sebastian kadener lab

sebastian kadener lab

He then pursued a PhD in chemistry at Caltech (17) under the mentorship of Dr. Jackie Barton. 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. Advantages of CRISPRi as compared with RNAi are that the level of knockdown can be more tightly controlled and the system appears to have reduced off-target effects. and Torres H.N. . 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. Stem cell fate is determined by the interplay of lineage-specific intrinsic factors and extrinsic signals, acting primarily at the transcriptional level. Mezan S., Feuz JD, Deplancke B. and Kadener S. PDF signaling is an integral part of the. * Corresponding authors. Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays. In the Bandopadhay Lab, Marissa is working to study drivers of Diffuse Midline Gliomas, including the mechanisms through which MYC isoforms are activated. In this context, the most important question looking forward are: Afik S. 1, Bartok O. View 129 related references Ask authors/readers for more resources. *, Bartok O. Dec 2017. For doing this, we study the circadian clock from a systemic point of view, including studies at the molecular and neural levels. Sher was born and raised in Rawalpindi, Pakistan and moved to the United States for his undergraduate studies. Cohen-Hadad Y., Altarescu G., Eldar-Geva T., Levi-Lahad E., Zhang M., Rogaeva, E. Gotkine M., Bartok O., Ashwal-Fluss R., Kadener S., Epsztejn-Litman S., Eiges R. Marked differences in C9orf72 methylation status and isoform expression between C9/ALS human embryonic and induced pluripotent stem cells. S Kadener, P Cramer, G Nogus, D Cazalla, M de la Mata, JP Fededa, . SRA: Mus musculus; 1: GPL21103; GSE154616; TXT; SRA Run Selector; Sebastian Kadener: Sep 09, 2021 Transcriptional activators differ in their abilities to control alternative splicing. The Kadener laboratory studies how molecular processes in the brain determines behavior with a special emphasis on RNA metabolism. ( 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. * Corresponding authors. Litovchenko M, Meireles-Filho ACA, Frochaux MV, Bevers RPJ, Prunotto A, Anduaga AM, Hollis B, Gardeux V, Braman VS, Russeil JMC, Kadener S, Dal Peraro M, Deplancke B. Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells. Mosquito cell lines exist that are able to become infected with viruses and are susceptible to mosquitocidal toxins, parasites, and drugs, but tools to allow deeper understanding of pathogen interactions with mosquito cells are lacking. 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. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. Among the next significant questions to address are how complex phenotypes arise in the context of the whole organism and how the programs regulating these phenotypes are influenced by genetic background and environment. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? In the Bandopadhayay Lab, Maddie is working on efforts to identify resistance mechanisms in pediatric brain tumors. Maddie received her MS and BS in Biology from Brandeis University in 2021. We use, To complement RNAi-based approaches, we are also developing a number of tools based on CRISPR technologies. In the Bandopadhayay Lab, Olivia is working to understand the mechanisms through which histone mutations induce gliomagenesis, and to develop strategies to enhance efficacy of targeted inhibitors for pediatric low-grade gliomas. 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. Selected for Faculty of 1000 (Factor 6 Must Read). 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. 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. Joined June 2011. This dual reporter can be used in either fixed or live tissues to monitor spatio-temporal activity of signaling pathways at an unprecedented resolution. Transcriptional activators differ in their abilities to control alternative splicing. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. 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. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. Perelman School of Medicine at the University of Pennsylvania These questions are: Circadian clocks organize cellular, physiological, and behavioral timing in 24-hour cycles. Our laboratory is interested in understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. We showed that miRNAs have a key role in providing robustness to the circadian system both during development and in adults. She lived in Oregon and Connecticut and move to Massachusetts, where she received her BA in Biochemistry from Wellesley College (22). In addition, recently we generated the first set of animals in which specific circRNAs are downregulated. 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. April received her BS in Cellular and Molecular Biology from Beloit College in 2017, where she worked in the lab of Dr. Amy Briggs studying the role offpgsgenes inArabidopsis thaliana. Antibodies allow protein visualization by immunostaining, biochemical study by immunoprecipitation and western blot, and proteomic study by IP-MS. 178: Selected for Faculty of 1000 (Factor 3.0 Recommended). de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. Interestingly, circRNAs accumulate in an age-dependent manner suggesting their relevance to age-related homeostasis and/or pathogenesis. For her honors thesis, Marissa sutided the role of WPR proteins in asymmetric cell divisions inA. thalianaroots. 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. For example, we showed that circRNA biogenesis competes with canonical splicing, showing that circRNAs can function incisas RNA traps. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. Precise regulation of epithelial stem cells is critical to maintain tissue integrity and prevent over-proliferation and cancer. Nogues G., Kadener S., Cramer P., Bentley D. and Kornblihtt A.R. 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 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. Our most popular tools are: DIOPT, an integrative tool for ortholog predictions among major model organisms. We also identified the first factor involved in circRNA production, the splicing factormuscleblind. First, we developed a new method to visualize the dynamic activation of pathway activities. He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania. 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. 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. Associate Professor, Brandeis University. Lic. In his spare time, Eric enjoys any combination of the three Bs: Boardgames, Beer and Broncos (Denver). 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. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. 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. 