Applications in Cell Physiology

App Notes & Tech Briefs

• Functional validation of Genomic and Proteomic data

  A platform to validate proteins and pathways that alter mitochondrial function

  Comparative genomic and proteomic analyses have identified approximately half of the estimated 1500 mitochondrial proteins encoded by the human nuclear genome. In recently published studies, XF assays have extended these estimates via the identification of functional roles of some of the nuclear and mtDNA-encoded proteins, and in one case, clarifying assumptions about their activity that had been based on sequence homology data...

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• Measuring mitochondrial respiration in intact skeletal muscle fibers

  Assessment of mitochondrial function in skeletal muscle is a powerful tool for modeling neuromuscular conditions including muscular dystrophy, aging and cachexia. Similarly, skeletal muscle plays an important role in normal and pathological metabolism, such as obesity and diabetes. The majority of investigations use measurements of single mitochondrial enzymes as a surrogate to measuring mitochondrial function which does not provide a complete physiological readout of the mitochondria...

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• Assessing mitochondrial dysfunction in primary cardiomyocytes

  Mitochondrial reserve capacity is a sensitive measure of cellular stress

  This Application Note describes a method for profiling mitochondrial function in cells responding to stress. The mitochondrial profile generated in this way provides four parameters of mitochondrial function that can be measured in one experiment...

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• Defining metabolic phenotypes in cancer cells

  Kinetic assay reveals the dynamic interplay of oxidative phosphorylation and glycolytic pathways

  Malignant transformation of cells is often characterized by aerobic glycolysis, the conversion of glucose into lactate, despite the presence of oxygen. This metabolic shift, known as the Warburg effect, [1] can occur as a result of the activation or mutation of oncogenes or tumor suppressor genes, or as an adaptive response to hypoxia...

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• Measuring glycolysis and oxidative metabolism in cancer cells

  Real-time assay enables scientists to connect metabolic pathways with oncogenic phenotypes

  Measuring the metabolic pathways in cancer cells, and their co-dependent or compensatory interplay, is important for understanding transformation mechanisms, mechanisms of malignant growth, cancer cell drug resistance, and for discovering potential drugs that are relatively specific for cancer cells...

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• Analyzing microgram quantities of isolated mitochondria in the XF24 Analyzer

  Enhanced appreciation of the role of altered mitochondrial function in tumorigenesis, aging, neurodegenerative, metabolic, and cardiovascular diseases has stimulated the development of a variety of new approaches for assessing mitochondrial function and dysfunction. As the field moves towards the discovery of mitochondrial-related, molecular mechanisms that underlie disease, and drugs to prevent or reverse disease development, the demand for higher throughput and more sensitive assay methods increases...

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Publications

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• Fission and selective fusion govern mitochondrial segregation and elimination by autophagy

  Twig G, Elorza A, Molina A J, Mohamed H, Wikstrom J D, Walzer G, Stiles L, Haigh S E, Katz S, Las G, Alroy J, Wu M, Py B F, Yuan J, Deeney J T, Corkey B E and Shirihai O S

  EMBO J; 2008 Jan 23. 27 (2):433-446.

• Experimental assessment of bioenergetic differences caused by the common European mitochondrial DNA haplogroups H and T

  Amo T, Yadava N, Oh R, Nicholls D G and Brand M D

  Gene; 2008 Mar 31. 411 (40545):69-76.

• Negative feedback maintenance of heme homeostasis by its receptor, Rev-erbα

  Wu N, Yin L, Hanniman E A, Joshi S and Lazar M A

  Genes Dev; 2009 Sep 15. 23 (18):2201-2209.

• MicroRNA-210 controls mitochondrial metabolism during hypoxia by repressing the iron-sulfur cluster assembly proteins ISCU1/2

  Chan S Y, Zhang Y Y, Hemann C, Mahoney C E, Zweier J L and Loscalzo J

  Cell Metab; 2009 Oct 1. 10 (4):273-284.

• Interdependence of AMPK and SIRT1 for metabolic adaptation to fasting and exercise in skeletal muscle

  Canto C, Jiang L Q, Deshmukh A S, Mataki C, Coste A, Lagouge M, Zierath J R and Auwerx J

  Cell Metab; 2010 Mar 3. 11 (3):213-219.

