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Item Premature endocycling of Drosophila follicle cells causes pleiotropic defects in oogenesis(bioRxiv, 2024-01-03) Herriage, Hunter C.; Calvi, Brian R.; Biology, School of ScienceEndocycling cells grow and repeatedly duplicate their genome without dividing. Cells switch from mitotic cycles to endocycles in response to developmental signals during the growth of specific tissues in a wide range of organisms. The purpose of switching to endocycles, however, remains unclear in many tissues. Additionally, cells can switch to endocycles in response to conditional signals, which can have beneficial or pathological effects on tissues. However, the impact of these unscheduled endocycles on development is underexplored. Here, we use Drosophila ovarian somatic follicle cells as a model to examine the impact of unscheduled endocycles on tissue growth and function. Follicle cells normally switch to endocycles at mid-oogenesis. Inducing follicle cells to prematurely switch to endocycles resulted in lethality of the resulting embryos. Analysis of ovaries with premature follicle cell endocycles revealed aberrant follicular epithelial structure and pleiotropic defects in oocyte growth, developmental gene amplification, and the migration of a special set of follicle cells known as border cells. Overall, these findings reveal how unscheduled endocycles can disrupt tissue growth and function to cause aberrant development.Item ApoA5 lowers triglyceride levels via suppression of ANGPTL3/8-mediated LPL inhibition(Elsevier, 2021) Chen, Yan Q.; Pottanat, Thomas G.; Zhen, Eugene Y.; Siegel, Robert W.; Ehsani, Mariam; Qian, Yue-Wei; Konrad, Robert J.; Biology, School of ScienceTriglyceride (TG) molecules represent the major storage form of fatty acids, and TG metabolism is essential to human health. However, the mechanistic details surrounding TG metabolism are complex and incompletely elucidated. Although it is known that angiopoietin-like protein 8 (ANGPTL8) increases TGs through an ANGPTL3/8 complex that inhibits LPL, the mechanism governing ApoA5, which lowers TGs, has remained elusive. Current hypotheses for how ApoA5 acts include direct stimulation of LPL, facilitation of TG-containing particle uptake, and regulation of hepatic TG secretion. Using immunoprecipitation-MS and Western blotting, biolayer interferometry, functional LPL enzymatic assays, and kinetic analyses of LPL activity, we show that ApoA5 associates with ANGPTL3/8 in human serum and most likely decreases TG by suppressing ANGPTL3/8-mediated LPL inhibition. We also demonstrate that ApoA5 has no direct effect on LPL, nor does it suppress the LPL-inhibitory activities of ANGPTL3, ANGPTL4, or ANGPTL4/8. Importantly, ApoA5 suppression of ANGPTL3/8-mediated LPL inhibition occurred at a molar ratio consistent with the circulating concentrations of ApoA5 and ANGPTL3/8. Because liver X receptor (LXR) agonists decrease ApoA5 expression and cause hypertriglyceridemia, we investigated the effect of the prototypical LXR agonist T0901317 on human primary hepatocytes. We observed that T0901317 modestly stimulated hepatocyte ApoA5 release, but markedly stimulated ANGPTL3/8 secretion. Interestingly, the addition of insulin to T0901317 attenuated ApoA5 secretion, but further increased ANGPTL3/8 secretion. Together, these results reveal a novel intersection of ApoA5 and ANGPTL3/8 in the regulation of TG metabolism and provide a possible explanation for LXR agonist-induced hypertriglyceridemia.Item Essential Oils Produce Developmental Toxicity in Zebrafish Embryos and Cause Behavior Changes in Zebrafish Larvae(MDPI, 2023-10-18) da Silva, Ivanildo Inacio, Jr.; da Silva, Niely Priscila Correia; Marrs, James A.; Cadena, Pabyton Gonçalves; Biology, School of ScienceEssential oils have gained significant popularity in various industries due to their biological properties, but their potential toxic effects on living organisms have been poorly investigated. This study aimed to evaluate the effects of lemongrass, thyme, and oregano essential oils on zebrafish embryos and larvae as animal models. Embryos were exposed to different concentrations of essential oils, and various endpoints were assessed, including epiboly, mortality (LC50), morphometry, and behavioral changes. All three essential oils reduced epiboly, affecting embryonic development. LC50 values were calculated for lemongrass (3.7 