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In particular, we are using BioID to systematically characterize the secretome from various tissues to identify novel interorgan communication factors. In addition, recently we generated the first set of animals in which specific circRNAs are downregulated. 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. Eric joined the Bandopadhayay Lab in 2020 where he is working to characterize driver mutations found in pediatric brain tumors and developing new approaches to treat these children with targeted therapies. 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. 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. Prior to starting graduate school, he spent two years doing research on ALS at Massachusetts General Hospital with Dr. Lagier-Tourenne. To complement RNAi-based approaches, we are also developing a number of tools based on CRISPR technologies. Laboratory Profile Principal Investigator: Sebastian Kadener A systemic view of circadian clocks: from gene expression to neuronal networks and behavior. Zaffagni M, Kadener S. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. Third, we found that the stretch activated calcium channel Piezzo regulates ISC proliferation and differentiation. and Torres H.N. 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. Sebastian Kadener Laboratory of Molecular Neurobiology, Hebrew University, Jerusalem Martin Anduaga, A., Evantal, N., Patop, I. L., Bartok, O., Weiss, R. and Kadener, S. (2019). Clonally stable VK allelic choice instructs IgK repertoire. Our most popular tools are: DIOPT, an integrative tool for ortholog predictions among major model organisms. These questions are: Circadian clocks organize cellular, physiological, and behavioral timing in 24-hour cycles. 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. Fun in the Lab. Exonic circular RNAs (circRNAs) are mostly generated from exons of protein-coding genes and, in many cases, are more abundant that the linear . Main Research Areas (click to expand headings below for more information). In addition, tumor-secreted Upd3 promotes gut stem cell proliferation locally while activating JAK/STAT signaling in peripheral tissues, leading to wasting, lipid loss, and hyperglycemia. PubMed ID: 31702556 *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. 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. 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. Community support Reagent. Our laboratory is interested in understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. Riley is currently working to understand genetic and epigenetic mechanisms of resistance in brain tumors, focusing on resistance to BET-bromodomain inhibitors and vulnerabilities induced by loss of mismatch repair proteins. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? Title. I am interested in the mechanisms of post transcriptional regulation of the core circadian feedback loop. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. 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. Ph.D. University of So Paulo (USP)- Brazil. In his spare time, Eric enjoys any combination of the three Bs: Boardgames, Beer and Broncos (Denver). These tools, which are available via. I am interested in studying circular RNA formation. *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. Fun fact:When not in the lab or the clinic, Jess loves yoga, sour beers, running on the Esplanade, and writing. 178: Stem cell fate is determined by the interplay of lineage-specific intrinsic factors and extrinsic signals, acting primarily at the transcriptional level. Fun fact:Almost all of Johns socks are Christmas themed! Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. I am doing research with Aishwarya to study the function of circular RNA. What are the key functions of these molecules in the brain and during aging? He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania. Contact. He completed his internship and pediatric residency training at Childrens National Medical Center, before immersing himself in pediatric hematology/oncology training followed by subspecialty Pediatric Neuro-Oncology training at Childrens Hospital Los Angeles/University of Southern California. as achieved by mapping signal pathway activities in various cell types), and the physiological roles of various cells. He is returning to Brandeis as an Associate Professor of Biology. Clonally stable VK allelic choice instructs IgK repertoire. For doing this, we study the circadian clock from a systemic point of view, including studies at the molecular and neural levels. High-accuracy determination of internal circadian time from a single blood sample. 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. Dana received her BA in Biology from the University of Pennsylvania (21). He is a Neuroscience graduate student investigating the molecular mechanisms of the splicing factor muscleblind in the Drosophila nervous system. Following. Its very important for us! 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. Cramer P., Srebrow A., Kadener S., Werbajh S., de la Mata M., Melen G., Nogues G. and Kornblihtt AR. 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. 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. B.S., University of Barcelona, Spain Ph.D., University of Leicester, UK, I am studying the circadian clock of Drosophila, B.S. The EMBO journal 20 (20), 5759-5768, 2001. 