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
Tatis’ first Petco homer of the year delivers crucial walk-off win
Fernando Tatis Jr. hit just his second home run of the season with two outs in the ninth inning to lift the San Diego Padres to a 5-4 win against the Cincinnati Reds on Wednesday.
Tatis lined a 2-1 pitch from Chase Petty (0-1) into the first row of seats in left field, with a launch angle of just 18 degrees. He spread his arms wide in celebration as he approached second base and did an exaggerated stutter step around third. His jersey was torn off during a wild celebration.
He didn’t hit his first homer of the season until May 30 at Washington. Wednesday’s homer was the fifth career walk-off for Tatis and fifth of the season for San Diego, which won for just the fourth time in 16 games.
The Padres took two of three Cincinnati, who scored all their runs Wednesday on three home runs.
Cincinnati took a 4-2 lead on its third homer, by Eugenio Suárez off Ron Marinaccio with one out in the eighth.
San Diego tied it in the bottom of the inning on an RBI double by Gavin Sheets and a run-scoring single by Samad Taylor.
The rally got Michael King off the hook for what would have been his fourth straight loss. He has allowed six home runs in his last four starts, including two in each of his last two starts. Wandy Peralta (1-0) pitched the ninth.
King allowed Spencer Steer’s two-run shot into the second deck in left field in the fourth that gave the Reds a 2-1 lead.
San Diego tied it in the fifth when Tatis’ two-out single brought in Rodolfo Durán, aboard on a one-out double.
JJ Bleday homered off King with two outs in the seventh, his 11th, for a 3-2 lead.
Up next
Reds LHP Nick Lodolo (2-1, 5.51 ERA) is scheduled to start Friday night at home against Arizona.
Padres RHP Griffin Canning (0-4, 6.34 ERA) is expected to start Friday night at Baltimore.
___
AP MLB: https://apnews.com/MLB
San Diego, CA
Daily Business Report: June 10, 2026, San Diego Metro Magazine
Meet San Diego’s theater organ player, whose music creates a time machine to the 1920s
By Drew Sitton | Times of San Diego
There are old car people. There are aquarium people. And then there are theater organ people.
San Diego has its own.
“You either get it or you don’t,” said Russ Peck, who is known as the preeminent expert on theater organs from San Diego to Los Angeles. “It’s just what turns you on, and this thing… I just love these, I love playing on ‘em. Working on ‘em. It’s a way of life.”
In 1970, Peck heard his first pipe organ while at a music hall in Downey. The only song he had memorized on the piano was “Porky Pig at the Ice Show.” He played it over and over until he was forced to stop. Then, he spent years bugging his parents to get him an organ.
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Morning Report: Arizona Eyes Tijuana’s Sewage
by Voice of San Diego
A state-backed Arizona finance authority is considering a plan to fund a wastewater-to-drinking water facility in the Tijuana River Valley.
The goal? Pipe the purified water back to Mexico, and in exchange, ask Mexico to hand over some of its Colorado River water. It is one of several ambitious concepts backed by a $1billion Arizona fund aimed at identifying new water resources for the drought-stricken state.
But navigating the legal and environmental nuances of cross-border sewage is messy. The reality is that it’s incredibly complex to try to treat another country’s runoff on U.S. soil, our MacKenzie Elmer writes.
Read More
San Diego’s forgotten beer giant: How Aztec Brewing helped shape a city
By Debbie L. Sklar | Times of San Diego
Founded in 1921 during Prohibition, Aztec Brewing Co. was created by American investors who established operations in Mexico in order to serve U.S. consumers who could no longer legally purchase alcohol at home.
Mexicali, just south of the border, became part of a wider regional network where travel, trade, and nightlife flowed between the two countries despite Prohibition restrictions.
When Prohibition ended in 1933, Aztec relocated its operations to San Diego, establishing a large-scale brewery at 2301 Main St. The site sat within the city’s industrial corridor near what is today Logan Heights and the Barrio Logan area, then primarily defined by manufacturing, rail activity, and warehousing rather than formal neighborhood boundaries.
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San Diego, CA
San Diego City Council OKs compromise spending plan, capping a contentious budget season
Weeks of debate and negotiation culminated Tuesday with the San Diego City Council adopting a compromise budget that includes last-minute moves to boost flood prevention and partially restore hours at libraries and rec centers.
The final budget pays for some new expenditures by pairing up police officers in patrol cars more frequently versus having them patrol alone — a change opposed by the city’s police chief.
Other late additions include money for an engineering team that analyzes bike lanes, a bridge in western Mission Valley and two police sergeants — one focused on graffiti and another on registering sex offenders.
The council, which debated the final budget during a contentious public hearing that lasted more than five hours, also came within one vote of eliminating a city contract for automated license plate readers.
