*** This version of Confluence is for testing only and contains a copy of content from June 29th 2026. No changes will be preserved. ***
...
For any questions about these protocols, please contact Emily Wright at emw85@cornell.edu.
Current Cornell Food Safety Protocols & SOPS:
1-Animal Studies
1.1-Infection of Guinea Pigs with Listeria monocytogenes
2-Bacterial Growth & Preservation
2.1-Antibiotic Code System
2.2- Beckman Spectrophotometer DU-640 Protocol
2.3- Determining bacterial ODs using the Spectronic 20D+
2.4-Formulating media with growth inhibitors
2.4.1- Formulating media with growth inhibitors chart
2.5- FSL Isolate Designation, ID Assignment & Maintenance
2.6-Growth curve using the plate reader
2.7-Protocol for Freezing Bacterial Isolates
2.8-Spiral Plater & QCount
2.9-Standardized Growth Protocol for Bacterial Cultures & ODs
3-Bacteriophage
3.1- Listeriaphage isolation, purification, high-titer phage lysate preparation, and host range determination
3.2- Preparing High Titer Phage Stocks on M. smegmatis
3.3- Salmonella phage DNA extraction and PFGE
3.4- Salmonella Phage isolation, purification and host range characterization
3.5- Salmonella phage transduction
4- Commercial SOPs & LMT
4.1- actA PCR Assay to Differentiate Listeria monocytogenes
4.2- Generic Procedure for Automated Ribotyping Using the RiboPrinter
4.3- Molecular Subtyping of E.coli, Salmonella, and Shigella by Pulsed field Gel Electrophoresis (PFGE)
4.4- Molecular Subtyping of Listeria monocytogenes and Listeria species by Pulsed field Gel Electrophoresis (PFGE)
4.5- Procedure for Automated Ribotyping Using the RiboPrinter and Purified DNA Samples
4.6- Receiving External DNA
4.7-Receiving External Isolate
4.8- RiboPrinter Software Cheat Sheet
5-Lab Manuals & Safety SOPs
5.1-BSL1 &BSL2
5.2-Critical Laboratory Orientation
5.3-Exiting Student Checklist
5.4-Freezer emergency Plan
5.5- General safety procedures and handling and disposal of laboratory waste, including biohazard materials (BSL-1 and BSL-2 pathogens)
5.6- Laboratory Orientation Checklist
5.7-Offical Lab Manual
5.8-Poster Guidelines
5.9-Preparing Dangerous Goods for Shipping
5.10-Required and Suggested Readings
6- Microbial Detection & Isolation
6.1- Detection and Isolation of L. monocytogenes from Food and Environmental samples using the BAX system
6.2- Detection and Isolation of Listeria, Salmonella, Escherichia coli O157H7, non-O157 shiga toxin producing Ecoli (STEC) from Grazing Pastures, Pristine Environments an
6.3- Detection of Listeria monocytogenes from silage and other feeds
6.4- Detection of Listeria monocytogenes in milk
6.5- Detection of V parahaemolyticus O3K6 in oyster samples
6.6- Procedure to detect and isolate Listeria, Salmonella, Escherichia coli O157:H7, and non-O157 shiga toxin producing E. coli (STEC) from samples collected from pristine environments.
6.7- Surface swap detection for L. monocytogenes
7- Milk Quality
7.1- 2nd floor-16S GreenMaster Procedure
7.2- 16s Identification Using RDP database
7.3- 96 Well Plate Procedure
7.3.1- 96 well plate template
7.4- Checking Reports Protocol
7.5- Colony PCR
7.6- Dried milk — Enumeration of the specially thermoresistant spores of thermoresistant bacteria
7.7- Endospore Stain - cold
7.8- Endospore Staining -- Steam Method
7.9- Final rpoB GreenMaster Protocol
7.10- Growth Rate L.mono in Milk
7.11- Highly Heat Resistant Spore Pasteurization SOP
7.12- Identification of rpoB Sequences using Bioedit
7.13- Lab Pasteurization
7.14- PCR Procedure and Touble-shooting Guide for rpoB and 16S
7.15- Primer Ordering
7.16- Primer Reconstitution
7.17- Procedure for Lysis of Bacterial Cells
7.18- Purified Lysates Procedure
7.19- Spiral Plating for raw and powdered dairy products
7.20- Spore Count SOP
7.21- Spore Media Protocol
7.22- VSL Microbiological and Chemical Analysis
7.23-Sensory Analysis SOPs
7.23.1- Defective Milk, Reference Flavor & Basic Tastes Sample Preparation Protocol - in progress
7.23.2- MQIP VSL Sensory Analysis Panelist Training Protocol - in progress
7.23.3- Pouring instructions - computer set-up - short version
7.23.4- Sensory Analysis SOP
