Ravi Allada (born 1967) is an Indian-American chronobiologist studying the circadian and homeostatic regulation of sleep primarily in the fruit fly Drosophila. He is currently the executive director of the Michigan Neuroscience Institute (MNI), a collective which connects neuroscience investigators across the University of Michigan to probe the mysteries of the brain on a cellular, molecular, and behavioral level. Working with Michael Rosbash, he positionally cloned the Drosophila Clock gene. In his laboratory at Northwestern, he discovered a conserved mechanism for circadian control of sleep-wake cycle, as well as circuit mechanisms that manage levels of sleep.
Early life Allada was born on August 20, 1967, in Midland, Michigan, to Indian immigrant parents, Sambasiva Rao and Jayalakshmi. Allada has two brothers, Vivek and Gopal, who both currently work as physicians. At the age of 11, Allada won 3rd place in a free throw competition.Allada, Ravi (April 22, 2021). (Personal Interview). Hallie Cohn. Allada's interest in sports also led him to track baseball statistics, which triggered Ravi Allada's interest in math and later, his research on jet lag for MLB players.
Education Allada graduated from H. H. Dow High School in 1985. Following high school, Allada attended the University of Michigan where he was awarded his B.S. degree.
Allada was also awarded his M.D. by the University of Michigan. While attending University of Michigan Medical School, Allada spent two years as an HHMI-NIH Research Scholar working with Howard Nash on a molecular genetics project relating to general anesthesia in Drosophila. Before the end of medical school, he returned to NIH as a HHMI-NIH Continued Support Fellow working with Carl Wu at the NCI. Following medical school, he completed his residency in clinical pathology at Brigham and Women's Hospital in Boston. Thereafter, he completed an HHMI Physician Postdoctoral Fellowship with Michael Rosbash at Brandeis University.
Career Allada is currently the executive director of the Michigan Neuroscience Institute. He also holds an professorship in the University of Michigan's Department of Anesthesiology and is the Theophile Raphael, M.D., Collegiate Professor of Neurosciences.
Prior to joining MNI in September 2023, Allada was a Professor and Chair of Neurobiology and a Professor and Associate Director of the Center for Sleep and Circadian Biology at Northwestern University. Allada also served on the NIH Sleep Disorders Research Advisory Board, the Society for Research on Biological Rhythms Board as a member and Secretary, and the Sleep Research Society's Board of Directors from 2020-2023.
The Allada lab focuses on finding molecular components of the circadian clock and their impacts on neurodegenerative diseases, sleep, jet lag, and memory processing. His lab has begun to shift its focus to research regarding sleep homeostasis. Allada's research has been supported financially by the NIH, the Defense Advanced Research Projects Agency, and other private foundations.
Early research
Drosophila circadian rhythms
Molecular identification of the Drosophila Clock Gene (1998) Using Drosophila melanogaster as a model organism, Allada and his team used forward genetics to discover a circadian rhythm gene called Drosophila Clock (dClock; Clk). Forward genetics screens for observable phenotypes that could potentially correspond to underlying genetic differences typically resulting from randomly induced mutagenesis. dClock (Clk) was discovered when Allada and his colleagues were completing a forward genetic screen of EMS mutagenized flies. The mutation found by Allada, that abolishes fly circadian rhythms is termed Jrk.
Functioning, CLOCK proteins encoded by the Clk gene form a dimer with CYCLE proteins. The formed dimer will bind to the E-box sequence which will activate the enhancers of per and tim genes. per and tim have been shown in Drosophila, to have daily rhythms of transcription. These per and tim mRNA transcripts are translated into proteins, PER and TIM, which heterodimerize and are essential for the circadian rhythms. The Jrk mutation within Clk, eliminates the cycling of per and tim mRNA transcripts which disrupts molecular and behavioral outputs of the circadian clock.
The studies of the Jrk mutation in the Clk gene showed dominant effects on the Drosophila. Half of the heterozygous flies demonstrate arrhythmic activity and reduce amplitude levels of per/tim transcripts in constant darkness. While all homozygous flies showed arrhythmic activity in constant darkness. Coupled with complementation data with a null deletion. Data suggests that the Jrk mutation has a negative dominant effect, meaning that only one copy of the gene is sufficient for phenotype interference. Further studies of the output of other clock proteins, namely, PERIOD (PER) and TIMELESS (TIM), showed very low expression levels.
In Drosophila, the two well studied clock genes, period (per) and timeless (tim) undergo circadian oscillations. The low levels of PER and TIM could be explained by lower protein stability or reduced protein synthesis due to mutant strains. To distinguish that from transcription levels, Allada et al conducted experiments measuring the levels of per and tim RNA. Experiment showed low levels and non-cycling levels of RNA which suggested reduced synthesis rather than stability. To compare its function to mouse CLOCK gene, in situ cloning and DNA sequencing was performed. A point mutation that changes a triplet codon to a premature stop codon. Allada et al concluded that the Jrk mutation disrupts the transcription cycling of per and tim, since it encodes a premature stop codon that abolished the function of the truncated C-terminal activation domain of the transcription factor bHLH-PAS.
