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. In the Bandopadhayay Lab, Michelle is interested in using computational efforts to better characterize pediatric brain tumors. Is the category for this document correct. NanoTags, VHH05- and 127D01-tagsthat are 14 and 10 amino acids in length, and their corresponding nanobodies (NbVHH05 and Nb127D01) are excellent reagents for both, We have developed a series of bioinformatics tools that provide the research community with well-designed, user-friendly resources that impact research at all stages, from project design to data analysis and integration. Chikne V.*, Doniger T.*, Bartok O. 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. 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. Im a Masters student studying the expression of Ultradian Genes and their role in Canton-S flies. We continue to evaluate and create new methods for genome engineering. Biogenesis and functions of circular RNAs. 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. 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. *, Bartok O. Fun fact: Outside the lab, Adam is an avid soccer fan and enjoys watching the English Premier League. 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. Chem. UAS-gypsy structure and functional test. For her honors thesis, Marissa sutided the role of WPR proteins in asymmetric cell divisions inA. thalianaroots. PubMed ID: 31702556 Belacortu Y., Weiss R., Kadener S. and Paricio N. Transcriptional activity and nuclear localization of Cabut, the, Belancortu Y., Weiss R., Kadener S. and Paricio N. Expression of, Van der Linden A.M., Beverly M., Kadener S., Rodriguez J., Wasserman S., Rosbash M. and Sengupta P. Genome-Wide Analysis of Light and Temperature-Entrained Circadian Transcripts in, Fathallah-Shaykh H.M., Bona J.L. 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. . This work, led by Sebastian Kadener, summarizes years of development of a pipeline that improves upon current tools. 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. Our laboratory is interested in understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. Sebastian Kadener, PhD, was trained at the University of Buenos Aires, Argentina, and at Brandeis University in Waltham, Massachusetts. 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 Bando Lab, Adam is studying how alterations in chromatin factors lead to pediatric gliomagenesis with the ultimate goal of discovering novel therapeutic approaches. For his PhD, he then moved south to the Max Planck Institute in Freiburg (then to the IGMC in Strasbourg, France) where he worked in the lab of Dr. Robert Schneider characterizing novel types of histone post-translational modifications, earning his PhD in 2016. She also loves bagels and is always on the hunt for the best bagel. Last but not least, we recently showed that some circRNAs are translated. Fun fact: Anna is a gardening nerd on hold, as she does not have a garden in Boston. 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. Studying transcription, chromatin and gene expresion in the brain. Following. 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. snguyen [at]brandeis [dot]edu Michelle Chukwu Research Technician 178: 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. *, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. Pseudouridylation in. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. This plasticity is the result of the existence of very efficient input pathways that convey the external signals into the core oscillator machinery. September 2018. Chikne V.*, Doniger T.*, Bartok O. I am interested in studying circular RNA formation. Cs. Cramer P., Srebrow A., Kadener S., Werbajh S., de la Mata M., Melen G., Nogues G. and Kornblihtt AR. During her time at Brandeis, Maddie worked in the lab of Sebastian Kadener studying RNA metabolism and the circadian rhythm. She lived in Oregon and Connecticut and move to Massachusetts, where she received her BA in Biochemistry from Wellesley College (22). DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. 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. Statuses. Fun fact: In his native language of Urdu, Shers full name translates to lion/tiger brave. Dana received her BA in Biology from the University of Pennsylvania (21). I am interested in studying circular RNAs and neurological disorders. 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. Gene activation is triggered by co-expression of catalytically dead Cas9 (dCas9) fused to an activator domain. What are the key functions of these molecules in the brain and during aging? 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. Further, our work and that of others has suggested functions of these moleculesin vivo. 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. 178: In addition, recently we generated the first set of animals in which specific circRNAs are downregulated. Molecular Neurobiology and RNA metabolism. I am a junior who is majoring in biochemistry. High-accuracy determination of internal circadian time from a single blood sample. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. Sebastian Kadener. 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. 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. Olivia received her B.A. Antibodies allow protein visualization by immunostaining, biochemical study by immunoprecipitation and western blot, and proteomic study by IP-MS. 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. Riley was born and raised in Seoul, South Korea, and moved to the U.S when she was 11 years old. 