ZFIN Lab: Farber Lab

ZFIN ID: ZDB-LAB-000330-2

Farber Lab

PI/Director:	Farber, Steven
Co-PI / Senior Researcher:	Shuda, Jamie
Contact Person:	Farber, Steven
Email:	farber@ciwemb.edu
URL:	http://www.ciwemb.edu/labs/farber/index.php
Address:	Carnegie Institution Department of Embryology 3520 San Martin Drive Baltimore, MD 21218 USA
Country:	United States
Phone:	(410) 246-3028
Fax:	(410) 243-6311
Line Designation:	c

GENOMIC FEATURES ORIGINATING FROM THIS LAB

Show all 18 genomic features

STATEMENT OF RESEARCH INTERESTS

LAB MEMBERS

Feltes, McKenna Post-Doc	Kelpsch, Daniel Post-Doc	Kozan, Darby Graduate Student
Thierer, James (Jay) Graduate Student	Shen, Meng-Chieh Research Staff	Butler, Valerie

ZEBRAFISH PUBLICATIONS OF LAB MEMBERS

Jawahar, J., McCumber, A.W., Lickwar, C.R., Amoroso, C.R., de la Torre Canny, S.G., Wong, S., Morash, M., Thierer, J.H., Farber, S.A., Bohannan, B.J.M., Guillemin, K., Rawls, J.F. (2022) Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding. BMC Genomics. 23:225

Wilson, M.H., Ekker, S.C., Farber, S.A. (2021) Imaging cytoplasmic lipid droplets in vivo with fluorescent perilipin 2 and perilipin 3 knock-in zebrafish. eLIFE. 10:

Shao, W., Hwang, J., Liu, C., Mukhopadhyay, D., Zhao, S., Shen, M.C., Alpergin, E.S.S., Wolfgang, M.J., Farber, S.A., Espenshade, P.J. (2020) Serum lipoprotein-derived fatty acids regulate hypoxia-inducible factor. The Journal of biological chemistry. 295(52):18284-18300

Ichino, N., Serres, M.R., Urban, R.M., Urban, M.D., Treichel, A.J., Schaefbauer, K.J., Greif, L.E., Varshney, G.K., Skuster, K.J., McNulty, M.S., Daby, C.L., Wang, Y., Liao, H.K., El-Rass, S., Ding, Y., Liu, W., Anderson, J.L., Wishman, M.D., Sabharwal, A., Schimmenti, L.A., Sivasubbu, S., Balciunas, D., Hammerschmidt, M., Farber, S.A., Wen, X.Y., Xu, X., McGrail, M., Essner, J.J., Burgess, S.M., Clark, K.J., Ekker, S.C. (2020) Building the vertebrate codex using the gene breaking protein trap library. eLIFE. 9:

Wilson, M.H., Rajan, S., Danoff, A., White, R.J., Hensley, M.R., Quinlivan, V.H., Recacha, R., Thierer, J.H., Tan, F.J., Busch-Nentwich, E.M., Ruddock, L., Hussain, M.M., Farber, S.A. (2020) A point mutation decouples the lipid transfer activities of microsomal triglyceride transfer protein. PLoS Genetics. 16:e1008941

Thierer, J.H., Ekker, S.C., Farber, S.A. (2020) Author Correction: The LipoGlo reporter system for sensitive and specific monitoring of atherogenic lipoproteins. Nature communications. 11:3707

Walsh, M.T., Celestin, O.M., Thierer, J.H., Rajan, S., Farber, S.A., Hussain, M.M. (2019) Model systems to study assembly, trafficking and secretion of apoB-lipoproteins using fluorescent fusion proteins. Journal of Lipid Research. 61(3):316-327

Thierer, J.H., Ekker, S.C., Farber, S.A. (2019) The LipoGlo reporter system for sensitive and specific monitoring of atherogenic lipoproteins. Nature communications. 10:3426

Otis, J.P., Shen, M.C., Caldwell, B.A., Reyes Gaido, O.E., Farber, S.A. (2019) Dietary cholesterol and apolipoprotein A-I are trafficked in endosomes and lysosomes in the live zebrafish intestine. American journal of physiology. Gastrointestinal and liver physiology. 316(3):G350-G365

Sæle, Ø., Rød, K.E.L., Quinlivan, V.H., Li, S., Farber, S.A. (2018) A novel system to quantify intestinal lipid digestion and transport. Biochimica et biophysica acta. 1863(9):948-957

Anderson, J.L., Mulligan, T.S., Shen, M.C., Wang, H., Scahill, C.M., Tan, F.J., Du, S.J., Busch-Nentwich, E.M., Farber, S.A. (2017) mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay. PLoS Genetics. 13:e1007105

