Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

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Fiji: an open-source platform for biological-image analysis

Forward genetic screens in model organisms have provided important insights into numerous aspects of development, physiology and pathology. With the availability of complete genome sequences and the introduction of RNA-mediated gene interference (RNAi), systematic reverse genetic screens are now also possible. Until now, such genome-wide RNAi screens have mostly been restricted to cultured cells and ubiquitous gene inactivation in Caenorhabditis elegans. This powerful approach has not yet been applied in a tissue-specific manner. Here we report the generation and validation of a genome-wide library of Drosophila melanogaster RNAi transgenes, enabling the conditional inactivation of gene function in specific tissues of the intact organism. Our RNAi transgenes consist of short gene fragments cloned as inverted repeats and expressed using the binary GAL4/UAS system. We generated 22,270 transgenic lines, covering 88% of the predicted protein-coding genes in the Drosophila genome. Molecular and phenotypic assays indicate that the majority of these transgenes are functional. Our transgenic RNAi library thus opens up the prospect of systematically analysing gene functions in any tissue and at any stage of the Drosophila lifespan.

/pdf/a-genome-wide-transgenic-rnai-library-for-conditional-gene-20svjywsa1.pdf

A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila

SUMMARY The mitogen-activated protein kinases (MAPKs) regulate diverse cellular programs by relaying extracellular signals to intracellular responses. In mammals, there are more than a dozen MAPK enzymes that coordinately regulate cell proliferation, differentiation, motility, and survival. The best known are the conventional MAPKs, which include the extracellular signal-regulated kinases 1 and 2 (ERK1/2), c-Jun amino-terminal kinases 1 to 3 (JNK1 to -3), p38 (α, β, γ, and δ), and ERK5 families. There are additional, atypical MAPK enzymes, including ERK3/4, ERK7/8, and Nemo-like kinase (NLK), which have distinct regulation and functions. Together, the MAPKs regulate a large number of substrates, including members of a family of protein Ser/Thr kinases termed MAPK-activated protein kinases (MAPKAPKs). The MAPKAPKs are related enzymes that respond to extracellular stimulation through direct MAPK-dependent activation loop phosphorylation and kinase activation. There are five MAPKAPK subfamilies: the p90 ribosomal S6 kinase (RSK), the mitogen- and stress-activated kinase (MSK), the MAPK-interacting kinase (MNK), the MAPK-activated protein kinase 2/3 (MK2/3), and MK5 (also known as p38-regulated/activated protein kinase [PRAK]). These enzymes have diverse biological functions, including regulation of nucleosome and gene expression, mRNA stability and translation, and cell proliferation and survival. Here we review the mechanisms of MAPKAPK activation by the different MAPKs and discuss their physiological roles based on established substrates and recent discoveries.

Activation and Function of the MAPKs and Their Substrates, the MAPK-Activated Protein Kinases

https://hal-pasteur.archives-ouvertes.fr/pasteur-01799353/document

TrackMate: An open and extensible platform for single-particle tracking.

Helicobacter pylori infection is associated with a variety of clinical outcomes including gastric cancer and duodenal ulcer disease. The reasons for this variation are not clear, but the gastric physiological response is influenced by the severity and anatomical distribution of gastritis induced by H. pylori. Thus, individuals with gastritis predominantly localized to the antrum retain normal (or even high) acid secretion, whereas individuals with extensive corpus gastritis develop hypochlorhydria and gastric atrophy, which are presumptive precursors of gastric cancer. Here we report that interleukin-1 gene cluster polymorphisms suspected of enhancing production of interleukin-1-beta are associated with an increased risk of both hypochlorhydria induced by H. pylori and gastric cancer. Two of these polymorphism are in near-complete linkage disequilibrium and one is a TATA-box polymorphism that markedly affects DNA-protein interactions in vitro. The association with disease may be explained by the biological properties of interleukin-1-beta, which is an important pro-inflammatory cytokine and a powerful inhibitor of gastric acid secretion. Host genetic factors that affect interleukin-1-beta may determine why some individuals infected with H. pylori develop gastric cancer while others do not.

