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Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset
(2018)
With the advent of neurogenetic methods, the neural basis of behavior is presently being analyzed in more and more detail. This is particularly true for visually driven behavior of Drosophila melanogaster where cell-specific driver lines exist that, depending on the combination with appropriate effector genes, allow for targeted recording, silencing and optogenetic stimulation of individual cell-types. Together with detailed connectomic data of large parts of the fly optic lobe, this has recently led to much progress in our understanding of the neural circuits underlying local motion detection. However, how such local information is combined by optic flow sensitive large-field neurons is still incompletely understood. Here, we aim to fill this gap by a dense reconstruction of lobula plate tangential cells of the fly lobula plate. These neurons collect input from many hundreds of local motion-sensing T4/T5 neurons and connect them to descending neurons or central brain areas. We confirm all basic features of HS and VS cells as published previously from light microscopy. In addition, we identified the dorsal and the ventral centrifugal horizontal, dCH and vCH cell, as well as three VSlike cells, including their distinct dendritic and axonal projection area.
Aims: Somatic mutations in haematopoietic stem cells can lead to the clonal expansion of mutated blood cells, known as clonal haematopoiesis (CH). Mutations in the most prevalent driver genes DNMT3A and TET2 with a variant allele frequency (VAF) ≥ 2% have been associated with atherosclerosis and chronic heart failure of ischemic origin (CHF). However, the effects of mutations in other driver genes for CH with low VAF (<2%) on CHF are still unknown.
Methods and results: Therefore, we analysed mononuclear bone marrow and blood cells from 399 CHF patients by deep error-corrected targeted sequencing of 56 genes and associated mutations with the long-term mortality in these patients (3.95 years median follow-up). We detected 1113 mutations with a VAF ≥ 0.5% in 347 of 399 patients, and only 13% had no detectable CH. Despite a high prevalence of mutations in the most frequently mutated genes DNMT3A (165 patients) and TET2 (107 patients), mutations in CBL, CEBPA, EZH2, GNB1, PHF6, SMC1A, and SRSF2 were associated with increased death compared with the average death rate of all patients. To avoid confounding effects, we excluded patients with DNMT3A-related, TET2-related, and other clonal haematopoiesis of indeterminate potential (CHIP)-related mutations with a VAF ≥ 2% for further analyses. Kaplan–Meier survival analyses revealed a significantly higher mortality in patients with mutations in either of the seven genes (53 patients), combined as the CH-risk gene set for CHF. Baseline patient characteristics showed no significant differences in any parameter including patient age, confounding diseases, severity of CHF, or blood cell parameters except for a reduced number of platelets in patients with mutations in the risk gene set in comparison with patients without. However, carrying a mutation in any of the risk genes remained significant after multivariate cox regression analysis (hazard ratio, 3.1; 95% confidence interval, 1.8–5.4; P < 0.001), whereas platelet numbers did not.
Conclusions: Somatic mutations with low VAF in a distinct set of genes, namely, in CBL, CEBPA, EZH2, GNB1, PHF6, SMC1A, and SRSF2, are significantly associated with mortality in CHF, independently of the most prevalent CHIP-mutations in DNMT3A and TET2. Mutations in these genes are prevalent in young CHF patients and comprise an independent risk factor for the outcome of CHF, potentially providing a novel tool for risk assessment in CHF.
Dendritic spines are considered a morphological proxy for excitatory synapses, rendering them a target of many different lines of research. Over recent years, it has become possible to image simultaneously large numbers of dendritic spines in 3D volumes of neural tissue. In contrast, currently no automated method for spine detection exists that comes close to the detection performance reached by human experts. However, exploiting such datasets requires new tools for the fully automated detection and analysis of large numbers of spines. Here, we developed an efficient analysis pipeline to detect large numbers of dendritic spines in volumetric fluorescence imaging data. The core of our pipeline is a deep convolutional neural network, which was pretrained on a general-purpose image library, and then optimized on the spine detection task. This transfer learning approach is data efficient while achieving a high detection precision. To train and validate the model we generated a labelled dataset using five human expert annotators to account for the variability in human spine detection. The pipeline enables fully automated dendritic spine detection and reaches a near human-level detection performance. Our method for spine detection is fast, accurate and robust, and thus well suited for large-scale datasets with thousands of spines. The code is easily applicable to new datasets, achieving high detection performance, even without any retraining or adjustment of model parameters.
Background: Serotonin plays a pivotal role in regulating and modulating physiological and behavioral processes in both vertebrates and invertebrates. In the honeybee (Apis mellifera), serotonin has been implicated in division of labor, visual processing, and learning processes. Here, we present the cloning, heterologous expression, and detailed functional and pharmacological characterization of two honeybee 5-HT2 receptors.
