Welcome to the Fall 2024 edition of the Institute for the Biology of Stem Cells (IBSC) newsletter
Happy Holidays from the IBSC!
IBSC Hosted Annual Research Review Day on November 15th, 2024
Research Review Day is the IBSC’s annual event to allow for trainees and mentors to come together to learn about the research projects being funded by our training programs. This years event took place at Seymour Marine Discovery Center, where we heard talks from our CIRM postdocs and predocs, our T32 postdocs, and our IRACDA postdocs. We also had two fantastic keynote speakers, Dr. Sergiu Pasca from Stanford University and Dr. Alexander Payumo from San Jose State University.
Several IBSC Faculty receive funding from the UCSC Genomic’s Institute
IBSC Faculty (in bold) have recently received funding from the UCSC Genomic’s Institute for their collaborative research projects!
Professors Ali Shariati, Russell Corbett-Detig, and Manuel Ares aim to determine “How Introns Change the Function of the Human Genome”
Professors Shaheen Sikandar and David Boyd along with GI Xena Broswer researchers Jing Zhu and Mary Goldman are Using Single-Cell Transcriptomics to “Elucidate the Role of Post-Viral Lung Disease in Promoting Metastasis”
Professors Raquel Chamorro-Garcia and Upasna Sharma are “Developing Tools for the Study of the Epigenome and its Response to Environmental Cues”
Professors Jeremy Sanford and Michael Stone are investigating the “Druggable RNA Atlas”
Professors Yuying Zhou and Olena Vaske are performing “Molecular Classification of Osteosarcoma using Artificial Intelligence”
Read more about these exciting projects here
UC Santa Cruz scientists Secure R01 Funding from the National Eye Institute
The Feldheim Lab has recently been awarded an NIH R01 grant from the National Eye Institute (NEI) titled “Developmental mechanisms underlying visual and auditory topographic map alignment and accurate spatialorienting behavior” . The grant aims to understand how the brain develops the ability to locate an object in space using visual and auditory cues.
IBSC Faculty Upasna Sharma and current cIRM trainee Publish two new Papers on Small RNAs
Current CIRM Postdoctoral Trainee Alka Gupta has made exciting progress in her field with her recent manuscript “Epididymis-specific RNase A family genes regulate fertility and small RNA processing“. This work is currently available on bioRxiv but has been accepted to Journal of Biological Chemistry (JBC). The Sharma Lab also has another publication titled “A sperm-enriched 5’fragment of tRNA-Valine regulates preimplantation embryonic transcriptome and development” which is available on bioRxiv. Congrats to the Sharma Lab on their exciting findings!
As a CIRM Trainee, Alka works to decipher the mechanism of soma-germline communication via the small RNA, potentially carried by the extracellular vesicles of epididymis known as epididymosomes. Alka also works to understand the effect of external and environmental stressors on modulating the payload of small RNAs in sperm.
IBSC Welcomes new program manager and previous UCSC Alumni, Taylor Cool
The IBSC is excited to welcome back Dr. Taylor Cool as the new Program Manager for the IBSC! Taylor completed her PhD in the UCSC PBSE Program in June of 2022. She then spent two years as an NIH T32- funded Postdoc at Stanford University in the Pediatrics Department where she investigated the role of the microenvironment in targeted hematopoietic stem cell (HSC) depletion using anti-CD117 monoclonal antibodies. Read her most recent publication in Stem Cell Research and Therapy here.
Dr. Cool is excited to bring her love of Stem Cell Biology and knowledge of diverse training mechanisms back to UCSC in this new role. Have a question for her or the IBSC? Send an email to ibsc@ucsc.edu or taycool@ucsc.edu or stop by Biomed 444.
IBSC Welcomes new Flow Cytometry Manager, Patty Lovelace
The IBSC is thrilled to welcome Patty Lovelace as the new flow Cytometry Manager. Patty earned a BS in Biology/Clinical Lab Science at San Jose State University. Following that she completed the 1-year internship to become a licensed clinical lab scientist (CLS). She was a Clinical Lab Scientist for 9 years after that at El Camino Hospital in Mountain View before making the leap to a research/clinical mix flow cytometry lab in the Cellular Immunity lab located above the Stanford Blood Center. Patty has 25+ years of flow cytometry experience and has worked at many prestigious facilities, including UCSF, DNAX, Geron, Stanford, and BD.
