Wet Lab
What is a Luekopak
It is the blood sack that gets received from the blood bank - around 10 times the volume of a PVI standard blood draw
How many total IRB approved human subjects research protocols do we have with Dr. Simon as PI?
11 - 5 are participant facing (PARIS, UMBRELLA, HEALTHY DONORS, APOLLO, ANTIVIRALS), 2 are clinical cores (CRIPT, VIVA), 4 support secondary research on existing biospecimen (SPI, GIHSN, VIRAL RNA, PLUTO)
How does PTO work in the Simon Lab?
Email your manager for approval
Once approved, update the PTO tracker, google calendar, and Sinai Cloud
If you are out for longer than a couple of days you need to provide a coverage plan. If you are hourly, the cloud will prohibit you on time off - talk to Komal
What samples are collected in the Pathogen Surveillance program - type(s) and reason for collection
Bacteria and Nasal Swabs that are done with clinical testing and have tested positive for a pathogen, Serum from specific cases of interest
How many columns in the Specimen Dashboard of the Processing Notebook should be blank/missing 24 hours after a sample is processed on a Tuesday?
0
From what sample types do we isolate microglia and monocytes
From leukopaks and brain tissue
What does IRB stand for and what are its two primary responsibilities?
IRB = Institutional Review Board
A coalition of trained professionals who convene under a Chair for review of human subjects research and humanitarian use devices.
How do you request supplies to be ordered?
Using Quartzy!
What nasal swab samples get accessioned in the Simon Lab vs the PSP room in CML (led by Anna)
All the samples that test positive for SARS-CoV-2 come to the simon lab, all the biofire samples go to Anna
Give the primary key (the column / set of columns that make a unique index) for:
Sample Intake Log
APOLLO Participant Tracker (approximate name okay)
A tab in the New Import Sheet
Sample ID
Participant ID
(Row, Column) or Position
What is the difference between the digital PCR and the qPCR
Digital PCR gives you absolute counts of DNA and qPCR gives you relative quantities
What is the definition of a human subject?
According to 45 CFR 46,
a human subject is "a living individual about whom an investigator (whether professional or student) conducting research:
Where can you find the holiday schedule, various handbooks and user guides on Sharepoint?
Under Resources >> General Resources
Who are the directors of the Pathogen Surveillance program, what departments are they a part of and what is the workflow across their respective teams that makes up the PSP pipeline?
Mia Sordillo - clinical interface, running CLIA lab operations and ensuring samples transfer from clinical settings to research once all standard of care diagnostic and support testing is complete
Viviana Simon - sample processing, de-identifying virology samples and biobanking them for eventual sequencing with the van Bakel lab and culturing in our lab.
Harm Van Bakel - sample sequencing, harmonizing data from the medical record, lims and research data sources, creating data visualizions and phylogenetic trees, reporting to GISAID and analyzing current sequences
What are the steps to calculate an IC50 or ID50, starting from OD readings from a plate reader after a serial dilution?
1. Average the positive and negative controls for the plate.
2.Normalize the OD values for each well to be between 0 and 1: (positive mean - [well OD]) / (positive mean - negative mean)
3. Fit a logistic curve to your data for each sample (using Prism, e.g.) and find the midpoint.
What is a library prep and how is it used in the lab?
A library prep is the first stage of preparing a sample for sequencing. In our lab we do library prep for experiments under pMorpheus and HERVs - sequencing is currently done by Takara.
When did PVI Start and how many visits does PVI have in total? (+/-300)
2016 and 18,303 as of last week!
Name six of the quick links on the homepage of the Sharepoint Site
Lab Notebooks
Cloud Resources
Sinai Cloud Login
Quartzy
Inventory
Requested Samples
Sample Intake Log
SCC Result Reporting
REDCap
PSP Sequencing Request Form
Metadata Library
NGS List
Pathogen Surveillance Program
SARS-CoV-2 Virus Farming
PVI - Personalized Virology Inititative
Wet Lab
PVID Dashboard
Website
Intranet
PTO
When did the pathogen surveillance program start?
2013
What is the difference between a biological replicate and a technical replicate? What makes a good one, and what are they good for?
Technical replicates run the same assay on the same sample, biological replicates use a different sample / individual / organism. Technical replicates identify or reduce assay variability; biological replicates ensure your findings hold true for more than one person.
You get a shocking, almost nonsensical result on your favorite assay (microneuts, digital PCR, qPCR, sequencing). What steps do you take to debug and confirm that the result is real or figure out what went wrong?
[assay dependent]
Name the kit types we use and the vacutainers that are in them
SeroNet MARS - 3 CPT 2 SST
SeroNet GAEA - 2 CPT 3 SST
Cells - 4 EDTA 1 SST
Serum - 2 SSTs
Acute -2 EDTA 1 SST
Standard - 3 EDTA 2 SST
APOLLO - 5 SST
Name all the Simon/Mulder lab external funding sources, what they aim to do, and what type of funding they are.
Grants
VIVA - Understanding immune responses to different viral vaccines (SARS-CoV-2, Influenza, Dengue)
PLUTO - Developing a pancoronavirus vaccine
SPI - Understanding the drivers of persistant SARS-CoV-2 infections
pMorpheus - Understanding HIV Latency
GIHSN - Contributing to global tracking of influenza cases, sequences and severity
HERVs - HERVs proteogenomics
Contracts
CRIPT - Base & Options - Understanding Influenza severity and pathogenesis
CIVIC - Options - Developing a universal Influenza Vaccine
SeroNet - Leveraging serology based technology to characterize SARS-CoV-2 in populations of interest
When we say biofire - what does that mean and what does it test?
It is called the biofire respiratory virus panel and it is a commercial test that is FDA approved to detected a host of viruses and bacteria.
VIRUSES
Adenovirus
Coronavirus 229E
Coronavirus HKU1
Coronavirus NL63
Coronavirus OC43
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Human metapneumovirus
Human rhinovirus/enterovirus
Influenza A virus
Influenza A virus A/H1
Influenza A virus A/H3
Influenza A virus A/H1-2009
Influenza B virus
Parainfluenza virus 1
Parainfluenza virus 2
Parainfluenza virus 3
Parainfluenza virus 4
Respiratory syncytial virus
BACTERIA
Bordetella parapertussis
Bordetella pertussis
Chlamydia pneumoniae
Mycoplasma pneumoniae
What is a Mann Whitney U test? What is it good for, what assumptions does it rely on, and how does it work?
A non-parametric two-sample test evaluating differences in the central tendency of two groups (the median, assuming i.i.d samples). Relies on the two samples being independent and the data being ordinal. Transforms data into ranks and compares a statistic based on the sum of the ranks of each group to a known distribution under the null hypothesis (samples drawn from the same distribution)