sebastian kadener lab
My diverse. Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer. 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. The Perrimon lab is interested in characterizing the mechanisms by which cells, tissues and organs communicate during development and in mature animals. Prior to coming to Brandeis, Sayan worked in the Bangalore Life Science Cluster, India as a research fellow. Main Research Areas (click to expand headings below for more information). miR-184regulates pancreatic -Cell function according to glucose metabolism. Eric studied how the interaction of cell surface proteins expressed by different cell types can regulate blood vessel formation in normal cells and tumors. Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. April received her BS in Cellular and Molecular Biology from Beloit College in 2017, where she worked in the lab of Dr. Amy Briggs studying the role offpgsgenes inArabidopsis thaliana. Samar was awarded the Neubauer doctoral fellowship . Dana joined the Bandopadhayay Lab in 2021 where is she working to apply single-cell methods to evaluate the heterogeneity of pediatric gliomas, and to understand spatial associations. In the Bandopadhayay Lab, Michelle is interested in using computational efforts to better characterize pediatric brain tumors. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. What is their mechanisms of action? 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. September 2018. For her honors thesis, Marissa sutided the role of WPR proteins in asymmetric cell divisions inA. thalianaroots. Antibodies allow protein visualization by immunostaining, biochemical study by immunoprecipitation and western blot, and proteomic study by IP-MS. We are now using this tool to establish sensors of each signaling pathway involved in gut homeostasis, and will use these reagents to examine pathway crosstalk. Metazoan MicroRNAs (2018) David P. Bartel CELL Non-canonical functions of microRNA pathway enzymes - Drosha, DGCR8, Dicer and Ago proteins Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. How do circRNAs work at the molecular level? With this advance, we hope to enable the mosquito community to easily perform genome-wide loss- or gain-of-function screens in cells, for example to discover entry and infection mechanisms of pathogens and drugs, as well as to aid in the functional annotation of mosquito genomes. UAS-gypsy structure and functional test. Molecular Neurobiology and RNA metabolism. I am a PhD student in the lab since 2018 after graduating from The College of Wooster. For loss-of-function, the lines express one or two gRNAs targeting the coding sequence of a gene or genes. de Educ. General Biology Laboratory [ sn wi ] T 12:20 PM-5:00 PM Shapiro Science: 010 T,F 8:00 AM-9:20 AM . Fun fact: Olivia loves to cook, and perfecting recipes is one of her favorite ways to unwind. In the Bandopadhayay Lab, Jess is applying genomic approaches to optimize novel treatment approaches for pediatric brain tumors, and is also working to characterize the role long non-coding RNAs play in the formation of Diffuse Intrinsic Pontine Gliomas. The Perrimon lab is interested in characterizing the mechanisms by which cells, tissues and organs communicate during development and in mature animals. These experiments will provide a system-wide understanding of the factors originating from tumors and how they perturb systemic energy balance, and how peripheral organs in turn respond to initiate cachectic phenotypes. Our lab is interested in determining how molecular and neural circadian components regulate each other and generate a system that is both robust and plastic. * Corresponding authors. Nov, 2017. This plasticity is the result of the existence of very efficient input pathways that convey the external signals into the core oscillator machinery. For example, the vertebrate CNS receives information regarding the status of peripheral metabolic processes via hormonal signaling and direct macromolecular sensing. 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. Zaffagni M, Kadener S. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. Chem. Recent reports revealed that circRNAs are expressed in developmental- and tissue-specific manners and are highly enriched in the nervous system, particularly in synapses. Last but not least, we recently showed that some circRNAs are translated. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. Dr. Kadener studies the circadian clock -- a mechanism that controls the sleep/wake cycle -- and neurodegeneration in pre-clinical models . The EMBO journal 20 (20), 5759-5768, 2001. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. During her free time, Riley enjoys watching documentaries, cooking Korean food, and visiting cafes to drink iced vanilla latte. 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. 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. Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. Im an undergraduate in the Class of 2023 majoring in Chemical Biology at Brandeis. Contact. Sher also loves watching European football and is a die-hard Chelsea football club fan. 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. She also enjoys amateur photography. Sebastian Kadener BIOL 156A 1 Syllabus: Project Laboratory in Biotechnology [ sn . PubMed ID: 31702556 I am in the Class of 2024 studying neuroscience and biology. A polar mechanism coordinates different regions of alternative splicing within a single gene. Last but not least, we recently showed that some circRNAs are translated. 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. She received her BA in Molecular and Cell Biology from the University of California, Berkeley in 2019. View 129 related references Ask authors/readers for more resources. Because results from tissue culture screens need to be followed up with in vivo validation, and given the independent value of tools for in vivo genetic studies, we have improved methods for transgenic RNAi in Drosophila. She then obtained her the PhD from Cancer Biology PhD program at the University of Michigan in 2022. 