Quinlivan, V.H., Farber, S.A. (2017) Lipid Uptake, Metabolism, and Transport in the Larval Zebrafish. Frontiers in endocrinology. 8:319

O'Hare, E.A., Yang, R., Yerges-Armstrong, L., Sreenivasan, U., McFarland, R., Leitch, C.C., Wilson, M.H., Narina, S., Gorden, A., Ryan, K., Shuldiner, A.R., Farber, S.A., Wood, G.C., Still, C.D., Gerhard, G.S., Robishaw, J.D., Sztalryd, C., Zaghloul, N.A. (2017) TM6SF2 rs58542926 impacts lipid processing in liver and small intestine. Hepatology (Baltimore, Md.). 65(5):1526-1542

Quinlivan, V.H., Wilson, M.H., Ruzicka, J., Farber, S.A. (2017) An HPLC-CAD/Fluorescence Lipidomics Platform Using Fluorescent Fatty Acids as Metabolic Tracers. Journal of Lipid Research. 58(5):1008-1020

Otis, J.P., Shen, M.C., Quinlivan, V., Anderson, J.L., Farber, S.A. (2017) Intestinal epithelial cell Caveolin 1 regulates fatty acid and lipoprotein cholesterol plasma levels. Disease models & mechanisms. 10(3):283-295

Shuda, J.R., Butler, V.G., Vary, R., Farber, S.A. (2016) Project BioEYES: Accessible Student-Driven Science for K-12 Students and Teachers. PLoS Biology. 14:e2000520

Zeituni, E.M., Wilson, M.H., Zheng, X., Iglesias, P.A., Sepanski, M., Siddiqi, M.A., Anderson, J.L., Zheng, Y., Farber, S.A. (2016) Endoplasmic reticulum lipid flux influences enterocyte nuclear morphology and lipid-dependent transcriptional responses. The Journal of biological chemistry. 291(45):23804-23816

Otis, J.P., Farber, S.A. (2016) High-fat Feeding Paradigm for Larval Zebrafish: Feeding, Live Imaging, and Quantification of Food Intake. Journal of visualized experiments : JoVE. (116)

Anderson, J.L., Carten, J.D., Farber, S.A. (2016) Using fluorescent lipids in live zebrafish larvae: From imaging whole animal physiology to subcellular lipid trafficking. Methods in cell biology. 133:165-178

Zeituni, E.M., Farber, S.A. (2016) Studying Lipid Metabolism and Transport During Zebrafish Development. Methods in molecular biology (Clifton, N.J.). 1451:237-55

Otis, J.P., Zeituni, E.M., Thierer, J.H., Anderson, J.L., Brown, A.C., Boehm, E.D., Cerchione, D.M., Ceasrine, A.M., Avraham-Davidi, I., Tempelhof, H., Yaniv, K., Farber, S.A. (2015) Zebrafish as a model for apolipoprotein biology: Comprehensive expression analysis and a role for ApoA-IV in regulating food intake. Disease models & mechanisms. 8(3):295-309

Miyares, R.L., de Rezende, V.B., Farber, S.A. (2014) Zebrafish yolk lipid processing: a tractable tool for the study of vertebrate lipid transport and metabolism. Disease models & mechanisms. 7(7):915-27

Miyares, R.L., Stein, C., Renisch, B., Anderson, J.L., Hammerschmidt, M., and Farber, S.A. (2013) Long-Chain Acyl-CoA Synthetase 4A Regulates Smad Activity and Dorsoventral Patterning in the Zebrafish Embryo. Developmental Cell. 27(6):635-647

Sadler, K.C., Rawls, J.F., and Farber, S.A. (2013) Getting the inside tract: new frontiers in zebrafish digestive system biology. Zebrafish. 10(2):129-131

Otis, J.P., and Farber, S.A. (2013) Imaging vertebrate digestive function and lipid metabolism in vivo.. Drug Discovery Today: Disease Models. 10(1):e11-e16

Semova, I., Carten, J.D., Stombaugh, J., Mackey, L.C., Knight, R., Farber, S.A., and Rawls, J.F. (2012) Microbiota regulate intestinal absorption and metabolism of Fatty acids in the zebrafish. Cell Host & Microbe. 12(3):277-288

Walters, J.W., Anderson, J.L., Bittman, R., Pack, M., and Farber, S.A. (2012) RETRACTION: Visualization of lipid metabolism in the zebrafish intestine reveals a relationship between NPC1L1-mediated cholesterol uptake and dietary fatty acid. Chemistry & Biology. 19:913-925

Avraham-Davidi, I., Ely, Y., Pham, V.N., Castranova, D., Grunspan, M., Malkinson, G., Gibbs-Bar, L., Mayseless, O., Allmog, G., Lo, B., Warren, C.M., Chen, T.T., Ungos, J., Kidd, K., Shaw, K., Rogachev, I., Wan, W., Murphy, P.M., Farber, S.A., Carmel, L., Shelness, G.S., Iruela-Arispe, M.L., Weinstein, B.M., and Yaniv, K. (2012) ApoB-containing lipoproteins regulate angiogenesis by modulating expression of VEGF receptor 1. Nature medicine. 18(6):967-973

Delous, M., Yin, C., Shin, D., Ninov, N., Debrito Carten, J., Pan, L., Ma, T.P., Farber, S.A., Moens, C.B., and Stainier, D.Y. (2012) sox9b Is a Key Regulator of Pancreaticobiliary Ductal System Development. PLoS Genetics. 8(6):e1002754

Carten, J.D., Bradford, M.K., and Farber, S. (2011) Visualizing digestive organ morphology and function using differential fatty acid metabolism in live zebrafish. Developmental Biology. 360(2):276-85

Anderson, J.L., Carten, J.D., and Farber, S.A. (2011) Zebrafish lipid metabolism: from mediating early patterning to the metabolism of dietary fat and cholesterol. Methods in cell biology. 101:111-141

Anderson, J.L., Macurak, M.L., Halpern, M.E., and Farber, S.A. (2010) A Versatile Aquatics Facility Inventory System with Real-Time Barcode Scan Entry. Zebrafish. 7(3):281-287

Clifton, J.D., Lucumi, E., Myers, M.C., Napper, A., Hama, K., Farber, S.A., Smith, A.B. 3rd, Huryn, D.M., Diamond, S.L., and Pack, M. (2010) Identification of novel inhibitors of dietary lipid absorption using zebrafish. PLoS One. 5(8):e12386

Mulligan, T., Blaser, H., Raz, E., and Farber, S.A. (2010) Prenylation-deficient G protein gamma subunits disrupt GPCR signaling in the zebrafish. Cellular Signalling. 22(2):221-233

Carten, J.D., and Farber, S.A. (2009) A new model system swims into focus: using the zebrafish to visualize intestinal metabolism in vivo. Clinical lipidology. 4(4):501

Shuda, J., and Kearns-Sixsmith, D. (2009) Outreach: empowering students and teachers to fish outside the box. Zebrafish. 6(2):133-138

Hama, K., Provost, E., Baranowski, T.C., Rubinstein, A.L., Anderson, J.L., Leach, S.D., and Farber, S.A. (2009) In vivo imaging of zebrafish digestive organ function using multiple quenched fluorescent reporters. American journal of physiology. Gastrointestinal and liver physiology. 296(2):G445-G453

Barresi, M.J., Farber, S.A., Hutson, L.D., Hyde, D.R., Liang, J.O., and Morris, J.K. (2008) Zebrafish in the Classroom. Zebrafish. 5(3):205-208

Ouyang, M., Garnett, A.T., Han, T.M., Hama, K., Lee, A., Deng, Y., Lee, N., Liu, H.Y., Amacher, S.L., Farber, S.A., and Ho, S.Y. (2008) A web based resource characterizing the zebrafish developmental profile of over 16,000 transcripts. Gene expression patterns : GEP. 8(3):171-180

Robu, M.E., Larson, J.D., Nasevicius, A., Beiraghi, S., Brenner, C., Farber, S.A., and Ekker, S.C. (2007) p53 activation by knockdown technologies. PLoS Genetics. 3(5):e78

Pickart, M.A., Klee, E.W., Nielsen, A.L., Sivasubbu, S., Mendenhall, E.M., Bill B.R., Chen, E., Eckfeldt, C.E., Knowlton, M., Robu, M.E., Larson, J.D., Deng, Y., Schimmenti, L.A., Ellis, L.B., Verfaillie, C.M., Hammerschmidt, M., Farber, S.A., and Ekker, S.C. (2006) Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome. PLoS One. 1(1):e104

Schaefer, J. and Ryan, A. (2006) Developmental plasticity in the thermal tolerance of zebrafish Danio rerio. Journal of Fish Biology. 69(3):722-734

Ho, S.Y., Lorent, K., Pack, M., and Farber, S.A. (2006) Zebrafish fat-free is required for intestinal lipid absorption and Golgi apparatus structure. Cell Metabolism. 3(4):289-300

