Abstracts as of 9/19/23

Please check back for updates

Julie Auger, Andy Chitty and Craige Mazur: Maximizing Core Impact with Metrics Integration and Effective Communication

Cores and Shared Resources exist at the intersection of science, education, and business. Providing cutting edge services and training to the scientific community is challenging, made more so by the need to employ business skills and juggle communications with core users and those who support the cores centrally. How do we make sure our user base gives appropriate credit to our work? How do we communicate the value of our cores to executive leadership? 

In this session, we will cover a variety of metrics, including a model for tracking publications, tracking grants supported by cores, and tracking other core impact metrics in the research environment. We will share some examples and ideas of how to communicate the impact of our operations to various stakeholders such as core users and executive leadership. The session will end with an open discussion, where we invite others to share their challenges and success stories, as well as discuss emerging ideas from previous sessions.

Peter Barr-Gillespie: KEYNOTE: Balancing how to hear and be heard: Stories from the cores

Peter Barr-Gillespie is Chief Research Officer (CRO) at Oregon Health & Science University (OHSU), and has ultimate oversight over the core resources there. Barr-Gillespie is also a basic scientist whose lab heavily uses several core facilities at OHSU. The presentation will start out with a brief introduction to the auditory and vestibular research carried out by the Barr-Gillespie lab, with a particular focus on projects that use specific cores (mass spectrometry, light microscopy, electron microscopy). Barr-Gillespie will then switch to describing the OHSU University Shared Resources (USR) program, which is run out of his office. Topics will include organization and management, financial support, and relationships with the faculty. He will describe how his experiences with using the cores have assisted in his oversight role. Because there is particular interest in how cores can communicate with research leadership at the university, Barr-Gillespie will discuss how core leaders can best ensure that leaders like the CRO know the issues within all of the cores, not just the ones he has personal experience with. 

Most of all, this keynote is intended to lead to an informal dialog between Barr-Gillespie and the audience, and the audience should plan to ask questions of Barr-Gillespie that are normally difficult to address to research leadership because of access.

Pamela Canaday: The Benefits of a Core Career Track

Core laboratories are an indispensable tool for modern research. They allow the latest technology and expertise to be shared between multiple labs. Experienced core specialists are essential to a well-functioning core. It can take years for someone to become not just proficient, but expert, at operating instruments and consulting on assays. Due to the high demand for these skills, core labs need to be competitive in order to retain valued staff.

 In order to meet this need, OHSU has introduced a new series of job designations. Rather than working as Research Associates, the people who are essential for operating the cores are given the title of Core Scientist. This title change also comes with competitive salaries and recognition that core staff are an essential part of a well-running core and research community. This talk will focus on this transition from the perspective of a Flow Cytometry Core Scientist. 

Britt Daughtry: Incorporating a Clinical Project into Your Core Lab

Are you thinking about adding clinical samples to your core services? Accreditation from the College of American Pathologists (CAP) is essential for laboratories that want to process clinical samples. It is a rigorous program that helps labs meet and exceed the highest quality standards, ensuring the accuracy and reliability of test results for high-quality patient care. While the process of CAP accreditation can seem costly, time-consuming, and daunting, the payoff is well worth it if you enter the process prepared. These benefits can include increased opportunities for contracts, partnerships, collaborations, and revenue; improved management of the core laboratory and staff training; and enhanced resumes and career development for staff.

In this talk, we will share our experience at Oregon Health & Science University’s Integrated Genomics Laboratory with becoming CAP accredited in order to process clinical samples for the Healthy Oregon Project. We will discuss the steps involved in the application and accreditation process, as well as the work involved with maintaining accreditation. We will also highlight some of the requirements of CAP accreditation and provide general guidance on what to expect as you make your core laboratory CAP-compliant. In addition, we will share lessons learned along the way and discuss the benefits of CAP accreditation for core laboratory operations. CAP accreditation is well worth the effort, as it can open many doors and opportunities, and bring you the satisfaction of knowing that your work is having an immediate impact on patient care.

