Mouse Metabolic Research Unit Guidelines and Resources


Users’ Responsibilities

  • Inform yourself on how to get the best results from these measurements.
    • For CLAMS studies, watch an on-line a webinar about this.
      Read through this website carefully.

  • Obtain the appropriate institutional approvals for experiments to be conducted in the MMRU (e.g., IACUC protocol, X-ray protocol). For reference, the MMRU IACUC protocol number is AN-5020 and X-ray protocol is AX124

  • You must leave all equipment you use clean and decontaminated as instructed by MMRU staff so that it is ready for the next user.

  • You must also complete the instrument log with the information requested every time you use MMRU equipment.

  • For non-CLAMS MMRU equipment, you must also complete the instrument’s log with the information requested every time you use it.

  • For mice not currently housed within the CNRF, investigator must organize the transfer as described in CLAMS Measurement Request Protocol.

  • Non-CNRC investigators also must get authorization from CNRC security to enter the CNRF as described in CLAMS Use and Measures.


For CLAMS Experiments

  • Coordinate your experiment “set-up” times with MMRU staff ( At this time, you will:
    • Transfer your mice to the CLAMS cages.
    • Learn how to fill feeders and interrupt the measurements to refill feeders.
    • Learn how to stop the experiment at the end and prepare your cages for washing.
    • Fill out cage cards with your name and contact information, protocol number, mouse id, and any other information you want.
  • At least two days before the experiment, inform the MMRU staff person running your experiment, the approximate weight range that you expect the mice to be.
  • On the day the experiment will start:
    • Print and fill out a log sheet with the mouse IDs, Experimental group, diet, sex, date-of-birth of the mice (if relevant), body weight at the start of the study, and the CLAMS chamber # that the mouse will be in. This information is required to program the operation of the instrument and should be made available to MMRU staff when ready.
    • Provide the correct diet in a powdered form (in accordance with your approved IACUC protocol) and fill the appropriate feeders. Fill water bottles.
    • For long-term studies, change cages and water a minimum of once every six days. Note (with a “C”) on the provided daily room log the day(s) when the change occurred.
  • You MUST check the mouse in each cage daily (including weekends). You will then complete the daily room log for each cage to verify that the food, water, and health status of each mouse is OK. If sheets are not available, please contact CNRF manager.
  • At the end of the experiment, after you have taken care of the mice, complete the following:
    • Remove cages from the racks, and place on a CNRF cart.
    • Unlock the floor from each cage, remove it, and leave it in the cage.
    • Empty feed from the feeder, disassemble the feeder and place all parts in the cage it came from. The springs should go in the “Feeder Spring” box (not to wash).
    • Loosen nut on cage lid just enough to remove water bottle. Re-tighten the nut and place water bottle in the cage it came from.
    • Remove cage cards from chamber racks.
    • Take cart with dirty cages to the area outside the dirty cage wash area in the CNRF.

Publications Acknowledgment

In publications that include data that were generated using MMRU resources please acknowledge the use of the facility. The following is suggested:

“Measurements of (select as appropriate: body composition / energy balance / food intake) were performed in the Mouse Metabolic Research Unit at the USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, which is supported by funds from the USDA ARS  The authors acknowledge the expert assistance of the MMRU core director, Dr. Marta Fiorotto, and staff.”

Please send Dr. Fiorotto a copy of the resulting publication at


General Guidelines to Ensure Accurate, Reproducible and Valid Data


We have carried out an extensive series of measurements to identify factors that can influence your data and offer the following suggestions to ensure that your measurements reflect the "true" metabolic state of your animals.

  • If you transfer your mice to the CNRC, this should be done at least (5-7 days), prior to the start of your measurements.
  • Prior to the start of your measurements, your mice should be individually housed and fed the powdered diet that you will use while they are in the CLAMS.
  • If you are going to implant a telemetry device, this should be done at least two weeks before you start your measurements.
  • Adapt mice to food monitoring/calorimetry cages for three days before you perform indirect calorimetry measurements. The first day's data will not be representative of the mouse's intake and should be discarded.
  • Weigh mice when they go in and when they come out of the feeder cages.
  • On the fourth day (e.g., Monday a.m., if you start on Friday) transfer mice from the feeder to the calorimetry cages. Collect data for 3-4 days (unless you do RMR~see below). The first day's data will not be representative of the mouse's energy expenditure and normal activity levels and should be discarded.
  • Weigh mice when they begin and finish calorimetry. Measure mouse body composition at the beginning AND end if they are still growing. Just once is sufficient if they are not growing.
  • If you request measurements of resting metabolic rate, feed access will be blocked at 6 a.m. on day 4 or 5, and O2 consumption and CO2 production monitored for an additional 6-8 hours. Put the provided notice on the door that no one is to enter the room during this time, but you may want to check as early as possible that the anti-foraging collars are all in place. The average of 2-3 lowest energy expenditure values (heat) after the first 4 hours of fasting will give a close approximation of resting metabolic rate.
  • If you are going to do exercise testing, we recommend you read The American Physiological Society’s "Resource Book for the Design of Animal Exercise Protocols" (available upon request).

All your calorimetry data will be reviewed for aberrant values and summarized to give you average daily values for all the parameters measured on each mouse as well as the average day and night values. You can also have all your raw data files, and access to computer software to analyze the data as you wish.



  • The American Physiological Society’s "Resource Book for the Design of Animal Exercise Protocols" (available upon request).
  • Mini Miter implant manual (available upon request).
  • App to analyze energy expenditure data.