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https://www.readbyqxmd.com/read/28227973/improving-odorant-chemical-class-prediction-with-multi-layer-perceptrons-using-temporal-odorant-spike-responses-from-drosophila-melanogaster-olfactory-receptor-neurons
#1
Luqman R Bachtiar, Richard D Newcomb, Andrew V Kralicek, Charles P Unsworth, Luqman R Bachtiar, Richard D Newcomb, Andrew V Kralicek, Charles P Unsworth, Charles P Unsworth, Andrew V Kralicek, Richard D Newcomb, Luqman R Bachtiar
In this work, we examine the possibility of improving the prediction performance of an olfactory biosensor through the use of temporal spiking data. We present an Artificial Neural Network (ANN), in the form of an optimal hybrid Multi-Layer Perceptron (MLP) system for the classification of chemical odorants from olfactory receptor neuron spike responses of the Drosophila melanogaster fruit fly (DmOrs). The data used in this study contains the responses to 34 odorants from 6 individual DmOrs, of which we exploit the temporal spiking responses of a 500ms odorant stimulus window...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227815/lab-on-chips-for-manipulation-of-small-scale-organisms-to-facilitate-imaging-of-neurons-and-organs
#2
Ramtin Ardeshiri, Pouya Rezai, Ramtin Ardeshiri, Pouya Rezai, Ramtin Ardeshiri, Pouya Rezai
Caenorhabditis elegans (C. elegans) and Drosophila melanogaster (D. melanogaster) are widely-used model organisms for neurological and cardiac studies due to their simple neuronal (302 neurons in C. elegans) and cardiac (simple tubular organ in D. melanogaster) systems. However, their small sizes and continuous mobility impede their precise and timely manipulation, hence, limiting the assays that can be done using conventional manual methods. This has resulted in a need for technologies that allow multidirectional manipulation of model organisms to enable studies on target neurons and organs throughout the body...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226201/genomewide-association-study-of-alcohol-dependence-identifies-risk-loci-altering-ethanol-response-behaviors-in-model-organisms
#3
Amy E Adkins, Laura M Hack, Tim B Bigdeli, Vernell S Williamson, G Omari McMichael, Mohammed Mamdani, Alexis Edwards, Fazil Aliev, Robin F Chan, Poonam Bhandari, Richard C Raabe, Joseph T Alaimo, GinaMari G Blackwell, Arden A Moscati, Ryan S Poland, Benjamin Rood, Diana G Patterson, Dermot Walsh, John B Whitfield, Gu Zhu, Grant W Montgomery, Anjali K Henders, Nicholas G Martin, Andrew C Heath, Pamela A F Madden, Josef Frank, Monika Ridinger, Norbert Wodarz, Michael Soyka, Peter Zill, Marcus Ising, Markus M Nöthen, Falk Kiefer, Marcella Rietschel, Joel Gelernter, Richard Sherva, Ryan Koesterer, Laura Almasy, Hongyu Zhao, Henry R Kranzler, Lindsay A Farrer, Brion S Maher, Carol A Prescott, Danielle M Dick, Silviu A Bacanu, Laura D Mathies, Andrew G Davies, Vladimir I Vladimirov, Mike Grotewiel, M Scott Bowers, Jill C Bettinger, Bradley T Webb, Michael F Miles, Kenneth S Kendler, Brien P Riley
BACKGROUND: Alcohol Dependence (AD) shows evidence for genetic liability, but genes influencing risk remain largely unidentified. METHODS: We conducted a genomewide association study in 706 related AD cases and 1748 unscreened population controls from Ireland. We sought replication in 15,496 samples of European descent. We used model organisms to assess the role of orthologous genes in ethanol response behaviors. We tested one primate-specific gene for expression differences in case/control post-mortem brain tissue...
