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. I am a PhD student in the lab since 2018 after graduating from The College of Wooster. @skadener. Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. Alexander M. van der Linden, Matthew Beverly, Sebastian Kadener, Joseph Rodriguez, Sara Wasserman, Michael Rosbash, Piali Sengupta. 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. Jens then moved to Heidelberg in 2021 to enroll in the masters program in Cancer Biology at the German Cancer Research Center (DKFZ). Sebastian Kadener Principal Investigator M.Sc., The University of Buenos Aires, Buenos Aires, Argentina Ph.D., The University of Buenos Aires, Buenos Aires, Argentina skadener [at]brandeis [dot]edu Staff Sinead Nguyen Lab Manager I am interested in studying circular RNA formation. Fun fact: Outside the lab, Adam is an avid soccer fan and enjoys watching the English Premier League. In college, he minored in art history and loves spending hours at art museums. 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. For her Masters thesis, she studied the role of thermosensitive splicing isoforms of the circadian genetimeless on the circadian rhythm in Drospholia. Our laboratory is interested in understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. M.Sc., The University of Buenos Aires, Buenos Aires, Argentina Ph.D., The University of Buenos Aires, Buenos Aires, Argentina. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. 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. Michael earned a BA in cellular biology and neuroscience from Rutgers University. 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. Selected for Faculty of 1000 (Factor 3.0 Recommended). Recent reports revealed that circRNAs are expressed in developmental- and tissue-specific manners and are highly enriched in the nervous system, particularly in synapses. Transcriptional activators differ in their abilities to control alternative splicing. Moreover, we also showed that the neural and molecular circadian systems compensate and interact with each other. 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 Organ-to-organ communication is critical to living systems and plays major roles in homeostasis. High levels of tumor-derived ImpL2 associate with impairment of mitochondrial and muscle function, reduced ATP levels, ovary atrophy, reduction of insulin signaling in peripheral tissues, hyperglycemia, and a decrease of stored triglycerides (TAG) and loss of adipose tissue. Circadian Regulation and Biological Timing, 2013 - 2023 studylib.net all other trademarks and copyrights are the property of their respective owners. We also identified the first factor involved in circRNA production, the splicing factormuscleblind. 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. Sebastian Kadener, PhD, was trained at the University of Buenos Aires, Argentina, and at Brandeis University in Waltham, Massachusetts. Despite the importance of antibodies in biology study, antibodies are not available for most fly proteins. Anna moved to Boston in 2022 to continue her career as a scientist focused on pediatric neuro-oncology and hopes to make a difference for the young patients affected by this diverse group of devastating diseases. 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. Our Funds. Hanan M, Simchovitz A, Yayon N, Vaknine S, Cohen-Fultheim R, Karmon M, Madrer N, Rohrlich TM, Maman M, Bennett ER, Greenberg DS, Meshorer E, Levanon EY, Soreq H, Kadener S. Past, present, and future of circRNAs. We showed that miRNAs have a key role in providing robustness to the circadian system both during development and in adults. 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. Nucleic Acids Research47(11): e95; 1-16 (2017). Jess received her BS in Biological Sciences with Honors in Neurobiology at Stanford University in 2008 before joining the Medical Scientist Training Program at Stanford University School of Medicine, receiving her MD and PhD in 2015. Feel free to send suggestions. 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. In October 2021, Anna defended her PhD thesis (and Mimi had the honor of being her faculty opponent!!). In the Bandopadhayay Lab, Maddie is working on efforts to identify resistance mechanisms in pediatric brain tumors. During his time at Dickinson, Sher worked in Dr. Michael Roberts lab, investigating gene targets for potential Acute Myeloid Leukemia therapies. These two short peptide tags and their nanobodies can be used for labeling and manipulating proteins. 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. Third, more recently we used single-cell RNAseq (scRNAseq) to describe all the cell types and their transcriptomes in the Drosophila gut. dsGFP, because of its short half-life, captures real-time signaling, while stable RFP labels cells in which signaling activity has occurred. 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. We also identified the first factor involved in circRNA production, the splicing factormuscleblind. In this context, the most important question looking forward are: Afik S. 1, Bartok O. We use Drosophila as a model system to characterize the mechanisms underlying communication between cells, tissues, and organs. Cramer P., Cceres J.F., Cazalla D., Kadener S., Muro, A., Baralle F. and Kornblihtt A. *, Bartok O. We continue to evaluate and create new methods for genome engineering. In the Bandopadhayay Lab, Michelle is interested in using computational efforts to better characterize pediatric brain tumors. *, Afik S., Menet J., Wolfson V., Weissbein U., Haimovich D., Gafni C., Friedman N., Rosbash M. and Kadener S. . Explore trending content on Musk Viewer 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). 