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Congratulations to Christian Gallardo for a Successful PhD Dissertation Defense!

(July 10, 2020)

The Torbett Lab would like to congratulate Christian Gallardo for successfully defending his doctoral dissertation on July 10, 2020, entitled: “Novel Sequencing Strategies for Interrogating HIV Activation Dynamics in Infected Host Cells and Tracing Viral Evolution at the Single Molecule Level”.

His work sought to address the potential role of alternative splicing during HIV latency and reactivation from latency. To undertake these studies, he developed a quantitative full-length RNA-seq methodology allowing simultaneous profiling of poly-adenylated HIV and host cell transcripts from the J-Lat cell line model of viral latency. These studies resulted in the identification of what appears to be a novel pathway that may modulate Gag assembly. Christian’s work also sought to address the role of novel mechanisms of drug resistance to antiretrovirals in circulating HIV virions. For this, he developed a nanopore-based long-range sequencing methodology to obtain accurate HIV cDNA sequences covering the entire Gag-Pol region from clinical isolates, with the goal of tacing of novel evolutionary pathways that result in drug failure.

Dr. Bruce Torbett supervised his research. The disseration committee included Juan C. de la Torre, Ph.D., Brian M. Paegel, Ph.D. and Ali Torkamani, Ph.D., while Jesse Bloom, Ph.D. of the Fred Hutchinson Cancer Research Center, served as an external examiner.

Christian began his studies at the Torbett Laboratory as a Graduate Student in 2015 through the Scripps Research Institute’s Skaggs Graduate School of Chemical and Biological Sciences. He plans to continue his work on viral genomics, with an emphasis on decoding how viral RNAs modulate fitness at different stages of the viral lifecycle.

Resveratrol Trimer Caraphenol A Study Enhancing Gene Delivery in Blood (October 17, 2019)

Press Release from Scripps Research: When added to gene therapy, plant-based compound may enable faster, more effective treatments

Access the paper here: Resveratrol trimer enhances gene delivery to hematopoietic stem cells by reducing antiviral restriction at endosomes 

Torbett Lab Welcomes Three New Members (August 1, 2019)

As the Torbett Lab expands, three new members have been recruited. Each of therm brings knowledge, experience and skills that add a unique perspective to advance the lab’s research projects.

Christina Garza

Christina Garza is a MD/PhD graduate student of University of California San Diego. She is currently working on her doctoral degree through the Scripps Research Institute’s Skaggs Graduate Program. Her co-mentored project will combine faculty expertise in HIV structure and function (Torbett) and molecular modeling (Forli) and will allow her to perform studies of the HIV capsid. Christina’s project will focus on evaluating the contribution of Gag/Pol proteins and viral RNA forming and contributing to the functional capsid structure. This will allow the identification of sites for potential drug targets and orientation of protein-protein and protein-RNA interfaces. Docking simulations will serve to identify binding sites, as well as potential drug candidates that fit into the sites. Existing screening methods can then assess whether these high-scoring drugs bind to their target proteins.

Before joining Torbett and Forli lab, Christina studied proton transporters with multiscale QM/MM (quantum mechanical/molecular mechanical) molecular dynamics simulations with Dr. Hai Lin at the University of Colorado Denver. Christina earned her Bachelor of Science in Public Health with a minor in Chemistry. She likes to spend her free time climbing, playing board games and participating in competitive jigsaw puzzling.

Anh-Viet Nguyen

Anh-Viet Nguyen is the new research assistant in the Torbett lab. Viet brings to the lab his experience in providing direction and training for team of interns, assistant and technicians on various research-related tasks. He started his scientific research career in 2017 as a lab technician in Shresta lab at La Jolla Institute for Immunology where he assisted in the collaboration on various projects regarding flaviviruses (Dengue and Zika) including vaccine development, mouse pregnancy studies and drug efficacy tests. He has relevant skills on experimental assays, mouse procedures, maintaining mammalian and insect lines for use in various experiments, viral production and concentration in both mammalian and insect cell cultures, and drafting and submitting administrative, biohazard and human protocols for research projects and biohazard materials.

