San Diego, CA

Illumina and the San Diego Zoo are sequencing koala genomes to investigate disease

Published

2 years ago

January 17, 2024

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Illumina and the San Diego Zoo are sequencing koala genomes to investigate disease

Credit: Pixabay/CC0 Public Domain

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

Padres roster review: Miguel Andujar

Published

9 hours ago

March 11, 2026

Press Room

Padres roster review: Miguel Andujar – San Diego Union-Tribune

MIGUEL ANDUJAR

Position(s): Third base, left field, first base
Bats / Throws: Right / Right
2026 opening day age: 31
Height / Weight: 6-foot / 211 pounds
How acquired: Signed as a free agent in February 2026
Contract status: Will make $1.5 million in 2026, with the opportunity to earn another $2 million-plus in performance bonuses; his $4 million guarantee includes a $2.5 million buyout against an $8 million mutual option for 2027.
fWAR in 2025: 1.1
Key 2025 stats: .318 AVG, .352 OBP, .470 SLG, 10 HRs, 44 RBIs, 36 runs, 17 walks, 49 strikeouts, 1 steal (94 games, 341 plate appearances)

STAT TO NOTE

.986 — Andujar’s OPS against left-handed pitching in 2025, the second-highest mark of his career and well above his career .807 OPS against southpaws. Andujar had been below .600 in 2021 and 2022 before jumping to .871 in 2023 and a career-high .995 in 2024.

Up — Signed for $700,000 out of the Dominican Republic as a 16-year-old in the international amateur market, Andujar needed two years to get out of the Yankees’ rookie-ball affiliate in the Gulf Coast League and finally cracked top-100 lists ahead of the 2018 season — No. 59 at Baseball America and No. 65 at MLB.com — after reaching Triple-A following a 16-homer season (.850 OPS). Andujar even made his MLB debut as a 22-year-old in 2017 and looked like he’d be a big part of the Yankees’ future after pairing 27 homers and 92 RBIs with an .855 OPS in finishing second to Shohei Ohtani in AL Rookie of the Year voting in 2018. But a right shoulder labrum tear derailed Andujar in 2019 and Andujar was never able to grab a starting job again in New York. The Pirates claimed him late in 2022 and then the Athletics claimed him after the 2023 season. By then, he’d developed into a platoon player with defensive limitations. Andujar had a .697 OPS in 75 games in his first year with the Athletics and a .765 OPS in 60 games last year when, after missing time with a right oblique strain, he was shipped to the Reds for a minor league pitcher. Andujar went on to hit .359/.400/.544 with four homers and 17 RBIs in 34 games to help the Reds lock up a wild-card spot. He was 0-for-4 with a walk and a strikeout in the NL Wild Card Series sweep at the hands of the Dodgers.

Miguel Andujar #41 of the San Diego Padres participates in drills during spring training workouts at the Peoria Sports Complex on Thursday, Feb. 12, 2026 in Peoria, Ariz.(Meg McLaughlin / The San Diego Union-Tribune)

2026 OUTLOOK

The need for right-handed balance in the lineup was painfully obvious in the Padres’ NL Wild Card Series loss to the Cubs, so Andujar became a target after 1B/OF Ryan O’Hearn walked as a free agent. Expect Andujar to get at-bats against lefties as either a DH, first base, third base or left field — the spots he’s been playing in spring training.

ROSTER RANKINGS

1. OF Fernando Tatis Jr.
2. 3B Manny Machado
3. OF Jackson Merrill
4. RHP Nick Pivetta
5. RHP Michael King
6. RHP Mason Miller
7. OF Ramón Laureano
8. SS Xander Bogaerts
9. LHP Adrián Morejón
10. RHP Jeremiah Estrada
11. RHP Jason Adam
12. 2B Jake Cronenworth
13. RHP Joe Musgrove
14. RHP Randy Vásquez
15. INF Miguel Andujar
16. OF Gavin Sheets
17. LHP JP Sears
18. RHP Yu Darvish
19. RHP Bradgley Rodriguez
20. RHP David Morgan
21. C Freddy Fermin
22. LHP Wandy Peralta
23. C Luis Campusano
24. LHP Yuki Matsui
25. INF Sung-Mun Song
26. RHP German Marquez
27. RHP Matt Waldron
28. OF Bryce Johnson
29. OF/1B Nick Castellanos
30. RHP Ron Marinaccio
31. RHP Bryan Hoeing
32. LHP Kyle Hart
33. INF Will Wagner
34. RHP Garrett Hawkins
35. RHP Miguel Mendez
36. RHP Daison Acosta
37. RHP Ty Adcock
38. RHP Alek Jacob
39. INF Mason McCoy

Removed from 40-man roster

OF Tirso Ornelas (designated for assignment)
RHP Jhony Brito (60-day injured list)