Ghiselli, G., and Farber, S.A. (2005) D-glucuronyl C5-epimerase acts in dorso-ventral axis formation in zebrafish. BMC Developmental Biology. 5:19

Duffy, K.T., McAleer, M.F., Davidson, W.R., Kari, L., Kari, C., Liu, C.G., Farber, S.A., Cheng, K.C., Mest, J.R., Wickstrom, E., Dicker, A.P., and Rodeck, U. (2005) Coordinate control of cell cycle regulatory genes in zebrafish development tested by cyclin D1 knockdown with morpholino phosphorodiamidates and hydroxyprolyl-phosphono peptide nucleic acids. Nucleic acids research. 33(15):4914-4921

McAleer, M.F., Davidson, C., Davidson, W.R., Yentzer, B., Farber, S.A., Rodeck, U., and Dicker, A.P. (2005) Novel use of zebrafish as a vertebrate model to screen radiation protectors and sensitizers. International journal of radiation oncology, biology, physics. 61(1):10-13

Mulligan, T.S., and Farber, S.A. (2005) A "Block and Rescue" Pharmacogenetic Approach to Dissecting a Biochemical Pathway Controlling Germ Cell Migration. Zebrafish. 1(4):343-347

Wickstrom, E., Choob, M., Urtishak, K.A., Tian, X., Sternheim, N., Talbot, S., Archdeacon, J., Efimov, V.A., and Farber, S.A. (2004) Sequence specificity of alternating hydroyprolyl/phosphono peptide nucleic acids against zebrafish embryo mRNAs. Journal of drug targeting. 12(6):363-372

Guo, Y., Cheong, N., Zhang, Z., De Rose, R., Deng, Y., Farber, S.A., Fernandes-Alnemri, T., Alnemri, E.S. (2004) Tim50, a component of the mitochondrial translocator, regulates mitochondrial integrity and cell death. The Journal of biological chemistry. 279(23):24813-24825

Smart, E.J., De Rose, R.A., and Farber, S.A. (2004) RETRACTED: Annexin 2-caveolin 1 complex is a target of ezetimibe and regulates intestinal cholesterol transport. Proceedings of the National Academy of Sciences of the United States of America. 101(10):3450-3455

Thorpe, J.L., Doitsidou, M., Ho, S.-Y., Raz, E., and Farber, S.A. (2004) Germ Cell Migration in Zebrafish Is Dependent on HMGCoA Reductase Activity and Prenylation. Developmental Cell. 6:5-302

Ho, S.Y., Thorpe, J.L., Deng, Y., Santana, E., DeRose, R.A., and Farber, S.A. (2004) Lipid metabolism in zebrafish. The Zebrafish: Cellular and Developmental Biology,2nd Ed. Methods Cell Biol.. 76:87-108

Urtishak, K.A., Choob, M., Tian, X., Sternheim, N., Talbot, W.S., Wickstrom, E., and Farber, S.A. (2003) Targeted gene knockdown in zebrafish using negatively charged peptide nucleic acid mimics. Developmental dynamics : an official publication of the American Association of Anatomists. 228(3):405-413

Farber, S.A., De Rose, R.A., Olson, E.S., and Halpern, M.E. (2003) The zebrafish annexin gene family. Genome research. 13(6):1082-1096

Ho, S.Y., Pack, M., and Farber, S.A. (2003) Analysis of small molecule metabolism in zebrafish. Methods in enzymology. 364:408-426

Farber, S.A., Pack, M., Ho, S.Y., Johnson, I.D., Wagner, D.S., Dosch, R., Mullins, M.C., Hendrickson, H.S., Hendrickson, E.K., and Halpern, M.E. (2001) Genetic analysis of digestive physiology using fluorescent phospholipid reporters. Science (New York, N.Y.). 292(5520):1385-1388

Ho, S.Y., Pack, M., and Farber, S.A. (2001) Real-time imaging of lipid processing in wild type and mutant zebrafish. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 15(5):A1102

Hendrickson, H.S., Hendrickson, E.K., Johnson, I.D., and Farber, S.A. (1999) Intramolecularly quenched BODIPY-labeled phospholipid analogs in phospholipase A(2) and platelet-activating factor acetylhydrolase assays and in vivo fluorescence imaging. Analytical biochemistry. 276(1):27-35

Farber, S.A., Olson, E.S., Clark, J.D., and Halpern, M.E. (1999) Characterization of Ca2+-dependent phospholipase A2 activity during zebrafish embryogenesis. The Journal of biological chemistry. 274(27):19338-19346