@article{everett_huang_zhou_carbone_lyman_arya_geisz_ma_morgante_st armour_et al._2020, title={Gene expression networks in the Drosophila Genetic Reference Panel}, volume={30}, ISSN={["1549-5469"]}, DOI={10.1101/gr.257592.119}, abstractNote={A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. This question is best addressed in a genetic mapping population in which all molecular polymorphisms are known and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable elements, and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, as well as genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses.}, number={3}, journal={GENOME RESEARCH}, author={Everett, Logan J. and Huang, Wen and Zhou, Shanshan and Carbone, Mary Anna and Lyman, Richard F. and Arya, Gunjan H. and Geisz, Matthew S. and Ma, Junwu and Morgante, Fabio and St Armour, Genevieve and et al.}, year={2020}, month={Mar}, pages={485–496} }
 @article{tallo_duncan_yamamoto_slaydon_arya_turlapati_mackay_carbone_2021, title={Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy}, volume={11}, ISSN={["2160-1836"]}, DOI={10.1093/g3journal/jkaa014}, abstractNote={Abstract
               In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.}, number={1}, journal={G3-GENES GENOMES GENETICS}, author={Tallo, Christian A. and Duncan, Laura H. and Yamamoto, Akihiko H. and Slaydon, Joshua D. and Arya, Gunjan H. and Turlapati, Lavanya and Mackay, Trudy F. C. and Carbone, Mary A.}, year={2021}, month={Jan} }
 @article{gabrawy_campbell_carbone_morozova_arya_turlapati_walston_starz-gaiano_everett_mackay_et al._2019, title={Lisinopril Preserves Physical Resilience and Extends Life Span in a Genotype-Specific Manner in Drosophila melanogaster}, volume={74}, ISSN={["1758-535X"]}, DOI={10.1093/gerona/glz152}, abstractNote={Abstract
               Physical resiliency declines with age and comorbid conditions. In humans, angiotensin-converting enzyme (ACE) has been associated with attenuation of the decline in physical performance with age. ACE-inhibitor compounds, commonly prescribed for hypertension, often have beneficial effects on physical performance however the generality of these effects are unclear. Here, we tested the effects of the ACE-inhibitor Lisinopril on life span, and age-specific speed, endurance, and strength using three genotypes of the Drosophila melanogaster Genetic Reference Panel. We show that age-related decline in physical performance and survivorship varies with genetic background. Lisinopril treatment increased mean life span in all Drosophila Genetic Reference Panel lines, but its effects on life span, speed, endurance, and strength depended on genotype. We show that genotypes with increased physical performance on Lisinopril treatment experienced reduced age-related protein aggregation in muscle. Knockdown of skeletal muscle-specific Ance, the Drosophila ortholog of ACE, abolished the effects of Lisinopril on life span, implying a role for skeletal muscle Ance in survivorship. Using transcriptome profiling, we identified genes involved in stress response that showed expression changes associated with genotype and age-dependent responsiveness to Lisinopril. Our results demonstrate that Ance is involved in physical decline and demonstrate genetic variation in phenotypic responses to an ACE inhibitor.}, number={12}, journal={JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES}, author={Gabrawy, Mariann M. and Campbell, Sarah and Carbone, Mary Anna and Morozova, Tatiana V and Arya, Gunjan H. and Turlapati, Lavanya B. and Walston, Jeremy D. and Starz-Gaiano, Michelle and Everett, Logan and Mackay, Trudy F. C. and et al.}, year={2019}, month={Dec}, pages={1844–1852} }
 @article{lavagnino_arya_korovaichuk_fanara_2013, title={Genetic Architecture of Olfactory Behavior in Drosophila melanogaster: Differences and Similarities Across Development}, volume={43}, ISSN={["1573-3297"]}, DOI={10.1007/s10519-013-9592-z}, abstractNote={In the holometabolous insect Drosophila melanogaster, genetic, physiological and anatomical aspects of olfaction are well known in the adult stage, while larval stages olfactory behavior has received some attention it has been less studied than its adult counterpart. Most of these studies focus on olfactory receptor (Or) genes that produce peripheral odor recognition. In this paper, through a loss-of-function screen using P-element inserted lines and also by means of expression analyses of larval olfaction candidate genes, we extended the uncovering of the genetic underpinnings of D. melanogaster larval olfactory behavior by demonstrating that larval olfactory behavior is, in addition to Or genes, orchestrated by numerous genes with diverse functions. Also, our results point out that the genetic architecture of olfactory behavior in D. melanogaster presents a dynamic and changing organization across environments and ontogeny.}, number={4}, journal={BEHAVIOR GENETICS}, author={Lavagnino, N. J. and Arya, G. H. and Korovaichuk, A. and Fanara, J. J.}, year={2013}, month={Jul}, pages={348–359} }
 @article{garlapow_everett_zhou_gearhart_fay_huang_morozova_arya_turlapati_st armour_et al., title={Genetic and genomic response to selection for food consumption in Drosophila melanogaster}, volume={47}, number={2}, journal={Behavior Genetics}, author={Garlapow, M. E. and Everett, L. J. and Zhou, S. S. and Gearhart, A. W. and Fay, K. A. and Huang, W. and Morozova, T. V. and Arya, G. H. and Turlapati, L. and St Armour, G. and et al.}, pages={227–243} }
 @article{shorter_dembeck_everett_morozova_arya_turlapati_st armour_schal_mackay_anholt, title={Obp56h modulates mating behavior in Drosophila melanogaster}, volume={6}, number={10}, journal={G3-Genes Genomes Genetics}, author={Shorter, J. R. and Dembeck, L. M. and Everett, L. J. and Morozova, T. V. and Arya, G. H. and Turlapati, L. and St Armour, G. E. and Schal, C. and Mackay, T. F. C. and Anholt, R. R. H.}, pages={3335–3342} }
 @article{arya_magwire_huang_serrano-negron_mackay_anholt, title={The genetic basis for variation in olfactory behavior in Drosophila melanogaster}, volume={40}, number={4}, journal={Chemical Senses}, author={Arya, G. H. and Magwire, M. M. and Huang, W. and Serrano-Negron, Y. L. and Mackay, T. F. C. and Anholt, R. R. H.}, pages={233–243} }