Glossary
Catalyzing Discovery & Understanding
13C
Refers to the naturally-occurring heavier stable isotopic form of carbon atoms that contain 7 neutrons. This atom accounts for approximately 1% of the carbon atoms found in living organisms.
18O
Refers to one of the naturally occurring heavy stable isotopes of oxygen that contains 10 neutrons. This atom accounts for approximately 0.2% of the oxygen atoms found in living organisms.
Absolute humidity
A measure of the actual amount of water vapor in a given volume of air typically expressed in terms of g/m3. Contrast with ‘Relative humidity’.
Absolute temperature
refers to a measure of thermal energy relative to the theoretical lowest possible temperature where all molecular motion ceases. Quantitively it is equivalent to -273.15C.
Acclimation
The process of becoming accustomed to a new environment, often in a laboratory, experimental, or simulation setting. Acclimation usually refers to adjustments made to one specific factor in a controlled environment. Contrast with ‘acclimatization’.
Acclimatization
The process of adjusting to natural environmental changes, such as altitude, temperature, or humidity, over time. Acclimatization is generally used to describe adaptations to natural, complex, multi-factor, or long-term environmental changes. Contrast with ‘acclimation’.
Accuracy
Refers to the ability for a sensor to report a value that is close to a known or theoretical value. Accuracy can be maximized using careful and frequent calibrations. Note that a sensor with high Accuracy does not necessarily have high ‘Precision’ or ‘Resolution’.
Adaptation
The evolutionary process whereby a species becomes better suited to its habitat through heritable changes in structure, function, or behavior. Driven by natural selection, these inherited traits enhance an organism’s survival and fitness in specific environments.
Adaptive thermogenesis
Adaptive thermogenesis is the process where the body adjusts its metabolism and energy expenditure in response to environmental changes (like cold) or changes in energy intake (like dieting). It often manifests as metabolic slowing during calorie restriction, causing weight loss to stall because the body burns fewer calories.
Algorithm
Generally refers to a precise, step-by-step set of instructions or rules followed to perform a calculation or generate an output. In practice, algorithms are used in the field of respirometry to convert data outputs from various flow sensors and gas composition sensors into outputs that are readily useful to scientists (e.g., VO2, VCO2, RER).
Alkaline tide
Ambient pressure
Refers to the atmospheric gas pressure measured at a specified location. Note that it may be lower than 1 atmosphere above sea-level and may be higher than 1 atmosphere when a gas stream is being pushed through a tube or across a sensor.
Analog
A signal or measurement that is continuous (e.g., voltage outputs between 0 and 5V). These signals may be prone to distortion or noise. Contrast with ‘digital’.
Analyzer chain
Refers to a series of gas analyzers through which a gas stream is routed. A series is used rather than parallel routing to ensure homogeneity of the gas stream. Typically the order of the individual sensors is dependent on their response time and their sensitivity to gas sample pressure.
Anoxia
Refers to the general condition whereby oxygen molecules are absent. In terrestrial environments as well as most tissues within an animal’s body perfectly anoxic conditions are rare. Exceptions may include some small regions of cecum or large intestine.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Area under the curve
Typically refers to the integral of a complex curve in a time-series measurement. In stop-flow respirometry AUC refers to the amount of a particular gas measured during an acute injection of a bolus sample. In tracer approaches AUC usually refers to the total amount of tracer measured over a given time period.
Ascarite
A granulated material used for scrubbing CO2 from a gas stream that consists of silica coated with sodium hydroxide. It can absorb more than 30% of its weight in CO2 and exhibits a color change from light brown to ashy white when it is exhausted.
Atmospheric pressure
Refers either to a standard value of 1 atmosphere at sea-level (e.g., expressed in units of 101.3 kPa, 760 mmHg, 14.7 psi, 1.013 bar), or the measured environmental gas pressure measured at a specific time and location.
Background baselining
The practice whereby two gas analyzer chains are working in tandem to allow continuous measurement of a subject. In practice this is done by allowing only one of the analyzer chains to temporarily switch to measure incurrent gas in a repeated series. A macro is used to ‘stitch’ together the data vectors generating a continuous trace of excurrent gas and a near-continuous trace of incurrent gas (which is less susceptible to change).
Barometric pressure compensation
An approach to correct a sensor’s measured partial pressure to 1 atmosphere if ambient barometric pressure is known. In practice because ambient BP tends to be less than 1 atmosphere the corrected value increases the partial pressure measured by the sensor. For example – Xcorrected = [(Xmeasured * 101.325) / BPmeasured]
Basal metabolic rate (BMR)
The metabolic rate of an postabsorptive, resting endothermic animal that is ‘awake’ and within its thermoneutral zone. (Compare with Standard Metabolic Rate for ectotherms). Note that ‘overnight metabolic rate’ is approximately 5-10% lower than BMR.
Baselining
The process of periodically and temporarily switching from measuring a stream of excurrent gas in place of incurrent gas for the purposes of characterizing changes in ambient gas composition. Baselining periods should be as brief as possible and should be done as frequently as possible without compromising the quality of the metabolic measurements. See also ‘background baselining.’
Behavioral enrichment
The practice of enhancing the welfare of a captive animal by providing it with stimuli that encourage natural behaviors, and improve mental and physical well being. In behavioral and metabolic phenotyping systems behavioral enrichment can be achieved by adding running wheels, body mass habitats, and chewing/gnawing materials.
Bioremediation
The practice of using various microorganisms or their enzymes to neutralize contaminated environments or undesirable waste products.
Blood glucose
Refers to the amount of glucose molecules in a volume of blood (expressed in units of mg/dL or mmol/L). Blood glucose levels are generally similar in the arterial and venous blood. Typical blood glucose levels in healthy humans and mice are 70-100mg/dL, but can vary with nutritional and physiological state.
Blood pressure
Refers to the force (typically reported in units of mmHg) of blood on vessels. Pressure fluctuates as a result of the cyclic heart contractions. Peak and minimum values are the greatest in the aorta and are reported as systolic and diastolic values respectively (e.g., 120/80mmHg). Note that blood pressure continually decreases as it travels through systemic circulation (e.g., to 2-4mmHg in humans) before returning to the heart.
Body mass index (BMI)
A numerical value derived from an adult’s height and weight, used as a screening tool to estimate if they are at a healthy weight, underweight, overweight, or obese. It acts as a general indicator of body fatness, although it has been criticized in literature for failing to account for differences in body composition.
Bomb calorimetry
Refers to an analytical method used to measure the heat of combustion of solid or liquid samples by burning them in a high-pressure, oxygen-filled, sealed container known as a ‘bomb’. It calculates the energy released by measuring the temperature rise in a surrounding water bath. Heats of combustion for unknown samples are typically compared with those of known amount of benzoic acid standards.
Brown Adipose Tissue (BAT)
A type of mitochondria-rich adipose tissue that when triggered by adrenaline oxidizes fatty acids in order to generate heat. BAT is typically present in small mammals, hibernators, and newborns of larger mammals.
Bubble flow meter
A device used to measure the volumetric flow rate of gases. It works by measuring the time it takes for a soap bubble to travel between two calibrated markings in a tube with a known diameter. Its application tends to be limited to relatively low flow rates (e.g., < 1LPM) and measurements need to be corrected for temperature and pressure to determine mass flow.
Cachexia
An involuntary wasting syndrome characterized by the loss of more than 5% to 10% of body weight, primarily muscle mass with or without fat loss, commonly driven by chronic illnesses like cancer, heart failure, or COPD
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Caching behavior
The phenomenon whereby an animal (typically a rodent) obtains and scatters or hides bits of food to consume at a later time. While this behavior has adaptive significance for wild animals surviving unpredictable food supplies, it is problematic for accurate determinations of food intake in controlled laboratory experiments.