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. 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. Fun in the Lab. Im working on aging-related circRNA knockdown fly behavior and physiology. 369. Our studies on Drosophila gut led us to establish a model of tumor-induced organ wasting that is relevant to cachexia. Clonally stable VK allelic choice instructs IgK repertoire. miR-184regulates pancreatic -Cell function according to glucose metabolism. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? 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. Selected for Faculty of 1000 (Factor 3 Recommended). Lic. 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. In the Bandopadhay Lab, Marissa is working to study drivers of Diffuse Midline Gliomas, including the mechanisms through which MYC isoforms are activated. de Educ. Interestingly, mechanical stress caused by overfeeding flies with 10% methylcellulose, which distorts the gut, induces ISC proliferation. 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. In October 2021, Anna defended her PhD thesis (and Mimi had the honor of being her faculty opponent!!). Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila. Don't wanna be here? What is their mechanisms of action? tested regenerative limb interventions to restore form and function to the amputated hindlimbs in adult African clawed frogs. de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. Lerner I. 2018-10-18 DOI. Murugan et al. Selected for Faculty of 1000 (Factor 3.0 Recommended). During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. For example, the vertebrate CNS receives information regarding the status of peripheral metabolic processes via hormonal signaling and direct macromolecular sensing. We have also generated stable nuclease-dead Cas9 activator (dCas9a) cell lines that can be used, after transfection with gRNAs, to perform overexpression screens - thus complementing loss of function screens. Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. Title. In this context, the most important question looking forward are: Afik S. 1, Bartok O. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. Strikingly, these phenotypes are reminiscent of the pathophysiology of cystic fibrosis (CF), as in CF the non-functional CF transmembrane conductance regulator (CFTR) increases ENaC activity resulting in chronic dehydration of the intraluminal surface liquid in organs such as kidney, colon, lung and sweat glands. This plasticity is the result of the existence of very efficient input pathways that convey the external signals into the core oscillator machinery. 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. For her Masters studies, she moved to Uppsala and finisher her MSc in Medicine in 2014 after spending a semester in Dr. Fredrik Swartlings lab with a degree project focused on BET and CDK2 inhibition in MYC/N-driven medulloblastoma. Sebastian Kadener. 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. She is also working to evaluate the role of altered metabolic signaling to driving formation of pediatric tumors such as Diffuse Intrinsic Pontine Gliomas. In the lab of Dr. William Kinlaw, Leslie studied lipid metabolism in breast cancer cells. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F. In mature animals, cells and organs interact to maintain homeostasis and coordinate their physiological roles. Sebastian Kadener. Molecular Neurobiology and RNA Metabolism Laboratory. 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 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. Rosi is attending the structural MS workshop in Finland. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. What are the differences at the molecular level between the individual circadian neurons? A phenotypic selection is then applied and gRNAs enriched following selection are identified via next-generation sequencing. We use Drosophila as a model system to characterize the mechanisms underlying communication between cells, tissues, and organs. Simchovitz A, Hanan M, Niederhoffer N, Madrer N, Yayon N, Bennett ER, Greenberg DS, Kadener S, Soreq H. Thermosensitive alternative splicing senses and mediates temperature adaptation in, Reconfiguration of a Multi-oscillator Network by Light in the. Mouse-olfactory bulb, brain stem, and thalamus-Mock. Interestingly, JAK/STAT signaling in the muscle or fat body directly triggers the expression of ImpL2, which in turn impairs local insulin signaling and its associated energy balance. Nucleic Acids Research47(11): e95; 1-16 (2017). DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. Precise regulation of epithelial stem cells is critical to maintain tissue integrity and prevent over-proliferation and cancer. She is also contributing to efforts to understand how the FOXR2 transcription factors enhances formation of tumors across pediatric and adult cancers, including in pediatric brain tumors. Genome-Wide Analysis of Light- and Temperature-Entrained . Despite the importance of antibodies in biology study, antibodies are not available for most fly proteins. 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. She makes a mean pour over coffee, and her favorite animal is a tie between a sloth and a quokka. In addition to ImpL2, we have also identified two additional factors produced from, because major organ types and signaling pathways in physiology (e.g. 