Rodent Husbandry
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Rodent Husbandry

Last modified on July 10, 2010

Diets    
Rat and mouse husbandry 
Woodchucks    
Guinea pigs

Hamsters

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In general, the environmental, housing and bedding requirements for rodents are similar. Notable exceptions are listed with each species.

Biologic response to the environment can be grouped by the source of the response modifiers: physical, chemical, and microbial.{3584}

Physical factors include the facility, cage, food and water, and shipping containers. Buildings should be constructed or arranged so as to limit traffic between clean and dirty areas; be constructed using monolithic finishes on walls, ceilings and floor; have windowless rooms and be lighted by fluorescent fixtures.{3584}

Diet

Types of laboratory animal diets

Natural product diets are made from farm-grown ingredients, and are the most commonly-used and economical feeds. Under usual manufacturing conditions, natural diets will vary widely in nutrient content, and can significantly modify biologic responses.{3584}  The term "purified"{3580} (or "semisynthetic" or "semipurified"{3584}) is used to describe animal diets composed of ingredients extracted from natural feedstuffs which are not necessarily chemically pure, combined with minerals and chemically pure vitamins. An example is a diet formulated of vitamin-free casein, gelatin, D,L-methionine, sucrose, dextrose, dextrin, cornstarch, cellulose vegetable oil, salts mix and vitamin mix. The term "chemically defined" is used to describe diets composed of amino acids, sucrose or other mono- or disaccharides, triglycerides or fatty acids, mineral salts, and vitamins of a high degree of purity.{3580}

Diets are classified as "open-formula" or "closed formula".  Open-formula diets specify the concentration of each ingredient. The manufacturer uses the same source of protein, carbohydrate and fat in each batch of the diet. Closed-formula diets are those for which, because of proprietary concerns, detailed information on ingredients is not available. The list of ingredients is specified but the concentrations of each are not. Concentrations of individual ingredients may vary between lots.{4134} Diets may be formed as pellets, meal (which makes adding extra ingredients possible), semimoist or gel (to which water and agar are added) and fully liquid diets.{3584

Examples of types of diets {4134}

Closed-formula natural-ingredient diets

Purina Rodent Lab Chow No. 5001 Maintenance
Purina Certified Rodent Chow No. 5002 Maintenance
Purina Mouse Chow No. 5015 Breeder
Purina Pico Mouse Chow 20, No. 5058 Irradiated breeder
Harlan Teklad No. 7012 Autoclavable breeder/maintenance

Open-formula natural-ingredient diets

Zeigler Brothers NIH-31 Autoclavable breeder/maintenance
Zeigler Brothers NIH-07 Breeder/maintenance, toxicology and carcinogenesis
Zeigler Brothers NTP-88 Maintenance
Zeigler Brothers NTP-2000 Toxicology and carcinogenesis

Note: The Jackson Laboratory recommends using NIH-31 for breeding inbred mice, especially C57BL/6J.{4181}
NTP= National Toxicology Program

Purified diets

Research Diets, Inc. AIN-76A soy-protein
Research Diets, Inc. AIN-93M casein maintenance

AIN= American Institute of Nutrition

Guide recommendations

User should monitor the supplier's procedures for ensuring diet quality
Food should be stored off the floor
Open bags should be stored in vermin-proof containers at <21°C and away from light, humidity and unsanitary conditions
Most natural-ingredient, dry diets with preservatives can be stored for up to 6 months
Vitamin C degrades in 3 months, although stabilized forms can extend shelf-life
Purified and chemically defined diets are less stable and should be stored for <6 months at 4°C
Moderate restriction in calorie and protein intake can increase longevity. This can be achieved through either decreasing metabolizable energy, protein density, or both. Decreasing the amount fed or the frequency can also be used.  Caloric restriction is an accepted practice for rodents and rabbits.
Treats can be offered to some species, i.e. NHPs, but caution should be used in varying diets. It is "well documented that many animals offered a cafeteria of unbalanced foods do not select a balanced diet and become obese through selection of high-energy, low-protein foods."{3948}

Rats used in long-term toxicology studies will live longer if they are limit-fed. One method is to offer 75% of what they eat when fed ad lib, i.e. by feeding 20 grams to male Sprague-Dawleys and 15 grams to females. Powdered feed seems to result in higher body weights at the end of the study than pelleted feed. Interestingly, males have different daily eating patterns than females. Males eat more than half of the daily amount during the first 4 hours (8am-noon) and had finished everything by 16 hours. Females have a more or less straight line consumption over 24 hours. This has implications for studies in which a test compound may depend on food consumption in some way.{4544}

Contaminants

Extraneous chemical contaminants in ordinary commercial diets may include nitrates, cadmium, lead, selenium, arsenic, aluminum, mercury, nickel, insecticides, mycotoxins, herbicides, chloroform, estrogenic substances, polycyclic hydrocarbons, PCBs, and antibiotics. For example, subclinical doses of lead have been found to cause decreased Salmonella resistance in mice, increased susceptibility of rats and chicks to endotoxin, decreased phagocytosis in rats and decreased antibody formation in mice. The National Center for Toxicologic Research has established maximal concentrations of these contaminants in research animal diets.{3584}

Water itself may introduce contaminants such as minerals and chemicals that leach from plumbing and utensils.{3584}