Calibration gas
Refers to a compressed gas mixture or a gas blend prepared in real-time that has a accurately and precisely specified composition. Common calibration gases in respirometry are 1%CO2 balanced with Nitrogen or 1% CO2 balanced with air. Generally pure gases (e.g., 100% N2 or 100% O2) are not considered to be calibration gases.
Carbon dioxide
Refers to one of the gaseous products of aerobic and anaerobic respiration. While fresh outdoor air may contain CO2 levels of ~420ppm, typical indoor air in a laboratory tends to range between 500-700ppm depending on occupancy and HVAC conditions. CO2 may occur in various isotopologues that have use as biochemical tracers.
Check valve
A check valve is a mechanical device that allows fluids to flow in only one direction, automatically preventing backflow. It operates without human intervention, using pressure differentials to open and seal,
Chronobiology
The scientific study of internal biological rhythms and their interactions with environmental, solar, and lunar cycles, with a focus on ~24-hour cycles (e.g., circadian, ultradian, infradian) that regulate behavior, physiology, and health.
Chronotherapy
The strategic scheduling of treatments—such as light therapy, medication, or sleep-wake adjustments to align with the body’s 24-hour circadian rhythms to maximize efficacy and minimize side effects. It is primarily used to treat circadian rhythm sleep disorders and depression,
Circadian
Relating to the approximate 24-h periodicity of a biological rhythm.
Constant volume respirometry
The process of sealing an organism inside an airtight metabolic chamber for a given amount of time and comparing the composition of the gas before and after the chamber. Contrast with ‘Flow-through respirometry’.
Deriving the Respirometry Equations
Core temperature
Refers to the internal temperature of an animals deep tissues and organs (e.g., liver, stomach, or lungs). It is generally higher and more stable than temperatures in the limbs or skin temperatures. The brain is usually not considered a ‘core’ organ. Core temperatures of mammals typically ranges between 36-40C and in birds ranges from 40-43C.
Coulometric respirometry
A sensitive method for continuously measuring oxygen consumption that requires an electrolytic O2 generator, a CO2 absorbent, and a precise pressure sensor. In practice an animal is placed inside rigid chamber where it continually consumes oxygen. The electrical charge used to generate O2 and restore the air pressure is proportional to VO2.
Countercurrent exchange
Refers to a structural configuration where two fluids flow in opposite directions in close proximity, allowing for maximum transfer of energy or fluids. Maintaining a constant diffusion gradient along the entire exchange surface is more efficient than alternate configurations (e.g., concurrent and cross-current).
Critical temperature
see ‘upper critical temperature’ or ‘lower critical temperature’.
Crossover concept
The idea that that as exercise intensity increases, the body switches from relying primarily on fat oxidation to burning carbohydrates for fuel. As energy demands rise, metabolic shifts favor glycogenolysis and fast-twitch fiber recruitment, resulting in a ‘crossover point’ (typically around 60-75% of VO2max).
Dalton’s law
Dead space
Dead space in the respiratory system refers to the volume of inspired air that does not participate in respiratory gas exchange and
exchange) with the blood. It consists of air trapped in conducting airways (anatomical dead space) or in non-functional alveoli (alveolar dead space) and in eupneic humans is roughly 150 mL. In animals with long necks it can be proportionally larger.
Delta value
In respirometry it refers to the magnitude of the compositional difference (typically O2, WVP, CO2)measured in incurrent and excurrent gas streams. In the field of stable isotopes it refers to the relative difference in the ratios of heavy to light isotopes in a sample.
Introduction to Stable Isotopes
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Depletion
Refers to the decrease in a rare isotope’s concentration relative to a standard. For example the 13C levels in organic components of fossil fuels are highly depleted.
Dew point
Refers to the amount of water vapor in the air and more specifically to the temperature at which air becomes saturated with water vapor and water vapor condenses into a liquid. Air chemically dried using a chemical like magnesium perchlorate may have a dew point of less than -70°C.
Diaphragm pump
A type of positive displacement pump that uses a reciprocating, flexible membrane (made of rubber or flexible plastic) and check valves to move fluids. It typically possesses a vacuum port to suck fluid in and a pressure port opposite port to push fluid out. These pumps cause pulsatile flows that may be undesirable for some applications.
Diet induced thermogenesis
The increase in metabolic rate and energy expenditure above resting levels that occurs after consuming food. It accounts for roughly 5–15% of daily energy expenditure, used for digesting, absorbing, and storing nutrients. It is also known as ‘specific dynamic action’, ‘postprandial thermogenesis’, and ‘thermic effect of food’.
Differential analyzer
A type of analyzer with two sensors making concurrent measurements on different samples. In respirometry a differential analyzer is capable of measuring incurrent and excurrent and determining the difference in gas composition between the two gas streams thereby precluding the need for periodic ‘baselining’.
Digital signal
A signal or measurement that is characterized by discrete values (e.g., 0 or 1). It is not continuous, but is less susceptible to interference and easier to transmit over long distances. Contrast with ‘analog’.
Diphosphoglycerate
Typically abbreviated 2,3-DPG it is a molecule constitutively found inside red blood cells that facilitates oxygen release in peripheral tissues. Levels of this molecule become adaptively upregulated during high-altitude acclimation and in response to exercise and/or anemia to improve oxygen delivery.
Direct calorimetry
A method for measuring an organisms metabolic rate by directly quantifying total heat produced by the body (via radiation, conduction, convection, and evaporation) while confined within a specialized, insulated chamber. It is considered a ‘gold standard’ because it measures both aerobic and anaerobic metabolism. [Compare with ‘Indirect calorimetry’]
Direct injection
A method during the validation of a metabolic chamber whereby a known amount of tracer gas is directly injected into the a main flow stream thereby bypassing the metabolic chamber. As such, a direct injection sets a theoretical threshold for gas recovery when injecting a tracer gas into a metabolic chamber.
Discontinuous gas exchange cycle
Diurnal
Refers to an organism that is primarily active during the ‘photophase’. Contrast with ‘nocturnal’.
Doubly-labeled water technique
Refers to an approach using stable isotopes of hydrogen (2H) and oxygen (18O) to estimate total daily energy expenditure in free-living humans and animals. In practice it works on the principle that the an ingested dose of water results in differential elimination of 2H (by way of water only) and 18O (by way of water and CO2). Although it is considered to be less accurate than respirometry, it is uniquely suited for studying ‘normal life’.
Introduction to Stable Isotopes
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Dry flow rate
This value can be calculated if WVP and BP are known following the equation FR dry = FR raw *[(BP-WVP)/BP]. It always results in a lower value than the raw flow rate.
Dry gas fraction
This value can be calculated if WVP and BP are known following the equation Gas dry = Gas raw * [BP/(BP-WVP)]. It always results in a higher value than the raw gas fraction.
Dwell time
Refers to the period of time (in seconds or minutes) that an automated respirometry system allows a given gas stream (e.g., incurrent or excurrent) is diverted through an analyzer chain. In a multiplexed system dwell times also refer to the duration that each sequential metabolic chamber is measured.
Ecophysiology
Refers to the study of how an organism’s internal physiological processes adapt to external environmental factors like temperature, light, water availability, and nutrient levels. It blends ecology and physiology to understand how organisms survive, function, and reproduce in specific habitats.
Eddy currents
Circular, swirling, or reverse currents that flow against the main fluid direction, commonly occurring in turbulent flow systems. Inside metabolic chambers they result in plumes of non-homogenous gas mixtures that can result in unwanted variations in respiratory gas measurement.
Energetics
Refers to a broad area of study of energy, focusing on is flow, transformation, and storage in physical, chemical, and biological systems. Among the branches of energetics, bioenergetics has the greatest involvement with respirometry and metabolic and behavioral phenotyping.