Methods: Honeybee 5-HT2 receptor cDNAs were amplified from brain cDNA. Recombinant cell lines were established constitutively expressing receptor variants. Pharmacological properties of the receptors were investigated by Ca2+ imaging experiments. Quantitative PCR was applied to explore the expression patterns of receptor mRNAs.
Results: The honeybee 5-HT2 receptor class consists of two subtypes, Am5-HT2α and Am5-HT2β. Each receptor gene also gives rise to alternatively spliced mRNAs that possibly code for truncated receptors. Only activation of the full-length receptors with serotonin caused an increase in the intracellular Ca2+ concentration. The effect was mimicked by the agonists 5-methoxytryptamine and 8-OH-DPAT at low micromolar concentrations. Receptor activities were blocked by established 5-HT receptor antagonists such as clozapine, methiothepin, or mianserin. High transcript numbers were detected in exocrine glands suggesting that 5-HT2 receptors participate in secretory processes in the honeybee.
Conclusions: This study marks the first molecular and pharmacological characterization of two 5-HT2 receptor subtypes in the same insect species. The results presented should facilitate further attempts to unravel central and peripheral effects of serotonin mediated by these receptors.
In the past decade, tissue-resident innate lymphoid cells (ILC) have become a central field of immunological research. ILC are a family of innate immune cells comprising cytotoxic Natural Killer (NK) cells and the non-cytotoxic helper like ILC1, ILC2 and ILC3. They mirror the functions and phenotypes of T cells, but do not require rearranged antigen-specific receptors for their rapid response to signals from injured or infected tissue. As potent cytokine producers being enriched in mucosal tissue, ILC play an essential role in tissue maintenance and regulating immunity to chronic inflammation and infection (Vivier et al., 2018). Although heterogeneity and plasticity of ILC complicates their classification, the pathophysiology of a broad variety of autoimmune and chronic inflammatory diseases have been associated with dysregulations in ILC subset distribution and functions (Dzopalic et al., 2019). This highlights their importance in human health and disease and accounts for the need for markers unambiguously describing the different ILC subtypes. This work introduces NKp65, a C-type lectin-like receptor (CTLR) encoded in the natural killer gene complex by the KLRF2 gene, as an exclusive marker for human ILC3. NKp65 expression especially discerns ILC3-like NK cell precursor from mature NK cells which express the NKp65-relative NKp80. Moreover, flow cytometric analysis of NKp65 expression aids in the demarcation of natural cytotoxicity receptor (NCR) expressing ILC3, from the closely related but functionally distinct RORt+ LTi cells and NCR- ILC3. This work further provides insights into NK cell development by in vitro differentiation studies in which NKp65 expressing cells are generated in presence of OP9 feeder cells and cytokines to support development. In such cultures, NKp65 expressing in vitro ILC (ivILC) acquire NKp80 expression in a Notch-dependent manner indicating their differentiation into mature NK cells. Acquisition of NK cell phenotypic markers is accompanied by NKp65 downregulation which leads to the mutually exclusive expression of NKp80 on NK cells and NKp65 on ILC3-like cells. Further insights are provided into the functional consequences of NKp65 engagement by its cognate high affinity ligand ‘keratinocyte-associated C-type lectin’ (KACL) which is selectively expressed on human keratinocytes (Bauer et al., 2015; Spreu et al., 2010). Expressed on ivILC, NKp65 mediates killing of KACL expressing target cells, suggesting that NKp65-KACL interaction promotes cellular cytotoxicity. In this context, the observed metalloproteinase dependent shedding of NKp65 might play a role in the termination of the cellular interaction. The findings on the regulation of NKp65 expression demonstrate the presence of a functional STAT5 response element in the KLRF2 promoter endowing a transcriptional control of NKp65 expression by IL-7 signaling. This provides an interesting link between the dependency of ILC3 on IL-7 signaling for their maintenance and the specific expression of NKp65 on these cells.
In summary, this study provides new insights into the physiologic expression of the CTLR NKp65 on human ILC3. The dependency of NKp65 surface expression on sustained STAT5 signaling provided by IL-7 underlines the connection of NKp65 expression and an ILC3 phenotype which might contribute to promote future research in discerning the interspersed pathways of ILC3 and NK cell development. The tissue and cell specific expression of NKp65 on ILC3 and its ligand KACL on keratinocytes of the human skin further suggests an important role of this genetically coupled receptor-ligand pair in tissue specific immunosurveillance.