• Characterization of the murine SIRT3 mitochondrial localization sequence and comparison of mitochondrial enrichment and deacetylase activity of long and short SIRT3 isoforms

  Bao J, Lu Z, Joseph J J, Carabenciov D, Dimond C C, Pang L, Samsel L, McCoy J P, Jr., Leclerc J, Nguyen P, Gius D and Sack M N

  J Cell Biochem; 2010 May 1. 110 (1):238-247.

• Use of cells expressing gamma subunit variants to identify diverse mechanisms of AMPK activation

  Hawley S A, Ross F A, Chevtzoff C, Green K A, Evans A, Fogarty S, Towler M C, Brown L J, Ogunbayo O A, Evans A M and Hardie D G

  Cell Metab; 2010 Jun 9. 11 (6):554-565.

• Forward operation of adenine nucleotide translocase during F0F1-ATPase reversal: critical role of matrix substrate-level phosphorylation

  Chinopoulos C, Gerencser A A, Mandi M, Mathe K, Torocsik B, Doczi J, Turiak L, Kiss G, Konrad C, Vajda S, Vereczki V, Oh R J and Adam-Vizi V

  FASEB J; 2010 Jul 1. 24 (7):2405-2416.

• Fibroblast growth factor 21 regulates energy metabolism by activating the AMPK-SIRT1-PGC-1α pathway

  Chau M D, Gao J, Yang Q, Wu Z and Gromada J

  Proc Natl Acad Sci U S A; 2010 Jul 13. 107 (28):12553-12558.

• Wnt signaling regulates mitochondrial physiology and insulin sensitivity

  Yoon J C, Ng A, Kim B H, Bianco A, Xavier R J and Elledge S J

  Genes Dev; 2010 Jul 15. 24 (14):1507-1518.

• Essential regulation of cell bioenergetics by constitutive InsP3 receptor Ca2+ transfer to mitochondria

  Cardenas C, Miller R A, Smith I, Bui T, Molgo J, Muller M, Vais H, Cheung K H, Yang J, Parker I, Thompson C B, Birnbaum M J, Hallows K R and Foskett J K

  Cell; 2010 Jul 23. 142 (2):270-283.

• Bioenergetic characterization of mouse podocytes

  Abe Y, Sakairi T, Kajiyama H, Shrivastav S, Beeson C and Kopp J B

  Am J Physiol Cell Physiol; 2010 Aug 1. 299 (2):C464-476.

• Pyruvate suppresses PGC1α expression and substrate utilization despite increased respiratory chain content in C2C12 myotubes

  Philp A, Perez-Schindler J, Green C, Hamilton D L and Baar K

  Am J Physiol Cell Physiol; 2010 Aug 1. 299 (2):C240-250.

• Alterations in bioenergetics due to changes in mitochondrial DNA copy number

  Qian W and Van Houten B

  Methods; 2010 Aug 1. 51 (4):452-457.

• MICU1 encodes a mitochondrial EF hand protein required for Ca(2+) uptake

  Perocchi F, Gohil V M, Girgis H S, Bao X R, McCombs J E, Palmer A E and Mootha V K

  Nature; 2010 Sep 16. 467 (7313):291-296.

• SIRT4 regulates fatty acid oxidation and mitochondrial gene expression in liver and muscle cells

  Nasrin N, Wu X, Fortier E, Feng Y, Bare O C, Chen S, Ren X, Wu Z, Streeper R S and Bordone L

  J Biol Chem; 2010 Oct 15. 285 (42):31995-32002.

• Fast kinase domain-containing protein 3 is a mitochondrial protein essential for cellular respiration

  Simarro M, Gimenez-Cassina A, Kedersha N, Lazaro J B, Adelmant G O, Marto J A, Rhee K, Tisdale S, Danial N, Benarafa C, Orduna A and Anderson P

  Biochem Biophys Res Commun; 2010 Oct 22. 401 (3):440-446.

• Mitochondrial matrix pH controls oxidative phosphorylation and metabolism-secretion coupling in INS-1E clonal beta cells

  Akhmedov D, Braun M, Mataki C, Park K S, Pozzan T, Schoonjans K, Rorsman P, Wollheim C B and Wiederkehr A

  FASEB J; 2010 Nov 1. 24 (11):4613-4626.