Energy balance
Refers to the energy surplus of deficit (typically reported in terms of ±kcal) measured in an individual in a metabolic and behavioral phenotyping system. It is calculated as the energy in the food consumed minus the metabolic energy measured using indirect calorimetry. In general, a positive energy balance means body mass is occurring whereas a negative energy balance the animal has not met its metabolic demands with its food intake.
Energy expenditure
Refers to an organisms metabolic energy per unit time (usually in kcal/day) calculated from measurements of rates of oxygen consumption and carbon dioxide production.
Enrichment
In the field of stable isotopes, it refers to the increase in a rare isotope’s concentration relative to a standard. In metabolic and behavioral phenotyping it typically refers to an object or material introduced into a animal cage to improve its welfare by reducing stress or increasing activity. See also ‘behavioral enrichment’.
Eurythermy
Refers to the ability of an organism to tolerate and function within a wide range of ambient environmental temperatures. Contrast with ‘stenothermy’.
Evaporation
Refers to the physical process whereby a liquid changes into a gas at a temperature below its boiling point. It is a cooling process because the highest-energy molecules escape, reducing the average temperature of the remaining liquid. It is used by many animals as a mechanism to reduce body temperature.
Excurrent
Refers to the gas stream leaving a metabolic chamber. If an animal is in the chamber, this gas stream generally contains lower oxygen, and higher CO2 and water content than the ambient gas. Contrast with ‘incurrent’.
Expedata
Refers to a graphical software package developed by Sable Systems that is used to collect and analyze data and signals by Classic Line instruments.
Setting up a Small Animal Respirometry System: The Expedata Setup File
Factorial increase
In the literature of bioenergetics it typically refers to the multiple that an elevated metabolic rate (e.g., during exercise, digestion, cold stress) is higher than a lower metabolic rate (e.g., RMR, BMR, etc.). For example a mouse maintained at 10C may have a factorial increase of 3, meaning its metabolic rate is 3 times its basal metabolic rate measured within its thermoneutral zone.
Fasting
Refers the situation whereby a postabsorptive animal, through some intrinsic mechanism, foregoes an opportunity to eat. It is distinguished from ‘starvation’ not in it severity but rather the fact that is voluntary allotting animals to allocate their time and energy to other activities.
Fat free mass
Refers to the total amount of all non-lipid components in the body. While often used interchangeably with ‘lean body mass’ LBM may sometimes be used to include a small percentage of structural lipids (e.g., in cell membranes).
Feedforward effect
Refers to an anticipatory, proactive regulatory mechanism where the body detects a change in the environment and adjusts physiological responses before a significant disturbance occurs. A textbook example is the rapid increase in ‘minute ventilation’ that takes place at the onset of exercise in humans.
Fermentation
The cellular process by which organic substrates are catabolized in the absence of oxygen. It typically involves bacteria or fungi but also includes the process of animals generating lactic acid.
Fiber photometry
An in-vivo optical technique that measures real-time neural activity in freely behaving animals. By implanting a fiber optic cannula, it record fluorescent signals form genetically modified molecules to map neural circuit dynamic and behavioral collections in specific cell populations. Contrast with ‘optogenetics’.
Fick’s Law of Diffusion
Refers to the phenomenon by which molecules move from an area of higher concentration to an area of lower concentration across a biological membrane. Specifically it describes the relationship between the concentration gradients, the diffusion coefficient of a membrane and the surface area across which diffusion occurs.
Field metabolic rate (FMR)
A measurement of the total energy expenditure of a free-living organism in its natural habitat for one or more days. It is typically made using the doubly-labeled water method or the bicarbonate method.
First-order kinetics
In respirometry it refers to a situation where the elimination or appearance of a substance in a mixture changes exponentially as the concentration of the substance changes. This can be contrasted with zero-order kinetics whereby a constant amount of a substance is added or removed from a system, and second-order kinetics where the change may be concentration-dependent.
Flow through respirometry
A type of indirect calorimetry whereby an organism is placed inside a metabolic chamber and air is continually entering or leaving the chamber at a constant rate. Contrast with ‘Constant-volume respirometry’.
Deriving the Respirometry Equations
Setting up a small animal respirometry system
An Introduction to Animal Respirometry Course
Food quotient (FQ)
A unitless value that accounts for the compostion of the daily dietary intake, specifically calculating the proportions of protein, fat, carbohydrate, and alcohol consumed. In practice the stoichiometric relationship of each macronutrient can be used to estimate a value typically ranging from 0.70 to 1.0 that should approximate the RER of an organism.
Food restriction
Refers to an experimental approach whereby food is either removed or access to food is mechanically controlled. It is frequently used to study the effects of intermittent feeding in rodents.
Fractionation
Refers to the physical or biochemical processes that alter the relative abundance of isotopes in a substance. In general the heavier isotopic siblings are less likely to take part in chemical reactions.
Introduction to Stable Isotopes
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Fuel cell
A device that generates an electrical voltage when gaseous oxygen crosses a membrane and triggers a reaction between a lead anode and gold cathode. These sensors typically have a limited lifespan of 1-2 years.
Futile cycle
A futile cycle in biochemistry occurs when two opposing metabolic reactions run simultaneously, resulting in a net consumption of ATP and the release of heat without producing a significant, net, useful chemical product. Though once thought to be merely wasteful, these cycles are now recognized for regulating metabolic flux and generating heat.
Germ free
Typically refers to a laboratory rodent that has been raised in a completely sterile environment and is devoid of all microorganisms (e.g., bacterial, viruses, fungi, and parasites). They typically have weakened immune systems and reduced metabolic rates. Germ-free rodents may be the starting point for ‘gnotobiotic’ studies where they are inoculated only with selected microorganisms. Also known as ‘axenic’.
Glucose tolerance test
An experimental procedure whereby a subject is administered (usually orally) a relatively large bolus of glucose to study how it regulates circulating blood glucose levels. It is one of the diagnostic tests for diabetes.
Gnotobiotic
Typically refers to a laboratory rodent raised in a sterile environment where all life forms are fully controlled by the researcher. A gnotobiotic rodent may either be germ-free/axenic or have been colonized with one ‘monocolonized’ or multiple microbial strains.
Graded exercise test
A standardized protocol (often abbreviated GXT)used to observe the dynamic relationship between exercise workload and the integrated cardiovascular, pulmonary, musculoskeletal, and neuropsychological systems. During a typical test running or cycling speed and incline or resistance, respectively, are stepwise increased until VO2max is achieved. Heart rate, ECG, and blood metabolites may also be measured.
Mouse Graded Exercise Test to Obtain VO2 max
Sable Announces the Release of New Metabolic Treadmill for Mice
Gut-brain axis
The gut-brain axis is a bidirectional communication network linking the central nervous system (brain) with the enteric nervous system (gut “second brain”). It facilitates constant, two-way signaling via neural (vagus nerve), hormonal, and immune pathways. This interaction regulates digestion, immune function, mood, stress, and cognitive health and is thus a fertile area for metabolic and behavioral phenotyping research
Habituation
Refers to the phenomenon whereby an organism decreases or ceases its response to a repetitive, harmless stimulus over time. It is considered to an adaptive response to conserve energy and focus on more relevant stimuli.
Heliox
Heliox id a mixture of helium and oxygen (typically 80/20 or 70/30) which reduces air flow resistance and decreases ventilatory work. In studies of summit metabolic rate, it causes significantly higher body heat loss than air due to helium’s high thermal conductivity, which is approximately five times greater than air.
Hess’s law
The concept that the total energy released in a chemical reaction is independent of the of the number of steps in a reaction. One implication of this is that the heat energy released during immediate combustion of food using a bomb calorimeter is equivalent to the energy gradually released when an animal oxidizes the same food.
High fat diet
Typically refers to a commercially prepared rodent diet that has 32-60% of calories from lipids, designed to rapidly induce obesity, metabolic syndrome, and insulin resistance. These diets can become viscid at warm environmental temperatures.
