Institute of Ecology, and Oak Ridge National Laboratory reviewed the potential impacts of warming on viruses and how these might alter scientific understanding of ecosystem responses to climate change. Warming likely affects several different stages of the viral infection cycle, as well as virus-host dynamics. However, there are still many gaps in our understanding about these effects. Because viruses are ubiquitous across all habitats and have strong effects on microbial functioning, filling these gaps is critical to understanding how warming will affect the flow of energy and matter within ecosystems. The researchers’ preliminary models show that viruses could potentially tip the scales on natural carbon balances, causing some ecosystems to switch from being net carbon sources (releasing more carbon than they store) to being net carbon sinks (absorbing carbon). This study shows how incorporating viruses into predictive models can lead to new and unexpected effects on ecosystems in response to climate change.

This work was supported by the Department of Energy Office of Science, Biological and Environmental Research program.

DNAzymes are nucleic acid enzymes that cut other molecules. Through chemistry, UCI’s team developed the Dz 46 enzyme, which specifically targets the allele-specific RNA mutation in the KRAS gene, the master regulator of cell growth and division, found in 25 percent of all human cancers. A description of how the team achieved this enzyme evolution was recently published in the online journal Nature Communications.

“Generating DNAzymes that can effectively function in the natural conditions of cell systems has been more challenging than expected,” said corresponding author John Chaput, UCI professor of pharmaceutical sciences. “Our results suggest that chemical evolution could pave the way for development of novel therapies for a wide range of diseases.”

Gene silencing has been available for more than 20 years and some FDA-approved drugs incorporate various versions of the technology, but none can distinguish a single point mutation in an RNA strand. The benefit of the Dz 46 enzyme is that it can identify and cut a specific gene mutation, offering patients an innovative, precision medicine treatment.

The DNAzyme resembles the Greek letter omega and acts as a catalyst by accelerating chemical reactions. The “arms” on the left and right bind to the target region of the RNA. The loop binds to magnesium, and folds and cuts the RNA at a very specific site. But generating DNAzymes with robust multiple turnover activity under physiological conditions required some ingenuity, because DNAzymes are normally very dependent on concentrations of magnesium not found inside a human cell.

“We solved that problem by re-engineering the DNAzyme using chemistry to reduce its dependency on magnesium and did so in such a way that we could maintain high catalytic turnover activity,” Chaput said. “Ours is one of the very first, if not the first, example of achieving that. The next steps are to advance Dz 46 to a point that it’s ready for pre-clinical trials.”

Team members Kim Thien Nguyen, project scientist, and Turnee N. Malik, postdoctoral scholar, both from the Department of Pharmaceutical Sciences, also participated in this study.

The researchers and UCI have filed provisional patent applications on the chemical composition and cleavage preference of Dz 46. Chaput is a consultant for drug development company 1E Therapeutics, which supported this work.

A paper published today in the journal Nature Energy examines the cost to plug 14,000 wells that are inactive, have not produced for five years and are unlikely to be reactivated in the Gulf of Mexico region, which is the epicenter of U.S. offshore oil and gas operations.

The wells could pose future environmental and financial risks to the public, and the cost differential for plugging onshore wells versus those in offshore waters is large, said Mark Agerton, an assistant professor at UC Davis and lead author of the paper.

Leaks from wells closer to shore are more likely to damage coastal ecosystems and release greenhouse gases like methane into the atmosphere, compared to wells in deep waters. The study found that more than 90% of inactive wells are in shallow areas, and the cost to plug those would be $7.6 billion, or 25% of a total $30 billion.

Informing policy decisions

“The wells aren’t supposed to be leaking into the environment, but sometimes they do,” said Agerton, of the Department of Agricultural and Resource Economics. “How do you get the most environmental benefit for the least amount of money?”

The findings could help states decide cleanup priorities, especially as they access $4.7 billion in federal money authorized by the Infrastructure Investment and Jobs Act. That money is set aside for methane reduction programs, including cleanup of old oil and gas wells, said Gregory Upton, an associate research professor at the Louisiana State University Center for Energy Studies and co-author of the paper.

“States have a pretty good idea of what it costs to plug these wells on land, but there is really a lot of uncertainty as to what the costs were for these offshore wells,” Upton said during a media briefing about the paper.

Liability for cleaning up wells abandoned in federal waters falls to prior owners if the current owner becomes insolvent and is unable to cover costs. Large American oil companies currently own or have owned 88% of the wells in federal Gulf of Mexico waters and would legally shoulder cleanup liabilities before taxpayers, Agerton said.

But in state waters, each jurisdiction handles liability differently, and prior ownership doesn’t come into play. States oversee plugging programs for orphaned wells whose owners have gone bankrupt, though the cost to plug an abandoned offshore well increases with the length of the well and the depth of the water.