• Loss of manganese superoxide dismutase leads to abnormal growth and signal transduction in mouse embryonic fibroblasts

  Zhang Y, Zhang H M, Shi Y, Lustgarten M, Li Y, Qi W, Zhang B X and Van Remmen H

  Free Radic Biol Med; 2010 Nov 1. 49 (8):1255-1262.

• The Lkb1 metabolic sensor maintains haematopoietic stem cell survival

  Gurumurthy S, Xie S Z, Alagesan B, Kim J, Yusuf R Z, Saez B, Tzatsos A, Ozsolak F, Milos P, Ferrari F, Park P J, Shirihai O S, Scadden D T and Bardeesy N

  Nature; 2010 Dec 2. 468 (7324):659-663.

• Cytoprotective effect of gamma-tocopherol against tumor necrosis factor alpha induced cell dysfunction in L929 cells

  Olah G, Modis K, Gero D, Suzuki K, Dewitt D, Traber D L and Szabo C

  Int J Mol Med; 2011 Jan 1. 28 (5):711-720.

• ChChd3, an Inner Mitochondrial Membrane Protein, Is Essential for Maintaining Crista Integrity and Mitochondrial Function

  Darshi M, Mendiola V L, Mackey M R, Murphy A N, Koller A, Perkins G A, Ellisman M H and Taylor S S

  J Biol Chem; 2011 Jan 28. 286 (4):2918-2932.

• A reduction in ATP demand and mitochondrial activity with neural differentiation of human embryonic stem cells

  Birket M J, Orr A L, Gerencser A A, Madden D T, Vitelli C, Swistowski A, Brand M D and Zeng X

  J Cell Sci; 2011 Feb 1. 124 (Pt 3):348-358.

• Exercise and PGC-1alpha-independent synchronization of type I muscle metabolism and vasculature by ERRgamma

  Narkar V A, Fan W, Downes M, Yu R T, Jonker J W, Alaynick W A, Banayo E, Karunasiri M S, Lorca S and Evans R M

  Cell Metab; 2011 Mar 2. 13 (3):283-293.

• Glutamate Transport Decreases Mitochondrial pH and Modulates Oxidative Metabolism in Astrocytes

  Azarias G, Perreten H, Lengacher S, Poburko D, Demaurex N, Magistretti P J and Chatton J Y

  J Neurosci; 2011 Mar 9. 31 (10):3550-3559.

• Assessing mitochondrial dysfunction in cells

  Brand M D and Nicholls D

  Biochem J; 2011 Mar 29. 435 (1):297-312.

• PARP-1 Inhibition Increases Mitochondrial Metabolism through SIRT1 Activation

  Bai P, Canto C, Oudart H, Brunyanszki A, Cen Y, Thomas C, Yamamoto H, Huber A, Kiss B, Houtkooper R H, Schoonjans K, Schreiber V, Sauve A A, Menissier-de Murcia J and Auwerx J

  Cell Metab; 2011 Apr 6. 13 (4):461-468.

• TEFM (c17orf42) is necessary for transcription of human mtDNA

  Minczuk M, He J, Duch A M, Ettema T J, Chlebowski A, Dzionek K, Nijtmans L G, Huynen M A and Holt I J

  Nucleic Acids Res; 2011 May 1. 39 (10):4284-4299.

• Mitochondrial Matrix Calcium Is an Activating Signal for Hormone Secretion

  Wiederkehr A, Szanda G, Akhmedov D, Mataki C, Heizmann C W, Schoonjans K, Pozzan T, Spat A and Wollheim C B

  Cell Metab; 2011 May 4. 13 (5):601-611.

• Mitochondrial c-Jun N-terminal Kinase (JNK) Signaling Initiates Physiological Changes Resulting in Amplification of Reactive Oxygen Species Generation

  Chambers J W and Lograsso P V

  J Biol Chem; 2011 May 6. 286 (18):16052-16062.

• Negative Regulation of STAT3 Protein-mediated Cellular Respiration by SIRT1 Protein

  Bernier M, Paul R K, Martin-Montalvo A, Scheibye-Knudsen M, Song S, He H J, Armour S M, Hubbard B P, Bohr V A, Wang L, Zong Y, Sinclair D A and de Cabo R

  J Biol Chem; 2011 Jun 3. 286 (22):19270-19279.