Chris Harrington and Jackie Shannon: Cores in Support of Impactful Innovation: The Healthy Oregon Project

The Healthy Oregon Project (HOP) is a large initiative that seeks to understand the root causes of cancer and other diseases through the collection of population survey data combined with biological sampling of up to 100,000 volunteers across the state of Oregon.  This project harnesses and integrates the power of the people, the knowledge of disease experts and specialized core facilities to make an impact on human health.  This talk will describe the origins of the HOP, it’s goals, how the project has evolved, how the different participating factions have been integrated, and the role that core facilities have played in the process.  We will also discuss the outreach that has been critical in moving this project forward as well as the current and projected future impact of this project on human health.

Claudia Lopez: How to Successfully Manage a University Shared Resource and a National NIH Electron Microscopy Facility and Survive in the Process 

The Multiscale Microscopy Core (MMC) is a state-of-the-art electron microscopy university shared resource core that was established at OHSU in 2013. This core provides imaging services, technical support and training to academic users. The MMC was initially located on the OHSU main campus and in 2014 was re located to a brand new 5,023 sq ft specially designed low-vibration imaging suite in the basement of the Robertson Life Sciences Building (RLSB) situated at the OHSU South Waterfront campus. This microscopy suite was designed and built to provide a low-vibration environment for high-end instrumentation and included a separate foundation of 2,600 sq ft that is isolated from the rest of the RLSB building by a 50 ft air moat. This moat serves the purpose of isolating the microscopy suite from vibrations occurring in the main the building, surface streets, and public transit systems. This microscopy suite was originally shared between the MMC other research labs, including the advanced light microscopy core. Then, in 2018 the NIH Transformative High-Resolution Cryoelectron Microscopy (cryoEM) Program awarded to OHSU one of the three multiyear/multimillion grant dedicated to broadening access to high-resolution cryoEM to the research community. The Pacific Northwest Cryo-EM Center (PNCC) was then established at OHSU on the same year. In order to build this new national center, OHSU invested funds and the low vibration suite had to be redesign to accommodate three new large high-end cryo-electron microscopes. In this talk I will share my experience as Director of both centers regarding, day-to-day managing activities, lessons learn during relocation of major instrumentation, remodeling of spaces for high-end instruments, hiring and retaining highly skilled personnel, synergistic interactions between the two centers and strategic budget and planning.

Karen Mosier: Power Skills in Academic Environments

Personal skill sets, whether utilized within a team setting or organization, are crucial to foster a collaborative, productive and creative work environment. Previously defined as Soft Skills, these skill sets increasingly designated as Power Skills, in recognition of their critical importance in the workplace.

Power Skills are timeless, non-technical aptitudes that enable individuals to evolve effortlessly in increasingly diverse and interdisciplinary organizations. As such, Power Skills are essential to today’s Research Administrators. They are one of the keys to unlock our potential at work, as an individual or as part of a team. These invaluable skills are inescapable on our path to a successful career, and intimately tied to the success of companies, organizations and institutions alike.

Honing your Power Skills does not come naturally to everyone, but with reflection, learning, and practice any employee can acquire and sharpen these skills. Without them, you may not achieve success, and developing them takes a lifelong commitment.

This talk cover the basics of Power Skills that will enable you to be successful in your career and unlock your individual potential in the workplace. This presentation will focus on five core components: Communication, Leadership, Resiliency & Adaptability, Professionalism & Integrity, and Collaboration & Promotion. This session will highlight Power Skills in a dual framework in terms of team goals versus personal career goals.


Mike Munks: Multi-Core Experiments: Synergistic Outcomes, or Just Squared Degree of Difficulty?

Scientific research continues to become more collaborative over time, and also more focused on large datasets. As a half-time core director and half-time research scientist, I will describe two projects. One is a completed project involving RNA-seq data generated by sequentially combining flow cytometry, RNA isolation and bulk RNA-seq. The second is a current project utilizing patient-derived cancer cell lines, used for 3D bioprinting of tumors. The samples are analyzed in parallel by single-cell RNA-seq, cyclic immunofluorescence and/or flow cytometry. I will highlight both the struggles and successes, with a goal of facilitating a conversation about the dos, the don’ts, and factors to consider for feasibility.