“The bulk of the costs comes from plugging wells in deeper water where the environmental consequences are less than for a shallow well closer to shore,” Agerton said. “That money is probably better spent on state waters where they can’t go after prior owners for cleanup costs and it’s going to be a cheaper cleanup job with more environmental benefit.”

Siddhartha Narra, Brian Snyder and Gregory B. Upton Jr. of Louisiana State University, are co-authors on the research.

Led by the College Transition Collaborative and the IU Equity Accelerator, the research team offered a brief online reading and writing exercise to nearly 27,000 students from 22 diverse colleges and universities across the United States in fall 2015 and 2016, including IU. These results, the country’s largest multi-site randomized controlled trial of this belonging intervention, were published May 5 in Science.

“There are hundreds of thousands of students being left behind and not supported by institutions in the way they need to be supported,” said IU Equity Accelerator founder Mary Murphy, professor of psychological and brain sciences and Class of 1948 Herman B Wells Endowed Professor in the IU Bloomington College of Arts and Sciences. “The Equity Accelerator is helping institutions understand what they can do to help students feel like they belong, that they are supported academically.

“It is important that students never feel alone, and that the institution offers tangible affordances that are recognized and used by students to help them feel a sense of belonging and to be academically successful in college.”

The researchers found significant effects on students’ persistence, course taking and sense of belonging after engaging with the reading and writing exercise. The intervention increased the rate at which students completed their first year of college as full-time students, especially among students in groups that had historically progressed at lower rates. However, across the 22 institutions, the impacts were much greater when the institutions had strategies and resources in place to help students feel like they belong.

The researchers have calculated that their results can be generalized to more than 1 million students annually at 749 four-year colleges and universities in the United States, where the 12-month drop-out rate for first-time undergraduate freshmen is 24.1 percent, according to the Education Data Initiative. If all schools in the generalizability sample implemented the online social-belonging intervention, 12,136 more full-time students would complete the first year of college each year. The benefits are greatest among historically lower-performing groups — students whose combined race/ethnicity and generation status is historically lower performing at a particular institution — which helps to reduce inequality on campuses.

The social-belonging intervention was delivered through an online module in the summer before students began college, typically as part of a pre-semester checklist of necessary forms and requirements. It included survey results from older students showing that everyday worries about belonging are normal in the transition to college and can improve over time; carefully curated stories from older students describing these worries and how they improved from them; and an opportunity to reflect on these stories in writing.

Results varied across the 22 institutions, since each offers different strategies, resources and programs to support the particular groups of students who historically struggle with first-year college completion. The researchers say institutional transformation and increasing support for students on campus — as well as students’ knowledge of, attitudes about and usage of these resources — are critical to improving student success.

“This work is globally reimagining the role of institutions on student outcomes, not just from an academic perspective but also students’ life outcomes,” said Sara Woodruff, chief strategy officer at the IU Equity Accelerator. “This is a call to action for the ways in which institutions take their power and use it to really move students. Through the Equity Accelerator, we’re helping institutions reexamine the contract they are creating with students, helping them call out inequities that exist and telling them in real, granular terms what they can do to change.”

The IU Equity Accelerator, formed in July 2022, is a focused research organization whose mission is to use and apply social and behavioral science to provide more equitable learning and working environments where everyone can meet their full potential. Institutions nationwide that are working to improve students’ belonging can work with the Equity Accelerator to identify, from their own students’ perspectives, what resources and strategies are needed to facilitate student belonging on campus.

“In addressing equity, it is important to have actionable results that can be used to improve student experiences and outcomes and help them be the people they are meant to be,” Murphy said. “We hope institutions can build on our findings and the work of the IU Equity Accelerator to identify better ways to support their students.”

The advance — which was recently announced in the journal Nature — uses bacteria to combine natural enzymatic reactions with a new-to-nature reaction called the “carbene transfer reaction.” This work could also one day help reduce industrial emissions because it offers sustainable alternatives to chemical manufacturing processes that typically rely on fossil fuels.

“What we showed in this paper is that we can synthesize everything in this reaction — from natural enzymes to carbenes — inside the bacterial cell. All you need to add is sugar and the cells do the rest,” said Jay Keasling, a principal investigator of the study and CEO of the Department of Energy’s Joint BioEnergy Institute (JBEI).

Carbenes are highly reactive carbon-based chemicals that can be used in many different types of reactions. For decades, scientists have wanted to use carbene reactions in the manufacturing of fuels and chemicals, and in drug discovery and synthesis.

But these carbene processes could only be carried out in small batches via test tubes and required expensive chemical substances to drive the reaction.

