Refinement Database

Database on Refinement of Housing, Husbandry, Care, and Use of Animals in Research

This database, created in 2000, is updated every four months with newly published scientific articles, books, and other publications related to improving or safeguarding the welfare of animals used in research.

Tips for using the database:

  • This landing page displays all of the publications in the database.
  • Use the drop-down menus to filter these publications by Animal Type, Setting, and/or Topic.
  • Clicking on a parent category (e.g., Rodent) will include publications relating to all the items in that category (e.g., Chinchilla, Gerbil, Guinea Pig, etc.).
  • You may also add a keyword to further narrow your search.
  • Please note that at this time, only publications dated 2010 or later (with some exceptions) can be filtered by Animal Type and Topic, and only publications dated 2020 or later (with some exceptions) can be filtered by Setting. Most publications older than 2010 can only be searched by keyword. 
Philippe, C., Vergauwen, L., Huyghe, K. et al. 2023. Chronic handling stress in zebrafish Danio rerio husbandry. Journal of Fish Biology 103(2), 367–377.

The zebrafish (Danio rerio, Hamilton, 1822) is one of the most important fish model species in scientific research, with millions of fish housed in laboratory animal facilities around the world. During husbandry, it is necessary...

Shishis, S., Tsang, B., Ren, G. J. et al. 2023. Effects of different handling methods on the behavior of adult zebrafish. Physiology & Behavior 262, 114106.

The zebrafish is an important biomedical research organism. In most research, zebrafish are removed from their home tank and subsequently their phenotype is measured. The method of handling the fish, however, may significantly affect a...

Buckmaster, C. L., Levesque, D., LaFollette, M. et al. 2022. Five hot topics in refinement of nonhuman primate neuroscience research. Laboratory Animal Science Professional 10(1) (January/February), 24-26.

Members of the North American 3Rs Collaborative (NA3RsC) refinement initiative have chosen to summarize developments in five hot topics of interest: 1. Tips for welfare-friendly transport, chairing, and restraint; 2. Guidance on refining food and...

Jang, J. Y., Liang, T., Kim, M.-K. et al. 2022. A rapid and noninvasive method that extracts polymerase chain reaction-ready genomic DNA from adult zebrafish. Zebrafish 19(4), 160-164.

Genotyping usually entails analysis of the products of polymerase chain reaction (PCR) carried out with genomic DNA (gDNA) as template, and is employed for validation of mutant or transgenic organisms. For genotyping of adult zebrafish...

Sørensen, D., Cloutier, S., Gaskill, B. (Eds.). 2021. Animal-centric Care and Management - Enhancing Refinement in Biomedical Research. CRC Press, Boca Raton, FL.

The concept of the 3Rs (Refinement, Reduction and Replacement) has been used as a framework for improving the welfare of laboratory animals for the last half century. By establishing an animal-centric view on housing and...

Falendysz, E. A., Calhoun, D. M., Smith, C. A. et al. 2020. Outside the box: Working with wildlife in biocontainment. ILAR Journal 61(1), 72-85.

Research with captive wildlife in Animal Biosafety Level 2 (ABSL2) and 3 (ABSL3) facilities is becoming increasingly necessary as emerging and re-emerging diseases involving wildlife have increasing impacts on human, animal, and environmental health. Utilizing...

Tilley, C. A., Carreño Gutierrez, H., Sebire, M. et al. 2020. Skin swabbing is a refined technique to collect DNA from model fish species. Scientific Reports 10(1), 18212.

Model fish species such as sticklebacks and zebrafish are frequently used in studies that require DNA to be collected from live animals. This is typically achieved by fin clipping, a procedure that is simple and...

McIntosh, M. K., Armitage-Brown, B., Levy, R. 2019. Refinements of equipment and methodology to reduce risk during pole-guided chair transfer of nonhuman primates. JAALAS 58(4), 462-468.

Neurophysiologic studies of NHP commonly involve their transfer from a housing enclosure to a laboratory by using a mobile chair. This transfer should be performed in a manner that is safe and minimizes stress for...

Stevens, C. 2019. Refining handling for small laboratory fishes. Animal Technology and Welfare 18(3), 191-193.

Fishes in captivity, such as those used in laboratory research, may experience handling on a regular basis. In the laboratory, handling is usually done with dip-nets, and involves pursuit, confinement and capture and removal of...

Lambert, C. J., Freshner, B. C., Chung, A. et al. 2018. An automated system for rapid cellular extraction from live zebrafish embryos and larvae: Development and application to genotyping. PLOS ONE 13(3), e0193180.

Zebrafish are a valuable model organism in biomedical research. Their rapid development, ability to model human diseases, utility for testing genetic variants identified from next-generation sequencing, amenity to CRISPR mutagenesis, and potential for therapeutic compound...

O’Rourke, D. P., Baccanale, C. L., Stoskopf, M. K. 2018. Nontraditional laboratory animal species (cephalopods, fish, amphibians, reptiles, and birds). ILAR Journal 59(2), 168-176.

Aquatic vertebrates and cephalopods, amphibians, reptiles, and birds offer unique safety and occupational health challenges for laboratory animal personnel. This paper discusses environmental, handling, and zoonotic concerns associated with these species.

Breacker, C., Barber, I., Norton, W. H. J. et al. 2017. A low-cost method of skin swabbing for the collection of DNA samples from small laboratory fish. Zebrafish 14(1), 35-41.