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. Cramer P., Srebrow A., Kadener S., Werbajh S., de la Mata M., Melen G., Nogues G. and Kornblihtt AR. Articles Cited by Public access Co-authors. View 129 related references Ask authors/readers for more resources. Kadener, Sebastian / Brandeis University Publications. This plasticity is the result of the existence of very efficient input pathways that convey the external signals into the core oscillator machinery. Fun in the Lab. Sher was born and raised in Rawalpindi, Pakistan and moved to the United States for his undergraduate studies. I am interested in understanding how proteins and miRNAs regulate and can be regulated by circRNAs. This dual reporter can be used in either fixed or live tissues to monitor spatio-temporal activity of signaling pathways at an unprecedented resolution. 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. Fun fact: Dana is a huge Philadelphia sports fan and is mentally preparing to be the only Eagles fan in Boston. 369. Laboratory Profile Principal Investigator: Sebastian Kadener A systemic view of circadian clocks: from gene expression to neuronal networks and behavior. Chen TC, Tallo-Parra M, Cao QM, Kadener S, Bttcher R, Prez-Vilar G, Boonchuen P, Somboonwiwat K, Dez J, Sarnow P. A lncRNA survey finds increases in neuroprotective LINC-PINT in Parkinson's disease substantia nigra. 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. 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. Sebastian Kadener. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? 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. She then obtained her the PhD from Cancer Biology PhD program at the University of Michigan in 2022. Its very important for us! I am researching the role of circular RNAs (circRNAs) in aging processes in Drosophila melanogaster. 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. Followers. Chikne V.*, Doniger T.*, Bartok O. Fun fact: In his native language of Urdu, Shers full name translates to lion/tiger brave. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. Transcriptional activators differ in their abilities to control alternative splicing. 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. Circadian clocks are also exceptionallyplasticas they can quickly and specifically adjust to specific environmental cues. What is their mechanisms of action? Nogues G., Kadener S., Cramer P., Bentley D. and Kornblihtt A.R. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. 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. Fun fact: Like many Swedish people, Eric has completed Vasaloppet, a 60-mile cross-country skiing race (twice!). 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. Cramer P., Cceres J.F., Cazalla D., Kadener S., Muro, A., Baralle F. and Kornblihtt A. Olivia received her B.A. 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. She also loves sleeping in, making guacamole, and reading about art history. Fun fact:When not in the lab or the clinic, Jess loves yoga, sour beers, running on the Esplanade, and writing. 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. 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. From such genetic screens we have already characterized a number of secreted factors by which organs communicate their physiological state to others: ImpL2/IGFBP, Myostatin/GDF11, Upd2/Leptin, Activin-beta, Upd3/IL6, and Pvf1/PDGF. My diverse. , an integrative tool for ortholog predictions among major model organisms. in English and Anthropology from Washington University in St. Louis (22). 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. The EMBO journal 20 (20), 5759-5768, 2001. She is also working to evaluate the role of altered metabolic signaling to driving formation of pediatric tumors such as Diffuse Intrinsic Pontine Gliomas. CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. In mature animals, cells and organs interact to maintain homeostasis and coordinate their physiological roles. Murugan et al. Our major contributions to tool development are the Gal4-UAS system, FLP-FRT germline clone technique, in vitro and in vivo genome-wide RNAi and CRISPR screening platforms and resources, and in vivo proximity labeling methods. Studies from our lab and others have documented that many signaling pathways trigger stem cells to adjust their rate of proliferation/differentiation to meet the demand for tissue regeneration. 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. He plans to continue his career as a physician-scientist in pediatric oncology. 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. 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. 