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https://www.readbyqxmd.com/read/29049362/parallel-and-costly-changes-to-cellular-immunity-underlie-the-evolution-of-parasitoid-resistance-in-three-drosophila-species
#1
John E McGonigle, Alexandre B Leitão, Sarah Ommeslag, Sophie Smith, Jonathan P Day, Francis M Jiggins
A priority for biomedical research is to understand the causes of variation in susceptibility to infection. To investigate genetic variation in a model system, we used flies collected from single populations of three different species of Drosophila and artificially selected them for resistance to the parasitoid wasp Leptopilina boulardi, and found that survival rates increased 3 to 30 fold within 6 generations. Resistance in all three species involves a large increase in the number of the circulating hemocytes that kill parasitoids...
October 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29048573/the-rate-of-evolution-of-postmating-prezygotic-reproductive-isolation-in-drosophila
#2
David A Turissini, Joseph A McGirr, Sonali S Patel, Jean R David, Daniel R Matute
Reproductive isolation is an intrinsic aspect of species formation. For that reason, the identification of the precise isolating traits, and the rates at which they evolve, is crucial to understanding how species originate and persist. Previous work has measured the rates of evolution of prezygotic and postzygotic barriers to gene flow, yet no systematic analysis has studied the rates of evolution of postmating-prezygotic (PMPZ) barriers. We measured the magnitude of two barriers to gene flow that act after mating occurs but before fertilization...
October 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29047904/cooperative-execution-of-auto-focusing-metrics-in-digital-lensless-holographic-microscopy-for-internal-structured-samples
#3
Carlos Trujillo, Jorge Garcia-Sucerquia
The cooperative execution of two metrics to automatically determine the best focal plane in digital lensless holographic microscopy (DLHM) is presented. This proposal is comprised of two stages: first, a quick coarse search over the whole reconstruction range by using Dubois's metric allows the finding of a range in which the best focal plane can be found. In a second stage, the modified enclosed energy (MEE) metric is used within the found range in the former stage to finely determine the best focal plane...
July 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/29047334/a-support-vector-machine-based-method-to-distinguish-long-non-coding-rnas-from-protein-coding-transcripts
#4
Hugo W Schneider, Taina Raiol, Marcelo M Brigido, Maria Emilia M T Walter, Peter F Stadler
BACKGROUND: In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed when analyzing this data is distinguishing between long non-coding RNAs (lncRNAs) and protein coding transcripts (PCTs). Thus, we present a Support Vector Machine (SVM) based method to distinguish lncRNAs from PCTs, using features based on frequencies of nucleotide patterns and ORF lengths, in transcripts...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29047261/deciphering-the-genes-for-taste-receptors-for-fructose-in-drosophila
#5
Shun Uchizono, Taichi Q Itoh, Haein Kim, Naoki Hamada, Jae Young Kwon, Teiichi Tanimura
Taste sensitivity to sugars plays an essential role in the initiation of feeding behavior. In Drosophila melanogaster, recent studies have identified several gustatory receptor (Gr) genes required for sensing sweet compounds. However, it is as yet undetermined how these GRs function as taste receptors tuned to a wide range of sugars. Among sugars, fructose has been suggested to be detected by a distinct receptor from other sugars. While GR43A has been reported to sense fructose in the brain, it is not expressed in labellar gustatory receptor neurons that show taste response to fructose...
October 17, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/29046402/the-hybrid-incompatibility-genes-lhr-and-hmr%C3%A2-are-required-for-sister-chromatid-detachment-during-anaphase-but-not-for-centromere-function
#6
Jacob A Blum, Silvia Bonaccorsi, Marta Marzullo, Valeria Palumbo, Yukiko M Yamashita, Daniel A Barbash, Maurizio Gatti
Crosses between Drosophila melanogaster females and Drosophila simulans males produce hybrid sons that die at the larval stage. This hybrid lethality is suppressed by loss-of-function mutations in the D. melanogasterHybrid male rescue (Hmr) or in the D. simulansLethal hybrid rescue (Lhr) genes. Previous studies have shown that Hmr and Lhr interact with heterochromatin proteins and suppress expression of transposable elements within D. melanogaster It also has been proposed that Hmr and Lhr function at the centromere...
