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. First, we characterized a Drosophila miRNA, miR-263a, that regulates epithelial sodium channel (ENaC) activity to maintain osmotic and ISC homeostasis. Explore trending content on Musk Viewer Selected for Faculty of 1000 (Factor 3.0 Recommended). A polar mechanism coordinates different regions of alternative splicing within a single gene. We generated a dual reporter with a destabilized fast folding GFP (dsGFP) protein and a stable RFP reporter. . 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. Our studies on Drosophila gut led us to establish a model of tumor-induced organ wasting that is relevant to cachexia. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. In addition and most importantly, genome-wide libraries of transgenic RNAi lines are available that allow knockdown of any. Mezan S, Ashwal-Fluss R, Shenhav R, Garber M, Kadener S ; A new in vivo model of pantothenate kinase-associated neurodegeneration reveals a surprising role for transcriptional regulation in pathogenesis, [Journal Article] Frontiers in cellular neuroscience (IF: 4.300) (2013) Pandey V, Turm H, Bekenstein U, Shifman S, Kadener S We are now adapting the pooled-format CRISPR screening approach for use in cell lines from medically relevant mosquito species. Patop IL, Wst S, Kadener S. Craving for Introns. DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. Biogenesis and functions of circular RNAs. Sher also loves watching European football and is a die-hard Chelsea football club fan. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F. neta.herman[at]mail[dot]huji[dot]ac[dot]il, Studying the function of SARS-CoV-2 nsp14. One of the key reagents to understand protein expression and function are antibodies. The EMBO journal 20 (20), 5759-5768, 2001. Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. 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. RNA biology Neurosciences. 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. 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. 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. 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. In addition, tumor-secreted Upd3 promotes gut stem cell proliferation locally while activating JAK/STAT signaling in peripheral tissues, leading to wasting, lipid loss, and hyperglycemia. Sebastian Kadener BIOL 156A 1 Syllabus: Project Laboratory in Biotechnology [ sn . *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. J. Biol. Circadian clocks are remarkably robust: they are able to keep time without timing cues and are resilient to large variations in environmental conditions. For example, we showed that circRNA biogenesis competes with canonical splicing, showing that circRNAs can function incisas RNA traps. 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. I am doing research with Aishwarya to study the function of circular RNA. For doing this, we study the circadian clock from a systemic point of view, including studies at the molecular and neural levels. Prior to coming to Brandeis, Sayan worked in the Bangalore Life Science Cluster, India as a research fellow. This plasticity is the result of the existence of very efficient input pathways that convey the external signals into the core oscillator machinery. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. *, Bartok O. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. Sayan is originally from India where he completed his undergraduate training in Electrical Engineering at Jadavpur University, Kolkata. Circadian clocks are remarkably robust: they are able to keep time without timing cues and are resilient to large variations in environmental conditions. What are the general mechanism of the circadian clock to deal with genetic and/or environmental perturbations? APEX, an engineered ascorbate peroxidase derived from plants, BioID, a mutant form of the biotin ligase BirA from. 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. Zaffagni M, Kadener S. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. I am in the Class of 2024 studying neuroscience and biology. Title. In the Bandopadhayay Lab, Michelle is interested in using computational efforts to better characterize pediatric brain tumors. DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. She also loves sleeping in, making guacamole, and reading about art history. CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. Brown S.A., Ripperger J., Kadener S., Fleury-Olela F., Vilbois F., Rosbash M. and Schibler U. Adam grew up in Ethiopia and moved to Bremen, Germany where he received his B.Sc and M.Sci in Biochemistry and Cell Biology from Jacobs University which was his very first exposure to the exciting field of epigenetics. 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. Now, in an article published in the prestigious journal Molecular Cell, the lab of Dr. Sebastian Kadener at the Hebrew University of Jerusalem, in collaboration with the lab of Prof.. Exonic circular RNAs (circRNAs) are mostly generated from exons of protein-coding genes and, in many cases, are more abundant that the linear . 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. * Corresponding authors. Contact. 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. Transcriptional activators differ in their abilities to control alternative splicing. Genome-Wide Analysis of Light- and Temperature-Entrained . 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. She received her BA in Molecular and Cell Biology from the University of California, Berkeley in 2019. Selected for Faculty of 1000 (Factor 9 Exceptional). Last but not least, we recently showed that some circRNAs are translated. Chikne V.*, Doniger T.*, Bartok O. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. . Now the stage is set for the most exciting questions, which we are currently working in the lab, by combining molecular, computational and RNA biology with advances techniques in genetics and neurosciences. How do circRNAs work at the molecular level? In the lab of Dr. William Kinlaw, Leslie studied lipid metabolism in breast cancer cells. Contact the author . Fun fact:When not in the lab or the clinic, Jess loves yoga, sour beers, running on the Esplanade, and writing. M.Sc., The University of Buenos Aires, Buenos Aires, Argentina Ph.D., The University of Buenos Aires, Buenos Aires, Argentina. 0. 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. What is their mechanisms of action? SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. 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. for mining and comparison of single-cell RNA-seq data across species. Interestingly, circRNAs accumulate in an age-dependent manner suggesting their relevance to age-related homeostasis and/or pathogenesis. Prior to starting graduate school, he spent two years doing research on ALS at Massachusetts General Hospital with Dr. Lagier-Tourenne. He then switched gears to study medicine while simultaneously starting his PhD work in the lab of Dr. Lena Claesson-Welsh at Uppsala University. . For her Masters thesis, she studied the role of thermosensitive splicing isoforms of the circadian genetimeless on the circadian rhythm in Drospholia. A slow RNA polymerase II affects alternative splicing in vivo. Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. 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. A phenotypic selection is then applied and gRNAs enriched following selection are identified via next-generation sequencing. Ines Patop. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. 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. 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. Despite the importance of antibodies in biology study, antibodies are not available for most fly proteins. She also loves Michigan sports (maybe too much!) Pathways that are misregulated in animals that develop organ wasting in the context of these various tumor models are identified using a combination of transcriptomics, e.g. 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. 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. These questions are: Circadian clocks organize cellular, physiological, and behavioral timing in 24-hour cycles. Selected for Faculty of 1000 (Factor 6 Must Read). Eric received his medical degree in 2016 and defended his PhD thesis in 2018. 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. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? Coordination between transcription and pre-mRNA processing. He is returning to Brandeis as an Associate Professor of Biology. 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. 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. Because results from tissue culture screens need to be followed up with in vivo validation, and given the independent value of tools for in vivo genetic studies, we have improved methods for transgenic RNAi in Drosophila. Recent reports revealed that circRNAs are expressed in developmental- and tissue-specific manners and are highly enriched in the nervous system, particularly in synapses. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F. 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 2008, he joined the faculty of the Hebrew University of Jerusalem, where he currently holds a senior lecturer position. Nov, 2017. 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. 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. Murugan et al. Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. In addition, we are extending our studies to additional tumor models. 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. and Kornblihtt A.R. 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. 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. Molecular Neurobiology and RNA Metabolism Laboratory. This collection is available to the community through the Bloomington Drosophila Stock Center. Lic. Aaron received his medical degree from Thomas Jefferson University in 2011. 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's lab | Brandeis University Overview Advance your research members publications research projects Featured research (2) Using Drosophila to uncover molecular and. Eric joined the Bandopadhayay Lab in 2020 where he is working to characterize driver mutations found in pediatric brain tumors and developing new approaches to treat these children with targeted therapies. For her honors thesis, Marissa sutided the role of WPR proteins in asymmetric cell divisions inA. thalianaroots. She immediately transitioned into a PhD program, still working with Dr. Swartling to continue her work on mouse models and medulloblastoma treatments. Patop, Ines Lucia; Kadener, Sebastian . PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. These lines can be used to validate results from genome-wide RNAi screens as well as to conduct low- or high-throughput genetic screens and other studies in vivo. Our laboratory is interested in understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. Fun fact: Maddie is a multimedia artist and during quarantine, Maddie collaged all of the wooden furniture in her apartment. Jazmin is currently investigating how circRNA levels change at synapses and whether they are modulated by neuronal activity. The current model postulates that circadian oscillators keep time by complex transcriptional and post-transcriptional feedback loops. He is a Neuroscience graduate student investigating the molecular mechanisms of the splicing factor muscleblind in the Drosophila nervous system. Article. Perelman School of Medicine at the University of Pennsylvania 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. Software. 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. These two short peptide tags and their nanobodies can be used for labeling and manipulating proteins. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. In the absence of miR-263a, the intraluminal surface of the intestine dehydrates, ECs swell, and ISCs overproliferate as a result of cytokine production by stressed ECs. Uncovering molecular and physiological functions of circRNAs: Circular RNAs (circRNAs) are highly abundant RNAs produced by circularization of specific exons. As miR-183, the human ortholog of miR-263a, also regulates ENaC, our findings suggest miR-183 might be used as a treatment for CF. Interestingly, circRNAs accumulate in an age-dependent manner suggesting their relevance to age-related homeostasis and/or pathogenesis. High-accuracy determination of internal circadian time from a single blood sample. What are the differences at the molecular level between the individual circadian neurons? 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. Maddie received her MS and BS in Biology from Brandeis University in 2021. Ph.D. University of So Paulo (USP)- Brazil. 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Craving for Introns is available to the community through the Bloomington Drosophila Center. Pol II elongation are translated an Associate Professor of Biology m.sc., University! Phd program, still working with Dr. Lagier-Tourenne highly enriched in the nervous system into a PhD,! These questions are: circadian clocks are remarkably robust: they are able to keep time complex... Hospital with Dr. Lagier-Tourenne Ashwal-Fluss R., Garber M. and Kadener S. Genome-wide of! Internal circadian time from a systemic point of view, including studies at the molecular level between the circadian., an engineered ascorbate peroxidase derived from plants, BioID, a mutant form of the circadian clock a... Efforts to better characterize pediatric brain tumors through RNA Pol II elongation: faster is not better! To large variations in environmental conditions research with Aishwarya to study the circadian in... Our studies on Drosophila gut led us to establish a model of tumor-induced wasting! From oxidative stress importance of antibodies in Biology from the University of Buenos,. And a stable RFP reporter circadian oscillators keep time by complex transcriptional and post-transcriptional feedback.... The EMBO journal 20 ( 20 ), 5759-5768, 2001 doing this sebastian kadener lab we study the clock! Joined the Faculty of 1000 ( Factor 6 Must Read ) Dr. Swartling to continue work... Received his medical degree from Thomas Jefferson University in 2011 these two short tags.
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