I am a PhD student in the lab since 2018 after graduating from The College of Wooster. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. To facilitate these studies, we are developing various techniques and resources in functional genomics and proteomics. Article. snguyen [at]brandeis [dot]edu Michelle Chukwu Research Technician *, Bartok O. tested regenerative limb interventions to restore form and function to the amputated hindlimbs in adult African clawed frogs. Determine the nature of circadian rhythms within organisms. 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. Jazmin is currently investigating how circRNA levels change at synapses and whether they are modulated by neuronal activity. DIOPT has been well received by the scientific community and has been integrated into FlyBase, PomBase, MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration) and AGR (Alliance of Genome Resources); Gene2Function integrates annotation information for orthologs of multiple species in unified interfaces; RSVP allows scientists to mine the validation and phenotype data for in vivo RNAi and sgRNA stocks; MIST (Molecular Interaction Search Tool) for mining, visualization and analysis of network data, iProteinDB for mining protein post-translational modification (PTM) data and comparison of PTM data across species and DRscDB for mining and comparison of single-cell RNA-seq data across species. Avigayel Rabin, Michela Zaffagni, Reut Ashwal-Fluss, Ines Lucia Patop, Aarti Jajoo, Shlomo Shenzis, Liran Carmel and Sebastian Kadener (2021). 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. Ph.D. University of So Paulo (USP)- Brazil. 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. For gain-of-function, the lines express gRNAs targeting upstream of a gene transcription start site. 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. 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. 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. Cramer P., Srebrow A., Kadener S., Werbajh S., de la Mata M., Melen G., Nogues G. and Kornblihtt AR. To date more than 120 screens have been performed by our lab and others, underscoring the success of the center. In particular, we are using BioID to systematically characterize the secretome from various tissues to identify novel interorgan communication factors. Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer. We continue to evaluate and create new methods for genome engineering. Last but not least, we recently showed that some circRNAs are translated. Jens then moved to Heidelberg in 2021 to enroll in the masters program in Cancer Biology at the German Cancer Research Center (DKFZ). More recently in collaboration Andy McMahons lab at USC we have extended this approach to the mouse. , an integrative tool for ortholog predictions among major model organisms. 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. 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. During her time at Brandeis, Maddie worked in the lab of Sebastian Kadener studying RNA metabolism and the circadian rhythm. Additional unpublished work from my lab demonstrates that a subset of circRNAs is translated. 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. 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. 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. 10.1261/rna.068692.118 References. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. BOX 39.4 CHRONOPHARMACOLOGY Many drugs, toxins, and, Academic Degrees - Dartmouth Medical School, BOX 39.2 MOLECULAR MECHANISMS OF CIRCADIAN, Evolutionary mechanisms underlying the functional divergence of, Trainee Professional Development Day Session Information, Naslov projekta: Defining the role of circadian genes in behavioral, Supplementary Information - Word file (66 KB ), INTRODUCTION TO CHRONOPHARMACOLOGY - Copy, Fall 2012 Application for Associate Editors, BOX 39.1 NEURONAL CONTROL OF DROSOPHILA CIRCADIAN, Biological Rhythms - Cornell University Ergonomics Web. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. During her undergraduate studies, she studied the role of the soluble adenyl cyclase (sAC) pathway in pH homeostasis in Dr. Katie Barotts lab. RNA biology Neurosciences. In his spare time, Eric enjoys any combination of the three Bs: Boardgames, Beer and Broncos (Denver). Cs. UAS-gypsy structure and functional test. Followers. Sebastian Kadener. As miR-183, the human ortholog of miR-263a, also regulates ENaC, our findings suggest miR-183 might be used as a treatment for CF. Aaron received his medical degree from Thomas Jefferson University in 2011. 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. 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. He also enjoys playing handball and online chess. 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. What are the neural and molecular basis of temperature adaptation and compensation? 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. in English and Anthropology from Washington University in St. Louis (22). 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. Previously, Kadener was a Professor in the Biological Chemistry department at the Hebrew University of Jerusalem. 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. Fun fact: Olivia loves to cook, and perfecting recipes is one of her favorite ways to unwind. Lacadie S.A., Tardiff D.F., Kadener S. and Rosbash M. In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. 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. 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. We showed that miRNAs have a key role in providing robustness to the circadian system both during development and in adults. 2018-10-18 DOI. He is a Neuroscience graduate student investigating the molecular mechanisms of the splicing factor muscleblind in the Drosophila nervous system. 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. The Perrimon lab is interested in characterizing the mechanisms by which cells, tissues and organs communicate during development and in mature animals. 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. Sebastian Kadener. Contact. 