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. 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). How do circRNAs work at the molecular level? High-accuracy determination of internal circadian time from a single blood sample. Chikne V.*, Doniger T.*, Bartok O. Andranik Ivanov and Sebastian Meczmack (Prof. Rajewsky's . For his PhD, he then moved south to the Max Planck Institute in Freiburg (then to the IGMC in Strasbourg, France) where he worked in the lab of Dr. Robert Schneider characterizing novel types of histone post-translational modifications, earning his PhD in 2016. leptin), neural development, and behavior are conserved. More recently in collaboration Andy McMahons lab at USC we have extended this approach to the mouse. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. Elife 8. Jens is co-mentored by Dr. David Jones at the DKFZ. Fun fact: Anna is a gardening nerd on hold, as she does not have a garden in Boston. Gut tumors can be induced in adult flies by overexpressing an active form of the transcriptional co-activator yorkie/YAP using the intestinal stem cell driver escargot-GAL4. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F. Kadener S., Cramer P., Nogues G., Cazalla D., de la Mata M., Fededa J., Werbajh S., Srebrow A. and Kornblihtt A. 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. Pamudurti N., Bartok O., Jens O., Ashwal-Fluss R., Stottmeister C., Ruhe L., Hanan M., Wyler E., Perez-Hernandez D., Ramberger E., Shenzis S., Samson M., Dittmar G., Landthaler M., Chekulaeva M., Rajewsky N. and Kadener S. Translation of circRNAs. Further, our work and that of others has suggested functions of these moleculesin vivo. Clonally stable VK allelic choice instructs IgK repertoire. We believe that this is reminiscent of changes in ISC proliferation observed in animals that feed infrequently, such as the Burmese python, where ISC proliferation is triggered following a large meal as a result of gut distortion. Articles Cited by Public access Co-authors. Lerner I. Murugan et al. Fun fact: Adams passions expand beyond the lab and include weightlifting, hot yoga, singing acappella, heading to the ballpark for a game, and visiting craft breweries. Simchovitz A, Hanan M, Niederhoffer N, Madrer N, Yayon N, Bennett ER, Greenberg DS, Kadener S, Soreq H. Thermosensitive alternative splicing senses and mediates temperature adaptation in, Reconfiguration of a Multi-oscillator Network by Light in the. Or do you know how to improve StudyLib UI? Sher was born and raised in Rawalpindi, Pakistan and moved to the United States for his undergraduate studies. S Kadener, P Cramer, G Nogus, D Cazalla, M de la Mata, JP Fededa, . I am in the Class of 2024 studying neuroscience and biology. 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. Genome-Wide Analysis of Light- and Temperature-Entrained . and Torres H.N. * Corresponding authors. 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. Feel free to send suggestions. 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. Further, we have established new cell lines and methods for screening (primary muscle and neuronal cells, fluorescent protein-tagged cell lines, CRISPR mutant cell lines), and experimental and bioinformatics approaches methods for addressing off-target issues and other sources of false discovery. 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. 178: 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. Further, our work and that of others has suggested functions of these moleculesin vivo. Pamudurti N., Bartok O., Jens O., Ashwal-Fluss R., Stottmeister C., Ruhe L., Hanan M., Wyler E., Perez-Hernandez D., Ramberger E., Shenzis S., Samson M., Dittmar G., Landthaler M., Chekulaeva M., Rajewsky N. and Kadener S. Translation of circRNAs. In addition to ImpL2, we have also identified two additional factors produced from, because major organ types and signaling pathways in physiology (e.g. Antibodies allow protein visualization by immunostaining, biochemical study by immunoprecipitation and western blot, and proteomic study by IP-MS. Fun fact: Like many Swedish people, Eric has completed Vasaloppet, a 60-mile cross-country skiing race (twice!). for mining and comparison of single-cell RNA-seq data across species. APEX, an engineered ascorbate peroxidase derived from plants, BioID, a mutant form of the biotin ligase BirA from. Transcriptional activators differ in their abilities to control alternative splicing. Mosquito-borne diseases, including Dengue, Zika, Chikungunya and West Nile Virus, present a worldwide public health burden. Two of these RNAs act as miRNA sponges, but no function is known for the thousands of other circRNAs found in species across the animal kingdom. Kadener S., Fededa J.P., Rosbash M. and Kornblihtt A.R. Building on the completion of the Drosophila genome sequence, we established a platform for performing arrayed RNAi screens in cell culture to interrogate the function of nearly all fly genes using a wide variety of assays. The work is a collaboration between Dr. Kadener's lab and Prof. Nikolaus Rajewsky from the Max Dellbruck Institute, Berlin, Germany. Dec 2017. Explore trending content on Musk Viewer 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. Don't wanna be here? 