I am studying potential applications of the CRISPR/Cas13 system. What are the neural and molecular basis of temperature adaptation and compensation? M.Sc., The University of Buenos Aires, Buenos Aires, Argentina Ph.D., The University of Buenos Aires, Buenos Aires, Argentina. I am interested in studying circular RNA formation. 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. Rosi is accepted to attend the Autumn Workshop in Structural Proteomics in Nurmes, Finland and was chosen to receive a COST scholarship. DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. Studying transcription, chromatin and gene expresion in the brain. Jazmin is currently investigating how circRNA levels change at synapses and whether they are modulated by neuronal activity. Regulation of RNA metabolism is emerging as a major regulatory hub for gene expression control in tissues like the brain and the muscle, which don't undergo cel. 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. She also loves sleeping in, making guacamole, and reading about art history. Moreover, we also showed that the neural and molecular circadian systems compensate and interact with each other. At the lab, I research the role of temperature in the synchronization of the Drosophila circadian clock. 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. Coordination between transcription and pre-mRNA processing. Transcription factor Dam fusions of the major proliferative signaling pathways will be used to address questions about crosstalk and target co-regulation. Moreover, in 2019, we were funded to function as the Drosophila Research and Screening Center-Biomedical Technology Research Resource (DRSC-BTRR), which focuses on development of new screening and other technologies. During her free time, Riley enjoys watching documentaries, cooking Korean food, and visiting cafes to drink iced vanilla latte. Second, we identified 53 transcription factors, specifically expressed or enriched in the ISCs, and are characterizing how they cooperate to integrate signal inputs. ( 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. single nuclei sequencing (snRNAseq) of entire flies, and proteomics approaches, e.g. 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. Despite the importance of antibodies in biology study, antibodies are not available for most fly proteins. @skadener. For example, the vertebrate CNS receives information regarding the status of peripheral metabolic processes via hormonal signaling and direct macromolecular sensing. PANGEA: A New Gene Set Enrichment Tool for Drosophila and Common Research Organisms Aaron was born and raised in Kuantan, a small beach town on the east coast of peninsular Malaysia. 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. 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. In addition to ImpL2, we have also identified two additional factors produced from, because major organ types and signaling pathways in physiology (e.g. For example, we showed that circRNA biogenesis competes with canonical splicing, showing that circRNAs can function incisas RNA traps. In addition to her passion for medicine and science, Jess is also passionate about advocacy for science. Marissa received her BS in Biochemistry and Molecular Biology from UMass Amherst in 2022. tested regenerative limb interventions to restore form and function to the amputated hindlimbs in adult African clawed frogs. Fun fact:Almost all of Johns socks are Christmas themed! DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. and Torres H.N. The Perrimon lab is interested in characterizing the mechanisms by which cells, tissues and organs communicate during development and in mature animals. How do circRNAs work at the molecular level? What is their mechanisms of action? Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. 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. The EMBO journal 20 (20), 5759-5768, 2001. In addition, we are extending our studies to additional tumor models. S Kadener, P Cramer, G Nogus, D Cazalla, M de la Mata, JP Fededa, . . He then switched gears to study medicine while simultaneously starting his PhD work in the lab of Dr. Lena Claesson-Welsh at Uppsala University. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. Fun fact: Maddie is a multimedia artist and during quarantine, Maddie collaged all of the wooden furniture in her apartment. 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. Sebastian Kadener. For example, we identified a number of ion channels that either directly or indirectly regulate stem cell proliferation. *, Bartok O. in English and Anthropology from Washington University in St. Louis (22). 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. Is the category for this document correct. 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. In the Bandopadhay Lab, Marissa is working to study drivers of Diffuse Midline Gliomas, including the mechanisms through which MYC isoforms are activated. We are now adapting the pooled-format CRISPR screening approach for use in cell lines from medically relevant mosquito species. We showed that miRNAs have a key role in providing robustness to the circadian system both during development and in adults. 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. 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. Explore trending content on Musk Viewer For loss-of-function, the lines express one or two gRNAs targeting the coding sequence of a gene or genes. leptin), neural development, and behavior are conserved, . We showed that miRNAs have a key role in providing robustness to the circadian system both during development and in adults. Harvard Medical SchoolHoward Hughes Medical Institute, Communication between cells, tissues and organs in Drosophila. The work is a collaboration between Dr. Kadener's lab and Prof. Nikolaus Rajewsky from the Max Dellbruck Institute, Berlin, Germany. Fsica, Tcnico Sup. In the Bandopadhayay Lab, Maddie is working on efforts to identify resistance mechanisms in pediatric brain tumors. The latest Tweets from Kadener Lab (@kadenerlab): "https://t.co/VOExAyFxj9" 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. High-accuracy determination of internal circadian time from a single blood sample. Articles Cited by Public access Co-authors. The current model postulates that circadian oscillators keep time by complex transcriptional and post-transcriptional feedback loops. One of the key reagents to understand protein expression and function are antibodies. Sebastian Kadener. 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. He can also be found doing crossword puzzles at odd hours. Aaron received his medical degree from Thomas Jefferson University in 2011. neta.herman[at]mail[dot]huji[dot]ac[dot]il, Studying the function of SARS-CoV-2 nsp14. She also loves Michigan sports (maybe too much!) Uncovering molecular and physiological functions of circRNAs: Circular RNAs (circRNAs) are highly abundant RNAs produced by circularization of specific exons. 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. Selected for Faculty of 1000 (Factor 3.0 Recommended). 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. Antibodies allow protein visualization by immunostaining, biochemical study by immunoprecipitation and western blot, and proteomic study by IP-MS. 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. Selected for Faculty of 1000 (Factor 3.0 Recommended). Patop IL, Wst S, Kadener S. Craving for Introns. What are the neural and molecular basis of temperature adaptation and compensation? 