Name: rapid generation of amyloid from native proteins in vitro
Uploaded: 2013-12-05T16:30:00
Description: Watch this Scientific Journal Video about Rapid Generation of Amyloid from Native Proteins In vitro at JoVE.com

This work is supported by grants to W.C. from National Institutes of Health Grant AI074809 and The University of Texas M. D. Anderson Cancer Center Institutional Research Grant Program.

1. Prepare MES Buffer
<ol>
	<li>Use MES buffer (0.1 M 2-(N-morpholino)ethanesulfonic acid and 0.9 M NaCl) to prepare both protein-only amyloid as well as stabilized soluble protein oligomers. Weigh 1.95 g of MES and 5.27 g of NaCl. Add H2O and adjust pH to 4.7. Make up the final volume to 100 ml. Store at 4&#186; C for up to 6 months.</li>
</ol>
2. Prepare Protein-only Amyloid Directly from Native Proteins
<ol>
	<li>Weigh protein of choice (any native protein or peptide) and reconst...

<ol>
	<li>Selkoe, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+proteins+in+fatal+ways.">Folding proteins in fatal ways.</a> Nature. 426, 900-904 (2003).</li><li>Schnabel, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+folding:+The+dark+side+of+proteins.">Protein folding: The dark side of proteins.</a> Nature. 464, 828-829 (2010).</li><li>Goldberg, A. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+degradation+and+protection+against+misfolded+or+damaged+proteins.">Protein degradation and protection against misfolded or damaged proteins.</a> Nature. 426, 895-899 (2003).</li><li>Chiti, F., Dobson, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+misfolding,+functional+amyloid,+and+human+disease.">Protein misfolding, functional amyloid, and human disease.</a> Annu. Rev. Biochem. 75, 333-366 (2006).</li><li>Goldschmidt, L., Teng, P. K., Riek, R., Eisenberg, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identifying+the+amylome,+proteins+capable+of+forming+amyloid-like+fibrils.">Identifying the amylome, proteins capable of forming amyloid-like fibrils.</a> Proc. Natl. Acad. Sci. U.S.A. 107, 3487-3492 (2010).</li><li>Fowler, D. M., Koulov, A. V., Balch, W. E., Kelly, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+amyloid+-+from+bacteria+to+humans.">Functional amyloid - from bacteria to humans.</a> Trends Biochem. Sci. 32, 217-224 (2007).</li><li>Chapman, M. R., 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=Role+of+Escherichia+coli+Curli+Operons+in+Directing+Amyloid+Fiber+Formation.">Role of Escherichia coli Curli Operons in Directing Amyloid Fiber Formation.</a> Science. 295, 851-855 (2002).</li><li>Barnhart, M. M., Chapman, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Curli+Biogenesis+and+Function.">Curli Biogenesis and Function.</a> Annu. Rev. Microbiol. 60, 131-147 (2006).</li><li>Claessen, D., 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+n	olved+in+aerial+hyphae+formation+in+Streptomyces+coelicolor+by+forming+amyloid-like+fibrils.">A n	olved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils.</a> Genes Dev. 17, 1714-1726 (2003).</li><li>Maji, S. K., 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=Functional+Amyloids+As+Natural+Storage+of+Peptide+Hormones+in+Pituitary+Secretory+Granules.">Functional Amyloids As Natural Storage of Peptide Hormones in Pituitary Secretory Granules.</a> Science. 325, 328-332 (2009).</li><li>Badtke, M. P., Hammer, N. D., Chapman, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+Amyloids+Signal+Their+Arrival.">Functional Amyloids Signal Their Arrival.</a> Sci. Signal. 2, pe43 (2009).</li><li>Li, J., 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=The+RIP1/RIP3+Necrosome+Forms+a+Functional+Amyloid+Signaling+Complex+Required+for+Programmed+Necrosis.">The RIP1/RIP3 Necrosome Forms a Functional Amyloid Signaling Complex Required for Programmed Necrosis.</a> Cell. 150, 339-350 (2012).</li><li>Hou, F., 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=MAVS+forms+functional+prion-like+aggregates+to+activate+and+propagate+antiviral+innate+immune+response.">MAVS forms functional prion-like aggregates to activate and propagate antiviral innate immune response.</a> Cell. 146, 448-461 (2011).</li><li>Stefani, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biochemical+and+biophysical+features+of+both+oligomer/fibril+and+cell+membrane+in+amyloid+cytotoxicity.">Biochemical and biophysical features of both oligomer/fibril and cell membrane in amyloid cytotoxicity.</a> FEBS J. 277, 4602-4613 (2010).</li><li>Glabe, C. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+classification+of+toxic+amyloid+oligomers.">Structural classification of toxic amyloid oligomers.</a> J. Biol. Chem. 283, 29639-29643 (1074).