Junior Specialist/Emerson lab

We seek to hire a Junior Specialist to conduct research in viral (mostly bacteriophage) communities in the healthy human microbiome, using molecular biology equipment and techniques, as well as bioinformatics, as part of a project focused on characterizing viral roles in human-associated microbial ecosystems. Primary duties will involve co-designing and undertaking laboratory protocols for human biosamples (mostly human gut, some urine, saliva, and other sample types); receiving and logging biosamples; entering data into spreadsheets; analyzing experimental and metagenomic (viromic) data; and supervising and training undergraduate assistants. Apart from the primary project supporting this position, our research group is predominantly focused on soil viral (bacteriophage) communities, such that experience with viromes (metagenomes from the viral size fraction) and/or phage-host dynamics and/or microbiomes in any ecosystem would be good preparation for this human virome-focused position.

Research (90%):

The incumbent of this position will be actively and significantly involved in publishable research activities through the following roles and duties:

* Assist the PI by performing viral particle purification and nucleic acid extractions of viral and other microbial communities from healthy human biosamples (mostly human gut samples, also including urine, saliva, and other biosamples from healthy humans), using autoclaves, molecular biology equipment, and molecular biology techniques as part of larger projects focused on characterizing viral roles in human microbiome ecology, and in order to establish the best laboratory protocols for studying viromes from human biosamples.

* Assist the PI by obtaining and maintaining (in culture) ~10-20 viruses and their hosts from existing culture collections to generate and test viral "spike-in" standards to facilitate absolute quantification of viral abundances in viromes.

* Assist the PI by performing other laboratory procedures related to human and/or soil viral ecology, for example, microscopy, cultivation, and microfluidics.

* Maintain a well-organized lab notebook detailing laboratory procedures, results (e.g., DNA and RNA extraction yields), and sample IDs, and share lab notebook information with the PI during regular meetings (approximately every 1-2 weeks).

* Adhere to laboratory safety standards, follow standard operating procedures (SOPs), and adhere to safety guidelines for all laboratory work, with special care taken to adhere to the SOP for processing healthy human biosamples, including a requirement that those samples be processed under a chemical fume hood.

* Assist the PI and project team in retrieving human biosamples, most often from our collaborators at the UC Davis Medical School in Sacramento, CA.

* Assist the PI with bioinformatics data processing and analysis of sequencing and other omic data, for example using our high-performance computing (HPC) cluster and the R programming language.

* Assist the PI and project collaborators in manuscript preparation, including but not limited to: preparing tables and figures, statistically analyzing data, reading scholarly literature, writing methods and results sections, and revising manuscripts.

* Assist the PI and other lab members in shared tasks required for running a safe research laboratory, such as eyewash checks, fire extinguisher checks, ensuring secondary containment for hazardous chemicals, and appropriate storage and disposal of hazardous waste.

* Assist the PI by acting as a logistical liaison to the NIH Human Virome Project Consortium team, including attending team meetings and reporting back to the PI; this role will complement the roles of other liaisons to that consortium team, including the scientific liaison (PI Emerson) and the bioinformatics liaison (a postdoctoral researcher).

* Work collaboratively with other members of the Emerson group, particularly the postdoctoral researcher, and with our collaborators at UC Davis, the University of Colorado at Boulder, and other institutions.

Professional competence (5%):

* The incumbent will participate in weekly lab meetings and will be encouraged to attend weekly seminars in the Department of Plant Pathology (and/or seminars in other programs of interest on campus).

* The incumbent will be encouraged to read scientific literature to assist with experimental design and interpretation.

University and Public Service (5%):

* As a component of university service, the incumbent will be available to serve on one or more departmental committees as suggested by department administration.

* As a public service, the incumbent will also be encouraged to provide occasional research updates at public events such as those held by UC Cooperative Extension.

Minimum requirements to fit the position would be a Bachelor's degree in Molecular Biology, Microbiology, Genomics, or a related field.

Preferred qualifications would include research lab experience with DNA extractions and bioinformatics research experience in viral (bacteriophage) community ecology and/or phage-host dynamics and/or microbiomes, DNA and RNA extraction from microorganisms and/or microbiomes, high-performance computing (HPC) experience, and programming experience in R.

• 3-4 required (contact information only)

As a condition of employment, the finalist will be required to disclose if they are subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct, are currently being investigated for misconduct, left a position during an investigation for alleged misconduct, or have filed an appeal with a previous employer.

• "Misconduct" means any violation of the policies or laws governing conduct at the applicant's previous place of employment, including, but not limited to, violations of policies or laws prohibiting sexual harassment, sexual assault, or other forms of harassment, discrimination, dishonesty, or unethical conduct, as defined by the employer.
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