2017 Lab 2
- 1 Preparation/Fixation
- 2 Objectives
- 3 Health and Safety (H&S)
- 4 Three Main Techniques
- 5 Fresh Frozen
- 6 Precipitation
- 7 Aldehyde Cross-Linked
- 8 Other Fixation Considerations
- 9 Tissue Embedding
- 10 Histology Stains
- 11 2017 Group Projects
- 12 ANAT3231 Project Archive
- 13 References
- 14 External Links
- 15 2017 Course Content
This lab is introduction to histological techniques and tissue/cell fixation. The lab will also introduce Health and Safety (H&S) issues in relation to chemicals used in this process. More information is available from the School of Medical Sciences H&S webpage. Later analysis and immunhistochemistry will be covered in a future Laboratories.
Ideally we would like to look at dynamic cellular processes in living cells, but this is not always possible as many analytical techniques are not compatible with cell viability. There is also the question of being able to preserve and analyse the material at an appropriate time or all at once from a series of experiments. This is where "fixation" is a useful technique.
In general the Fixation process should:
- Preserve cell structure by prevention of tissue autodigestion (autolysis)
- Inhibits bacterial and fungal growth (preserves)
- Make the tissue resistant to damage during subsequent processing (hardy)
- Allow access of stains and antibodies (permeable)
It is critical to match the method of fixation with the intended analytical technique. Firstly, some types of analysis are totally incompatible with certain fixation techniques. Secondly, always consider that "artefacts" can be introduced by the actual fixation process.
- Brief understanding of chemical H&S issues
- Brief understanding of histological staining techniques
- Brief understanding of tissue preparation and sectioning
- Understanding of fixation techniques
Health and Safety (H&S)
- School of Medical Sciences, Health and Safety Consultation Committee
- "To facilitate a safe work environment by developing and documenting H&S programs to coordinate training of staff and students and by overseeing the implementation of H&S procedures and policies in the School of Medical Sciences."
- Australian Acts and Standards
- A Health and Safety Management System is a set of plans, actions and procedures to systematically manage health and safety in the workplace that is actively endorsed by a committed employer to achieve:
- Provision of a safe and health workplace and the prevention/reduction of illness and injury equally for employees and contractors.
- Identification of workplace hazards, assessment and control of all risks.
- Active involvement in health and safety matters by managers, supervisors and employees and their representatives.
- Provision of information and training for employees at all levels so they can work safely.
- Audit and review of the HSMS.
- UNSW UNSW Health and Safety Management System | Student Training | Policies
Safety Data Sheets (SDS)
- Safety Data Sheets (SDS) replace the original term and classification Material Safety Data Sheets (MSDS)
- Updated as part of "Globally Harmonized System of Classification and Labelling of Chemicals (GHS)"
- A set of standardised safety information prepared for each of the chemicals used within the laboratory.
- Each research laboratory is required to keep either a hardcopy or electronic copy of these MSDS's available within the laboratory.
- Before carrying out any new research technique, in particular for students, should be taken through the location and use of SDSs.
- the risks and hazards involved with specific chemicals.
- the correct storage, handling, labeling and disposal of each chemical.
- ideally they should keep an electronic copy or link to each of these SDS's for their own reference.
- There is currently no coordinated international standard and different countries may have different requirements.
SDS must state:
- a hazardous substance's product name
- the chemical and generic name of certain ingredients
- the chemical and physical properties of the hazardous substance
- health hazard information
- precautions for safe use and handling
- the manufacturer's or importer's name, Australian address and telephone number.
Note that while information found on internet chemical SDS pages may be very similar, international sites may not conform to Australian Worksafe format.
