Name: determining basal energy expenditure and the capacity of thermogenic adipocytes to expend energy in obese mice
Uploaded: 2021-11-11T13:00:00
Description: Watch this Scientific Journal Video about Determining Basal Energy Expenditure and the Capacity of Thermogenic Adipocytes to Expend Energy in Obese Mice at JoVE.com

ML is funded by the Department of Medicine at UCLA, pilot grants from P30 DK 41301 (UCLA:DDRC NIH) and P30 DK063491 (UCSD-UCLA DERC).

All experiments were approved by the Institutional Animal Care and Use Committee at the University of California, Los Angeles (UCLA). Mice were administered their diet and water ad libitum in the metabolic cage, housed in a temperature-controlled environment (~21-22 or 30 &#176;C) with a 12h light/dark cycle. 8 week-old female mice fed a high-fat diet or chow diet for 8 weeks were used for this study.
1. Measurement of the Basal Metabolic Rate (BMR)
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	<li>Rolfe, D. F., Brown, G. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellular+energy+utilization+and+molecular+origin+of+standard+metabolic+rate+in+mammals.">Cellular energy utilization and molecular origin of standard metabolic rate in mammals.</a> Physiological Reviews. 77 (3), 731-758 (1997).</li><li>Heymsfield, S. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+energy+expenditure:+advances+in+organ-tissue+prediction+models.">Human energy expenditure: advances in organ-tissue prediction models.</a> Obesity Reviews. 19 (9), 1177-1188 (2018).</li><li>Kummitha, C. M., Kalhan, S. C., Saidel, G. M., Lai, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relating+tissue/organ+energy+expenditure+to+metabolic+fluxes+in+mouse+and+human:+experimental+data+integrated+with+mathematical+modeling.">Relating tissue/organ energy expenditure to metabolic fluxes in mouse and human: experimental data integrated with mathematical modeling.</a> Physiological Reports. 2 (9), 12159 (2014).</li><li>Tschop, M. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+guide+to+analysis+of+mouse+energy+metabolism.">A guide to analysis of mouse energy metabolism.</a> Nature. 9 (1), 57-63 (2011).</li><li>Mina, A. I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CalR:+A+Web-Based+Analysis+Tool+for+Indirect+Calorimetry+Experiments.">CalR: A Web-Based Analysis Tool for Indirect Calorimetry Experiments.</a> Cell Metabolism. 28 (4), 656-666 (2018).</li><li>Shum, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ABCB10+exports+mitochondrial+biliverdin,+driving+metabolic+maladaptation+in+obesity.">ABCB10 exports mitochondrial biliverdin, driving metabolic maladaptation in obesity.</a> Science Translational Medicine. 13 (594), (2021).</li><li>Assali, E. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NCLX+prevents+cell+death+during+adrenergic+activation+of+the+brown+adipose+tissue.">NCLX prevents cell death during adrenergic activation of the brown adipose tissue.</a> Nature Communication. 11 (1), 3347 (2020).</li><li>Clark, J. D., Gebhart, G. F., Gonder, J. C., Keeling, M. E., Kohn, D. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Special+Report:+The+1996+Guide+for+the+Care+and+Use+of+Laboratory+Animals.">Special Report: The 1996 Guide for the Care and Use of Laboratory Animals.</a> ILAR Journal. 38 (1), 41-48 (1997).</li><li>Schena, G., Caplan, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Everything+You+Always+Wanted+to+Know+about+beta3-AR+*+(*+But+were+afraid+to+ask).">Everything You Always Wanted to Know about beta3-AR * (* But were afraid to ask).</a> Cells. 8 (4), 357 (2019).</li><li>Granneman, J. G., Burnazi, M., Zhu, Z., Schwamb, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=White+adipose+tissue+contributes+to+UCP1-independent+thermogenesis.">White adipose tissue contributes to UCP1-independent thermogenesis.</a> American Journal of Physiology-Endocrinology and Metabolism. 285 (6), 1230-1236 (2003).</li><li>Szentirmai, E., Kapas, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+the+brown+adipose+tissue+in+beta3-adrenergic+receptor+activation-induced+sleep,+metabolic+and+feeding+responses.">The role of the brown adipose tissue in beta3-adrenergic receptor activation-induced sleep, metabolic and feeding responses.</a> Scientific Reports. 7 (1), 958 (2017).</li></ol>

Indirect calorimetry has been used for years to assess whole-body energy expenditure4. This protocol described herein provides a straightforward method of measuring the basal metabolic rate and determining BA thermogenic capacity in vivo using metabolic cages.
The indirect calorimetry method described here confirms that dividing energy expenditure values by body weight values can be misleading. For example, it can conclude that energy expenditure is systematica...