µg/mL), thyme (14.4 µg/mL), and oregano (5.3 µg/mL) oils. Larvae exposed to these oils displayed morphological defects, including growth reduction, spinal deformation, pericardial edema, eye size reduction, and reduced swim-bladder inflation. Morphometric analysis confirmed reduced larval length at higher oil concentrations. Essential-oil exposure altered zebrafish larval swimming behavior, with lemongrass oil reducing dark-cycle activity and oregano oil increasing light-cycle activity, suggesting neurodevelopmental toxicity. These findings illustrate the adverse effects of these oils on zebrafish embryos and larvae and reveal essential-oil toxicity, indicating careful use should be considered, particularly during pregnancy.Item Characterization of spray-dried Gac aril extract and estimated shelf life of β-carotene and lycopene(PeerJ, 2021-03-24) Thumthanaruk, Benjawan; Laohakunjit, Natta; Chism, Grady W.; Biology, School of ScienceBackground: Fresh Gac (Momordica cochinchinensis) fruit is rich in carotenoids, mainly β-carotene and lycopene, but these compounds are sensitive to degradation. Spray drying is used to encapsulate the sensitive β-carotene and lycopene with different materials. Only a few reports of using highly branched cyclodextrin (HBCD) have been published. Additionally, studies of β-carotene and lycopene losses in Gac powders during storage are limited. Therefore, the encapsulation of β-carotene and lycopene of Gac aril with HBCD by spray drying at different inlet temperatures were compared. The shelf life of β-carotene and lycopene during storage was also calculated. Methods: The fresh Gac aril was separated and kept frozen before the experiment. Gac aril and water (1:5 w/v) were centrifuged at 8,000 g at 20 °C for 15 min using a high-speed centrifuge (Sorval; Dupont, Wilmington, DE, USA). The supernatant was filtered twice and concentrated until 15° Brix using a rotary evaporator (R-200; Buchi, Flawil, Switzerland). The mixture of concentrated aril extract and highly branched cyclodextrin at 5% (w/v) was dried at three inlet temperatures by a spray dryer (B-290; Buchi, Flawil, Switzerland) with drying air flow rate, compressor air pressure, and feed rate set at 473 L/h, 40 m3/h, and 3 mL/min, respectively . The physicochemical qualities, particle image morphology, and estimated storage time of β-carotene and lycopene were determined. Results: Increased inlet temperatures of spray drying decreased the bulk density, β-carotene, and lycopene content of spray-dried powders significantly. The color values of dried powders had significant differences in yellowness (b*) and chroma, but not lightness (L*), redness (a*), and hue when the inlet temperature increased from 160 °C to 180 °C. The maximum reduction of β-carotene and lycopene observed during storage at 55 °C was 90.88% and 91.11% for 33 and 18 days. For β-carotene, the estimated shelf-life (retention of 50% of β-carotene) was 9.9, 48.4, and 91.6 days at 25 °C, 10 °C, and 4 °C. The shelf-life of lycopene was 26, 176, and 357 days at 25 °C, 10 °C, and 4 °C, respectively. HBCD could be potentially used as an encapsulating agent in spray-dried Gac aril, but the shelf-life of β-carotene and lycopene needs to be improved to be useful as a food ingredient.Item Shared heritability of human face and brain shape(Springer Nature, 2021) Naqvi, Sahin; Sleyp, Yoeri; Hoskens, Hanne; Indencleef, Karlijne; Spence, Jeffrey P.; Bruffaerts, Rose; Radwan, Ahmed; Eller, Ryan J.; Richmond, Stephen; Shriver, Mark D.; Shaffer, John R.; Weinberg, Seth M.; Walsh, Susan; Thompson, James; Pritchard, Jonathan K.; Sunaert, Stefan; Peeters, Hilde; Wysocka, Joanna; Claes, Peter; Biology, School of ScienceEvidence from model organisms and clinical genetics suggests coordination between the developing brain and face, but the role of this link in common genetic variation remains unknown. We performed a multivariate genome-wide association study of cortical surface morphology in 19,644 individuals of European ancestry, identifying 472 genomic loci influencing brain shape, of which 76 are also linked to face shape. Shared loci include transcription factors involved in craniofacial development, as well as members of signaling pathways implicated in brain-face cross-talk. Brain shape heritability is equivalently enriched near regulatory regions active in either forebrain organoids or facial progenitors. However, we do not detect significant