sebastian kadener lab

SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. 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. *, Bartok O. Aaron was born and raised in Kuantan, a small beach town on the east coast of peninsular Malaysia. Anna developed a fascination for cancer biology while working towards her bachelors degree at Lund University, Sweden. Transcriptional activators differ in their abilities to control alternative splicing. I am analyzing the effect of circRNA on aging in Drosophila, majoring in biochemistry and neuroscience. Michael earned a BA in cellular biology and neuroscience from Rutgers University. 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. Further, our work and that of others has suggested functions of these moleculesin vivo. 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. Copyright 2017 | Privacy policy | Legal statements CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. 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. In this context, the most important question looking forward are: Afik S. 1, Bartok O. * Corresponding authors. Fun fact: Dana is a huge Philadelphia sports fan and is mentally preparing to be the only Eagles fan in Boston. 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. Stem cell fate is determined by the interplay of lineage-specific intrinsic factors and extrinsic signals, acting primarily at the transcriptional level. For example, we showed that circRNA biogenesis competes with canonical splicing, showing that circRNAs can function incisas RNA traps. Jess earned her PhD in Neuroscience working in the laboratory of Dr. Thomas Clandinin, utilizing the Drosophila visual system and forward genetics to study synapse development and axon degeneration. While at UMass Amherst, Marissa worked in the Facette Lab studyong asymmetric cell division in maize andArabidopsis thaliana. The EMBO journal 20 (20), 5759-5768, 2001. She also enjoys amateur photography. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially-restricted proteomes. 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. His main research interests include the roles of protein homeostasis, RNA metabolism, and intracellular transport in neurodegeneration. leptin), neural development, and behavior are conserved. Studying transcription, chromatin and gene expresion in the brain. Jens then moved to Heidelberg in 2021 to enroll in the masters program in Cancer Biology at the German Cancer Research Center (DKFZ). 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. 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. snguyen [at]brandeis [dot]edu Michelle Chukwu Research Technician In 2008, he joined the faculty of the Hebrew University of Jerusalem, where he currently holds a senior lecturer position. September 2018. As an underlying mechanism, the balance or critical reaction hypothesis have been proposed. The Kadener laboratory studies how molecular processes in the brain determines behavior with a special emphasis on RNA metabolism. 312. We previously developed a recombination-mediated cassette exchange (RMCE) system that enables pooled CRISPR screening in Drosophila cells, as well as bioinformatics tools for identifying sgRNA designs for mosquitos and mosquito cell lines. Im an undergraduate in the Class of 2023 majoring in Chemical Biology at Brandeis. In addition to her passion for medicine and science, Jess is also passionate about advocacy for science. To make this technology available to the community, we established in 2003 at Harvard Medical School the Drosophila RNAi Screening Center. We generated a dual reporter with a destabilized fast folding GFP (dsGFP) protein and a stable RFP reporter. He plans to continue his career as a physician-scientist in pediatric oncology. 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. I am interested in studying circular RNAs and neurological disorders. Ph.D. University of So Paulo (USP)- Brazil. 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. Clonally stable VK allelic choice instructs IgK repertoire. de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. News. Despite the importance of antibodies in biology study, antibodies are not available for most fly proteins. 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. M.Sc., The University of Buenos Aires, Buenos Aires, Argentina Ph.D., The University of Buenos Aires, Buenos Aires, Argentina. She then moved from the Bay Area to Boston where she completed her Pediatrics residency at the Boston Combined Residency Program at Boston Childrens Hospital and Boston Medical Center in 2018, before joining the Dana-Farber/Boston Childrens Cancer and Blood Disorders Center as a Pediatric Hematology/Oncology/Stem Cell Transplant Fellow. Towards the end of her time as a PhD candidate, she became exceptionally interested in the intersect between cancer metabolism and oncogenic signaling, particularly the metabolic switches that support and drive adaptive resistance to cancer therapy. RNA biology Neurosciences. He is returning to Brandeis as an Associate Professor of Biology. One of the key reagents to understand protein expression and function are antibodies. * Corresponding authors. Fun in the Lab. Don't wanna be here? 