Metabolism can be defined as the integration of the biochemical reactions responsible for nutrient uptake, storage, transformation, and breakdown that cells use to grow and perform their functions. Metabolic reactions transform the energy contained in nutrients into a form that can be used by cells to synthesize new molecules and execute work. These biochemical reactions are inherently inefficient in transforming this energy into a usable form to sustain life1. Such inefficiency results in energy dissipation in the form of heat, with this heat production being used to quantify the Standard Metabolic Rate (SMR) of an organism1. The Standard condition was classically defined as heat production occurring in an awake but resting adult, not ingesting or digesting food, at thermoneutrality and without any stress1. The Basal Metabolic Rate (BMR) or basal energy expenditure in mice is referred to as the SMR but in individuals ingesting and digesting food under mild thermal stress (ambient temperatures 21-22 &#176;C)1. The challenges and difficulties of directly measuring heat production made indirect calorimetry, namely calculating heat production from oxygen consumption measurements, to become the most popular approach to determine the BMR. Calculating the BMR from oxygen consumption is possible because the oxidation of nutrients by mitochondria to synthesize ATP is responsible for 72% of the total oxygen consumed in an organism, with 8% of total oxygen consumption also occurring in mitochondria but without generating ATP (uncoupled respiration)1. The majority of the remaining 20% of oxygen consumed can be attributed to nutrient oxidation in other subcellular locations (peroxisomal fatty acid oxidation), anabolic processes, and reactive oxygen species formation1. Thus, in 1907, Lusk established an equation, based on empirical measurements, widely used to transform oxygen consumption and CO2 production into energy dissipation as heat. In humans, the brain accounts for ~25% of the BMR, the musculoskeletal system for ~18.4%, the liver for ~20 %, the heart for ~10%, and the adipose tissue for ~3-7%2. In mice, the tissue contribution to BMR is slightly different, with the brain representing ~6.5%, the skeletal muscle ~13%, the liver ~52%, the heart ~3.7%, and adipose tissue ~5%3.
Remarkably, the biochemical reactions defining the BMR are not fixed and change in response to different needs, such as external work (physical activity), development (tissue growth), internal stresses (counteracting infections, injuries, tissue turnover), and changes in ambient temperature (cold defense)1. Some organisms actively recruit processes to generate heat in cold exposure, implying that heat produced by metabolism is not just an accidental byproduct. Instead, evolution selected regulatory mechanisms that could specifically upregulate heat production by changing the rate of metabolic reactions1. Thus, these same oxygen consumption measurements can be used to determine the capacity of an organism to generate heat in response to cold.
Two major processes contribute to heat generation upon cold exposure. The first one is shivering, which generates heat by increasing mitochondrial oxidative phosphorylation and glycolysis in muscle to cover the physical work done by involuntary muscle contraction. Therefore, cold exposure will increase oxygen consumption in muscles1. The second is Non-Shivering Thermogenesis, which occurs through an increase in oxygen consumption in brown and beige adipocytes (BA). Dissipation of energy into heat in BA is mediated by the mitochondrial uncoupling protein 1 (UCP1), which allows proton re-entry into the mitochondrial matrix, decreasing the mitochondrial proton gradient. The dissipation of the mitochondrial proton gradient by UCP1 increases heat production by the elevation in electron transfer and oxygen consumption and the energy released by proton dissipation per se without generating ATP (uncoupled). Moreover, thermogenic BA can recruit additional mechanisms that elevate oxygen consumption without causing a large dissipation in the proton gradient, by activating futile oxidative ATP synthesis and consumption cycles. The metabolic cages described here, namely the CLAMS-Oxymax system from Columbus Instruments, offer the possibility to measure energy expenditure at different ambient temperatures. However, to determine BA thermogenic capacity using whole-body oxygen consumption measurements, one needs to: (1) eliminate the contribution of shivering, and other non-BA metabolic processes to energy expenditure, and (2) specifically activate BA thermogenic activity in vivo. Thus, a second protocol describes how to selectively activate BA in vivo using pharmacology in anesthetized mice at thermoneutrality (30 &#176;C), with anesthesia and thermoneutrality limiting other non-BA thermogenic processes (i.e., physical activity). The pharmacological strategy to activate BA is treating mice with the &#946;3-adrenergic receptor agonist CL-316,246. The reason is that cold exposure promotes a sympathetic response releasing norepinephrine to activate &#946;-adrenergic receptors in BA, which activates UCP1 and fat oxidation. Furthermore, &#946;3-adrenergic receptor expression is highly enriched in adipose tissue in mice.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>CLAMS-Oxymax System</td>
			<td>Columbus Instruments</td>
			<td>CLAMS-center feeder-ENC</td>
			<td>Including enviromental enclosure and Zirconia oxygen sensor</td>
		</tr>
		<tr>
			<td>Desktop PC with Oxymax Software</td>
			<td>HP/Columbus</td>
			<td>N/A</td>
			<td>PC needed to be purchased separately</td>
		</tr>
		<tr>
			<td>Drierite jug (Calcium Sulfate with Cobalt Chloride Indicator)</td>
			<td>Fisher Scientific</td>
			<td>23-116681</td>
			<td>Needed to dry the gas entering the oxygen sensor, humidity can damage the sensor</td>
		</tr>
		<tr>
			<td>NMR for body composition</td>
			<td>Echo-MRI</td>
			<td>Echo-MRI 100</td>
			<td>Measure lean and fat mass in alive mice. It is necessary for ANCOVA analyses.</td>
		</tr>
		<tr>
			<td>CL-316-243</td>
			<td>Sigma</td>
			<td>C5976</td>
			<td>Injected to the mice subcutaneously to activate thermogenesis</td>
		</tr>
		<tr>
			<td>High fat diet</td>
			<td>Research Diets</td>
			<td>D12266B</td>
			<td>Provided to the mice prior and during measurements</td>
		</tr>
		<tr>
			<td>Pentobarbital/Nembutal</td>
			<td>Pharmacy at DLAM</td>
			<td>N/A</td>
			<td>Anesthesia for the mice</td>
		</tr>
		<tr>
			<td>Primary standard grade gas (tank and regulator)</td>
			<td>Praxair</td>
			<td>NI CD5000O6P-K/PRS 2012-2331-590</td>
			<td>20.50% Oxygen, 0.50% CO2 balanced with nitrogen used for calibration</td>
		</tr>
	</tbody>
</table>