7.23.5- VSL Sensory Analysis Protocol - in progress
7.24-SOPs for USDEC
7.24.1- 16S rDNA PCR-Go Taq
7.24.2- HHR Spore Count SOP
7.24.3- Dried milk — Enumeration of the specially thermoresistant spores of thermoresistant bacteria
7.24.4- Spiral Plating for raw and powdered dairy products
7.24.5- Spore Count SOP
8-Molecular Biology Techniques
8.1-Characterization & DNA Amplification
8.1.1-PCR
8.1.1.1-General PCR Methods & Guidelines
8.1.1.1.1-16S rDNA PCR-Go Taq
8.1.1.1.2-16S rDNA PCR-modified for Taq gold
8.1.1.1.3-Basic GoTaq PCR Protocol
8.1.1.1.4-Colony PCR Protocol
8.1.1.1.5-Guidelines for Primer Design
8.1.1.1.6-Primer Naming, Reconstitution & Storage Protocol
8.1.1.1.7-Primer Reconstitution
8.1.1.1.8-Sample Submission to BRC
8.1.1.1.9-Ten Things That Can Kill Your PCR
8.1.1.1.10- Submitting sequences to GenBank
8.1.1.2-Listeria PCRs
8.1.1.2.1-Ten gene MLST Listeria
8.1.1.2.1.1-New MLST Scheme
8.1.1.2.1.2-addB PCR with GoTaq
8.1.1.2.1.3-ldh PCR with GoTaq
8.1.1.2.1.4--lmo490 PCR with GoTaq Hotstart
8.1.1.2.1.5-lmo1555 PCR-GoTaq
8.1.1.2.1.6-lmo2763 PCR-GoTaqhotstart
8.1.1.2.1.7-pbpA PCR-GoTaqhotstart
8.1.1.2.1.8-pbpA PCR-J1-208 GoTaqhotstart
8.1.1.2.1.9-polC PCR-GoTaq
8.1.1.2.1.10-prs PCR-GoTaq
8.1.1.2.1.11-rarA PCR-GoTaq
8.1.1.2.2- PCR by Gene Name
8.1.1.2.2.1- Fact Sheet on ActA Differentiation PCR & Interpretation of Results
8.1.1.2.2.2- Gap PCR protocol for Listeria monocytogenes
8.1.1.2.2.3- Hly ab gene PCR for Listeria monocytogenes
8.1.1.2.2.4- inlA ORF & Gene Fragment PCR & Sequencing
8.1.1.2.2.5- Modified SigB PCR Protocol-Taq Gold 10uM primers
8.1.1.2.2.6- Multiplex PCR for inlH screening
8.1.1.2.2.7- Nested hly PCR for Listeria monocytogenes
8.1.1.2.2.8- Protocol for sequencing actA gene most polymorphic region
8.1.1.2.2.9- Protocol for Sequencing actA gene region with best discrimination
8.1.1.2.2.10- Protocol for Sequencing inlA gene region with the best discrimination
8.1.1.2.2.11- Prs PCR Protocol for Listeria monocytogenes
8.1.1.2.2.12- PurM PCR Protocol for lineage II Listeria monocytogenes
8.1.1.2.2.13- PurM PCR Protocol for Listeria monocytogenes
8.1.1.2.2.14- RibC PCR Protocol for Listeria monocytogenes
8.1.1.2.2.15- SigB PCR Protocol GoTaq
8.1.1.3-Salmonella PCRs
8.1.1.3.1-fimA PCR & DNA sequencing of Salmonella enterica
8.1.1.3.2-manB PCR & DNA sequencing of Salmonella enterica
8.1.1.3.3-mdh PCR & DNA sequencing of Salmonella enterica
8.1.1.3.4-7 Gene MLST for Salmonella
8.1.1.3.4.1-7 gene MLST for Salmonella- Primers and PCR
8.1.1.3.4.2-Salmonella 7 gene MLST Template
8.1.1.3.5-PCR detection of the presence or absence of antibiotic resistance genes in Salmonella
8.1.1.3.6- InvA colony PCR for Salm 4-13-10
8.1.1.3.7-PCR identification of common Salmonella serogroups
8.1.1.3.8-PCR determination of H1 and H2-antigens for Salmonella
8.1.1.4-PCRs for Other Organisms
8.1.1.4.1- E. coli 6-gene multiplex PCR
8.1.1.4.2- ipaH colony PCR for Shigella
8.1.1.4.3-SodA PCR Protocol for S. agalactiae
8.1.2-Phenotypic Characterization
8.1.2.1-Restriction Digest and Cloning of PCR amplified 16S rDNA
8.1.2.2-Semi-Quantitative Hemolysis Assay for Listeria
8.1.3-RLFP
8.1.3.1-Polymerase Chain Reaction- Restriction Fragment Length Polymorphism
8.1.4-Southern Blot
8.1.4.1-Southern Blotting by Electrophoretic Transfer and non-radioactive Detection
8.1.4.2-Southern Blotting
8.1.4.3-SouthernBlot Hybridization
8.2-DNA Labeling & Modification
8.2.1-3' end labeling of oligonucleotides
8.2.2-Kinasing and DIG labeling of LCR primer
8.2.3-Poly-T tailing of oligonucleotides
8.2.4-Protocol for Fluorescein labeling of oligonucleotides carrying an aminolink
8.2.5-Protocol for Geneclean (USB)
8.3-DNA Preparation, Purification & Quantification
8.3.1-Chelex DNA extraction from blood
8.3.2-Chelex DNA extraction from semen
8.3.3-Detailed Preparation of Chromosomal Listeria DNA (5_05_2011)
8.3.4-DNA Preparation from Listeria using Guanidinium Isothiocyanate
8.3.5-Listeria Lysis Methods and Procedures
8.3.6-PCR product purification using ExoSAP
8.3.7-PCR Purification Protocol for DNA Sequencing
8.3.8- Preparation of chromosomal Listeria DNA according to Flamm et al.