Home cage
Refers to the standard, familiar living environment where laboratory mice or rats are housed, typically consisting of a cage, bedding, water, food, and environmental enrichment. The home cage is considered the primary, undisturbed environment where rodents spend most of their time and is the most appropriate habitat to study the effects of experimental manipulations.
Rodent Metabolic and Behavioral Cages Time and Locomotion Budgets
Huddling behavior
Refers to the purposeful aggregation of conspecifics of heterothermic animals with the goal of conserving body heat, minimizing energy expenditure, and increasing survival. It is commonly used by rodents and birds.
Hyperbaric
Refers to a condition whereby the pressure of a gaseous environment is significantly greater than 1 atmosphere (typically 1.5 to 3 atmospheres). Note that the partial pressures of all constituent gases in that hyperbaric environment are increased. Contrast with ‘hypobaric’.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Hypercapnia
Refers to the condition of elevated CO2 in the body, that is typically caused by inadequate ventilation. It may also refer to a situation of environmentally elevated CO2 levels. In respirometry both situations can occur if the flow rates are too low. In the short term hypercapnia tends to decrease blood pH and has been linked with cognitive impairment.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Hyperoxia
May refer either to 1) a condition whereby inhaled gas (near normobaric conditions) is above normal (e.g., 25-35% O2), or 2) a situation whereby tissue oxygen levels are substantially higher than they should be near sea level. The latter condition can be caused by either elevated O2 content at normal atmospheric pressure, atmospheric pressures greater than ~1.5ATM, or both. Contrast with hypoxia.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Hyperthermia
A pathological condition occurring when core body temperature above a setpoint that cannot be defended using behavioral or physiological mechanisms. It is distinct from a fever where setpoint is endogenously elevated. Contrast with ‘hypothermia’.
Hypobaric
Refers to a condition whereby the pressure of a gaseous environment is less than 1 atmosphere. This naturally occurs at high altitudes. Note that the partial pressures of all constituent gases in that hyperbaric environment are decreased. Contrast with ‘hyperbaric’.
Hypothermia
Refers to the general condition whereby behavioral and physiological mechanisms are unable to maintain the core body temperature at its preferred setpoint. A core temperature of 35C may be considered hypothermic in humans. Contrast with ‘hyperthermia’.
Hypoxia
May refer either to 1) a condition whereby O2 levels in inhaled gas (near normobaric or conditions) is below normal (e.g., 10-15% O2), or 2) a situation whereby tissue oxygen levels are substantially lower than they should be near sea level. The latter condition can be caused by numerous environmental conditions as well as pathological conditions related to O2 binding in the blood.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Incurrent
Refers the both the direction and the composition of stream of gas entering a metabolic chamber. Incurrent gas should ideally be the same composition as gas sampled during ‘baselining’.
Deriving the Respirometry Equations
Indirect calorimetry
Indirect calorimetry is the method by which metabolic rate is estimated from measurements of oxygen consumption and carbon dioxide production. [Contrast with ‘Direct calorimetry’] [Compare with ‘respirometry’]
Deriving the Respirometry Equations
Inline filter
Refers to a cylindrical device installed directly onto a fluid supply line to remove contaminants. In respirometry inline filters are typically used to prevent hair and dust from entering the gas analyzer chain. Typically they are replaced annually.
Insensible water loss
Refers to the continuous and unconscious loss of body fluid through constitutive skin evaporation (not active sweating) and breathing. It represents about 30–50% of all daily water loss, averaging 600–800 mL/day in adults. Contrast with ‘sensible water loss’.
Instantaneous correction
see ‘Z-transformation’
Intermittent fasting
Refers to an eating pattern cycling between periods of eating and fasting, designed to promote weight loss and metabolic health by creating a calorie deficit. Periods of fasting may last several hours to a couple of days.
Isotope
A variant of a particular chemical element that has the same number of protons in their atomic nuclei but different numbers of neutrons. These differences in atomic mass cause slight differences in biochemical properties of the element.
Introduction to Stable Isotopes
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Isotopologue
Refers to molecules that differ only in their isotopic composition. Contrast with ‘isotopomer’.
Introduction to Stable Isotopes
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Isotopomers
Refers to molecules that have the same number of isotopic substitutions, but differ in the location of the substitutions. Contrast with ‘isotopologue’.
Introduction to Stable Isotopes
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Kleiber’s Law
The principle that a the metabolic rate of a given species of organism scales allometrically to the 0.75 power of its body mass, and not in a 1:1 ratio. In short, it explains that larger organisms of a given group (e.g., endothermic vertebrates, ectothermic vertebrates, invertebrates, plants, unicellular organisms, etc.) have lower metabolic rates per unit of mass than smaller ones.
Lactic acid
Refers to a molecule with the formula C3H6O3, that resembles half of a glucose molecule, it is technically not a carbohydrate but rather an organic acid. During moderate or intense exercise pyruvate generated by glycolysis may be anaerobically converted into lactate rather than being oxidized in the citric acid cycle. Eventually circulating lactate travels to the liver where it is used for gluconeogenesis.
Lag correction
Refers to a time correction in a data stream that accounts for differences in response times of different sensors. Typically if a chain of analyzers are positioned in series the last analyzer in the chain is given the largest lag correction to synchronize data.
Lag time
Refers to the time delay that occurs between with a sensor is initially expose to a stimulus and when it begins to register meaningful changes. Analyzers in series may have different lag times that need to be considered during data analysis.
Load cell
A transducer that converts mechanical force (e.g., weight, tension, compression, or pressure) into a measurable electrical signal, usually a voltage output. In practice they are used inside devices that monitor food and water intake as well as body mass.
Longitudinal study
A research design that involves repeated observations or measurements of the same individuals, variables, or subjects over an extended period, ranging from weeks to decades. These observational studies track changes, development, and trends, allowing researchers to establish sequences of events and potential cause-and-effect relationships. Although they require more time than ‘cross-sectional’ studies, they offer the statistical benefit of ‘repeated measures’.
Lower critical temperature
The ambient temperature below which the rate of metabolic hat production of a resting thermoregulating tachymetabolic animal must be increase either by shivering or nonshivering thermogenesis
Lowest observed metabolic rate
Refers to the lowest rate of metabolism measured during a defined time period with the aim of quantifying periods of minimal movement or activity. In practice, a 10-minute window for LOMR might be selected from a continuous recording lasting a couple of hours.
Luer connector
Refers to a standardized, threaded medical fitting used to create secure, leak-proof, and detachable connections between syringes, catheters, and tubing. The locking types consist of a male tapered tip that screws into a female hub, ensuring components stay connected even under pressure. Slip connections rely only on friction between the male and female surfaces and are more prone to separate.
Macro
A customized software program designed to take a large batch of time-series datasets and correct, calculate, and collate raw data into processed data in a format that is easy to evaluate by an end-user. Some macros may also include post-hoc statistical analyses of the data.
Setting up a Small Animal Respirometry System: The Expedata Setup File
Macrointerpreter
A Sable Systems software package that allows users to visualize raw Promethion data and to run macros to analyze data.
Setting up a Small Animal Respirometry System: The Expedata Setup File
Magnesium perchlorate
A powerful, white, crystalline inorganic oxidizing agent and highly effective, regenerable drying agent used for gas analysis and moisture absorption. It is commonly used as a desiccant in laboratory and industrial settings, is highly soluble in water, and can explode under heat or fire. More effective, but also substantially more expensive than Drierite or silica gel.
Manifold
A rigid structure that connects three or more tubes. Manifolds are often used to split a single fluid stream into multiple streams or to combine multiple fluid streams into a single stream.
Mass flow controller
A mass flow meter that is paired with a proportional control valve that uses a feedback loop to ensure constant flow rates at a user-defined set point.
Mass flow meter
An electronic device that measures the mass flow rate of a fluid through a tube. As opposed to volumetric flow it is unaffected by changes in temperature, pressure, or viscosity.