determining basal energy expenditure and the capacity of thermogenic adipocytes to expend energy in obese mice

Energy expenditure measurements are necessary to understand how changes in metabolism can lead to obesity. Basal energy expenditure can be determined in mice by measuring whole-body oxygen consumption, CO2 production, and physical activity using metabolic cages. Thermogenic brown/beige adipocytes (BA) contribute significantly to rodent energy expenditure, particularly at low ambient temperatures. Here, measurements of basal energy expenditure and total BA capacity to expend energy in obese mice are described in two detailed protocols: the first explaining how to set up the assay to measure basal energy expenditure using analysis of covariance (ANCOVA), a necessary analysis given that energy expenditure co-varies with body mass. The second protocol describes how to measure BA energy expenditure capacity in vivo in mice. This procedure involves anesthesia, needed to limit expenditure caused by physical activity, followed by the injection of beta3-adrenergic agonist, CL-316,243, which activates energy expenditure in BA. These two protocols and their limitations are described in sufficient detail to allow a successful first experiment.

Figure 4 shows VO2, VCO2, Heat production/Energy expenditure (EE), Respiratory Exchange Ratio (RER), and X, Y, Z physical activity values obtained using the metabolic cages of the CLAMS system. The VO2 and VCO2 provided by the CLAMS system is the volume of gas (mL) per minute and can be already divided by the body weight or the lean mass values by entering these weight values in the CLAMS software before starting the measurements. However, body wei...

Watch this Scientific Journal Video about Determining Basal Energy Expenditure and the Capacity of Thermogenic Adipocytes to Expend Energy in Obese Mice at JoVE.com

Determining Basal Energy Expenditure and the Capacity of Thermogenic Adipocytes to Expend Energy in Obese Mice

This manuscript describes a protocol to measure the basal metabolic rate and the oxidative capacity of thermogenic adipocytes in obese mice.

Energy expenditure measurements are necessary to understand how changes in metabolism can lead to obesity. Basal energy expenditure can be determined in ...