8.3.9-Preparation of chromosomal Listeria DNA
8.3.10-Quantification of Purified DNA by NanoDrop
8.3.11-Single Stranded DNA preparation from M13
8.3.12-Small-scale phenolchloroform extraction of chromosomal DNA from Listeria monocytogenes
8.4-DNA Recombination
8.4.1-Cloning of DNA Flanking Tn917-LTV3
8.4.2-Cloning of DNA Fragments
8.4.3-Cloning PCR products for Sequencing using pCR 2.1
8.4.4- Cloning Protocol for Transformation of E. coli DH5aF
8.4.5- Electroporation L mono
8.4.6- Electroporation of E coli
8.4.7- Electroporation of Mycobacterium paratuberculosis
8.4.8- General Cloning DNA
8.4.9- GUS promoter fusions in Listeria monocytogenes
8.4.10- Integration of pPL2 derivatives into L. monocytogenes 10403S
8.4.11- Listeria Genomic Alterations
8.4.12- Overview-Making a mutant in Listeria monocytogenes
8.4.13- Part II-Making a mutant in Listeria monocytogenes
8.4.14- Part III-Making a mutant in Listeria monocytogenes
8.4.15- Part IV-Making a mutant in Listeria monocytogenes
8.4.16-pMJG2 vector map
8.4.17-pMJG3 vector map
8.4.18-pMJG4 vector map
8.4.19- Procedure for cloning with pDH32
8.4.20-Whole Mutant- SoeingPCR for L. mono
8.5-Microarrays
8.5.1-Analyzing Microarrays
8.5.2-Creating Microarrays
8.5.3-Labeling RNA with Cy3Cy5 and Hybridization for Microarrays
8.5.4-Microarray Slide Blocking
8.6-Protein Methods
8.6.1-Assay for beta-galactosidase activity of B. subtilis transformed with lacZ reporter plasmid
8.6.2-Beta Galactosidase Assay
8.6.3-His tagged sigma factor protein purification protocol
8.7-RNA Prep & Analysis
8.7.1-DNase treatment and phenolchloroform extractions for high purity RNA
8.7.2-Isolation of RNA from Listeria monocytogenes infected mammalian cells
8.7.3-Preparation of infected tissue culture cells for bacterial RNA collection
8.7.4-Preperation of Listeria RNA
8.7.5-RNA extraction, clean-up and storage using Turbo DNase for TaqMan
8.7.6-RNA Prep with RNeasy Midi Kit instructions
8.7.7-RNeasy kit total RNA isolation from Listeria monocytogenes with on-column DNase treatment
8.7.8-RT-PCR for the detection of cytokine mRNA
8.7.9-Synthesis of large amounts of RNA
8.7.10-Taqman- Quantitative Real-Time RT-PCR Protocol
9- Food Microbe Tracker
9.1- Food Microbe Tracker Batch Upload & Help Guide
10- Tissue Culture
10.1-Caco-2
10.1.1- Listeria monocytogenes Caco-2 cell invasion assay
10.1.2- Maintenance of Caco-2 Cells_22NOV10
10.1.3- Salmonella Caco-2 cell invasion assay
10.2-Hela
10.2.1- Culturing Conditions, Splitting and Freezing of Hela
10.2.2- Tissue culture assay to quantify bacterial adhesion to HeLa cells
10.3-J774
10.3.1- J774 cells Culturing Conditions, Splitting and Freezing
10.3.2- Label Listerial Protein J774 Cells
10.3.3- Labeling of listerial proteins in J774 cells
10.4-L2 Mouse
10.4.1- Listeria monocytogenes Intercellular Growth Assay in L2
10.4.2- Mouse L cells Culturing Conditions, Splitting and Freezing
10.4.3- Passage of Mouse L Cells for Plaque Assay
10.4.4- Passage of Mouse L Cells for Plaque Assay
10.5-Other Cell Lines
10.5.1- Culturing Conditions, Splitting and Freezing of L929
10.5.2- Growth of Primary Sheep Neurons in Cell Culture
10.5.3- L. monocytogenes Infection of Primary Neuronal Cell Culture(DRG)
10.5.4- Lmono Intracellular Infection Assay in Fish Cells
10.5.5- PC12 cells Culturing Conditions, and Freezing
10.6-Tissue Culture Media & Reagents
10.6.1- Preparation of 0.1% Trypsin-EDTA_22NOV10