overlap between shared brain-face genome-wide association study signals and variants affecting behavioral-cognitive traits. These results suggest that early in embryogenesis, the face and brain mutually shape each other through both structural effects and paracrine signaling, but this interplay may not impact later brain development associated with cognitive function.Item Evaluation of supervised machine-learning methods for predicting appearance traits from DNA(Elsevier, 2021) Katsara, Maria-Alexandra; Branicki, Wojciech; Walsh, Susan; Kayser, Manfred; Nothnagel, Michael; VISAGE Consortium; Biology, School of ScienceThe prediction of human externally visible characteristics (EVCs) based solely on DNA information has become an established approach in forensic and anthropological genetics in recent years. While for a large set of EVCs, predictive models have already been established using multinomial logistic regression (MLR), the prediction performances of other possible classification methods have not been thoroughly investigated thus far. Motivated by the question to identify a potential classifier that outperforms these specific trait models, we conducted a systematic comparison between the widely used MLR and three popular machine learning (ML) classifiers, namely support vector machines (SVM), random forest (RF) and artificial neural networks (ANN), that have shown good performance outside EVC prediction. As examples, we used eye, hair and skin color categories as phenotypes and genotypes based on the previously established IrisPlex, HIrisPlex, and HIrisPlex-S DNA markers. We compared and assessed the performances of each of the four methods, complemented by detailed hyperparameter tuning that was applied to some of the methods in order to maximize their performance. Overall, we observed that all four classification methods showed rather similar performance, with no method being substantially superior to the others for any of the traits, although performances varied slightly across the different traits and more so across the trait categories. Hence, based on our findings, none of the ML methods applied here provide any advantage on appearance prediction, at least when it comes to the categorical pigmentation traits and the selected DNA markers used here.Item 3D Facial Matching by Spiral Convolutional Metric Learning and a Biometric Fusion-Net of Demographic Properties(IEEE, 2021) Mahdi, Soha Sadat; Nauwelaers, Nele; Joris, Philip; Bouritsas, Giorgos; Gong, Shunwang; Bokhnyak, Sergiy; Walsh, Susan; Shriver, Mark D.; Bronstein, Michael; Claes, Peter; Biology, School of ScienceFace recognition is a widely accepted biometric verification tool, as the face contains a lot of information about the identity of a person. In this study, a 2-step neural-based pipeline is presented for matching 3D facial shape to multiple DNA-related properties (sex, age, BMI and genomic background). The first step consists of a triplet loss-based metric learner that compresses facial shape into a lower dimensional embedding while preserving information about the property of interest. Most studies in the field of metric learning have only focused on 2D Euclidean data. In this work, geometric deep learning is employed to learn directly from 3D facial meshes. To this end, spiral convolutions are used along with a novel mesh-sampling scheme that retains uniformly sampled 3D points at different levels of resolution. The second step is a multi-biometric fusion by a fully connected neural network. The network takes an ensemble of embeddings and property labels as input and returns genuine and imposter scores. Since embeddings are accepted as an input, there is no need to train classifiers for the different properties and available data can be used more efficiently. Results obtained by a to-fold cross-validation for biometric verification show that combining multiple properties leads to stronger biometric systems. Furthermore, the proposed neural-based pipeline outperforms a linear baseline, which consists of principal component analysis, followed by classification with linear support vector machines and a Naïve Bayes-based score-fuser.Item Insights into the genetic architecture of the human face(Springer Nature, 2021) White, Julie D.; Indencleef, Karlijne; Naqvi, Sahin; Eller, Ryan J.; Hoskens, Hanne; Roosenboom, Jasmien; Lee, Myoung Keun; Li, Jiarui; Mohammed, Jaaved; Richmond, Stephen; Quillen, Ellen