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. Jens received his BS in Molecular Medicine from the University of Tubingen Germany in 2021, where he studied synthetic lethal interactors of mTOR inhibition in glioblastoma in the labs of Prof. Ghazaleh Tabatabai and Dr. Daniel Merk. Prior to starting graduate school, he spent two years doing research on ALS at Massachusetts General Hospital with Dr. Lagier-Tourenne. 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. Ph.D. University of So Paulo (USP)- Brazil. In October 2021, Anna defended her PhD thesis (and Mimi had the honor of being her faculty opponent!!). 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. *, Bartok O. Dana received her BA in Biology from the University of Pennsylvania (21). Selected for Faculty of 1000 (Factor 3 Recommended). Cs. High-accuracy determination of internal circadian time from a single blood sample. 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. Patop IL, Wst S, Kadener S. Craving for Introns. Molecular Neurobiology and RNA metabolism. One point of focus for DRSC-BTRR efforts is establishment of CRISPR pooled screening in cell lines from mosquito vectors of infectious diseases. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. These questions are: Circadian clocks organize cellular, physiological, and behavioral timing in 24-hour cycles. Sebastian Kadener Activities Collapse all Works (11) sort Sort The chromatin factor ROW cooperates with BEAF 32 in regulating longrange inducible genes EMBO reports 2022-12-06 | Journal article DOI: 10.15252/embr.202254720 Contributors : Neta Herman; Sebastian Kadener; Sagiv Shifman Show more detail Source : Crossref Recent reports revealed that circRNAs are expressed in developmental- and tissue-specific manners and are highly enriched in the nervous system, particularly in synapses. S Kadener, P Cramer, G Nogus, D Cazalla, M de la Mata, JP Fededa, . 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. 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. leptin), neural development, and behavior are conserved. She also loves bagels and is always on the hunt for the best bagel. In the Bando Lab, Adam is studying how alterations in chromatin factors lead to pediatric gliomagenesis with the ultimate goal of discovering novel therapeutic approaches. Kadener, Sebastian / Brandeis University Publications. Michael earned a BA in cellular biology and neuroscience from Rutgers University. Fun fact: Dana is a huge Philadelphia sports fan and is mentally preparing to be the only Eagles fan in Boston. *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. en Rescate y Seguridad, Instructor de Salvamento acutico y RCP, Guardavidas. The current model postulates that circadian oscillators keep time by complex transcriptional and post-transcriptional feedback loops. 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. 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. *, Afik S., Menet J., Wolfson V., Weissbein U., Haimovich D., Gafni C., Friedman N., Rosbash M. and Kadener S. . neta.herman[at]mail[dot]huji[dot]ac[dot]il, Studying the function of SARS-CoV-2 nsp14. Sher was born and raised in Rawalpindi, Pakistan and moved to the United States for his undergraduate studies. Sebastian Kadener. Third, more recently we used single-cell RNAseq (scRNAseq) to describe all the cell types and their transcriptomes in the Drosophila gut. For doing this, we study the circadian clock from a systemic point of view, including studies at the molecular and neural levels. During her time at Brandeis, Maddie worked in the lab of Sebastian Kadener studying RNA metabolism and the circadian rhythm. Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. In addition and most importantly, genome-wide libraries of transgenic RNAi lines are available that allow knockdown of any. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. 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 mature animals, cells and organs interact to maintain homeostasis and coordinate their physiological roles. A polar mechanism coordinates different regions of alternative splicing within a single gene. Andranik Ivanov and Sebastian Meczmack (Prof. Rajewsky's . Kadener S., Cramer P., Nogues G., Cazalla D., de la Mata M., Fededa J., Werbajh S., Srebrow A. and Kornblihtt A. CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. Olivia worked in two labs during her time at WashU: Dr. Natalie Muellers paleoethnobotany lab where she analyzed plant samples from Late Archaic food sites in modern-day Mississippi, and Dr. Crickette Sanzs Digital Lab for Primatology where she studied captive and wild chimpanzee ecology and ontogeny. and Kornblihtt A.R. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. 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. I am studying translational activators of the circadian clock in Drosophila. Further, our work and that of others has suggested functions of these moleculesin vivo. * Corresponding authors. Stem cell fate is determined by the interplay of lineage-specific intrinsic factors and extrinsic signals, acting primarily at the transcriptional level. Rosi is attending the structural MS workshop in Finland. Community support Reprint. Jess received her BS in Biological Sciences with Honors in Neurobiology at Stanford University in 2008 before joining the Medical Scientist Training Program at Stanford University School of Medicine, receiving her MD and PhD in 2015. 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. 