United Nations - Globally Harmonized System of Classification and Labelling of Chemicals
(GHS) The new system, which was called "Globally Harmonized System of Classification and Labelling of Chemicals (GHS)", addresses classification of chemicals by types of hazard and proposes harmonized hazard communication elements, including labels and safety data sheets. It aims at ensuring that information on physical hazards and toxicity from chemicals be available in order to enhance the protection of human health and the environment during the handling, transport and use of these chemicals. The GHS also provides a basis for harmonization of rules and regulations on chemicals at national, regional and worldwide level, an important factor also for trade facilitation.
|GHS08 Health Hazard|
|Of the 9 pictogram codes, this relates to systemic health hazard as well as reproductive and developmental effects.
Germ cell mutagenicity (State route of exposure if it is conclusively proven that no other routes of exposure cause the hazard)
Carcinogenicity (State route of exposure if it is conclusively proven that no other routes of exposure cause the hazard)
Reproductive toxicity (state specific effect if known)(state route of exposure if it is conclusively proven that no other routes of exposure cause the hazard)
- Commercial Example - Sigma - Paraformaldehyde | SDS
- UNSW Chemical Safety
- UNSW ChemAlert
- PubChem - PubChem provides information on the biological activities of small molecules.
- When dealing with biological materials, in particular human specimens, are a set of precautions designed to prevent transmission of human immunodeficiency virus (HIV), hepatitis B virus (HBV), and other bloodborne pathogens when providing first aid or health care. These precautions should also be used when carrying out basic research on these tissues.
- Universal precautions involve the use of protective barriers (PPE, personal protective equipment) such as gloves, gowns, aprons, masks, or protective eyewear, which can reduce the risk of exposure of the health care worker's skin or mucous membranes to potentially infective materials. In addition, under universal precautions, it is recommended that all health care workers take precautions to prevent injuries caused by needles, scalpels, and other sharp instruments or devices.
Three Main Techniques
Techniques for tissue and cell fixation.
- Fresh Frozen
- Aldehyde Cross-linked
See also videos
- Used in surgical biopsies of tissue and research - cells are preserved and hardened by rapid freezing
- Advantages - rapid processing, retention of some enzyme and protein function, retention of epitopes, retention of fat
- Disadvantages - requires a cryotome (freezing microtome) for sectioning, thicker sections (8+ micrometers), tissue distortion with cutting, thawing can degrades tissue.
|See also Using Unfixed, Frozen Tissues to Study Natural Mucin Distribution PMID 23023050|
- Immersion in cooled organic solvents- methanol or acetone or acids
- Acidic precipitation does not preserve cellular structures well, rarely used (except for specific protocols, such as mitotic chromosome spreads)
- Fixation by precipitation does not preserve the three-dimensional organization of specimens, therefore not recommended for confocal microscopy.
- Cultured cells fixed with cold methanol shrink by as much as 50%.
- Advantages- speed -(fixation usually taking a few minutes), retention of epitopes (antibody binding sites) not covalently modified as they might be with aldehyde fixation,
simultaneous permeabilization of cellular membranes (no need for detergent-treatment), precipitation will not introduce autofluorescence
(Text modified from Cell Biology Applications of Fluorescence Microscopy by Stephen Rogers)
- Precipitation fixation
- Methanol dehydrates, coagulates and precipitates cellular proteins, nucleic acids and carbohydrates
- The process involves no covalent bonding between methanol fixative and tissue components
- Permeabilises cells
- Immunochemistry - some epitopes are very sensitive to methanol as it can disrupt epitope structure. (alternative is acetone for permeabilization if required).
- will also permeabilize.
- -20C, 4C or RT.
- fresh acetone is better, as open acetone absorbs water and increases backgrounds.
- Carnoy’s fixative
- rapid tissue penetration (small tissue pieces in minutes not hours)
- can damage tissues when transferred from aqueous solution (extreme hydrophobicity of chloroform and rapid dehydration)
- Chloroform 30%
- Ethanol (100%) 60%
- Acetic Acid (Glacial) 10%
- Aldehydes form covalent bonds between adjacent amine-containing groups through a Schiff acid-base reaction.
- Cross-links are generated between several reactive groups (mainly -NH2 groups) such as found in protein lysine residues.
- good fixatives for proteins and nucleic acids.
