Role of Adaptor TrfA and ClpPC in Controlling Levels of SsrA-Tagged Proteins and Antitoxins in Staphylococcus aureus

Staphylococcus aureus responds to changing extracellular environments in part by adjusting its proteome through alterations of transcriptional priorities and selective degradation of the preexisting pool of proteins. In Bacillus subtilis, the proteolytic adaptor protein MecA has been shown to play a role in assisting with the proteolytic degradation of proteins involved in competence and the oxidative stress response. However, the targets of TrfA, the MecA homolog in S. aureus, have not been well characterized. In this work, we investigated how TrfA assists chaperones and proteases to regulate the proteolysis of several classes of proteins in S. aureus. By fusing the last 3 amino acids of the SsrA degradation tag to Venus, a rapidly folding yellow fluorescent protein, we obtained both fluorescence-based and Western blot assay-based evidence that TrfA and ClpCP are the adaptor and protease, respectively, responsible for the degradation of the SsrA-tagged protein in S. aureus. Notably, the impact of TrfA on degradation was most prominent during late log phase and early stationary phase, due in part to a combination of transcriptional regulation and proteolytic degradation of TrfA by ClpCP. We also characterized the temporal transcriptional regulation governing TrfA activity, wherein Spx, a redox-sensitive transcriptional regulator degraded by ClpXP, activates trfA transcription while repressing its own promoter. Finally, the scope of TrfA-mediated proteolysis was expanded by identifying TrfA as the adaptor that works with ClpCP to degrade antitoxins in S. aureus. Together, these results indicate that the adaptor TrfA adds temporal nuance to protein degradation by ClpCP in S. aureus

Photoperiodism and overwintering in boreal and sub-Arctic Calanus finmarchicus populations

The copepod Calanus finmarchicus, a key species in the North Atlantic, generally spends the non-productive season by descending into deep waters and entering diapause, a physiological state characterized by reduced metabolism and arrested development. In the open ocean, overwintering depths are below 600 m, where temperature and light conditions are favourable to initiate diapause. However, C. finmarchicus has also been reported diapausing in areas with shallow water depth such as fjords, coastal waters and shelf seas. In these environments, the temperature and light conditions are different, and it has been hypothesized that under such conditions C. finmarchicus may remain active throughout winter. Here, we investigated changes in the swimming activity of C. finmarchicus from shallow fjords in the eastern North Atlantic during overwintering in response to ambient photoperiod. We conducted monthly experiments with populations from 2 fjords from different latitudes (sub-Arctic Ramfjord, 69°N and boreal Loch Etive, 56°N), measuring the locomotor activity of individual C. finmarchicus stage CVs exposed to a natural light:dark cycle. At both locations, peaks in activity in response to the light cycle were observed to shift from nocturnal during the early overwintering phase to diurnal during mid and late overwintering phase, with a minimal intensity observed during the mid-overwintering phase. In Ramfjord, activity and rhythmicity were generally lower than in Loch Etive. We conclude that C. finmarchicus remains active throughout its overwintering period when in shallow (<200 m) locations but down-regulates its locomotor activity during the main overwintering phase, which we describe as a winter resting state as distinct from classical diapause

Nicotine in the Endoplasmic Reticulum

Nicotine activates plasma membrane (PM) nicotinic receptors (nAChRs), but also permeates into the endoplasmic reticulum (ER) and cis-Golgi, and there binds to nascent nAChRs. Other psychiatric and abused drugs may also enter the ER and bind their classical targets. Further progress requires direct proof, quantification, and time resolution of these processes in live cells and in the brain of animals. Therefore, we are developing genetically encoded fluorescent biosensors to study the subcellular pharmacokinetics of neural drugs

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Powering sub-Saharan Africa’s urban revolution: An energy transitions approach