Viet earned a B.S. in Microbiology from the University of California San Diego. In addition to his research endeavors, he also volunteers with the International Health Collective, a non-profit organization which hosts free clinics within the San Diego-Tijiuana area. In his spare time, he enjoys surfing and rock climbing, and is a competitive ballroom and Latin dancer.

Richie Othanh

Richie Othanh, a recent graduate from The Preuss School UCSD joined for an internship position. Before joining Scripps Research, he also worked as an intern at the Molecular Biology lab with Dr. Jose Pruneda-Paz at UCSD Muir Biology. His interest in developing a lab experience motivated him to pursue a chemistry major at UCSD and a medical profession in the future. He is an upcoming UCSD freshman in the Ravelle campus with a pharmacological chemistry major. In his free time, Richie likes to lift weights at the gym, play the guitar and ukelele, and cook for friends and family. Alongside this, he likes to volunteer with the Ocean Discovery Institute whenever he can to help preserve the environment.

Torbett Lab Hosts Graduate Student and Summer Interns (June 6, 2019)

The Torbett Laboratory is pleased to welcome graduate student and interns for summer 2019. The rotation allowed stduents to become immersed in the lab environment, gain exposure to techniques, research programs and culture of the lab. Meanwhile, the internship program is designed to provide closely supervised training with the purpose of providing an environment where interns can develop professional skills and gain research-related experience.

Shiyi Wang

Shiyi Wang, Graduate Student of Scripps Research Graduate Program, has joined the Torbett laboratory for a lab rotation. The major part of the rotation includes the practice of techniques in handling RNA, specifically for the purpose of sequencing HIV RNA present in virions. The end result would be to follow anti-retroviral mutations in HIV, overtime, from HIV-infected patient sera isolates. Moreover, Shiyi will utilize her knowledge on basic bioinformatics in order to analyze and understand the sequencing results.

Shiyi earned her B.A. in Biotechnology in Zhejiang University in China in 2018. Before that, she studied the correlation between chitin synthase (CHS) genes and fungal adaption abilities to the environment back in 2015 (Liu R, et al. Sci Rep. 2017). Also, she joined Dr. Xu’s lab in University of Michigan as a visiting scholar, studying lysomal Two-Pore Channel 2 (TPC2)’s effects on lysosome membrane potential change, lysosome membrane trafficking, cellular cholesterol trafficking and amino acid efflux across lysosomal membrane.

Prior to joining the Torbett lab, she has finished three rotations covering studying the antibodies targeting on LASV membrane glycoprotein from the structural biological perspective, studying the molecular mechanism of cellular circadian rhythm, and using high throughput screening to discover small molecular regulars targeting on specific cellular pathways. She enjoys spending her free time on reading and writing novels.

Fatima Mohammed

Fatima Mohammed is part of the Scripps Research’s Summer Undergraduate Research Fellows (SURF) internship program. The ten-week SURF program aims to provide students an opportunity to experience cutting edge research in one of 220 laboratories at Scripps while being monitored by world-renowned faculty. Fatima decided to join the Torbett lab because of her interest in the HIV-related projects. The aim of her project is to assist in distinguishing host factors that interact with HIV proteins, such as the Gag precursor protein. The approach utilizes biotin tagging in order to identify virus-host interactions.

Fatima is a senior undergraduate student working towards a B.A. in Spanish and B.S. in Biology at Wofford College, Spartanburg, South Carolina. After completing her degree, she plans to continue her education in the field of medicine. In her free time, Fatima enjoys traveling with friends and family as well as volunteering with organizations that aim to aid underprivileged school districts.

Joshua Pelletier

Joshua Pelleter is a high school student from the Bishop’s School, La Jolla, California. He began interning at the Torbett laboratory in June. He is interested in science and engineering and has experience with basic molecular techniques. He is also active in ecology-based service projects. After completing high school in 2020, Joshua intends to pursue and education in science. Joshua is an avid sailor, enjoys fishing, studying fish ecology and behavior and kayaking in his spare time.

John Majernik

John Majernik is currently a high-school student attending Bishop’s School, La Jolla, California taking part in an internship in the Torbett laboratory. He has relevant skills on biological lab techniques and also held various positions for the San Diego Yacht Club Junior Board, where he actively planned and organized outreach activities and community service projects. He is looking forward to his college experience after completing high school next year. John likes to spend his free time doing various outdoor activities such as sailing and playing water polo.