- most commonly used aldehydes are formaldehyde (formalin), paraformaldehyde and glutaraldehyde
- The degree of cross-linking produced in a tissue is also proportional to fixation time.
- Aldehydes are suspected carcinogens, to be used only in well-ventilated areas or fume hoods and contact with skin or eyes avoided
- Aldehyde Cross-Link fixation
- Formalin is a 37% aqueous solution of formaldehyde, which fixes by cross-linking like other aldehyde fixatives and is suitable for most histological purposes
- Neutral buffered formalin (fixation time 12-24 hours) is preferred to formol-saline (a single 10% solution of formalin in 9% aqueous NaCl) as formalin pigment is avoided
- Specimens may be stored in this fluid and the solution is isotonic.
- Can be combined with a precipitation step (acetone etc) for permeabilization
- Synonyms: bvf, FA, fannoform, formalith, formalin, formalin 40, formic aldehyde, formol, fyde, hoch, karsan, lysoform, methyl aldehyde, methylene glycol, methylene oxide, methanal, morbicid, oxomethane, oxymethylene, paraform, polyoxymethylene glycols, superlysoform
- Molecular formula: CH2O CAS No: 50-00-0 MSDS: Formaldehyde MSDS
- Aldehyde Cross-Link fixation
- Used generally fresh
- generates less fluorescent artifacts than formaldehyde
- preferred technique for many uses: immunochemistry, in situ hybridization, cell staining
- Immunochemistry - fixation for more than 10-15 min will cross-link the proteins to the point where antigen retrieval may be required.
Synonyms: paraform, polyoxymethane, polymerised formaldehyde, alacide, flo-mor, formagene
Molecular formula: (CH2O)n CAS No: 30525-89-4
- Aldehyde Cross-Link fixation
Other Fixation Considerations
- Detergents are not really "fixative", but a number of different types are often used in the fixation process.
- Detergents can selectively remove components from the material to be fixed or already fixed, as a method of preserving or accessing antigenic sites that may be blocked or effected by the fixation process itself.
- Detergent's charge (nonionic, anionic, cationic, zwitterionic or amphoteric) is determined by the charge of the emulsifier or surfactant.
- The 2 major detergent classes
- ionic detergents (anionic, cationic)
- nonionic detergents (uncharged, hydrophilic head groups) Tween, Triton, and the Brij series
- Generally a phosphate buffered saline (PBS) is used but wil differ for some specific fixatives. Changes in osmolality can affect tissue structure and introduce artefacts.
- hypertonic solutions may cause cells to shrink.
- hypotonic solutions may cause the cells may swell and burst.
- Cell cultures are usually only a layer or two of cells thick and are generally not embedded in a support media, except for electron microscopic (EM) preparation.
- This tissue thickness also means that fixation can be quite rapid.
- Paraffin waxes can allow easy long-term tissue storage and ease of sectioning by supporting the tissue during cutting.
- Often requires a large number of steps in fixation, series of steps for embedding, sectioning and finally removal of embedding matrix for staining.
- There are automated paraffin embedding systems that remove many of the preparation steps.
- Can sometimes not be suitable for immunochemistry fluorescence techniques.
- Possible freezing artifact, ice crystal formation if not controlled chilling. Freezing can be critical.
- vapor phase of liquid nitrogen
- thawing isopentane
- OCT (Optimal Cutting Temperature) commercial Cryo Embedding Medium
- Not suitable for large amounts, by volume) of tissue (usually 0.5 cm x 0.5 cm x 0.5 cm max)
You would have previously covered Histology stains in your Histology course. The information below and on the linked page is provided for revision purposes.