/pdf/interleukin-1-polymorphisms-associated-with-increased-risk-42608maro7.pdf

Interleukin-1 polymorphisms associated with increased risk of gastric cancer

The world is permanently changing. Laboratory experiments on learning and memory normally minimize this feature of reality, keeping all conditions except the conditioned and unconditioned stimuli as constant as possible1. In the real world, however, animals need to extract from the universe of sensory signals the actual predictors of salient events by separating them from non-predictive stimuli (context2). In principle, this can be achieved ifonly those sensory inputs that resemble the reinforcer in theirtemporal structure are taken as predictors. Here we study visual learning in the fly Drosophila melanogaster, using a flight simulator3,4, and show that memory retrieval is, indeed, partially context-independent. Moreover, we show that the mushroom bodies, which are required for olfactory5,6,7 but not visual or tactile learning8, effectively support context generalization. In visual learning in Drosophila, it appears that a facilitating effect of context cues for memory retrieval is the default state, whereas making recall context-independent requires additional processing.

Context generalization in Drosophila visual learning requires the mushroom bodies

We propose that inDrosophila melanogaster the optomotor response to both horizontal and vertical movement is mediated predominantly by the 6 large retinula cells (R1–6) in each facet of the compound eye. Evidence is presented which indicates that this may also be true for most of the other visual responses which at present can be quantitatively studied. These responses include visually controlled landing, pattern-induced orientation of flying and walking animals, the abnormal jump reflex of the mutant Hk1 (Kaplan, 1976) and probably also phototaxis. The only function for which the small retinula cells R7 and/or R8 seem to be required so far is spectral wavelength discrimination in phototaxis at high light intensity. Our hypothesis is based on studies of the receptor deficient mutantssevenless, outer rhabdomeres absent andreceptor degeneration B as well as on results of bleaching experiments by which the retinula cells R1–6 of the eye color mutantwhite can be reversibly blocked. Visual performance of wild typeDrosophila in the optomotor response reflects receptor properties (visual acuity, spectral sensitivity and polarization sensitivity) expected for the R1–6 receptor subsystem. The notion of a ‘high sensitivity’ and a ‘high acuity’ state which was proposed earlier on the basis of experiments on various visual mutants is in agreement with the present results but their interpretation as reflecting properties of different receptor subsystems must be abandoned. Experimental data on wild type also suggest the existence of such an adaptational mechanism; this, however, remains to be demonstrated more conclusively.

The rôle of retinula cell types in visual behavior of Drosophila melanogaster

Octopamine in male aggression of Drosophila

Dissection of the peripheral motion channel in the visual system of Drosophila melanogaster.

Adult fruit flies and Drosophila larvae have very different bodies and behaviour patterns. The question therefore arises: how much reorganization does the brain undergo during pupation? Some apparent shape changes have been documented, for example, the growth of the optic lobes and the separation of the prothoracic and suboesophageal ganglia1,2. In the central brain, the issue is less clear. Most neurone cell bodies persist through metamorphosis3, and the general shape of certain neuropil regions is conserved. However an identified motoneurone in another holometabolous insect (Manduca) has been shown to change its dendritic arborization patterns during pupation4. Here we report that the mushroom body, a major neuropil area in the insect brain, is extensively reorganized during pupation (that is, many of the intrinsic fibres are broken down and made anew). This reorganization is cryptic—the overall morphology of the mushroom body is apparently constant throughout pupation. We have now studied this reorganization by examining two mutations (mbd, mud) which cause derangement of this structure during metamorphosis, and we report that this reorganization is one of the most extensive yet found in insect metamorphosis.

Martin Heisenberg

Papers

Context generalization in Drosophila visual learning requires the mushroom bodies

The rôle of retinula cell types in visual behavior of Drosophila melanogaster

Octopamine in male aggression of Drosophila

Dissection of the peripheral motion channel in the visual system of Drosophila melanogaster.

Neural reorganization during metamorphosis of the corpora pedunculata in Drosophila melanogaster