John and Joshua are closely supervised by Dr. Tony Pelletier, Professional Scientific Collaborator and former faculty at The Scripps Research Institute. Their current work focuses on improving lentiviral-based expression vectors.

Alexandra Joyce Stream

Alexandra Stream, a MD/PhD Graduate Student of University of California through the Medical Scientist Training Program, has joined the Torbett laboratory for an internship. As part of her internship, Alexandra will focus on gene delivery of an anti-HIV entry inhibitor, eCD4-Ig to hematopoietic stem and pregenitor cells.

Alexandra earned her B.S. in Microbiology, Immunology and Molecular Genetics at the University of California, Los Angeles. Prior to joining UCSD, she worked as an undergraduate research at UCLA, specifically the laboratories of Drs. Kent Hill (Department of Microbiology, Immunology and Molecular Genetics) and Cho-Lea Tso (Department of Surgery) and the laboratory of Dr. Robert Yarchoan at the National Cancer Institute, National Institutes of Health through the Postbaccalaureate Cancer Resarch Training Award Program.

She enjoys spending her free time doing yoga, hiking and watching musical theater.

Saumya Jani

Saumya Jani has joined the Torbett lab as an intern. She is currently a MD/PhD Graduate Student through the Medical Scientist Training Program at University of California San Diego. Saumya’s internship will focus on the impact of opioids on T cells.

Before joining UCSD, Saumya served at various laboratories, inluding under the mentorship of Dr. Marcelo Tolmasky at CSUF, Dr. Robert Bonomo at the Louis Stokes Cleveland Veterans Affiars Medical Center as a Sally Casanova Pre-Doctoral Scholar , and Dr. Carolyn Carr of the Cardiac Metabolism Research Group at the University of Oxford as a Minority Health and Health Disparitites International Research Program trainee.

Saumya likes to spend her free time traveling, swimming, trying new foods and listening to true-crime podcasts.

Torbett Lab Celebrates Stosh Ozog’s Dissertation Completion (April 16, 2019)

Stosh Ozog successfully defended his doctoral thesis titled “Innate Immune Modulation and Lentiviral Vector Modification to Improve Anti-HIV Gene Therapy” at the Committee Lecture Hall on April 16, 2019. His work sought to investigate factors that prevent efficient gene modification of hematopoietic stem cells, and develop methods to overcome those barriers to improve clinical gene therapy of blood diseases.

His research was supervised by Dr. Bruce Torbett. The dissertation committee included Juan C. de La Torre, Ph.D., Erica Ollmann Saphire, Ph.D., and Michael Farzan, Ph.D., while David J. Rawlings, M.D. of Seattle Children’s Research Institute served as an external examiner. 

Stosh began his studies at the Torbett Laboratory as a Graduate Student in 2015 through the Scripps Research Institute’s Skaggs Graduate Program. He will return to the UC San Diego School of Medicine to complete his medical training through the Medical Scientist Training Program.

Swiss Postdoctoral Scholar Nicolas Niklaus Joins Torbett Lab (April 1, 2019)

Nicolas Niklaus, a Ph.D. student in Experimental Pathology at the University of Bern, Switzerland has begun a 3-month stint in the Scripps Research-Torbett Laboratory as an external graduate student through the support of the Swiss National Science Foundation. Nicolas’ thesis study in Prof. Mario Tschan’s lab concentrates on the versatile roles of the alternative spliced DMTF1 isoforms in breast cancer and acute myeloid leukemia.

As part of his fellowship study in Scripps Research, Nicolas will focus on understanding howPu.1 (Spi-B) regulates Caspase 8 and c-Flip transcriptional regulation and c-Flip transcript splicing during myeloid development and in monocytes/macrophages in collaboration with Prof. Tschan. He aims to employ the panel of PU.1 domains to determine which domain may regulate Caspase 8 and c-Flip transcriptional regulation. He will also take advantage of the primary CD34 cells for additional studies via knockdown and gain og function studies to study Pu.1-mediated regulation of Caspase 8 and c-Flip as well as c-Flip splicing.