• Glutathionylation acts as a control switch for uncoupling proteins UCP2 and UCP3

  Mailloux R J, Seifert E L, Bouillaud F, Aguer C, Collins S and Harper M E

  J Biol Chem; 2011 Jun 17. 286 (24):21865-21875.

• Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter

  Baughman J M, Perocchi F, Girgis H S, Plovanich M, Belcher-Timme C A, Sancak Y, Bao X R, Strittmatter L, Goldberger O, Bogorad R L, Koteliansky V and Mootha V K

  Nature; 2011 Jun 19. 476 (7360):341-345.

• Hexokinase II acts through UCP3 to suppress mitochondrial reactive oxygen species production and maintain aerobic respiration

  Mailloux R J, Dumouchel T, Aguer C, deKemp R, Beanlands R and Harper M E

  Biochem J; 2011 Jul 15. 437 (2):301-311.

• The Rate of Oxygen Utilization by Cells

  Wagner B A, Venkataraman S and Buettner G R

  Free Radical Biology and Medicine; 2011 Aug 1. 51 (3):700-712.

• PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria

  Rorbach J, Nicholls T J and Minczuk M

  Nucleic Acids Res; 2011 Sep 1. 39 (17):7750-7763.

• Identification and characterization of a functional mitochondrial angiotensin system

  Abadir P M, Foster D B, Crow M, Cooke C A, Rucker J J, Jain A, Smith B J, Burks T N, Cohn R D, Fedarko N S, Carey R M, O'Rourke B and Walston J D

  Proc Natl Acad Sci U S A; 2011 Sep 6. 108 (36):14849-14854.

• Uncoupling proteins and the control of mitochondrial reactive oxygen species production

  Mailloux R J and Harper M E

  Free Radic Biol Med; 2011 Sep 15. 51 (6):1106-1115.

• Apoptosis induced by persistent single-strand breaks in the mitochondrial genome: Critical role of EXOG (5' EXO/Endonuclease) in their repair

  Tann A W, Boldogh I, Meiss G, Qian W, Van Houten B, Mitra S and Szczesny B

  J Biol Chem; 2011 Sep 16. 286 (37):31975-31983.

• NF-kappaB controls energy homeostasis and metabolic adaptation by upregulating mitochondrial respiration

  Mauro C, Leow S C, Anso E, Rocha S, Thotakura A K, Tornatore L, Moretti M, De Smaele E, Beg A A, Tergaonkar V, Chandel N S and Franzoso G

  Nat Cell Biol; 2011 Oct 1. 13 (10):1272-1279.

• The PGC-1{alpha}-related coactivator promotes mitochondrial and myogenic adaptations in C2C12 myotubes

  Philp A, Belew M Y, Evans A, Pham D, Sivia I, Chen A, Schenk S and Baar K

  Am J Physiol Regul Integr Comp Physiol; 2011 Oct 1. 301 (4):R864-872.

• The Transcriptional Coactivators, PGC-1? and ?, Cooperate to Maintain Cardiac Mitochondrial Function During the Early Stages of Insulin Resistance

  Mitra R, Nogee D P, Zechner J F, Yea K, Gierasch C M, Kovacs A, Medeiros D M, Kelly D P and Duncan J G

  J Mol Cell Cardiol. 2011 Oct 20; [Epub ahead of print].

• Assessing bioenergetic function in response to oxidative stress by metabolic profiling

  Dranka B P, Benavides G A, Diers A R, Giordano S, Zelickson B R, Reily C, Zou L, Chatham J C, Hill B G, Zhang J, Landar A and Darley-Usmar V M

  Free Radic Biol Med; 2011 Nov 1. 51 (9):1621-1635.

• NCoR1 Is a Conserved Physiological Modulator of Muscle Mass and Oxidative Function

  Yamamoto H, Williams E G, Mouchiroud L, Canto C, Fan W, Downes M, Heligon C, Barish G D, Desvergne B, Evans R M, Schoonjans K and Auwerx J

  Cell; 2011 Nov 11. 147 (4):827-839.

• A critical role of mitochondrial phosphatase ptpmt1 in embryogenesis reveals a mitochondrial metabolic stress-induced differentiation checkpoint in embryonic stem cells

  Shen J, Liu X, Yu W M, Liu J, Groot Nibbelink M, Guo C, Finkel T and Qu C K

  Mol Cell Biol; 2011 Dec 1. 31 (24):4902-4916.