February 22, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28225068/relish2-mediates-bursicon-homodimer-induced-prophylactic-immunity-in-the-mosquito-aedes-aegypti
#4
Hongwei Zhang, Shengzhang Dong, Xi Chen, David Stanley, Brenda Beerntsen, Qili Feng, Qisheng Song
Bursicon is a neuropeptide hormone consisting of two cystine-knot proteins (burs α and burs β), responsible for cuticle tanning and other developmental processes in insects. Recent studies show that each bursicon subunit forms homodimers that induce prophylactic immunity in Drosophila melanogaster. Here, we investigated the hypothesis that bursicon homodimers act in prophylactic immunity in insects, and possibly arthropods, generally, using the mosquito, Aedes aegypti. We found that burs α and burs β are expressed in larvae, pupae and newly emerged adults...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224717/tissue-specific-expression-and-silencing-phenotypes-of-mitochondrial-phosphate-carrier-paralogues-in-several-insect-species
#5
R Sugahara, A Jouraku, T Nakakura, M Minaba, T Yamamoto, Y Shinohara, H Miyoshi, T Shiotsuki
The mitochondrial phosphate carrier gene (PiC) encodes a membrane protein that mediates the supply of inorganic phosphate from the cytosol into the mitochondrial matrix. This substrate-specific transport system plays an important role in efficient ATP synthesis. Mammals appear to have only one PiC with two alternative splicing variants whose functional differences remain unclear. The present study is the first to characterize the multiple genes that encode PiC in insects. Bombyx mori was found to have two PiC paralogues, one ubiquitous and one testis-specific, the latter seeming to be present only in Lepidoptera...
February 22, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/28223318/a-drosophila-model-of-fragile-x-syndrome-exhibits-defects-in-phagocytosis-by-innate-immune-cells
#6
Reed M O'Connor, Elizabeth F Stone, Charlotte R Wayne, Emily V Marcinkevicius, Matt Ulgherait, Rebecca Delventhal, Meghan M Pantalia, Vanessa M Hill, Clarice G Zhou, Sophie McAllister, Anna Chen, Jennifer S Ziegenfuss, Wesley B Grueber, Julie C Canman, Mimi M Shirasu-Hiza
Fragile X syndrome, the most common known monogenic cause of autism, results from the loss of FMR1, a conserved, ubiquitously expressed RNA-binding protein. Recent evidence suggests that Fragile X syndrome and other types of autism are associated with immune system defects. We found that Drosophila melanogaster Fmr1 mutants exhibit increased sensitivity to bacterial infection and decreased phagocytosis of bacteria by systemic immune cells. Using tissue-specific RNAi-mediated knockdown, we showed that Fmr1 plays a cell-autonomous role in the phagocytosis of bacteria...
February 21, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28222763/the-discovery-of-novel-lpmo-families-with-a-new-hidden-markov-model
#7
Gerben P Voshol, Erik Vijgenboom, Peter J Punt
BACKGROUND: Renewable biopolymers, such as cellulose, starch and chitin are highly resistance to enzymatic degradation. Therefore, there is a need to upgrade current degradation processes by including novel enzymes. Lytic polysaccharide mono-oxygenases (LPMOs) can disrupt recalcitrant biopolymers, thereby enhancing hydrolysis by conventional enzymes. However, novel LPMO families are difficult to identify using existing methods. Therefore, we developed a novel profile Hidden Markov model (HMM) and used it to mine genomes of ascomycetous fungi for novel LPMOs...
February 21, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28222282/transcriptional-pre-patterning-of-drosophila-gastrulation
#8
Bomyi Lim, Michael Levine, Yuji Yamazaki
No abstract text is available yet for this article.
February 20, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28222093/active-zone-proteins-are-transported-via-distinct-mechanisms-regulated-by-par-1-kinase
#9
Kara R Barber, Julia Tanquary, Keegan Bush, Amanda Shaw, Michael Woodson, Michael Sherman, Yogesh P Wairkar
Disruption of synapses underlies a plethora of neurodevelopmental and neurodegenerative disease. Presynaptic specialization called the active zone plays a critical role in the communication with postsynaptic neuron. While the role of many proteins at the active zones in synaptic communication is relatively well studied, very little is known about how these proteins are transported to the synapses. For example, are there distinct mechanisms for the transport of active zone components or are they all transported in the same transport vesicle? Is active zone protein transport regulated? In this report we show that overexpression of Par-1/MARK kinase, a protein whose misregulation has been implicated in Autism spectrum disorders (ASDs) and neurodegenerative disorders, lead to a specific block in the transport of an active zone protein component- Bruchpilot at Drosophila neuromuscular junctions...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28221375/circadian-deep-sequencing-reveals-stress-response-genes-that-adopt-robust-rhythmic-expression-during-aging
#10
Rachael C Kuintzle, Eileen S Chow, Tara N Westby, Barbara O Gvakharia, Jadwiga M Giebultowicz, David A Hendrix
Disruption of the circadian clock, which directs rhythmic expression of numerous output genes, accelerates aging. To enquire how the circadian system protects aging organisms, here we compare circadian transcriptomes in heads of young and old Drosophila melanogaster. The core clock and most output genes remained robustly rhythmic in old flies, while others lost rhythmicity with age, resulting in constitutive over- or under-expression. Unexpectedly, we identify a subset of genes that adopted increased or de novo rhythmicity during aging, enriched for stress-response functions...