Mathematical scrubbing
A computational method to account for the dilution effect of water vapor (and sometimes other gas species) without having to chemically scrub water vapor from a gas stream prior to compositional analysis. It is one of the key differentiators of the Sable Systems approach.
Metabolic acidosis
Refers to the general condition whereby the pH of the blood falls below its typical lower range. It may be caused by excessive secretion and elimination of bicarbonate or increased accumulation of acids (e.g., as a result of ingestion, ketoacidosis, or lactic acid production). Contrast with ‘metabolic alkalosis’ and ‘respiratory acidosis’.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Metabolic alkalosis
Refers to the general condition whereby the pH of the blood increases above its typical upper range. It may be caused by excessive loses of gastric acid (e.g., during vomiting), severe dehydration, or secondary effects of hypokalemia. Contrast with ‘metabolic acidosis’ and ‘respiratory alkalosis’.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Metabolic and behavioral phenotyping
The simultaneous measurement of energy expenditure (e.g., using indirect calorimetry), and activity patterns (e.g., food/water intake, locomotion, and wheel running), primarily in rodents, to study metabolic syndrome, obesity, and pharmacological targets.
Metabolic canopy
A metabolic canopy (or canopy hood system) is a clear plastic tent or dome placed over a subjects head and shoulders, typically paired with a plastic or fabric veil to ensure complete breath collection. In practice excurrent gas is pulled from one end of the dome at a rate of 30-80 LPM to measure resting or basal energy expenditure. While it tends to be more comfortable than a mask or mouthpiece, it is not well suited for measuring metabolic rates during activity.
Metabolic flexibility
Generally refers to the ability for an organism to adaptively switch between oxidizing carbohydrates or lipids to fuel energy requirements. These shifts in fuel selection may be driven by dietary shifts, activity levels, and therapeutic interventions.
Metabolic hood
See ‘metabolic canopy’
Metabolic syndrome
Metabolic syndrome is a cluster of at least three concurrent conditions from the following list: increased waist circumference, high blood pressure, high triglycerides, low HDL cholesterol, or high fasting blood sugar. The condition significantly raises the risk of heart disease, stroke, and type 2 diabetes. It is closely linked to obesity, inactivity, and insulin resistance
Metabolic treadmill
A treadmill that is sufficiently enclosed enabling it to collect all of the exhaled breath from an animal for purposes of respirometry. The treadmill may adjust speed and incline and use various adverse stimuli (e.g., lights, sounds, push rods, electrical shocks) to motivate the animal to run.
Mouse Graded Exercise Test to Obtain VO2 max
Sable Announces the Release of New Metabolic Treadmill for Mice
Methane
A colorless, odorless, flammable gas [CH4] that is the primary component of natural gas and is produced by methanogenic microbes. It is produced in large quantities in the guts of ruminant animals and its production in humans and mice is highly variable.
Promethion Methane Gas Analyzer
Microbiome
Refers to the communities of microorganisms (e.g., bacteria, archaea, fungi) and viruses that inhabit the body of a metazoan. It includes the microorganisms as well as their respective environments (e.g., intestine, cecum, skin, mouth, etc.)
Mixing chamber
Refers to a device used in respirometry to blend excurrrent gas samples, eliminating breath-by-breath fluctuations to provide a stable, averaged, and accurate measurement. These devices are particulalry useful when using masks and canopies where the excurrent gas may otherwise have limited opportunity to become mixed in the incurrent stream.
Moving average
Refers to a statistical calculation used to analyze time-series data by creating a constantly updated average of a user-defined subset of data points. It smooths out short-term fluctuations and sensor noise. In the most common case all data points within a subset are weighted equally.
Setting up a Small Animal Respirometry System: The Expedata Setup File
Multiplexing
The practice of using an automated device to sequentially select a single fluid stream from multiple streams and diverting it into a single pathway, typically for the purpose of measurement (e.g., flow rate and/or fluid composition) by a common analyzer.
RM-8 Respirometry Flow Multiplexer
Nafion
Refers to a chemical polymer, typically formed into a tube, that selectively permits transfer of water molecules from one side of the membrane to another leaving most gas species (e.g., CO2, O2 and N2) in a stream untouched. The diffusion follows a first order kinetic reaction and thus conveniently allows for equilibrium of the partial pressure of water vapor on either side of its membrane.
Natural abundance
Refers to the naturally occurring molar ratio of isotope in a sample. Because ‘fractionation’ is inevitable, natural abundance generally refers to a narrow range of values rather than a fixed value.
Introduction to Stable Isotopes
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Needle valve
A needle valve is a precision flow-control device that uses a slender, tapered, needle-shaped plunger to regulate, restrict, or shut off the flow of liquids or gases through a small orifice. Unlike proportional valves they tend to require periodic manual adjustments and do not ensure flow rates remain constant over long periods.
Non-shivering thermogenesis
Obesity
Refers to a chronic, complex disease defined by an excessive accumulation of body fat that increases the risk of serious health conditions like type 2 diabetes, heart disease, and certain cancers. It is generally diagnosed in adults with a Body Mass Index (BMI) of 30. Mice, rats, and other model species are also capable of exibiting obesity.
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
On-demand regulator
A gas control device that automatically supplies compressed gas only when a downstream vacuum pump activates it. Because these vales remain ‘off/closed’ until needed these regulators can be constitutively connected to a cylinder, providing a “ready state” for quick calibration.
Optogenetics
A technique used in neuroscience research that uses light to control the activity of specific, genetically modified neurons in living tissue. In practice light sensitive proteins are periodically exposed to specific wavelengths of light to elicit a biochemical response. Contrast with ‘fiber photometry’.
Oral gavage
A technique for delivering substances (drugs, food, or compounds) directly into the stomach of laboratory animals (e.g., typically rodents) using a rigid feeding needle or semi-rigid tube inserted through the mouth and esophagus. It is primarily used in toxicological and pharmacological studies to ensure exact dosing volume and time.
Overnight metabolic rate
Also referred to as ‘sleeping metabolic rate’ is approximately 5-10% lower than a subjects basal metabolic rate. Note that for nocturnal animals, it may be more appropriate to use the term ‘sleeping metabolic rate’ to avoid confusion.
Oxygen debt
Refers to the amount of extra oxygen required by the body during the post-exercise states to restore oxygen levels to pre-exercise conditions. It may also be referred to as ‘excess post-exercise oxygen consumption’ (EPOC), and in humans the duration of the response may last for several minutes. Contrast with ‘oxygen deficit’.
Oxygen deficit
Refers to the difference between the oxygen taken into the body at the onset of exercise and the oxygen that is actually consumed to meet the energy demands of the exercise. Contrast with ‘oxygen debt’.
Pair feeding
Pair-feeding is an experimental design used in animal studies to ensure that, when testing a treatment that may reduce appetite, any observed differences in outcomes (like weight loss or metabolism) are due to the treatment itself rather than differences in food intake. A “pair-fed” group is restricted to eating only the same, typically smaller, amount of food consumed by a treated group.
Parabronchi
Parabronchi are tiny, open-ended, parallel tubes in the lungs of birds and some reptiles that allow for continuous, one-way airflow, facilitating highly efficient, cross-current gas exchange. Unlike mammalian alveoli (dead-end sacs), parabronchi allow constant gas exchange to support high-metabolism flight
Paramagnetic oxygen analyzer
a sensor that measures oxygen concentration by leveraging oxygen molecules’ unique, strong magnetic susceptibility. In short a nitrogen-filled glass dumbbell suspended in a magnetic field rotates when oxygen enters the chamber and displaces it. Although these analyzers are long-lasting and particularly useful for their ability to measure a wide range of oxygen concentration, they are relatively expensive and tend to require frequent calibrations because of drift.