</li><li>Di Domizio, J., 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=Binding+with+nucleic+acids+or+glycosaminoglycans+converts+soluble+protein+oligomers+to+amyloid.">Binding with nucleic acids or glycosaminoglycans converts soluble protein oligomers to amyloid.</a> J. Biol. Chem. 287, 736-747 (2012).</li><li>Zhang, X., Li, J. -. P., Lijuan, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Heparan+sulfate+proteoglycans+in+amyloidosis.">Heparan sulfate proteoglycans in amyloidosis.</a> Prog. Mol. Biol. Transl. Sci. 93, 309-334 (2010).</li><li>Jim&#233;nez, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein-DNA+Interaction+at+the+Origin+of+Neurological+Diseases:+A+Hypothesis.">Protein-DNA Interaction at the Origin of Neurological Diseases: A Hypothesis.</a> J. Alzheimer's Dis. 22, 375-391 (2010).</li><li>Bhattacharya, M., Jain, N., Mukhopadhyay, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Insights+into+the+Mechanism+of+Aggregation+and+Fibril+Formation+from+Bovine+Serum+Albumin.">Insights into the Mechanism of Aggregation and Fibril Formation from Bovine Serum Albumin.</a> J. Phys. Chem. B. 115, 4195-4205 (2011).</li><li>Vetri, V., 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=Bovine+Serum+Albumin+protofibril-like+aggregates+formation:+Solo+but+not+simple+mechanism.">Bovine Serum Albumin protofibril-like aggregates formation: Solo but not simple mechanism.</a> Arch. Biochem. Biophysics. 508, 13-24 (2011).</li><li>Bucciantini, 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=Inherent+toxicity+of+aggregates+implies+a+common+mechanism+for+protein+misfolding+diseases.">Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases.</a> Nature. 416, 507-511 (2002).</li><li>McParland, V. J., Kalverda, A. P., Homans, S. W., Radford, S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+properties+of+an+amyloid+precursor+of+b2-microglobulin.">Structural properties of an amyloid precursor of b2-microglobulin.</a> Nat. Struct. Mol. Biol. 9, 326-331 (2002).</li><li>Chiti, F., 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=Designing+conditions+for+in+vitro+formation+of+amyloid+protofilaments+and+fibrils.">Designing conditions for in vitro formation of amyloid protofilaments and fibrils.</a> Proc. Natl. Acad. Sci. U.S.A. 96, 3590-3594 (1999).</li><li>McParland, V. J., 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=Partially+Unfolded+States+of+b2-Microglobulin+and+Amyloid+Formation+in+vitro.">Partially Unfolded States of b2-Microglobulin and Amyloid Formation in vitro.</a> Biochemistry. 39, 8735-8746 (2000).</li><li>Liu, K., Cho, H. S., Lashuel, H. A., Kelly, J. W., Wemmer, D. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+glimpse+of+a+possible+amyloidogenic+intermediate+of+transthyretin.">A glimpse of a possible amyloidogenic intermediate of transthyretin.</a> Nat. Struct. Mol. Biol. 7, 754-757 (2000).</li><li>Pfefferkorn, C. M., McGlinchey, R. P., Lee, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+pH+on+aggregation+kinetics+of+the+repeat+domain+of+a+functional+amyloid.">Effects of pH on aggregation kinetics of the repeat domain of a functional amyloid.</a> Pmel17. Proc. Natl. Acad. Sci. U.S.A. 107, 21447-21452 (2010).</li><li>Di Domizio, J., 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=Nucleic+acid-containing+amyloid+fibrils+potently+induce+type+I+interferon+and+stimulate+systemic+autoimmunity.">Nucleic acid-containing amyloid fibrils potently induce type I interferon and stimulate systemic autoimmunity.</a> Proc. Natl. Acad. Sci. U.S.A. 109, 14550-14555 (2012).</li><li>Halle, A., Hornung, V., Petzold, G. C., Stewart, C. R., Monks, B. G., Reinheckel, T., Fitzgerald, K. A., Latz, E., Moore, K. J., Golenbock, D. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+NALP3+inflammasome+is+involved+in+the+innate+immune+response+to+amyloid-&#946;.">The NALP3 inflammasome is involved in the innate immune response to amyloid-&#946;.</a> Nat. Immunol. 9, 857 (2008).</li><li>Masters, S. L., O'Neill, 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=Disease-associated+amyloid+and+misfolded+protein+aggregates+activate+the+inflammasome.">Disease-associated amyloid and misfolded protein aggregates activate the inflammasome.</a> Trends Mol. Med. 17, 276-282 (2011).</li></ol>

The method described here offers a rapid and flexible means to prepare amyloid fibrils in vitro from virtually any protein or peptide of choice. Several different types of amyloid can be reliably prepared - protein-only fibrils or hybrid aggregates containing DNA, RNA, &#160;or glycosaminoglycans. The procedures involved are simple, straight forward, and do not require advanced technical training. The amyloid prepared by this method is quite stable and can be safely stored at 4 &#186;C or frozen at -80 &#186;C f...