February 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28220999/the-drosophila-divalent-metal-ion-transporter-malvolio-is-required-in-dopaminergic-neurons-for-feeding-decisions
#11
Eirik Søvik, Angela LaMora, Gurpreet Seehra, Andrew B Barron, Jennifer G Duncan, Yehuda Ben-Shahar
Members of the Natural resistance-associated macrophage protein (NRAMP) family are evolutionarily-conserved metal ion transporters that play an essential role in regulating intracellular divalent cation homeostasis in both prokaryotes and eukaryotes. Malvolio (Mvl), the sole NRAMP family member in insects, plays a role in food choice behaviors in Drosophila and other species. However, the specific physiological and cellular processes that require the action of Mvl for appropriate feeding decisions remain elusive...
February 21, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28220806/on-the-long-term-stability-of-clines-in-some-metabolic-genes-in-drosophila-melanogaster
#12
Rodrigo Cogni, Kate Kuczynski, Spencer Koury, Erik Lavington, Emily L Behrman, Katherine R O'Brien, Paul S Schmidt, Walter F Eanes
Very little information exists for long-term changes in genetic variation in natural populations. Here we take the unique opportunity to compare a set of data for SNPs in 15 metabolic genes from eastern US collections of Drosophila melanogaster that span a large latitudinal range and represent two collections separated by 12 to 13 years. We also expand this to a 22-year interval for the Adh gene and approximately 30 years for the G6pd and Pgd genes. During these intervals, five genes showed a statistically significant change in average SNP allele frequency corrected for latitude...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28219985/activity-induced-synaptic-structural-modifications-by-an-activator-of-integrin-signaling-at-the-drosophila-neuromuscular-junction
#13
Joo Yeun Lee, Junhua Geng, Juhyun Lee, Andrew R Wang, Karen T Chang
Activity-induced synaptic structural modification is crucial for neural development and synaptic plasticity, but the molecular players involved in this process are not well defined. Here, we report that a protein named Shriveled, Shv, regulates synaptic growth and activity-dependent synaptic remodeling at the Drosophila neuromuscular junction. Depletion of Shv causes synaptic overgrowth and an accumulation of immature boutons. We find that Shv physically and genetically interacts with βPS integrin. Furthermore, Shv is secreted during intense, but not mild, neuronal activity to acutely activate integrin signaling, induce synaptic bouton enlargement, and increase postsynaptic glutamate receptor abundance...
February 20, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28219947/phosphorylation-potential-of-drosophila-e-cadherin-intracellular-domain-is-essential-for-development-and-regulating-adherens-junction-biosynthetic-dynamics
#14
Yi-Jiun Chen, Juan Huang, Lynn Huang, Erin Austin, Yang Hong
E-Cadherin intracellular domain contains a highly conserved serine cluster whose phosphorylations are essential for binding to β-Catenin in vitro. In cultured cells phosphorylations of specific serine residues within the cluster are also required for regulating adherens junction (AJ) stability and dynamics. However, much less is known how such phosphorylations of E-Cadherin regulate the AJ formation and dynamics in vivo. In this report we generated an extensive array of Drosophila E-Cadherin (DE-Cad) endogenous knock-in alleles that carry mutations targeting this highly conserved serine cluster...
February 20, 2017: Development
https://www.readbyqxmd.com/read/28219118/bmcalpains-are-involved-in-autophagy-and-apoptosis-during-metamorphosis-and-after-starvation-in-bombyx-mori
#15
Hui-Yu Yi, Wan-Ying Yang, Wen-Mei Wu, Xing-Xia Li, Xiao-Juan Deng, Qing-Rong Li, Yang Cao, Yang-Jin Zhong, Ya-Dong Huang
Apoptosis and autophagy play crucial roles during Bombyx mori metamorphosis and in response to various adverse conditions, including starvation. Recently, calpain, one of the major intracellular proteases, has been reported to be involved in apoptosis and autophagy in mammals. BmATG5 and BmATG6 have been identified to mediate apoptosis following autophagy induced by 20-hydroxyecdysone and starvation in B. mori. However, B. mori calpains and their functions remain unclear. In this study, phylogenetic analysis of calpains from B...