E.; Norton, Heather L.; Feingold, Eleanor; Swigut, Tomek; Marazita, Mary L.; Peeters, Hilde; Hens, Greet; Shaffer, John R.; Wysocka, Joanna; Walsh, Susan; Weinberg, Seth M.; Shriver, Mark D.; Claes, Peter; Biology, School of ScienceThe human face is complex and multipartite, and characterization of its genetic architecture remains challenging. Using a multivariate genome-wide association study meta-analysis of 8,246 European individuals, we identified 203 genome-wide-significant signals (120 also study-wide significant) associated with normal-range facial variation. Follow-up analyses indicate that the regions surrounding these signals are enriched for enhancer activity in cranial neural crest cells and craniofacial tissues, several regions harbor multiple signals with associations to different facial phenotypes, and there is evidence for potential coordinated actions of variants. In summary, our analyses provide insights into the understanding of how complex morphological traits are shaped by both individual and coordinated genetic actions.Item Ciliary ARL13B prevents obesity in mice(bioRxiv, 2023-08-04) Terry, Tiffany T.; Gigante, Eduardo D.; Alexandre, Coralie M.; Brewer, Kathryn M.; Engle, Staci E.; Yue, Xinyu; Berbari, Nicolas F.; Vaisse, Christian; Caspary, Tamara; Biology, School of ScienceCilia are near ubiquitous small, cellular appendages critical for cell-to-cell communication. As such, they are involved in diverse developmental and homeostatic processes, including energy homeostasis. ARL13B is a regulatory GTPase highly enriched in cilia. Mice expressing an engineered ARL13B variant, ARL13BV358A which retains normal biochemical activity, display no detectable ciliary ARL13B. Surprisingly, these mice become obese. Here, we measured body weight, food intake, and blood glucose levels to reveal these mice display hyperphagia and metabolic defects. We showed that ARL13B normally localizes to cilia of neurons in specific brain regions and pancreatic cells but is excluded from these cilia in the Arl13bV358A/V358A model. In addition to its GTPase function, ARL13B acts as a guanine nucleotide exchange factor (GEF) for ARL3. To test whether ARL13B’s GEF activity is required to regulate body weight, we analyzed the body weight of mice expressing ARL13BR79Q, a variant that lacks ARL13B GEF activity for ARL3. We found no difference in body weight. Taken together, our results show that ARL13B functions within cilia to control body weight and that this function does not depend on its role as a GEF for ARL3. Controlling the subcellular localization of ARL13B in the engineered mouse model, ARL13BV358A, enables us to define the cilia-specific role of ARL13B in regulating energy homeostasis.Item Development of a three-dimensional organoid model to explore early retinal phenotypes associated with Alzheimer’s disease(Springer Nature, 2023-08-24) Lavekar, Sailee S.; Harkin, Jade; Hernandez, Melody; Gomes, Cátia; Patil, Shruti; Huang, Kang‑Chieh; Puntambekar, Shweta S.; Lamb, Bruce T.; Meyer, Jason S.; Biology, School of ScienceAlzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of Aβ plaques and neurofibrillary tangles, resulting in synaptic loss and neurodegeneration. The retina is an extension of the central nervous system within the eye, sharing many structural similarities with the brain, and previous studies have observed AD-related phenotypes within the retina. Three-dimensional retinal organoids differentiated from human pluripotent stem cells (hPSCs) can effectively model some of the earliest manifestations of disease states, yet early AD-associated phenotypes have not yet been examined. Thus, the current study focused upon the differentiation of hPSCs into retinal organoids for the analysis of early AD-associated alterations. Results demonstrated the robust differentiation of retinal organoids from both familial AD and unaffected control cell lines, with familial AD retinal organoids exhibiting a significant increase in the Aβ42:Aβ40 ratio as well as phosphorylated Tau protein, characteristic of AD pathology. Further, transcriptional analyses demonstrated the differential expression of many genes and cellular pathways, including those associated with synaptic dysfunction. Taken together, the current study demonstrates the ability of retinal organoids to serve as a powerful model for the identification of some of the earliest retinal alterations associated with AD.