Phytoestrogens

The two main classes of phytoestrogens are lignans and isoflavonoids. Soybeans are the chief source of phytoestrogens in rodent diets; flax, wheat, barley, corn, alfalfa and oats have also been reported to contain phytoestrogens. These isoflavones include daidzein, genistein, formononetin and biochanin A. Their common mechanism of action is to bind to the estrogen receptors on cells; they have weak activity compared with steroidal estrogens. However, it has been documented that phytoestrogens can affect study results. They reduce the rate of mammary tumor development as well as liver, colon and prostate tumors. They reduce serum cholesterol in NHPs, rats and humans. They increase bone density in aged rats. They also act as antioxidants and suppress angiogenesis. These effects can be dramatic: 10% soybean meal in a rat diet resulted in a 40% reduction in mammary tumors in two rat models of breast cancer. Daidzein and genistein were reputed to be responsible. Daidzein levels in typical diets ranged from 38-277µg/g of diet; genistein levels varied from 31-214µg/g. There can be great variability among different lots of the same diet; the mean levels are around 20-30 but the range can be from 30-200µg/g.{4134}

Rodent diets differ in estrogenic activity. One way of measuring this is by comparing uterine to body weight ratios in 15-day-old mice (CD-1). Open-formula diets with standardized phytoestrogen levels are suggested for reproductive, toxicologic and carcinogenesis studies, as there is less chance of variability. {3998}

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Rat and Mouse Husbandry{3987}

Environment

Breeding systems

Caging

HVAC

Identification

Environment

Guide recommends 64°-79°F (17.8°-26°C) for rats and mice ; Euroguide recommends 20°-24°C{4770}
Relative humidity 30-70%. If raised to over 70% ammonia will be produced no matter what the bedding used. If lowered to under 50%, little ammonia will be produced regardless of bedding type.{3742} Euroguide specifies 45-65%.
Light: 30 foot candles 1 meter off the floor for most activities, 37fc if cages are rotated around; 75-100fc for husbandry activities. Note that in experiments involving tumor growth, light leaks at as little as 0.2 lux can have very significant effects due to decreased melatonin secretion{3835}

Caging

Cage design for rats is either wire-bottom or solid-bottom. If metals are used in caging, they should not be galvanized, as the zinc in the metal will be a source of dietary zinc for the animals. Plastic is popular because of economy, smoothness, seamlessness, and chemical inertness. Polycarbonate is clear, whereas polypropylene is translucent. Wire bar lids restrict airflow within the cage up to 25%, plus further restriction by the presence of food and water bottles. Filter tops (also called "bonnets" or "caps") were invented by Kraft to control viral diarrhea in infant mice, and work well to limit fomite transmission of pathogens. However, they also limit air circulation; the higher ammonia levels may predispose animals to mycoplasmal pneumonia.

The toxicology industry often houses their rodents in wire-bottom caging. A survey indicated that toxicologists preferred it because of: (1) ease of sanitation, (2) better animal health assessment, (3) serviceability of the equipment, (4) labor savings, (5) controlled exposure to drugs, (6) more accurate feed consumption data, (7) reduced staff allergies, (8) elimination of bedding ingestion, (9) better air circulation and ammonia control, (10) denser cage census, (11) reduced fecal and urine exposure, (12) no significant water accidents, and (13) the existence of baseline data. There is little compelling evidence to support the belief that rodents prefer solid-bottom caging, and when housed for <1 year there are fewer foot lesions.{4540} An ACLAM-sponsored study showed that lesions developed only after 1 year on wire flooring, and were more common in heavier strains, i.e. CD rats, than in Sprague-Dawleys. The recommendation of the Guide to house rodents in solid-bottom cages was based on only three papers using small numbers of animals. One such paper indicated the presence of Renaut bodies, defined as "loosely textured, whorled, cell-sparse structures located in the subperineurial space of peripheral nerves." These were thought to be related to nerve compression.{4542}

Performance of routine cage-changing causes increased heart rate, mean arterial pressure and activity level in rats. This lasts for 45-60 minutes. Addition of a cup of dirty bedding from the old cage makes no difference, so olfactory cues are not important. Changing cages every 2 weeks instead of weekly results in a somewhat higher and more prolonged effect. Rats in the same room that just "witness" the cage changes have hardly any response. This is therefore probably a response to a novel environment, known to cause behavior changes in rats. The response wasn't different the fourth time from the first, meaning that rats do not habituate to cage changing.{4490}

Microisolators

The first isolator cage was developed by Kraft in the 1950s. The modern filter top was developed by Robert Sedlacek; this top has a polycarbonate frame containing a piece of Reemay fabric, which is spun polyester in different weights. The top also fits over the cage with a lip arrangement, similar to a Petri dish. When used with a class 100 mass air displacement unit (MADU) it is extraordinarily effective in maintaining rodents.{3742}

Unfortunately, the biggest disadvantage of static isolators is buildup of ammonia from bacterial urease, which converts urine urea into ammonia (NH3). Organisms incriminated are fecal Proteus mirabilis and Pasteurella pneumotropica.{4205} Mr. Sedlacek's mice were free of these bacteria. In the 1980s there was much interest in the cage microenvironment. Air exchange takes place mostly at the interface between lid and cage, rather than through the filter. NH3 may rise to over the acceptable human limit (25ppm 8-hr time weighted average) in 3-4 days, depending on the number of animals, the relative humidity, and the air flow.{3742} Note that another source reports the OSHA TWA limit is 50ppm (CTLAS 39(4):7 letter, July 2000). Ammonia concentrations over 25ppm promote growth of infective agents in the respiratory tract of rats. Formation of ammonia is also strain-dependent; in microisolators, DBA and CD-1 mice produce >160ppm, whereas BALB/c produce only 10ppm on the seventh day.{4205

