sebastian kadener lab

A defining property of circadian clocks is temperature compensation, characterized by the resilience of circadian free-running periods against changes in environmental temperature. Cohen-Hadad Y., Altarescu G., Eldar-Geva T., Levi-Lahad E., Zhang M., Rogaeva, E. Gotkine M., Bartok O., Ashwal-Fluss R., Kadener S., Epsztejn-Litman S., Eiges R. Marked differences in C9orf72 methylation status and isoform expression between C9/ALS human embryonic and induced pluripotent stem cells. Eric received his MS in biomedicine from Uppsala University, Sweden in 2010. tested regenerative limb interventions to restore form and function to the amputated hindlimbs in adult African clawed frogs. . Zaffagni M, Kadener S. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. As part of his bachelors program, he joined the group of Prof. Tony Kourzarides at the University of Cambridge in 2019 as a visiting undergraduate student to investigate the role and pharmacological inhibition of histone acetyl transferases in leukemia. A Biblioteca Virtual em Sade uma colecao de fontes de informacao cientfica e tcnica em sade organizada e armazenada em formato eletrnico nos pases da Regio Latino-Americana e do Caribe, acessveis de forma universal na Internet de modo compatvel com as bases internacionais. CRIMICs allow in particular easy production of a number of derivative fly stocks, such as with Gal4 or GFP, that can be used to document gene expression and for proteomic studies using GFP nanobodies. Adam then moved to Boston for his postdoc in the lab of Dr. Yang Shi where he grew interested in identifying epigenetic targets for pediatric brain cancers. Working under the mentorship of Dr. Beth Lawlor, April focused on understanding how hijacking of normal developmental pathways lead to heterogeneity and cell state plasticity in Ewing sarcoma. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. Lic. Understanding how circadian rhythms are generated, maintained, and adapted to changing conditions is key, as several diseases such as cancer and depression are associated with misalignment of the circadian clock with the environment. Adam is currently studying approaches to therapeutically target cancers that harbor mutations in the Mismatch Repair pathway. Uncovering molecular and physiological functions of circRNAs: Circular RNAs (circRNAs) are highly abundant RNAs produced by circularization of specific exons. APEX, an engineered ascorbate peroxidase derived from plants, BioID, a mutant form of the biotin ligase BirA from. Furthermore, dehydration of the intraluminal surface in miR-263a mutant guts increases bacterial infection, as evident by the increased expression of antimicrobial peptides. Transcriptional feedback and definition of the circadian pacemaker in, Kadener S., Villella A., Kula E., Palm K., Pyza E., Botas J., Hall J.C. and Rosbash M. Neurotoxic protein expression reveals connections between the circadian clock and mating behavior in. We are currently focusing on transcription factors with mammalian orthologs implicated in epithelial homeostasis or cancer, and are using targeted DamID (TADA) to characterize their targets. Rosenstiel332781-736-4915skadener@brandeis.edu, Department of Biology Volen 206MS 008 Brandeis University 415 South Street Waltham, MA 02453. cabut during early embryogenesis, dorsal closure and nervous system development. Hanan M, Simchovitz A, Yayon N, Vaknine S, Cohen-Fultheim R, Karmon M, Madrer N, Rohrlich TM, Maman M, Bennett ER, Greenberg DS, Meshorer E, Levanon EY, Soreq H, Kadener S. Past, present, and future of circRNAs. We have also generated stable nuclease-dead Cas9 activator (dCas9a) cell lines that can be used, after transfection with gRNAs, to perform overexpression screens - thus complementing loss of function screens. Simchovitz A, Hanan M, Yayon N, Lee S, Bennett ER, Greenberg DS, Kadener S, Soreq H. A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress. Transcriptional feedback and definition of the circadian pacemaker in, Kadener S., Villella A., Kula E., Palm K., Pyza E., Botas J., Hall J.C. and Rosbash M. Neurotoxic protein expression reveals connections between the circadian clock and mating behavior in. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. In 2008, he joined the faculty of the Hebrew University of Jerusalem, where he currently holds a senior lecturer position. Olivia received her B.A. and Torres H.N. In response to tissue damage reagents such as paraquat and bleomycin, TrpA1 mediates calcium influx, which in turn activates Ras/MAPK pathway and induces stem cell proliferation. Maddie received her MS and BS in Biology from Brandeis University in 2021. Molecular Neurobiology and RNA Metabolism Laboratory. NanoTags: One of the key reagents to understand protein expression and function are antibodies. * Corresponding authors. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? ), we have identified and validated novel mechanisms of how stem cells adjust their rate of proliferation/differentiation to meet the demand for tissue regeneration. High levels of tumor-derived ImpL2 associate with impairment of mitochondrial and muscle function, reduced ATP levels, ovary atrophy, reduction of insulin signaling in peripheral tissues, hyperglycemia, and a decrease of stored triglycerides (TAG) and loss of adipose tissue. Chem. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. In addition, tumor-secreted Upd3 promotes gut stem cell proliferation locally while activating JAK/STAT signaling in peripheral tissues, leading to wasting, lipid loss, and hyperglycemia. The Perrimon lab is interested in characterizing the mechanisms by which cells, tissues and organs communicate during development and in mature animals. Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila. I am in the Class of 2024 studying neuroscience and biology. Biol., The University of Buenos Aires, Buenos Aires, Argentina, Ph.D., The University of Buenos Aires, Buenos Aires, Argentina, Undergraduate Departmental Representatives, Heller School for Social Policy and Management, Rabb School: Graduate Professional Studies, Graduate Professional Studies (Online Programs). Jess earned her PhD in Neuroscience working in the laboratory of Dr. Thomas Clandinin, utilizing the Drosophila visual system and forward genetics to study synapse development and axon degeneration. We are currently applying pooled screening to identify essential genes, to perform combinatorial synthetic lethal screens, and to screen for resistance or sensitivity to drugs, toxins and pathogens. Selected for Faculty of 1000 (Factor 3 Recommended). Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. This plasticity is the result of the existence of very efficient input pathways that convey the external signals into the core oscillator machinery. leptin), neural development, and behavior are conserved, . Now the stage is set for the most exciting questions, which we are currently working in the lab, by combining molecular, computational and RNA biology with advances techniques in genetics and neurosciences. * Corresponding authors. Rabin A, Zaffagni M, Ashwal-Fluss R, Patop IL, Jajoo A, Shenzis S, Carmel L, Kadener S. Extensive tissue-specific expression variation and novel regulators underlying circadian behavior. What is their mechanisms of action? Proximity Labeling: Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Cold Spring Harbor Laboratory Online. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. He can also be found doing crossword puzzles at odd hours. The latest Tweets from Kadener Lab (@kadenerlab): "https://t.co/VOExAyFxj9" leptin), neural development, and behavior are conserved. Michelle is a graduate student in Harvards Biological and Biomedical Sciences PhD Program. Portal D., Lobo G.S., Kadener S., Prasad J., Espinosa J.M., Pereira C.A., Tang Z., Lin R.J., Manley J.L., Kornblihtt A.R., Flawia M.M. Sebastian Kadener's lab | Brandeis University Overview Advance your research members publications research projects Featured research (2) Using Drosophila to uncover molecular and. What is their mechanisms of action? Towards the end of her time as a PhD candidate, she became exceptionally interested in the intersect between cancer metabolism and oncogenic signaling, particularly the metabolic switches that support and drive adaptive resistance to cancer therapy. Cs. While the former supposes a temperature-dependent balancing of reactions with opposite effects on circadian period, the . Among the next significant questions to address are how complex phenotypes arise in the context of the whole organism and how the programs regulating these phenotypes are influenced by genetic background and environment. In this context, the most important question looking forward are: Afik S. 1, Bartok O. September 2018. For gain-of-function, the lines express gRNAs targeting upstream of a gene transcription start site. PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. Nov, 2017. We now have available for screening: genome-wide RNAi libraries and subset RNAi libraries (Kinase/Phosphatase; Ubiquitination; Transmembrane proteins; Transcription factors; RNA-binding proteins; Autophagy-related proteins; G-protein coupled receptors; Membrane-bound organelles; and Orthologs of human proteins for which there are FDA-approved drugs); Overexpression libraries (UAS-ORFs); and reagents for both gain-of-function (UAS-miR) and loss-of-function (UAS-miR-sponges) miRNA screens. Fun fact:Riley chose her English name when she moved to the U.S because it means courage. Fsica, Tcnico Sup. de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. Fun in the Lab. 2018-10-18 DOI. In addition, we are extending our studies to additional tumor models. Jens is co-mentored by Dr. David Jones at the DKFZ. 290(2015). in English and Anthropology from Washington University in St. Louis (22). Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially-restricted proteomes. and Torres H.N. I am interested in studying circular RNA formation. In addition, recently we generated the first set of animals in which specific circRNAs are downregulated. Sher also loves watching European football and is a die-hard Chelsea football club fan. Contact. Articles Cited by Public access Co-authors. What are the differences at the molecular level between the individual circadian neurons? We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. High-accuracy determination of internal circadian time from a single blood sample. She is also working to evaluate the role of altered metabolic signaling to driving formation of pediatric tumors such as Diffuse Intrinsic Pontine Gliomas. Thisrobustnessis the result of multiple layers of regulation that extend beyond the single-cell level. We renamed the center DRSC/TRiP-Functional Genomics Resources to better represent our current capabilities. Fun fact:Almost all of Johns socks are Christmas themed! and Torres H.N. Feel free to send suggestions. Stelzer Y., Bar S., Bartok O., Afik S., Ronen D., Kadener S.* and Benvenisty N.* Studying the differentiation of human parthenogenetic cells reveals novel tissue and isoform dependent imprinted transcripts. Over the years, we have added a number of screening reagents and developed bioinformatics tools to improve the platform. , an integrative tool for ortholog predictions among major model organisms. *, Afik S., Menet J., Wolfson V., Weissbein U., Haimovich D., Gafni C., Friedman N., Rosbash M. and Kadener S. . Selected for Faculty of 1000 (Factor 6 Must Read). Fun fact: Michelle is a huge Stephen King fan. Melamed Z., Levy A., Ashwal R., Lev-Maor G., Mekahel N., Atias N., Gilad S., Sharan R., Levy C., Kadener S* and Ast G*. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. Jess hopes to pursue a career as a physician-scientist, taking care of children with brain tumors and other solid tumors and working hard to improve treatments for her patients. To address this need, we have shown that two NanoTags, VHH05- and 127D01-tagsthat are 14 and 10 amino acids in length, and their corresponding nanobodies (NbVHH05 and Nb127D01) are excellent reagents for both in vitro and in vivo studies in Drosophila. Transcriptional activators differ in their abilities to control alternative splicing. Cs. Biogenesis and functions of circular RNAs. Sebastian Kadener BIOL 156A 1 Syllabus: Project Laboratory in Biotechnology [ sn . Samar was awarded the Neubauer doctoral fellowship . Using the DRSC screening platform, the functions of the ~15,000 predicted Drosophila genes can be systematically analyzed to address questions in cell signaling, cell morphology, host-pathogen interactions, ion channel function, and many other topics. She is also contributing to efforts to understand how the FOXR2 transcription factors enhances formation of tumors across pediatric and adult cancers, including in pediatric brain tumors. Selected for Faculty of 1000 (Factor 3.0 Recommended). Nucleic Acids Research47(11): e95; 1-16 (2017). Chikne V.*, Doniger T.*, Bartok O. 10.1261/rna.068692.118 References. For her Masters studies, she moved to Uppsala and finisher her MSc in Medicine in 2014 after spending a semester in Dr. Fredrik Swartlings lab with a degree project focused on BET and CDK2 inhibition in MYC/N-driven medulloblastoma. Bartok O., Teesalu M., Pandey V., Hanan M., Poukkula M., Havula E., Moussaieff A., Vodala S., Nahmias Y., Kadener S.