369. Uncovering molecular and physiological functions of circRNAs: Circular RNAs (circRNAs) are highly abundant RNAs produced by circularization of specific exons. We chose to use peripheral blood monocytes as source material for gene expression profiling, because (a) blood is an easily accessible source of human cells and (b) monocytes constitute a homogenous blood cell population and have been shown to possess a high-amplitude circadian clock ( 24, 25) in contrast to other PBMCs, such as B or T cells. Cramer P., Srebrow A., Kadener S., Werbajh S., de la Mata M., Melen G., Nogues G. and Kornblihtt AR. 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. Patop IL, Wst S, Kadener S. Craving for Introns. 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. PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. ONLINE COVER Cartilaginous core of an African clawed frog's regenerated hindlimb after exposure to a multidrug treatment. 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. The work is a collaboration between Dr. Kadener's lab and Prof. Nikolaus Rajewsky from the Max Dellbruck Institute, Berlin, Germany. 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). Murugan et al. 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. Sebastian Kadener Associate Professor of Biology Research Description Molecular Neurobiology and RNA metabolism Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. Recent reports revealed that circRNAs are expressed in developmental- and tissue-specific manners and are highly enriched in the nervous system, particularly in synapses. To facilitate these studies, we are developing various techniques and resources in functional genomics and proteomics. Copyright 2017 | Privacy policy | Legal statements 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. Verified email at brandeis.edu - Homepage. 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. 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. He can also be found doing crossword puzzles at odd hours. Anna developed a fascination for cancer biology while working towards her bachelors degree at Lund University, Sweden. What is their mechanisms of action? in English and Anthropology from Washington University in St. Louis (22). 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. Brown S.A., Ripperger J., Kadener S., Fleury-Olela F., Vilbois F., Rosbash M. and Schibler U. Article. We are now adapting the pooled-format CRISPR screening approach for use in cell lines from medically relevant mosquito species. Statuses. Hu, Comjean, Attrill, Antonazzo, Jim Thurmond, Li, Chao, Mohr, Brown, Perrimon Software. Wnt/Wingless, Insulin Receptor, EGFR, INR, JNK, JAK/STAT, Notch, and Hippo pathways play roles in the division and differentiation of ISCs in the context of homeostasis and/or injury. Selected for Faculty of 1000 (Factor 3 Recommended). Explore trending content on Musk Viewer Kadener S., Fededa J.P., Rosbash M. and Kornblihtt A.R. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. 312. at USC we have extended this approach to the mouse. For example, little is understood about how the simultaneous growth and differentiation of different tissues and organs are coordinated and how the development of different cell types and tissues is integrated within an organ. Cramer P., Cceres J.F., Cazalla D., Kadener S., Muro, A., Baralle F. and Kornblihtt A. Followers. Explore tweets Explore followers Explore following. Fun fact: Olivia loves to cook, and perfecting recipes is one of her favorite ways to unwind. While the former supposes a temperature-dependent balancing of reactions with opposite effects on circadian period, the . 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. The EMBO journal 20 (20), 5759-5768, 2001. B.S., University of Barcelona, Spain Ph.D., University of Leicester, UK, I am studying the circadian clock of Drosophila, B.S. 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: Michelle is a huge Stephen King fan. Samar was awarded the Neubauer doctoral fellowship . leptin), neural development, and behavior are conserved. [email protected], Neuroscience Program Volen 206 Mailstop 013 Brandeis University 415 South Street Waltham, MA 02453 [email protected]. 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. Sebastian Kadener. Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila. High-accuracy determination of internal circadian time from a single blood sample. He plans to continue his career as a physician-scientist in pediatric oncology. * Corresponding authors. and Kornblihtt A.R. I am analyzing the effect of circRNA on aging in Drosophila, majoring in biochemistry and neuroscience. 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. Title. 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. Sebastian Kadener E-mail (s) [email protected] 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 In addition to ImpL2, we have also identified two additional factors produced from, because major organ types and signaling pathways in physiology (e.g. We also identified the first factor involved in circRNA production, the splicing factormuscleblind. 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. Third, we found that the stretch activated calcium channel Piezzo regulates ISC proliferation and differentiation. Circadian Regulation and Biological Timing, 2013 - 2023 studylib.net all other trademarks and copyrights are the property of their respective owners. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? For example, little is understood about how the simultaneous growth and differentiation of different tissues and organs are coordinated and how the development of different cell types and tissues is integrated within an organ. 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. 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. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. 0. 2012- Lab manager at Ami Citri laboratory at the Hebrew University of Jerusalem 2010- 2012 Postdoc at the Hebrew University of Jerusalem at Sebastian Kadener Lab; research topic-studying neodegenerative diseases using fruit flies as a model 2000-2003 Research assistant at QBI company; I was part of research From a number of screens (receptome-wide RNAi screen, miRNA screens, etc. Studying the function of circRNAs in the brain. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. She immediately transitioned into a PhD program, still working with Dr. Swartling to continue her work on mouse models and medulloblastoma treatments. What are the general mechanism of the circadian clock to deal with genetic and/or environmental perturbations? Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. What is their mechanisms of action? September 2018. 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. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. This plasticity is the result of the existence of very efficient input pathways that convey the external signals into the core oscillator machinery.

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