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

SUMMARY In stationary flight Drosophila rnelunogusfer produces yaw torque in response to visual movement stimuli. The residual optomotor yaw torque response of the mutant optomofor-blindH3’ (omb), which lacks the horizontal (HS) and vertical (VS) giant fibers in the lobula plate, differs from that of wild-type in several aspects: it is restricted to the frontal visual field, it is only elicited by front-to-back motion and appears to be mediated by a different set of elementary movement detectors (EMDs). Using a single black stripe as motion stimulus the torque response is, even in wild-type flies, dominated by the frontal visual field and by front-to-back motion. We thus propose that Drosophila’s optomotor yaw control is organized as two partially parallel subunits. The component still displayed by omb is called ‘‘object response”; the component missing in the mutant (which is presumably mediated by the giant HS-cells in the wild-type) is called “large field response”. Several properties of the object response are described.

Genetic Dissection of Optomotor Behavior in Droso- phila melanogaster Studies on Wild-Type and the

Behaviour of humans and most animals can be free. Behaviour is free if the subject does of her/his own accord what must be done. Action selection is the main task of a brain. The search for the right behaviour is demanding because it requires assessing the possible consequences of the available behavioural options. Freedom is reduced externally, if fewer adaptive behavioural options are available or internally, if the search process in the brain is impaired. Most animal societies enforce cooperation at the expense of individual freedom. In contrast, human societies can base cooperation on shared intentions. In this way the individuals can cooperate without sacrificing behavioural freedom.

The Origin of Freedom in Animal Behaviour

The Flybrain Project

In Drosophila melanogaster, adult or larval rearing conditions influence brain structure. In particular, larval density affects the number of fibers forming the mushroom bodies, a neuropil structure involved in olfactory learning. The mushroom bodies receive chemosensory inputs from the antennal lobes at the level of the calyx. In this study we report that larval density affects calyx volume measured shortly after eclosion from the pupal case. We observe that in the memory mutant amnesiac this form of experience-dependent structural plasticity is missing, whereas it is not affected in the learning mutant rutabaga and in the memory mutant radish. Independent of the plasticity effect, the calyces are on average slightly bigger than wild type in amnesiac and smaller in rutabaga flies.

Abnormal mushroom body plasticity in the Drosophila memory mutant amnesiac.

Starvation causes a motivational state that facilitates diverse behaviors such as feeding, walking, and search. Starved Drosophila can form odor/feeding-time associations but the role of starvation in encoding of "time" is poorly understood. Here we show that the extent of starvation is correlated with the fly's ability to establish odor/feeding-time memories. Prolonged starvation promotes odor/feeding-time associations after just a single cycle of reciprocal training. We also show that starvation is required for acquisition but is dispensable for retrieval of odor/feeding-time memory. Finally, even with extended starvation, a functional circadian oscillator is indispensable for establishing odor/feeding-time memories.

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Martin Heisenberg

Papers

Genetic Dissection of Optomotor Behavior in Droso- phila melanogaster Studies on Wild-Type and the

The Origin of Freedom in Animal Behaviour

The Flybrain Project

Abnormal mushroom body plasticity in the Drosophila memory mutant amnesiac.

Starvation promotes odor/feeding-time associations in flies.