Advancing environmental justice by making fisheries more equitable

ASU PhD student selected to Global Human Rights Hub Fellows Program for her work on human rights in the seafood industry

October 30, 2020

Growing up in Arizona, Gabrielle “Gabby” Lout was fascinated with the ocean.

“Not having the ocean right in my backyard magnified my interest and wonder about it,” said Lout, a Human and Social Dimensions of Science and Technology doctoral student at ASU’s School for the Future of Innovation in Society in the College of Global Futures. “It was something so different than the desert, but the marine environment can be just as harsh and even more unpredictable.” Gabby Lout at the Pyramid of the Sun in Teotihuacan, Mexico Gabby Lout at the Pyramid of the Sun in Teotihuacan, Mexico. Lout was in Mexico for a case study examining novel approaches for sustainable resource use in seafood supply chains. Download Full Image

Lout spent summers with her family on the beaches of Florida. Her grandfather taught her about the ocean and listening to the energy of the Earth. She knew from a young age that she wanted to pursue marine conservation. After earning her Bachelor of Science in marine and conservation biology in Seattle and her Master of Arts in global leadership and sustainable development in Hawaii, she returned to Arizona. She wasn’t planning to go straight into her PhD, but when she came across an ASU research assistant position working in small scale fisheries, she was drawn to the HSD program and the type of research she could do.

“I'm interested in the complexity between social and natural sciences, and the social issues that are present in conservation, specifically fisheries,” Lout said.

She is now focusing her research on human rights in the seafood industry and will continue her work as a Global Human Rights Hub Graduate Fellow

“It’s exciting to be acknowledged for this less-known and advancing field around human rights, the ocean and conservation,” Lout said. “It’s an opportunity that lines up with my research, and I believe it will be pivotal in my development within the human rights space.”

The fellows program is part of the new Global Human Rights Hub, which brings together ASU faculty members and graduate students researching global human rights issues. The hub will highlight the important work that graduate students are conducting and provide a network of scholars to help students develop their research and knowledge on human rights.

“The field of human rights is incredibly interdisciplinary,” said Associate Professor Heather Smith-Cannoy, director of the Global Human Rights Hub and Lout’s mentor for the program. “We think that there is high value in finding ways to connect faculty who are working on these topics with graduate students. Lout’s work will contribute to a field of critical concern: environmental justice. Her work forces us to think specifically about human rights abuses at sea and how nonsustainable practices can harm marine ecology and human rights. We think she will be a future leader in the field.”

In the program, Lout will also highlight her current research in a series of blog posts.

“One project I’ve been leading in Guyana with Conservation International is looking at the marine ecosystem and sustainable fisheries, and focusing on social well-being and livelihoods,” Lout said. “I’ve been working with local stakeholders and fishing cooperatives to identify social risks and areas of improvement, which will then inform fisheries management of ways to be more inclusive and equitable.”

Lout is also leading a project for the Food and Agriculture Organization of the United Nations on decent work in fisheries in Guyana, Suriname, and Trinidad and Tobago to identify ways to improve working conditions for fishers. ASU and the Human and Social Dimensions of Science and Technology program have helped her further her research.

“Being surrounded by peers and faculty that are working on such diverse issues has pushed me to think differently. I have been so impressed and appreciative of the vast opportunities at ASU and have felt supported to pursue work that is not cookie-cutter or linear.”

After she graduates, Lout wants to continue working in the nonprofit sector.

“I think everybody wants to make an impact and a difference, regardless of how small or large it can be. The ocean and the natural world are changing so rapidly, and social issues are becoming more complex. I want to give small scale fisheries and marine conservation the attention they deserve and make an impact any way I can.”

Ashley Richards

Communications Specialist , School for the Future of Innovation in Society


Criss-crossing viruses give rise to peculiar hybrid variants

October 30, 2020

For millions of years, viruses have participated in a far-flung, import-export business, exchanging fragments of themselves with both viral and nonviral agents and acquiring new features. What these tiny entities lack in outward complexity, they make up for with their astonishing abilities to swap out modular genomic components and ceaselessly reinvent themselves.

In new research appearing in the journal mBioArvind Varsani and his colleagues investigate a recently discovered class of viruses that have taken the characteristic versatility of the viral world to new heights. Cruciviruses are a hybrid form containing both RNA and DNA genomic material. Here, a single-stranded DNA virus (yellow) containing a Rep protein sequence, which directs the virus's replication, borrows genetic information from an RNA virus (blue) , specifically, a coding sequence for the RNA virus's capsid protein. The result is a chimerical virus with both DNA and RNA components — a crucivirus (seen in the right panel). Graphic by Shireen Dooling for the Biodesign Institute. Download Full Image

Referred to as cruciviruses, these minute forms reveal a fusion of components from both RNA and DNA viruses, proving that these previously distinct genomic domains can, under proper conditions, intermingle, producing a hybrid or chimeric viral variant.

Varsani, a virologist at the Arizona State Univeristy Biodesign Center for Fundamental and Applied Microbiomics, is deeply intrigued with these new viruses, which are starting to crop up in greater abundance and diversity in a wide range of environments. 

“It is great to see the research groups that first identified cruciviruses around the same time teaming up for the sharing and mining of metagenomic data with an aim to identify a larger diversity of cruciviruses,” said Varsani, an associate professor with the ASU School of Life Sciences.

Arvind Varsani is a virologist with the Biodesign Center for Fundamental and Applied Microbiomics and ASU's School of Life Sciences.