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. High-accuracy determination of internal circadian time from a single blood sample. 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. 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. Fun fact:Almost all of Johns socks are Christmas themed! In addition, these gRNA fly stock resources can be used for genome engineering of the promoter or coding regions. The EMBO journal 20 (20), 5759-5768, 2001. Fun fact: In his native language of Urdu, Shers full name translates to lion/tiger brave. 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. The challenge is now to understand how these pathways intersect and cooperate, as it is not clear if some pathways regulate the activity of others, or if they act concomitantly. CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. 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. 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. Mosquito-borne diseases, including Dengue, Zika, Chikungunya and West Nile Virus, present a worldwide public health burden. and Kornblihtt A.R. Send us removal request. For example, we identified a number of ion channels that either directly or indirectly regulate stem cell proliferation. * Corresponding authors. Joined June 2011. dsGFP, because of its short half-life, captures real-time signaling, while stable RFP labels cells in which signaling activity has occurred. Regulation of RNA metabolism is emerging as a major regulatory hub for gene expression control in tissues like the brain and the muscle, which don't undergo cel. Biogenesis and functions of circular RNAs. In a collaboration with Sebastian Kadener's 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. For doing this, we study the circadian clock from a systemic point of view, including studies at the molecular and neural levels. These nanobodies and NanoTags can be expressed as chromobodies that enable detecting NanoTags at the N-terminus, C-terminus, or internal site of protein of interest. Organ-to-organ communication is critical to living systems and plays major roles in homeostasis. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. RNAseq of specific organs and more recently, whole-body snRNAseq, allow us to define the transcriptional signatures corresponding to homeostatic states, various stress conditions, and changes to the diet and environment. Laboratory Profile Principal Investigator: Sebastian Kadener A systemic view of circadian clocks: from gene expression to neuronal networks and behavior. Eric studied how the interaction of cell surface proteins expressed by different cell types can regulate blood vessel formation in normal cells and tumors. View 129 related references Ask authors/readers for more resources. High-accuracy determination of internal circadian time from a single blood sample. In this context, the most important question looking forward are: Afik S. 1, Bartok O. Metazoan MicroRNAs (2018) David P. Bartel CELL Non-canonical functions of microRNA pathway enzymes - Drosha, DGCR8, Dicer and Ago proteins 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. Molecular Neurobiology and RNA metabolism. I am analyzing the effect of circRNA on aging in Drosophila, majoring in biochemistry and neuroscience. Nucleic Acids Research47(11): e95; 1-16 (2017). 1 / 3 Looking for Postdoctoral researchers Lic. cabut during early embryogenesis, dorsal closure and nervous system development. We have further established pooled loss- and gain-of-function CRISPR screens (CRISPR and CRISPRa, respectively), whereby gRNAs from a library are introduced into a specific docking site in cells. For her Masters thesis, she studied the role of thermosensitive splicing isoforms of the circadian genetimeless on the circadian rhythm in Drospholia. 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. What is their mechanisms of action? Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? 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. What are the key functions of these molecules in the brain and during aging? * Corresponding authors. This work, led by Sebastian Kadener, summarizes years of development of a pipeline that improves upon current tools. Adam received his BS with honors in chemistry from Trinity College (12), where he worked in the lab of Dr. Tim Curran exploring the coordination of tungsten to diphenylacetylene -turn peptidomimetics. *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. In October 2021, Anna defended her PhD thesis (and Mimi had the honor of being her faculty opponent!!). PubMed ID: 31702556 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. In addition and most importantly, genome-wide libraries of transgenic RNAi lines are available that allow knockdown of any Drosophila gene in an organ or tissue-specific manner. Samar was awarded the Neubauer doctoral fellowship . single nuclei sequencing (snRNAseq) of entire flies, and proteomics approaches, e.g. He then pursued a PhD in chemistry at Caltech (17) under the mentorship of Dr. Jackie Barton. at USC we have extended this approach to the mouse. For his honors thesis, Sher characterized the role of the MAPK/ERK signaling modulator SPRY2 in regulating the transcriptome of the HL-60 Acute Myeloid Leukemia cell line. In mature animals, cells and organs interact to maintain homeostasis and coordinate their physiological roles. for mining and comparison of single-cell RNA-seq data across species. Second, we identified 53 transcription factors, specifically expressed or enriched in the ISCs, and are characterizing how they cooperate to integrate signal inputs. Furthermore, dehydration of the intraluminal surface in miR-263a mutant guts increases bacterial infection, as evident by the increased expression of antimicrobial peptides. Although Celiac disease put a damper on her plans to be a foodie, Dana loves to eat and is always on the hunt for new gluten-free restaurants. Fsica, Tcnico Sup. What are the general mechanism of the circadian clock to deal with genetic and/or environmental perturbations? Cramer P., Srebrow A., Kadener S., Werbajh S., de la Mata M., Melen G., Nogues G. and Kornblihtt AR. 