Elizabeth Silva

Universities are at long last undertaking efforts to collect and disseminate information about student career outcomes, after decades of calls to action. Organizations such as Rescuing Biomedical Research and Future of Research brought this issue to the forefront of graduate education, and the second Future of Biomedical Graduate and Postdoctoral Training conference (FOBGAPT2) featured the collection of career outcomes data in its final recommendations, published in this journal (Hitchcock et al., 2017). More recently, 26 institutions assembled as the Coalition for Next Generation Life Science, committing to ongoing collection and dissemination of career data for both graduate and postdoc alumni. A few individual institutions have shared snapshots of the data in peer-reviewed publications (Mathur et al., 2018; Silva, des Jarlais, Lindstaedt, Rotman, Watkins, 2016) and on websites. As more and more institutions take up this call to action, they will now be looking for tools, protocols, and best practices for ongoing career outcomes data collection, management, and dissemination. Here, we describe UCSF's experiences in conducting a retrospective study, and in institutionalizing a methodology for annual data collection and dissemination. We describe and share all tools we have developed, and we provide calculations of the time and resources required to accomplish both retrospective studies and annual updates. We also include broader recommendations for implementation at your own institutions, increasing the feasibility of this endeavor.

The oversupply of postdoctoral scholars relative to available faculty positions has led to calls for better assessment of career outcomes. Here, we report the results of a study of postdoctoral outcomes at the University of California, San Francisco, and suggest that institutions have an obligation to determine where their postdoc alumni are employed and to share this information with current and future trainees. Further, we contend that local efforts will be more meaningful than a national survey, because of the great variability in training environment and the classification of postdoctoral scholars among institutions. We provide a framework and methodology that can be adopted by others, with the goal of developing a finely grained portrait of postdoctoral career outcomes across the United States.

There is growing concern about lack of scientific rigor and transparent reporting across many preclinical fields of biological research. Poor experimental design and lack of transparent reporting can result in conscious or unconscious experimental bias, producing results that are not replicable. The Analgesic, Anesthetic, and Addiction Clinical Trial Translations, Innovations, Opportunities, and Networks (ACTTION) public-private partnership with the U.S. Food and Drug Administration sponsored a consensus meeting of the Preclinical Pain Research Consortium for Investigating Safety and Efficacy (PPRECISE) Working Group. International participants from universities, funding agencies, government agencies, industry, and a patient advocacy organization attended. Reduction of publication bias, increasing the ability of others to faithfully repeat experimental methods, and increased transparency of data reporting were specifically discussed. Parameters deemed essential to increase confidence in the published literature were clear, specific reporting of an a priori hypothesis and definition of primary outcome measure. Power calculations and whether measurement of minimal meaningful effect size to determine these should be a core component of the preclinical research effort provoked considerable discussion, with many but not all agreeing. Greater transparency of reporting should be driven by scientists, journal editors, reviewers, and grant funders. The conduct of high-quality science that is fully reported should not preclude novelty and innovation in preclinical pain research, and indeed, any efforts that curtail such innovation would be misguided. We believe that to achieve the goal of finding effective new treatments for patients with pain, the pain field needs to deal with these challenging issues.

Apoptosis, a genetically programmed cell death, allows for homeostasis and tissue remodelling during development of all multi-cellular organisms. Phagocytes swiftly recognize, engulf and digest apoptotic cells. Yet, to date the molecular mechanisms underlying this phagocytic process are still poorly understood. To delineate the molecular mechanisms of apoptotic cell clearance in Drosophila, we have carried out a deficiency screen and have identified three overlapping phagocytosis-defective mutants, which all delete the fly homologue of the ced-12 gene, known as Dmel\ced12. As anticipated, we have found that Dmel\ced-12 is required for apoptotic cell clearance, as for its C. elegans and mammalian homologues, ced-12 and elmo, respectively. However, the loss of Dmel\ced-12 did not solely account for the phenotypes of all three deficiencies, as zygotic mutations and germ line clones of Dmel\ced-12 exhibited weaker phenotypes. Using a nearby genetically interacting deficiency, we have found that the polycystic kidney disease 2 gene, pkd2, which encodes a member of the TRPP channel family, is also required for phagocytosis of apoptotic cells, thereby demonstrating a novel role for PKD2 in this process. We have also observed genetic interactions between pkd2, simu, drpr, rya-r44F, and retinophilin (rtp), also known as undertaker (uta), a gene encoding a MORN-repeat containing molecule, which we have recently found to be implicated in calcium homeostasis during phagocytosis. However, we have not found any genetic interaction between Dmel\ced-12 and simu. Based on these genetic interactions and recent reports demonstrating a role for the mammalian pkd-2 gene product in ER calcium release during store-operated calcium entry, we propose that PKD2 functions in the DRPR/RTP pathway to regulate calcium homeostasis during this process. Similarly to its C. elegans homologue, Dmel\Ced-12 appears to function in a genetically distinct pathway.