In the new study, the researchers replaced expensive chemical reactants with natural products that can be produced by an engineered strain of the bacteria Streptomyces. Because the bacteria use sugar to produce chemical products through cellular metabolism, “this work enables us to perform the carbene chemistry without toxic solvents or toxic gases typically used in chemical synthesis,” said first author Jing Huang, a Berkeley Lab postdoctoral researcher in the Keasling Lab. “This biological process is much more environmentally friendly than the way chemicals are synthesized today,” Huang said.

During experiments at JBEI, the researchers observed the engineered bacterium as it metabolized and converted sugars into the carbene precursor and the alkene substrate. The bacterium also expressed an evolved P450 enzyme that used those chemicals to produce cyclopropanes, high-energy molecules that could potentially be used in the sustainable production of novel bioactive compounds and advanced biofuels. “We can now perform these interesting reactions inside the bacterial cell. The cells produce all of the reagents and the cofactors, which means that you can scale this reaction to very large scales” for mass manufacturing, Keasling said.

Recruiting bacteria to synthesize chemicals could also play an integral role in reducing carbon emissions, Huang said. According to other Berkeley Lab researchers, close to 50% of greenhouse gas emissions come from the production of chemicals, iron and steel, and cement. Limiting global warming to 1.5 degrees Celsius above pre-industrial levels will require severely cutting greenhouse gas emissions in half by 2030, says a recent report by the Intergovernmental Panel on Climate Change.

Huang said that while this fully integrated system can be envisioned for a large number of carbene donor molecules and alkene substrates, it is not yet ready for commercialization.

“For every new advance, someone needs to take the first step. And in science, it can take years before you succeed. But you have to keep trying — we can’t afford to give up. I hope our work will inspire others to continue searching for greener, sustainable biomanufacturing solutions,” Huang said.

This work was supported by the DOE Office of Science and DOE Office of Biological and Environmental Research. Additional support was provided by the National Science Foundation.

“The advantage of organoids is that we can intervene in their development and test active substances on them, which allows us to learn more about healthy tissue as well as diseases,” explains Barbara Treutlein, Professor of Quantitative Developmental Biology at the Department of Biosystems Science and Engineering at ETH Zurich in Basel.

To help produce such an atlas, Treutlein, together with researchers from the Universities of Zurich and Basel, has now developed an approach to gather and compile a great deal of information about organoids and their development. The research team applied this approach to the organoids of the human retina, which they derived from stem cells.

Many proteins visible simultaneously

At the heart of the methods the scientists used for their approach was the 4i technology: iterative indirect immunofluorescence imaging. This new imaging technique can visualise several dozen proteins in a thin tissue section at high resolution using fluorescence microscopy. The 4i technology was developed a few years ago by Lucas Pelkmans, a professor at the University of Zurich and coauthor of the study that has just been published in the scientific journal Nature Biotechnology. It is in this study that the researchers applied this method to organoids for the first time.

Typically, researchers use fluorescence microscopy to highlight three proteins in a tissue, each with a different fluorescent dye. For technical reasons, it is not possible to stain more than five proteins at a time. In 4i technology, three dyes are used, but these are washed from the tissue sample after measurements have been taken, and three new proteins are stained. This step was performed 18 times, by a robot, and the process took a total of 18 days. Lastly, a computer merges the individual images into a single microscopy image on which 53 different proteins are visible. They provide information on the function of the individual cell types that make up the retina; for example, rods, cones, and ganglion cells.

The researchers have supplemented this visual information of retinal proteins with information on which genes are read in the individual cells.

High spatial and temporal resolution

The scientists performed all these analyses on organoids that were of different ages and thus at different stages of development. In this way, they were able to create a time series of images and genetic information that describes the entire 39-week development of retinal organoids. “We can use this time series to show how the organoid tissue slowly builds up, where which cell types proliferate and when, and where the synapses are located. The processes are comparable to those of retinal formation during embryonic development,” says Gray Camp, a professor at the University of Basel and a senior author of this study.

The researchers published their image information and more findings on retinal development on a publicly accessible website: EyeSee4is.

Further tissue types planned

So far, the scientists have been studying how a healthy retina develops, but in the future, they hope to deliberately disrupt development in retinal organoids with drugs or genetic modifications. “This will give us new insights into diseases such as retinitis pigmentosa, a hereditary condition that causes the retina’s light-sensitive receptors to gradually degenerate and ultimately leads to blindness,” Camp says. The researchers want to find out when this process begins and how it can be stopped.

Treutlein and her colleagues are also working on applying the new detailed mapping approach to other tissue types, such as different sections of the human brain and to various tumour tissues. Step by step, this will create an atlas that provides information on the development of human organoids and tissues.