Aaron Nilsen: Access to Synthetic Chemistry Can Expand the Services Offered by Your Core Facilities

By working synergistically with other core facilities, a synthetic chemistry core can expand both the services offered by core facilities and the research approaches available to their customers. The OHSU Medicinal Chemistry Core helps researchers investigate interactions between small molecules or peptides and biological systems by providing medicinal chemistry and chemical biology expertise and small molecule and peptide synthesis support. The core synthesizes custom fluorescent or pull-down molecular probes that can be used in light microscopy or proteomics cores to visualize or analyze protein targeting. The core synthesizes ‘heavy’ versions of druglike molecules for use in pharmacokinetics experiments performed by mass spectrometry cores. The core also prepares custom synthetic intermediates that can be converted to radiolabeled materials by a radiochemical synthesis core. Using these approaches, a synthetic chemistry core can give biological researchers access to techniques that are otherwise only available to research labs that already possess synthetic chemistry capabilities.

Brett Phinney: Developing Proteomic Genotyping for the Common Good

The Proteomics core at UC Davis Genome Center is involved in a wide variety of collaborative research. Several of our major collaborative projects involve extracting genetic and species information from proteomics samples where DNA is either absent or degraded (collaborating lab = Dr Glendon Parker UC Davis). This technology called “proteomic genotyping” can be used in a wide variety of applications. These applications include species identification of fur’s confiscated in illegal fur trafficking in California, using human hair to molecularly identify individuals in crime scenes, analyzing sexual assault kits where DNA is degraded, and estimating biological sex in archology and paleontology applications. Here we will present our recent research in this area and demonstrate how our proteomics core facility has helped develop and enable this technology and its real-world applications in forensics, archaelogy, and wildlife enforcement.

Beverley Rabbitts: Surf’s Up in Academic Drug Discovery

As a core facility designed to meet the goal of drug discovery, the UCSC Chemical Screening Center (RRID SCR_021114) hosts a suite of resources spanning end-to-end workflows, from large compound libraries to fast data acquisition modalities. To make high throughput sample preparation possible, we integrated instruments from several vendors onto a single custom robotic workstation. Our resources are applied to a wide variety of projects by trained users with varying areas of expertise, and this presents unique challenges and opportunities for the director of this single-person core. We will present what we have learned along the way, in the context of our macrophage platform, in which we explore image-based analysis with machine learning as a powerful method of identifying novel natural product modulators of the innate immune response. 

Scale: RNA, Methylation, and CRISPR, oh my! New Technologies to Enable Scalable Single Cell Studies
Mary Arrastia, Dominic Skinner, Sanika Khare, Nick Pervolarakis, Jerushah Thomas, Dmitry Pokholok, Hosu Sin, Ashley Woodfin, Eric Pu, Lin Lin, Phuong Dang, Aimee Beck, Margaret Nakamoto, Beth Walczak, Felix Schlesinger

Single-cell sequencing technology has uncovered new biology across a wide range of disciplines. However, cell and sample throughput of experiments has not scaled rapidly due to high costs and complex workflows, restricting utility of this technology for screens, cell atlases, or large patient cohorts which can be prohibitively expensive. To meet this need combinatorial indexing has been established as a cost-effective method to increase throughput. Here, we present three applications of combinatorial indexing technology from Scale Biosciences (ScaleBio) that enables high-throughput single cell studies: RNA, CRISPR, and methylation. ScaleBio’s RNA Sequencing Kit allows users to process upwards to 125,000 cells, nuclei, or both in one experiment with low multiplet rates. ScaleBio’s CRISPR Guide Enrichment Kit can amplify a CRISPR guide sequence derived from a CROP-style vector along with the whole transcriptome in upwards to 500,000 single cells. Lastly, ScaleBio’s Single Cell Methylation Kit is the first single cell DNA methylation kit on the market, allowing profiling of single-cell methylation states in tens of thousands of cells. With these kits, we have processed a variety of sample types, including macaque brain samples from UCLA and prenatal & adult human brain tissue from Duke University. Together these data show that combinatorial barcoding can be effectively applied to a variety of samples and tissues, significantly increasing sample and cell throughput and reducing bench time and cost without compromising data quality.  