Proteins are the most abundant biological macromolecules present in all types of cells. They occur in a great variety of sizes, structures, and post-translational modifications, and fulfill an enormous range of important biological functions when in their native forms. More than two dozens of aberrant polypeptides have been implicated in numerous human pathological conditions, such as Alzheimer&#39;s disease, Parkinson disease, &#160;and Type 2 Diabetes1-4. The terminal misfolded proteins accumulate as amyloid fibrils&#160;the insoluble stable aggregates that occur extracellularly or intracellularly.
Despite the implication of specific proteins in certain diseases, increasing evidence supports the notion that all polypeptides have intrinsic properties that enable amyloid transformation. A genome-wide sequence survey identified the &#8220;amylome&#8221;, by which amyloid-prone fragments constitute roughly 15% of all coding peptide segments from E. coli to humans5. Accordingly, an increasing number of functional amyloids, which participate in various important cellular processes, have been discovered in recent years. For example, bacteria assemble amyloids to form biofilm and spore structures that are critical for their survival and pathogenesis6-9. Peptide hormones form amyloid deposits during storage within mammalian secretory granules before being released, further implying that the protein amyloid form can serve beneficial biological functions6,10,11. Moreover, proteins can also assemble into amyloid fibrils to relay critical cellular signals12,13.
For many years, the most studied amyloids are prepared from individual peptides that are associated with human diseases, such as amyloid beta or prion peptide. These peptides usually lack well defined structure and spontaneously form amyloid in solution over time, a process mediated by a partially misfolded intermediate that serves as the precursor of insoluble amyloid. The precursor of amyloid is also called soluble protein oligomer, which is rare and unstable when generated from natural peptides14,15. However, as described earlier, almost any protein in principle can adopt amyloid conformation under the appropriate conditions. We recently established a method to prepare stabilized soluble oligomers of native proteins, which readily form amyloid in the presence of various cofactors16. The resulting amyloid fibrils reflect the complex nature of the terminal protein misfolding aggregates17,18. Here we use the term protein-only amyloid to refer the protein fibrils without cofactors and hybrid amyloid for the fibrils containing nonproteinaceous components.
Previously, various methods have been developed to generate amyloid in vitro by applying conditions known to favor protein misfolding, such as high temperature, hydrophobic environment, and pH variations19-23. However, they associate with various problems, such as low efficiency, reversible folding, large batch variations or slow kinetics. The approach described here is reproducible, easy to scale up, and allows one to precisely control the timing and condition of amyloid conversion.

<table border="0" cellpadding="0" cellspacing="0" width="795">
	<colgroup>
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="31">
			<td height="31" style="height:31px;width:487px;">2-(N-morpholino)ethanesulfonic acid (MES)</td>
			<td style="width:145px;">Sigma-Aldrich</td>
			<td style="width:164px;">M8250</td>
		</tr>
		<tr height="31">
			<td height="31" style="height:31px;width:487px;">NaCl</td>
			<td style="width:145px;">Fisher</td>
			<td style="width:164px;">BP358-10</td>
		</tr>
		<tr height="31">
			<td height="31" style="height:31px;width:487px;">1-ethyl-3-[3-dimethyl-aminopropyl] carbodiimide hydrochloride (EDC)</td>
			<td style="width:145px;">Thermo/Pierce</td>
			<td style="width:164px;">22980</td>
		</tr>
		<tr height="31">
			<td height="31" style="height:31px;width:487px;">DNA from salmon sperm</td>
			<td style="width:145px;">Sigma</td>
			<td style="width:164px;">D1626</td>
		</tr>
		<tr height="31">
			<td height="31" style="height:31px;width:487px;">RNA from torula yeast</td>
			<td style="width:145px;">Sigma</td>
			<td style="width:164px;">R6625</td>
		</tr>
		<tr height="31">
			<td height="31" style="height:31px;width:487px;">Heparin from porcine intestinal mucosa</td>
			<td style="width:145px;">Sigma</td>
			<td style="width:164px;">H3149</td>
		</tr>
		<tr height="31">
			<td height="31" style="height:31px;width:487px;">Tris base</td>
			<td style="width:145px;">Fisher</td>
			<td style="width:164px;">BP152-1</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;"></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="36">
			<td height="36" style="height:36px;">Equipment:</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:487px;">Material Name</td>
			<td style="width:145px;">Company</td>
			<td style="width:164px;">Catalogue Number</td>
		</tr>
		<tr height="29">
			<td height="29" style="height:29px;width:487px;">Water bath</td>
			<td style="width:145px;">Fisher Science</td>
			<td style="width:164px;">Isotemp 210</td>
		</tr>
		<tr height="33">
			<td height="33" style="height:33px;width:487px;">Slide-A-Lyzer dialysis cassette</td>
			<td style="width:145px;">Thermo/Pierce</td>
			<td style="width:164px;">66380</td>
		</tr>
	</tbody>
</table>