HIVE Center Holds 2019 Trainee Retreat Program and Winter Face-to-Face Meeting (Jan. 9, 2019)

The HIV Interactions in Viral Evolution (HIVE) Center, Directors Bruce Torbett, Ph.D. (Scripps Research California) and Stefan Sarafianos, Ph.D. (Emory University) as well as Coordinator Arthur Olson, Ph.D. (Scripps Research California), hosted the 2019 Trainee Retreat Program and Winter Face-to-Face Meeting in La Jolla, California on January 9-11, 2019.

The HIVE Trainee Retreat Program is held 2 times per year to introduce postdocs and graduate students from HIVE laboratories to technologies and methodologies utilized by the HIVE Center. The meeting was part of the training and professional development initiatives of the HIVE Center. A total of 20 postodcs and graduate students from HIVE laboratories participated in the training workshop. Drs. Dmitry Lyumkis, Darios Passos and Jessica Bruhn of the Salk Institute discussed the overview and applications of Cryo-EM and provided a Chimera tutorial. Drs. Patrick Griffin, Douglas Kojetin and Jie Zheng of the Scripps Research Florida presented the overview and applications of Hydrogen Deuterium Exchange (HDX) mass spectrometry, the use of protein cross-linking mass spectrometry, as well as know to analyze HDX data. Overall, the training workshop was considered a success by the trainees.

The 2-day HIVE Center Winter Face-to-Face total was attended by 63 HIVE Center members comprised of PIs, Collaborative Development Program (CDP) awardees, postdoctoral fellows and graduate students. The purpose of the meeting was to discuss collaborative progress on understanding the structural and dynamic relationships between interacting macromolecules in the HIV life cycle. Presentatioins by HIVE Center members updated all as to the Center’s progress during the past year. The meeting also featured poster sessions which allowed the postdocs and graduate students to share the results of their respective scientific researches. The breakout sessions also provided the opportunity to foster discussion among collaborating groups and explore new collaborative activities.

The HIVE Center holds bi-annual face-to-face conferences. The HIVE Summer Face-to-Face Meeting and Trainee Retreat will be held on June 26, 2019 in conjunction with the Structural Biology Related to HIV/AIDS Meeting sponsored by National Institute of General Medicine Sciences (NIGMS) and National Institute of Allergy and Infectious Diseases (NIAID) on June 27-28, 2019 in Bethesda, Maryland.

Torbett Laboratory Welcomes Kristina Seiler, MD as External Graduate Student (Jan. 4, 2019)

Kristina Seiler, a medical doctor, has joined the Torbett Laboratory in Scripps Research as an external graduate student. Kristina is currently a postdoctoral scholar at the Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland. Kristina’s thesis studies in Prof. Mario Tschan’s lab involves studying glycolytic metabolism and autophagy in AML – considerations for AML biology and therapy.

Kristina’s Fellowship studies in Scripps Research will focus on determining the roles that hexokinases, a group of glycolytic enzymes, play in human neutrophils and during myeloid development in general. She will continue following up on the studies previously done at Scripps Research in collaboration with Prof. M. Tschan. Kristina will also participate in additional studies using mass spectrometry to determine the metabolic and proteomic changes as a result of disrupting the different hexokinase isoforms.

Prior to joining her current role, she started her scientific research career in 2014 where she was involved in a study investigating the implementation of a risk assessment tool for osteoporosis patients at University of Bern, Switzerland. She also worked on the recovery of cell populations from archived formalin-fixed paraffin-embedded colorectal cancer tissue for downstream analysis of pure cell populations in 2015 at Institute of Pathology, University of Bern, Switzerland. Kristina was previously employed at The Scripps Research Institute, La Jolla, California in 2016 and studied the knockout of hexokinase 2 and 3 and evaluation of the effect of altered hexokinase expression on proliferation and differentiation of CD34+ cells.

Kristina was born and raised in Switzerland and earned her bachelor’s and master’s degrees in medicine from the University of Bern, Switzerland. She passed the United States Medical Licensing Examination and obtained her medical license in 2017.

Kristina likes to spend her free time doing various outdoor activities such as camping or hiking and is looking forward to exploring the California coast with her bike. She is also a qualified skipper and avid sailor and plays competitive tennis for the women’s team in her hometown.

Dr. Johanna Heideker Joins Torbett Laboratory (November 9, 2018)

Dr. Christine Johanna Heideker, a molecular biologist, has joined the Torbett Laboratory as a Staff Scientist.