This paper develops a geographic understanding of urban energy transitions in subSaharan African towns and cities. In doing so this paper seeks to critically reflect on the value and limits of urban transitions analysis as a framework for understanding energy networks beyond the largely integrated systems across the Global North. We explore how these potentials and deficits can be addressed by examining promising developments across a series of debates in urban studies that can help sensitise this approach to energyscapes in the African context. By reviewing urban transi- tions analysis through these debates the paper offers four important contributions to expand existing ways of understanding energy transition. These include the particular urbanisation dynamics of African towns ands cities, the need to locate the urban across energy regimes, the agencies of various intermediaries and urban actors and the contested politics inherent in the governing of energy networks. In the conclusion we reflect on the specific directions that have emerged from the paper in relation to our contributions, offering a geographically informed framework that allows us to better examine the challenges and specificities of transition across these rapidly growing urban regions

Volume-transmitted GABA waves pace epileptiform rhythms in the hippocampal network

Mechanisms that entrain and pace rhythmic epileptiform discharges remain debated. Traditionally, the quest to understand them has focused on interneuronal networks driven by synaptic GABAergic connections. However, synchronized interneuronal discharges could also trigger the transient elevations of extracellular GABA across the tissue volume, thus raising tonic conductance (Gtonic) of synaptic and extrasynaptic GABA receptors in multiple cells. Here, we monitor extracellular GABA in hippocampal slices using patch-clamp GABA "sniffer" and a novel optical GABA sensor, showing that periodic epileptiform discharges are preceded by transient, region-wide waves of extracellular GABA. Neural network simulations that incorporate volume-transmitted GABA signals point to a cycle of GABA-driven network inhibition and disinhibition underpinning this relationship. We test and validate this hypothesis using simultaneous patch-clamp recordings from multiple neurons and selective optogenetic stimulation of fast-spiking interneurons. Critically, reducing GABA uptake in order to decelerate extracellular GABA fluctuations-without affecting synaptic GABAergic transmission or resting GABA levels-slows down rhythmic activity. Our findings thus unveil a key role of extrasynaptic, volume-transmitted GABA in pacing regenerative rhythmic activity in brain networks

Controlled environments: an urban research agenda on microclimatic enclosure

Controlled environments create specialist forms of microclimatic enclosure that are explicitly designed to transcend the emerging limitations and increasing turbulence in existing modes of urban climatic conditions. Across different urban contexts, anthropogenic change is creating urban conditions that are too hot, cold, humid, wet, windy etc. to support the continued and reliable environments that are suitable for the reproduction of food, ecologies and human life. In response, there are emerging forms of experimentation with new logics of microclimatic governance that seek to enclose environments within membranes and develop artificially created internal ecologies that are precisely customized to meet the needs of the plant, animal or human occupants of these new forms of enclosure. While recognizing that enclosure has a long history in urbanism, design and architecture, we ask in this paper if a new logic of microclimatic governance is emerging in specific response to the ecological changes of the Anthropocene. The paper sets out a research agenda to investigate whether the ability of cities, states and corporates to design and construct internalized environments is now a strategic capacity that is critical to developing the knowledge, practices and technologies to reconfigure new forms of urban climatic governance that address the problems of climate change and ensure urban reproduction under conditions of turbulence

A Model for Type 2 Coronal Line Forest (CLiF) AGNs

We present a model for the classification of Coronal Line Forest Active Galactic Nuclei (CLiF AGNs). CLiF AGNs are of special interest due to their remarkably large number of emission lines, especially forbidden highionization lines (FHILs). Rose et al. suggest that their emission is dominated by reflection from the inner wall of the obscuring region rather than direct emission from the accretion disk. This makes CLiF AGNs laboratories to test AGN-torus models. Modeling an AGN as an accreting supermassive black hole surrounded by a cylinder of dust and gas, we show a relationship between the viewing angle and the revealed area of the inner wall. From the revealed area, we can determine the amount of FHIL emission at various angles. We calculate the strength of [Fe VII]λ6087 emission for a number of intermediate angles (30°, 40°, and 50°) and compare the results with the luminosity of the observed emission line from six known CLiF AGNs. We find that there is good agreement between our model and the observational results. The model also enables us to determine the relationship between the type 2:type 1 AGN fraction vs the ratio of torus height to radius, h/r

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs