Biofluorimetry Lab
Dipartimento di Fisiopatologia MedicaUniversity of Rome 'La Sapienza'page created and maintained by Leopoldo Silvestroni & Simonetta Palleschi
last update May 3, 2010
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Lab equipments, techniques and protocols |
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Lab animals & Safety |
Acids and bases: strengths of common solutions
Acronyms of analytical instrumentation and techniques
Actin:
nonmuscle sources, preparation
Alkaline phosphatase and phospholipase C Assays
Antibodies:
affinity purification of antibodies (1) (2)
binding to protein A and protein G
product guide (PDF file, 505K)
production (monoclonal & polyclonal)
purification (1) (2) (3)
purification by affinity binding to proteins bound to nitrocellulose
Autoradiography and fluorography:
32P Autoradiographic exposure times
Balance:
Blood smear preparation and staining
Buffers (see Solutions below)
Calcium (45Ca2) uptake analysis
Centrifugation/ultracentrifugation:
percoll (equilibrium density)
sucrose (density and refractive indexes)
Chemiluminescence & Biochemiluminescence:
qualitative analysis of chr. data
quantitative analysis of chr. data
technical tips
affinity chromatography (1) (2):
peptide coupling to Affigel-10 Resin
field flow fractionation
forum:
liquid chromatography
gas chromatography
hyphenated techniques
data systems
Capillary Column Installation
Guide
capillary GC
Column Characteristics calculator
Column Selection Guide
columns
flow control
GC/MS QTmovie (1)
(2)
Kovats retention index
McReynolds constants
Pressure Calculator
Pressure Conversion Factors
Setting Dead Time for Optimum Linear Velocity
Splitless Injection Animation
temperature programming
HPLC:
reversed phase for Peptides (PDF)
ion exchange chromatography (1) (2) (3)
introduction
types of interactions
solvent selection
Snyder method
gradient elution
troubleshooting guide (1)
(2)
(3)
Colloidal gold:
Comet assay:
after single-cell electrophoresis (PDF)
introduction
protocols:
alkaline comet assay (pH > 13) (1) (2)
neutral comet assaY (pH 7-10)
image analysis software
Covalent labeling of biomolecules
Coverslip coating (polylysine) see Slide
Distillation
Distillation theory &
practice
agarose gel electrophoresis (1 basic method) (2) (3)
capillary electrophoresis (1) (2) (QTime - ShockW)
capillary electrophoresis injection evaluation (QTime - ShockW)
capillary electrophoresis modes (QTime - ShockW)
documentation by Polaroid camera
formaldehyde gel electrophoresis and non-radioactive northern blotting of RNA
mass spectrometry of tryptic digests from electroph. gels
protein transfer to PVDF membranes
SDS-PAGE (1) (2) (minigel & semidry transfer):
databases of 2D gel maps of proteins (27 links)
pouring and running protein gels/electrotransfer
separation of protein standards
staining with coomassie blue (1) (2)
staining with ethanol-based coomassie blue
staining with silver (1) (2) (3) (4)
Electroporation of mammalian cells
development guide (PDF file, 152k)
product guide (PDF file, 160k)
reference guide (PDF file, 672k)
successful running (PDF file, 245k)
troubleshooting guide (PDF file, 66k)
Experimental methods (concepts)
Extraction with supercritical fluids
FACS
standard
protocol
Flasks in practice (volumetric)
centrifugation: simulation of filtering centrifuge
constant pressure filtration
constant rate filtration
sedimentation: continuous sedimentation - thickening
solid-liquid separation
specific surface area per unit volume
Flow cytometry (87 links) (commonly used fluorochromes)
Fluorescence: see also our Fluorescence / Spectroscopy and Microscopy pages
fluorescein labeling of proteins (1) (2)
green fluorescent protein (GFP) applications
Ganglioside purification (micro scale)
Getting started and staying organized at the bench
Glass properties & technical data
Glutaraldehyde conjugation of oligopeptides to proteins
Glycolipids separated by TLC: immunostaining
Glycoprotein deglycosylation using endoglycosidases
Histone H1 kinase activity assay
Immunoprecipitation buffers & protocol
In-gel tryptic digest for mass spectrometry (from electrophoretic gels)
Lipid analysis (1, Thin layer chromatography) (2, Gas liquid chromatography)
Lipid separation and quantification by gas chromatography
Lipid separation and quantification by TLC
Lipid Transmethylation and extraction of methyl derivatives
Lipoproteins isolation (from plasma) and analysis
Log P and pKa measurements and their use
Mass spectrometry (see Spectroscopy below)
Metric system:
metric square and cube units conversion
Micro-scale isolation and purification of gangliosides
Molarity, molality, or normality?