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. This dual reporter can be used in either fixed or live tissues to monitor spatio-temporal activity of signaling pathways at an unprecedented resolution. From a number of screens (receptome-wide RNAi screen, miRNA screens, etc. 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. I am analyzing the effect of circRNA on aging in Drosophila, majoring in biochemistry and neuroscience. and Kornblihtt A.R. Aaron was born and raised in Kuantan, a small beach town on the east coast of peninsular Malaysia. Kadener S., Fededa J.P., Rosbash M. and Kornblihtt A.R. 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. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. 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. 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. 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. My diverse. 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. In addition and most importantly, genome-wide libraries of transgenic RNAi lines are available that allow knockdown of any Drosophila gene in an organ or tissue-specific manner. Second, we showed that the calcium channel TrpA1 is expressed in ISCs and is required for their proliferation. Moreover, we also showed that the neural and molecular circadian systems compensate and interact with each other. Eric studied how the interaction of cell surface proteins expressed by different cell types can regulate blood vessel formation in normal cells and tumors. 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. The EMBO journal 20 (20), 5759-5768, 2001. and Torres H.N. 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. Verified email at brandeis.edu - Homepage. In the Bandopadhayay Lab, Anna will be expanding her skills to apply genomic approaches to understand the mechanisms through which gliomas develop, and to develop strategies to overcome therapeutic resistance. 0. Aaron is an Attending Pediatric Neuro-Oncologist at the Dana-Farber/Boston Childrens Cancer and Blood Disorders Center. I am in the Class of 2024 studying neuroscience and biology. Interestingly, circRNAs accumulate in an age-dependent manner suggesting their relevance to age-related homeostasis and/or pathogenesis. 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. Or do you know how to improve StudyLib UI? A slow RNA polymerase II affects alternative splicing in vivo. Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays. We previously developed a recombination-mediated cassette exchange (RMCE) system that enables pooled CRISPR screening in Drosophila cells, as well as bioinformatics tools for identifying sgRNA designs for mosquitos and mosquito cell lines. Fun fact: Leslie played basketball through college and is now an avid cyclist. SRA: Mus musculus; 1: GPL21103; GSE154616; TXT; SRA Run Selector; Sebastian Kadener: Sep 09, 2021 Lic. 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. To complement RNAi-based approaches, we are also developing a number of tools based on CRISPR technologies. 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. At the lab, I research the role of temperature in the synchronization of the Drosophila circadian clock. 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. M.Sc., The University of Buenos Aires, Buenos Aires, Argentina Ph.D., The University of Buenos Aires, Buenos Aires, Argentina. *, Bartok O. First, we characterized a Drosophila miRNA, miR-263a, that regulates epithelial sodium channel (ENaC) activity to maintain osmotic and ISC homeostasis. Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. I am studying translational activators of the circadian clock in Drosophila. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D. and Kornblihtt A.R. He is also contributing to efforts to characterize chromatin complexes as therapeutic targets for pediatric brain tumors. Studying the neuronal functions of circular RNA. Fun fact: Dana is a huge Philadelphia sports fan and is mentally preparing to be the only Eagles fan in Boston. Our most popular tools are: DIOPT, an integrative tool for ortholog predictions among major model organisms. Cold Spring Harbor Laboratory Online. Further, fat-derived adipokines leptin and adiponectin serve as inter-organ secreted metabolic regulators. 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. While at Caltech, Adam studied luminescent ruthenium complexes that function as light switch probes for DNA mismatches. Fun fact: One of the first things Jens did when he arrived in Boston was to buy a bike. 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. 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. at USC we have extended this approach to the mouse. 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. 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. Rosenstiel332781-736-4915skadener@brandeis.edu, Neuroscience Program Volen 206 Mailstop 013 Brandeis University 415 South Street Waltham, MA 02453 781-736-2352neuroscience@brandeis.edu. Perelman School of Medicine at the University of Pennsylvania Rybak-Wolf A., Stottmeister C., Glazar P., Jens M., Pino N., Giusti S., Hanan M., Behm M., Bartok O., Ashwal R., Herzog M., Schreyer L., Papavasileiou P., Ivanov A., Ohman M., Refojo D., Kadener S. and Rajewsky N. Circular RNAs in the mammalian brain are highly abundant, conserved, dynamically expressed, and regulated by ADAR1. Relevant to cachexia into a target genomic location a mean pour over coffee and... Create new methods for genome engineering when she was 11 years old Michelle is interested in circular! 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