Biology subjects

Keene, A.

Publications and source records attributed to Keene, A..

8 recordsLinked to original sources

bioRxiv2025

The fat-body secreted neuropeptide CCHa2 signals insulin-producing cells in the brain to promote sleep

Sleep is a fundamental behavior regulated by diverse environmental and physiological cues. While the central mechanisms underlying sleep regulation have been investigated in detail, far less is known about how nutrient signals from the periphery are communicated to the brain to modulate sleep. Here, we perform a targeted RNAi screen of genes enriched in the fat body and regulated by feeding state to identify genes that function in the fat body to regulate sleep in Drosophila. This analysis found that body-specific knockdown of CCHa2 significantly reduced sleep duration and sleep depth in fed flies, phenocopying sleep in starved flies. CCHa2-deficient flies exhibited reduced glycogen stores and diminished feeding drive. Analysis of single-cell transcriptomic atlases confirms that the CCHa2 receptor (CCHa2-R) is selectively expressed in Insulin Producing Cells (IPCs) of the fly brain. We find that knockdown of CCHa2-R in IPCs recapitulates the sleep loss phenotype of CCHa2 mutants, supporting a role in adipose-brain signaling. Further screening of genes identified in single cell atlases as being enriched in IPCs led to the identification of numerous genes that function in IPCs to regulate sleep including modulators of wnt and insulin signaling. Together, these findings identify a fat body-IPC axis that is a critical modulator of sleep duration and intensity.

neuroscience↗

bioRxiv2025

Cryptic and Ecologically Relevant Locomotor Activity Patterns in Lake Malawi Cichlids Revealed Through Computer Vision Pipeline

Cichlid fishes have long been a popular model for ecology and evolutionary biology. Not only do they exhibit nearly unparalleled taxonomic diversity, but their community structures are both complex and extremely dense. Niche partitioning along dietary axes has been credited in maintaining cichlid biodiversity in a broad sense; however, it is common for cichlid species with overlapping diets to co-exist, leading to the search for other mechanisms to explain the maintenance of cichlid biodiversity. Behavioral variation has the potential to lead to fine-scale (i.e., micro-) habitat partitioning, but analyzing complex animal behavior poses several challenges, including time, cost and reproducibility. Modern tools, such as Machine Learning (ML), ease the burden of behavioral analyses, and are increasingly used in the field. Here, we present the application of tools from a well-developed sub-field of ML, Computer Vision (CV), to extract locomotor behavioral data from four Lake Malawi cichlid species. Our dataset consisted of low-resolution (320x240), twenty-four-hour infrared videos of activity in 4 cichlid species. We first analyzed a pair of species with divergent behaviors, diets and habitats (i.e., Abactochromis labrosus versus Tropheops kumwera), representing a proof-of-concept comparison. Next we analyzed activity in two closely related species with broadly similar behaviors and overlapping diets and habitats (i.e., Maylandia sp. Daktari versus Maylandia faiaziberi). In both comparisons, our analysis involved the quantification of tank usage patterns and stop/rest activity. Not only did our data align with the known ecologies and behaviors of the species in our proof-of-concept comparison, but they revealed novel behavioral differences between all species, especially as related to variation in tank usage from day to night. Our approach provides a window into potential cryptic behavioral niche partitioning, as well as a foundation for future, high-throughput analyses to study the genetic basis and evolution of behavior.

animal behavior and cognition↗

bioRxiv2024

Circadian rhythm disruption alters mammary gland morphology and accelerates cold aggressive tumorigenesis through a LILRB4-dependent pathway

