A single fixation protocol for proteome-wide immunofluorescence localization studies

Immunofluorescence microscopy is a valuable tool for analyzing protein expression and localization at a subcellular level thus providing information regarding protein function, interaction partners and its role in cellular processes. When performing sample fixation, parameters such as difference in accessibility of proteins present in various cellular compartments as well as the chemical composition of the protein to be studied, needs to be taken into account. However, in systematic and proteome-wide efforts, a need exists for standard fixation protocol(s) that works well for the majority of all proteins independent of subcellular localization. Here, we report on a study with the goal to find a standardized protocol based on the analysis of 18 human proteins localized in 11 different organelles and subcellular structures. Six fixation protocols were tested based on either dehydration by alcohols (methanol, ethanol or iso-propanol) or cross-linking by paraformaldehyde followed by detergent permeabilization (Triton X-100 or saponin) in three human cell lines. Our results show that cross-linking is essential for proteome-wide localization studies and that cross-linking using paraformaldehyde followed by Triton X-100 permeabilization successfully can be used as a single fixation protocol for systematic studies.     

Prediction of partial membrane protein topologies using a consensus approach

We have developed a method to reliably identify partial membrane protein topologies using the consensus of five topology prediction methods. When evaluated on a test set of experimentally characterized proteins, we find that approximately 90% of the partial consensus topologies are correctly predicted in membrane proteins from prokaryotic as well as eukaryotic organisms. Whole-genome analysis reveals that a reliable partial consensus topology can be predicted for approximately 70% of all membrane proteins in a typical bacterial genome and for approximately 55% of all membrane proteins in a typical eukaryotic genome. The average fraction of sequence length covered by a partial consensus topology is 44% for the prokaryotic proteins and 17% for the eukaryotic proteins in our test set, and similar numbers are found when the algorithm is applied to whole genomes. Reliably predicted partial topologies may simplify experimental determinations of membrane protein topology.     

Caspase-1-driven neutrophil pyroptosis and its role in host susceptibility to Pseudomonas aeruginosa

Multiple regulated neutrophil cell death programs contribute to host defense against infections. However, despite expressing all necessary inflammasome components, neutrophils are thought to be generally defective in Caspase-1-dependent pyroptosis. By screening different bacterial species, we found that several Pseudomonas aeruginosa (P. aeruginosa) strains trigger Caspase-1-dependent pyroptosis in human and murine neutrophils. Notably, deletion of Exotoxins U or S in P. aeruginosa enhanced neutrophil death to Caspase-1-dependent pyroptosis, suggesting that these exotoxins interfere with this pathway. Mechanistically, P. aeruginosa Flagellin activates the NLRC4 inflammasome, which supports Caspase-1-driven interleukin (IL)-1β secretion and Gasdermin D (GSDMD)-dependent neutrophil pyroptosis. Furthermore, P. aeruginosa-induced GSDMD activation triggers Calcium-dependent and Peptidyl Arginine Deaminase-4-driven histone citrullination and translocation of neutrophil DNA into the cell cytosol without inducing extracellular Neutrophil Extracellular Traps. Finally, we show that neutrophil Caspase-1 contributes to IL-1β production and susceptibility to pyroptosis-inducing P. aeruginosa strains in vivo. Overall, we demonstrate that neutrophils are not universally resistant for Caspase-1-dependent pyroptosis.     

A small skull from Flores dated to the 20th century

A human skull with mandible from the Ngada District on the island of Flores, Indonesia, is described in order to contribute to the knowledge of variation in cranial architecture, which is important in interpretations of evolutionary cerebralisation. The skull was excavated in 1924 and sent to the National Museum in Copenhagen. The “Copenhagen Flores” (CF) male skull is radiocarbon-dated and of modern age. The cranium is small, but larger than e.g. Liang Bua skull (LB1) in every measurement. The (CT-scan based) cranial capacity of 1258 ml is normal for modern humans, but somewhat lower than values from the middle or upper Palaeolithics. The metric cranial data analysed in FORDISC, characterize the skull as a male Vietnamese rather than a Chinese or White individual. Tooth morphology shows the sundadont pattern and tooth size corresponds to that of teeth from Bali, Java and Malayan Orang Asli. Remarkable are the marked asymmetries in the dentition with rotation of an upper premolar and congenital absence of a third molar. In these respects the CF skull is similar to dentitions belonging to the pygmoid villagers of Rampasasa, a village not far from the Liang Bua cave, and to LB1.     

Temporal and spatial variation in coastal macrobenthic community structure,hanö bay (southern Baltic)

Quantitative (0.1-m²) samples of benthic macrofauna were taken at three depths (5, 10, 17 m) off the eastern coast of Scania, southern Baltic, in the period April 1974 to August 1978. Altogether 20 sampling cruises were made. Spatial and temporal species composition, abundance and biomass were compared. The number of species increased significantly with increasing depth. Zonation of the species was due to their zoogeographical origin and capacity to withstand exposure. Abundance was highest at 5 m depth whereas biomass increased with depth due to the dominance of large bivalves. Variation in abundance within years was large at all three depths and connected with reproductive recruitment for all species except Bathyporeia pilosa Lindström which migrated towards the shore in summer.     

