text: Biorxiv.: auth.: group Benton
  – 08/30/2018Posted in: Recent CIG publications
  View ORCID ProfileJuan Antonio Sanchez-Alcaniz, Ana F Silbering, Vincent Croset, Giovanna Zappia, Anantha K Sivasubramaniam, Liliane Abuin, Saumya Y Sahai, Thomas O Auer, Steeve Cruchet, G. Larisa Neagu-Maier, View ORCID ProfileSimon G Sprecher, View ORCID ProfileNilay Yapici, View ORCID ProfileRichard Benton
  MBio.: co-auth.: GTF
  MBio. 2018 Mar 20;9(2). pii: e00024-18. doi: 10.1128/mBio.00024-18.
  Masson F1, Calderon Copete S2, Schüpfer F3, Garcia-Arraez G3, Lemaitre B1.
  Endosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbionts. Spiroplasma poulsonii is a maternally transmitted bacterial endosymbiont that is naturally associated with several Drosophila species. S. poulsonii strongly affects its host's physiology, for example by causing male killing or by protecting it against various parasites. Despite intense work on this model since the 1950s, attempts to cultivate endosymbiotic Spiroplasma in vitro have failed so far. Here, we developed a method to sustain the in vitroculture of S. poulsonii by optimizing a commercially accessible medium. We also provide a complete genome assembly, including the first sequence of a natural plasmid of an endosymbiotic Spiroplasma species. Last, by comparing the transcriptome of the in vitro culture to the transcriptome of bacteria extracted from the host, we identified genes putatively involved in host-symbiont interactions. This work provides new opportunities to study the physiology of endosymbiotic Spiroplasma and paves the way to dissect insect-endosymbiont interactions with two genetically tractable partners.IMPORTANCE The discovery of insect bacterial endosymbionts (maternally transmitted bacteria) has revolutionized the study of insects, suggesting novel strategies for their control. Most endosymbionts are strongly dependent on their host to survive, making them uncultivable in artificial systems and genetically intractable. Spiroplasma poulsonii is an endosymbiont of Drosophilathat affects host metabolism, reproduction, and defense against parasites. By providing the first reliable culture medium that allows a long-lasting in vitro culture of Spiroplasma and by elucidating its complete genome, this work lays the foundation for the development of genetic engineering tools to dissect endosymbiosis with two partners amenable to molecular study. Furthermore, the optimization method that we describe can be used on other yet uncultivable symbionts, opening new technical opportunities in the field of host-microbes interactions.
  Spiroplasma; endosymbiosis; host-symbiont interaction
  PMID: 29559567
  Sci Rep.: co-auth.: C. Dessimoz and group Herr
  Klopfenstein DV1, Zhang L2, Pedersen BS3, Ramírez F4, Warwick Vesztrocy A5, Naldi A6, Mungall CJ7, Yunes JM8, Botvinnik O9, Weigel M10, Dampier W1,11, Dessimoz C5, Flick P12, Tang H13.
  The biological interpretation of gene lists with interesting shared properties, such as up- or down-regulation in a particular experiment, is typically accomplished using gene ontology enrichment analysis tools. Given a list of genes, a gene ontology (GO) enrichment analysis may return hundreds of statistically significant GO results in a "flat" list, which can be challenging to summarize. It can also be difficult to keep pace with rapidly expanding biological knowledge, which often results in daily changes to any of the over 47,000 gene ontologies that describe biological knowledge. GOATOOLS, a Python-based library, makes it more efficient to stay current with the latest ontologies and annotations, perform gene ontology enrichment analyses to determine over- and under-represented terms, and organize results for greater clarity and easier interpretation using a novel GOATOOLS GO grouping method. We performed functional analyses on both stochastic simulation data and real data from a published RNA-seq study to compare the enrichment results from GOATOOLS to two other popular tools: DAVID and GOstats. GOATOOLS is freely available through GitHub: https://github.com/tanghaibao/goatools .
  PMID: 30022098
  Diabetes.: co-auth.: group Thorens
  Hamilton A1, Zhang Q1, Salehi A2, Willems M1, Knudsen JG1, Ringgaard AK3,4, Chapman CE1, Gonzalez-Alvarez A1, Surdo NC5, Zaccolo M5, Basco D6, Johnson PRV1,7, Ramracheya R1, Rutter GA8, Galione A9, Rorsman P10,2,7, Tarasov AI10,7.
  Adrenaline is a powerful stimulus of glucagon secretion. It acts by activation of β-adrenergic receptors, but the downstream mechanisms have only been partially elucidated. Here, we have examined the effects of adrenaline in mouse and human α-cells by a combination of electrophysiology, imaging of Ca2+ and PKA activity, and hormone release measurements. We found that stimulation of glucagon secretion correlated with a PKA- and EPAC2-dependent (inhibited by PKI and ESI-05, respectively) elevation of [Ca2+]i in α-cells, which occurred without stimulation of electrical activity and persisted in the absence of extracellular Ca2+ but was sensitive to ryanodine, bafilomycin, and thapsigargin. Adrenaline also increased [Ca2+]i in α-cells in human islets. Genetic or pharmacological inhibition of the Tpc2 channel (that mediates Ca2+ release from acidic intracellular stores) abolished the stimulatory effect of adrenaline on glucagon secretion and reduced the elevation of [Ca2+]i Furthermore, in Tpc2-deficient islets, ryanodine exerted no additive inhibitory effect. These data suggest that β-adrenergic stimulation of glucagon secretion is controlled by a hierarchy of [Ca2+]i signaling in the α-cell that is initiated by cAMP-induced Tpc2-dependent Ca2+ release from the acidic stores and further amplified by Ca2+-induced Ca2+ release from the sarco/endoplasmic reticulum.
  PMID: 29563152
  Diabetologia.: co-auth.: B. Thorens
  Diabetologia. 2018 May 12. doi: 10.1007/s00125-018-4629-8. [Epub ahead of print]
  Bellini L1, Campana M1, Rouch C1, Chacinska M2,3, Bugliani M4, Meneyrol K1, Hainault I5, Lenoir V6,7,8, Denom J1, Véret J1, Kassis N1, Thorens B9, Ibberson M10, Marchetti P4, Blachnio-Zabielska A2,3, Cruciani-Guglielmacci C1, Prip-Buus C6,7,8, Magnan C1, Le Stunff H11,12.
  AMPK; Apoptosis; Ceramide; DHA; ELOVL2; Glucolipotoxicity; Mitochondrial β-oxidation; Pancreatic beta cells; Type 2 diabetes