Other contaminants have been investigated but are of unknown importance; of these, acetic acid off-gassed from corncob bedding and sulfur dioxide were both increased. Carbon dioxide levels rise, but not to dangerous levels. The standard for carbon dioxide exposure to humans is 5,000ppm over a working day.{4205} The NIH published a paper using computational fluid dynamics to examine airflow in isolators. They found that historical assumptions about what was good macroenvironment did not apply to the microenvironment within the cages. High-level exhausts, for example, reduce intracage ventilation.{3742}

Static isolators are still useful especially for hazardous agent research, as they can be placed into a cabinet acting as a secondary enclosure. To address the poor environment, four steps can be taken: (1) increase cage change frequency; (2) use a contact bedding with desirable characteristics, not just absorbency (best are corncob, virgin cellulose and hardwood chips); (3) reduce macroenvironmental relative humidity; and (4) increase macroenvironmental temperature.{3742} Increasing the air changes/hour in the room does not result in improved intracage ventilation (at least when bonnet-top cages are used); rather, it may lower relative humidity too much. Heat load generated by the mice themselves is sufficient in a bonnet-top to change the air, even when room ventilation is turned off.{4205}

Cage change frequency should be based upon frequent monitoring of ammonia inside cages, which requires a monitor and cages with ports.{3742} Brüel and Kjær in Denmark make a multi-point doser/sampler to inject 1% sulfur hexafluoride (SF6), measuring decay of the tracer gas with a photoacoustic infrared gas monitor. SKC Inc., in Pennsylvania, make a low range (0.5-60ppm) ammonia sorbent sampler tube to measure ammonia.{4205}

Cage sizes

Cage sizes for rats, according to the Guide and Euroguide, must be as shown. Interior height must be at least 7" (17.78cm; Euroguide requires 18cm). The density of housing greatly affects both stress levels and the immune responsiveness of the animals; either too crowded or not enough company will affect the rats. The cages should be identified with cage cards. If individual ID is required for the research, a tattoo, ear punch, or ear tag can be considered.{3584}

Body wt., gm Floor area/rat 
in2 (cm2) (Guide)
Floor area/rat cm2 (Euroguide) (min. area 800cm2)
<100 17 (110)
100-200 23 (148) 200
200-300 29 (187) 250
300-400 40 (258) 350
400-500 60 (387) 450 (401-600gm)
>500 >=70 (452) 600 (>600gm)

Cage sizes for group-housed mice are shown below. Height must be 5" (12.7cm; Euroguide requires 12cm). To convert square inches to square centimeters, multiply by 6.45. According to the Guide, "If they are housed individually or exceed the weights in the table, animals might require more space."{3948}

Body wt., gm Floor area/mouse
in2 (cm2)(Guide)
Floor area/mouse cm2 (Euroguide) (min. area 330 cm2)
<10 6 (38.7)  
10-15 8 (51.6) 60 (<20gm)
16-25 12 (77.4) 70 (21-25gm)
>25 >15 (97)

80 (26-30gm); 100 (>30gm)

A recent advertisement for mouse caging listed a floor area of 75 in2. This would be technically sufficient to house 5 mice >25 grams, 6 mice weighing 16-25 gm, 9 mice weighing 10-15 grams or 12 mice weighing <10 gm each. Another article{4175} gave measurements of 12"x9"x6", or 108in2. Although they housed 5 mice (>25gm) per cage, they would technically be large enough to house 7. 

Data supporting the cage sizes for mice are lacking. New studies with C57BL6 and BALB/cJ mice support the conclusion that smaller cage sizes than those recommended in the Guide are sufficient to preserve performance standards such as growth, immune status and perhaps low mortality rates. BALB/cJ mice were grouped in blocks of three mice per cage at weaning, and the cage size adjusted using a plastic panel to provide 5, 15 or 20 in2 per mouse. Males were followed for 42 days, and slower-growing females for 49 days. Immune measures included RBC and WBC counts, hemoglobin, hematocrit, RBC volume, lymphocyte proliferation (by both PHA and LPS) and NK cell cytotoxicity. Water use and feed intake was measured and body weight was followed. The only statistically significant difference between mice caged at the three cage sizes was in high-dose PHA lymphocyte proliferation in female mice (it was higher in the smaller cages). Mice were videotaped and behavioral activities monitored.  Similar amounts of time were spent in all groups feeding, drinking and engaging in social behaviors such as grooming and agonistic behavior).  Females spent more time grooming in smaller cages; the meaning is unknown but grooming increases when anti-anxiety drugs are given, so it may indicate comfort. Grooming increases with age in mice.{4504}

Cage sizes for group-housed hamsters is shown below. Height must be 6"(15.24cm; Euroguide requires 14cm) according to the Guide.{3948}

Body wt., gm Floor area/hamster
in2 (cm2) (Guide)
Floor area/hamster
cm2 (Euroguide; min size 800cm2)
<60 10 (64.5) 150
61-80 13 (84) 200 (61-100gm)
81-100 16 (103)  
>100 >19 (122) 250

Guinea pigs weighing less than 350 grams need 60in2 (387cm2); those >350 grams need >101 in2 (652cm2). Height must be 7" (17.78cm) according to the Guide.{3948}. The Euroguide requires a minimum enclosure size of 1800 cm2 and 23cm high.

Body wt, gm Floor area/g pig, cm2 (Guide) Floor area/g pig, cm2 (Euroguide)
<200 387 200
201-300 387 350
301-450 652 500
451-700 652 700
>700 652 900

According to the Euroguide, hamsters require a minimum enclosure of 800 cm2 and a height of 14cm. Floor area per hamster varies from 150cm2 (<60gm) to 250cm2 (>100gm).

Bedding

Bedding is usually made of sterilized wood chips. Cedar is not used because of its content of aromatic hydrocarbons such as cedrene and cedrol, which induce hepatic microsomal enzymes. Some toxicity studies require the use of wire bottoms to prevent animals from being exposed to dust, organisms and chemicals present in all wood bedding.{3584}

Shipping can cause dehydration and weight loss in rats, particularly during hot weather. Older rats and those shipped by air usually lose more weight. Therefore, the most important challenge in shipping rats is the provision of adequate water, which can be provided with fruit or vegetables, gels, canned diets, or a source of fresh liquid water.{3584}

Once animals arrive in the new facility, equilibration time must be allowed. This is defined as the length of time for body weight to recover to within 1 standard deviation of age-matched unshipped adolescent controls. Equilibration time normally varies between one and five days.{3584}

Special facilities and equipment may be necessary when housing immunodeficient rodents. Filtered "microisolators" are recommended by ILAR, in part because their clear plastic materials allow the animals to be observed without opening the cage. Microisolators are the simplest way to house pathogen-free rodents, but they must be used properly. HEPA-filtered laminar-flow hoods place the animals under a positive flow of filtered air, and can be used during cage changing. HEPA-filtered housing is also available. Important maintenance includes (1) following the scheduled change of prefilters, (2) monitoring the air velocity gauge, and (3) annual recertification of the unit by a qualified person to ensure the HEPA filter is intact, properly seated and not leaking. If animals must be maintained with complete exclusion of microbes, a germfree isolator is used. This is usually constructed of flexible plastic which can be chemically sterilized. Food and supplies are passed in through a sterile entry chamber. While these units are ideal for pathogen-free housing, they are labor intensive and impair the ability to handle animals. Individually-ventilated cage racks are the newest way to house immunodeficient rodents. Cages are enclosed and supplied with either positive or negative-pressure airflow.{4162}

Back to rat/mouse

HVAC

The recommended temperature range for rats is 65-75°F (18-42°C). Even though rats can be acclimated to temperatures outside this range, the time needed is on the order of 3 weeks, so sudden fluctuations are to be avoided. If relative humidity is too low (<40%), young rats can develop ringtail, annular constrictions which may result in tail sloughing.{3584} Features of ringtail include epidermal and dermal lesions. Epidermal hyperplasia is the common finding in all cases, but can be caused by a plethora of things: ectoparasites, nutritional deficiencies (zinc, vitamin A, essential fatty acids), fungi (dermatophytes), seborrhea, endocrinopathy, Corynebacterium, mutation, oncogenes, or environmental stimuli such as low humidity. Activated keratinocytes may then secrete cytokines that cause vascular dilatation and dermal edema. In severe cases this leads to thrombosis and necrosis.{4110}

Rooms housing rats should have 10-15 air changes per hour (0.815 ft3/min/250gm rat). There is controversy over whether the rooms should be slightly positive or negative compared to the hallway. Lighting should be 13/11 or 14/10 for breeding. Environmental influences can have profound effects upon drug action; for example, sleeping time of rats given pentobarbital varies by 100% in relationship to the light/dark periodicity. Light intensity, although recommended to be between 75-125 foot candles at cage level, can still be too high and cause photoreceptor cell degeneration.{3584}

Rats have an acute sense of hearing. High noise level (i.e. >85db) is associated with increased eosinophil counts, serum cholesterol, and adrenal weight. Rats are known to be disturbed by fire alarms. Alarms in lower ranges (450Hz), which are audible to humans but not rats, may help alleviate the startle response.{3584}

Hepatic microsomal enzymes are those found in highest concentrations in the liver, and which function in metabolism and removal of exogenous substances from the body. Hence, alteration of the chemical environment of an animal may have serious effects upon metabolic, immunologic and toxicity studies. In addition to careful consideration of gaseous chemicals in the animal room, the levels of ammonia and carbon dioxide inside the cages should be considered as hepatic microsomal enzyme inducers. The maximum exposure limit of man to ammonia is 25ppm. In rat cages, after six days without changing the bedding, levels can reach 150-700ppm depending upon the size and number of the animals therein, and the air circulation. The first documented observation of alterations in drug metabolism caused by an environmental chemical resulted from use of the pesticide chlordane in an animal facility. If chemical pesticides must be used, the investigators should be informed and only approved forms of preferably nonvolatile chemicals used.{3584}

When drugs are used in a study it may be important to have pair-fed and watered controls. It may be necessary to reduce the feed amounts in the controls to match the feed intake of the test animals. Also, unmetabolized drugs may be excreted and then re-consumed through coprophagy, resulting in unexpected drug exposures. {3584}

Subclinical infections with microbial factors were tremendous problems in laboratory animal science until the advent of gnotobiotic technology in the 1950s as an offshoot of "germ-free life" research. In rats, mycoplasmosis and hemobartonellosis were particularly difficult to diagnose, yet had subtle to profound effects upon research projects. Some definitions are in order:

  1. Axenic or germfree rats= those with no flora; born by hysterectomy and reared in germfree barriers
  2. Gnotobiotic rats= those with more than one known bug; sometimes axenic to begin with and then known microbes are added back
  3. Barrier-reared (BR) or defined-flora (DF)=rats reared from conception as gnotobiotes; generally act as breeding stock to produce gnotobiotes
  4. Specific pathogen-free (SPF)= rats freed of specific pathogens by the use of gnotobiotic technology (because true gnotobiotes often differed significantly from "normal")
  5. Conventional rats (CV)=animals which usually maintain an assortment of pathogens as either latent or overt infections{3584}

 Sanitation

Cage cleaning: the Guide says solid-bottom cages, bottles and sipper tubes usually require sanitation at least once a week{3948}
Racks: once a month for solid bottom, twice a month for wire cage rack

Cleaners and deodorizers smell nice because they contain volatile hydrocarbons or essential oils, which are well known inducers of hepatic microsomal enzymes.{3584

The ACLAM rat book says that cages should be sanitized at least twice a week. Water bottles and sipper tubes should be sanitized biweekly as well, to account for chlorine degradation and microbial buildup. Bleach can be used at a concentration of 6ppm (certainly not less than 2ppm), at a pH of 2.5-3.5 to prevent growth of Pseudomonas in water bottles (according to a slide at the CL Davis workshop). Detergents and chemicals used for sanitizing, if used, must be thoroughly rinsed away. If water reaches a temperature of 180° F, known rat pathogens will be eliminated.{3584}

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Back to rodent husbandry

Breeding systems

Outbred

Mutant

Inbred

    Congenic

    Coisogenic

    Segregating inbred

    Recombinant inbred

    Transgenic

Genetic monitoring

This topic, perhaps because it is very confusing to me, is also covered on the Muridae biology page. For a review of Mendelian genetics, click here.

Outbred stocks

Laboratory rodents are either inbred strains or outbred stock depending upon the breeding system used and the genetic makeup of the animal. There may be good reasons for investigators to select a particular type depending upon the nature of their research. The laboratory animal medical staff must be able to assist in this process by first understanding the basics of animal genetics and the differences between breeding systems; and second by being able to find particular strains of rodents that the researcher needs.

Outbred (random-bred, non-inbred) stocks of rodents are those having a large degree of genetic variation presumably arising from random matings within the population as a whole. The term "non-inbred" may be preferred because in many cases animals are produced by breeding systems designed to avoid inbreeding in finite populations{3564}. Most rodent vendors have closed colonies, thus limiting the size of the population to choose from, and so true random breeding can no longer occur.

Non-inbred rodents are very important in laboratory animal science and in research. They are the base population from which interesting new genetic variations can be selected. They are generally much more vigorous animals, and may be critical for use in radiation or mutagenesis experiments to keep the test animals viable{3564}. Examples include: NMRI, OF, CD-1 and Swiss-Webster mice; Sprague-Dawley rats; and most higher animals. They are designated by a stock code consisting of 2-4 capital letters (i.e. NMRI) which may be preceded by a lab code consisting of a capital and 1-3 lower case letters (Tif:NMRI). This prefix code and the colon distinguishes an outbred stock from an inbred strain.Many outbred stocks have a restricted distribution within a country, so that direct comparison of research results in the "same" stock is not truly possible because different animals were used, albeit of the same stock name.{4535}

Traditionally, non-inbred animals have been used in toxicology experiments on the assumption that such populations are a good representation of human populations. One might consider, however, performing factorial experiments, using several inbred strains to test a particular substance for toxicity. In so doing it might be determined that the response to the substance is under genetic control{3564}. Non-inbred rodents are widely available, less expensive, and have high vigor and reproductive performance. On the other hand, they show phenotypic variation that may contribute to high variance in results, thereby requiring higher animal numbers to achieve statistical significance. {3564}

Non-inbred rodents are often produced by a circular system of breeding. In this system, males from one colony are mated with females of colonies opposite theirs in a circular diagram. Any breeding system that avoids inbreeding and is recorded accurately will maintain non-inbred stocks{3564}. Deliberate selection should be avoided, except that abnormal or unhealthy animals should not be used for breeding. The colony should be as large as possible. In a closed colony maintained by random mating, the rate of inbreeding per generation is given by the equation

Fg=

1

+

1

8Nm 8Nf

in which Fg is the increase in inbreeding and Nm and Nf are the number of males and females chosen for the next generation, excluding those to be used to generate experimental subjects. Note that the rate of inbreeding is mostly dependent upon the numbers of the least numerous sex chosen. With four males and four females, the inbreeding will be 6.25% per generation; with 4 males and 40 females the inbreeding will be 3.44%.

Genetic contamination is a potentially catastrophic problem which can be avoided in part by housing animals with the same coat color in different rooms.

Outbred stocks usually carry some deleterious recessive genes. Getting rid of these genes is nearly impossible using selection. The best method is to use a known homozygote or heterozygote to progeny-test potential breeding stock. As long as sufficiently large litters are produced, the statistical chance of detecting a recessive gene can be quantified.{4535}

Back to breeding systems

Mutant stocks

A mutant stock is an outbred stock carrying a mutation, such as nude or obese. If the mutation is carried in an inbred strain, it is called a segregating inbred or congenic strain.  There are >700 mouse and >100 rat mutants and polymorphisms. The main advantage of maintaining these outbred mutants is their good breeding performance; however, these animals are histo-incompatible so cannot be used for transplantation studies.{4535}

For a list of mouse mutants, click here. Rat mutants are on another page.

Mutants are maintained in different ways depending on how viable and fertile the homozygotes are. Albinos, for example, are usually maintained by mating homozygotes. In the nu mutation, the females tend to be poor mothers and less fertile than normal. Mating heterozygous (phenotypically normal) nu/+ females to homozygous nu/nu males is the usual method of maintaining the stock. Half the offspring will be homozygous and can be used for experiments, with the males used for breeding. The leftover heterozygotes may be considered for experimental controls; however, at the biochemical or immunological level, heterozygotes of some mutants may be only partially recessive. When both sexes are infertile, heterozygous mating schemes must be used. This will produce a ratio of 1m/m: 2m/+: 1+/+. Telling the difference between the useful m/+ and the useless +/+ offspring is most easily done by performing a few test matings and then culling those pairs that do not produce mutant offspring. Another way is to use a known m/+ parent and do test matings. This requires meticulous record keeping and a well-trained staff to avoid genetic contamination during all the pairing up.{4535}

One advantage of using mutants in research is that their phenotypically normal littermates may be excellent controls. This is not the case with inbreds carrying polygenic traits, for which there is usually no reasonable "control" aside from studying several different inbred strains. Even better is to develop mutations on inbred backgrounds (i.e. segregating inbreds or congenics), which are then genetically identical except for the mutant locus.{4535}

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Inbred strains

Inbred strains are designated by capital letters or combinations of capital letters and numbers. Some older strains, such as 129, got "grandfathered in" with numerical designations.  Substrains are designated by the name of the parent strain followed by a slash and a substrain symbol that may be numeric and/or the letters designating the individual or institution maintaining the strain (i.e. DBA/1J is substrain 1 held by Jax; DBA/LacJ was transferred from the Laboratory Animal Center in the UK to Jax).{4181} Another reference states that the strain and lab code are to be separated by the @ sign, e.g. CBA/Ca@J. {4535} It is customary when designating rodent strains to show the female parent first, followed by the male parent, i.e. (C57BL/6J x C3H/HeJ)F1 denotes a mother C57BL/6J and a father C3H/HeJ. This may be abbreviated as B6C3F1 if it is defined in the document at the first use of the term.{4162}

Inbred or isogenic strains are produced by 20 or more successive generations of brother-sister matings, a definition put forth by the Committee on Standardised Genetic Nomenclature for Mice in 1952.{3564} Examples include: CBA, NOD (non-obese diabetic), NOR (non-obese diabetes resistant), AKR, and C57BL mice; and F344 and LEW rats. The extent of inbreeding is expressed by the coefficient of inbreeding, which is the probability that two genes at any locus are identical by descent, i.e., that the two genes in one individual originate from one of its ancestors. With successive inbreeding, reproductive capacity and vigor decrease as a result of uncovering deleterious recessive genes by making them homozygous. However, the trait of choice also increases in homozygosity.

Inbred strains have the following characteristics:{4535}

Isogenicity: all animals are identical at more than 99% of the genetic loci which were segregating in the initial founding colony. They accept transplants from each other, and genotyping one individual should hold true for all others
Homozygosity: Each inbred animal is homozygous at more than 99% of the loci which were segregating in the initial founding colony. They do not carry any hidden recessive genes, and will breed true.
Long-term stability: An inbred strain remains genetically constant; it cannot change as a result of selection, inbreeding or random drift as do outbred stocks. Mutation, however, does occur, and generally has an effect very slowly. It is best to maintain frozen embryos to resuscitate the strain from time to time.
Phenotypic uniformity: fewer animals are needed to achieve a level of statistical significance. Festing has estimated that, using mandible shape as a measure, equal precision can be achieved using 34 F2 hybrids, 25 outbreds, 16 inbreds or 13 F1 hybrid mice.
Individuality: Each strain differs from every other strain
Identifiability: There is a unique genetic profile for each inbred strain, using biochemical, immunological and microsatellite markers. Microsatellites are simple short sequences of bases that are repeated many times at each locus; they are detected with PCR and are a very convenient way of profiling strains.
International distribution: Unlike outbred stocks, inbred strains are stable for a long time and can be sent all over the world. Genetic control is easy, so data can be compared among labs.

The most popular (i.e. the largest number of holders in 1993) rat and mouse strains are listed in the following table.

Rank Rat strain # of holders Mouse strain # of holders
1 F344 51 BALB/c 162
2 LEW 37 C3H 154
3 SHR 34 C57BL/6 128
4 WKY 31 CBA 112
5 DA 28 DBA/2 92
6 BN 26 C57BL/10 56
7 WAG 21 AKR 52
8 PVG 17 A 49
9 BUF 17 SJL 40
10 WF 15 129 38
11 SHRSP 14 B6C3F1 32
12 ACI 14 NOD 30
13 LOU/C 12 DBA/1 28
14 BDIX 11 B6D2F1 27
15 COP 10 NZB 24
16 LOU/M 9 FVB 23

Inbred strains are usually produced using backcrossing (breeding back to the parent, or breeding homozygotes with heterozygotes) and/or intercrossing (breeding two heterozygotes). The system used depends upon the gene of interest, particularly whether it is dominant, codominant, or recessive. In some cases (i.e. when homozygotes for the gene are infertile) the breeding system can become quite complicated.

Inbred strains are maintained by successive brother x sister matings. A breeding pair should be kept together for life if possible, as this will minimize the chance of mis-mating. Alternatively, consecutive backcrossing may be used, as long as the younger parent is always selected (i.e. the mouse bred to its parent is the one subsequently used as the parent in the next generation).{4748} Selection for good breeding performance should be done by selecting the most productive sub-lines rather than the best pairs.{4535} Some, such as C57BL/6J, are very susceptible to environmental stress. Better results may be obtained if exposure to sudden noise, excessive handling and vibration from equipment are minimized. Extending the light/dark cycle from 12:12 to 14:10 may also help. Dietary fat and nutritional makeup may also affect breeding performance. The Jackson Laboratory uses NIH31 6% diet.{4181}

If an inbred mother mouse is not caring for her young, they may be fostered onto another mother. Tips for success include:{4181}

Choose a foster mother that has recently successfully weaned a litter
Match the age of the litter to be fostered with the foster mom's natural litter
Foster litter should be of a different coat color if they are to be left together
Be sure the foster mom has finished delivery (may deliver up to 6 hours apart)
Critical: have the same number of pups, as a change in litter size of 2 pups may affect the foster mom's milk supply
Keep the foster mom in her cage, remove the natural litter, and add the foster litter to the cage; transfer to a clean cage the next day if needed. Avoid disturbing her for 24 hours, but check to be sure she is caring for the litter.
Alternatively, remove the entire nest with the natural litter and keep it under a heat lamp. Place the foster litter in the nest and mingle the pups together. Rub some maternal feces on the foster pups' backs. Place the fostered nest back with the mother.

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Congenic Strains

If a strain of rodent carrying a gene of interest is mated by either repetitive backcrossing or intercrossing with a different strain acting as the background, the resulting strain is congenic with the parent strain that donated the genetic background. For example, the AKR/N strain carrying a dominant allele k/k was backcrossed (i.e., k/+ x +/+) for approximately 10 generations with C57BL/6J carrying the b/b allele. Continuing to backcross with the C57BL/6J and selecting the b/k offspring, the eventual congenic strain was almost all C57Bl/6J background genes with the b/k gene. A final intercross between these heterozygous animals produced some that were homozygous for the k gene. If the allele is recessive, i.e. nu/nu, a system of alternating backcrosses with the parent BALB/c genotype and intercrosses between the heterozygous siblings eventually produced BALB/c nu/nu mice.{3564}{4162}

Coisogenic Strains

Coisogenic strains arise as a result of a mutation in an established inbred strain. The two strains are then absolutely identical except for the affected locus.

If two inbred strains are bred, the resulting F1 hybrids have the advantage of higher vigor, longer lifespan, and larger litters. The F1s are all isogenic, albeit heterozygous at each locus at which their parents differed. As long as the parental strains are maintained, F1s can be produced for research use, particularly in chemical carcinogenesis studies.{3564}

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Segregating Inbred Strains

If F1s are mated by continuous intercrossing and selection, i.e. for the diabetic db mutation, a segregating inbred strain will be produced. These animals are similar to other inbred strains except that because of the use of brother-sister mating they are more nearly homozygous except for a segment of the chromosome with the gene of interest. The nomenclature indicates the number or backcrosses or cross-intercrosses with the letter N, and the number of succeeding inbred generations by the letter F: i.e. BALB/cA nu/+ N20F15 indicates that there were 20 cycles of cross-intercrossing, followed by 15 inbred generations.{3564}

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Recombinant Inbred Strains

If F2s are mated by selecting out pairs of brothers and sisters and then inbreeding, a collection of new strains called recombinant inbred or RI strains will result.{3564} Most RI strains were produced by randomly selecting two inbred strains and mating F2 pairs by continuous brother-sister mating. After 20+ generations, these strains should be genetically fixed at more than 98% of the loci that distinguish the two parental strains. Each RI strain is equally likely to have inherited either the maternal or paternal progenitor strain allele at each autosomal locus. Linked genes will tend to remain in the parental combination, making RI strains very useful for studies of segregation and genetic linkage. They are particularly useful for studying and mapping genes controlling phenotypic traits that differed between the two progenitor strains. However, they are only useful if the progenitors differed with respect to the gene of interest, and often there are not enough strains available for rigorous hypothesis testing. Phenotypic traits under the control of multiple loci are too complicated to study with RI strains. Finally, undetected mutations may become fixed by the multiple generations of inbreeding.{4181}

RI strains are denoted by one or two-letter abbreviations of the progenitor strains with an X in the middle. A hyphen is used to separate this from the individual member number. A slash separates the number from any substrain symbols that may follow. For example, a cross between an AKR/J female and a DBA/2J male, the first individual in a substrain called Ty is denoted AKXD-1/Ty.{4181}

RI strains are usually maintained as are other inbred colonies. Many of them breed poorly. The strains are a mixture of parental coat color loci, and may therefore vary in color.{4181}

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Transgenic Strains

Transgenic animals have had foreign DNA inserted into the genome, which may subsequently be inherited by their offspring if the germ cells carry the DNA. There are many techniques for producing transgenic (Tg) animals. Micro-injection of DNA into the pronucleus of fertilized eggs is the most common method. DNA may also be carried by retroviral vectors into the fertilized embryos or embryonic stem cells, and then transferred into blastocysts to form chimeras.{3564}

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Genetic Monitoring

Coat color

Coat color loci of common inbred strains. a=agouti, Aw=white-bellied agouti, Tyrp1b=brown, Tyrc=albino, Myo5ad=dilute, p=pinkeye{4765}

Strain

a

Tyrp1b

Tyrc

Myo5ad

p

Phenotype

A/J

a

Tyrp1b Tyrc + +

Albino

AKR/J

a

+ Tyrc + + Albino

BALB/cJ

+ Tyrp1b Tyrc + + Albino

SJL/J

+ + Tyrc +

p

Albino

129P3/J

Aw

+ Tyrc-ch/Tyrc +

p

Light chinchilla or albino

CBA/J

+ + + + + Agouti

CBA/CaJ

+ + + + + Agouti

C3H/HeJ

+ + + + + Agouti

C57BL/6J

a

+ + + + Non-agouti black

NZB/B1nJ

a

+ + + + Non-agouti black

DBA/1J

a

Tyrp1b + Myo5ad + Dilute brown non-agouti

DBA/2J

a

Tyrp1b + Myo5ad + Dilute brown non-agouti

Some albino mouse strains carry "hidden" coat color alleles which can be uncovered by test mating to a colored strain: {4535}

Parent Parent F1 Genotype
DBA/2 A chocolate aabbCc
DBA/2 AKR black aaBbCc
DBA/2 BALB/c cinnamon AabbCc
DBA/2 SJL agouti AaBbCc

Skin grafts

Exchange of skin grafts will tell whether the two animals are of the same strain, but not which strain it is. This technique can be used if DNA methods are not available to verify that a strain is fully inbred.{4535} MHC differences will be rejected right away, but minor histocompatability differences may take up to 100 days to manifest, so this is slow. Additionally, C57BL/10 and BALB/cByJ-Rb mice are famous for nibbling on each others' grafts and must be singly-housed.{4765}

Biochemical markers

Proteins produced by animals that have differing loci can be examined using gel electrophoresis; more than 20 such proteins have been described. Examples include esterase-1 (Es1), glucose phosphate dehydrogenase (Gpd1), histocompatibility-2 (H2), hemoglobin alpha chain (Hba), hemoglobin beta chain (Hbb), hemolytic complement (Hc), and malic enzyme (Mod1). These have generally been superceded by the use of microsatellite markers.{4535, 4765}

Immunologic methods

Alloantisera can be produced by inoculating fluids from the strain of interest into another strain. Some monoclonal antibodies that detect strain differences are also available. Immunological tests such as hemagglutination, immunofluorescent antibody and cytotoxicity are then used to distinguish differences. This is particularly useful to distinguish strains that differ at the H2 loci, such as H2 congenic strains.{4535, 4765}

Morphology

Festing developed a series of measures of the right mandible of the mouse and rat which was used in the UK for several years. However, he now says this is only of historical interest, having been replaced by DNA methods.{4535, 4765}

Breeding performance

Monitoring of breeding performance may uncover unexpected increases in litter size. This may indicate that genetic contamination has occurred and that hybrid vigor of the F1 crosses is the reason for the increase in litter size.{4535, 4765}

DNA fingerprinting

Minisatellite markers are DNA sequences of a few to several hundred base pairs in length, which are present at multiple locations in the chromosomes of an individual. These can be identified using labelled probes on a Southern blot. Members of the same inbred strain should be identical at all minisatellite loci. This is a difficult technique to do well. RFLP analysis, which allowed the first linkage maps based on DNA polymorphism to be constructed, are still used to monitor genetic quality.{4535, 4765}

Microsatellites are short DNA sequences, usually 50-200 base pairs in length, which unique sequence flanking DNA. There are several thousand microsatellites in vertebrate DNA; about 6000 have been identified in the mouse and nearly as many in the rat. Examples include D1Mit3, D2Mit14, etc. They are often highly polymorphic in the number of repeats. They are detected using PCR. PCR-amplified SSLP markers are now the standard way to do genetic mapping in rodents, and characterize and monitor the genetic background. This was the technique used to re-work the 129 substrain designations in the late 1990s. Single nucleotide polymorphisms (SNPs) are replacing SSLP analysis (cheaper) as soon as the number of mouse SNPs is increased.{4535, 4765}

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Animal Identification

In addition to cage cards for rodent identification, holes and notches may be placed in the ears following a code established by Dickie. Toe snipping has fallen from favor because of the likelihood of infection. Tattoos or small aluminum ear studs may also be used.{3762}

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Guinea Pig Husbandry{3983}

Environment{3977}

Temperature 64.4°-78.8°, or average around 70° F; USDA says 60°-85° 
Humidity 40-70% 
Ventilation: 10-15 ACH
Light: dark from 12:12 to 16:8
Housing and caging: either plastic polycarbonate or stainless steel; solid or wire mesh floors but don’t change them after established because they don’t adapt well
Cage size for <350 gm=60 sq in; >350 gm or nursing moms=101 sq in, all 7" high
Feed in J feeders as they are messy and poop in their food 
Water in bottles (they spit in them) or lixits

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Syrian Hamster Husbandry{3990}

Environment guidelines differ, with textbook values narrower than AWA (18-26° C). Adults prefer it cool but are comfortable at 20-24° C and 45-55% RH. Light:dark should be 14:10. House away from excessive noise as they are sensitive to that. Dwarf hamsters (Phodopus) should be housed at 18°C; at warmer temperatures the stress results in reproductive deficits and death of pups.{4091}

Caging: NOT mouse cages, as they are only 5 ½ inches tall and hamsters require 6 inches. Solid-bottom with bedding is better than wire mesh. Floor space: base 10 in2, for every 20gm increase in body weight over 60 g, an extra 3 in2 is needed. Nursing dams and litters: 121 in2
House individually after weaning at 21-28 days as they are aggressive.
Cleaning: Guide says weekly, group-housed need it more often. Acid prewash may be needed for urine.
Diet: 18-19% protein, rat or mouse diet is okay. Make sure there’s enough vitamin E. They need 10-15 gm per day. They are coprophagic. Best to feed on the floor as their noses are too broad to fit through the wires.
Water supplied at 7-10 days when young start eating dry food.
14 light:10 dark hours {3988}
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Woodchuck Husbandry

Adults can be housed in a variety of cages, including cat, dog or rabbit cages. Doors must be secured, and food containers securely attached. Raised slats or wire are preferable to bedding, which they will dig and throw out. They can also be housed outdoors in concrete runs, although if so housed they will need nestboxes and hay. Weanlings can be housed in rodent boxes and kept in groups. They must be separated the following spring after hibernation. Adult males cannot be housed together. Adult females can be housed in groups, but some will dominate the food bowls. Photoperiod is extremely important for reproduction; weekly adjustments must be made in indoor lighting to simulate photoperiodicity.{3560}

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©1999, Janet Becker Rodgers, DVM, MS, DipACLAM, MRCVS

All rights reserved.

Comments? Send an email to janet.rodgers@vet.ox.ac.uk