Cyclin D1 and cyclin D3 show divergent responses to distinct mitogenic stimulation

D‐type cyclins predominantly regulate progression through the cell cycle by their interactions with cyclin‐dependent kinases (cdks). Here, we show that stimulating mitogenesis of Swiss 3T3 cells with phorbol esters or forskolin can induce divergent responses in the expression levels, localization and activation state of cyclin D1 and cyclin D3. Phorbol ester‐mediated protein kinase C stimulation induces S phase entry which is dependent on MAPK activation and increases the levels and activation of cyclin D1, whereas forskolin‐mediated cAMP‐dependent protein kinase A stimulation induces mitogenesis that is independent of MAPK, but dependent upon mTor and specifically increases the level and activation of cyclin D3. These findings uncover additional levels of complexity in the regulation of the cell cycle at the level of the D‐type cyclins and thus may have important therapeutic implications in cancers where specific D‐cyclins are overexpressed. J. Cell. Physiol. 225: 638–645, 2010. © 2010 Wiley‐Liss, Inc.     

Rap1 Can Bypass the FAK-Src-Paxillin Cascade to Induce Cell Spreading and Focal Adhesion Formation

We developed new image analysis tools to analyse quantitatively the extracellular-matrix-dependent cell spreading process imaged by live-cell epifluorescence microscopy. Using these tools, we investigated cell spreading induced by activation of the small GTPase, Rap1. After replating and initial adhesion, unstimulated cells exhibited extensive protrusion and retraction as their spread area increased, and displayed an angular shape that was remodelled over time. In contrast, activation of endogenous Rap1, via 007-mediated stimulation of Epac1, induced protrusion along the entire cell periphery, resulting in a rounder spread surface, an accelerated spreading rate and an increased spread area compared to control cells. Whereas basal, anisotropic, spreading was completely dependent on Src activity, Rap1-induced spreading was refractory to Src inhibition. Under Src inhibited conditions, the characteristic Src-induced tyrosine phosphorylations of FAK and paxillin did not occur, but Rap1 could induce the formation of actomyosin-connected adhesions, which contained vinculin at levels comparable to that found in unperturbed focal adhesions. From these results, we conclude that Rap1 can induce cell adhesion and stimulate an accelerated rate of cell spreading through mechanisms that bypass the canonical FAK-Src-Paxillin signalling cascade.     

Uncovering Atomic‐Scale Stability and Reactivity in Engineered Zinc Oxide Electrocatalysts for Controllable Syngas Production

In this study, scalable, flame spray synthesis is utilized to develop defective ZnO nanomaterials for the concurrent generation of H₂ and CO during electrochemical CO₂ reduction reactions (CO₂RR). The designed ZnO achieves an H₂/CO ratio of ≈1 with a large current density (j) of 40 mA cm^?2 during long‐term continuous reaction at a cell voltage of 2.6 V. Through in situ atomic pair distribution function analysis, the remarkable stability of these ZnO structures is explored, addressing the knowledge gap in understanding the dynamics of oxide catalysts during CO₂RR. Through optimization of synthesis conditions, ZnO facets are modulated which are shown to affect reaction selectivity, in agreement with theoretical calculations. These findings and insights on synthetic manipulation of active sites in defective metal‐oxides can be used as guidelines to develop active catalysts for syngas production for renewable power‐to‐X to generate a range of fuels and chemicals.     

Forecasting intensifying disturbance effects on coral reefs

Anticipating future changes of an ecosystem's dynamics requires knowledge of how its key communities respond to current environmental regimes. The Great Barrier Reef (GBR) is under threat, with rapid changes of its reef‐building hard coral (HC) community structure already evident across broad spatial scales. While several underlying relationships between HC and multiple disturbances have been documented, responses of other benthic communities to disturbances are not well understood. Here we used statistical modelling to explore the effects of broad‐scale climate‐related disturbances on benthic communities to predict their structure under scenarios of increasing disturbance frequency. We parameterized a multivariate model using the composition of benthic communities estimated by 145,000 observations from the northern GBR between 2012 and 2017. During this time, surveyed reefs were variously impacted by two tropical cyclones and two heat stress events that resulted in extensive HC mortality. This unprecedented sequence of disturbances was used to estimate the effects of discrete versus interacting disturbances on the compositional structure of HC, soft corals (SC) and algae. Discrete disturbances increased the prevalence of algae relative to HC while the interaction between cyclones and heat stress was the main driver of the increase in SC relative to algae and HC. Predictions from disturbance scenarios included relative increases in algae versus SC that varied by the frequency and types of disturbance interactions. However, high uncertainty of compositional changes in the presence of several disturbances shows that responses of algae and SC to the decline in HC needs further research. Better understanding of the effects of multiple disturbances on benthic communities as a whole is essential for predicting the future status of coral reefs and managing them in the light of new environmental regimes. The approach we develop here opens new opportunities for reaching this goal.