This protocol allows a researcher to determine whether there are differences in the energetic balance of mice, which can help identifying the physiological processes responsible for a change in body weight. It can also be used to determine the capacity of brown fat to expend energy. This technique quantifies the oxygen consumed and the CO2 produced by an individual mouse in a controlled environment.It allows users to calculate the energy expenditure in this individual mouse and determine whether different treatments or genetic manipulations can change energy expenditure. To begin, open the software controlling the enclosure and the airflow and let the software test the computer's communication with the equipment. Once communication is established, click file, then open experiment configuration and select the experiment configuration pre-designed by the vendor or set up from a previous assay.Next, click on experiment, then click on properties to open the experiment properties window. In the properties window, set up the parameters of the environmental enclosure including the ambient temperature and 12-hour light cycles. Then click on experiment, followed by setup to open the experiment setup window where the parameters of each metabolic cage are defined.Next, add a pre-weighed amount of food to the feeders in the metabolic cages housing eight-week-old female mice. Also, place the water bottles and check that the bottles are sealed correctly and do not leak. After 24 hours, weigh the food remaining in the cages and weigh the mice.Two to three days after the mice have been housed in the system, start indirect calorimetry and activity measurements. First, calibrate the CLAMS systems oxygen and carbon dioxide zirconia-based detector using a calibration gas of known composition. After turning on and ensuring that the tank output pressure is between 5 to 10 pounds per square inch, open the calibration utility software for calibrating and testing the gas sensors.Click on experiment, then calibrate and press start. Wait for the sensors to be tested and for the software to ask the user to turn the knobs of the gas sensor until the value of oxygen identity is one. Click next when the step is complete.After measuring the body weight and composition of the mice, start the oxygen, carbon dioxide, and activity measurements by clicking on experiment and run. After a minimum of 48 hours, stop the experiment by clicking experiment, then stop. To export the data, click on file, then export and export all subjects as a CSV file.During the dark phase, mice have higher oxygen consumption and carbon dioxide production, and thus have higher energy expenditure. Mice on a regular diet and a fed state with food ingestion occurring in the dark cycle are characterized by respiratory exchange range ratio values close to one, indicating a preference to use carbohydrates. During the light cycle when mice mostly sleep and thus fast, there is a shift to fat oxidation with RER values being closer to 0.7.Accordingly, physical activity measured as XYZ laser beam break counts increases during the dark phase and decreases during the light phase. High-fat diet feeding increases body weight and fat mass without changing the lean mass. High-fat diet-fed mice ate more kilocalories per day, mainly due to higher caloric density per gram of food.However, physical activity is similar between the chow and high-fat diet-fed mice even during the dark period. Lower respiratory coefficient ratio values of high-fat diet-fed mice indicate a preference to use fat as the primary substrate for oxidation. Oxygen consumption, but not carbon dioxide production, increases in high-fat diet-fed mice, which results in a significant increase in energy expenditure per mouse.Energy expenditure is increased by a beta-3 agonist injection, mainly as a result of the adrenergic activation of thermogenic adipocytes, which raises oxygen consumption, carbon dioxide production, and thus energy expenditure itself. To measure energy expenditure with the CLAMS, the calibration must be completed and body weight should be measured to perform the ANCOVA analysis. Also, food intake must be measured in both the adaptation period and during measurements.The adaptation period is over when mice recover the initial food intake and body weight. This procedure can also be used to test the acute effects of drugs on mouse activity and behavior. We also use this system in a collaborative study that demonstrated which population of neurons controlled This technique is essential to study diseases related to weight gain and for identifying processes controlling nutrient preference as well as physical activity, thermogenesis, and energy balance.

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Investigating Tissue- and Organ-specific Phytochrome Responses using FACS-assisted Cell-type Specific Expression Profiling in Arabidopsis thaliana

Light mediates an array of developmental and adaptive processes throughout the life cycle of a plant. Plants utilize light-absorbing molecules called photoreceptors to sense and adapt to light. The red/far-red light-absorbing phytochrome photoreceptors have been studied extensively. Phytochromes exist as a family of proteins with distinct and overlapping functions in all higher plant systems in which they have been studied1. Phytochrome-mediated light responses, which range from seed germination through flowering and senescence, are often localized to specific plant tissues or organs2. Despite the discovery and elucidation of individual and redundant phytochrome functions through mutational analyses, conclusive reports on distinct sites of photoperception and the molecular mechanisms of localized pools of phytochromes that mediate spatial-specific phytochrome responses are limited. We designed experiments based on the hypotheses that specific sites of phytochrome photoperception regulate tissue- and organ-specific aspects of photomorphogenesis, and that localized phytochrome pools engage distinct subsets of downstream target genes in cell-to-cell signaling. We developed a biochemical approach to selectively reduce functional phytochromes in an organ- or tissue-specific manner within transgenic plants. Our studies are based on a bipartite enhancer-trap approach that results in transactivation of the expression of a gene under control of the Upstream Activation Sequence (UAS) element by the transcriptional activator GAL43. The biliverdin reductase (BVR) gene under the control of the UAS is silently maintained in the absence of GAL4 transactivation in the UAS-BVR parent4. Genetic crosses between a UAS-BVR transgenic line and a GAL4-GFP enhancer trap line result in specific expression of the BVR gene in cells marked by GFP expression4. BVR accumulation in Arabidopsis plants results in phytochrome chromophore deficiency in planta5-7. Thus, transgenic plants that we have produced exhibit GAL4-dependent activation of the BVR gene, resulting in the biochemical inactivation of phytochrome, as well as GAL4-dependent GFP expression. Photobiological and molecular genetic analyses of BVR transgenic lines are yielding insight into tissue- and organ-specific phytochrome-mediated responses that have been associated with corresponding sites of photoperception4, 7, 8. Fluorescence Activated Cell Sorting (FACS) of GFP-positive, enhancer-trap-induced BVR-expressing plant protoplasts coupled with cell-type-specific gene expression profiling through microarray analysis is being used to identify putative downstream target genes involved in mediating spatial-specific phytochrome responses. This research is expanding our understanding of sites of light perception, the mechanisms through which various tissues or organs cooperate in light-regulated plant growth and development, and advancing the molecular dissection of complex phytochrome-mediated cell-to-cell signaling cascades.