• Poly(ADP-ribose) polymerase-2 depletion reduces doxorubicin-induced damage through SIRT1 induction

  Szanto M, Rutkai I, Hegedus C, Czikora A, Rozsahegyi M, Kiss B, Virag L, Gergely P, Toth A and Bai P

  Cardiovasc Res; 2011 Dec 1. 92 (3):430-438.

• Perilipin 5, a lipid droplet-associated protein, provides physical and metabolic linkage to mitochondria

  Wang H, Sreenevasan U, Hu H, Saladino A, Polster B M, Lund L M, Gong D W, Stanley W C and Sztalryd C

  J Lipid Res; 2011 Dec 1. 52 (12):2159-2168.

• The nuclear receptor PPARbeta/delta programs muscle glucose metabolism in cooperation with AMPK and MEF2

  Gan Z, Burkart-Hartman E M, Han D H, Finck B, Leone T C, Smith E Y, Ayala J E, Holloszy J and Kelly D P

  Genes Dev; 2011 Dec 15. 25 (24):2619-30.

• The role of nuclear lamin B1 in cell proliferation and senescence

  Shimi T, Butin-Israeli V, Adam S A, Hamanaka R B, Goldman A E, Lucas C A, Shumaker D K, Kosak S T, Chandel N S and Goldman R D

  Genes Dev; 2011 Dec 15. 25 (24):2579-2593.

• Silencing of nicotinamide nucleotide transhydrogenase impairs cellular redox homeostasis and energy metabolism in PC12 cells

  Yin F, Sancheti H and Cadenas E

  Biochim Biophys Acta; 2011 Dec 16. 1817 (3):401-409.

• C7orf30 is necessary for biogenesis of the large subunit of the mitochondrial ribosome

  Rorbach J, Gammage P A and Minczuk M

  Nucleic Acids Res. 2012 Jan 11; [Epub ahead of print].

• Integrin-Dependent Akt1 Activation Regulates PGC-1 Expression and Fatty Acid Oxidation

  Beeson C C, Beeson G C, Buff H, Eldridge J, Zhang A, Seth A, Demcheva M, Vournakis J N and Muise-Helmericks R C

  J Vasc Res. 2012 Jan 13; [Epub ahead of print].

• Hemin causes mitochondrial dysfunction in endothelial cells through promoting lipid peroxidation: The protective role of autophagy

  Higdon A N, Benavides G A, Chacko B K, Ouyang X, Johnson M S, Landar A, Zhang J and Darley-Usmar V M

  Am J Physiol Heart Circ Physiol. 2012 Jan 13; [Epub ahead of print].

• Role of mitofusin 2 in the renal stress response

  Gall J M, Wang Z, Liesa M, Molina A, Havasi A, Schwartz J H, Shirihai O, Borkan S C and Bonegio R G

  PLoS One; 2012 Jan 26. 7 (1):e31074.

• SirT1 catalytic activity is required for male fertility and metabolic homeostasis in mice

  Seifert E L, Caron A Z, Morin K, Coulombe J, Hong He X, Jardine K, Dewar-Darch D, Boekelheide K, Harper M E and McBurney M W

  FASEB J; 2012 Feb 1. 26 (2):555-66.

• Altered mitochondrial function and metabolic inflexibility associated with loss of caveolin-1

  Wernstedt Asterholm I, Mundy D I, Weng J, Anderson R G and Scherer P E

  Cell Metab; 2012 Feb 8. 15 (2):171-185.

• Cellular bioenergetics is regulated by PARP1 under resting conditions and during oxidative stress

  Modis K, Gero D, Erdelyi K, Szoleczky P, Dewitt D and Szabo C

  Biochem Pharmacol; 2012 Mar 1. 83 (5):633-643.