When Patty is not thinking about flow cytometry, she spends a lot of time with her 2 favorite buddies, Kermit and Mochi. They are Formosan Mountain Dog Mixes rescued from the streets of Taiwan. She also enjoys river rafting and mountain biking. Need help with a fly cytometry experiment? Stop by Biomed 450 to chat with Patty!
IBSC Welcomes new T32, CIRM, and IRACDA Fellows
The IBSC is delighted to announce the addition of new Predoctoral & Postdoctoral fellows to our Training Programs!
Greta has joined the T32 Postdoctoral Training Program and is performing her research in the Feldheim Lab. Her project aims to determine how different auditory brainstem regions contribute to sound localization in the mouse superior colliculus.
Bryce finished his tenure as an IRACDA postdoctoral scholar and is now joining our crew of T32 Postdoctoral Scholars, performing his research in the Forsberg Lab. He is investigating the ways in which aging and inflammation influence blood cell production in mice and humans.
Carly has joined the CIRM Postdoctoral Training Program and is performing her research in the Shariati Lab. Her research focuses on studying cell fate decisions during human embryogenesis using stem cell-based embryo models and epigenome editing tools.
Mojtaba has joined the CIRM Postdoctoral Training Program and is performing his research in the Teodorescu Lab. Mojtaba’s research focuses on developing a scalable, fully automated microfluidic system for tissue culture inside incubators, designed to improve the fidelity and reliability of organoid models for studying brain development and disease.
Carlismari has joined the CIRM Postdoctoral Training Program and is performing her research in the Sanchez Lab. Her project investigates how lipid-mediated interactions, driven by β-adrenergic signaling and metabolic exchanges between iPSC-derived fallopian tube organoids and omental tissues, contribute to the metastasis of high-grade serous ovarian cancer using advanced 3D co-culture models and mass spectrometry-based lipidomics.
Saran, a previous IBSC T32 trainee, is now joining our crew of CIRM Postdoctoral Scholars, performing his research in the Forsberg Lab. He is investigating the causes and consequences of age-specific megakaryocyte progenitors.
Ethan has joined the IRACDA Postdoctoral Training Program and is performing research in the Sanchez Lab. His work aims to develop an in vitro microbe-mammalian co-culture system to study host-microbe interactions, leveraging mass spectrometry imaging and multimodal imaging to visualize microbial metabolite distribution and co-localization with host targets.
Raana has joined the CIRM Predoctoral Training Program and is performing her research in the Forsberg Lab. Her project aims to understand the mechanisms that regulate platelet production and hyper-reactivity upon aging, with the goal of better controlling platelet-related disorders.
Eva has joined the CIRM Predoctoral Training Program and is performing her research in the Stone Lab. Her project aims to understand how human telomerase RNA folds, trafficks, and interacts with proteins to understand how variants of this RNA precipitate disease in patients with telomere biology disorders
Nicholas has joined the CIRM Predoctoral Training Program and is performing his research in the Wang Lab. His project aims to understand the cell-type-specific functions of miR-205 in prostate epithelial homeostasis and cancer initiation.
We look forward to welcoming the new trainees within the IBSC and hope you take a chance to say hello as you cross paths in the lab and in the halls!
What to do with that one figure that’s been sitting on your hard drive for too long? MicroPub it!
We’ve all had that one figure that has been sitting in our data pile for far too long! That one that we continually reference in lab meeting but has never made its way into our publications. Thankfully, microPublication Biology has created a journal for this very reason! Their mission is to publish brief articles on research findings and in this way rapidly disseminate experimentally sound results to the community. These can be novel findings, negative results, replication successful (including being scooped), replication unsuccessful – perceived impact is not relevant. The key is that it must be presented in a single figure. Each article is peer-reviewed, assigned a DOI, and your data is curated and deposited in third-party authoritative scientific databases upon publication. Over 1,000 microPublication Biology articles are now discoverable through PMC, PubMed, EuropePMC, Google Scholar, and university library catalogs. The Hinck lab recently published one on SLIT proteins regulating lactation that you can see here.
Research Updates: Publication/Manuscript Roll Call
The IBSC is home to a wide array of research areas that are not limited to stem cell biology. The following preprints and papers have recently been published by our affiliated labs. IBSC Labs/trainees are indicated in bold.