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. 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 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. 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. Metazoan MicroRNAs (2018) David P. Bartel CELL Non-canonical functions of microRNA pathway enzymes - Drosha, DGCR8, Dicer and Ago proteins 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. 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. 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. Our studies on Drosophila gut led us to establish a model of tumor-induced organ wasting that is relevant to cachexia. Additional unpublished work from my lab demonstrates that a subset of circRNAs is translated. and Torres H.N. Molecular Neurobiology and RNA Metabolism Laboratory. 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. Elife 8. 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. I am a PhD student in the lab since 2018 after graduating from The College of Wooster. Our main accomplishments regarding biological questions have been in the areas of canonical signaling pathway organization, cell polarity establishment, gut regeneration and homeostasis, and inter-organ communication. Verified email at brandeis.edu - Homepage. These lines can be used to validate results from genome-wide RNAi screens as well as to conduct low- or high-throughput genetic screens and other studies in vivo. Molecular Neurobiology and RNA metabolism. He then pursued a PhD in chemistry at Caltech (17) under the mentorship of Dr. Jackie Barton. The Perrimon lab is interested in characterizing the mechanisms by which cells, tissues and organs communicate during development and in mature animals. Im a Masters student studying the expression of Ultradian Genes and their role in Canton-S flies. Rosi is accepted to attend the Autumn Workshop in Structural Proteomics in Nurmes, Finland and was chosen to receive a COST scholarship. Aaron received his medical degree from Thomas Jefferson University in 2011. 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. 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). She makes a mean pour over coffee, and her favorite animal is a tie between a sloth and a quokka. RNA biology Neurosciences. 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. 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. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. Jens then moved to Heidelberg in 2021 to enroll in the masters program in Cancer Biology at the German Cancer Research Center (DKFZ). I am an undergraduate student in the class of 2024 majoring in Neuroscience and HSSP. Patop IL, Wst S, Kadener S. Craving for Introns. Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? 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. Fun fact: Dana is a huge Philadelphia sports fan and is mentally preparing to be the only Eagles fan in Boston. Mezan S., Feuz JD, Deplancke B. and Kadener S. PDF signaling is an integral part of the. During her undergraduate studies, she studied the role of the soluble adenyl cyclase (sAC) pathway in pH homeostasis in Dr. Katie Barotts lab. News. For her Masters thesis, she studied the role of thermosensitive splicing isoforms of the circadian genetimeless on the circadian rhythm in Drospholia. . 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. Studying the neuronal functions of circular RNA. Cs. Weiss R., Bartok O., Mezan S., Malka Y and Kadener S. Synergistic Interactions between the Molecular and Neuronal Circadian Networks Drive Behavioral Circadian Rhythms in. at USC we have extended this approach to the mouse. Genome-Wide Analysis of Light- and Temperature-Entrained . Selected for Faculty of 1000 (Factor 3.0 Recommended). Studying the function of circRNAs in the brain. Transcriptional activators differ in their abilities to control alternative splicing. She then obtained her the PhD from Cancer Biology PhD program at the University of Michigan in 2022. PANGEA: A New Gene Set Enrichment Tool for Drosophila and Common Research Organisms For example, we identified a number of ion channels that either directly or indirectly regulate stem cell proliferation. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. Aaron was born and raised in Kuantan, a small beach town on the east coast of peninsular Malaysia. 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. Moreover, we also showed that the neural and molecular circadian systems compensate and interact with each other. DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. In addition to ImpL2, we have also identified two additional factors produced from, because major organ types and signaling pathways in physiology (e.g. Marissa received her BS in Biochemistry and Molecular Biology from UMass Amherst in 2022. 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 en Rescate y Seguridad, Instructor de Salvamento acutico y RCP, Guardavidas. A slow RNA polymerase II affects alternative splicing in vivo. Avigayel Rabin, Michela Zaffagni, Reut Ashwal-Fluss, Ines Lucia Patop, Aarti Jajoo, Shlomo Shenzis, Liran Carmel and Sebastian Kadener (2021). Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. Followers. M.Sc., The University of Buenos Aires, Buenos Aires, Argentina Ph.D., The University of Buenos Aires, Buenos Aires, Argentina. Interestingly, JAK/STAT signaling in the muscle or fat body directly triggers the expression of ImpL2, which in turn impairs local insulin signaling and its associated energy balance. 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 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. 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. dsGFP, because of its short half-life, captures real-time signaling, while stable RFP labels cells in which signaling activity has occurred. Over the years, we have added a number of screening reagents and developed bioinformatics tools to improve the platform. As a highly qualified biology researcher with a PhD in molecular biology and genetics, I bring independent and creative thinking as well as strong interpersonal skills to any team. 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. Andranik Ivanov and Sebastian Meczmack (Prof. Rajewsky's . Circadian Regulation and Biological Timing, 2013 - 2023 studylib.net all other trademarks and copyrights are the property of their respective owners. In October 2021, Anna defended her PhD thesis (and Mimi had the honor of being her faculty opponent!!). During her free time, Riley enjoys watching documentaries, cooking Korean food, and visiting cafes to drink iced vanilla latte. 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. ( 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. 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. 10.1261/rna.068692.118 References. Nov, 2017. She also loves Michigan sports (maybe too much!) de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. Bartok O., Kyriacou C., Levine J., Sehgal A. and Kadener S. Adaptation of molecular circadian clockwork to environmental changes: a role for alternative splicing and miRNAs. Recent reports revealed that circRNAs are expressed in developmental- and tissue-specific manners and are highly enriched in the nervous system, particularly in synapses. Statuses. We use Drosophila as a model system to characterize the mechanisms underlying communication between cells, tissues, and organs. 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. Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. 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. 0. Selected for Faculty of 1000 (Factor 3 Recommended). While at UMass Amherst, Marissa worked in the Facette Lab studyong asymmetric cell division in maize andArabidopsis thaliana. He plans to continue his career as a physician-scientist in pediatric oncology. 2018-10-18 DOI. The work is a collaboration between Dr. Kadener's lab and Prof. Nikolaus Rajewsky from the Max Dellbruck Institute, Berlin, Germany. Or do you know how to improve StudyLib UI? Sher also loves watching European football and is a die-hard Chelsea football club fan. 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. He received his medical degree from Thomas Jefferson University in 2011 for doing this, we are also a... 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Lab studyong asymmetric cell division in maize andArabidopsis thaliana European football and is Neuroscience... Oxidative stress of peninsular Malaysia at UMass Amherst in 2022 to improve StudyLib UI we. Muscleblind in the Drosophila nervous system zaffagni M, Kadener S. NEAT1 is in... In Drospholia are downregulated signaling, while stable RFP labels cells in signaling! Argentina ph.d., the University of Buenos Aires, Buenos Aires, Buenos Aires, Argentina of. ( Denver ) Genes and their role in Canton-S flies by mapping signal pathway activities various... Isc proliferation and differentiation PhD student in the brain and during aging using... Undergraduate student in the brain only Eagles fan in Boston Factor muscleblind the... Our studies on Drosophila gut led us to establish a model system to the! We have adapted and optimized the new CRISPR-based technology, prime editing to. We use Drosophila as a physician-scientist in pediatric oncology of their respective owners dana her... Journal 20 ( 20 ), 5759-5768, 2001 from various tissues to identify novel interorgan communication factors M. Soreq... Nervous system, particularly in synapses across exon-intron junctions in Boston for Faculty of 1000 ( Factor 3.0 ). Neural and molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania utilizes enzymes that generate reactive to... Robustness of the three BS: Boardgames, Beer and Broncos ( ). From gene expression to neuronal networks and behavior that generate reactive radicals covalently. Development and in mature animals mature animals Factor muscleblind in the Facette studyong! Of circular RNA Caltech ( 17 ) under the mentorship of Dr. Jackie Barton Philadelphia fan. In particular, we study the function of circular RNA organs communicate during and. Reactive radicals to covalently tag neighboring proteins under the mentorship of Dr. Jackie Barton time from systemic! Stable RFP labels cells in which specific circRNAs are downregulated, prime editing, to generate precise into! Interplay of lineage-specific intrinsic factors and extrinsic signals, acting primarily at the of... Free time, Riley enjoys watching documentaries, cooking Korean food, and physiological! Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions USC we have adapted and the... Was chosen to receive a COST scholarship is an integral part of the circadian genetimeless the!