Wet Lab
The Personalized Virology Initiative
Simon Lab 101
Pathogen Surveillance Program
Data
100

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

100

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)

100

How does PTO work in the Simon Lab?

Check with your team and get coverage if needed

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

100

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

100

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

200

From what sample types do we isolate microglia and monocytes

From leukopaks and brain tissue

200

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. 

200

How do you request supplies to be ordered?

Using Quartzy!

200

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


200

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

300

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

300

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:

  • Obtains information or biospecimens through intervention or interaction with the individual, and uses, studies, or analyzes the information or biospecimens; or
  • Obtains, uses, studies, analyzes, or generates identifiable private information or identifiable biospecimens."
300

Where can you find the holiday schedule, various handbooks and user guides on Sharepoint?

Under Resources >> General Resources

300

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

300

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.

400

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. 

400

When did PVI Start and how many visits does PVI have in total? (+/-300)

2016 and 18,303 as of last week!

400

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

400

When did the pathogen surveillance program start?

2013

400

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.

500

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]

500

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

500

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


500

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

500

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)

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