Molecular weight calculator - interactive
NIOSH Manual of Analytical Methods
Nuclear extract preparation (1 - 2 - 3)
Peptide mapping with 2D Western blot
Peptide separations on a stable, aqueous-compatible C18 column (PDF)
pH readings in practice (digital) (analogic)
Phosphate assay (molybdate-based) (1) (2)
Phosphoamino acid(32P) analysis in SDS PAGE
Phosphoamino acid analysis of non-TCA precipitable proteins from gel slices
differential-pulse polarography
pH meters
Proteases, substrates and inhibitors assays
Proteins:
acetylation (or succinylation) of amino groups
analysis by immunoprecipitation
assays by:
Biuret (1)
Bradford (1) (2) (3) (4, microtiter plastes) (5) (6)
dot blotting, semi-quantitative
Lowry (1) (2) (3) (4 for membrane extracts) (5 for SDS)
UV spectrophotometry at 280 nm (1) (2) and 205 nm
databases:
3D structure classification browsers
locating 3d structure information
online protein structure courses
protein sequence patterns and motifs
secondary structure prediction
determination, comparison of different methods
microarrays: technology adoption and utilization
product guide (PDF file, 181K)
radioiodination of cell surface proteins
radioiodination of protein in solution
subcellular fractionation from cells
Quantitative pipetting and spectrophotometry
radioiodination of cell surface proteins
radioiodination of protein in solution
Receptor binding: basic principles and techniques (PDF)
Scientific method (1) (2)
Sephadex G-50 spun column purification
Serum preparation from whole blood
titration-Henderson-Hasselbalch
Significant figures & scientific notation (expanded in Analysis of data and Statistics page)
Single component solutions (calculator)
Single vesicle analysis (Optical Trap)
Slide (microscopy) coating with polyacrylamide substrates
Slide (microscopy) coating with poly-L-lysine and silane
Slide (microscopy) preparation (washing and polylysine coating)
Slide (microscopy) silanization
Solutions & solution recipes:
acids and bases: strengths of common solutions
blocking buffer stock solution for Western
buffer calculator (java)
chloroform-isoamyl alcohol mix (24:1)
Church prehybridization buffer
concentration measurements and preparation
CTAB/NaCl (hexadecyltrimethyl ammonium bromide)
denaturation solution 2 (0.4M NaOH/1M NaCl)
DNA digestion: core reaction buffers
DNA digestion: enzyme dilution buffer
eluotropic strength of solvents on various sorbents
hybridization solution (Zappe)
IPTG, isopropyl-á-D-thio-galactopyranoside
lauryl sulphate, see sodium dodecyl sulphate
media, solutions and stains (also fluorescent) for cell biology
minimal medium 5x salts, E. coli
molecular weight – g/mol - calculator (java)
Mungbean nuclease dilution/storage buffer
Mungbean nuclease reaction buffer
phenol (buffered pH 7.6, 10mM Tris)
phosphate (sodium) buffer chart
Reagents and Standards Preparation and Documentation
SDS, see sodium dodecyl sulphate
ST1 Southern transfer solution 1
ST2 Southern transfer solution 2
ST3 Southern transfer solution 3
various salts in common buffers:
various salts calculator (part 1, part 2) (another)
X-gal, 5-bromo-4-chloro-3-indolyl-á-D-galactoside
Spectroscopy: Fluorescence / Spectroscopy and Chemistry pages
atomic:
atomic absorption spectroscopy (QTmovie)
atomic fluorescence spectroscopy
electron paramagnetic resonance (EPR, ESR)
electron:
X-ray absorption spectroscopy (QTmovie)
X-ray photoelectron spectroscopy
in general:
history
limit of detection (PDF)
laser:
cavity-ringdown laser absorption spectroscopy
intracavity-absorption spectroscopy
mass:
electrospray mass spectra interpretation
ion-cyclotron resonance Fourier transform
1H NMR interpretation tutorial
