ZFIN ID: ZDB-LAB-120112-1
Yaksi Lab
PI/Director: Yaksi, Emre
Co-PI / Senior
Jurisch-Yaksi, Nathalie
Contact Person: Yaksi, Emre
Email: emre.yaksi@ntnu.no
URL: http://yaksilab.com/
Address: Kavli Institute for Systems Neuroscience /Centre for Neural Computation/Egil and Pauline Braathen and Fred Kavli Centre for Cortical Microcircuits, NTNU Norwegian University of Science and Technology Olav Kyrres gate 9 Postboks 8905 7030 Trondheim Norway
Country: Norway
Line Designation: nw

Show all 5 genomic features

Sensory computations: Our primary goal is to understand how sensory world (smell, vision and taste) is represented in animal brain and how these computations regulate different behavioral programs (e.g. fear, arousal, feeding). Moreover, we are interested in understanding how these representations are modulated by behavioral states of animals (e.g, stress, reproduction and hunger). We achieve this by focusing on those brain areas that integrate information from multiple sensory modalities and closely relate to behavior (e.g. telencephalon, habenula, brainstem). Small and accessible brain of zebrafish provides an exceptional framework for studying the neural circuit computations both locally and across multiple brain regions simultaneously.

The role of cilia in brain development and function: The cilium is a small cellular appendage projecting from the surface of most cells, like a tiny antenna. It can generate flow or play a structural, sensory or signaling role in many tissues. Hence, defects in cilia observed in ciliopathy patients affect multiple organs and result in developmental defects, heart and kidney disease, respiratory dysfunction, anosmia and neurological disorders. Using a combination of genetics and imaging techniques, we investigate cellular and physiological mechanisms regulating ciliary function and motility, in vivo. Altogether we expect our work to set a framework for studying and characterizing human ciliopathies using zebrafish as a model organism.

Neural circuit mechanisms underlying neurological diseases: Finally, our laboratory is always open to reach out to the local and international science community for providing the expertise in studying neural circuit function and architecture to investigate the changes in brain circuits underlying neurological diseases. A small core in our laboratory is interested in applying systems neuroscience tools to zebrafish and fruitfly models of neurological diseases (e.g. Fragile X syndrome and epilepsy). Our aim is to understand the alterations in neural circuit computations and connectivity in these disease models.

Kermen, Florence Post-Doc Lal, Pradeep Post-Doc Bartoszek, Ewelina Graduate Student
Palumbo, Fabrizio Graduate Student Pelgrims, Robbrecht Graduate Student Andresen, Merethe Administrative Staff
Ringers, Christa Sommers, Tom Wiest, Christoph

Myren-Svelstad, S., Jamali, A., Ophus, S.S., D'gama, P.P., Ostenrath, A.M., Mutlu, A.K., Hoffshagen, H.H., Hotz, A.L., Neuhauss, S.C.F., Jurisch-Yaksi, N., Yaksi, E. (2022) Elevated photic response is followed by a rapid decay and depressed state in ictogenic networks. Epilepsia. 63:2543-2560
