San Diego, CA
Illumina and the San Diego Zoo are sequencing koala genomes to investigate disease
Two world-class institutions that call San Diego home have joined forces on an investigation into the DNA of koalas.
The San Diego Zoo Wildlife Alliance and DNA-sequencing giant Illumina are examining the genetic information of nearly 100 koalas spanning 30 years to get a better understanding of koala retrovirus, or KoRV.
Scientists suspect through growing evidence that certain variants of koala retrovirus—all koalas carry some form of it—are associated with common diseases and health issues they have, such as leukemia, lymphoma and deadly fungal infections.
KoRV is baked into the genes of koalas and gets passed along to the next generation. This boat load of genetic data will help researchers examine patterns of how KoRV is getting integrated into koala genes. In turn, having a better understanding of KoRV will help inform conservation plans for koalas in the wild and in human care.
Dr. Cora Singleton, senior veterinarian at the San Diego Zoo Wildlife Alliance, works primarily with marsupials, including koalas. Singleton has cared for koalas for years and witnessed them struggle with the health effects of KoRV.
In order to sequence the genome, the San Diego Zoo used samples from 91 current koalas living at the zoo as well as samples from the frozen zoo—a bank of living cells—going back to the 1970s. These samples were then sent to Illumina’s laboratory in San Diego, where researchers extracted the DNA to prepare it for sequencing in their machines. Those sequencing instruments break the DNA down into the basic alphabet that makes up all genetic information.
Ashley Van Zeeland, vice president of corporate development at Illumina, said there is a lot less known about the koala genome than the human genome. That mass amount of data was then sent to collaborators in other countries, who are now studying the koala genomes.
“(They) take the data that our instruments generate and put it together into kind of the full picture of that species,” Van Zeeland said.
Van Zeeland, who has worked in genomics for two decades, explained the unique offering of this dataset is that it pairs generations of genetic data alongside meticulously documented medical records. For instance, researchers can examine the cause of death for a koala and its parents to see if there’s a connection.
Researchers are looking for patterns of where KoRV has inserted itself into the koala’s DNA because it’s not entering at the same spot for every koala. More specifically, researchers are comparing the patterns of how KoRV integrated into koala genes in a way that may be associated with certain diseases.
Van Zeeland explained that looking at where KoRV inserted itself in the genome may give researchers an idea of which genes might be disrupted, turned on or off in the koala and the resulting effect on their health.
Having that knowledge of which integration patterns correlate with certain adverse health effects could inform how conservationists pair up koala populations for reproduction. As koalas already face pressures from climate change and a disappearing habitat in the wild, this would tackle one more stressor on the endangered population.
While the koala genome had already been sequenced previously, the scale of this project wasn’t feasible even a few years ago, explained Singleton.
“One of the questions everybody always said from a research perspective: ‘wouldn’t it be great if we could see what’s going on in the genome?’ But for many, many years it was very expensive and very labor intensive,” Singleton said.
Illumina has been focused on getting the cost of sequencing the genome down so this kind of technology is more accessible and applicable for researchers. Van Zeeland said that in 2015 it cost roughly $1,000 to $2,000 to sequence a genome, but now that cost is down to about $200 using the latest technology. (Illumina’s work on the project is through its Illumina iConserve initiative, which focuses on environmental and wildlife conservation.)
Singleton characterizes this project as a career highlight to be a part of a network of collaborators trying to solve the same puzzle. While it’s been years in the making, she always knew “there was something special in there that we had to uncover at the right time and the right place.”
“It’s the moment for genetics to take off in the world of conservation,” Singleton said.
The effort to compile and analyze a database of the North American koala population will be the largest koala pedigree genomic database in the world. The project spans continents and is also aided by the University of Sydney, Australian Museum Research Institute, University of Nottingham, Leibniz Institute for Zoo and Wildlife Research and ZooParc de Beauval.
2024 The San Diego Union-Tribune. Distributed by Tribune Content Agency, LLC.
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San Diego, CA
An Apprentice Program for Commercial Fishing
Despite San Diego’s abundant marine life, the region’s commercial fishing industry is in decline.
In 2020, the Scripps Institution of Oceanography started an apprentice program to help reverse the trend — but the program has had mixed results, reports Deborah Brennan at our partner CalMatters.
Globalization is partly to blame for the busted economics of San Diego’s fishing industry. Higher wages and stricter regulations in the U.S. mean that fish caught in other countries are often cheaper. A 2016 report found that just 10 percent of seafood consumed in San Diego is caught locally.