Camilla Urbaniak: Harnessing Core Facilities for Advancing Space Biology Research

The adaptation of microorganisms to the space environment is a critical factor affecting the feasibility and sustainability of both short and long-duration space missions. Understanding the impact of deep space stressors on the human and built microbiome necessitates sophisticated techniques, advanced equipment, and interdisciplinary expertise, all of which are provided by core facilities. As a result, core facilities play a pivotal role in space biology research.

The Biotechnology and Planetary Protection Group at NASA’s Jet Propulsion Laboratory exemplifies the integration of core facilities in space biology research. Leveraging these facilities, the group processes and analyzes experiments conducted on the International Space Station, spacecraft clean rooms, and analog environments. One such project is the ODYSSEY Project, set to launch to the ISS in early 2024. This study aims to compare biofilm formation and horizontal gene transfer of select bacteria grown on the ISS and in simulated microgravity devices on Earth. Collaborating with core facilities, the research team plans to employ advanced techniques such as confocal microscopy, transcriptomics, and metabolomics to analyze samples obtained from space.

By utilizing core facilities for space biology research, scientists gain access to state-of-the-art instrumentation and specialized services that are vital for conducting space-related experiments. These facilities streamline research processes and enhance efficiency, thereby optimizing the utilization of limited resources available during space missions. Additionally, the standardization and reproducibility ensured by core facilities are crucial when dealing with precious and challenging-to-obtain samples from space. This consistency in research practices facilitates reliable data generation, enabling accurate comparisons between samples and across different studies.

The significance of core facilities in space biology research cannot be overstated, especially when it comes to advancing scientific knowledge and contributing to the broader field of space exploration. The insights gained from studying microbial adaptation in space have far-reaching implications, from optimizing human health and safety during space travel to ensuring the habitability of spacecraft and extraterrestrial habitats. As humanity ventures further into the cosmos, the role of core facilities will continue to be pivotal in unraveling the mysteries of space biology and shaping the future of space exploration.

 
Victoria Vesna: Visualizing Frequencies: Bridging Art and Science from Atomic to Cosmic Dimensions

 In this talk, I venture into the captivating intersection of science labs and media artists, with an accentuated focus on the visualization and imaging of frequencies and waves, spanning scales from the atomic to the vast expanses of space. Interestingly, where artists once encountered barriers, there now stands an invitation. Scientists, who once held their research close, are now welcoming these artists to collaborate within the lab environment. This evolving synergy is fueled by a shared toolkit of technological instruments and a rhythm of interdisciplinary teamwork, funding challenges, and looming deadlines. These shared endeavors dissolve past communication barriers, sparking the birth of a novel, third cultural nexus. This burgeoning culture not only amplifies the art-science connection but also introduces fresh challenges for both realms. As technology, fortified by AI, surges ahead at an unparalleled pace, delving deep into this alliance becomes crucial. Through a lens that captures the intricacies of our universe, from its tiniest particles to its boundless galaxies, I will illuminate this bond by presenting my collaborative journeys with scientists and spotlighting the pioneering endeavors of the UCLA Art | Sci research center.

Erin Weisbart: From Lots of Pictures to Lots of Numbers to Lots of Answers: Advances in quantitative high content imaging

Dr. Weisbart will discuss the quantitative power of bioimages and how software, data science, and machine learning advances have improved our ability to extract meaningful biological insights from high content imaging. She will touch on the importance of public data and open source software and how cross-discipline collaboration improves science for all.

 
Ryan Zervakos: The Roadmap to Career Success and Mobility

This talk will encompass the following themes related to core usage of LinkedIn : Why One Should be on LinkedIn, Creating an Authentic Profile, Using LinkedIn to Network, Using LinkedIn Like Social Media