Why do we sleep?
Why we sleep remains one of the most enduring mysteries in science. Sleep is homeostatically regulated where the duration of wakefulness drives subsequent sleep. Here we aim to determine how waking experience is sensed to trigger sleep and how sleep restores the brain? How the circadian clock interacts with sleep homeostasis? How impaired sleep leads to human diseases such as Alzheimer’s disease?
why do we sleep?
Why we sleep remains one of the most enduring mysteries in science. Sleep is homeostatically regulated where the duration of wakefulness drives subsequent sleep. Here we aim to determine how waking experience is sensed to trigger sleep and how sleep restores the brain? How the circadian clock interacts with sleep homeostasis? How impaired sleep lead to human diseases such as Alzheimer’s disease?
Research
Nearly every organism examined, even the jellyfish that lacks a centralized nervous system, exhibits a restorative sleep-like state. While asleep, we cannot eat, mate, defend ourselves from predators or care for our young. Inadequate sleep contributes to brain disease such as Alzheimer’s and depression, and even diseases outside of the brain, such as diabetes and obesity. Sleep is homeostatically regulated, i.e., sleep is driven by the duration and intensity of prior waking experience. Our principal goals are to identify the neuronal and molecular components of the sleep homeostat, to understand how those components cooperate to sense and control sleep-wake state, and to reveal how molecular and neural homeostatic pathways impact brain function, health, and disease. Our strategy employs genetic tools primarily in the fruit fly Drosophila to dissect, manipulate and monitor the homeostatic machinery. This approach builds on our research to understand the molecular basis of circadian (~24 h) behavior which have revealed sleep mechanisms conserved between invertebrates and vertebrates and incorporates work in both mice and humans.
Circadian Rhythms
Circadian clocks dictate when we wake up and when we fall asleep. Using molecular to behavioral approaches primarily in the fruit fly we aim to reveal the molecular and neuronal mechanisms by which circadian clocks keep time and convey that information to control sleep/wake? We are also determining the mechanistic role of disrupted circadian clocks in neurodevelopmental (e.g. autism) and neurodegenerative (e.g. Huntington’s disease disorders.
Sleep Homeostasis
The elusive sleep homeostat drives sleep as a function of prior wakefulness. How does the homeostat sense waking experience, trigger sleep and restore the brain to a baseline healthy state? By combining genetics, genomics, real-time imaging, and high resolution behavior analysis, we aim to identify the locus of the sleep homeostat and understand the molecular mechanisms that govern homeostat function. We are also determining how disrupted sleep can contribute to neurodegenerative disorders such as Alzheimer’s disease.
Humans: Diagnostics/Jet Lag
Disrupted sleep and circadian rhythms have been increasingly associated with neural (depression and Alzheimer’s) and even non-neural disorders (diabetes and obesity). Here we are combining RNA-sequencing with machine learning algorithms to discover biomarker signatures of sleep and circadian disorders. We are also using publicly available data to assess the effects of sleep/circadian disruption on athletic performance.
Team
Ravi Allada
Principal Investigator
BA, University of Michigan, Ann Arbor
MD, University of Michigan, Ann Arbor
On his way to becoming a medical doctor, Ravi decided to take a year (and then two) off during medical school to do research at the NIH. There he caught the research ”bug” and began his career-long interest in sleep, working on mechanisms of general anesthesia in the fruit fly Drosophila. After completing his M.D and a short residency in Clinical Pathology, he did his postdoctoral training with Nobel laureate Michael Rosbash, cloning the core circadian clock gene Clock in Drosophila. He joined the faculty at Northwestern in 2000 where his lab has discovered core gears of the circadian clock, how those gears drive sleep and wake, and how those pathways are linked to neurodegenerative disease. He applies similar approaches to reveal the molecular basis of the sleep homeostat, key to understanding the elusive function of sleep. In his spare time, he has served or is serving on various Boards including for the Society for Research on Biological Rhythms, the Sleep Research Society and the NIH Sleep Disorders Research Advisory Board.
Bridget Lear
Research Associate Professor
BS, University of California at Los Angeles
PhD, University of Chicago
As a Ph.D. student, Bridget studied nervous system development and evolution with Dr. Nipam Patel. She then moved to the field of circadian rhythms, where she has focused on understanding the neural mechanisms regulating circadian behavior. As a postdoctoral fellow (Allada lab), Bridget helped identify the receptor for the PDF neuropeptide, a critical component of clock neuron communication in Drosophila. Her postdoctoral work also established an important role for the sodium leak channel Narrow Abdomen (aka NALCN) in circadian neuron output. As a faculty member (U. of Iowa 2010-2018; Northwestern U. 2009-10, 2018-present) she has continued to study the regulation and function of the Narrow Abdomen ion channel complex in the circadian system. She has also focused on understanding the complex relationship between neuronal network communication, environmental input, and circadian behavioral output.