|Common Stains and Their Reactions|
|Haematoxylin||mucins - light blue|
|Eosin||colloid - pink muscle - red|
|Van Gieson||muscle: yellow/browncartilage - pink|
|Verhoeff's Elastin||elastic fibres - black|
|Silver Impregnation||reticular fibres - black|
|Nuclear Fast Red|
|Gomori's Trichrome||keratin - redmuscle - purple/red|
|Heidenhain's Azan||muscle - red|
|Osmium tetroxide||myelin, lipids - black|
|Alcian Blue||mucins, - blue|
|Periodic acid-Schiff's reagent (PAS)||mucins, glycogen, glycocalyx - magenta|
|PTAH||muscle bands - blue|
|Masson's Trichrome||cartilage, mucins - blue or green; muscle - red|
|Luxol Fast Blue||myelin - blue~|
|Aldehyde Fuchsin||elastic fibres, mast cells - deep purple|
|Gallocyanin||nucleic acids, Nissl granules - dark blue|
|Romanowsky(e.g. Leishman's stain)||acidophils - redbasophils - blueazurophilic - purple|
|Aldehyde Pararosanilin||elastic fibres - purple|
- UK - Haematoxylin, USA - Hematoxylin
- Stains nuclei blue to dark-blue.
- Stains the matrix of hyaline cartilage, myxomatous, and mucoid material pale blue.
- Stains myelin weakly but is not noticeable if combined with eosin stain.
- Stains cytoplasm pink to red; red blood cells are also bright red.
- Common counterstain to hematoxylin.
- Stain intensity varies with the formula as well as the fixative.
A bacterial staining procedure using crystal violet and pink safranin counterstain that generally divides bacteria into either gram-positive or gram-negative and useful for considering associated pharmacology. The procedure was named after Hans Christian Gram (1853 - 1938).
- Purple crystal violet stain is trapped by layer of peptidoglycan (peptidoglycan forms outer layer of the cell).
- Outer membrane prevents stain from reaching peptidoglycan layer in the periplasm.
- outer membrane is composed of four major components: lipopolysaccharide, phospholipids, beta-barrel proteins, and lipoproteins.
- outer membrane then permeabilized.
- Pink safranin counterstain is trapped by peptidoglycan layer.
2017 Group Projects
|Group 1||Group 2||Group 3||Group 4|
This week we will begin the group project work. The main topic will be "Cells of the Pancreas". Together with your group members you should selecta a specific cell type from the pancreas and describe the specific cell type cell biology. Some examples of possible sub-heading could include: structure, function, history, development, abnormalities, signaling, cell-matrix interactions, current research.
Cells of the Pancreas
- The Endocrine Pancreas - pancreatic islets (islets of Langerhans)
- The Exocrine Pancreas
- Nussey S, Whitehead S. Endocrinology: An Integrated Approach. Oxford: BIOS Scientific Publishers; 2001. Chapter 2, The endocrine pancreas. Available from: https://www.ncbi.nlm.nih.gov/books/NBK30/
- Pandol SJ. The Exocrine Pancreas. San Rafael (CA): Morgan & Claypool Life Sciences; 2010. Available from: https://www.ncbi.nlm.nih.gov/books/NBK54128/ doi: 10.4199/C00026ED1V01Y201102ISP014
Lab 2 Individual Assessment
- Identify a chemical SDS and the risks and hazards of that chemical in text. Add a link to the original SDS
- Select 4 reference papers papers related to your selected group project topic sub-section. Read the research papers and write a brief description of their findings and relevance to the selected topic sub-section. The reference along with your description should then be pasted on both your group discussion page and your own personal page.
This assessment will be due by the next lab (Lab 3).
ANAT3231 Project Archive
2016 Blood Cells: Group 1 - Megakaryocytes | Group 2 - Red Blood Cells | Group 3 - Lymphocyte B-Cell | Group 4 - Natural Killer Cells | Group 5 - Mast Cells | Group 6 - Lymphocyte T-Cell | Group 7 - Eosinophils
2015 Extracellular Matrix: Group 1 - Small Leucine-Rich Proteoglycans | Group 2 - Integrins | Group 3 - Elastic Fibres | Group 4 - Fibronectin | Group 5 - Laminin | Group 6 - Collagen | Group 7 - Basement Membrane
2013 Cell Division: Group 1 - Regulation of Cell Division | Group 2 - Cytokinesis | Group 3 - Golgi Apparatus | Group 4 - Spindle Apparatus | Group 5 - Nuclear Envelope | Group 6 - Anaphase | Group 7 - Mitochondria
2012 Signaling: Group 1 - Testosterone | Group 2 - Vascular Endothelial Growth Factor | Group 3 - Extrinsic Apoptosis | Group 4 - Notch | Group 5 - Wnt-Beta catenin | Group 6 - Insulin | Group 7 - G protein (beta adrenergic) | Group 8 - Leukocyte Extravasation | Group 9 - p53
2010 Cell Methods: Group 1 - Fluorescent-PCR | Group 2 - RNA Interference | Group 3 - Immunohistochemistry | Group 4 - Cell Culture | Group 5 - Electron Microsopy | Group 6 - Confocal Microscopy | Group 7 - Monoclonal Antibodies | Group 8 - Microarray | Group 9 - Fluorescent Proteins | Group 10 - Somatic Cell Nuclear Transfer
Essential Cell Biology
Molecular Biology of the Cell
Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter New York and London: Garland Science; c2002
Molecular Cell Biology
Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E. New York: W. H. Freeman & Co.; c1999
The Cell- A Molecular Approach
Cooper, Geoffrey M. Sunderland (MA): Sinauer Associates, Inc.; c2000
Search Online Textbooks
- "tissue fixation" Molecular Biology of the Cell | Molecular Cell Biology | The Cell- A molecular Approach | Bookshelf
- "cell fixation" Molecular Biology of the Cell | Molecular Cell Biology | The Cell- A molecular Approach | Bookshelf
- PubMed is a service of the U.S. National Library of Medicine that includes over 18 million citations from MEDLINE and other life science journals for biomedical articles back to 1948. PubMed includes links to full text articles and other related resources. PubMed
- PubMed Central (PMC) is a free digital archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health (NIH) in the National Library of Medicine (NLM) allowing all users free access to the material in PubMed Central. PMC
- Online Mendelian Inheritance in Man (OMIM) is a comprehensive compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM
- Entrez is the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others Entrez
- "tissue+fixation" PubMed reviews | PubMed all articles | PMC reviews | PMC all articles | OMIM | Entrez all databases
- "cell+fixation" PubMed reviews | PubMed all articles | PMC reviews | PMC all articles | OMIM | Entrez all databases
- Sample preparation for scanning electron microscopy of plant surfaces--horses for courses. Pathan AK, Bond J, Gaskin RE. Micron. 2008 Dec;39(8):1049-61. Epub 2008 May 27. Review. PMID 18586502
- Correlated light and electron microscopy of the cytoskeleton. Auinger S, Small JV. Methods Cell Biol. 2008;88:257-72. Review. PMID 18617038
- Tissue microdissection. Erickson HS, Gillespie JW, Emmert-Buck MR. Methods Mol Biol. 2008;424:433-48. Review. PMID 18369881
External Links Notice - The dynamic nature of the internet may mean that some of these listed links may no longer function. If the link no longer works search the web with the link text or name.
2017 Course Content
Lectures: Cell Biology Introduction | Cells Eukaryotes and Prokaryotes | Cell Membranes and Compartments | Cell Nucleus | Cell Export - Exocytosis | Cell Import - Endocytosis | Cytoskeleton Introduction | Cytoskeleton - Microfilaments | Cytoskeleton - Microtubules | Cytoskeleton - Intermediate Filaments | Cell Mitochondria | Cell Junctions | Extracellular Matrix 1 | Extracellular Matrix 2 | Cell Cycle | Cell Division | Cell Death 1 | Cell Death 2 | Signal 1 | Signal 2 | Stem Cells 1 | Stem Cells 2 | Development | 2017 Revision
Dr Mark Hill 2015, UNSW Cell Biology - UNSW CRICOS Provider Code No. 00098G