Partial pressure
Refers to the pressure that a single component of a gas mixture would exert on a fixed volume container at a given temperature. Note that the sum of partial pressures of all constituent gases is equal to total gas pressure. See also, ‘Daltons law’.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Pathogen free
Refers to an organism that is free only of specific disease-causing organisms, while still harboring a normal, undefined, non-pathogenic microbiome. Ther term Specific Pathogen Free (SPF) is used to refer to animals that lack a defined list of pathogens. Contrast with ‘germ free’.
Pejus
Refers to a range of environmental conditions, typically temperatures, where physiological performance begins to decline, reducing its aerobic scope and overall fitness. Unlike optimal conditions, the pejus range causes acute stress although the organism can still survive there, albeit with restricted activity
Peltier effect
A thermoelectric phenomenon where passing an electric current through a junction of two dissimilar conductors or semiconductors causes heat to be absorbed at one junction (cooling) and released at the other (heating). In practice the Peltier effect can be used to heat or cool a given object relatively rapidly and with high precision.
Photoperiod
Refers to the duration of natural or laboratory manipulated light periods (i.e., photophase) and dark periods (i.e., scotophase) in a 24-hour cycle. It may be expressed in the form where ‘14L:10D’ refers to 14 hours of light followed by 10 hours of darkness.
Photophase
Refers to the light period within a 24-hour light/dark cycle, representing the ‘day’ portion of a photoperiod. Contrast with ‘scotophase’.
Piloerection
refers to the involuntary bristling of hairs on the skin’s surface, usually caused by fear, cold, or strong emotions. It occurs when arrector pili muscles at the base of hair follicles contract, often as a sympathetic nervous system reaction. Functionally it serves to increase the boundary layer to trap heat when the body is exposed to cold temperatures.
Postabsorptive
Refers to a nutritional state where the stomach and upper small intestine have emptied their contents from the previous meal and most dietary nutrients have already been absorbed into circulation. It is sometimes referred to as ‘fasted-state’ alghouth fasting has a unique definition. Postabsorptive is a requirement for measuring basal and standard metabolic rates of animals.
Postprandial thermogenesis
The increase in metabolic rate and energy expenditure above resting levels that occurs after consuming food. It accounts for roughly 5–15% of daily energy expenditure, used for digesting, absorbing, and storing nutrients. It is also known as ‘diet induced thermogenesis’, ‘postprandial thermogenesis’, and ‘thermic effect of food’
Postprandial thermophily
Precision
Refers to the consistency or repeatability of multiple measurements made by a sensor. Note that Precision is different from ‘Resolution’ and ‘Accuracy’ and generally cannot be improved by doing ‘Calibrations’.
Preclinical research
Refers to a stage of drug development that takes place before human testing, using laboratory (in vitro) and animal (in vivo) studies to evaluate a compound’s safety, toxicity, and effectiveness. It does not require FDA-approved devices.
Pressure
In physiology and respirometry this term generally refers to the force exerted per unit area by a fluid. Liquid pressure includes blood pressure and osmotic pressure. Gas pressures may refer to dissolved gases as well as those inside and around the body. There are more type of units to express pressure than perhaps any other measureable variable in science.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Propane burn
The practice of combusting liquid propane gas to consume oxygen and generate carbon dioxide. The change in mass of the propane tank is used to generate a theoretical VO2 and VCO2. Propane burns are most effective at generating conditions where RER is 0.60 but because of safety issue are being replaced by direct gas injections using N2 and CO2. (see N2 dilution technique) (See also ‘butane burn’.)
Proportional integral derivative control
Refers to a closed-loop feedback mechanism in automation that maintains a desired variable (e.g., temperature or speed) by constantly calculating the difference between a setpoint and a measured value, adjusting the output accordingly.
Proportional valve
A proportional valve is an electro-pneumatic device that controls fluid flow or pressure in direct proportion to an electrical input signal (voltage or current). Unlike standard “bang-bang” solenoids that only open or close, these valves allow for precise, continuous, and adjustable regulation of flow or pressure.
Pseudoreplication
Pseudoreplication occurs when data points in an experiment are not statistically independent, yet are treated as such, artificially inflating the apparent sample size. In metabolic measurements it may occur by taking repeated measurements over time from a single subject but treating them as independent replicates.
Pull mode system
A flow through respirometry system where gas is actively pulled from a metabolic chamber. Pull systems are less susceptible to leaks and flow rate is typically measured in the excurrent gas stream. Contrast with Push mode system.
Deriving the Respirometry Equations
Purge gas generator
Refers to a system designed to continuously produce dry, purified gas (e.g., CO2-free air or nitrogen) from a standard compressed air supply. Most systems use alternating pressurized chambers containing molecular sieves specific to the desired gas outputs. It offers a relatively inexpensive alternative to high pressure gas cylinders for high output demands.
Push mode system
A flow through respirometry system where incurrent gas is actively pushed into a metabolic chamber. Push systems require a sealed chamber and flow rate is measured either on the incurrent or excurrent locations. Contrast with Pull mode system
Deriving the Respirometry Equations
Q10
A quantitative method of characterizing the thermal sensitivity of a given physiological or behavioral parameter over a temperature range of 10°C.
Rearing
Refers to a vertical, exploratory action where the mouse stands on its hind legs, often lifting its forelimbs to investigate its environment, sniff the air, or look for distant cues. It is a key indicator of cognitive function, environmental curiosity, and anxiety levels.
Reed switch
A compact, magnetically operated electrical switch consisting of two magnetic, flexible metal reeds sealed inside a small, nitrogen-filled glass envelope. When a magnetic field approaches, the reeds attract, closing the circuit, and they open when the field is removed. These sensors can measure very rapid signals and have long life.
Relative humidity
Refers to the amount of water vapor actually in the air, relative to the maximum amount of water the air can possibly hold at a given temperature. It is expressed as a percentage where conditions of 100% RH results in condensation. Constrast with ‘absolute humidity’.
Resolution
Refers to the smallest change a sensor can detect. Like ‘Precision’ Resolution is generally inherent to a given sensor and cannot be ‘improved’ by ‘Calibration’ or other means.
Respiration
Refers to the cellular process in which cells break down organic molecules using to produce energy in the form of adenosine triphosphate (ATP). Aerobic respiration typically involves all three or the final two of the following stages: glycolysis, Krebs cycle, and oxidative phosphorylation. Anaerobic respiration is known as ‘fermentation’.
Deriving the Respirometry Equations
Setting up a small animal respirometry system
Respiratory acidosis
A condition where the lungs do not release enough CO2 causing the accumulation in the blood which leads to reductions in blood pH. It is typically an acute condition and is corrected by changes in ventilation. Contrast with ‘respiratory alkalosis’.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Respiratory alkalosis
A condition caused by rapid and/or deep breathing that leads to excessive loss of CO2 from the blood stream. This reduction in CO2 is typically manifested as an increase in blood pH. It is typically an acute condition and is corrected by changes in ventilation. Contrast with ‘respiratory acidosis’.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Respiratory exchange ratio (RER)
A unitless value that is calculated as rate of carbon dioxide production divided by rate of oxygen consumption measured at the organism level. Typical values range from 0.7 and 1.0 and are used to interpret the relative reliance on lipid oxidation and carbohydrate oxidation respectively. Contrast with ‘respiratory quotient’.
Deriving the Respirometry Equations
Setting up a small animal respirometry system
An Introduction to Animal Respirometry Course
Respirometry
Refers to the general technique for measuring rates of oxygen consumption and carbon dioxide production but not necessarily calculate ‘energy expenditure’. It is distinct from ‘indirect calorimetry’ in that all indirect calorimetry involves respirometry, but not all respirometry is intended to calculate energy expenditure.
Room calorimetry
Refers to the practice of using a room-sized, climate-controlled chamber to measure a human subject’s total energy expenditure, metabolism, and substrate oxidation over 24 hours to several days. Participants live inside these rooms, allowing for free movement and varied behaviors such as sleeping, exercising, and routine activities.