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. He went to college in Malaysia before moving to Philadelphia. Chem. In the Bandopadhayay Lab, Anna will be expanding her skills to apply genomic approaches to understand the mechanisms through which gliomas develop, and to develop strategies to overcome therapeutic resistance. in English and Anthropology from Washington University in St. Louis (22). We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. ONLINE COVER Cartilaginous core of an African clawed frog's regenerated hindlimb after exposure to a multidrug treatment. Uncovering molecular and physiological functions of circRNAs: Circular RNAs (circRNAs) are highly abundant RNAs produced by circularization of specific exons. 178: Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially-restricted proteomes. 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. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. Aaron is an Attending Pediatric Neuro-Oncologist at the Dana-Farber/Boston Childrens Cancer and Blood Disorders Center. 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. Sebastian Kadener. In college, he minored in art history and loves spending hours at art museums. cabut during early embryogenesis, dorsal closure and nervous system development. Advantages of CRISPRi as compared with RNAi are that the level of knockdown can be more tightly controlled and the system appears to have reduced off-target effects. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. Im a Masters student studying the expression of Ultradian Genes and their role in Canton-S flies. 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. J. Biol. 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. We demonstrated that shRNAs are more efficient and specific than long dsRNA when expressed as transgenes, and generated a genome scale collection of >13,000 lines covering 75% of the genome in our optimized VALIUM vectors (85% of highly conserved genes). and Kornblihtt A.R. We continue to evaluate and create new methods for genome engineering. 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. Fun fact:Riley chose her English name when she moved to the U.S because it means courage. 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). Second, we identified 53 transcription factors, specifically expressed or enriched in the ISCs, and are characterizing how they cooperate to integrate signal inputs. Transcriptional activators differ in their abilities to control alternative splicing. PANGEA: A New Gene Set Enrichment Tool for Drosophila and Common Research Organisms Biogenesis and functions of circular RNAs. Hu, Comjean, Attrill, Antonazzo, Jim Thurmond, Li, Chao, Mohr, Brown, Perrimon 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. Studying transcription, chromatin and gene expresion in the brain. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. Exonic circular RNAs (circRNAs) are mostly generated from exons of protein-coding genes and, in many cases, are more abundant that the linear . RNA biology Neurosciences. Our laboratory is interested in understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. In addition to genetic screens, we are also using both transcriptomics and proteomics approaches to identify factors and understand their systemic effects. 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. Fun fact: Leslie played basketball through college and is now an avid cyclist. Associate Professor, Brandeis University. 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 using CRISPR to mutate or engineer cell lines that can be used for screening, and have developed efficient protocols in Drosophila cells, which are particularly challenging as they are polyploid and difficult to grow following single-cell isolation. Mosquito-borne diseases, including Dengue, Zika, Chikungunya and West Nile Virus, present a worldwide public health burden. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. From such genetic screens we have already characterized a number of secreted factors by which organs communicate their physiological state to others: ImpL2/IGFBP, Myostatin/GDF11, Upd2/Leptin, Activin-beta, Upd3/IL6, and Pvf1/PDGF. Finally, as an alternative to RNAi for partial loss-of-function screens using a Cas system, we have shown that Cas13 is an effective tool for CRISPRi in Drosophila cells. I am interested in studying circular RNAs and neurological disorders. Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. Acquiring answers to these fascinating questions requires a deep understanding of the mechanisms by which cells integrate signals received from their inner selves, neighboring cells, other organs and the environment. 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. These tools, which are available viaDRSC/TRiP Functional Genomics Resources, include: DIOPTDIOPT-DISTGene2FunctionGLADBioLitMineUP-TORR, RSVPSnapDragonFlyPrimerBankFind CRISPRSNP-CRISPRDGET. Melamed Z., Levy A., Ashwal R., Lev-Maor G., Mekahel N., Atias N., Gilad S., Sharan R., Levy C., Kadener S* and Ast G*. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. Feel free to send suggestions. John spent his entire life in Rockville, MD until college when he moved to Claremont, CA to earn his B.S. Community support Reagent. Fun in the Lab. 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. Brown S.A., Ripperger J., Kadener S., Fleury-Olela F., Vilbois F., Rosbash M. and Schibler U. The EMBO journal 20 (20), 5759-5768, 2001. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. 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. 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. I am researching the role of circular RNAs (circRNAs) in aging processes in Drosophila melanogaster. Molecular Neurobiology and RNA Metabolism Laboratory. Olivia received her B.A. There, she studied the oncogenic role of certain signaling molecules in the Hedgehog signaling pathway, and became extremely interested in advancing cancer therapy research. Lab, Michelle is interested in understanding how molecular processes in the of!, he minored in art history and loves spending hours at art museums and understand their effects! 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sebastian kadener lab