Wages have plummeted for U.S. fishing captains and their crews in the last decade. A deckhand in San Diego can expect to earn between $15,000 and $50,000 per year.
The apprentice program doesn’t just teach people to fish, but to navigate, repair engines and even business skills. It hasn’t been without success — despite a Covid hiatus. Of 11 graduates, 6 are still fishing. But some of the captains who said the program was necessary have also been reluctant to mentor apprentices.
Peter Brownell used to be research director for San Diego’s Center for Policy Initiatives. He studied, incidentally, poverty. Wanting to transition away from a desk job, he entered the program and is now scratching out an existence on the water.
“If you’re entirely reliant on commercial fishing for all your economic needs, that’s a hard puzzle to put all the pieces together to make that work consistently year after year,” he said.
Read the full story here.
Council Considers Junk Fee Ordinance
The San Diego City Council heard details of a proposed “junk fee” ordinance that would cap extra fees for renters and require landlords to disclose fees before a lease is signed.
The proposal, introduced by Councilmembers Sean Elo-Rivera and Henry Foster, would cap fees at no more than five percent of the price of rent. It would also prohibit things like charges for basic building operating expenses, such as pest control.
“What I’ve heard is a general consensus around the transparency components and agreement that people should know what they’re going to be asked to pay,” said Elo-Rivera during a hearing on the fee Tuesday. “They should know that at the beginning of their search and before they sign a lease, not after.”
The Council only heard details on the new proposal. It did not vote on the ordinance.
AI-Powered Humanoid Robots Take Over the Web
It’s always strange when a story you write starts spreading. This week, I’ve been watching it happen with a story we published about a local charter network that spent $500,000 on two ChatGPT-powered humanoid robots.
I wasn’t shocked the story struck a nerve. It had a built-in, WTF factor that seemed guaranteed to draw eyeballs. But more importantly, it comes at a moment when people across the world are grappling with what it means to live alongside technology. It’s playing out in skirmishes over edtech, battles over data centers, and now the question of humanoid robots in the classroom.
The story has moved from the new media food chain. First came news aggregators like the New York Post, then aggregation scavengers you’ve never heard of, and now even AI aggregators, which create something akin to news hot dogs — if hot dogs used an excessive amount of subheads and bullet points.
Underneath that hollow feeding frenzy, though, are real, local news organizations. The reporters and editors report on the communities you love, because they love them too. If you haven’t already, you should consider supporting this one.
Rabbitholed
University Heights’ neon street sign — with its iconic trolley car logo — is set to go dark.
Locals were warned recently that city workers plan to turn off the 30-year-old sign due to wear and tear. Burned-out neon had already left some portions of the sign nonfunctioning.
Members of the University Heights Community Association say the city’s to blame. They allege city officials have drained funds from the neighborhood’s Maintenance Assessment District, which would normally pay for repairs. Now, they’re pressuring the city to pony up for fixes.
But behind the faulty neon is the fascinating, 130-year-plus origin of the sign’s trolley logo. It commemorates a time before the city was carved up by freeways — and instead had a thriving network of streetcars extending from Ocean Beach to La Jolla and Chula Vista. Many of those cars were repaired at a warehouse located at the site of Trolley Barn Park, hence the name – and the sign.
The streetcar network had plenty of ups and downs, like when John Spreckles, the richest man in San Diego at the time and owner of the network, ordered his workers to secretly dig up the tracks under the cover of night due to a dispute with city officials. Here’s an interesting story about how the actual streetcars evolved over the years.
The system ultimately went defunct in 1949.
What’s your take? Do you wish the city still had an urban streetcar system?
In Other News
- Two San Marcos residents say their homeowners association is violating their rights to fly American flags outside their home. But legal experts say people do have the right to fly their flags even in homes subject to rules by homeowners associations. (inewsource)
- Longer meetings are coming to San Diego City Hall. As part of a new set of policies to boost public participation, city officials will allow group presentations during online meetings. (Union-Tribune)
- Speaking of City Hall, the San Diego City Council will soon create an affordable housing preservation fund backed by $8.5 million. Along with other funding sources, the fund will work to preserve affordable housing. (KPBS)
- The former news director of KPBS, Terrence Shepherd, is suing the outlet, alleging he was wrongfully terminated after recommending a reporter be fired because they’d “staged a protest scene” during a television shot. Exactly what Shepherd’s claim of a “staged protest” entails isn’t entirely clear. A spokesperson for KPBS declined to comment on the situation. (Current)
The Morning Report was written by Jakob McWhinney, Mariana Martínez Barba and Will Huntsberry. It was edited by Will Huntsberry.