Andreassen, A.H., Hall, P., Khatibzadeh, P., Jutfelt, F., Kermen, F. (2022) Brain dysfunction during warming is linked to oxygen limitation in larval zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 119:e2207052119
Salman, H.E., Jurisch-Yaksi, N., Yalcin, H.C. (2022) Computational Modeling of Motile Cilia-Driven Cerebrospinal Flow in the Brain Ventricles of Zebrafish Embryo. Bioengineering (Basel, Switzerland). 9(9)
Hotz, A.L., Jamali, A., Rieser, N.N., Niklaus, S., Aydin, E., Myren-Svelstad, S., Lalla, L., Jurisch-Yaksi, N., Yaksi, E., Neuhauss, S.C.F. (2021) Loss of glutamate transporter eaat2a leads to aberrant neuronal excitability, recurrent epileptic seizures, and basal hypoactivity. Glia. 70(1):196-214
D'Gama, P.P., Qiu, T., Cosacak, M.I., Rayamajhi, D., Konac, A., Hansen, J.N., Ringers, C., Acuña-Hinrichsen, F., Hui, S.P., Olstad, E.W., Chong, Y.L., Lim, C.K.A., Gupta, A., Ng, C.P., Nilges, B.S., Kashikar, N.D., Wachten, D., Liebl, D., Kikuchi, K., Kizil, C., Yaksi, E., Roy, S., Jurisch-Yaksi, N. (2021) Diversity and function of motile ciliated cell types within ependymal lineages of the zebrafish brain. Cell Reports. 37:109775
Bartoszek, E.M., Ostenrath, A.M., Jetti, S.K., Serneels, B., Mutlu, A.K., Chau, K.T.P., Yaksi, E. (2021) Ongoing habenular activity is driven by forebrain networks and modulated by olfactory stimuli. Current biology : CB. 31(17):3861-3874.e3
Palumbo, F., Serneels, B., Yaksi, E. (2021) Optimized protocol for conditioned place avoidance learning in juvenile zebrafish. STAR protocols. 2:100465
Palumbo, F., Serneels, B., Pelgrims, R., Yaksi, E. (2020) The Zebrafish Dorsolateral Habenula Is Required for Updating Learned Behaviors. Cell Reports. 32:108054
Golla, A., Østby, H., Kermen, F. (2020) Chronic unpredictable stress induces anxiety-like behaviors in young zebrafish. Scientific Reports. 10:10339
Hansen, J.N., Kaiser, F., Klausen, C., Stüven, B., Chong, R., Bönigk, W., Mick, D.U., Möglich, A., Jurisch-Yaksi, N., Schmidt, F.I., Wachten, D. (2020) Nanobody-directed targeting of optogenetic tools to study signaling in the primary cilium. eLIFE. 9:
Kermen, F., Darnet, L., Wiest, C., Palumbo, F., Bechert, J., Uslu, O., Yaksi, E. (2020) Stimulus-specific behavioral responses of zebrafish to a large range of odors exhibit individual variability. BMC Biology. 18:66
Jurisch-Yaksi, N., Yaksi, E., Kizil, C. (2020) Radial glia in the zebrafish brain: Functional, structural, and physiological comparison with the mammalian glia. Glia. 68(12):2451-2470
Kermen, F., Lal, P., Faturos, N.G., Yaksi, E. (2020) Interhemispheric connections between olfactory bulbs improve odor detection. PLoS Biology. 18:e3000701
Thouvenin, O., Keiser, L., Cantaut-Belarif, Y., Carbo-Tano, M., Verweij, F., Jurisch-Yaksi, N., Bardet, P.L., van Niel, G., Gallaire, F., Wyart, C. (2020) Origin and role of the cerebrospinal fluid bidirectional flow in the central canal. eLIFE. 9:
Diaz Verdugo, C., Myren-Svelstad, S., Aydin, E., Van Hoeymissen, E., Deneubourg, C., Vanderhaeghe, S., Vancraeynest, J., Pelgrims, R., Cosacak, M.I., Muto, A., Kizil, C., Kawakami, K., Jurisch-Yaksi, N., Yaksi, E. (2019) Glia-neuron interactions underlie state transitions to generalized seizures. Nature communications. 10:3830
Fore, S., Yaksi, E. (2019) Habenula: A Role in Brain State Transitions during Coping Behavior. Current biology : CB. 29:R692-R694
Olstad, E.W., Ringers, C., Hansen, J.N., Wens, A., Brandt, C., Wachten, D., Yaksi, E., Jurisch-Yaksi, N. (2018) Ciliary Beating Compartmentalizes Cerebrospinal Fluid Flow in the Brain and Regulates Ventricular Development. Current biology : CB. 29(2):229-241.e6
Jin, Y.N., Schlueter, P.J., Jurisch-Yaksi, N., Lam, P.Y., Jin, S., Hwang, W.Y., Yeh, J.J., Yoshigi, M., Ong, S.E., Schenone, M., Hartigan, C.R., Carr, S.A., Peterson, R.T. (2018) Noncanonical translation via deadenylated 3' UTRs maintains primordial germ cells. Nature Chemical Biology. 14(9):844-852
Fore, S., Palumbo, F., Pelgrims, R., Yaksi, E. (2018) Information processing in the vertebrate habenula. Seminars in cell & developmental biology. 78:130-139
Lal, P., Tanabe, H., Suster, M.L., Ailani, D., Kotani, Y., Muto, A., Itoh, M., Iwasaki, M., Wada, H., Yaksi, E., Kawakami, K. (2018) Identification of a neuronal population in the telencephalon essential for fear conditioning in zebrafish. BMC Biology. 16:45
Bergboer, J.G.M., Wyatt, C., Austin-Tse, C., Yaksi, E., Drummond, I.A. (2018) Assaying sensory ciliopathies using calcium biosensor expression in zebrafish ciliated olfactory neurons. Cilia. 7:2
Muto, A., Lal, P., Ailani, D., Abe, G., Itoh, M., Kawakami, K. (2017) Activation of the hypothalamic feeding centre upon visual prey detection. Nature communications. 8:15029
Reiten, I., Uslu, F.E., Fore, S., Pelgrims, R., Ringers, C., Diaz Verdugo, C., Hoffman, M., Lal, P., Kawakami, K., Pekkan, K., Yaksi, E., Jurisch-Yaksi, N. (2017) Motile-Cilia-Mediated Flow Improves Sensitivity and Temporal Resolution of Olfactory Computations. Current biology : CB. 27(2):166-174
Kruger, M., Boney, R., Ordoobadi, A.J., Sommers, T.F., Trapani, J.G., Coffin, A.B. (2016) Natural Bizbenzoquinoline Derivatives Protect Zebrafish Lateral Line Sensory Hair Cells from Aminoglycoside Toxicity. Frontiers in Cellular Neuroscience. 10:83
Tanabe, H., Seki, M., Itoh, M., Deepak, A., Lal, P., Horiuchi, T., Suzuki, Y., Kawakami, K. (2016) Fluorescence-Activated Cell Sorting and Gene Expression Profiling of GFP-Positive Cells from Transgenic Zebrafish Lines. Methods in molecular biology (Clifton, N.J.). 1451:93-106
Vendrell-Llopis, N., Yaksi, E. (2015) Evolutionary conserved brainstem circuits encode category, concentration and mixtures of taste. Scientific Reports. 5:17825
Wyatt, C., Bartoszek, E.M., Yaksi, E. (2015) Methods for studying the zebrafish brain: past, present and future. The European journal of neuroscience. 42(2):1746-63
Takeuchi, M., Matsuda, K., Yamaguchi, S., Asakawa, K., Miyasaka, N., Lal, P., Yoshihara, Y., Koga, A., Kawakami, K., Shimizu, T., Hibi, M. (2015) Establishment of Gal4 transgenic zebrafish lines for analysis of development of cerebellar neural circuitry. Developmental Biology. 397(1):1-17
Hüsken, U., Stickney, H.L., Gestri, G., Bianco, I.H., Faro, A., Young, R.M., Roussigne, M., Hawkins, T.A., Beretta, C.A., Brinkmann, I., Paolini, A., Jacinto, R., Albadri, S., Dreosti, E., Tsalavouta, M., Schwarz, Q., Cavodeassi, F., Barth, A.K., Wen, L., Zhang, B., Blader, P., Yaksi, E., Poggi, L., Zigman, M., Lin, S., Wilson, S.W., Carl, M. (2014) Tcf7l2 Is Required for Left-Right Asymmetric Differentiation of Habenular Neurons. Current biology : CB. 24(19):2217-27
Dreosti, E., Vendrell Llopis, N., Carl, M., Yaksi, E., and Wilson, S.W. (2014) Left-right asymmetry is required for the habenulae to respond to both visual and olfactory stimuli. Current biology : CB. 24(4):440-445
Jetti, S.K., Vendrell-Llopis, N., and Yaksi, E. (2014) Spontaneous activity governs olfactory representations in spatially organized habenular microcircuits. Current biology : CB. 24(4):434-439
Kermen, F., Franco, L.M., Wyatt, C., and Yaksi, E. (2013) Neural circuits mediating olfactory-driven behavior in fish. Frontiers in neural circuits. 7:62
Jurisch-Yaksi, N., Rose, A.J., Lu, H., Raemaekers, T., Munck, S., Baatsen, P., Baert, V., Vermeire, W., Scales, S.J., Verleyen, D., Vandepoel, R., Tylzanowski, P., Yaksi, E., de Ravel, T., Yost, H.J., Froyen, G., Arrington, C.B., and Annaert, W. (2013) Rer1p maintains ciliary length and signaling by regulating γ-secretase activity and Foxj1a levels. The Journal of cell biology. 200(6):709-720
Blumhagen, F., Zhu, P., Shum, J., Schärer, Y.P., Yaksi, E., Deisseroth, K., and Friedrich, R.W. (2011) Neuronal filtering of multiplexed odour representations. Nature. 479(7374):493-8
Kawakami, K., Abe, G., Asada, T., Asakawa, K., Fukuda, R., Ito, A., Lal, P., Mouri, N., Muto, A., Suster, M.L., Takakubo, H., Urasaki, A., Wada, H., and Yoshida, M. (2010) zTrap: zebrafish gene trap and enhancer trap database. BMC Developmental Biology. 10:105
Friedrich, R.W., Yaksi, E., Judkewitz, B., and Wiechert, M.T. (2009) Processing of odor representations by neuronal circuits in the olfactory bulb. Annals of the New York Academy of Sciences. 1170:293-297
Yaksi, E., von Saint Paul, F., Niessing, J., Bundschuh, S.T., and Friedrich, R.W. (2009) Transformation of odor representations in target areas of the olfactory bulb. Nature Neuroscience. 12(4):474-482
Tabor, R., Yaksi, E., and Friedrich, R.W. (2008) Multiple functions of GABA(A) and GABA(A) receptors during pattern processing in the zebrafish olfactory bulb. The European journal of neuroscience. 28(1):117-127
Yaksi, E., Judkewitz, B., and Friedrich, R.W. (2007) Topological Reorganization of Odor Representations in the Olfactory Bulb. PLoS Biology. 5(7):e178
Yaksi, E. (2007) Analysis of odor evoked activity patterns in zebrafish olfactory system by calcium imaging. Ph.D. Thesis. :22p
Yaksi, E., and Friedrich, R.W. (2006) Reconstruction of firing rate changes across neuronal populations by temporally deconvolved Ca2+ imaging. Nature Methods. 3(5):377-383
Feng, B., Bulchand, S., Yaksi, E., Friedrich, R.W., and Jesuthasan, S.J. (2005) The recombination activation gene 1 (Rag1) is expressed in a subset of zebrafish olfactory neurons but is not essential for axon targeting or amino acid detection. BMC Neuroscience. 6:46
Li, J., Mack, J.A., Souren, M., Yaksi, E., Higashijima, S., Mione, M., Fetcho, J.R., and Friedrich, R.W. (2005) Early development of functional spatial maps in the zebrafish olfactory bulb. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25(24):5784-95
Tabor, R., Yaksi, E., Weislogel, J.M., and Friedrich, R.W. (2004) Processing of odor mixtures in the zebrafish olfactory bulb. The Journal of neuroscience : the official journal of the Society for Neuroscience. 24(29):6611-6620