Investigating Tissue- and Organ-specific Phytochrome Responses using FACS-assisted Cell-type Specific Expression Profiling in Arabidopsis thaliana

The molecular basis of spatial-specific phytochrome responses is being investigated using transgenic plants that exhibit tissue- and organ-specific phytochrome deficiencies. The isolation of specific cells exhibiting induced phytochrome chromophore depletion by Fluorescence-Activated Cell Sorting followed by microarray analyses is being utilized to identify genes involved in spatial-specific phytochrome responses.

Light mediates an array of developmental and adaptive processes throughout the life cycle of a plant. Plants utilize light-absorbing molecules called ...

OLIgo Mass Profiling (OLIMP) of Extracellular Polysaccharides

The direct contact of cells to the environment is mediated in many organisms by an extracellular matrix. One common aspect of extracellular matrices is that they contain complex sugar moieties in form of glycoproteins, proteoglycans, and/or polysaccharides. Examples include the extracellular matrix of humans and animal cells consisting mainly of fibrillar proteins and proteoglycans or the polysaccharide based cell walls of plants and fungi, and the proteoglycan/glycolipid based cell walls of bacteria. All these glycostructures play vital roles in cell-to-cell and cell-to-environment communication and signalling.
An extraordinary complex example of an extracellular matrix is present in the walls of higher plant cells. Their wall is made almost entirely of sugars, up to 75% dry weight, and consists of the most abundant biopolymers present on this planet. Therefore, research is conducted how to utilize these materials best as a carbon-neutral renewable resource to replace petrochemicals derived from fossil fuel. The main challenge for fuel conversion remains the recalcitrance of walls to enzymatic or chemical degradation due to the unique glycostructures present in this unique biocomposite.
Here, we present a method for the rapid and sensitive analysis of plant cell wall glycostructures. This method OLIgo Mass Profiling (OLIMP) is based the enzymatic release of oligosaccharides from wall materials facilitating specific glycosylhydrolases and subsequent analysis of the solubilized oligosaccharide mixtures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS)1 (Figure 1). OLIMP requires walls of only 5000 cells for a complete analysis, can be performed on the tissue itself2, and is amenable to high-throughput analyses3. While the absolute amount of the solubilized oligosaccharides cannot be determined by OLIMP the relative abundance of the various oligosaccharide ions can be delineated from the mass spectra giving insights about the substitution-pattern of the native polysaccharide present in the wall.
OLIMP can be used to analyze a wide variety of wall polymers, limited only by the availability of specific enzymes4. For example, for the analysis of polymers present in the plant cell wall enzymes are available to analyse the hemicelluloses xyloglucan using a xyloglucanase5, 11, 12, 13, xylan using an endo-&beta;-(1-4)-xylanase 6,7, or for pectic polysaccharides using a combination of a polygalacturonase and a methylesterase 8. Furthermore, using the same principles of OLIMP glycosylhydrolase and even glycosyltransferase activities can be monitored and determined 9.

OLIgo Mass Profiling OLIMP of Extracellular Polysaccharides

A rapid way is described to gain insights into the structure of polysaccharides in an extracellular matrix. The method takes advantage of the specificity of glycosylhydrolases and the sensitivity of mass spectrometry allowing minute amounts of materials to be analyzed. This technique is adaptable to be used directly on tissue itself.

The direct contact of cells to the environment is mediated in many organisms by an extracellular matrix. One common aspect of extracellular matrices is ...