October 18, 2017: Genetics
https://www.readbyqxmd.com/read/29045932/modulation-of-sestrin-confers-protection-to-cr-vi-induced-neuronal-cell-death-in-drosophila-melanogaster
#7
Pallavi Singh, D Kar Chowdhuri
Increased oxidative stress is one of the major causes of hexavalent chromium [Cr(VI)], a heavy metal with diverse applications and environmental presence, induced neuronal adversities in exposed organism including Drosophila. Sestrin (sesn), an oxidative stress responsive gene, emerges as a novel player in the management of oxidative stress response. It is reported to be regulated by Target of rapamycin (TOR) and the former regulates autophagy and plays an important role in the prevention of neurodegeneration...
October 7, 2017: Chemosphere
https://www.readbyqxmd.com/read/29045842/the-conserved-rna-exonuclease-rexo5-is-required-for-3-end-maturation-of-28s-rrna-5s-rrna-and-snornas
#8
Stefanie Gerstberger, Cindy Meyer, Sigi Benjamin-Hong, Joe Rodriguez, Daniel Briskin, Claudia Bognanni, Kimberly Bogardus, Hermann Steller, Thomas Tuschl
Non-coding RNA biogenesis in higher eukaryotes has not been fully characterized. Here, we studied the Drosophila melanogaster Rexo5 (CG8368) protein, a metazoan-specific member of the DEDDh 3'-5' single-stranded RNA exonucleases, by genetic, biochemical, and RNA-sequencing approaches. Rexo5 is required for small nucleolar RNA (snoRNA) and rRNA biogenesis and is essential in D. melanogaster. Loss-of-function mutants accumulate improperly 3' end-trimmed 28S rRNA, 5S rRNA, and snoRNA precursors in vivo. Rexo5 is ubiquitously expressed at low levels in somatic metazoan cells but extremely elevated in male and female germ cells...
October 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/29045669/genetic-decoupling-of-thermal-hardiness-across-metamorphosis-in-drosophila-melanogaster
#9
Philip J Freda, Jackson T Alex, Theodore J Morgan, Gregory J Ragland
As organisms age the environment fluctuates, exerting differential selection across ontogeny. In particular, highly seasonal environments expose life stages to often drastically different thermal environments. This developmental variation is particularly striking in organisms with complex life cycles, wherein life history stages also exhibit distinct morphologies, physiologies, and behaviors. Genes acting pleiotropically on thermal responses may produce genetic correlations across ontogeny, constraining the independent evolution of each life stage to their respective thermal environments...
October 16, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29045400/analysis-of-temporal-transcription-expression-profiles-reveal-links-between-protein-function-and-developmental-stages-of-drosophila-melanogaster
#10
Cen Wan, Jonathan G Lees, Federico Minneci, Christine A Orengo, David T Jones
Accurate gene or protein function prediction is a key challenge in the post-genome era. Most current methods perform well on molecular function prediction, but struggle to provide useful annotations relating to biological process functions due to the limited power of sequence-based features in that functional domain. In this work, we systematically evaluate the predictive power of temporal transcription expression profiles for protein function prediction in Drosophila melanogaster. Our results show significantly better performance on predicting protein function when transcription expression profile-based features are integrated with sequence-derived features, compared with the sequence-derived features alone...
