Methane Clumped Isotopes: Progress and Potential for a New Isotopic Tracer

The isotopic composition of methane is of longstanding geochemical interest, with important implications for understanding petroleum systems, atmospheric greenhouse gas concentrations, the global carbon cycle, and life in extreme environments. Recent analytical developments focusing on multiply substituted isotopologues (‘clumped isotopes’) are opening a valuable new window into methane geochemistry. When methane forms in internal isotopic equilibrium, clumped isotopes can provide a direct record of formation temperature, making this property particularly valuable for identifying different methane origins. However, it has also become clear that in certain settings methane clumped isotope measurements record kinetic rather than equilibrium isotope effects. Here we present a substantially expanded dataset of methane clumped isotope analyses, and provide a synthesis of the current interpretive framework for this parameter. In general, clumped isotope measurements indicate plausible formation temperatures for abiotic, thermogenic, and microbial methane in many geological environments, which is encouraging for the further development of this measurement as a geothermometer, and as a tracer for the source of natural gas reservoirs and emissions. We also highlight, however, instances where clumped isotope derived temperatures are higher than expected, and discuss possible factors that could distort equilibrium formation temperature signals. In microbial methane from freshwater ecosystems, in particular, clumped isotope values appear to be controlled by kinetic effects, and may ultimately be useful to study methanogen metabolism

TCR and CD28 Concomitant Stimulation Elicits a Distinctive Calcium Response in Naive T Cells

T cell activation is initiated upon ligand engagement of the T cell receptor (TCR) and costimulatory receptors. The CD28 molecule acts as a major costimulatory receptor in promoting full activation of naive T cells. However, despite extensive studies, why naive T cell activation requires concurrent stimulation of both the TCR and costimulatory receptors remains poorly understood. Here, we explore this issue by analyzing calcium response as a key early signaling event to elicit T cell activation. Experiments using mouse naive CD4+ T cells showed that engagement of the TCR or CD28 with the respective cognate ligand was able to trigger a rise in fluctuating calcium mobilization levels, as shown by the frequency and average response magnitude of the reacting cells compared with basal levels occurred in unstimulated cells. The engagement of both TCR and CD28 enabled a further increase of these two metrics. However, such increases did not sufficiently explain the importance of the CD28 pathways to the functionally relevant calcium responses in T cell activation. Through the autocorrelation analysis of calcium time series data, we found that combined but not separate TCR and CD28 stimulation significantly prolonged the average decay time (τ) of the calcium signal amplitudes determined with the autocorrelation function, compared with its value in unstimulated cells. This increasement of decay time (τ) uniquely characterizes the fluctuating calcium response triggered by concurrent stimulation of TCR and CD28, as it could not be achieved with either stronger TCR stimuli or by co-engaging both TCR and LFA-1, and likely represents an important feature of competent early signaling to provoke efficient T cell activation. Our work has thus provided new insights into the interplay between the TCR and CD28 early signaling pathways critical to trigger naive T cell activation