Label-free in situ Imaging of Lignification in Plant Cell Walls

Meeting growing energy demands safely and efficiently is a pressing global challenge. Therefore, research into biofuels production that seeks to find cost-effective and sustainable solutions has become a topical and critical task. Lignocellulosic biomass is poised to become the primary source of biomass for the conversion to liquid biofuels1-6. However, the recalcitrance of these plant cell wall materials to cost-effective and efficient degradation presents a major impediment for their use in the production of biofuels and chemicals4. In particular, lignin, a complex and irregular poly-phenylpropanoid heteropolymer, becomes problematic to the postharvest deconstruction of lignocellulosic biomass. For example in biomass conversion for biofuels, it inhibits saccharification in processes aimed at producing simple sugars for fermentation7. The effective use of plant biomass for industrial purposes is in fact largely dependent on the extent to which the plant cell wall is lignified. The removal of lignin is a costly and limiting factor8 and lignin has therefore become a key plant breeding and genetic engineering target in order to improve cell wall conversion.
Analytical tools that permit the accurate rapid characterization of lignification of plant cell walls become increasingly important for evaluating a large number of breeding populations. Extractive procedures for the isolation of native components such as lignin are inevitably destructive, bringing about significant chemical and structural modifications9-11. Analytical chemical in situ methods are thus invaluable tools for the compositional and structural characterization of lignocellulosic materials. Raman microscopy is a technique that relies on inelastic or Raman scattering of monochromatic light, like that from a laser, where the shift in energy of the laser photons is related to molecular vibrations and presents an intrinsic label-free molecular "fingerprint" of the sample. Raman microscopy can afford non-destructive and comparatively inexpensive measurements with minimal sample preparation, giving insights into chemical composition and molecular structure in a close to native state. Chemical imaging by confocal Raman microscopy has been previously used for the visualization of the spatial distribution of cellulose and lignin in wood cell walls12-14. Based on these earlier results, we have recently adopted this method to compare lignification in wild type and lignin-deficient transgenic Populus trichocarpa (black cottonwood) stem wood15. Analyzing the lignin Raman bands16,17 in the spectral region between 1,600 and 1,700 cm-1, lignin signal intensity and localization were mapped in situ. Our approach visualized differences in lignin content, localization, and chemical composition. Most recently, we demonstrated Raman imaging of cell wall polymers in Arabidopsis thaliana with lateral resolution that is sub-&mu;m18. Here, this method is presented affording visualization of lignin in plant cell walls and comparison of lignification in different tissues, samples or species without staining or labeling of the tissues.

Label-free in situ Imaging of Lignification in Plant Cell Walls

A method based on confocal Raman microscopy is presented that affords label-free visualization of lignin in plant cell walls and comparison of lignification in different tissues, samples or species.

Meeting growing energy demands safely and efficiently is a pressing global challenge. Therefore, research into biofuels production that seeks to find ...

Patch Clamp and Perfusion Techniques for Studying Ion Channels Expressed in Xenopus oocytes

The protocol presented here is designed to study the activation of the large conductance, voltage- and Ca2+-activated K+ (BK) channels. The protocol may also be used to study the structure-function relationship for other ion channels and neurotransmitter receptors1. BK channels are widely expressed in different tissues and have been implicated in many physiological functions, including regulation of smooth muscle contraction, frequency tuning of inner hair cells and regulation of neurotransmitter release2-6. BK channels are activated by membrane depolarization and by intracellular Ca2+ and Mg2+ 6-9. Therefore, the protocol is designed to control both the membrane voltage and the intracellular solution. In this protocol, messenger RNA of BK channels is injected into Xenopus laevis oocytes (stage V-VI) followed by 2-5 days of incubation at 18&deg;C10-13. Membrane patches that contain single or multiple BK channels are excised with the inside-out configuration using patch clamp techniques10-13. The intracellular side of the patch is perfused with desired solutions during recording so that the channel activation under different conditions can be examined. To summarize, the mRNA of BK channels is injected into Xenopus laevis oocytes to express channel proteins on the oocyte membrane; patch clamp techniques are used to record currents flowing through the channels under controlled voltage and intracellular solutions.

Patch Clamp and Perfusion Techniques for Studying Ion Channels Expressed in Xenopus oocytes

Ionic current of BK channels is recorded using patch clamp techniques. BK channels are expressed in Xenopus oocytes by injecting messenger RNA. The intracellular solution during patch clamp recordings is controlled by a perfusion system.

The protocol presented here is designed to study the activation of the large conductance, voltage- and Ca2+-activated K+ (BK) channels. The protocol may ...

Determining the Contribution of the Energy Systems During Exercise

One of the most important aspects of the metabolic demand is the relative contribution of the energy systems to the total energy required for a given physical activity. Although some sports are relatively easy to be reproduced in a laboratory (e.g., running and cycling), a number of sports are much more difficult to be reproduced and studied in controlled situations. This method presents how to assess the differential contribution of the energy systems in sports that are difficult to mimic in controlled laboratory conditions. The concepts shown here can be adapted to virtually any sport.
The following physiologic variables will be needed: rest oxygen consumption, exercise oxygen consumption, post-exercise oxygen consumption, rest plasma lactate concentration and post-exercise plasma peak lactate. To calculate the contribution of the aerobic metabolism, you will need the oxygen consumption at rest and during the exercise. By using the trapezoidal method, calculate the area under the curve of oxygen consumption during exercise, subtracting the area corresponding to the rest oxygen consumption. To calculate the contribution of the alactic anaerobic metabolism, the post-exercise oxygen consumption curve has to be adjusted to a mono or a bi-exponential model (chosen by the one that best fits). Then, use the terms of the fitted equation to calculate anaerobic alactic metabolism, as follows: ATP-CP metabolism = A1 (mL . s-1) x t1 (s). Finally, to calculate the contribution of the lactic anaerobic system, multiply peak plasma lactate by 3 and by the athlete&#x2019;s body mass (the result in mL is then converted to L and into kJ).
The method can be used for both continuous and intermittent exercise. This is a very interesting approach as it can be adapted to exercises and sports that are difficult to be mimicked in controlled environments. Also, this is the only available method capable of distinguishing the contribution of three different energy systems. Thus, the method allows the study of sports with great similarity to real situations, providing desirable ecological validity to the study.

This protocol allows researchers focused on exercise and sports sciences to determine the relative contribution of three different energy systems to the total energy expenditure during a large variety of exercises.

One of the most important aspects of the metabolic demand is the relative contribution of the energy systems to the total energy required for a given ...

Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids

Microbes have complex metabolic pathways that can be investigated using biochemistry and functional genomics methods. One important technique to examine cell central metabolism and discover new enzymes is 13C-assisted metabolism analysis 1. This technique is based on isotopic labeling, whereby microbes are fed with a 13C labeled substrates. By tracing the atom transition paths between metabolites in the biochemical network, we can determine functional pathways and discover new enzymes. 
As a complementary method to transcriptomics and proteomics, approaches for isotopomer-assisted analysis of metabolic pathways contain three major steps 2. First, we grow cells with 13C labeled substrates. In this step, the composition of the medium and the selection of labeled substrates are two key factors. To avoid measurement noises from non-labeled carbon in nutrient supplements, a minimal medium with a sole carbon source is required. Further, the choice of a labeled substrate is based on how effectively it will elucidate the pathway being analyzed. Because novel enzymes often involve different reaction stereochemistry or intermediate products, in general, singly labeled carbon substrates are more informative for detection of novel pathways than uniformly labeled ones for detection of novel pathways3, 4. Second, we analyze amino acid labeling patterns using GC-MS. Amino acids are abundant in protein and thus can be obtained from biomass hydrolysis. Amino acids can be derivatized by N-(tert-butyldimethylsilyl)-N-methyltrifluoroacetamide (TBDMS) before GC separation. TBDMS derivatized amino acids can be fragmented by MS and result in different arrays of fragments. Based on the mass to charge (m/z) ratio of fragmented and unfragmented amino acids, we can deduce the possible labeled patterns of the central metabolites that are precursors of the amino acids. Third, we trace 13C carbon transitions in the proposed pathways and, based on the isotopomer data, confirm whether these pathways are active 2. Measurement of amino acids provides isotopic labeling information about eight crucial precursor metabolites in the central metabolism. These metabolic key nodes can reflect the functions of associated central pathways.
13C-assisted metabolism analysis via proteinogenic amino acids can be widely used for functional characterization of poorly-characterized microbial metabolism1. In this protocol, we will use Cyanothece 51142 as the model strain to demonstrate the use of labeled carbon substrates for discovering new enzymatic functions.

Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids

13C-isotope labeling is a useful technique for determining the cell central metabolism for various types of microorganisms. After cells have been cultured with a specific labeled substrate, GC-MS measurement can reveal functional metabolic pathways based on unique labeling patterns in proteinogenic amino acids.

Microbes have complex metabolic pathways that can be investigated using biochemistry and functional genomics methods. One important technique to examine ...

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

One of the major questions in microbial ecology is &#8220;who is there?&#8221; This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. Traditionally, this was performed by cloning and Sanger (capillary electrophoresis) sequencing of PCR amplicons. The advent of next-generation sequencing has tremendously simplified and increased the sequencing depth for 16S rRNA gene sequencing. The introduction of benchtop sequencers now allows small labs to perform their 16S rRNA sequencing in-house in a matter of days. Here, an approach for 16S rRNA gene amplicon sequencing using a benchtop next-generation sequencer is detailed. The environmental DNA is first amplified by PCR using primers that contain sequencing adapters and barcodes. They are then coupled to spherical particles via emulsion PCR. The particles are loaded on a disposable chip and the chip is inserted in the sequencing machine after which the sequencing is performed. The sequences are retrieved in fastq format, filtered and the barcodes are used to establish the sample membership of the reads. The filtered and binned reads are then further analyzed using publically available tools. An example analysis where the reads were classified with a taxonomy-finding algorithm within the software package Mothur is given. The method outlined here is simple, inexpensive and straightforward and should help smaller labs to take advantage from the ongoing genomic revolution.

Characterizing microbial community has been a longstanding goal in environmental microbiology. Next-generation sequencing methods now allow for the characterization of microbial communities at an unprecedented depth with minimal cost and labor. We detail here our approach to sequence bacterial 16S ribosomal RNA genes using a benchtop sequencer.

One of the major questions in microbial ecology is &#8220;who is there?&#8221; This question can be answered using various tools, but one of the ...