Yong-Kyu Kim
Research Associate Senior
BS, Sung Kyun Kwan University
PhD, City University of New York
Yong-Kyu’s research areas are multidisciplinary in behavior genetics, evolutionary biology and neurobiology; and include the evolution of mating behavior, aggressive behavior, sleep and memory. He grew up in Seoul, Korea and graduated from Sung Kyun Kwan University. Yong-Kyu moved to USA for graduate work and got a Ph.D. degree at the City University of New York, New York. He has research and teaching experience at State University of New York, University of Georgia, Emory University and Janelia Research Campus. He joined the Allada lab to investigate neural mechanisms of how sleep enhances memory using Drosophila as a model system.
Clark Rosensweig
Postdoctoral Fellow
BA, Harvard University
PhD, University of Texas Southwestern Medical Center
Clark grew up in a sleepy beach community in South Florida. After college, he dropped out of science to pursue a career in stand up comedy, then dropped out of stand up comedy to pursue a career in science. As a graduate student in Carla Green’s lab, he performed structure/function studies of the circadian repressors Cryptochrome 1 and 2 and identified a subtle structural divergence between the two with a major role in determining periodicity in the mammalian circadian clock. Clark brought his penchant for biochemistry to the Allada lab to determine why we sleep. He has subsequently become a more interesting dinner party guest.
Shiju Sisobhan
Research Area Specialist
PhD, Indraprastha Institute of Information Technology, Delhi
BTech, Cochin University of Science and Technology, Kochi
I grew up in the beautiful state of Kerala (India) where I received my bachelor’s and master’s degree in electronics engineering. Then I relocate to Delhi, where I did my Ph.D. in computational biology under Dr. K. Sriram. My work in Ph.D. studies focused on the mathematical modeling of the mammalian circadian rhythm. Then I worked as postdoc at Northwesern University, Chicago and at University of Michigan. In the Allada lab, I am focusing on developing computational tools for analyzing sleep and circadian behavior of Drosophila and human being. I am also working on bioinformatics analysis on bulk and single cell RNA sequencing data, machine learning and biomarker discovery.
Gregory Wesseling
Research Specialist, Lab Manager
Masters, Grand Valley State University
Bachelors, Central Michigan University
In graduate school at GVSU, Greg dissected larval drosophila brains to investigate histamine expression in deletion mutants generated through transposon-excision mutagenesis. When Greg joined the Allada lab, he dissected adult drosophila brains to investigate PER expression. Greg now works on project ENCODE to help document where transcription factors act in the fly genome. Before graduate school, Greg spent a summer at the University of Cambridge to study evolution. In his spare time, Greg enjoys watching college football and basketball.
Aldeb Perera
Ph.D. Candidate
BS, University of Illinois at Chicago
A Belizean native, Aldeb moved to Chicago in 2013 where he completed is BS in Biochemistry at the University of Illinois at Chicago. After graduating college, Aldeb worked in Dr. Wei Qiu’s lab at Loyola University Chicago for two years investigating liver cancer, after which he began his PhD work at Northwestern University in the Fall of 2020. He joined the Allada lab the following year, where he currently uses molecular biology and omics approaches to deconvolute sleep homeostasis. Outside of lab, Aldeb serves as the president of Northwestern’s SACNAS chapter, studies classical piano at Northwestern’s Bienen School of Music, and is a member of NEIU’s Judo Club. In his free time, he enjoys videogames, time outdoors, and game nights with his siblings.
Tuhin Chakraborty
Research Specialist
Ph.D. in Neurobiology from the National Center for Biological Sciences (NCBS), Bangalore, India.
Master’s degree in Zoology from Viswa-Bharati University, Santiniketan, India
Dr. Tuhin Subhra Chakraborty is a Research Specialist at the Michigan Neuroscience Institute (MNI). He received a master’s degree in Zoology from Visva-Bharati University, Santiniketan, India and the Ph.D. in Neurobiology from the National Center for Biological Sciences (NCBS), Bangalore, India. After completing a postdoctoral fellowship in System Neuroscience at the University of California, San Diego, Tuhin joined the Department of Molecular and Integrative Physiology (MIP), University of Michigan in Ann Arbor where he uses Drosophila melanogaster as a model organism to study the impacts of severe experiences on an organism’s survival and quality of life. This is achieved through unraveling links between perception and homeostatic control.
Jordan Munroe
Postdoctoral Fellow
PhD in Biology from University of Oregon (2023)
BS in Biology from Boise State University (2018)
My research is focused on understanding the inter/intracellular molecular mechanisms that drive sleep homeostasis in Drosophila. I love working with Drosophila and think it’s a stellar model organism for studying the brain and nervous system in both the adult fly and during development!