Fin clipping of live fish under anesthesia is widely used to collect samples for DNA extraction. An alternative, potentially less invasive, approach involves obtaining samples by swabbing the skin of nonanesthetized fish. However, this method...

Lawton, S. 2017. Do Buccal swabs from Zebrafish give enough of a sample of DNA to be used as a viable non-invasive method of genotyping? Animal Technology and Welfare 16(3), 155-164.

The zebrafish has become a valuable research model within the laboratory. Currently the proven method of genotyping involves taking a tail fin clip from the fish to gain the sample. This involves surgically removing a...

Breacker, C., Tilley, C. 2017. DNA sampling by skin swabbing for Zebrafish (Danio rerio) and sticklebacks (Gasterosteus aculeatus). Animal Technology and Welfare 16(3), 211-213.

Fin clipping of live fish under anaesthesia is widely used to collect tissues samples for DNA extraction. However, this technique raises a number of ethical concerns, since the use of anaesthetic and/or physical fin damage...

Lidster, K., Readman, G. D., Prescott, M. J. et al. 2017. International survey on the use and welfare of zebrafish Danio rerio in research. Journal of Fish Biology 90(5), 1891-1905.

A survey was conducted regarding zebrafish Danio rerio use for scientific research with a focus on: anaesthesia and euthanasia; housing and husbandry; breeding and production; refinement opportunities. A total of 98 survey responses were received...

McMillan, J. L., Perlman, J. E., Galvan, A. et al. 2014. Refining the pole-and-collar method of restraint: Emphasizing the use of positive training techniques with rhesus macaques (Macaca mulatta). JJAALAS 53(1), 61-68.

The pole-and-collar method is one of several techniques that enable the safe transfer of a nonhuman primate from its home environment into a restraint chair without the need for sedation. It has been used within...

Andrews, C. 2014. Using positive reinforcement training to refine daily medical treatment of a cynomolgus macaque. American Association for Laboratory Animal Science [AALAS] Meeting Official Program, 565-566. (Abstract #P63).

Medical care of nonhuman primates in a laboratory setting can be challenging due to the safety concerns inherent in handling conscious animals. A mature, adult male cynomolgus macaque presented with a chronic foot condition that...

Bliss-Moreau, E., Moadab, G., Theil, J. 2013. Efficient cooperative chair training. American Journal of Primatology 75(S1), 67. (36th Meeting of the American Society of Primatologists Scientific Program, Abstract #118)

Traditional procedures for training nonhuman primates to be restrained in chairs typically involve very little use of positive reinforcement. In this talk, we detail a refined chair training procedure which uses a mix of positive...

NC3Rs, University of Stirling. 2011. Common Marmoset Care [Online resource].

The three main divisions of 'marmosetcare.com' aim respectively to promote: an understanding of the range of behaviour in this species, placing this behaviour in the context of its natural habitat and promoting good welfare in...

Watts, A. 2010. Thinking outside the box in box training. Tech Talk [The Newsletter for Laboratory Animal Science Technicians] 15(2), 3.

At the Oregon National Primate Research Center, we train animals to enter transfer boxes using positive reinforcement training (PRT), a type of training in which the trainer reinforces desired behaviors (such asentering the transfer box)...

Moreau, E. 2010. To squeeze or not to squeeze? A Discussion on LAREF, September, 2009. Laboratory Primate Newsletter 49(2), 3-4.

The discussion was started by the following questions: "Is the squeeze-back mechanism more or less stressful than the pole and collar system for removing a macaque from his cage for an IM (intramuscular) injection?" and...

McMillan, J. L., Galvan, A., Wichmann, T. et al. 2010. The use of positive reinforcement during pole and collar training of rhesus macaques (Macaca mulatta). American Association for Laboratory Animal Science [AALAS] Meeting Official Program, 705-706 (Abstract #P78).

The pole and collar method enables safe transfer of a monkey from their home environment to a restraint chair without sedation. The ability to conduct procedures with a conscious and cooperative subject is cost effective...

Egeler, J. L., Hoekwater, S., Hoffman, H. D. 2010. A novel approach for utilizing large group-housing style cages for nonhuman primates in toxicology studies. American Association for Laboratory Animal Science [AALAS] Meeting Official Program, 716 (Abstract #P110).

The ability to provide permanent group-housed caging for nonhuman primates involved in toxicology research is quickly becoming an important step in improving the overall quality of life for these animals. This type of caging offers...

LAREF [Laboratory Animal Refinement and Enrichment Forum] 2007. Chapter 7.4. Pole-and-collar training of macaques. In: Making Lives Easier for Animals in Research Labs: Discussions by the Laboratory Animal Refinement & Enrichment Forum. Baumans, V., Coke, C., Green, J., Moreau, E., Morton, D., Patterson-Kane, E., Reinhardt, A., Reinhardt, V., Van Loo, P. (eds), 127-130. Animal Welfare Institute, Washington, DC.

While strictly using positive reinforcement and applying patient gentle-firmness, most macaques can be trained to cooperate during the pole-attachment-chairing procedure. Some cannot be trained, because they have problems overcoming their often-legitimate mistrust of humans.

Reinhardt, V. 2002. The myth of the aggressive monkey. Journal of Applied Animal Welfare Science 5(4), 321-330.

Captive rhesus macaques are not intrinsically aggressive, but poor husbandry and handling practices can trigger their aggression towards conspecifics and towards the human handler. The statement 'rhesus macaques are so aggressive animals' is probably based...