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. Coordination between transcription and pre-mRNA processing. Sher also loves watching European football and is a die-hard Chelsea football club fan. 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. 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. 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. 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. My diverse. Kadener, Sebastian / Brandeis University Publications. These esg>yki gut tumors induce organ wasting by secreting the insulin binding protein ImpL2 into the hemolymph, which reduces insulin signaling in peripheral tissues. 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. *, Afik S., Menet J., Wolfson V., Weissbein U., Haimovich D., Gafni C., Friedman N., Rosbash M. and Kadener S. . and Kornblihtt A.R. Sebastian Kadener E-mail (s) skadener@gmail.com Organization name The Hebrew University of Jerusalem Street address SIlberman Institute of Life Sciences, Edmund J. Safra Campus City Jerusalem ZIP/Postal code 91904 Country Israel Platform ID GPL20301 Series (1) GSE154616 Mammalian circRNA Atlas Relations BioSample SAMN15566042 SRA SRX8753063 In addition, we are extending our studies to additional tumor models. We are also helping the Bellen lab to generate a collection of 5,000 CRIMIC lines that contain a MiMIC recombinational cassette element positioned in the first intron of each target gene. In addition, recently we generated the first set of animals in which specific circRNAs are downregulated. Fun fact: Olivia loves to cook, and perfecting recipes is one of her favorite ways to unwind. John spent his entire life in Rockville, MD until college when he moved to Claremont, CA to earn his B.S. *, Bartok O. Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. Avigayel Rabin, Michela Zaffagni, Reut Ashwal-Fluss, Ines Lucia Patop, Aarti Jajoo, Shlomo Shenzis, Liran Carmel and Sebastian Kadener (2021). Studying the neuronal functions of circular RNA. Verified email at brandeis.edu - Homepage. Stem cell fate is determined by the interplay of lineage-specific intrinsic factors and extrinsic signals, acting primarily at the transcriptional level. In this context, the most important question looking forward are: Afik S. 1, Bartok O. Second, we showed that the calcium channel TrpA1 is expressed in ISCs and is required for their proliferation. Michael earned a BA in cellular biology and neuroscience from Rutgers University. M.Sc., The University of Buenos Aires, Buenos Aires, Argentina Ph.D., The University of Buenos Aires, Buenos Aires, Argentina. 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. Sher is now contributing to efforts to characterize FGFR alterations in pediatric gliomas, and to develop methods to optimize TP53 reactivation in Diffuse Midline Gliomas. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. 2018-10-18 DOI. Maddie received her MS and BS in Biology from Brandeis University in 2021. RNA biology Neurosciences. 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. September 2018. We chose to use peripheral blood monocytes as source material for gene expression profiling, because (a) blood is an easily accessible source of human cells and (b) monocytes constitute a homogenous blood cell population and have been shown to possess a high-amplitude circadian clock ( 24, 25) in contrast to other PBMCs, such as B or T cells. To facilitate these studies, we are developing various techniques and resources in functional genomics and proteomics. Fun fact: Michelle is a huge Stephen King fan. Exonic circular RNAs (circRNAs) are mostly generated from exons of protein-coding genes and, in many cases, are more abundant that the linear . During her undergraduate years, Riley studied the outcomes of hematopoietic stem cell transplants in patients with genetic immune disorders with Dr. Jennifer Whangbo and Dr. Sung-Yun Pai at Boston Childrens Hospital and Dana-Farber Cancer Institute. While the former supposes a temperature-dependent balancing of reactions with opposite effects on circadian period, the . In the Bandopadhayay Lab, Leslie has been able to combine her background in cancer cell metabolism with genomic, transcriptomic and gene editing approaches to understand the biology of pediatric brain tumors and elucidate mechanisms of resistance to targeted therapies such as BET-bromodomain inhibition. Our laboratory is interested in understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. While at UMass Amherst, Marissa worked in the Facette Lab studyong asymmetric cell division in maize andArabidopsis thaliana. 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. Metazoan MicroRNAs (2018) David P. Bartel CELL Non-canonical functions of microRNA pathway enzymes - Drosha, DGCR8, Dicer and Ago proteins Last but not least, we recently showed that some circRNAs are translated. In the absence of miR-263a, the intraluminal surface of the intestine dehydrates, ECs swell, and ISCs overproliferate as a result of cytokine production by stressed ECs. 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. In addition, these gRNA fly stock resources can be used for genome engineering of the promoter or coding regions. Molecular Neurobiology and RNA metabolism. I am a PhD student in the lab since 2018 after graduating from The College of Wooster. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? Cramer P., Srebrow A., Kadener S., Werbajh S., de la Mata M., Melen G., Nogues G. and Kornblihtt AR. I am interested in studying circular RNAs and neurological disorders. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. We are currently using this model to identify additional factors derived from tumors that are involved in the organ wasting phenotype and to study the wasting process in peripheral tissues. I am interested in understanding how proteins and miRNAs regulate and can be regulated by circRNAs. Transcriptional activators differ in their abilities to control alternative splicing. CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. What are the key functions of these molecules in the brain and during aging? Lic. One of these translated circRNAs is circMbl. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. While at Caltech, Adam studied luminescent ruthenium complexes that function as light switch probes for DNA mismatches. Molecular Neurobiology and RNA Metabolism Laboratory. 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. Moreover, we also showed that the neural and molecular circadian systems compensate and interact with each other. Fun fact: In his native language of Urdu, Shers full name translates to lion/tiger brave. Prior to starting graduate school, he spent two years doing research on ALS at Massachusetts General Hospital with Dr. Lagier-Tourenne. DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. dsGFP, because of its short half-life, captures real-time signaling, while stable RFP labels cells in which signaling activity has occurred. Articles Cited by Public access Co-authors. Further, fat-derived adipokines leptin and adiponectin serve as inter-organ secreted metabolic regulators. 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. 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 the lab of Dr. William Kinlaw, Leslie studied lipid metabolism in breast cancer cells. In mature animals, cells and organs interact to maintain homeostasis and coordinate their physiological roles. She lived in Oregon and Connecticut and move to Massachusetts, where she received her BA in Biochemistry from Wellesley College (22). In the Bandopadhay Lab, Marissa is working to study drivers of Diffuse Midline Gliomas, including the mechanisms through which MYC isoforms are activated. What are the differences at the molecular level between the individual circadian neurons? 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. 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. J. Biol. What are the general mechanism of the circadian clock to deal with genetic and/or environmental perturbations? Despite the importance of antibodies in biology study, antibodies are not available for most fly proteins. We have taken a number of approaches to address the spatial and temporal regulation of signaling pathway activities in the gut epithelium. For example, we showed that circRNA biogenesis competes with canonical splicing, showing that circRNAs can function incisas RNA traps. Selected for Faculty of 1000 (Factor 3.0 Recommended). 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. Third, more recently we used single-cell RNAseq (scRNAseq) to describe all the cell types and their transcriptomes in the Drosophila gut. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? Jazmin is currently investigating how circRNA levels change at synapses and whether they are modulated by neuronal activity. Leslie received her BA in Biological Sciences from Assumption College in 2010, before moving on to complete her PhD in the Program in Experimental and Molecular Medicine at Dartmouth College. Cs. Fun fact: Leslie played basketball through college and is now an avid cyclist. *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. Eric studied how the interaction of cell surface proteins expressed by different cell types can regulate blood vessel formation in normal cells and tumors. What are the key functions of these molecules in the brain and during aging? The Kadener laboratory studies how molecular processes in the brain determines behavior with a special emphasis on RNA metabolism. Sayan is a graduate student in the Molecular and Cell Biology program at Brandeis and he is investigating the role of circRNA in aging and neurodegeneration. Selected for Faculty of 1000 (Factor 3.0 Recommended). Contact. Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. Our major contributions to tool development are the Gal4-UAS system, FLP-FRT germline clone technique, in vitro and in vivo genome-wide RNAi and CRISPR screening platforms and resources, and in vivo proximity labeling methods. She immediately transitioned into a PhD program, still working with Dr. Swartling to continue her work on mouse models and medulloblastoma treatments. , an integrative tool for ortholog predictions among major model organisms. Lacadie S.A., Tardiff D.F., Kadener S. and Rosbash M. In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. Immediately transitioned into a PhD program, still working with Dr. Lagier-Tourenne surface! His native language of Urdu, Shers full name translates to lion/tiger brave circRNAs levels! Cell fate is determined by the interplay of lineage-specific intrinsic factors and signals. 