Aadish Mithil Shah
Associate Data Scientist
BSE Data Science, University of Michigan, Ann Arbor (c/o 2021)
I was born and raised in Bahrain but am of Indian descent. After moving to the US in 2017, I completed my BSE in data science eng. at UMich, unofficially focusing in AI, ML and computational methods. After graduating in 2021, I spent three years building a social networking startup, launching 8 software products, fueled by pre-seed funding secured through the Desai Accelerator program- an entrepreneurship investment arm of the Zell Lurie Institute at the Ross School of Business. At the Allada Lab, I leverage my data science and entrepreneurial experience to develop data applications that analyze fly scRNA/bulk RNA seq transcriptomics, model fly behavior, and automate experiments. My fascination with sleep and its profound impact on biology, inspired by personal experience, has deepened through my work at the Allada Lab, where I am driven to better understand the science behind why we sleep. Aside from work, I also enjoy preparing meals for family & friends, playing the guitar and watching soccer games (especially when Chelsea is winning.)
Alumni
Postdocs
- Dr. Jack Curran
Ph.D., University of Bristol - Dr. Sumit Saurabh
Ph.D., University of Houston - Dr. Bart van Alphen
Ph.D., University of Queensland - Dr. Dae-Sung Hwangbo
Ph.D., University of Rochester Medical School - Dr. Mikhail Koksharov
Ph.D., Moscow State University - Dr. Evrim Yildirim
Ph.D., Rutgers University - Dr. Jongbin Lee
Ph.D., Korea Advanced Institute of Science & Tech - Dr. Matthieu Flourakis
Ph.D., University of Lille - Dr. Taichi Itoh
Ph.D., Kyushu University - Dr. Elzbieta Kula-Eversole
Ph.D., Brandeis University - Dr. Yong Yang
Ph.D., Peking University - Dr. Alena Kobelkova
Ph.D., University of South Bohemia - Dr. Tae Hee Han
Ph.D., Seoul National University - Dr. Yong-Jae Kwon
Ph.D., Yonsei University - Dr. Lane Coffee
Ph.D., Vanderbilt University - Dr. Chunghun Lim
Ph.D., Korea Advanced Institute of Science & Tech - Dr. Beiyi Shen
Ph.D., Johns Hopkins University - Dr. Cory Pfeiffenberger
Ph.D., UC Santa Cruz - Dr. Gang Liu
Ph.D., Chinese Academy of Sciences - Dr. Bridget Lear
Ph.D., University of Chicago - Dr. Jena Pitman
Ph.D., Northwestern University - Dr. C. Elaine Smith (Merrill)
Ph.D., Vanderbilt University - Dr. J.Russel Keath
Ph.D., University of Massachusetts - Dr. Jui-Ming Lin
Ph.D., Illinois Institute of Technology - Dr. Valerie Kilman
Ph.D., Brandeis University
Research Technologists
- Vanessa Hernandez
- Michael Lin
- Elizabeth Williamson
- Khadijah Hamid
- Angelina Kim
- Jordan Robson
- Gabrielle Watkins
- Setong Mavong
- Namhee Ji
- Erin Petrik
- Monica Villar
- Jermaine McGill
Ph.D. Students
- Tomas Andreani
2014 – 2022 - Melanie Zhang
2015 – 2021 - Fangke Xu
2012 – 2019 - Adam Seluzicki
2007 – 2013 - Brian Chung
2006 – 2010 - Luoying Zhang
2004 – 2009 - Rose-Anne Meissner
2004 – 2009 - Jena Pitman
2002 – 2007 - Kevin Keegan
2003 – 2005 (grad 2009)
Master’s Students
- Stanley Chen, M.S.
- Austin Wen, M.S.
- Vanessa Hernandez, M.S.
- Zhichun (Michael) Lin, M.S.
- Zuoheng (Jack) Qin, M.S.
- Keyin Li, M. Biotech
- Nanjia Song, M. Biotech
- Wenhao Cao, M. Biotech
- Timothy Earl, M. Biotech
- Ling Kai Shih, M.S.
- Zachary Taub, M.S.
- Anuja Ganesan, M. Biotech
- Weichao Zhang, M. Biotech
- Matthew Hong, M. Biotech
- Samuel Stewart, M.S.
- Keya Raychaudhuri, M.S.
- Sihan Teng, M. Biotech
- Leigh Ann Guennewig, M. Biotech
- Daine Stevens, M.S.
- Adam Young, M. Biotech
- Ryan Tubman, M. Biotech
- Kevin Oelstrom, M. Biotech
- Tim Requarth, M.S.
- Anup Patel, M.S.
- Jeff Guzelian, M.S.
- Natalie Boone, M.S.
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