Environmental DNA as a tool for assessing microbial diversity & ecological impacts by contaminants at The Bowtie parcel Brownfield site in Southern California
Wayne Lab Post-doc, Maura Palacious, received the the La Kretz and Stunt Ranch Combined grant. Take a look at the project summary below! Project Summary: Urban planning considers the loss of open space, biodiversity, and pollution, as well as the demand of a growing populations in cities. Vacant Brownfields are properties with the presence of hazardous substances, pollutants, or contaminants that if remediated can be critical to urban revitalization. This study applies eDNA metabarcoding to soil samples from The Bowtie Parcel Brownfield adjacent to the L.A. River to explore biological community changes in relation to contaminants. This study will contribute to the redevelopment plan of The Bowtie Parcel, potentially generate a low-cost microbial bioremediation alternative, and incorporate a new tool for the assessment of Brownfields.
This past summer I attended a Barcoding Educator workshop, an effort between James Madison University and Cold Spring Harbor Laboratory (CSHL), to train and expand DNA barcoding (the use of a single region of DNA to identify a species as simple as scanning a supermarket barcode) to other institutions across the nation. I chose to focus our DNA Barcoding Project at a location in our backyard, Arroyo Seco, an urban stream that flows into the L.A. River. The students were tasked to collect one insect with the use of a D-net, sweep net, or trapping them in a collection tube. We also set up a Malaise trap in the event a student was unable to collect a sample. In addition, students made observations using the iNaturalist application, an easy tool to create unique class specific projects (https://www.inaturalist.org/projects/eeb-87-california-s-dna-a-field-course). In groups students also collected water quality data and sediment environmental DNA samples. To our surprise, this hidden gem harbored high levels of biodiversity which included chorus frogs, salamanders, dragonflies, wolf spiders, and even horses!
The expanding global human footprint is dividing the world’s flora and fauna into ever-smaller, more isolated populations that could wink out because of inbreeding, disease, or environmental change. For decades, conservationists have proposed revitalizing those holdouts by bringing in new blood from larger populations. But they’ve wondered whether it really works—and how to do it without swamping the genetic identity and unique adaptations of the group at risk. Last month at Evolution 2019 here, researchers described how genomic tools are refining what is known as genetic rescue.
A Surprising Idea About the Risks of Extinction. The tiny population of wolves on Isle Royale descended from a much larger group. What if that helped doom them?
The wolves of Isle Royale inspired Chris Kyriazis and his colleagues at UCLA to simulate animal populations over hundreds of generations. Their findings were counterintuitive: What doomed the wolves is not just the small number that have lived on the island in modern times, but perhaps also the large number of wolves that lived thousands of years ago. Kyriazis presented his study at the Evolution 2019 conference, and the team posted a preprint of the article, which has not been peer reviewed yet, on bioRxiv.
Sea otters have low genetic diversity, which could endanger their health as a species, a UCLA-led team of life scientists has discovered. The findings have implications for the conservation of rare and endangered species, in which low genetic diversity could increase the odds of extinction.
It’s estimated that a person sheds between 30,000 to 40,000 skin cells per day. These cells and their associated DNA leave genetic traces of ourselves in showers, dust — pretty much everywhere we go. Other organisms shed cells, too, leaving traces throughout their habitats. This leftover genetic material is known as environmental DNA, or eDNA. Research using eDNA began about a decade ago, but was largely limited to a small cadre of biologists who were also experts in computers and big data. However, a new tool from UCLA could be about to make the field accessible and useful to many more scientists. A team of UCLA researchers recently launched the Anacapa Toolkit — open-source software that makes eDNA research easier, allowing researchers to detect a broad range of species quickly and producing sortable results that are simple to understand.
Serieys began her genetic research on bobcats in the lab of Robert Wayne, a UCLA professor of ecology and evolutionary biology who collaborates regularly with the park service. She later studied the rodenticides’ effects on the immune system in labs at the UCLA AIDS Institute and the UCLA Jonsson Comprehensive Cancer Center. Analyzing samples from bobcats with and without traceable levels of poison in their systems, she looked at 65 biochemical markers, including immune function and organ function.
Volunteers throughout California are heeding a call by UCLA researchers to map California’s biodiversity and preserve the state’s environmental history. The project, CALeDNA, aims to assess Californian biodiversity across numerous habitats using soil samples collected by citizen scientists. CALeDNA is funded by the President’s Research Catalyst Awards. University of California President Janet Napolitano instituted the award in 2015 to grant funding to UC members pursuing leading research. “CALeDNA is about monitoring life in California, everything from the bacteria in the soil to the mammals that walk on it,” said Rachel Meyer, executive director of the UC Conservation Genomics Consortium. “We want to know what California looks like right now, because environmental changes are happening very quickly, especially with the current political climate.”
In the 1990s, drought, parasites, and disease brought in by a stowaway raccoon, and predation by golden eagles, triggered the drastic population crashes that led to the foxes’ endangered status. Elimination of nonnative livestock and feral animals, replacement of invasive plants with native ones, and capturing and translocating golden eagles (which had been drawn to the islands by livestock carcasses), stabilized populations. Foxes were also vaccinated against introduced canine distemper virus. While these human-caused problems were solved or removed, foxes were bred in captivity and then returned to their home islands. Comprehensive whole genome studies of nuclear DNA from the islands’ foxes, performed by Jacqueline Robinson and her colleagues in the genetics laboratory of Robert K. Wayne at the University of California, Los Angeles, uncovered additional factors in the near-extinction of the species. What they found was startling. Genetic diversity was low, and sequences from the two foxes from San Nicolas were so similar as to be almost identical genetically. The group calls it genetic flatlining