Clk and cctopic circadian rhythms (2003-2005) Further research on the dClock (Clk) gene and its role in the Drosophila transcription translation feedback loop (TTFL) revealed the gene's ability to stimulate gene expression of other components of the TTFL ectopically—or outside of pacemaker cells—and subsequently modify daily organismal behavior. Clk and other circadian genes are predominantly expressed in the "lateral" neurons (LN), the pacemaker neurons of the Drosophila central circadian clock.
Allada's research team worked to understand how the expression of certain clock genes influenced the expression of other clock genes and where these genes were expressed. They used the GAL4/UAS system to examine how the expression of certain clock genes, pigment dispersing factor gene (pdf) and long and short versions of the cry promoter DNA sequence, affected neuronal gene expression. Pdf-GAL4 and long cry-GAL4 were only active in known clock neurons, but the shorter cry sequence was also active in "non-circadian" neurons. When short cry-GAL4 was coupled with the UAS-Clk gene in these non-circadian neurons, these ectopic sites rhythmically expressed the genes Tim and even cry, a circadian clock component that is expressed antiphase to Tim. These results demonstrate that misexpression of Clk was sufficient to induce an ectopic circadian clock. Additionally, transgenic flies with misexpression of Clk displayed different patterns in locomotor activity to wild type files under light-dark conditions: they displayed a single peak of activity in the daytime, opposed to two peaks of activity in the morning and evening. These results suggest that the ectopic clocks were sufficient to influence behavioral circadian rhythms.
PDF receptor (2005) To gain a deeper understanding of PDF's function, Allada and his colleagues worked to identify the PDF receptor protein. The receptor was found to be a class II peptide G protein-coupled receptor. The location of the PDF receptor was identified while observing fruit flies with an inversion mutation in a known potassium channel that disrupted circadian processes. It found that flies with this mutation in the potassium channel had a genomic insertion in the gene for the PDF receptor which caused the disruption. Flies possessing this receptor mutation became known as groom-of-PDF or gop. Comparing the oscillation of clock proteins within pacemaker neurons in wild-type flies to those in gop flies revealed an advance in clock protein oscillation. Allada and colleagues measured differences between the peaks of behavioral rhythmicity after genetically modifying PDF neurons to have a slower clock in both wild-type and gop flies. Wild-type flies with the genetically modified PDF neurons were able to delay peak behavioral rhythmicity whereas gop flies were not. PDF neurons being able to alter rhythmicity within wild-type flies demonstrates PDF's role as a signaling molecule. PDF's lack of ability to change rhythmicity within gop flies provides support that gop is a downstream receptor of PDF.
Casein kinase 2 (2002-2008) casein kinase 2 (CK2) is a protein that helps to regulate key pacemaker proteins, TIM and PER. TIM and PER proteins form a heterodimer that serves to inhibit the further transcription of clock genes tim and per. Nuclear entry of the heterodimer inhibits CLK-CYC from activating any further transcription of tim and per. Therefore, regulation of TIM and PER genes is essential to regulating other clock genes and outputs. Allada sought to understand what molecular mechanisms underlie PER and TIM regulation. TIM and PER nuclear entry appears to be regulated by phosphorylation. Phosphorylation of this heterodimer is partially carried out by CK2, which is composed of different subunits CK2 and CK2. Allada studied fruit flies with a mutant CK2 gene, termed CK2Tik , and observed an abnormally long behavioral rhythm of about 33 hours. The lengthened period of the CK2Tik mutants helped to highlight the importance of CK2 in regulating daily PER and TIM oscillations.
A later study conducted by Allada and his colleagues, attempted to understand why CK2 was important for regulation of the PER and TIM complex. To determine CK2's significance, Allada investigated flies with mutations in CK2 target sites in PER and TIM proteins. Mutations of PER CK2 target sites did not lead to abnormal accumulation of PER, but mutations in the TIM CK2 target sites did. The mutation in tim that caused the accumulation of PER, termed timUL, has a mutation at a serine site thought to prevent CK2 phosphorylation. Accumulation of PER proteins as a result of TIM CK2 target sites being mutated provides evidence that the purpose of CK2 is to regulate the stability of the TIM protein.
Later research
How clocks control neuronal excitability (2005-2015) Allada and colleagues are credited with understanding the na (NARROW ABDOMEN) gene's integral role in Drosophila circadian clock output and normal rest: activity. The Drosophila gene na codes for an ion channel with homology to the mammalian sodium leak channel, nonselective (NALCN). Mutants of na show poor circadian rhythms, yet oscillations of the clock protein PER remain; pacemaker neurons were found to express na and inducing na in pacemaker neurons is sufficient to restore normal locomotor activity rhythms. This served as an indication that NA likely functions on the clock output and "the mutant is a result of disruption in the coupling between the central clock and the neuronal networks controlling locomotion."