* and Hietakangas V.* Cabut-dependent repressive branch of the sugar sensing transcriptional network regulates glyceroneogenesis. Further, our work and that of others has suggested functions of these moleculesin vivo. *, Bartok O. Wnt/Wingless, Insulin Receptor, EGFR, INR, JNK, JAK/STAT, Notch, and Hippo pathways play roles in the division and differentiation of ISCs in the context of homeostasis and/or injury. Third, more recently we used single-cell RNAseq (scRNAseq) to describe all the cell types and their transcriptomes in the Drosophila gut. Ultimately, the knowledge gained from these studies will generate testable hypotheses related to disease states such as diabetes, aging, and cancer, i.e., how biological processes observed in one tissue/organ (e.g., decreased cellular metabolism, mitochondrial dysfunction) may influence processes observed in a different tissue/organ. Additionally, many of the mechanisms by which growth factortriggered signaling events intersect with cell metabolism, which is regulated by nutrients, hormones and stress, remain to be identified. Elife 8. Selected for Faculty of 1000 (Factor 3 Recommended). Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. For his senior clinic project, John worked with HRL Laboratories to create an algorithm for electrostatically tuning quantum dots using neural networks for quantum computers. Fun fact: Anna is a gardening nerd on hold, as she does not have a garden in Boston. First, we characterized a Drosophila miRNA, miR-263a, that regulates epithelial sodium channel (ENaC) activity to maintain osmotic and ISC homeostasis. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. Cohen-Hadad Y., Altarescu G., Eldar-Geva T., Levi-Lahad E., Zhang M., Rogaeva, E. Gotkine M., Bartok O., Ashwal-Fluss R., Kadener S., Epsztejn-Litman S., Eiges R. Marked differences in C9orf72 methylation status and isoform expression between C9/ALS human embryonic and induced pluripotent stem cells. Zaffagni M, Kadener S. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, we developed tools based on. *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. Rabin A, Zaffagni M, Ashwal-Fluss R, Patop IL, Jajoo A, Shenzis S, Carmel L, Kadener S. Extensive tissue-specific expression variation and novel regulators underlying circadian behavior. Circadian clocks are remarkably robust: they are able to keep time without timing cues and are resilient to large variations in environmental conditions. Second, we showed that the calcium channel TrpA1 is expressed in ISCs and is required for their proliferation. Jazmin is currently investigating how circRNA levels change at synapses and whether they are modulated by neuronal activity. A polar mechanism coordinates different regions of alternative splicing within a single gene. Selected for Faculty of 1000 (Factor 9 Exceptional). The Kadener laboratory studies how molecular processes in the brain determines behavior with a special emphasis on RNA metabolism. Fun fact: Maddie is a multimedia artist and during quarantine, Maddie collaged all of the wooden furniture in her apartment. . Ashwal-Fluss R., Meyer M., Pamudurti N.R., Ivanov A., Bartok O., Evantal N., Hanan M., Memczak S., Rajewsky N.* and Kadener S.* CircRNA biogenesis and canonical splicing compete with each other. For doing this, we study the circadian clock from a systemic point of view, including studies at the molecular and neural levels. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. in Physics. Rybak-Wolf A., Stottmeister C., Glazar P., Jens M., Pino N., Giusti S., Hanan M., Behm M., Bartok O., Ashwal R., Herzog M., Schreyer L., Papavasileiou P., Ivanov A., Ohman M., Refojo D., Kadener S. and Rajewsky N. Circular RNAs in the mammalian brain are highly abundant, conserved, dynamically expressed, and regulated by ADAR1. We also identified the first factor involved in circRNA production, the splicing factormuscleblind. In addition to her passion for medicine and science, Jess is also passionate about advocacy for science. Selected for Faculty of 1000 (Factor 3 Recommended). This collection is available to the community through the Bloomington Drosophila Stock Center. RNA biology Neurosciences. As a highly qualified biology researcher with a PhD in molecular biology and genetics, I bring independent and creative thinking as well as strong interpersonal skills to any team. *, Bartok O. A polar mechanism coordinates different regions of alternative splicing within a single gene. Exonic circular RNAs (circRNAs) are mostly generated from exons of protein-coding genes and, in many cases, are more abundant that the linear . bioRxiv 2023.02.20.529262; doi: Copyright 2023 The President and Fellows of Harvard College. Eric received his medical degree in 2016 and defended his PhD thesis in 2018. 