High Throughput Danio Rerio Energy Expenditure Assay

Zebrafish are an important model organism with inherent advantages that have the potential to make zebrafish a widely applied model for the study of energy homeostasis and obesity. The small size of zebrafish allows for assays on embryos to be conducted in a 96- or 384-well plate format, Morpholino and CRISPR based technologies promote ease of genetic manipulation, and drug treatment by bath application is viable. Moreover, zebrafish are ideal for forward genetic screens allowing for novel gene discovery. Given the relative novelty of zebrafish as a model for obesity, it is necessary to develop tools that fully exploit these benefits. Herein, we describe a method to measure energy expenditure in thousands of embryonic zebrafish simultaneously. We have developed a whole animal microplate platform in which we use 96-well plates to isolate individual fish and we assess cumulative NADH2 production using the commercially available cell culture viability reagent alamarBlue. In poikilotherms the relationship between NADH2 production and energy expenditure is tightly linked. This energy expenditure assay creates the potential to rapidly screen pharmacological or genetic manipulations that directly alter energy expenditure or alter the response to an applied drug (e.g. insulin sensitizers).

High Throughput Danio Rerio Energy Expenditure Assay

Zebrafish are an important model organism for the study of energy homeostasis. By utilizing a NADH2 sensitive redox indicator, alamar Blue, we have developed an assay that measures the metabolic rate of zebrafish larvae in a 96 well plate format and can be applied to drug or gene discovery.

Zebrafish are an important model organism with inherent advantages that have the potential to make zebrafish a widely applied model for the study of ...

Measurement of Energy Metabolism in Explanted Retinal Tissue Using Extracellular Flux Analysis

High acuity vision is a heavily energy-consuming process, and the retina has developed several unique adaptations to precisely meet such demands while maintaining transparency of the visual axis. Perturbations to this delicate balance cause blinding illnesses, such as diabetic retinopathy. Therefore, the understanding of energy metabolism changes in the retina during disease is imperative to the development of rational therapies for various causes of vison loss. The recent advent of commercially-available extracellular flux analyzers has made the study of retinal energy metabolism more accessible. This protocol describes the use of such an analyzer to measure contributions to retinal energy supply through its two principle arms - oxidative phosphorylation and glycolysis - by quantifying changes in oxygen consumption rates (OCR) and extracellular acidification rates (ECAR) as proxies for these pathways. This technique is readily performed in explanted retinal tissue, facilitating assessment of responses to multiple pharmacologic agents in a single experiment. Metabolic signatures in retinas from animals lacking rod photoreceptor signaling are compared to wild-type controls using this method. A major limitation in this technique is the lack of ability to discriminate between light-adapted and dark-adapted energy utilization, an important physiologic consideration in retinal tissue.

This technique describes real time recording of oxygen consumption and extracellular acidification rates in explanted mouse retinal tissues using an extracellular flux analyzer.

High acuity vision is a heavily energy-consuming process, and the retina has developed several unique adaptations to precisely meet such demands while ...

A Labor-saving and Repeatable Touch-force Signaling Mutant Screen Protocol for the Study of Thigmomorphogenesis of a Model Plant Arabidopsis thaliana

Plants responding to both intracellular and extracellular mechanical stimulations (or force signals) and develop special morphological changes, a called thigmomorphogenesis. In past decades, several signaling components have been identified and reported for being involved in the mechanotransduction (e.g., calcium ion binding proteins and jasmonic acid biosynthesis enzymes). However, the relatively slow pace of research in the study of force signaling or thigmomorphogenesis is largely attributed to two reasons: the requirement for laborious human hand-manipulated touch induction of thigmomorphogenesis and the force strength errors associated with people&#8217;s hand-touch. To enhance the efficiency of external force loading on a plant organism, an automatic touch-force loading machine was built. This robotic arm-driven hair brush touches provide a labor-saving and easily repeatable touch-force simulation, unlimited rounds of touch repetition and adjustable touch strength. This hair touch-force loading machine can be used for both large scale screening of touch-force signaling mutants and the phenomics study of plant thigmomorphogenesis. In addition, touch materials such as human hair, can be replaced with other natural materials like animal hair, silk threads and cotton fibers. The automated moving arms on the machine may be equipped with water sprinkling nozzles and air blowers to mimic the natural forces of rain drops and wind, respectively. By using this automatic hair touch-force loading machine in combination with the hand-performed cotton swab touching, we have investigated the touch response of two force signaling mutants, MAP KINASE KINASE 1 (MKK1) and MKK2 plants. The phenomes of the touch-force loaded wild type plants and two mutants were evaluated statistically. They have exhibited significant differences in touch response.

A Labor-saving and Repeatable Touch-force Signaling Mutant Screen Protocol for the Study of Thigmomorphogenesis of a Model Plant Arabidopsis thaliana

A gentle touch-force loading machine is built from human hair brushes, robotic arms and a controller. The hair brushes are driven by robotic arms installed on the machine and move periodically to apply touch-force on plants. The strength of machine-driven hair touches is comparable to that of manually applied touches.

Plants responding to both intracellular and extracellular mechanical stimulations (or force signals) and develop special morphological changes, a called ...