Rotameter
Also known as a ‘variable area flow meter’ is a device used to measure volumetric flow rate of a fluid consisting of a hollow tube containing a spherical or bullet-shaped ‘float’ (often made of steel aluminum, glass, or PTFE depending on the viscosity of the fluid). In practice the float’s vertical position within the rotameter is correlated with the flow rate.
Ruminants
Refers to a functional group of mammals (e.g., cattle, sheep, and deer) that have a four-compartment stomach that works as a fermentation vat where microbes break down cellulose before traditional digestion.
Running wheel
A freely rotating wheel placed inside rodent cages to provide enrichment activity and voluntary exercise. When combined with a rotational counting device can also be used to quantify speed and distanced traveled. Contrast with ‘treadmill’.
Savitsky-Golay smoothing
Refers to a digital filtering technique that removes high-frequency noise from data while preserving essential signal features like peak height and width better than ‘moving average’ smoothing. It works by fitting a low-degree polynomial to adjacent data points via linear least-squares within a moving window.
Setting up a Small Animal Respirometry System: The Expedata Setup File
Scotophase
Refers to the dark period within a 24-hour light/dark cycle, representing the ‘night’ portion of a photoperiod. Contrast with ‘photophase’.
Sensible water loss
Sensible water loss refers to body fluid loss that is consciously perceived and noticeable. It includes, primarily, urine output, along with feces and vomit. Contrast with ‘insensible water loss’.
Set-point
Refers to an ‘target’ value for a given physiological value (e.g., temperature, blood pressure, or glucose level). It utilizes negative feedback loops, where receptors detect deviations and effectors reverse the trend to maintain stability. Set points may change during periods of acclimation or acclimatization.
Shivering thermogenesis
Refers to an involuntary physiological process where skeletal muscles rapidly contract and relax to generate body heat in response to cold exposure or early hypothermia. Contrast with ‘nonshivering thermogenesis’.
Shock grid
Refers to an electrified metal grid located at the rear of a laboratory rodent treadmill (usually used for mice or rats) designed to deliver a small, controlled electric shock. It serves as an aversive stimulus to motivate animals to continue running and avoid stopping during fatigue.
Sable Announces the Release of New Metabolic Treadmill for Mice
Shredding behavior
Refers to an instinctual behavior of tearing apart materials. In the case of rodents shredding chow blocks this can become problematic for accurate measurements of food intake because shredded food is not actually ingested.
Silica gel
Refers to a granular form of silicon dioxide that is used to chemically scrub water vapor from a gas stream.While it is relatively inexpensive and can absorm ~30% of its mass in water, it does not dry the air as well as other scrubber chemicals. Compare with ‘magnesium percholorate’ or ‘Drierite’.
Sleeping metabolic rate
Smoothing
Technique used to reduce noise and short-term volatility in time series data to reveal underlying, long-term trends and patterns. Common methods include ‘moving averages’, exponential smoothing, and ‘Savitsky-Golay’ filters.
Setting up a Small Animal Respirometry System: The Expedata Setup File
Soda lime
Refers to a white, granular, and highly corrosive mixture of calcium hydroxide and sodium hydroxide or potassium hydroxide. It is an effective chamical scrubber for removing carbon dioxide from gas streams. It can also have color-indicator added to visualize when its absorpbtive capacity is exhaused.
Solenoid valve
Typically refers to a valve that has an electromagnetic actuator to open or close a valve to control the flow of fluids. They often come in two configurations whereby they are either normally closed (NC) or normally open (NO). See also ‘proportional valve’.
Spanning
Typically refers to the process of correlating a sensor output to a non-zero stimulus with a known value. Note that spanning is most accurate at values that are slightly above the expected upper limits of the measured value. Spanning should be done only after ‘zeroing’ a sensor.
Specific dynamic action
The increase in metabolic rate and energy expenditure above resting levels that occurs after consuming food. It accounts for roughly 5–15% of daily energy expenditure, used for digesting, absorbing, and storing nutrients. It is also known as ‘diet induced thermogenesis’, ‘postprandial thermogenesis’, and ‘thermic effect of food’
Stable Isotope
A non-radioactive form of an atom of a given element that does not decay over time. Stable isotopes of an element contain the same numbers of protons, but differ in the number of neutrons and thus atomic mass. The heavier stable isotope of a given element is typically the less abundant species.
Introduction to Stable Isotopes
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Standard metabolic rate
The metabolic rate of an postabsorptive, resting ectothermic animal that is ‘awake’ and its body temperature is in equilibrium with a specified environmental temperature. (Compare with Basal metabolic rate for endotherms)
Standard pressure
A benchmark temperature of 0°C (273.15 K or 32°F) used to normalize comparisons where gas pressures may vary.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Standard temperature
A benchmark pressure of 1 atmosphere (atm) or 100 kPa (1 bar) used to normalize comparisons where gas temperatures may vary.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Steady state
Refers to a condition of dynamic equilibrium where an organism’s internal environment (e.g., such as metabolite concentrations, ion concentrations, or temperature) remains relatively constant over time.
Stenothermy
refers to the ability of an organism to tolerate and function within a narrow range of ambient environmental temperatures. Examples include organisms inhabiting caves, deep sea, and polar regions. Contrast with ‘eurythermy’.
Stop flow respirometry
The practice of placing an organism inside an fully sealed metabolic chamber flushed with room air for a given and measuring the composition of a subsample of the chamber gas after a given amount of time. It is typically reserved for situations where the metabolic rates are too low to be conveniently measured ‘flow through’ calorimetry.
Deriving the Respirometry Equations
Subcutaneous
Refers to the tissue layer below the epidermis and dermis but above the muscle layer. It may be referred to as ‘Sub q’.
Subsampling
An approach whereby a small portion of a larger fluid stream is routed away, often into a gas analyzer that can only accept a portion of the larger gas stream.
Summit metabolic rate
Refers to the highest metabolic rate that can be induced in a resting endothermic animal by a cold environment. Heliox mixtures are often used to create conditions that accelerate heat loss to the environment. Synonymous with ‘peak metabolic rate’.
Syringe filter
Refers to plastic device containing a particle filter that is used for filtration of small liquid or gas samples. It typically has Luer lock fittings. In respirometry it can be used to buffer some of the turbulence generated by diaphragm pumps or to prevent particles from entering an analyzer chain.
Tachypnea
Refers to rapid, shallow breathing, typically exceeding 20 breaths per minute in adults (higher in children), often signaling underlying respiratory distress, infection (pneumonia), heart failure, or anxiety. Because tidal volumes are reduced ventilatory dead space reduces overall alveolar ventilation.
Temperature
Refers to a measure of the average kinetic energy of the particles in an object. Note that temperature is not a measure of ‘heat’ which is dependent on the mass and material properties of the object.
Thermal neutral zone (TNZ)
A range of ambient temperatures at which temperature regulation can be controlled without changes in metabolic heat production or evaporative heat loss. An endotherm subjected to temperatures above or below its TNZ will exhibit elevated metabolic rate. (Note: TNZ conditions are required for measurement of ‘Basal metabolic rates’.)
Thermic effect of food
The increase in metabolic rate and energy expenditure above resting levels that occurs after consuming food. It accounts for roughly 5–15% of daily energy expenditure, used for digesting, absorbing, and storing nutrients. It is also known as ‘diet induced thermogenesis’, ‘postprandial thermogenesis’, and ‘specific dynamic action’.
Thermogenesis
Thermogenesis is the process of heat production within the body, which burns calories to maintain core temperature and fuel physiological functions. It acts as a primary component of energy expenditure, triggered by eating (thermic effect of food), physical activity, and cold exposure. It includes shivering and non-shivering (brown fat) mechanisms.