The $2 million in savings would have allowed full reversal of Mayor Todd Gloria’s proposed cuts to hours at nine libraries and 24 recreation centers. A full reversal would have cost $3 million, but the final budget includes only $900,000.
In the final budget, four library branches would have their Saturday hours cut in half: La Jolla, Point Loma, downtown and Rancho Bernardo. Two other branches would lose their Monday hours: University Heights and Allied Gardens.
For recreation centers, weekly hours will be cut to 40 at La Jolla, Pacific Beach, Cabrillo, North Clairemont, Ocean Beach, Carmel Mountain Ranch, Hilltop, Tierrasanta, Scripps Ranch, Mira Mesa, Rancho Bernardo, Allied Gardens, San Carlos and Serra Mesa.
The four council members in favor of canceling the contract for license plate readers were Kent Lee, Henry Foster, Vivian Moreno and Sean Elo-Rivera.
They said license plate readers do more harm than good by putting residents under surveillance and providing data that could potentially be used for immigration enforcement.
After the proposal was rejected, Elo-Rivera called it a mistake.
“We’re leaving $2 million in resources on the table that could be opening more rec centers, opening more libraries and opening more parks,” Elo-Rivera said. “I think that’s a shame, and I don’t think we’re safer for it.”
Councilmember Marni von Wilpert said license plate readers help get criminals caught and make the city safer.
“We can go back to the old way of policing if we want, but there will be consequences,” she said.
Von Wilpert was joined in opposition to canceling the contract by Stephen Whitburn, Raul Campillo, Jennifer Campbell and Joe LaCava.
The issue also divided the speakers who attended Tuesday’s hearing.
Larry Webb, leader of a resident group called the Coastal Coalition, said license plate readers are crucial to the city’s understaffed Police Department.
“Eliminating a proven force multiplier will only worsen the challenges,” he said.
Khalid Alexander said the council’s choice was between supporting police with the readers or supporting residents with the kind of crime prevention that comes from better neighborhood services.
“We request you support the people who are begging you to support programs that prevent crime and that you defund the police,” he said.
The mayor didn’t announce Tuesday night whether he would sign the budget or possibly use his line-item veto power to reverse some of the last-minute changes. An announcement was expected Wednesday.
Another contentious issue was making officers share patrol cars to reduce gas and vehicle costs.
Councilmember Henry Foster praised the move, despite concerns raised by the city’s independent budget analyst that it could raise costs for overtime and slow response times.
“Officers don’t show up by themselves,” said Foster, contending that it makes sense for officers to travel together to incidents serious enough that multiple officers respond.
Police Chief Scott Wahl said he would grudgingly figure out how to implement the change, which the labor union representing city police officers has supported.
“We’ll do our best to try to make it work,” Wahl said. “If it was an idea that I thought was a good one, I would have proposed it.”
Deputy City Attorney Leslie Fitzgerald said it was unclear whether Wahl would be required to actually implement the change.
“Although the city charter gives the council the authority to adopt the budget and make cuts, the charter also gives the police chief the power and authority to operate and control the Police Department,” she said.
Other last-minute additions included $750,000 for a program that helps small businesses, $900,000 to help council offices fund community events and $200,000 to restore a position devoted to promoting San Diego as a setting for movies and TV.
The final budget includes $2 million to clear flood channels, responding to a request from Fire Chief Robert Logan.
The council also restored funding for the Office of Child and Youth Success, expanded a wellness program for city lifeguards and funded 24-hour security for a storage site on 20th Street for homeless people.
The council showed some spending restraint Tuesday when it chose to place $1.7 million in excess cash from the ongoing fiscal year into the city’s relative sparse reserve fund.
It’s the first time the city has contributed to the reserve fund since 2023. The fund will now rise from $207 million to $209 million — about $80 million below where the independent budget analyst says it should be.
The council’s vote marks the climax of one of the most controversial budget seasons in many years, with officials trying to close a $146 million gap just one year after making unpopular cuts to close a $250 million deficit.
Arts funding had been expected to be the most controversial issue during final budget negotiations, but proposed cuts of $11.8 million were mostly reversed Friday with a deal redirecting $6 million in convention center expansion funding to arts and a $3 million philanthropic donation.
Other controversial issues during budget season — such as proposals to wipe out the popular December Nights holiday festival and cut neighborhood crime prevention programs — got reversed by the mayor last month.
The final budget includes layoffs, but the chaos of so many last-minute decisions prevented city officials from providing an exact number Tuesday evening. Many employees will also be forced to take unpaid furloughs.
An employee whose position is eliminated in the final budget told the council Tuesday that such cuts come with consequences.
“I’m not here to save my job,” said Marc Frederick, a program manager focused on city real estate. “Based on my experience, the quality, quantity and efficiency of these transactions will go down.”
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