November 7, 2016: Insect Science
https://www.readbyqxmd.com/read/28218282/calcium-spikes-waves-and-oscillations-in-a-large-patterned-epithelial-tissue
#16
Ramya Balaji, Christina Bielmeier, Hartmann Harz, Jack Bates, Cornelia Stadler, Alexander Hildebrand, Anne-Kathrin Classen
While calcium signaling in excitable cells, such as muscle or neurons, is extensively characterized, calcium signaling in epithelial tissues is little understood. Specifically, the range of intercellular calcium signaling patterns elicited by tightly coupled epithelial cells and their function in the regulation of epithelial characteristics are little explored. We found that in Drosophila imaginal discs, a widely studied epithelial model organ, complex spatiotemporal calcium dynamics occur. We describe patterns that include intercellular waves traversing large tissue domains in striking oscillatory patterns as well as spikes confined to local domains of neighboring cells...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28218276/natural-and-laboratory-mutations-in-kuzbanian-are-associated-with-zinc-stress-phenotypes-in-drosophila-melanogaster
#17
Hung Le Manh, Lain Guio, Miriam Merenciano, Quirze Rovira, Maite G Barrón, Josefa González
Organisms must cope with altered environmental conditions such as high concentrations of heavy metals. Stress response to heavy metals is mediated by the metal-responsive transcription factor 1 (MTF-1), which is conserved from Drosophila to humans. MTF-1 binds to metal response elements (MREs) and changes the expression of target genes. kuzbanian (kuz), a metalloendopeptidase that activates the evolutionary conserved Notch signaling pathway, has been identified as an MTF-1 target gene. We have previously identified a putatively adaptive transposable element in the Drosophila melanogaster genome, named FBti0019170, inserted in a kuz intron...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28217557/regulation-of-antimicrobial-peptides-in-aedes-aegypti-aag2-cells
#18
Rudian Zhang, Yibin Zhu, Xiaojing Pang, Xiaoping Xiao, Renli Zhang, Gong Cheng
Antimicrobial peptides (AMPs) are an important group of immune effectors that play a role in combating microbial infections in invertebrates. Most of the current information on the regulation of insect AMPs in microbial infection have been gained from Drosophila, and their regulation in other insects are still not completely understood. Here, we generated an AMP induction profile in response to infections with some Gram-negative, -positive bacteria, and fungi in Aedes aegypti embryonic Aag2 cells. Most of the AMP inductions caused by the gram-negative bacteria was controlled by the Immune deficiency (Imd) pathway; nonetheless, Gambicin, an AMP gene discovered only in mosquitoes, was combinatorially regulated by the Imd, Toll and JAK-STAT pathways in the Aag2 cells...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28216314/visual-working-memory-requires-permissive-and-instructive-no-cgmp-signaling-at-presynapses-in-the-drosophila-central-brain
#19
Sara Kuntz, Burkhard Poeck, Roland Strauss
The gaseous second messenger nitric oxide (NO) has been shown to regulate memory formation by activating retrograde signaling cascades from post- to presynapse that involve cyclic guanosine monophosphate (cGMP) production to induce synaptic plasticity and transcriptional changes. In this study, we analyzed the role of NO in the formation of a visual working memory that lasts only a few seconds. This memory is encoded in a subset of ring neurons that form the ellipsoid body in the Drosophila brain. Using genetic and pharmacological manipulations, we show that NO signaling is required for cGMP-mediated CREB activation, leading to the expression of competence factors like the synaptic homer protein...
February 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28215745/astrocyte-transport-of-glutamate-and-neuronal-activity-reciprocally-modulate-tau-pathology-in-drosophila
#20
Jason G Kilian, Heng-Wei Hsu, Kenneth Mata, Fred W Wolf, Masashi Kitazawa
Abnormal buildup of the microtubule associated protein tau is a major pathological hallmark of SAlzheimer's disease (AD)and various tauopathies. The mechanisms by which pathological tau accumulates and spreads throughout the brain remain largely unknown. Previously, we demonstrated that a restoration of the major astrocytic glutamate transporter, GLT1, ameliorated a buildup of tau pathology and rescued cognition in a mouse model of AD. We hypothesized thataberrant extracellular glutamate and abnormal neuronal excitatory activities promoted tau pathology...
February 16, 2017: Neuroscience
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