Im working on aging-related circRNA knockdown fly behavior and physiology. 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. bioRxiv 2023.02.20.529262; doi: Copyright 2023 The President and Fellows of Harvard College. Moreover, in 2019, we were funded to function as the Drosophila Research and Screening Center-Biomedical Technology Research Resource (DRSC-BTRR), which focuses on development of new screening and other technologies. Fun in the Lab. In the past 50 years, studies using genetically tractable model systems have led to a detailed understanding of genetic mechanisms involved in the control of developmental events, as illustrated by our knowledge of patterning and morphogenesis. . ( a) Simplified overview of three stages of the gypsy retrotransposon life cycle, (i) parent insertion in the genome, (ii) the transcribed RNA (genomic RNA), and (iii) the new copy inserted in the genome. I am a PhD student in the lab since 2018 after graduating from The College of Wooster. In the lab of Dr. William Kinlaw, Leslie studied lipid metabolism in breast cancer cells. Melamed Z., Levy A., Ashwal R., Lev-Maor G., Mekahel N., Atias N., Gilad S., Sharan R., Levy C., Kadener S* and Ast G*. 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. Transcriptional activators differ in their abilities to control alternative splicing. Olivia received her B.A. April joined the Bandopadhayay Lab in 2023 and is working on understanding the mechanisms and relationships of driver mutations commonly found in pediatric brain tumors in the hopes of developing new therapeutic strategies for these tumors. Antibodies allow protein visualization by immunostaining, biochemical study by immunoprecipitation and western blot, and proteomic study by IP-MS. Fsica, Tcnico Sup. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F. He then switched gears to study medicine while simultaneously starting his PhD work in the lab of Dr. Lena Claesson-Welsh at Uppsala University. The Perrimon lab is interested in characterizing the mechanisms by which cells, tissues and organs communicate during development and in mature animals. In addition to ImpL2, we have also identified two additional factors produced from yki-gut tumors that contribute to tissue wasting: the Pvr receptor tyrosine kinase ligand Pvf1 and the IL6-like cytokine Unpaired 3 (Upd3). I am interested in studying circular RNA formation. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. During her time at Brandeis, Maddie worked in the lab of Sebastian Kadener studying RNA metabolism and the circadian rhythm. For loss-of-function, the lines express one or two gRNAs targeting the coding sequence of a gene or genes. 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 APEX, an engineered ascorbate peroxidase derived from plants, and BioID, a mutant form of the biotin ligase BirA from E coli and demonstrated their use for in vivo studies. 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. Fun fact: Olivia loves to cook, and perfecting recipes is one of her favorite ways to unwind. We are particularly interested on the role of circular RNAs (circRNAs) at the molecular and neural levels as well as the mechanisms underlying circadian clocks. Ines Patop. Associate Professor, Brandeis University. Mezan S., Feuz JD, Deplancke B. and Kadener S. PDF signaling is an integral part of the. 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. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. In addition, these gRNA fly stock resources can be used for genome engineering of the promoter or coding regions. Chikne V.*, Doniger T.*, Bartok O. Rosi is attending the structural MS workshop in Finland. Fun fact: One of the first things Jens did when he arrived in Boston was to buy a bike. Send us removal request. Additionally, they study the role of circular RNAs (circRNAs) at the molecular and neural levels as well as the mechanisms underlying circadian clocks. Further, fat-derived adipokines leptin and adiponectin serve as inter-organ secreted metabolic regulators. Strikingly, these phenotypes are reminiscent of the pathophysiology of cystic fibrosis (CF), as in CF the non-functional CF transmembrane conductance regulator (CFTR) increases ENaC activity resulting in chronic dehydration of the intraluminal surface liquid in organs such as kidney, colon, lung and sweat glands. Is the category for this document correct. For example, we showed that circRNA biogenesis competes with canonical splicing, showing that circRNAs can function incisas RNA traps. Moreover, we also showed that the neural and molecular circadian systems compensate and interact with each other. 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. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. . Before joining the Bando Lab, John worked as a High Frequency Trader. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. Pathways that are misregulated in animals that develop organ wasting in the context of these various tumor models are identified using a combination of transcriptomics, e.g. Nov, 2017. What are the general mechanism of the circadian clock to deal with genetic and/or environmental perturbations? . An early ancestor in the evolution of splicing: a. Nogues G., Kadener S., Cramer P., de la Mata M., Fededa J.P., Blaustein M., Srebrow A. and Kornblihtt A.R. In addition, skeletal muscles produce various myokines that influence metabolic homeostasis, lifespan, and the progression of age-related diseases and aging in non-muscle tissues. The work is a collaboration between Dr. Kadener's lab and Prof. Nikolaus Rajewsky from the Max Dellbruck Institute, Berlin, Germany. 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. The Kadener laboratory studies how molecular processes in the brain determines behavior with a special emphasis on RNA metabolism. 1 / 3 Looking for Postdoctoral researchers John spent his entire life in Rockville, MD until college when he moved to Claremont, CA to earn his B.S. . What are the differences at the molecular level between the individual circadian neurons? In this context, the most important question looking forward are: Afik S. 1, Bartok O. 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. Riley was born and raised in Seoul, South Korea, and moved to the U.S when she was 11 years old. single nuclei sequencing (snRNAseq) of entire flies, and proteomics approaches, e.g. She is the Co-Director of Research for a non-profit, the STEM Advocacy Institute, which is focused on building a future where there is equitable access and exposure to science for all people. Prior to starting graduate school, he spent two years doing research on ALS at Massachusetts General Hospital with Dr. Lagier-Tourenne. Sebastian Kadener Prof. Nac. Fun fact: Michelle is a huge Stephen King fan. 2018-10-18 DOI. Studying transcription, chromatin and gene expresion in the brain. and Kadener S. Mathematical Model of the, Kadener S., Menet J., Sugino K., Horwich M.D., Weissbein U., Nawathean P., Vagin V., Zamore P., Nelson S. and Rosbash M. A role for miRNAs in the, Kadener S., Rodriguez J., Abruzzi K. and Rosbash M. Genome-wide identification of targets of the, Kadener S., Schoer R., Menet J. and Rosbash M. Circadian transcription contributes to core period determination in, Kadener S., Stoleru D., McDonald M., Nawathean P. and Rosbash M. , Rosbash M., Bradley S., Kadener S., Li Y., Luo W., Menet J.S., Nagoshi E., Palm K., Schoer R., Shang Y. and Tang C.H. Im an undergraduate in the Class of 2023 majoring in Chemical Biology at Brandeis. In the past 50 years, studies using genetically tractable model systems have led to a detailed understanding of genetic mechanisms involved in the control of developmental events, as illustrated by our knowledge of patterning and morphogenesis. Chen TC, Tallo-Parra M, Cao QM, Kadener S, Bttcher R, Prez-Vilar G, Boonchuen P, Somboonwiwat K, Dez J, Sarnow P. A lncRNA survey finds increases in neuroprotective LINC-PINT in Parkinson's disease substantia nigra. PubMed ID: 31702556 We use Drosophila as a model system to characterize the mechanisms underlying communication between cells, tissues, and organs. Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays. Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. Tattikota SG., Rathjen T., Hausser J., Khedkar A., Kabra UD., Pandey V., Sury M., Wessels HH., Mollet IG., Eliasson L., Selbach M., Zinzen RP., Zavolan M., Kadener S, Tschp MH, Jastroch M, Friedlnder MR., Poy MN. Circadian clocks are remarkably robust: they are able to keep time without timing cues and are resilient to large variations in environmental conditions. Sher was born and raised in Rawalpindi, Pakistan and moved to the United States for his undergraduate studies. Im a Masters student studying the expression of Ultradian Genes and their role in Canton-S flies. Its very important for us! Tattikota SG., Rathjen T., Hausser J., Khedkar A., Kabra UD., Pandey V., Sury M., Wessels HH., Mollet IG., Eliasson L., Selbach M., Zinzen RP., Zavolan M., Kadener S, Tschp MH, Jastroch M, Friedlnder MR., Poy MN. Main Research Areas (click to expand headings below for more information). 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. Dec 2017. We are also helping the, 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. Community support Reprint. Lic. News. Fun fact: Leslie played basketball through college and is now an avid cyclist. Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. Litovchenko M, Meireles-Filho ACA, Frochaux MV, Bevers RPJ, Prunotto A, Anduaga AM, Hollis B, Gardeux V, Braman VS, Russeil JMC, Kadener S, Dal Peraro M, Deplancke B. Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells. Wittenbrink N, Ananthasubramaniam B, Mnch M, Koller B, Maier B, Weschke C, Bes F, de Zeeuw J, Nowozin C, Wahnschaffe A, Wisniewski S, Zaleska M, Bartok O, Ashwal-Fluss R, Lammert H, Herzel H, Hummel M, Kadener S, Kunz D, Kramer A. Levin-Klein R., Fraenkel S., Lichtenstein M., Matheson L., Bartok O., Nevo Y., Kadener S., Corcoran A., Cedar H., Bergman Y. Our laboratory is interested in understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. From 2002 to 2008, Sebastian Kadener was a postdoc working in the Michael Rosbash laboratory. Selected for Faculty of 1000 (Factor 6 Must Read). Sebastian Kadener Associate Professor of Biology Research Description Molecular Neurobiology and RNA metabolism Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. SRA: Mus musculus; 1: GPL21103; GSE154616; TXT; SRA Run Selector; Sebastian Kadener: Sep 09, 2021 Cs. Software. Adam is currently studying approaches to therapeutically target cancers that harbor mutations in the Mismatch Repair pathway. For example, the vertebrate CNS receives information regarding the status of peripheral metabolic processes via hormonal signaling and direct macromolecular sensing. During her free time, Riley enjoys watching documentaries, cooking Korean food, and visiting cafes to drink iced vanilla latte. Feel free to send suggestions. One of these translated circRNAs is circMbl. Fun fact:In her free time, Marissa loves to go on bike rides, do yoga and walk her dog. Pvf1 produced by yki-gut tumors activates MEK/ERK signaling and enhances catabolism in multiple tissues. Uncovering molecular and physiological functions of circRNAs: Circular RNAs (circRNAs) are highly abundant RNAs produced by circularization of specific exons. Second, we identified 53 transcription factors, specifically expressed or enriched in the ISCs, and are characterizing how they cooperate to integrate signal inputs. In a collaboration with Sebastian Kadeners lab at Brandeis, we generated a new set of PspCas13b and RfxCas13d expression constructs that can be used to target RNA in cells and in vivo. 10.1261/rna.068692.118 References. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. Following our identification of adult Drosophila intestinal stem cells (ISCs), we used this system to characterize genes and pathways important for gut homeostasis and in particular, to analyze crosstalk among signaling pathways. Fun fact:April does not drink coffee or tea (which perplexes Mimi) and loves milk and the whole lab likes to make fun of her for it. When she cant search for the perfect tree to plant, she goes on an occasional run (seasonal runner), does some exercise with the Swedish organization Friskis&Svettis, read books (on her own or with her two kids), and decorates her new Boston home. Adam grew up in Ethiopia and moved to Bremen, Germany where he received his B.Sc and M.Sci in Biochemistry and Cell Biology from Jacobs University which was his very first exposure to the exciting field of epigenetics. More. 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. What is their mechanisms of action? Nogues G., Kadener S., Cramer P., Bentley D. and Kornblihtt A.R. Additional unpublished work from my lab demonstrates that a subset of circRNAs is translated. Zaffagni M, Kadener S. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. We showed that their translation is mediated by IRES-like sequences, is enhanced in response to starvation and happens in association with membranes and in synapses. This dual reporter can be used in either fixed or live tissues to monitor spatio-temporal activity of signaling pathways at an unprecedented resolution. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. Or do you know how to improve StudyLib UI? Kadener S., Fededa J.P., Rosbash M. and Kornblihtt A.R. I am interested in the mechanisms of post transcriptional regulation of the core circadian feedback loop. My diverse. 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. 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. Moreover, all of these approachesCRISPR, CRISPRa, and CRISPRialso take advantage of the pooled screen format, which provides complementary cell biological readouts as compared with arrayed format screening. Circadian clocks are remarkably robust: they are able to keep time without timing cues and are resilient to large variations in environmental conditions. What are the neural and molecular basis of temperature adaptation and compensation? Contact. Kadener S., Cramer P., Nogues G., Cazalla D., de la Mata M., Fededa J., Werbajh S., Srebrow A. and Kornblihtt A. . Sebastian Kadener Associate Professor of Biology Research Description Molecular Neurobiology and RNA metabolism Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. 369. at USC we have extended this approach to the mouse. These studies have allowed us to better characterize what cell types are present in different gut regions and provide us with new powerful data sets with which we can better characterize the transcriptional networks that define lineage relationships among cell types, cell-cell interactions among cell types (i.e. ( GEO ) is a database repository of High throughput gene expression and. 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