rapid generation of amyloid from native proteins in vitro

Proteins carry out crucial tasks in organisms by exerting functions elicited from their specific three dimensional folds. Although the native structures of polypeptides fulfill many purposes, it is now recognized that most proteins can adopt an alternative assembly of beta-sheet rich amyloid. Insoluble amyloid fibrils are initially associated with multiple human ailments, but they are increasingly shown as functional players participating in various important cellular processes. In addition, amyloid deposited in patient tissues contains nonproteinaceous components, such as nucleic acids and glycosaminoglycans (GAGs). These cofactors can facilitate the formation of amyloid, resulting in the generation of different types of insoluble precipitates. By taking advantage of our understanding how proteins misfold via an intermediate stage of soluble amyloid precursor, we have devised a method to convert native proteins to amyloid fibrils in vitro. This approach allows one to prepare amyloid in large quantities, examine the properties of amyloid generated from specific proteins, and evaluate the structural changes accompanying the conversion.

The ability to convert native proteins directly to amyloid relies on the conformational change incurred at high temperature in the MES buffer. Precipitation in the solution is a good indication of protein aggregation and possibly amyloid formation. On the other hand, to allow soluble protein oligomer to stabilize, EDC is used to crosslink the proteins to solidify the oligomeric conformation induced in MES buffer. As a result, the stabilized protein oligomers are multimeric proteins (Figure 1), distinct f...

Watch this Scientific Journal Video about Rapid Generation of Amyloid from Native Proteins In vitro at JoVE.com

Rapid Generation of Amyloid from Native Proteins In vitro

Proteins can either adopt a native structure or misfold into insoluble amyloid. Conditions that favor the misfolding pathway lead to the formation of different types of amyloid fibrils. The methods described here allow rapid conversion of native proteins into amyloid in vitro.

Rapid Generation of Amyloid from Native Proteins In vitro

Proteins carry out crucial tasks in organisms by exerting functions elicited from their specific three dimensional folds. Although the native structures ...

Research

JoVE Journal

Biology

Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for Analysis of Multiprotein Complexes from Cellular Lysates

Blue Native Polyacrylamide Gel Electrophoresis BN-PAGE for Analysis of Multiprotein Complexes from Cellular Lysates

Multiprotein complexes (MPCs) play a crucial role in cell signalling, since most proteins can be found in functional or regulatory complexes with other ...

Rapid and Efficient Generation of Neurons from Human Pluripotent Stem Cells in a Multititre Plate Format

Existing protocols for the generation of neurons from human pluripotent stem cells (hPSCs) are often tedious in that they are  multistep procedures ...

Rapid Genetic Analysis of Epithelial-Mesenchymal Signaling During Hair Regeneration

Hair follicle morphogenesis, a complex process requiring interaction between epithelia-derived keratinocytes and the underlying mesenchyme, is an ...

Rapid and Efficient Zebrafish Genotyping Using PCR with High-resolution Melt Analysis

Zebrafish is a powerful vertebrate model system for studying development, modeling disease, and performing drug screening. Recently a variety of genetic ...

Generation of Myospheres From hESCs by Epigenetic Reprogramming

Generation of a homogeneous and abundant population of skeletal muscle cells from human embryonic stem cells (hESCs) is a requirement for cell-based ...

Efficient Generation Human Induced Pluripotent Stem Cells from Human Somatic Cells with Sendai-virus

A few years ago, the establishment of human induced pluripotent stem cells (iPSCs) ushered in a new era in biomedicine. Potential uses of human iPSCs ...

In Vitro Pancreas Organogenesis from Dispersed Mouse Embryonic Progenitors

In Vitro Pancreas Organogenesis from Dispersed Mouse Embryonic Progenitors

The pancreas is an essential organ that regulates glucose homeostasis and secretes digestive enzymes. Research on pancreas embryogenesis has led to the ...

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

RNA-binding proteins (RBPs) are emerging as a regulatory layer in the development and function of adipose. RBPs play a key role in the gene expression ...

Filtration Isolation of Nucleic Acids:  A Simple and Rapid DNA Extraction Method

FINA, filtration isolation of nucleic acids, is a novel extraction method which utilizes vertical filtration via a separation membrane and absorbent pad ...

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

The human gut is colonized by trillions of bacteria that support physiologic functions such as food metabolism, energy harvesting, and regulation of the ...