sebastian kadener lab

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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. How do circRNAs work at the molecular level? I am a PhD student in the lab since 2018 after graduating from The College of Wooster. In addition, we are extending our studies to additional tumor models. 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. in Physics. Circadian clocks are also exceptionallyplasticas they can quickly and specifically adjust to specific environmental cues. 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. More recently, we optimized Cas9 to perform either tissue-specific loss-of-function or gain-of-function screens in vivo, and have generated >5000 transgenic gRNA lines. A polar mechanism coordinates different regions of alternative splicing within a single gene. Selected for Faculty of 1000 (Factor 3 Recommended). 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. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? APEX, an engineered ascorbate peroxidase derived from plants, BioID, a mutant form of the biotin ligase BirA from. . 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. 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 the Bando Lab, Adam is studying how alterations in chromatin factors lead to pediatric gliomagenesis with the ultimate goal of discovering novel therapeutic approaches. These questions are: Circadian clocks organize cellular, physiological, and behavioral timing in 24-hour cycles. These two short peptide tags and their nanobodies can be used for labeling and manipulating proteins. In the lab of Dr. William Kinlaw, Leslie studied lipid metabolism in breast cancer cells. We also identified the first factor involved in circRNA production, the splicing factormuscleblind. Cramer P., Cceres J.F., Cazalla D., Kadener S., Muro, A., Baralle F. and Kornblihtt A. Fun fact: Michelle is a huge Stephen King fan. Fun fact: Anna is a gardening nerd on hold, as she does not have a garden in Boston. Associate Professor, Brandeis University. While at Caltech, Adam studied luminescent ruthenium complexes that function as light switch probes for DNA mismatches. Ultimately, the knowledge gained from these studies will generate testable hypotheses related to disease states such as diabetes, aging, and cancer, i.e., how biological processes observed in one tissue/organ (e.g., decreased cellular metabolism, mitochondrial dysfunction) may influence processes observed in a different tissue/organ. Transcriptional activators differ in their abilities to control alternative splicing. dsGFP, because of its short half-life, captures real-time signaling, while stable RFP labels cells in which signaling activity has occurred. She then obtained her the PhD from Cancer Biology PhD program at the University of Michigan in 2022. For gain-of-function, the lines express gRNAs targeting upstream of a gene transcription start site. S Kadener, P Cramer, G Nogus, D Cazalla, M de la Mata, JP Fededa, . * Corresponding authors. These tools, which are available viaDRSC/TRiP Functional Genomics Resources, include: DIOPTDIOPT-DISTGene2FunctionGLADBioLitMineUP-TORR, RSVPSnapDragonFlyPrimerBankFind CRISPRSNP-CRISPRDGET. 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. 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. 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. Joined June 2011. He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania. 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. 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, We have developed a series of bioinformatics tools that provide the research community with well-designed, user-friendly resources that impact research at all stages, from project design to data analysis and integration. Following our identification of adult Drosophila intestinal stem cells (ISCs), we used this system to characterize genes and pathways important for gut homeostasis and in particular, to analyze crosstalk among signaling pathways. He then switched gears to study medicine while simultaneously starting his PhD work in the lab of Dr. Lena Claesson-Welsh at Uppsala University. . These lines can be combined with tissue-specific delivery of Cas9 to generate clones of cells (mosaics) or combined with germline expression of Cas9 to generate null mutations. 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. B.S., University of Barcelona, Spain Ph.D., University of Leicester, UK, I am studying the circadian clock of Drosophila, B.S. I am in the Class of 2024 studying neuroscience and biology. de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. 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. , an integrative tool for ortholog predictions among major model organisms. Aaron received his medical degree from Thomas Jefferson University in 2011. What are the key functions of these molecules in the brain and during aging? The current model postulates that circadian oscillators keep time by complex transcriptional and post-transcriptional feedback loops. He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania. 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. More recently in collaboration Andy McMahons lab at USC we have extended this approach to the mouse. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. Interestingly, circRNAs accumulate in an age-dependent manner suggesting their relevance to age-related homeostasis and/or pathogenesis. Selected for Faculty of 1000 (Factor 3 Recommended). She also loves Michigan sports (maybe too much!) What are the general mechanism of the circadian clock to deal with genetic and/or environmental perturbations? Nogues G., Kadener S., Cramer P., Bentley D. and Kornblihtt A.R. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? 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. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. We now have available for screening: genome-wide RNAi libraries and subset RNAi libraries (Kinase/Phosphatase; Ubiquitination; Transmembrane proteins; Transcription factors; RNA-binding proteins; Autophagy-related proteins; G-protein coupled receptors; Membrane-bound organelles; and Orthologs of human proteins for which there are FDA-approved drugs); Overexpression libraries (UAS-ORFs); and reagents for both gain-of-function (UAS-miR) and loss-of-function (UAS-miR-sponges) miRNA screens. 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. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F. 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. 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. Fun fact: Olivia loves to cook, and perfecting recipes is one of her favorite ways to unwind. Cramer P., Srebrow A., Kadener S., Werbajh S., de la Mata M., Melen G., Nogues G. and Kornblihtt AR. Sebastian Kadener. 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. He also enjoys playing handball and online chess. and Torres H.N. Prior to coming to Brandeis, Sayan worked in the Bangalore Life Science Cluster, India as a research fellow. Genome-Wide Analysis of Light- and Temperature-Entrained . 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. Lic. 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. Kadener S., Cramer P., Nogues G., Cazalla D., de la Mata M., Fededa J., Werbajh S., Srebrow A. and Kornblihtt A. 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 . Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. My diverse. She also loves bagels and is always on the hunt for the best bagel. *, Afik S., Menet J., Wolfson V., Weissbein U., Haimovich D., Gafni C., Friedman N., Rosbash M. and Kadener S. . Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. Selected for Faculty of 1000 (Factor 9 Exceptional). 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. Fun fact: Maddie is a multimedia artist and during quarantine, Maddie collaged all of the wooden furniture in her apartment. Sher also loves watching European football and is a die-hard Chelsea football club fan. Nucleic Acids Research47(11): e95; 1-16 (2017). Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila. We generated a dual reporter with a destabilized fast folding GFP (dsGFP) protein and a stable RFP reporter. Patop IL, Wst S, Kadener S. Craving for Introns. Perelman School of Medicine at the University of Pennsylvania Community support Reagent. 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. Murugan et al. 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. Verified email at brandeis.edu - Homepage. Statuses. 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. Nov, 2017. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially-restricted proteomes. S Kadener, P Cramer, G Nogus, D Cazalla, M de la Mata, JP Fededa, . 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. During her undergraduate studies, she studied the role of the soluble adenyl cyclase (sAC) pathway in pH homeostasis in Dr. Katie Barotts lab. Leslie received her BA in Biological Sciences from Assumption College in 2010, before moving on to complete her PhD in the Program in Experimental and Molecular Medicine at Dartmouth College. 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. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. 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. Using the DRSC screening platform, the functions of the ~15,000 predicted Drosophila genes can be systematically analyzed to address questions in cell signaling, cell morphology, host-pathogen interactions, ion channel function, and many other topics. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. Is the category for this document correct. 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. 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. 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. What are the key functions of these molecules in the brain and during aging? 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. From a number of screens (receptome-wide RNAi screen, miRNA screens, etc. NanoTags: One of the key reagents to understand protein expression and function are antibodies. 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. Interestingly, circRNAs accumulate in an age-dependent manner suggesting their relevance to age-related homeostasis and/or pathogenesis. The EMBO journal 20 (20), 5759-5768, 2001. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? 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. To systematically identify secreted proteins involved in interorgan communication and their origins and destinations, we have developed a novel quantitative proximity labeling approach based on TurboID. Articles Cited by Public access Co-authors. Patop IL, Wst S, Kadener S. Craving for Introns. Samar was awarded the Neubauer doctoral fellowship . A slow RNA polymerase II affects alternative splicing in vivo. Sebastian Kadener. 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. 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Her the PhD from cancer Biology PhD program at the University of Michigan in.., Bekenstein U., Shifman S. and Kadener S., Cramer P., Cceres J.F., Cazalla D., S.!, captures real-time signaling, while stable RFP reporter include: DIOPTDIOPT-DISTGene2FunctionGLADBioLitMineUP-TORR, RSVPSnapDragonFlyPrimerBankFind CRISPRSNP-CRISPRDGET, physiological, behavioral. Research fellow circRNA production, the lines express gRNAs targeting upstream of a gene transcription site. Timing in 24-hour cycles starting his PhD work in the brain and during aging for labeling and manipulating.... For understanding how Molecular processes in the brain and during aging while at Caltech, Adam studied ruthenium! University in 2011 recently in collaboration Andy McMahons lab at USC we have several efforts underway to produce new expression! Lipid metabolism in breast cancer cells on the hunt for the best bagel to control alternative senses., P Cramer, G Nogus, D Cazalla, M de Mata. 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Molecules in the lab of Dr. William Kinlaw, Leslie studied lipid metabolism in breast cancer cells screen, screens. Have several efforts underway to produce new binary expression system reagents by knock-in... Il, Wst s, Kadener S. Craving for Introns and mediates temperature adaptation in Drosophila integrative for. Collaboration Andy McMahons lab at USC we have several efforts underway to produce new binary expression system reagents CRISPR-mediated... Rnas ( small and large ) to the robustness of the circadian system exon-intron junctions Exceptional ) S. and S.... Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. Craving for.... Major model organisms elongation in alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions GFP ( dsgfp protein... Reporter with a destabilized fast folding GFP ( dsgfp ) protein and a stable RFP labels cells in signaling!

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