First Investigation of the Microbiology of the Deepest Layer of Ocean Crust

We would like to thank Frederick (Rick) Colwell for input on molecular analyses in low biomass environments, Donna Blackman, Benoît Ildefonse, Adélie Delacour, and Gretchen Früh-Green for discussions regarding geological and geochemical aspects of this manuscript, and the Integrated Ocean Drilling Program Expeditions 304/305 Science Party. We would also like to thank Captain Alex Simpson and the entire crew of the JOIDES Resolution.Conceived and designed the experiments: OUM MRF SJG. Performed the experiments: OUM TN MR JDVN AM. Analyzed the data: OUM TN MR JDVN AM. Contributed reagents/materials/analysis tools: TN MR JZ MRF SJG. Wrote the paper: OUM.The gabbroic layer comprises the majority of ocean crust. Opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. During the Integrated Ocean Drilling Program Expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at Hole 1309D, located on the Atlantis Massif (30 °N, 42 °W). Microbial diversity in the rocks was analyzed by denaturing gradient gel electrophoresis and sequencing (Expedition 304), and terminal restriction fragment length polymorphism, cloning and sequencing, and functional gene microarray analysis (Expedition 305). The gabbroic microbial community was relatively depauperate, consisting of a low diversity of proteobacterial lineages closely related to Bacteria from hydrocarbon-dominated environments and to known hydrocarbon degraders, and there was little evidence of Archaea. Functional gene diversity in the gabbroic samples was analyzed with a microarray for metabolic genes (“GeoChip”), producing further evidence of genomic potential for hydrocarbon degradation - genes for aerobic methane and toluene oxidation. Genes coding for anaerobic respirations, such as nitrate reduction, sulfate reduction, and metal reduction, as well as genes for carbon fixation, nitrogen fixation, and ammonium-oxidation, were also present. Our results suggest that the gabbroic layer hosts a microbial community that can degrade hydrocarbons and fix carbon and nitrogen, and has the potential to employ a diversity of non-oxygen electron acceptors. This rare glimpse of the gabbroic ecosystem provides further support for the recent finding of hydrocarbons in deep ocean gabbro from Hole 1309D. It has been hypothesized that these hydrocarbons might originate abiotically from serpentinization reactions that are occurring deep in the Earth's crust, raising the possibility that the lithic microbial community reported here might utilize carbon sources produced independently of the surface biosphere.Yeshttp://www.plosone.org/static/editorial#pee

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)

A critical regulatory role for the cytoplasmic domain of CD28 in ligand binding in naive T cells

International audienc

Fas acts as a T cell co-stimulatory receptor both via a death domain-independent and dependent mechanism

T cell responses are regulated by co-stimulatory and inhibitory signalling pathways, driven by receptors and their ligands designated as immune checkpoints. These receptors belong either to the immunoglobulin superfamily or the tumour necrosis factor receptor (TNFR) superfamily. Despite their crucial role in enhancing T effector cell activity, the molecular mechanisms triggered by TNFR costimulatory receptors, particularly their integration into the T cell receptor (TCR) signalling network, remain incompletely characterized. The receptor Fas is classically recognized as the prototypical TNFR death receptor due to the presence of an intracellular death domain (DD). While best known for its ability to trigger cell death, Fas has also been involved in non-death functions, including T cell co-stimulation. Despite its key role in dictating T cell fate, only few studies have explored its involvement as a TCR costimulatory receptor and the underlying molecular mechanisms have not been solved. We show here that Fas constitutively concentrates in plasma membrane domains at the immune synapse where it can be activated by antigen-presenting cell (APC) membrane-anchored FasL. This proximity to the TCR signalling molecules allows Fas, in a DD-independent manner, to lower the TCR activation threshold thereby enhancing the number of activated cells. Additionally, Fas triggers a DD-dependent signaling cascade composed of FADD, caspase-8 and RIPK1, ultimately leading to TAK1 activation. TAK1 in turn initiates gene-activating signalling pathways essential for a complete Fas co-stimulatory response.Moreover, we identified the catalytic activity of caspase-8 as a tipping point in Fas signalling during TCR co-stimulation. Indeed, inhibiting caspase 8 not only prevents cell death but also promotes T cell costimulation by favoring RIPK1-dependent signalling. Altogether, our findings reveal a complex mechanism by which Fas integrates at multiple levels of the TCR spatial organization and signalling network, synergizing with TCR signalling to achieve full T cell activation

Concorso Internazionale di idee per la definizione del Piano di Interventi per il Recupero, la Riqualificazione e la Valorizzazione della città vecchia di Taranto