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. leptin), neural development, and behavior are conserved, . During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. Contact. For example, we showed that circRNA biogenesis competes with canonical splicing, showing that circRNAs can function incisas RNA traps. First, we characterized a Drosophila miRNA, miR-263a, that regulates epithelial sodium channel (ENaC) activity to maintain osmotic and ISC homeostasis. A Biblioteca Virtual em Sade uma colecao de fontes de informacao cientfica e tcnica em sade organizada e armazenada em formato eletrnico nos pases da Regio Latino-Americana e do Caribe, acessveis de forma universal na Internet de modo compatvel com as bases internacionais. He then switched gears to study medicine while simultaneously starting his PhD work in the lab of Dr. Lena Claesson-Welsh at Uppsala University. News. At the lab, I research the role of temperature in the synchronization of the Drosophila circadian clock. Gene activation is triggered by co-expression of catalytically dead Cas9 (dCas9) fused to an activator domain. Fun fact: Anna is a gardening nerd on hold, as she does not have a garden in Boston. What is their mechanisms of action? I am studying translational activators of the circadian clock in Drosophila. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. Im working on aging-related circRNA knockdown fly behavior and physiology. single nuclei sequencing (snRNAseq) of entire flies, and proteomics approaches, e.g. 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. Fun fact: Michelle is a huge Stephen King fan. 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. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F. Over the years, we have added a number of screening reagents and developed bioinformatics tools to improve the platform. Prior to coming to Brandeis, Sayan worked in the Bangalore Life Science Cluster, India as a research fellow. 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. 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. The current model postulates that circadian oscillators keep time by complex transcriptional and post-transcriptional feedback loops. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? 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. Associate Professor, Brandeis University. 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. 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. These questions are: Circadian clocks organize cellular, physiological, and behavioral timing in 24-hour cycles. Nucleic Acids Research47(11): e95; 1-16 (2017). 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. ), we have identified and validated novel mechanisms of how stem cells adjust their rate of proliferation/differentiation to meet the demand for tissue regeneration. S Kadener, P Cramer, G Nogus, D Cazalla, M de la Mata, JP Fededa, . What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? 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. As an underlying mechanism, the balance or critical reaction hypothesis have been proposed. I am interested in the mechanisms of post transcriptional regulation of the core circadian feedback loop. Brown S.A., Ripperger J., Kadener S., Fleury-Olela F., Vilbois F., Rosbash M. and Schibler U. Media. 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. Determine the nature of circadian rhythms within organisms. 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 APEX, an engineered ascorbate peroxidase derived from plants, and BioID, a mutant form of the biotin ligase BirA from E coli and demonstrated their use for in vivo studies. Verified email at brandeis.edu - Homepage. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. 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. Biogenesis and functions of circular RNAs. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. Chikne V.*, Doniger T.*, Bartok O. Cold Spring Harbor Laboratory Online. A polar mechanism coordinates different regions of alternative splicing within a single gene. Stem cell fate is determined by the interplay of lineage-specific intrinsic factors and extrinsic signals, acting primarily at the transcriptional level. Molecular Neurobiology and RNA Metabolism Laboratory. She also loves bagels and is always on the hunt for the best bagel. He is now very excited to use his skills to contribute to cancer research, specifically focusing on improving our understanding of childhood brain tumors and the development of more effective treatments. and Kornblihtt A.R. Second, we showed that the calcium channel TrpA1 is expressed in ISCs and is required for their proliferation. 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. She also enjoys amateur photography. 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. 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. Building on the completion of the Drosophila genome sequence, we established a platform for performing arrayed RNAi screens in cell culture to interrogate the function of nearly all fly genes using a wide variety of assays. 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. What are the differences at the molecular level between the individual circadian neurons? What are the general mechanism of the circadian clock to deal with genetic and/or environmental perturbations? Eric studied how the interaction of cell surface proteins expressed by different cell types can regulate blood vessel formation in normal cells and tumors. Fun fact:Almost all of Johns socks are Christmas themed! Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially-restricted proteomes. 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. DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. Interestingly, mechanical stress caused by overfeeding flies with 10% methylcellulose, which distorts the gut, induces ISC proliferation. 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). NanoTags: One of the key reagents to understand protein expression and function are antibodies. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania.
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