Epidemiological studies have shown that circadian rhythm disruption (CRD) is associated with the risk of breast cancer. However, the role of CRD in mammary gland morphology and aggressive basal mammary tumorigenesis and the molecular mechanisms underlying CRD and cancer risk remain unknown. To investigate the effect of CRD on aggressive tumorigenesis, a genetically engineered mouse model that recapitulates the human basal type of breast cancer was used for this study. The effect of CRD on mammary gland morphology was investigated using wild-type mice model. The impact of CRD on the tumor microenvironment was investigated using the tumors from LD12:12 and CRD mice via scRNA seq. ScRNA seq was substantiated by multiplexing immunostaining, flow cytometry, and realtime PCR. The effect of LILRB4 immunotherapy on CRD-induced tumorigenesis was also investigated. Here we identified the impact of CRD on basal tumorigenesis and mammary gland morphology and identified the role of LILRB4 on CRD-induced lung metastasis. We found that chronic CRD disrupted mouse mammary gland morphology and increased tumor burden, and lung metastasis and induced an immunosuppressive tumor microenvironment by enhancing LILRB4a expression. Moreover, CRD increased the M2-macrophage and regulatory T-cell populations but decreased the M1-macrophage, and dendritic cell populations. Furthermore, targeted immunotherapy against LILRB4 reduced CRD-induced immunosuppressive microenvironment and lung metastasis. These findings identify and implicate LILRB4a as a link between CRD and aggressive mammary tumorigenesis. This study also establishes the potential role of the targeted LILRB4a immunotherapy as an inhibitor of CRD-induced lung metastasis.

cancer biology↗

bioRxiv2022

Sorting of plant mitochondrial and plastid heteroplasmy is extremely rapid and depends on MSH1 activity

The fate of new mitochondrial and plastid mutations depends on their ability to persist and spread among the numerous organellar genome copies within a cell (heteroplasmy). The extent to which heteroplasmies are transmitted across generations or eliminated through genetic bottlenecks is not well understood in plants, in part because their low mutation rates make these variants so infrequent. Disruption of MutS Homolog 1 (MSH1), a gene involved in plant organellar DNA repair, results in numerous de novo point mutations, which we used to quantitatively track the inheritance of single nucleotide variants in mitochondrial and plastid genomes in Arabidopsis. We found that heteroplasmic sorting (the fixation or loss of a variant) was rapid for both organelles, greatly exceeding rates observed in animals. In msh1 mutants, plastid variants sorted faster than those in mitochondria and were typically fixed or lost within a single generation. Effective transmission bottleneck sizes for plastids and mitochondria were N {approx} 1 and 4, respectively. Restoring MSH1 function further increased the rate of heteroplasmic sorting in mitochondria (N {approx} 1.3), potentially due to its hypothesized role in promoting gene conversion as a mechanism of DNA repair, which is expected to homogenize genome copies within a cell. Heteroplasmic sorting also favored GC base pairs. Therefore, recombinational repair and gene conversion in plant organellar genomes can potentially accelerate the elimination of heteroplasmies and bias the outcome of this sorting process. Significance statementMitochondria and plastids play essential roles in eukaryotic life; thus, mutations in these organellar genomes can have severe consequences. In animals, early germline sequestration creates genetic "bottlenecks" providing cell-to-cell variance in mitochondrial mutations upon which selection can act. However, the dynamics of organellar mutations in plants and other organisms that lack early germline segregation remain unclear. Here, we show that sorting of mutations in plant organellar genomes proceeds very rapidly - much faster than in animals. In mitochondria, this process is accelerated by MSH1, a gene involved in recombination and repair of organellar genomes. This suggests that in plants, recombinational repair creates cell-to-cell variance in the frequency of organellar mutations, facilitating selection in the absence of a classical germline bottleneck.

plant biology↗

bioRxiv2018

Starvation resistance is associated with developmentally specified changes in sleep, feeding and metabolic rate

Food shortage represents a primary challenge to survival, and animals have adapted diverse developmental, physiological, and behavioral strategies to survive when food becomes unavailable. Starvation resistance is strongly influenced by ecological and evolutionary history, yet the genetic basis for the evolution of starvation resistance remains poorly understood. The fruit fly, Drosophila melanogaster, provides a powerful model for leveraging experimental evolution to investigate traits associated with starvation resistance. While control populations only live a few days without food, selection for starvation resistances results in populations that can survive weeks. We have previously shown that selection for starvation resistance results in increased sleep and reduced feeding in adult flies. Here, we investigate the ontogeny of starvation resistance-associated behavioral and metabolic phenotypes in these experimentally selected flies. We find that selection for starvation resistance results in delayed development and a reduction in metabolic rate in larvae that persists into adulthood, suggesting that these traits may allow for the accumulation of energy stores and an increase in body size within these selected populations. In addition, we find that sleep is largely unaffected by starvation- selection and that feeding increases during the late larval stages, suggesting that experimental evolution for starvation resistance produces developmentally specified changes in behavioral regulation. Together, these findings reveal a critical role for development in the evolution of starvation resistance and indicate that selection can selectively influence behavior during defined developmental timepoints.\n\nSUMMARY STATEMENTDrosophila melanogaster selected for starvation resistance take longer to develop and exhibit development-specific changes in traits associated with the accumulation and conservation of energy stores.