Johanna brings to Torbett Laboratory more than 12 years of experience in protein expression and purification and cellular signaling. She will be responsible in generating protein expression vectors for both bacterial and eukaryotic systems, to generate and purify proteins, and undertake and run mass spectometry experiments for core and research studies of the University of California San Diego Center for AIDS Research (USCD CFAR).

Johanna hopes to become involved in a broad range of activities and initiatives at Torbett Laboratory and UCSD CFAR.

Johanna began her scientific research career in 2011 as a Postdoctoral Associate at Genentech, Inc. in South San Francisco. From there she moved back to San Diego where she joined forces as a Research Scientist at a small cancer vaccine startup company (ImmunoActiva) in 2016. Before joining Scripps Research, Johanna served as Scientist II for ThermoFisher Lifesciences. At ThermoFisher, she performed large scale protein purification for global sales.

Johanna earned a Diploma in Structural Biology from the University of Wurzburg in Germany and a Ph.D. in Biology from The Scripps Research Institute in La Jolla, California.

Johanna, a native of Germany, enjoys spending her free time on staying on top of the scientific literature, mentoring younger scientists, and attending local art events.

Torbett Laboratory Welcomes UCSD Student Interns (October 22, 2018)

The Torbett Laboratory is pleased to welcome two student interns from the University of California San Diego (UCSD). The student interns will undergo closely supervised training to help develop their professional skills and gain hands-on experience which advances scientific careers.

Isabel Mendoza

Isabel Mendoza is a junior at UCSD working towards a B.S. in Physiology and Neuroscience. Before joining Scripps Research, Isabel served at the California National Primate Research Center as summer research intern and helped in performing experiments for projects studying the Zika virus. She was also previously employed at The Scripps Research Institute from November 2017 to June 2018 as an undergraduate research intern through the UCSD Work Study Program.

At UCSD, Isabel holds the positions of Vice President of Scholarship for the Junior Panhellenic Council and Assistant Director of Membership Education within her sorority, Phi Sigma Rho. She is also active in planning and organizing social events and community service projects.

After completing her degree, she plans to attend veterinary school and earn her Doctorate of Veterinary Medicine. In her spare time, she likes to practice Brazilian jiu jitsu and work on her photography skills.

Hannah Finnegan

Hannah Finnegan is a third year student currently pursuing a B.S. in Human Biology at UCSD. Prior to joining Scripps Research, Hannah served as a student intern at the Motwani Lasik Institute and as a volunteer at Valley Children’s Hospital.

Hannah is also a licensed EMT. She intends to pursue a Physician’s Assistant school after completing her bachelor’s degree. In her free time, Hannah enjoys hiking and spending time at the beach.

Torbett Lab, UCSD, TSRI Florida, and VMRF Working with a New Research Grant from NIH (October 1, 2018)

Dr. Bruce Torbett, Associate Professor of The Scripps Research Institute (TSRI), has received a subaward from the National Institutes of Health (NIH) through the University of California San Diego (UCSD).

The three-year grant will help fund the project entitled, “Opioid Impacts on T-cell Pathways and Epigenetics to Modulate HIV Integration, Latency and Reservoirs.” The project is designed in a two-stage process (R61/R63) to tease out the mechanisms of how opioids impact cellular receptor signaling for opioids, cellular co-receptors for HIV, epigenetic control (chromatin packing and methylation), and gene expression. It will also determine how these processes impact HIV replication, integration and latency.

Dr. David Smith of the UCSD School of Medicine is the Principal Investigator of the project. Other Co-Investigators on the grant include Dr. Laura Bohn of TSRI Florida and Dr. Celsa Spina of Veterans Medical Research Foundation (VMRF). Dr. Nadejda Beliakova-Bethell of VMRF, Dr. David Gorkin of UCSD School of Medicine, and Dr. Amalio Telenti of TSRI California are also named as key personnel.

The Torbett Laboratory’s expertise will be provided in evaluating morphine like-agonists and their effect on CD4T cells and macrophages HIV infection, latency and viral persistence in collaboration with Drs. Bohn and Spina. The Torbett group’s experience in HIV sequencing and informatics to evaluate HIV populations from the “final gift” patient cohort will also be utilized. Furthermore, Dr. Torbett will utilize novel RTs to generate full-length cDNAs from patient HIV samples to address whether there is genetic evolution of individual viruses within the viral population of HIV-infected patients before and during opioid use.