New virus in town

Crucivirus sequences were identified by Varsani’s colleague and co-author Kenneth M. Stedman and his group at Portland State University. The team detected the viruses flourishing in an extreme environment — Boiling Springs Lake (BSL) in Lassen Volcanic National Park,  in northern California. Around the same time, Varsani and Mya Breitbart’s research group identified a crucivirus in a dragonfly sample from Florida.

Since their discovery in 2012, cruciviruses have been found in diverse environments around the world, from lakes in upstate New York and Florida, to the Antarctic and deep-sea sediments. Some 80 distinct cruciviruses had been identified, prior to the current study, which expands the number to 461.

The first cruciviruses were identified using a technique known as viral metagenomics, in which viral genetic material obtained directly from the environment is sequenced rather than being cultivated or cultured from a host species or natural reservoir. 

The results of these early investigations revealed peculiar genetic sequences, radically distinct from anything that had been seen before. These sequences clearly displayed the signature of a DNA virus, yet also contained a gene that appeared to be derived from an RNA virus.

Using a shotgun approach to trawl through a potentially vast sequence space, viral metagenomics enables researchers to identify all of the genomic patterns present in an environmental sample, then separate out distinct viral sequences, like a fisherman retrieving a variety of sea creatures from his net.

The technique has revolutionized the discipline of virology. In addition to identifying a galaxy of previously unknown viruses, metagenomics has offered up exciting clues about genetic diversity and is helping to unlock some of the secrets of viral evolution, all without the need to initially isolate viral species or cultivate viruses in the lab.

Form and function

Cruciviruses belong to a broader class of viruses known as CRESS, (for circular Rep-encoding single-stranded) DNA viruses which have recently been classified into the phylum Cressdnaviricota. The defining characteristic of such viruses is their mode of replication, which relies on a specific component, known as the Rep protein. The Rep protein is important for guiding the replication method of these viruses, known as rolling circle DNA replication. Presence of the Rep protein and rolling circle replication pinpoints a virus as belonging to cressdnaviruses and helps researchers untangle the devilishly complex relationships and lineages found in the viral world.

In addition to the Rep found in cressdnaviruses, cruciviruses contain another centrally important feature — a capsid protein that is similar to that previously found only in RNA viruses. Capsids are vitally important, forming the outer shell or envelope that encloses the virus’s identity — its genetic sequence. The capsid shelters the vital nucleic acids sequestered within from digestion by host cell enzymes, enables virus particles to attach themselves to host cells and allows viruses to evade host cell defenses. Finally, capsids contain specialized features that give the virus its ability to puncture the host cell membrane and inject viral nucleic acid into the cell’s cytoplasm.

Analysis indicates that the capsid protein of cruciviruses is closely related to the capsid protein of another virus from the family Tombusviridae — a single-stranded RNA virus known to infect plants. This hybrid viral character, containing both DNA- and RNA-virus-derived coding components, is what makes cruciviruses so unique.

Uncertain origins

But how did a run-of-the-mill cressdnavirus come to acquire its RNA virus capsid protein coding sequence? This remains an issue of considerable debate, though presumably some form of lateral gene transfer occurred.

Viruses can acquire genes from their immediate progenitors, the way genetic traits are passed from human parents to their offspring. Viruses, however, are far more genetically promiscuous, collecting new genes from the cells they infect, from other unrelated viruses and even from bacterial symbionts. (The phenomenon is also common among bacteria, which can use horizontal gene transfer to acquire antibiotic resistance.) 

Through some such mechanism, a cressdnavirus acquired an RNA virus capsid-like gene, creating the first crucivirus. It also appears that various cruciviruses have actively exchanged functional elements among themselves, further scrambling their evolutionary history.

While the HOW of crucivirus DNA-RNA recombination remains mysterious, the WHY may be more straightforward. Clearly, the ability to borrow genetic traits from such distantly related viral sources could provide single-stranded DNA viruses with a considerable adaptive edge.

Collector’s edition

In the current study, researchers explored a vast dataset including 461 cruciviruses and 10 capsid-encoding circular genetic elements identified from varied environments and organisms, making this the most expansive investigation of crucivirus sequences yet undertaken.

The samples were found in environments ranging from temperate lakes to permafrost and lurking within organisms including red algae and invertebrates. The study points to the stramenopiles/alveolates/Rhizaria or SAR supergroup, (a diverse assemblage of eukaryotes, including many photosynthetic organisms) as the plausible candidate hosts for these unusual viruses, though this has yet to be verified. 

After examining the windfall of sequences, the researchers assembled similarity networks of cruciviral proteins with related viruses to try to better understand the twisting evolutionary paths that may have given rise to them, finding a rich cross-pollination of viral traits between many large families of viruses including Geminiviridae, Circoviridae, Nanoviridae, Alphasatellitidae, Genomoviridae, Bacilladnaviridae, Smacoviridae and Redondoviridae.

Intriguing questions remain

The findings may provide new insights into the early transition from RNA as the primary hereditary molecule of life to the adoption of more complex DNA genomes that has come to dominate life in the cellular world. The existence and behavior of cruciviruses suggest that viruses may have played a crucial role in this all-important transition, acting as a kind of genomic bridge between the RNA and DNA worlds, during the earliest emergence of life, though much more work is needed to explore these possibilities.

Recombining in endless forms, viruses have become the planet’s most ubiquitous biological entities, affecting every living organism and occupying every ecological niche. Increasingly, viruses are revealing themselves not only as agents of disease but as drivers of species evolution and vital actors in the molding of ecosystems.

The expanded abilities of cruciviruses to borrow genomic elements from the most far-flung regions of viral sequence space suggest that entirely new virus groups may arise though prolific recombination events between distantly related forms.

Richard Harth

Science writer, Biodesign Institute at ASU