Technical Posters

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• MTCH2/MIMP: A novel regulator of liver apoptosis and metabolism

  Yehudit Zaltsman, Liat Shachnai and Atan Gross

  Cold Spring Harbor Laboratory Cell Death
  October 11-15, 2011
  Cold Spring Harbor, NY

• Quantitative Proteomics and Functional Consequences of Mitochondrial Protein Carbonylation

  Jessica Curtis, Matt Stone, Wendy Hahn, Jacob Inda, Timothy Griffin, And David Bernlohr

  Keystone Symposia on Type 2 Diabetes, Insulin Resistance and Metabolic Dysfunction
  January 13-15, 2011
  Keystone, CO

• Assessing Mitochondrial and Cellular Bioenergetics in Human Pluripotent Stem Cells

  Alessandro Prigione and James Adjay

  Targeting Mitochondria 2010
  November 18-19, 2010
  Berlin, DE

• Cellular Bioenergetics in Chicken Embryo Fibroblast (Cef) and Immortal CEF (DF-1) Cells

  K. Lassiter, J. Y. Lee, A. Piekarski , B-W. Kong, J. J. Song, and W. Bottje

  Society for Free Radical Biology's 17th Annual Meeting
  November 17-20, 2010
  Orlando, FL

• Reduction of mitochondrial reserve capacity in endothelial cells by nitric oxide and superoxide – detection and quantitation of peroxynitrite formed from co-generated NO and O2

  Jacek Zielonka, Brian P. Dranka, Monika Zielonka, Joy Joseph, Micael Hardy, Adam Sikora, and B. Kalyanaraman

  Society for Free Radical Biology's 17th Annual Meeting
  November 17-20, 2010
  Orlando, FL, US

• Abrupt Alcohol Withdrawal Suppresses Mitochondrial Repiration in an Estrogen Preventable Manner

  Xiaohua Ju, Daniel Metzger, Yi Wen, Shaohua Yang, James W. Simpkins and Marianna Jung

  Neuroscience 2010
  November 13-17, 2010
  San Diego, CA

• The Homeobox Protein Prox1 is a Negative Modulator of ERRα/PGC-1α Bioenergetic Functions

  Alexis Charest-Marcotte, Catherine R. Dufour, Brian J. Wilson, Annie M. Tremblay, Lillian J. Eichner, Daniel H. Arlow, Vamsi K. Mootha and Vincent Gigu

  Nuclear Receptors: Development, Physiology and Disease
  March 21-26, 2010
  Keystone, CO

Webinars

Sort by: Title | Speaker | Date
• 

  Adaptation of Microplate-based Respirometry for Hippocampal Brain Slices

  Brian Polster, PhD, University of Maryland Medical School
  May 12, 2011

• 

  Multidimensional control of mitochondrial energy production: learning from physiology and pathology

  Rodrigue Rossignol, PhD, Université de Bordeaux
  April 27, 2011

• 

  Profiling Mitochondrial Function has never been so Easy: A Tutorial on the New XF Mito Stress Test Kit

  David Ferrick, PhD, CSO, Seahorse Bioscience
  September 1, 2010

• 

  Mitochondrial Profiling in Cells Under Physiological Conditions and In Response to Stress

  Victor Darley-Usmar, PhD, University of Alabama at Birmingham
  August 4, 2010

• 

  Turbocharging your Mitochondrial Analysis: A Tutorial that Goes Beyond the Obvious

  Min Wu, PhD, Assay Development, Seahorse Bioscience
  David Ferrick, PhD, CSO, Seahorse Bioscience
  February 24, 2010

• 

  Importance of the Mitochondrial Reserve Capacity in Cardiovascular Cells Exposed to Oxidative Stress.

  Brad Hill, PhD, Center for Diabetes and Obesity Research, University of Louisville
  January 20, 2010

• 

  Spare Respiratory Capacity and the Bioenergetics of the Nerve Terminal

  David Nicholls, PhD, FRSE, Buck Institute for Age Research & Lund University
  December 3, 2009

• 

  Fluorescent Reporters of Mitochondrial Function in the Life and Death of Cells

  John J. LeMasters, MD, PhD, Medical University of South Carolina
  February 18, 2009

• 

  The Rate and Coupling Efficiency of Oxidative Phosphorylation in Mitochondria and Cells

  Martin Brand, PhD, Buck Institute, MRC Dunn Human Nutrition Unit
  December 8, 2008

• 

  The Response of the Mitochondrion to Oxidative Stress in Cardiovascular Cells

  Victor Darley-Usmar, PhD, University of Alabama at Birmingham
  November 11, 2008

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