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San Diego, CA
Marine missing after training activity off San Diego is declared dead
The U.S. military identified a Minnesota Marine stationed in Southern California who went missing off San Diego last week, and confirmed his death.
Lance Cpl. Armando Ortiz Canseco was declared deceased Saturday. It is believed he was lost at sea after a training exercise.
“On behalf of the Marines and sailors of the 13th Marine Expeditionary Unit, I extend our deepest condolences to the family and loved ones of Lance Cpl. Ortiz Canseco,” Col. Richard Alvarez, the commanding officer of the 13th Marine Expeditionary Unit, said in a statement.
Ortiz Canseco was reported missing from the amphibious transport dock ship USS Anchorage early Thursday morning. His disappearance resulted in an extensive search and rescue operation, with efforts beginning around 1:20 a.m. Thursday.
The search spanned roughly 2,400 square miles and involved officials from the Navy, Marine Corps, Coast Guard and Air Force who used three surface ships and 12 aircraft, according to the military.
The Marine went missing during a training operation involving the 13th Marine Expeditionary Unit and the Makin Island Amphibious Ready Group.
After nearly two full days of searching, the Navy transitioned to recovery operations.
“He earned the title of United States Marine and served his country with honor and commitment,” Alvarez said. “We mourn alongside his family, and we remain committed to bringing him home.”
This incident marks the second time in recent weeks that the U.S. military has searched for missing service members.
The remains of two Army soldiers who went missing while off duty from military exercises in Morocco were recovered in May, according to the Army.
Officials did not initially identify Ortiz Canseco on Thursday or disclose the circumstances surrounding his disappearance, saying his family needed to be notified first.
His death continues to be under investigation.
Ortiz Canseco enlisted in the Marine Corps in April 2023 and reported for training at Marine Corps Recruit Depot San Diego.
His individual awards include the Marine Corps Good Conduct Medal and Sea Service Deployment Ribbon.
Times staff writer Alene Tchekmedyian contributed to this report.
San Diego, CA
Adobe Falls: The elusive waterfall that briefly returns after San Diego rains
Blink, and you might miss it.
Adobe Falls isn’t Niagara Falls — or anything close — but after winter rains, a seasonal waterfall briefly appears in a narrow Del Cerro canyon, hidden beneath streets, homes, and San Diego State University property.
The waterfall forms along Alvarado Creek, which drains parts of eastern San Diego, including the SDSU area and surrounding neighborhoods. In wet months, runoff moves through a steep canyon and drops over a short rock ledge known locally as Adobe Falls. In dry periods, the flow often fades to a trickle or disappears entirely, leaving exposed sandstone and a shaded canyon bed.
What makes the site stand out is its setting. Above the canyon are Del Cerro residential streets and university property tied to San Diego State. Below it, Alvarado Creek continues west as part of the Mission Valley watershed, eventually feeding into the San Diego River system. Like many urban drainages in San Diego, its flow is shaped by stormwater runoff, paved surfaces, and altered drainage patterns tied to development.

Access is restricted. The canyon sits on a mix of SDSU and city-managed land and has long been closed to the public due to safety concerns, including steep terrain, erosion, and unstable footing after rain. Although widely referenced in maps and online posts, it is not an official trail or recreation site.
The canyon itself pre-dates modern development in Del Cerro. It is part of a broader network of inland waterways and canyon corridors used for thousands of years by the Kumeyaay, whose presence shaped movement and settlement patterns across the region.
In the mid-20th century, as Del Cerro developed, homes and roads were built along canyon rims rather than through them, leaving Alvarado Creek intact as a drainage system. Adobe Falls remained within that corridor even as surrounding hillsides filled with residential and institutional development.
Today, Adobe Falls remains a small but persistent reminder that San Diego’s natural drainage systems still function within a heavily built environment — appearing briefly after storms, then receding back into the canyon until the next rain.
Read more history stories here, and do you have a story to tell? Send an email to DebbieSklar@cox.net.
Sources:
City of San Diego – Stormwater & Watershed Division (Alvarado Creek / Mission Valley watershed)
San Diego State University – planning and environmental impact documentation for adjacent canyon areas
U.S. Geological Survey (USGS) – San Diego County watershed and hydrology mapping (Alvarado Creek / San Diego River system context)
San Diego History Center – Kumeyaay regional land use and inland canyon corridor history
City of San Diego Planning Department – land use records and access restrictions for Adobe Falls area
California State Historic Landmark files – Adobe Falls (Landmark No. 80)
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