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. As an underlying mechanism, the balance or critical reaction hypothesis have been proposed. Transcriptional activators differ in their abilities to control alternative splicing. Fun fact:When not in the lab or the clinic, Jess loves yoga, sour beers, running on the Esplanade, and writing. How do circRNAs work at the molecular level? CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. Selected for Faculty of 1000 (Factor 6 Must Read). Genome-Wide Analysis of Light- and Temperature-Entrained . 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. We generated a dual reporter with a destabilized fast folding GFP (dsGFP) protein and a stable RFP reporter. 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. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. You can add this document to your study collection(s), You can add this document to your saved list. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. These questions are: Circadian clocks organize cellular, physiological, and behavioral timing in 24-hour cycles. Lacadie S.A., Tardiff D.F., Kadener S. and Rosbash M. In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. 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. Verified email at brandeis.edu - Homepage. 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. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. A slow RNA polymerase II affects alternative splicing in vivo. 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. 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. During her undergraduate studies, she studied the role of the soluble adenyl cyclase (sAC) pathway in pH homeostasis in Dr. Katie Barotts lab. To complement RNAi-based approaches, we are also developing a number of tools based on CRISPR technologies. News. PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. 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. He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? Zaffagni M, Kadener S. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. To facilitate these studies, we are developing various techniques and resources in functional genomics and proteomics. Circadian clocks are also exceptionallyplasticas they can quickly and specifically adjust to specific environmental cues. 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. Selected for Faculty of 1000 (Factor 3 Recommended). 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. Lacadie S.A., Tardiff D.F., Kadener S. and Rosbash M. In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. 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. 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. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? Third, more recently we used single-cell RNAseq (scRNAseq) to describe all the cell types and their transcriptomes in the Drosophila gut. Sebastian Kadener's lab | Brandeis University Overview Advance your research members publications research projects Featured research (2) Using Drosophila to uncover molecular and. Fun fact: Michelle is a huge Stephen King fan. Chikne V.*, Doniger T.*, Bartok O. 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. In addition and most importantly, genome-wide libraries of transgenic RNAi lines are available that allow knockdown of any. Maddie received her MS and BS in Biology from Brandeis University in 2021. Kadener S., Cramer P., Nogues G., Cazalla D., de la Mata M., Fededa J., Werbajh S., Srebrow A. and Kornblihtt A. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. Our studies on Drosophila gut led us to establish a model of tumor-induced organ wasting that is relevant to cachexia. Followers. 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. My diverse. For gain-of-function, the lines express gRNAs targeting upstream of a gene transcription start site. General Biology Laboratory [ sn wi ] T 12:20 PM-5:00 PM Shapiro Science: 010 T,F 8:00 AM-9:20 AM . Fun in the Lab. Recent reports revealed that circRNAs are expressed in developmental- and tissue-specific manners and are highly enriched in the nervous system, particularly in synapses. Lic. Additional unpublished work from my lab demonstrates that a subset of circRNAs is translated. 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. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. 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. 312. 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. Over the years, we have added a number of screening reagents and developed bioinformatics tools to improve the platform. I am analyzing the effect of circRNA on aging in Drosophila, majoring in biochemistry and neuroscience. 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. 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. 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. Prior to starting graduate school, he spent two years doing research on ALS at Massachusetts General Hospital with Dr. Lagier-Tourenne. What are the general mechanism of the circadian clock to deal with genetic and/or environmental perturbations? 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. Kadener, Sebastian / Brandeis University Publications. Feel free to send suggestions. This collection is available to the community through the Bloomington Drosophila Stock Center. 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. She then obtained her the PhD from Cancer Biology PhD program at the University of Michigan in 2022. 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. Jens is co-mentored by Dr. David Jones at the DKFZ. Clonally stable VK allelic choice instructs IgK repertoire. Gut tumors can be induced in adult flies by overexpressing an active form of the transcriptional co-activator yorkie/YAP using the intestinal stem cell driver escargot-GAL4. Further, our work and that of others has suggested functions of these moleculesin vivo. 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. These tools, which are available via. 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. BOX 39.4 CHRONOPHARMACOLOGY Many drugs, toxins, and, Academic Degrees - Dartmouth Medical School, BOX 39.2 MOLECULAR MECHANISMS OF CIRCADIAN, Evolutionary mechanisms underlying the functional divergence of, Trainee Professional Development Day Session Information, Naslov projekta: Defining the role of circadian genes in behavioral, Supplementary Information - Word file (66 KB ), INTRODUCTION TO CHRONOPHARMACOLOGY - Copy, Fall 2012 Application for Associate Editors, BOX 39.1 NEURONAL CONTROL OF DROSOPHILA CIRCADIAN, Biological Rhythms - Cornell University Ergonomics Web. Simchovitz A, Hanan M, Yayon N, Lee S, Bennett ER, Greenberg DS, Kadener S, Soreq H. A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress. Nov, 2017. We have several efforts underway to produce new binary expression system reagents by CRISPR-mediated knock-in, including split-GAL4, LexA, and QF. He is also contributing to efforts to characterize chromatin complexes as therapeutic targets for pediatric brain tumors. Fun fact: Olivia loves to cook, and perfecting recipes is one of her favorite ways to unwind. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? 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. V. *, Bartok O in pediatric brain tumors of non-coding RNAs small... Comprehensive pipeline for accurate annotation and quantification of circRNAs making guacamole, and behavioral timing in 24-hour cycles knock-in... Biology study, antibodies are not available for most fly proteins from a single blood sample with a destabilized folding... Functional genomics and proteomics of miRNAs located across exon-intron junctions, provide a robust platform for combinatorial.... 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