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. I am a junior who is majoring in biochemistry. Cramer P., Cceres J.F., Cazalla D., Kadener S., Muro, A., Baralle F. and Kornblihtt A. ), we have identified and validated novel mechanisms of how stem cells adjust their rate of proliferation/differentiation to meet the demand for tissue regeneration. Dana received her BA in Biology from the University of Pennsylvania (21). Kadener S., Cramer P., Nogues G., Cazalla D., de la Mata M., Fededa J., Werbajh S., Srebrow A. and Kornblihtt A. Allada R., Kadener S., Nandakumar N. and Rosbash M. A recessive mutant of, Portal D., Espinosa J.M., Lobo G.S., Kadener S., Pereira C.A., de la Mata M., Tang Z., Lin R.J., Kornblihtt A.R., Baralle F.E., Flawia M.M. In college, he minored in art history and loves spending hours at art museums. 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). Chem. 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. 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. We use, To complement RNAi-based approaches, we are also developing a number of tools based on CRISPR technologies. Interestingly, circRNAs accumulate in an age-dependent manner suggesting their relevance to age-related homeostasis and/or pathogenesis. Circadian clocks are also exceptionallyplasticas they can quickly and specifically adjust to specific environmental cues. Michelle is a graduate student in Harvards Biological and Biomedical Sciences PhD Program. Dec 2017. and Kornblihtt A.R. Selected for Faculty of 1000 (Factor 3.0 Recommended). This plasticity is the result of the existence of very efficient input pathways that convey the external signals into the core oscillator machinery. I am interested in understanding how proteins and miRNAs regulate and can be regulated by circRNAs. Before joining the Bando Lab, John worked as a High Frequency Trader. Site developed by Health Communication Core, 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 of. The current model postulates that circadian oscillators keep time by complex transcriptional and post-transcriptional feedback loops. *, Afik S., Menet J., Wolfson V., Weissbein U., Haimovich D., Gafni C., Friedman N., Rosbash M. and Kadener S. . . Now, in an article published in the prestigious journal Molecular Cell, the lab of Dr. Sebastian Kadener at the Hebrew University of Jerusalem, in collaboration with the lab of Prof.. 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. 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. Brown S.A., Ripperger J., Kadener S., Fleury-Olela F., Vilbois F., Rosbash M. and Schibler U. Its very important for us! Allada R., Kadener S., Nandakumar N. and Rosbash M. A recessive mutant of, Portal D., Espinosa J.M., Lobo G.S., Kadener S., Pereira C.A., de la Mata M., Tang Z., Lin R.J., Kornblihtt A.R., Baralle F.E., Flawia M.M. Fun fact: Leslie played basketball through college and is now an avid cyclist. I am interested in studying circular RNA formation. 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. Belacortu Y., Weiss R., Kadener S. and Paricio N. Transcriptional activity and nuclear localization of Cabut, the, Belancortu Y., Weiss R., Kadener S. and Paricio N. Expression of, Van der Linden A.M., Beverly M., Kadener S., Rodriguez J., Wasserman S., Rosbash M. and Sengupta P. Genome-Wide Analysis of Light and Temperature-Entrained Circadian Transcripts in, Fathallah-Shaykh H.M., Bona J.L. Mezan S, Ashwal-Fluss R, Shenhav R, Garber M, Kadener S ; A new in vivo model of pantothenate kinase-associated neurodegeneration reveals a surprising role for transcriptional regulation in pathogenesis, [Journal Article] Frontiers in cellular neuroscience (IF: 4.300) (2013) Pandey V, Turm H, Bekenstein U, Shifman S, Kadener S Gene activation is triggered by co-expression of catalytically dead Cas9 (dCas9) fused to an activator domain. We also identified the first factor involved in circRNA production, the splicing factormuscleblind. To overcome the problem associated with the significant reduction of signal strength of dsGFP, we increased post-transcriptional production of the fluorescent protein by including several translational enhancing elements. You can add this document to your study collection(s), You can add this document to your saved list. A phenotypic selection is then applied and gRNAs enriched following selection are identified via next-generation sequencing. He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania. 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. He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania. Jens joined the Bando Lab in 2023 as a visiting graduate student to understand how distinct histone mutations influence gliomagenesis and also aims to exploit the dependence of pLGGs on the MAPK pathway. Fun fact: Like many Swedish people, Eric has completed Vasaloppet, a 60-mile cross-country skiing race (twice!). Don't wanna be here? Thisrobustnessis the result of multiple layers of regulation that extend beyond the single-cell level. de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. He is returning to Brandeis as an Associate Professor of Biology. 178: PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. Nogues G., Kadener S., Cramer P., Bentley D. and Kornblihtt A.R. In the lab of Dr. William Kinlaw, Leslie studied lipid metabolism in breast cancer cells. Fleury-Olela F., Rosbash M. and Schibler U ) of entire flies, and proteomics by Sebastian Kadener systemic. ; t wan na be here be here the molecular and neural.! A systemic view of circadian clocks: from gene expression to neuronal networks and behavior evident... Thermosensitive splicing isoforms of the center and the circadian clock from a systemic point of view, including Dengue Zika! 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Jazmin is currently investigating how circRNA levels change at synapses and whether they are modulated by neuronal activity,. And Schibler U lipid metabolism in breast cancer cells and others, underscoring the success the. Exceptionallyplasticas they can quickly and specifically adjust to specific environmental cues is to! Study collection ( s ), you can add this document to your saved list was a in...