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San Diego, CA

San Diego Bishop Is Out of a Job

Published

21 hours ago

March 10, 2026

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Pope Leo XIV has accepted the resignation of the Chaldean Catholic bishop of San Diego, California, a decision announced Tuesday by the Vatican after the bishop was arrested on embezzlement charges. The San Diego County Sheriff’s Office said last week it had arrested Bishop Emmanuel Shaleta on Thursday at San Diego International Airport as he tried to leave the country, reports the AP. The office said it acted after someone from Shaleta’s church provided a statement and documentation “showing potential embezzlement from the church.” Shaleta was being held on $125,000 bail on eight counts of embezzlement, money laundering, and aggravated white collar crime, the statement said. Shaleta pleaded not guilty on Monday, reports NBC San Diego.

“He was on his way to Germany,” prosecutor Joel Madero said. “Given his access to funds, the fact that he had over $9,000 in the bag when he was stopped, and the fact that he has these international ties … I do believe that some bail to ensure he shows up is appropriate.” There was no immediate reply to an email sent to Shaleta’s parish, St. Peter Chaldean Church, seeking comment and contact information for his attorney. The Vatican said in its daily bulletin Tuesday that Leo had accepted Shaleta’s resignation under the code of canon law for eastern rite churches that allows for the pope to agree if a bishop asks to step down.

Leo actually accepted the resignation when Shaleta presented it in February, but an announcement was not made until Tuesday, according to the Vatican embassy in Washington. The Holy See appears to have waited to announce the decision to avoid interfering with the police investigation. Leo named Bishop Saad Hanna Sirop as a temporary administrator. Shaleta, 69, was ordained a priest of the Chaldean Catholic Church in Detroit in 1984. He was named to the San Diego branch of the eastern rite Catholic Church in the US in 2017.

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San Diego, CA

Padres roster review: Germán Márquez

Published

1 day ago

March 10, 2026

Press Room

Padres roster review: Germán Márquez – San Diego Union-Tribune

GERMÁN MÁRQUEZ

Position(s): Right-handed pitcher
Bats / Throws: Right / Right
2026 opening day age: 31
Height / Weight: 6-foot-1 / 230 pounds
How acquired: Signed as a free agent in February 2026
Contract status: Will make $1 million in 2026 with a $750,000 buyout on a mutual option for 2027; can add up to $3.25 million in performance bonuses.
fWAR in 2025: 0.3
Key 2025 stats: 3-16, 6.70 ERA, 83 strikeouts, 48 walks, 1.71 WHIP, .317 opponent average, 126⅓ innings (26 starts)

STAT TO NOTE

36.9 — The percentage of groundballs that Márquez yielded in 2025, a career low and significantly below his career average (48%). Márquez’s groundball rate was regularly above 50% before requiring Tommy John surgery in early 2023. He made one start in 2024 and struggled mightily while making 26 starts last year.

Down — Márquez had a 4.40 ERA through his first seven years in the majors, not bad considering he pitched roughly half his games at one of the best hitting environments in the majors. In fact, Márquez has a 5.17 ERA in his career at Coors Field and a 4.22 ERA in road environments. But Márquez underwent Tommy John surgery early in 2023, made one start in the majors in mid-July in 2024 (4 IP, 3 ER) and struggled throughout his first full year back in the Rockies rotation. The season was so difficult for Márquez that he was actually worse on the road (7.32 ERA) than he was in 11 starts at Coors Field (5.98 ERA). His strikeout rate (5.9 per nine innings) and strikeout-to-walk ratio (1.73) were the worst of his careers, as was his walk rate (3.4 per nine innings), while his hit rate (12.0 per nine innings) was the second worst of his career. On top of that, Márquez’s groundball rate was also the lowest of his career (see stat to note) and ranked in the bottom 22nd percentile of the league and his hard-hit rate (48.5%) and average exit velocity (91.7 mph) both ranked in the bottom 2 percentile of the league. One reason: a 94.8 mph four-seamer is down a few ticks than the height of his effectiveness. Márquez reached free agency after the season and signed with the Padres in February.

2026 OUTLOOK

Márquez has a big-league deal with the Padres, but he’ll have to rediscover his pre-elbow-reconstruction form to hold onto a roster spot, as RHP Griffin Canning (Achilles) is expected to push for a spot at some point this season and the likes of LHP JP Sears, RHP Matt Waldron and minor league signees like Marco Gonzales could warrant looks if Márquez’s struggles continue into 2026.

German Marquez #33 of the San Diego Padres participates in drills during spring training workouts at the Peoria Sports Complex on Monday, Feb. 16, 2026 in Peoria, Ariz.(Meg McLaughlin / The San Diego Union-Tribune)