Protein ubiquitination is a post-translational modification that typically involves the conjugation of ubiquitin to substrate proteins via a three-enzyme cascade and regulates a wide variety of cellular processes. Recent studies have revealed that SidE family of Legionella effectors such as SdeA catalyzes novel phosphoribosyl-linked ubiquitination (PR-ubiquitination) of serines in host substrate proteins utilizing NAD+, without the need of E2, E3. The catalytic core of SdeA comprises a mono-ADP-ribosyltransferase (mART) domain that functions to ADP-ribosylate ubiquitin, and a phosphodiesterase (PDE) domain that processes ADP-ribosylated ubiquitin and transfers the resulting phosphoribosylated ubiquitin to serines of substrates.
To date, extensive efforts have been made to study the function of SdeA and mechanism of SdeA mediated PR-ubiquitination, however, the cellular effects of this novel ubiquitination and phosphoribosylation of ubiquitin remained poorly understood. In our study, using biochemical and cell biological approaches, we explored the biological effect of phosphoribosylation of ubiquitin caused by SdeA in cells. We found that phosphoribosylated ubiquitin is not available for conventional ubiquitination, thereby phosphoribosylation of ubiquitin impairs numerous classical ubiquitination related cellular processes including mitophagy, TNF-α signaling and proteasomal degradation.
The precise temporal regulation of the functions of bacterial effectors during Legionella infection by other effectors with antagonizing activities has been well studied so far. Not surprisingly, PR-ubiquitination catalyzed by SidE family effecters is tightly controlled as well, it has been long known that effector SidJ counteracts the toxicity of SdeA to yeast cells. Interestingly, in an experiment for verifying the activity of SidJ, we found that Legionella lysate lacking SidJ was still able to remove ubiquitin from PR-ubiquitinated substrates. Using biochemical approach we identified DupA and DupB, two Legionella bacterial effectors that specifically reverse the novel serine PR-ubiquitination catalyzed by SdeA. We found that DupA and DupB possess a highly homologous PDE domain that removes ubiquitin from PR-ubiquitinated substrates by cleaving the phosphodiester bond between the phosphoribosylated-ubiquitin and serines of substrates. Catalytically deficient mutant DupA H67A strongly binds to PR-ubiquitinated proteins but not capable of cleaving PR-ubiquitin, using it as a trapping bait we identified over 180 substrates of PR-ubiquitination, including a number of ER and Golgi proteins.
In particular, we found that exogenously expressed SdeA localizes to the Golgi apparatus via its C-terminal region and disrupts the Golgi. We validated the identified potential substrates of SidE effectors and found that SdeA modifies Golgi tethering proteins GRASP55 and GRASP65. Using mass spectrometry analyses we identified four serine targets (S3, S408, S409, S449) of GRASP55 PR-ubiquitinated by SdeA in vitro. Ubiquitination of GRASP55 serine mutant in cells co-expressing SdeA or infected with Legionella was markedly decreased, compared with that of the wild-type GRASP55. In addition, with co-immunoprecipitation analyses we found that SdeA-catalyzed ubiquitination regulates the function of GRASP55. PR-ubiquitinated GRASP55 exhibited reduced self-interaction compared to unmodified GRASP55, expression of GRASP55 serine mutant in cells in part rescued Golgi damage caused by SdeA. Furthermore, our study reveals that Golgi structure disruption caused by SdeA does not result in the recruitment of Golgi membranes to the Legionella-containing vacuoles. Instead, it affects cellular secretory pathway including cytokine secretion in cells.
Taken all together, this work expands the understanding of this unconventional PR-ubiquitination catalyzed by Legionella effectors and sheds light on the functions of PR-ubiquitination by which Legionella regulates the Golgi function and secretion pathway during bacterial infection.
Proton-translocating NADH:ubiquinone oxidoreductase (complex I) is the largest and least understood enzyme of the respiratory chain. Complex I from bovine mitochondria consists of more than forty different polypeptides. Subunit PSST has been suggested to carry iron-sulfur center N-2 and has more recently been shown to be involved in inhibitor binding. Due to its pH-dependent midpoint potential, N-2 has been proposed to play a central role both in ubiquinone reduction and proton pumping. To obtain more insight into the functional role of PSST, we have analyzed site-directed mutants of conserved acidic residues in the PSST homologous subunit of the obligate aerobic yeast Yarrowia lipolytica. Mutations D136N and E140Q provided functional evidence that conserved acidic residues in PSST play a central role in the proton translocating mechanism of complex I and also in the interaction with the substrate ubiquinone. When Glu89, the residue that has been suggested to be the fourth ligand of iron-sulfur center N-2 was changed to glutamine, alanine, or cysteine, the EPR spectrum revealed an unchanged amount of this redox center but was shifted and broadened in the gzregion. This indicates that Glu89 is not a ligand of N-2. The results are discussedin the light of structural similarities to the homologous [NiFe] hydrogenases.