Thermoregulation
The integrated response whereby an maintain a stable internal body temperature, even when surrounding temperatures differ. It is a critical aspect of homeostasis, ensuring that metabolic processes, enzymes, and cellular functions operate optimally. Organisms vary widely in their capacity to thermoregulate.
Tidal volume
Refers to the volume of air that moves in or out of the lungs with each normal, resting ventilatory cycle. It represents baseline breathing, averaging approximately 0.5L for healthy adult males and 0.4L for healthy females. For comparison, tidal volumes for mice and rats are ~0.15ml and ~7ml, respectively.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Time constant
A time constant (usually expressed in terms of minutes) for a metabolic chamber that is calculated by diving the volume of a chamber by the rate of air flow through the chamber. In practice one time constant (abbreviated ‘tau’) is the time required to reach approximately 63% of a steady state value.
Tracer
A general term for substances introduced into living organisms to track the movement, metabolism, and distribution of specific molecules within tissues or cells. They allow researchers and clinicians to study physiological processes, diagnose diseases, and map chemical pathways without altering the system being studied.
Introduction to Stable Isotopes
Utilizing Stable Isotope Tracers in Preclinical Models of Obesity
Tracheal system
The primary respiratory system in insects and many terrestrial arthropods, consisting of a network of air-filled tubes (tracheae) that deliver oxygen directly to tissues without using blood. Air enters through external valves called spiracles, branching into smaller tubes (tracheoles) that reach every cell for gas exchange
Translational physiology
Refers to a multidisciplinary field that bridges basic, molecular-level research with clinical applications to improve human health, often referred to as “bench to bedside”. It focuses on applying physiological insights to develop diagnostics, therapeutics, and public health strategies. This field involves studying mechanisms across the spectrum, from cell function to population health, often employing a bidirectional approach where clinical observations inform new laboratory studies.
Uncoupling protein
A specialized protein expressed in the mitochondrial membrane of brown adipose tissue and collapses the electrochemical proton gradient thereby disabling ATP production. Because the oxidative phosphorylation is uncoupled from ATP synthesis the metabolic energy is released as heat rather than chemical energy.
Upper critical temperature
The ambient temperature above which the rate of evaporative heat loss of a resting thermoregulating animal must be increased (e.g., by thermal tachypnea or by thermal sweating) in order to maintain thermal balance.
Vasoconstriction
Refers to the narrowing of blood vessels caused by smooth muscle contraction in (non-capillary) vessel walls, which reduces blood flow and increases pressure. Triggered by various endogenous and exogenous chemicals, it is one of the common responses to reduce heat loss to the environment. Contrast with ‘vasodilation’.
Vasodilation
Refers to the widening of blood vessels caused by smooth muscle relaxation in (non-capillary) vessel walls, which reduces blood flow and increases pressure. Triggered by various endogenous and exogenous chemicals, it is one of the common responses to reduce heat loss to the environment. Contrast with ‘vasodilation’.
Ventilation-perfusion matching
Ventilation-perfusion matching is the physiological coupling of alveolar airflow to blood flow within the lungs to ensure ample gas exchange. Inadequate blood flow or inadequate ventilation both result in hypoxemia.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Ventilatory rate
Refers to the number of complete breath cycles taken by an animal in a given time period (usually 1 minute). It is more descriptive than the term ‘respiratory rate’ which technically involves the exchange of respiratory gases at the cellular level. Contrast with ‘minute ventilation’.
Controlled Atmospheres: Hypoxia, Anoxia, Hypercapnic or Hyperoxic Research
Venturi effect
The principle where a fluid’s velocity increases and its static pressure decreases as it flows through a constricted (narrower) section of a tube. Thus, pressure differentials measured in different locations of a tube with different cross sections can be used to calculate fluid flow rates.
VO2 max
The maximum rate of oxygen an organism can oxidize during intense, incremental exercise. Note that because it is a measure of aerobic capacity, additional metabolic expenditure can be achieved for a short period using anaerobic respiration.
Mouse Graded Exercise Test to Obtain VO2 max
Sable Announces the Release of New Metabolic Treadmill for Mice
Volatile organic compounds (VOCs)
Refers to carbon-based chemicals that easily evaporate into the air as gases at room temperature. Most animals constantly exhale hundreds of different VOCs produced by metabolic processes, gut bacteria, and absorbed environmental exposures. These compounds are being increasingly evaluated as biomarkers for health status.
Materials Science Atmospheric and Air Quality Monitoring, Climatology
Volumetric flow
Measurement of fluid flow in terms of volume per unit time (e.g., Liters per minute) that are subject to changes in temperature and pressure. Volumetric flows of gas are typically made using a Rotameter or a Turbine flow meter. Contrast to ‘Mass flow’
Voluntary exercise
Refers to self-paced, optional physical activity—most commonly running on a cage-mounted wheel. Unlike forced treadmill running, which can introduce stress-related confounding factors, voluntary exercise is generally considered more natural and less stressful.
Mouse Graded Exercise Test to Obtain VO2 max
Sable Announces the Release of New Metabolic Treadmill for Mice
Water vapor dilution
The reduction in measured partial pressures of the non-water components in a gas mixture that is caused by the presence of water vapor in the mixture. See also ‘dry flow rate’ and ‘dry gas fraction’.
Water vapor pressure (WVP)
Refers to the partial pressure that water vapor contributes to a gas mixture (typically expressed in units kPa). For a gas sample at room temperature and 1 atmosphere WVP can range from 0 kPa for dry air to approximately 3 kPa for highly saturated air.
Weir equation
Refers to the fundamental equation in physiology used in indirect calorimetry to calculate the rate of energy expenditure of an organism (typically in kcal/day) based on measurements of VO2 and VCO2. Variations of the equation may also consider costs associated with nitrogen excretion. May also be referred to as the ‘Weir Formula’.
Work efficiency
Refers to the ratio of useful external mechanical work performed to the total metabolic energy expended, typically measuring how effectively humans convert food/oxygen into movement. It is generally 20-25% efficient, meaning 75-80% of metabolic energy is lost as heat, with higher efficiency allowing more work with less energy
Mouse Graded Exercise Test to Obtain VO2 max
Sable Announces the Release of New Metabolic Treadmill for Mice
Yoked feeding
Refers to an experimental design to minimize the variation in food intake whereby a ‘yoked’ subject is allowed to consume no more food as a ‘master’ or ‘leader’ subject. In practice, this may be accomplished by measuring food intake of the ‘leader’ subject and then applying the yoked regimen 24h later on the second subject. Note that yoked feeding does not ensure that the ‘yoked’ subject consumes as much as the ‘leader’ subject.
Z-transformation
Refers to an approach to describe measurements across time where ‘ZT 0’ usually marks the beginning of the day (e.g., sunrise or lights on) and ‘ZT 12’ marks the beginning of the night (e.g., sunset or lights off).
Zeitgeber time
Refers to the process of adjusting a sensor or instrument to read exactly zero when it is at its base, inactive, or no-load state. For gas analyzers N2 is a convenient zero gas for O2, CO2, CH4, H2, and WVP sensors. Zeroing should always be done prior to ‘spanning’ a sensor.
Zeroing
It measures oxygen concentrations using a heated zirconia solid electrolyte coated with platinum electrodes whereby oxygen ions migrate through the zirconia from a high-concentration reference (air) to a low-concentration sample gas, generating a voltage proportional to the oxygen difference. Although they do not require routine maintenance, they show unwanted responses in the presence of CO H2, and many VOCs.
Zirconia analyzer
A mathematical approach (also referred to as ‘instantaneous correction’) for accounting for washout and wash in times of a given signal whereby the signal’s first derivative is multiplied by an empirically derived constant ‘Z’ (which is related to the time constant of the system). It relies on the assumption that the volume of gas is homogenously mixed at all times, and that the signal only exhibits first-order kinetics. See also ‘first-order-kinetics’.