Research Assistant - Department of Research

The Comparative Pathology and Genomics Shared Resource (CPGSR) is housed within the Office of Research overseen by the Associate Dean of Research, Dr. Cheryl London and offers capacity for detailed assessment of animal models of human disease to Cummings School scientists and clinicians and the broader Tufts research community, other academic institutions, and regional biotech and pharmaceutical companies. The CPGSR aims to improve human translational outcomes (i.e., treatment and prevention) through detailed characterization of animal models across species at the clinical, pathologic and genomic levels. The core is housed in the newly renovated 3622 sq ft, Amelia Peabody Pavilion at Cummings School of Veterinary Medicine at Tufts University. The total space for histopathology research is 1303 sq ft with three dedicated research bays and two chemical hoods, specimen storage, and equipment benches designed to accommodate up to three microtomes.

The core is co-directed by Dr. Martinot (comparative pathology), a board-certified veterinary pathologist, with a staff of certified histotechnicians, and Dr. Gardner (boarded comparative oncology and genomics), a boarded veterinary internist and oncologist specializing in genetics. The shared resource provides advanced histopathology, digital imaging, hi-plex immunofluorescence (Panoramic Midi II Digital slide scanner), and comparative genomics including spatial profiling and analysis of RNA and DNA, (Nanostring GeoMx Spatial Profiler, Nanostring CosMx Spatial Molecular Imager, nCounter Max, Illumina NextSeq 2000, 10X chromium controller, Agilent tapestation and Biomek i7 liquid handling system) and image analysis (HALO Indicalabs quantitative image analysis software). Together, this resource brings a core set of services designed to assess, credential, and utilize a wide variety of animal model systems of disease more accurately. Services include processing of tissue samples (e.g. paraffin embedding, sectioning, routine hematoxylin and eosin staining, special stains, RNAscope in situ hybridization, and immunohistochemistry) optimized for a number of animal species including mouse, rat, hamster, canine, porcine, and non-human primates).

Reporting to the Associate Dean, the research assistant will work in the CPGSR under the day-to-day direction of Drs. Amanda Martinot and Heather Gardner at Cummings School of Veterinary Medicine at Tufts University. The primary focus of the position is to help optimize and complete research tasks in the laboratory focused on a variety of data management and molecular techniques. The individual will be expected to undertake basic histology techniques and NGS library preparation techniques after training. The individual will work independently under the direction of Drs. Martinot and Gardner to optimize new assays / techniques, analyze and interpret datasets, and assist in preparation of assay results for CPGSR users, monitor digital platforms for experiment requests and initiate experimental tasks. Additional work includes assisting lab members with general lab maintenance, coordinating on-site instrument maintenance, record keeping and ordering supplies. The position will require substantial digital data recording and general maintenance of equipment and lab records. The individual will be expected to take on new and/or additional duties as skills improve and as lab needs change. The research assistant must have a strong foundation in molecular laboratory techniques and digital data platforms. Additionally, the research assistants will need to perform a wide range of detailed techniques and must be able to learn new tasks / techniques rapidly. Prior histology or NGS experience is beneficial, but not required.

Essential functions as a Research Assistant in CPGSR will be:

• Perform benchtop experiments under the direction of the CPGSR co-directors (Martinot/Gardner), involving molecular techniques, histology, library preparation and sequencing. Detailed digital data recording of all experiments. Tasks will include:
  
  • Handling fixed animal tissues for preparation for glass slides (grossing, embedding, microtomy of paraffin blocks).
    
  • Preparation of glass slide labels, and cassette labeling.
    
  • Monitoring shared email for new histology and genomics requests, emailing researchers/clinicians about sample updates, and preparing quotes.
    
  • Learning Agilent, iLabs tracking of histology and genomics requests.
    
  • Accurate and precise use of a micropipette and multi-channel pipette.
    
  • Calculations of antibody dilutions, reagent preparation, NGS library preparation and following detailed staining protocols with accuracy and reproducibility.
    
  • Programming and operating Leica Bond and Intellipath for RNAscope and immunohistochemistry for diagnostic samples and research samples. Operating and troubleshooting the Biomeki7 liquid handling robot, Illumina sequencer, Sony SH800 flow sorter, Nanostring and 10X genomics equipment.
    
  • Willing to learn manual RNAscope and immunohistochemistry for protocols not validated for automation (and developing new protocols with Dr. Martinot for new species/sample validation). Willing to learn and independently perform manual NGS library preparation for protocols not validated or automated.
    
  • Processing of animal tissues (frozen or fixed) for nucleic acid isolation and NGS project input.
    
  • Developing skills to operate and perform functions associated with other key pieces of equipment necessary for histology activities including Leica Grosslab Grossing stations, Sakkura VIP5 Tissue Processor, Sakura Tissue-Tek TEC 5 Embedding Center, Sakura DRS-601 Automated Slide Stainer, Tissue Tek SCA Automated Film Coverslipper, Leica microtomes, an Olympus CH-2 microscope, a ACD HyBEZ II Hybridization System, Olympus VS200 with 100x magnification scanning capacity for cytology,Thermo Slide Mate cassette printer.
    
• Laboratory maintenance and organization; including ordering supplies and stocking the laboratory, maintenance of laboratory equipment, maintaining laboratory records. Tasks will include:
  
  • Proper recording of experimental details in digital lab notebooks (LabArchives).
    
  • Preparation of distribution/sample lists and block/slide inventory using Sharepoint.
    
  • Interfacing with vendors to troubleshoot equipment issues and repairs.
    
  • Coordinating repairs, meeting service technicians, and following up on routine equipment maintenance.
• Interface with CPGSR users as needed to support service requests including:
  
  • Performing quality assurance of data generated including both histology and genomics-related activities.
    
  • Assisting CPGSR users with obtaining data from servers and instruments.
    
• Perform various administrative activities including:
  
  • Working effectively in iLabs to review requests and generate appropriate quotes for service.
    
  • Working with the Senior Administrative Coordinator to ensure billing activities are current and accurate.
    
  • Working with CPGSR directors and other staff to facilitate workflow.
    

Basic Requirements:

• A bachelor's degree in science (preferably in biological sciences) and 3-5 years of related laboratory experience OR a master's degree in science and one year of related laboratory experience (preferably performing molecular techniques).
• Strong skills in data management and digital data recording are required. In particular, the position requires use of a variety of platforms, including Microsoft excel; Microsoft Outlook; Microsoft Sharepoint/OneDrive; high performance compute cluster; Agilent iLabs; labarchives; Protocols.io; multiple instrument computers (LycaBond, Illumina sequencer, Nanostring nCounter, Nanostring GeoMx/Atomx, Beckman Biomek i7 Hybrid liquid handling robot).

Preferred Qualifications:

• Be highly motivated to learn new methods, well-organized, very careful, and willing to accurately follow detailed instructions.
• No previous NGS library preparation experience is required, however, the successful candidate will have strong experience in molecular laboratory techniques (e.g. PCR, etc).