ultraviolet/visible spectroscopy
Stoichiometry (see also our Chemistry page)
differential-scanning calorimetry
Titration in practice (QTmovie)
Tubulin preparation (large scale)
Units and measures (expanded in Data analysis and Statistics)
Ultrafiltration cells (stirred, Amicon)
Vacuum portal
linear sweep
Western Blotting (1) (2) (3) (4) (5) (6) (7) (8):
band visualization with ecl & iodinated proteina
buffers
histones
troubleshooting (1) (2) (3)
visualization with ECL instead of iodinated Protein A
Alkaline Phosphatase Conjugates
sequence of a complete run:
membrane protein extraction from tissue
total protein extraction from tissue
electrophoretic transfer to PVDF membranes
coomassie brilliant blue
Knockout Mice - What is a knockout mouse?
Transgenic animals:
basic research and biotechnology
making a genetically modified animal
the illuminating power & controversy
restraint and handling of animals
guidelines for the prevention, assessment and relief of pain and distress in laboratory animals
guidelines for the use of anesthetics, analgesics and tranquilizers in laboratory animals
principles of aseptic technique
Work in progress….
Ethidium Bromide Decontamination (1) (2) (3) (4)
benchmark dose technical guidance document
chemical and other safety information
chemical labeling do's and don'ts
chemical labs safety (44 items)
chemical safety graphics
chemical safety manual
chemical storage area clining up
epoxy resin tabletops refinishing
eye injury picture sites (1) (2) (3)
faq:
cleanup and disposal of mercury
how to store chemicals properly
maintenance tips for acid storage cabinets
gas cylinder storage and handling
general laboratory health and safety
glossary of risk assessment-related terms
gloves resistance to chemicals: by glove material by chemical
guidelines for reproductive toxicity risk assessment
guidelines for neurotixicity risk assessment
guidelines for working with hazardous substances
hazardous and toxic substances
health risk assessment of chemical mixtures
lab safety manual (1) (2)
multiple iris substance report generation
niosh pocket guide to chemical hazards
noise and hearing loss prevention: niosh power tools database
occupational health guidelines for chemical hazards
personal protective equipment program
protective clothing for vapor and splash protection
recommendations for chemical protective clothing (a-z list from niosh)
basic chemical classifications
chemical accident prevention (environment)
chemical carcinogens (A-Z list)
chemical toxicity abbreviations
chemicals entry and fate in humans
chemicals which may form peroxides during storage
colour codes for compressed gas cylinders (Europe)
explosion & explosives:
A-Z terminology
compounds involved in unexpected explosions
shock-sensitive material lists (1) (2)
fire safety and fire extinguishers
gases A-Z lists (1 PDF) (2) (3)
gloves resistance to chemicals: by glove material by chemical
material safety data sheets:
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
reference links by chemical name (1) (2)
materials incompatible with widely-used chemicals
radioactivity decontamination procedures
Safety, Storage, and Disposal of Chemicals (FAQ)
Security of Hazardous Materials
Standard Operating Procedures (SOP's)
Storage and handling of laboratory chemicals
Where and why science accidents occur
Main sources for thie page:
biological procedures online - BioChemHub - CDC - cell biology techniques - colorimetric assays basics - Experimental Bioscience - HOSHA
Integrated Risk Information System: IRIS Substance A-Z List
laboratory methods - laboratory protocols - LabSafety - NIOSH - protocol books - virtual chemistry library