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JOB SUMMARY The incumbent in this position will independently execute research in the Upadhyay Laboratory investigating how gut bacterial metabolites regulate lung epithelial mitochondrial function during acute respiratory distress syndrome (ARDS). Building on published findings that Bifidobacterium adolescentis-derived L-lactate increases mitochondrial activity in lung epithelial cells and correlates with ARDS severity (Upadhyay et al., bioRxiv 2025Nat Cell Biol), the SRA 2 will work under general supervision to advance a mechanistic understanding of the gut-lung axis in critical illness. The SRA 2 is expected to bring demonstrated laboratory proficiency, execute experiments with independence, troubleshoot problems before escalating to the PI, and contribute to data analysis and scientific communication. This position will be working under the general supervision of Dr. Vaibhav Upadhyay at the Upadhyay Laboratory, Benioff Center for Microbiome Medicine and Division of Pulmonary and Critical Care Medicine, UCSF Parnassus campus. DUTIES & ESSENTIAL JOB FUNCTIONS Identify the functions or tasks that employees in the job perform. The essential functions should state the purpose of the work and the results to be accomplished, rather than how the function is performed. Of the tasks listed, what percentage of time is devoted to each? The more time employees spend on a function, the more likely it is that the function is essential. Generally, include those functions that account for 10% or more of the work, i.e., key items that contribute significantly to the achievement of the job. The functions should add up to 100%.
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Essential Function (Yes/No) |
Key Responsibilities (To be completed by Supervisor) |
75 |
Yes |
SRA 2: Works with the PI and alongside other lab members. Independently executes experiments after training; troubleshoots technical problems before escalating to PI; contributes to data summaries and figure preparation. Specific duties include:
Cell culture: Independently maintain and passage lung epithelial cell lines (BEAS2B, NHBE, primary ALI cultures); design and execute multi-condition treatment experiments; troubleshoot culture problems independently. Bacterial culture: Independently propagate and maintain Bifidobacterium adolescentis and related gut bacteria under anaerobic conditions; prepare conditioned media and metabolite fractions; verify metabolite production by enzymatic assay. Biochemical assays: Independently execute Seahorse XF respirometry, lactate quantification, ROS and ATP measurements; recognize invalid results and troubleshoot before consulting PI. Molecular analysis: Perform RNA/DNA/protein isolation, qPCR, western blotting, immunofluorescence; independently troubleshoot technical problems before escalating. Gnotobiotic mouse experiments: Participate in and eventually lead colonization, tissue harvest, BAL, and sample collection; train junior lab members in animal handling under PI oversight. |
10 |
Yes |
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15 |
Yes |
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100% |
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(To update total %, enter the amount of time in whole numbers (without the % symbol - e.g., 15, 20) then highlight the total sum (e.g., 1%) at the bottom of the column and press F9. The total sum should add up to 100%.) |
Required Qualifications
- BS/BA degree in biology, biochemistry, molecular biology, or related field and one or more years of recent, directly related work experience utilizing the techniques or methods required by the position; and/or equivalent experience/training.
- Ability to work independently, prioritize multiple tasks, and troubleshoot problems before escalating to supervisor.
- Experience in microbiology, metabolic assays, mouse handling, or bioinformatics preferred.
- Computer skills at the level of using spreadsheet programs
- Prior experience in a respiratory, microbiome, or metabolism-focused laboratory is a plus.
- Experience with image analysis software and basic statistics (GraphPad Prism or equivalent).
- Experience handling mice
- Familiarity with gnotobiotic mouse models or other specialized in vivo systems preferred
- Experience with metabolic assays (Seahorse XF respirometry, lactate quantification) - anesthesia, ear tagging, intratracheal and peritoneal injections, and euthanasia.
- Computer skills at the level of using spreadsheet programs
- Strong written and verbal communication skills for lab meeting presentations and figure preparation.
Preferred Qualifications
- Demonstrated proficiency in mammalian cell culture: independent maintenance, passaging, and troubleshooting of cell lines.
- Demonstrated proficiency in molecular biology techniques: RNA isolation, qPCR, western blotting.
- Experience with bacterial culture, including anaerobic techniques, preferred.
Required Qualifications
- BS/BA degree in biology, biochemistry, molecular biology, or related field and one or more years of recent, directly related work experience utilizing the techniques or methods required by the position; and/or equivalent experience/training.
- Ability to work independently, prioritize multiple tasks, and troubleshoot problems before escalating to supervisor.
- Experience in microbiology, metabolic assays, mouse handling, or bioinformatics preferred.
- Computer skills at the level of using spreadsheet programs
- Prior experience in a respiratory, microbiome, or metabolism-focused laboratory is a plus.
- Experience with image analysis software and basic statistics (GraphPad Prism or equivalent).
- Experience handling mice
- Familiarity with gnotobiotic mouse models or other specialized in vivo systems preferred
- Experience with metabolic assays (Seahorse XF respirometry, lactate quantification) - anesthesia, ear tagging, intratracheal and peritoneal injections, and euthanasia.
- Computer skills at the level of using spreadsheet programs
- Strong written and verbal communication skills for lab meeting presentations and figure preparation.
Preferred Qualifications
- Demonstrated proficiency in mammalian cell culture: independent maintenance, passaging, and troubleshooting of cell lines.
- Demonstrated proficiency in molecular biology techniques: RNA isolation, qPCR, western blotting.
- Experience with bacterial culture, including anaerobic techniques, preferred.
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University of California - San Francisco
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Apr 15, 2026