Taranto Azzurra. Attraverso una storia contraddistinta dal susseguirsi di ruoli diversi di volta in volta assunti o attribuiti, l’Isola si presenta oggi come “città vecchia”, gravemente depauperata dal punto di vista della popolazione e delle funzioni, sostanzialmente ridotta a “ponte” tra la Taranto moderna a sud est, la stazione e lo stabilimento dell’Ilva a nord ovest. L’interpretazione di quel che è stato e di quel che potrebbe essere suggerisce di ricomprendere questa pregevole e unica formazione urbana come parte integrante di Taranto, inclusa con un proprio specifico ruolo nelle dinamiche ordinarie della città e della sua area gravitazionale. “2022 l’Isola ritorna al centro” è modo sintetico per richiamare i cambiamenti relativi a economia, infrastrutture, società e ambiente: da quartiere monofunzionale a centro di sperimentazione creativa; da spazio congestionato di attraversamento a destinazione; da luogo in stato di abbandono a centro attrattivo e inclusivo; da unico accesso al mare a primo tassello di rigenerazione ambientale dei seni del Mar Piccolo. Riscoprire, Riunire, Riconfigurare, Rinnovare, Riabitare, Ripopolare sono le parole che riassumono le intenzioni della proposta Taranto azzurra. Un’offerta di spazi attraenti, adeguatamente infrastrutturati e salubri, la riorganizzazione dell’accessibilità, la riscoperta dei luoghi del risiedere e del lavorare per liberare nuove energie economiche creative, sono condizioni necessarie per fermare la deriva del decadimento; altra condizione è costituita dalla capacità di coinvolgere in questo “viaggio della rigenerazione” i Tarantini di oggi e di domani che dovranno trovare nell’operazione una risposta alle difficoltà attuali e una prospettiva convincente. L’invito all’esplorazione dell’isola attraverso installazioni e promozione di eventi artistici e culturali, tali da indurre l’allungamento della passeggiata degli abitanti locali e da richiamare visitatori curiosi, viene inteso come startup del processo

Concorso Internazionale di idee per la definizione del Piano di Interventi per il Recupero, la Riqualificazione e la Valorizzazione della città vecchia di Taranto

Taranto Azzurra. Attraverso una storia contraddistinta dal susseguirsi di ruoli diversi di volta in volta assunti o attribuiti, l’Isola si presenta oggi come “città vecchia”, gravemente depauperata dal punto di vista della popolazione e delle funzioni, sostanzialmente ridotta a “ponte” tra la Taranto moderna a sud est, la stazione e lo stabilimento dell’Ilva a nord ovest. L’interpretazione di quel che è stato e di quel che potrebbe essere suggerisce di ricomprendere questa pregevole e unica formazione urbana come parte integrante di Taranto, inclusa con un proprio specifico ruolo nelle dinamiche ordinarie della città e della sua area gravitazionale. “2022 l’Isola ritorna al centro” è modo sintetico per richiamare i cambiamenti relativi a economia, infrastrutture, società e ambiente: da quartiere monofunzionale a centro di sperimentazione creativa; da spazio congestionato di attraversamento a destinazione; da luogo in stato di abbandono a centro attrattivo e inclusivo; da unico accesso al mare a primo tassello di rigenerazione ambientale dei seni del Mar Piccolo. Riscoprire, Riunire, Riconfigurare, Rinnovare, Riabitare, Ripopolare sono le parole che riassumono le intenzioni della proposta Taranto azzurra. Un’offerta di spazi attraenti, adeguatamente infrastrutturati e salubri, la riorganizzazione dell’accessibilità, la riscoperta dei luoghi del risiedere e del lavorare per liberare nuove energie economiche creative, sono condizioni necessarie per fermare la deriva del decadimento; altra condizione è costituita dalla capacità di coinvolgere in questo “viaggio della rigenerazione” i Tarantini di oggi e di domani che dovranno trovare nell’operazione una risposta alle difficoltà attuali e una prospettiva convincente. L’invito all’esplorazione dell’isola attraverso installazioni e promozione di eventi artistici e culturali, tali da indurre l’allungamento della passeggiata degli abitanti locali e da richiamare visitatori curiosi, viene inteso come startup del processo