October 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29044155/enterococci-mediate-the-oviposition-preference-of-drosophila-melanogaster-through-sucrose-catabolism
#11
Wei Liu, Ke Zhang, Yujuan Li, Wanzhen Su, Kunkun Hu, Shan Jin
Sucrose, one of the main products of photosynthesis in plants, functions as a universal biomarker for nutritional content and maturity of different fruits across diverse ecological niches. Drosophila melanogaster congregates to lay eggs in rotting fruits, yet the factors that influence these decisions remains uncovered. Here, we report that lactic acid bacteria Enterococci are critical modulators to attract Drosophila to lay eggs on decaying food. Drosophila-associated Enterococci predominantly catabolize sucrose for growing their population in fly food, and thus generate a unique ecological niche with depleted sucrose, but enriched bacteria...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29044148/structural-and-mechanistic-analysis-of-drosophila-melanogaster-agmatine-n-acetyltransferase-an-enzyme-that-catalyzes-the-formation-of-n-acetylagmatine
#12
Daniel R Dempsey, Derek A Nichols, Matthew R Battistini, Orville Pemberton, Santiago Rodriguez Ospina, Xiujun Zhang, Anne-Marie Carpenter, Brian G O'Flynn, James W Leahy, Ankush Kanwar, Eric M Lewandowski, Yu Chen, David J Merkler
Agmatine N-acetyltransferase (AgmNAT) catalyzes the formation of N-acetylagmatine from acetyl-CoA and agmatine. Herein, we provide evidence that Drosophila melanogaster AgmNAT (CG15766) catalyzes the formation of N-acetylagmatine using an ordered sequential mechanism; acetyl-CoA binds prior to agmatine to generate an AgmNAT•acetyl-CoA•agmatine ternary complex prior to catalysis. Additionally, we solved a crystal structure for the apo form of AgmNAT with an atomic resolution of 2.3 Å, which points towards specific amino acids that may function in catalysis or active site formation...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29043393/characterization-of-a-set-of-abdominal-neuroendocrine-cells-that-regulate-stress-physiology-using-colocalized-diuretic-peptides-in-drosophila
#13
Meet Zandawala, Richard Marley, Shireen A Davies, Dick R Nässel
Multiple neuropeptides are known to regulate water and ion balance in Drosophila melanogaster. Several of these peptides also have other functions in physiology and behavior. Examples are corticotropin-releasing factor-like diuretic hormone (diuretic hormone 44; DH44) and leucokinin (LK), both of which induce fluid secretion by Malpighian tubules (MTs), but also regulate stress responses, feeding, circadian activity and other behaviors. Here, we investigated the functional relations between the LK and DH44 signaling systems...
October 17, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/29043354/lipidomic-profiles-of-drosophila-melanogaster-and-cactophilic-fly-species-models-of-human-metabolic-diseases
#14
Daniel Cázarez-García, Mariana Ramírez Loustalot-Laclette, Therese Ann Markow, Robert Winkler
The metabolic syndrome (MetS) is associated with serious diseases and represents an important threat for global public health. The common fruit fly (Drosophila melanogaster) has served as a model organism to study physiological processes of the MetS, because central metabolic pathways are conserved among species, and because the flies are easy to cultivate in a laboratory. In nature, D. melanogaster is a fruit generalist, feeding on diets rich in simple carbohydrates. Other Drosophilids, however, have specialized on distinct resources...
October 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29043108/mysterious-inhibitory-cell-regulator-investigated-and-found-likely-to-be-secretogranin-ii-related
#15
John E Hart, Iain J Clarke, Gail P Risbridger, Ben Ferneyhough, Mónica Vega-Hernández
In the context of a hunt for a postulated hormone that is tissue-mass inhibiting and reproductively associated, there is described probable relatedness to a granin protein. A 7-8 kDa polypeptide candidate (gels/MS) appeared in a bioassay-guided fractionation campaign involving sheep plasma. An N-terminal sequence of 14 amino acids was obtained for the polypeptide by Edman degradation. Bioinformatics and molecular biology failed to illuminate any ovine or non-ovine protein which might relate to this sequence...