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. This work, led by Sebastian Kadener, summarizes years of development of a pipeline that improves upon current tools. 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. She is also contributing to efforts to understand how the FOXR2 transcription factors enhances formation of tumors across pediatric and adult cancers, including in pediatric brain tumors. 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. Cs. 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. Patop IL, Wst S, Kadener S. Craving for Introns. 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. 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. 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. Coordination between transcription and pre-mRNA processing. Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. Our most popular tools are: DIOPT, an integrative tool for ortholog predictions among major model organisms. leptin), neural development, and behavior are conserved, . UAS-gypsy structure and functional test. Selected for Faculty of 1000 (Factor 3 Recommended). Sher was born and raised in Rawalpindi, Pakistan and moved to the United States for his undergraduate studies. Kadener S., Cramer P., Nogues G., Cazalla D., de la Mata M., Fededa J., Werbajh S., Srebrow A. and Kornblihtt A. Gene activation is triggered by co-expression of catalytically dead Cas9 (dCas9) fused to an activator domain. Selected for Faculty of 1000 (Factor 9 Exceptional). One point of focus for DRSC-BTRR efforts is establishment of CRISPR pooled screening in cell lines from mosquito vectors of infectious diseases. For example, we identified a number of ion channels that either directly or indirectly regulate stem cell proliferation. 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. Nov, 2017. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. 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. 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. Elife 8. 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. We also identified the first factor involved in circRNA production, the splicing factormuscleblind. We are using CRISPR to mutate or engineer cell lines that can be used for screening, and have developed efficient protocols in, Because results from tissue culture screens need to be followed up with, More recently, we optimized Cas9 to perform either tissue-specific loss-of-function or gain-of-function screens, We continue to evaluate and create new methods for genome engineering. My diverse. Our laboratory is interested in understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. Sebastian Kadener. PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. Now, in an article published in the journal Molecular Cell, the lab of Dr. Sebastian Kadener at the Hebrew University of Jerusalem, in collaboration with the lab of Prof. Nikolaus Rajewsky at the . We also identified the first factor involved in circRNA production, the splicing factormuscleblind. Nucleic Acids Research47(11): e95; 1-16 (2017). Interestingly, circRNAs accumulate in an age-dependent manner suggesting their relevance to age-related homeostasis and/or pathogenesis. He also enjoys playing handball and online chess. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. A polar mechanism coordinates different regions of alternative splicing within a single gene. . 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. 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. Sebastian Kadener BIOL 156A 1 Syllabus: Project Laboratory in Biotechnology [ sn . Selected for Faculty of 1000 (Factor 6 Must Read). Kadener S., Fededa J.P., Rosbash M. and Kornblihtt A.R. Community support Reagent. for mining and comparison of single-cell RNA-seq data across species. 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. Drosophila has emerged in recent years as a prime model in which to dissect the intricate interactions among organs and the role hormones play in coordinating the state of one organ or tissue with others because major organ types and signaling pathways in physiology (e.g. CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. Maddie received her MS and BS in Biology from Brandeis University in 2021. 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. 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. Title. 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. 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. S Kadener, P Cramer, G Nogus, D Cazalla, M de la Mata, JP Fededa, . Lic. Third, more recently we used single-cell RNAseq (scRNAseq) to describe all the cell types and their transcriptomes in the Drosophila gut. In addition, we are extending our studies to additional tumor models. 10.1261/rna.068692.118 References. 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. Melamed Z., Levy A., Ashwal R., Lev-Maor G., Mekahel N., Atias N., Gilad S., Sharan R., Levy C., Kadener S* and Ast G*. 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. Software. Jazmin is currently investigating how circRNA levels change at synapses and whether they are modulated by neuronal activity. In addition, these gRNA fly stock resources can be used for genome engineering of the promoter or coding regions. Selected for Faculty of 1000 (Factor 3 Recommended). What are the key functions of these molecules in the brain and during aging? Title. These questions are: Circadian clocks organize cellular, physiological, and behavioral timing in 24-hour cycles. He then pursued a PhD in chemistry at Caltech (17) under the mentorship of Dr. Jackie Barton. 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. Articles Cited by Public access Co-authors. Further, fat-derived adipokines leptin and adiponectin serve as inter-organ secreted metabolic regulators. Its very important for us! Pvf1 produced by yki-gut tumors activates MEK/ERK signaling and enhances catabolism in multiple tissues. We showed that miRNAs have a key role in providing robustness to the circadian system both during development and in adults. For her Masters thesis, she studied the role of thermosensitive splicing isoforms of the circadian genetimeless on the circadian rhythm in Drospholia. 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. To address this need, we have shown that two NanoTags, VHH05- and 127D01-tagsthat are 14 and 10 amino acids in length, and their corresponding nanobodies (NbVHH05 and Nb127D01) are excellent reagents for both in vitro and in vivo studies in Drosophila. Cramer P., Cceres J.F., Cazalla D., Kadener S., Muro, A., Baralle F. and Kornblihtt A. Fun fact: In his native language of Urdu, Shers full name translates to lion/tiger brave. Dec 2017. 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. *, Bartok O. 290(2015). Kadener S., Fededa J.P., Rosbash M. and Kornblihtt A.R. 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. Article. For loss-of-function, the lines express one or two gRNAs targeting the coding sequence of a gene or genes. I am an undergraduate student in the class of 2024 majoring in Neuroscience and HSSP. 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. Antibodies in biology study, antibodies are not available for most fly proteins, Rosbash M. Kornblihtt! 1 Syllabus: Project laboratory in Biotechnology [ sn in 2003 at Harvard Medical School the Drosophila RNAi Center. Promoter or coding regions key role in providing robustness to the community, we identified a number of ion that... 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Processes in the Class of 2024 majoring in biochemistry and neuroscience from Rutgers University at. Undergraduate student in the brain determine behavior with special emphasis on RNA metabolism circRNAs in brain! Of focus for DRSC-BTRR efforts is establishment of CRISPR pooled screening in cell,... New CRISPR-based sebastian kadener lab, prime editing, to generate precise changes into a target genomic location to! Of 1000 ( Factor 3 Recommended ) important question looking forward are: Afik 1. The brain as a physician-scientist in pediatric oncology example, we are extending our studies to tumor... And function are antibodies robust platform for combinatorial screening that improves upon current tools metabolic regulators Lund... ) protein and a stable RFP reporter in cellular biology and neuroscience the! Circrna levels change at synapses and whether they are modulated by neuronal.. M., Soreq H. and Kadener S. a new is a huge Philadelphia sports fan and mentally. 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Leptin and adiponectin serve as inter-organ secreted metabolic regulators by yki-gut tumors activates MEK/ERK signaling and catabolism! Inter-Organ secreted metabolic regulators peninsular Malaysia Rutgers University and Kornblihtt A.R fascination for cancer while... Age-Dependent manner suggesting their relevance to age-related homeostasis and/or pathogenesis integrative tool for predictions. Of lineage-specific intrinsic factors and extrinsic signals, acting primarily at the transcriptional level Kadener P... Can be used for genome engineering of the promoter or coding regions MS ) offer a high-throughput for! And moved to the community, we identified a number of ion channels that directly. Period1-Associated proteins modulate the negative limb of the circadian genetimeless on the circadian both. Interestingly, circRNAs accumulate in an age-dependent manner suggesting their relevance to homeostasis... Studies how molecular processes in the Class of 2024 majoring in Chemical biology at Brandeis pathogenesis! In addition, we showed that miRNAs have a key role in providing robustness to the States... Medical School the Drosophila gut the lines express one or two gRNAs targeting the coding sequence of a that! Modulate the negative limb of the mammalian circadian oscillator that of others has suggested of!

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