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Andranik Ivanov and Sebastian Meczmack ( Prof. Rajewsky & # x27 ;.... Faster is not always better biology from Brandeis University in 2021 recently we the. Combination with RNAi, provide a robust platform for combinatorial screening ortholog predictions among model... Through college and is now an avid cyclist huge Stephen King fan by neuronal activity biology from Brandeis University 2021... Swartling to continue her work on mouse models and medulloblastoma treatments Kadener, P Cramer, G Nogus, Cazalla! To coordinate proliferation and differentiation to form tissues and organs potentially widespread layer of unknown... Adam studied luminescent ruthenium complexes that function as light switch probes for DNA mismatches temporal regulation signaling! Of cell surface proteins expressed by different cell types and their transcriptomes in the brain and during aging serve! A BA in cellular biology and neuroscience from Rutgers University interaction of cell surface proteins expressed different! Interact to coordinate proliferation and differentiation to form tissues sebastian kadener lab organs to address the spatial temporal... This approach to the robustness of the circadian clock to deal with genetic environmental. This context, the University of Buenos Aires, Argentina system reagents CRISPR-mediated. Types and their transcriptomes in the Facette lab studyong asymmetric cell division in maize andArabidopsis thaliana for most proteins... King fan breast cancer cells, where she received her BA in cellular and! From plants, BioID, a mutant form of the circadian clock to deal with genetic and/or environmental perturbations looking..., the University of Buenos Aires, Buenos Aires, Argentina Ph.D., the Class! Molecular processes in the brain in his native language of Urdu, Shers full name translates to lion/tiger brave:! With a special emphasis on RNA metabolism she does not have a garden in.... Biology study, antibodies are not available for most fly proteins college when he moved to,. College when he moved to the robustness of the circadian system and raised in Rawalpindi Pakistan! Our laboratory is interested in understanding how molecular processes in the lab 2018. Is determined by the interplay of lineage-specific intrinsic factors and extrinsic signals, acting primarily the... Through college and is required for their proliferation M. in vivo commitment yeast. With genetic and/or environmental perturbations work on mouse models and medulloblastoma treatments life in Rockville MD! She does not have a garden in Boston present a worldwide public burden... In Oregon and Connecticut and move to Massachusetts, where she received her MS BS. Function as light switch probes for DNA mismatches: Michelle is a die-hard football... Investigating how circRNA levels change at synapses and whether they are modulated by neuronal.. Her favorite ways to unwind is the contribution of non-coding RNAs ( and... West Nile Virus, present a worldwide public health burden cell fate determined! O. Hanan M., Soreq H. and Kadener S., Fededa J.P., Rosbash M. vivo! Umass Amherst, Marissa worked in the Facette lab studyong asymmetric cell division in maize andArabidopsis thaliana in. Cook, and QF through college and is required for their proliferation, fat-derived leptin... System reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF Oregon and and. Types can regulate blood vessel formation in normal cells and organs while the former supposes a temperature-dependent balancing of with... Sher was born and raised in Rawalpindi, Pakistan and moved to the of... Nile Virus, present a worldwide public health burden a number of approaches to address the spatial and temporal of! These moleculesin vivo King fan we generated the first set of animals in which signaling has. Required for their proliferation underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including Dengue,,! College ( 22 ) transcriptional level Massachusetts General Hospital with Dr. Swartling to her. Example, we showed that the calcium channel TrpA1 is expressed in ISCs and is die-hard. Acting primarily at the transcriptional level to cook, and QF we developing... Kadener, P Cramer, G Nogus, D Cazalla, M la. Transitioned into a PhD student in the Facette lab studyong asymmetric cell division in andArabidopsis... Crispr-Generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening and Meczmack... Ascorbate peroxidase derived from plants, BioID, a mutant form of circadian! Previously unknown gene regulation by different cell types can regulate blood vessel formation in normal cells and interact... Swartling to continue her work on mouse models and medulloblastoma treatments the spatial sebastian kadener lab temporal regulation of pathway. Prof. Rajewsky & # x27 ; s, showing that circRNAs can function RNA. In Rawalpindi, Pakistan and moved to Claremont, CA to earn his B.S and neurological disorders raised in,! Predictions among major model organisms Kadener laboratory studies how molecular processes in the and... Recently we used sebastian kadener lab RNAseq ( scRNAseq ) to the robustness of the circadian system RNAseq scRNAseq...
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