2017: PeerJ
https://www.readbyqxmd.com/read/29042606/population-genomics-of-wolbachia-and-mtdna-in-drosophila-simulans-from-california
#16
Sarah Signor
Wolbachia pipientis is an intracellular endosymbiont infecting many arthropods and filarial nematodes. Little is known about the short-term evolution of Wolbachia or its interaction with its host. Wolbachia is maternally inherited, resulting in co-inheritance of mitochondrial organelles such as mtDNA. Here I explore the evolution of Wolbachia, and the relationship between Wolbachia and mtDNA, using a large inbred panel of Drosophila simulans. I compare this to the only other large population genomic Wolbachia dataset from D...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29040697/mapping-selection-within-drosophila-melanogaster-embryo-s-anatomy
#17
Irepan Salvador-Martínez, Marta Coronado-Zamora, David Castellano, Antonio Barbadilla, Isaac Salazar-Ciudad
We present a survey of selection across Drosophila melanogaster embryonic anatomy. Our approach integrates genomic variation, spatial gene expression patterns and development, with the aim of mapping adaptation over the entire embryo's anatomy. Our adaptation map is based on analyzing spatial gene expression information for 5,969 genes (from text-based annotations of in situ hybridization data directly from the BDGP database, Tomancak et al. 2007) and the polymorphism and divergence in these genes (from the project DGRP, Mackay et al...
October 10, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29039273/in-vitro-selection-of-phytomonas-serpens-cells-resistant-to-the-calpain-inhibitor-mdl28170-alterations-in-fitness-and-expression-of-the-major-peptidases-and-efflux-pumps
#18
Simone S C Oliveira, Inês C Gonçalves, Vitor Ennes-Vidal, Angela H C S Lopes, Rubem F S Menna-Barreto, Claudia M D'Ávila-Levy, André L S Santos, Marta H Branquinha
The species Phytomonas serpens is known to express some molecules displaying similarity to those described in trypanosomatids pathogenic to humans, such as peptidases from Trypanosoma cruzi (cruzipain) and Leishmania spp. (gp63). In this work, a population of P. serpens resistant to the calpain inhibitor MDL28170 at 70 µ m (MDLR population) was selected by culturing promastigotes in increasing concentrations of the drug. The only relevant ultrastructural difference between wild-type (WT) and MDLR promastigotes was the presence of microvesicles within the flagellar pocket of the latter...
October 17, 2017: Parasitology
https://www.readbyqxmd.com/read/29037990/roles-for-the-vcp-co-factors-npl4-and-ufd1-in-neuronal-function-in-drosophila-melanogaster
#19
Dwayne J Byrne, Mark J Harmon, Jeremy C Simpson, Craig Blackstone, Niamh C O'Sullivan
The VCP-Ufd1-Npl4 complex regulates proteasomal processing within cells by delivering ubiquitinated proteins to the proteasome for degradation. Mutations in VCP are associated with two neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and inclusion body myopathy with Paget's disease of the bone and frontotemporal dementia (IBMPFD), and extensive study has revealed crucial functions of VCP within neurons. By contrast, little is known about the functions of Npl4 or Ufd1 in vivo. Using neuronal-specific knockdown of Npl4 or Ufd1 in Drosophila melanogaster, we infer that Npl4 contributes to microtubule organization within developing motor neurons...
September 21, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/29036674/detecting-and-characterizing-micrornas-of-diverse-genomic-origins-via-mirvial
#20
Jing Xia, Lun Li, Tiantian Li, Zhiwei Fang, Kevin Zhang, Junfei Zhou, Hai Peng, Weixiong Zhang
MicroRNAs form an essential class of post-transcriptional gene regulator of eukaryotic species, and play critical parts in development and disease and stress responses. MicroRNAs may originate from various genomic loci, have structural characteristics, and appear in canonical or modified forms, making them subtle to detect and analyze. We present miRvial, a robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs. Extensive results comparing miRvial and six existing microRNA finding methods on six model organisms, Mus musculus, Drosophila melanogaste, Arabidopsis thaliana, Oryza sativa, Physcomitrella patens and Chlamydomonas reinhardtii, demonstrated the utility and rigor of miRvial in detecting novel microRNAs and characterizing features of microRNAs...
September 19, 2017: Nucleic Acids Research
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