- Mostajo-Radji Lab
- Sano T, Sampad MJN, Gonzalez-Ferrer J, Hernandez S, Vera-Choqqueccota S, Vargas PA, Urcuyo R, Montellano Duran N, Teodorescu M, Haussler D, Schmidt H, Mostajo-Radji MA. Internet-enabled lab-on-a-chip technology for education. Sci Rep. 2024 Jun 22;14(1):14364. doi: 10.1038/s41598-024-65346-0. PMID: 38906940; PMCID: PMC11192768.
- Carpenter Lab
- Faherty L, Zhang WZ, Salih MM, Robinson EK, Perez E, Kim K, Carpenter S, Cloonan SM. Transcriptomic analysis reveals distinct effects of cigarette smoke on murine airspace and bone-marrow derived macrophages. Respir Res. 2024 Aug 24;25(1):322. doi: 10.1186/s12931-024-02939-3. PMID: 39182076; PMCID: PMC11344945.
- Hinck Lab
- Cazares O, Chen M, Menendez J, Molinuevo R, Thomas G, Cervantes J, Yee M, Cadell M, Durham M, Zhu Y, Strietzel C, Bubolz JW, Hinck L. SLIT Loss or Sequestration Increases Mammary Alveologenesis and Lactogenesis. MicroPubl Biol. 2024 Sep 6;2024:10.17912/micropub.biology.001264. doi: 10.17912/micropub.biology.001264. PMID: 39381643; PMCID: PMC11461027.
- Forsberg Lab
- Manso B, Medina P, Smith-Berdan S, Rodrigues y Baena A, Bachinsky E, Mok L, Deguzman A, Avila SB, Chattopadhyaya S, Rommel M, Jonsson VD, Forsberg EC. A rare HSC-derived megakaryocyte progenitor accumulates via enhanced survival and contributes to exacerbated thrombopoiesis upon aging. bioRxiv [Preprint]. 2024 November 5. bioRxiv 2024.11.04.621964; doi: https://doi.org/10.1101/2024.11.04.621964.
- Sikandar Lab
- Olander A, Ramirez CM, Acosta VH, Medina P, Kaushik S, Jonsson VD, Sikandar SS. Pregnancy Reduces Il33+ Hybrid Progenitor Accumulation in the Aged Mammary Gland. bioRxiv [Preprint]. 2024 Aug 6:2024.08.01.606240. doi: 10.1101/2024.08.01.606240. PMID: 39149387; PMCID: PMC11326159.
- Liang CE, Hrabeta-Robinson E, Behera A, Arevalo C, Fetter IJ, Soulette CM, Thornton AM, Sikandar SS, Brooks AN. U2AF1 S34F enhances tumorigenic potential of lung cells by exhibiting synergy with KRAS mutation and altering response to environmental stress. bioRxiv [Preprint]. 2024 Sep 15:2024.09.11.612492. doi: 10.1101/2024.09.11.612492. PMID: 39314447; PMCID: PMC11419039.
- Rubin Lab
- Knudsen ES, Witkiewicz AK, Rubin SM. Cancer takes many paths through G1/S. Trends Cell Biol. 2024 Aug;34(8):636-645. doi: 10.1016/j.tcb.2023.10.007. Epub 2023 Nov 10. PMID: 37953123; PMCID: PMC11082069.
- Partch Lab
- Harold RL, Tulsian NK, Narasimamurthy R, Yaitanes N, Hernandez MGA, Lee HW, Crosby P, Tripathi SM, Virshup DM, Partch CL. Isoform-specific C-terminal phosphorylation drives autoinhibition of Casein Kinase 1. bioRxiv [Preprint]. 2024 Jul 29:2023.04.24.538174. doi: 10.1101/2023.04.24.538174. Update in: Proc Natl Acad Sci U S A. 2024 Oct 8;121(41):e2415567121. doi: 10.1073/pnas.2415567121. PMID: 39131317; PMCID: PMC11312495.
- Gomez Lab
- Lu F, Zlobina K, Rondoni NA, Teymoori S, Gomez M. Enhancing wound healing through deep reinforcement learning for optimal therapeutics. R Soc Open Sci. 2024 Jul 31;11(7):240228. doi: 10.1098/rsos.240228. PMID: 39086835; PMCID: PMC11289634.