The Torbett Laboratory Welcomes New Postdoctoral Associate (September 4, 2018)

The Torbett Laboratory welcomes Shentian Zhuang, a Beijing native and a recent Ph.D. graduate from Peking University in China. Shentian’s thesis studies in Prof. Chu Wang’s lab focused on developing chemoproteomic strategies that use photo-affinity probes in combination with quantitative proteomics for large-scale profiling of Bile acids (BAs)-interacting proteins in both mammalian cells and bacteria. The studies better informed the field on BA’s regulatory roles in human physiology and diseases.

Shentian’s Scripps Resesarch fellowship studies, in collaboration with HIVE Center members, are focused on the identification and characterization of host proteins involved in HIV-1 Gag assembly and trafficking. She will develop chemical proteomics strategies to study metabolite-protein and protein-protein interactions in HIV infected and myeloid cell as well.

In her free time, Shentian enjoys watching movies, listening to music, and bein an innovative chef.

Geraldine Goebrecht Receives Training Grant from National Institutes of Health (September 3, 2018)

Geraldine Goebrecht recently received a four-year training grant (F30) from the National Institutes of Health (NIH) in support of a research project entitled, ” Lymph node-targeted delivery of HIV vaccine candidates.” The grant will provide funds for her tuition and fees, stipend, and an institutional allowance.

Geraldine’s work in the Torbett Laboratory now focuses on tracking the HIV capsid core as it moves towards and docks at the nuclear pore. Using SuFEx chemistry, developed by the Barry Sharpless group, she looks to establish a novel labeling strategy for HIV capsid allowing for the detailed visualization of core degradation.

To further characterize the completeness of capsid cores able to facilitate infection, she has designed cell lines capable of inducibly and reversibly halting nuclear entry. By controlling HIV’s entry into the nucleus, she will be able to assess those capsid structures poised to enable integration in too the host genome.

Geraldine has been in the Torbett Laboratory as a Graduate Student since May 2018. She is currently working on her doctoral degree in Biology through the Scripps Research Institute’s Skaggs Graduate Program. Upon completion of her doctorate, she will return to the UC San Diego School of Medicine to complete her medical training through the Medical Scientist Training Program.

Graduate Student Christian Gallardo Receives 2018 Ellen Browning Scripps Foundation Fellowship Award (September 2, 2018)

Christian Gallardo, Graduate Student of Scripps Research Graduate Program, has received the 2018 Ellen Browning Scripps Foundation Fellowship Award.

The award recognizes Christian whose work focuses on the development and application of sequencing technologies in vivo HIV viral evolution.

Christian has been a member of the Torbett Laboratory since 2015.

Former Torbett Lab Research Intern Joins Duke Center for Neurodegeneration and Neurotherapeutics (September 1, 2018)

Craig Chen, a former Research Intern in the Torbett Laboratory, has taken a position as a Research Assistant at the Duke Center for Neurodegeneration and Neurotherapeutics. His current work focuses on the development of a palliative drug to treat HD and Parkinson’s patients.

Craig joined the Torbett laboratory in June 2017 and worked on gene delivery strategies and lentiviral vectors before moving to Duke University in September 2018. Craig is also currently enrolled at Duke University, taking dual major in Biomedical Engineering and Finance.

His other interests include pursuing vaccine and antiobiotic development research and playing musical instruments.

Craig Chen from Bishop H.S. is interning in the lab summer 2017.  Way to go Craig for wearing a lab coat instead of flip flops this summer.  Happy to have you.

Stosh Ozog, M.D./Ph.D. Graduate Student, received a F30 Fellowship from the NHLBI in April 2017 to support his Ph.D. graduate studies and medical education.

Theresa Sample, Ph.D., a former TSRI Fellow (2010-2017), has taken a position at Ionis Pharmaceuticals as a Technical Writer.

Nina Timberlake, Ph.D., a former TSRI Fellow (2015-2016), has taken a position at Poseida Therapeutics as a Research Scientist and will undertake studies in gene delivery.