neuroscience↗

bioRxiv2018

Ade2 functions in the Drosophila fat body to promote sleep

Metabolic state is a potent modulator of sleep and circadian behavior and animals acutely modulate their sleep in accordance with internal energy stores and food availability. Across phyla, hormones secreted from adipose tissue act in the brain to control neural physiology and behavior to modulate sleep and metabolic state. Growing evidence suggests the fat body is a critical regulator of complex behaviors, but little is known about the genes that function within the fat body to regulate sleep. To identify molecular factors functioning in the periphery to regulate sleep, we performed an RNAi screen selectively knocking down genes in the fat body. We found that knockdown of Phosphoribosylformylglycinamidine synthase/Pfas(Ade2), a highly conserved gene involved the biosynthesis of purines, reduces sleep and energy stores. Flies heterozygous for multiple Ade2 mutations are also short sleepers and this effect is partially rescued by restoring Ade2 to the fat body. Targeted knockdown of Ade2 in the fat body does not alter arousal threshold or the homeostatic response to sleep deprivation, suggesting a specific role in modulating baseline sleep duration. Together, these findings suggest Ade2 functions within the fat body to promote both sleep and energy storage, providing a functional link between these processes.

neuroscience↗

bioRxiv2018

A single pair of leucokinin neurons are modulated by feeding state and regulate sleep-metabolism interactions

Dysregulation of sleep and feeding has widespread health consequences. Despite extensive epidemiological evidence for interactions between sleep and metabolic function, little is known about the neural or molecular basis underlying the integration of these processes. Drosophila melanogaster potently suppress sleep in response to starvation, and powerful genetic tools allow for mechanistic investigation of sleep-metabolism interactions. We have previously identified neurons expressing the neuropeptide leucokinin (Lk) as being required for starvation-mediated changes in sleep. Here, we demonstrate an essential role for Lk neuropeptide in metabolic regulation of sleep. Further, we find that the activity of Lk neurons is modulated by feeding state and circulating nutrients, with reduced activity in response to glucose and increased activity under starvation conditions. Both genetic silencing and laser-mediated microablation localize Lk-mediated sleep regulation to a single pair of Lk neurons within the lateral horn (LHLK) that project near primary sleep and metabolic centers of the brain. A targeted screen identified a critical role for AMP-activated protein kinase (AMPK) in starvation-modulated changes in sleep. Disruption of AMPK function in Lk neurons suppresses sleep and increases LHLK activity in fed flies, phenocopying the starvation state. Taken together, these findings localize feeding state-dependent regulation of sleep to a single pair of neurons within the fruit fly brain and provide a system for investigating the cellular basis of sleep-metabolism interactions.

neuroscience↗

bioRxiv2017

Geographic variation in sleep and metabolic function is associated with latitude and temperature

Regulation of sleep and metabolic homeostasis are critical to an animals survival and under stringent evolutionary pressure. Animals display remarkable diversity in sleep and metabolic phenotypes; however, an understanding of the ecological forces that select for, and maintain, these phenotypic differences remain poorly understood. The fruit fly, Drosophila melanogaster, is a powerful model for investigating the genetic regulation of sleep and metabolic function, and screening in inbred fly lines has led to the identification of novel genetic regulators of sleep. Nevertheless, little is known about the contributions of naturally occurring genetic differences to sleep, metabolic phenotypes, and their relationship with geographic or environmental gradients. Here, we quantified sleep and metabolic phenotypes in 24 D. melanogaster populations collected from unique geographic localities. These studies reveal remarkable diversity in sleep, starvation resistance, and energy stores. We found that increased sleep duration is strongly associated with proximity to the equator and elevated average annual temperature, suggesting that environmental gradients strongly influence natural variation in sleep. Further, we found variation in metabolic regulation of sleep to be associated with free glucose levels, while starvation resistance associates with glycogen and triglyceride stores. Taken together, these findings reveal robust naturally occurring variation in sleep and metabolic traits in D. melanogaster and suggest that distance from the equator and median temperature is a significant evolutionary factor in sleep regulation and architecture.

ecology↗