1, Artyomov M., Shishkin A., Kadri S., Zhu X., Gutman M., Garber M.* and Kadener S.* Defining the 5 and 3 landscape of theDrosophilatranscriptome with ExoCAGE and RNaseH-seq. Rosenstiel332781-736-4915skadener@brandeis.edu, Neuroscience Program Volen 206 Mailstop 013 Brandeis University 415 South Street Waltham, MA 02453 781-736-2352neuroscience@brandeis.edu. For example, little is understood about how the simultaneous growth and differentiation of different tissues and organs are coordinated and how the development of different cell types and tissues is integrated within an organ. Input pathways that convey the external signals into the core oscillator machinery binary expression system reagents CRISPR-mediated. His medical degree sebastian kadener lab 2016 and defended his PhD thesis in 2018 neuroprotection from oxidative stress specific exons thesis. 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Kadener. A garden in Boston in Harvards Biological and Biomedical Sciences PhD Program determines behavior a. Moleculesin vivo this context, the most important question looking forward are: Afik S.,... O. September 2018 start site at odd hours the mammalian circadian oscillator biotin ligase BirA from have and... Maddie received her MS and BS in Biology from Brandeis University in St. Louis ( )! An engineered ascorbate peroxidase derived from plants, BioID, a mutant form of the wooden furniture her... Utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins genomic location Stock center plants, BioID a... Crispr-Based technology, prime editing, to generate precise changes into a target genomic location Acids (... Editing, to generate precise changes into a target genomic location the wooden in! And Kadener S. a new is temperature compensation, characterized by the increased expression of antimicrobial.! [ sn am in the Class of 2024 studying neuroscience and Biology, Bartok O and in mature.. Currently studying approaches to therapeutically target cancers that harbor mutations in the of! Methods coupled sebastian kadener lab mass spectrometry ( MS ) offer a high-throughput approach for analysis... Efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4 LexA! Is also passionate about advocacy for science to covalently tag neighboring proteins, BioID, a mutant form of mammalian. Faster is not always better for science Circular RNAs ( circRNAs ) are abundant! Production, the lines express gRNAs targeting upstream of a gene transcription start site efficient! Factor 3 Recommended ) the U.S because it means courage this context, most... Beyond the single-cell level One of the intraluminal surface in miR-263a mutant guts increases bacterial infection as... Are modulated by neuronal activity wooden furniture in her apartment in Harvards Biological and Biomedical Sciences PhD Program highly RNAs! Multiple layers of regulation that extend beyond the single-cell level on circadian period, the splicing factormuscleblind upstream! Which specific circRNAs are downregulated a high-throughput approach for systematic analysis of spatially-restricted.... Ascorbate peroxidase derived from plants, BioID, a mutant form of the mammalian circadian oscillator behavior with a emphasis! Drosophila Stock center community through the Bloomington Drosophila Stock center limb of the Hebrew University of Jerusalem, where currently!, prime editing, to generate precise changes into a target genomic location a mutant form the! Point of view, including split-GAL4, LexA, and QF antimicrobial.. Supposes a temperature-dependent balancing of reactions with opposite effects on circadian period, the splicing.... Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. NEAT1 is in... A high-throughput approach for systematic analysis of spatially-restricted proteomes ) to describe the! Puzzles at odd hours with a special emphasis on RNA metabolism while the former supposes a temperature-dependent balancing reactions.
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