ALBERT

Description: We report a novel hybrid, molecular and elemental mass spectrometry (MS) setup for the absolute quantification of snake venom proteomes shown here for two desert black cobra species within the genus Walterinnesia, Walterinnesia aegyptia and Walterinnesia morgani. The experimental design includes the decomplexation of the venom samples by reverse-phase chromatography independently coupled to four mass spectrometry systems: the combined bottom-up and top-down molecular MS for protein identification and a parallel reverse-phase microbore high-performance liquid chromatograph (RP-μHPLC) on-line to inductively coupled plasma (ICP-MS/MS) elemental mass spectrometry and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QToF MS). This allows to continuously record the absolute sulfur concentration throughout the chromatogram and assign it to the parent venom proteins separated in the RP-μHPLC-ESI-QToF parallel run via mass profiling. The results provide a locus-resolved and quantitative insight into the three desert black cobra venom proteome samples. They also validate the units of measure of our snake venomics strategy for the relative quantification of snake venom proteomes as % of total venom peptide bonds as a proxy for the % by weight of the venom toxins/toxin families. In a more general context, our work may pave the way for broader applications of hybrid elemental/molecular MS setups in diverse areas of proteomics.

Description: California hosts ∼124,000 abandoned and plugged (AP) oil and gas wells, ∼38,000 idle wells, and ∼63,000 active wells, whose methane (CH4) emissions remain largely unquantified at levels below ∼2 kg CH4 h–1. We sampled 121 wells using two methods: a rapid mobile plume integration method (detection ∼0.5 g CH4 h–1) and a more sensitive static flux chamber (detection ∼1 × 10–6 g CH4 h–1). We measured small but detectable methane emissions from 34 of 97 AP wells (mean emission: 0.286 g CH4 h–1). In contrast, we found emissions from 11 of 17 idle wells—which are not currently producing (mean: 35.4 g CH4 h–1)—4 of 6 active wells (mean: 189.7 g CH4 h–1), and one unplugged well—an open casing with no infrastructure present (10.9 g CH4 h–1). Our results support previous findings that emissions from plugged wells are low but are more substantial from idle wells. In addition, our smaller sample of active wells suggests that their reported emissions are consistent with previous studies and deserve further attention. Due to limited access, we could not measure wells in most major active oil and gas fields in California; therefore, we recommend additional data collection from all types of wells but especially active and idle wells.

Description: In 2013, the Pacific Northwest National Laboratory led a geologic carbon sequestration field demonstration where ∼1000 tonnes of CO2 was injected into several deep Columbia River Basalt zones near Wallula, Washington. Rock core samples extracted from the injection zone two years after CO2 injection revealed nascent carbonate mineralization that was qualitatively consistent with expectations from laboratory experiments and reactive transport modeling. Here, we report on a new detailed analysis of the 2012 pre-injection and 2015 post-injection hydrologic tests that capitalizes on the difference in fluid properties between scCO2 and water to assess changes in near-field, wellbore, and reservoir conditions that are apparent approximately two years following the end of injection. This comparative hydrologic test analysis method provides a new way to quantify the amount of injected CO2 that was mineralized in the field test. Modeling results indicate that approximately 60% of the injected CO2 was sequestered via mineralization within two years, with the resulting carbonates occupying ∼4% of the available reservoir pore space. The method presented here provides a new monitoring tool to assess the fate of CO2 injected into chemically reactive basalt formations but could also be adapted for long-term monitoring and verification within more traditional subsurface carbon storage reservoirs.

Description: Background and Aims Dysregulated mineral homeostasis is common in chronic kidney disease (CKD) and associated with bone demineralization and vascular calcification. The balance between bone formation and resorption, which reflect the bone calcium (Ca) balance (BCaB), cannot be determined without bone biopsy which is invasive and not easily repeatable. Recently, we have shown that stable (i.e. non-radioactive) Ca isotopes, 42Ca and 44Ca, can be measured in serum and their ratio (δ44/42Caserum) quantitatively determines net bone gain or loss of Ca. Thus, when bone formation exceeds bone resorption, the net BCaB is positive and δ44/42Caserum is high, and when bone resorption is the predominant process δ44/42Caserum is low compared to age-matched controls. In this study we compared δ44/42Caserum against δ44/42Cabone and arterial biopsy samples (δ44/42Caartery) and the sensitivity of δ44/42Ca in predicting changes in bone histology.

Description: Petroleum substances, as archetypical UVCBs (substances of unknown or variable composition, complex reaction products, or biological substances), pose a challenge for chemical risk assessment as they contain hundreds to thousands of individual constituents. It is particularly challenging to determine the biodegradability of petroleum substances since each constituent behaves differently. Testing the whole substance provides an average biodegradation, but it would be effectively impossible to obtain all constituents and test them individually. To overcome this challenge, comprehensive two-dimensional gas chromatography (GC × GC) in combination with advanced data-handling algorithms was applied to track and calculate degradation half-times (DT50s) of individual constituents in two dispersed middle distillate gas oils in seawater. By tracking 〉1000 peaks (representing ∼53–54% of the total mass across the entire chromatographic area), known biodegradation patterns of oil constituents were confirmed and extended to include many hundreds not currently investigated by traditional one-dimensional GC methods. Approximately 95% of the total tracked peak mass biodegraded after 64 days. By tracking the microbial community evolution, a correlation between the presence of functional microbial communities and the observed progression of DT50s between chemical classes was demonstrated. This approach could be used to screen the persistence of GC × GC-amenable constituents of petroleum substance UVCBs.

Description: The dynamics of marine systems at decadal scales are notoriously hard to predict—hence references to this timescale as the “grey zone” for ocean prediction. Nevertheless, decadal-scale prediction is a rapidly developing field with an increasing number of applications to help guide ocean stewardship and sustainable use of marine environments. Such predictions can provide industry and managers with information more suited to support planning and management over strategic timeframes, as compared to seasonal forecasts or long-term (century-scale) predictions. The most significant advances in capability for decadal-scale prediction over recent years have been for ocean physics and biogeochemistry, with some notable advances in ecological prediction skill. In this paper, we argue that the process of “lighting the grey zone” by providing improved predictions at decadal scales should also focus on including human dimensions in prediction systems to better meet the needs and priorities of end users. Our paper reviews information needs for decision-making at decadal scales and assesses current capabilities for meeting these needs. We identify key gaps in current capabilities, including the particular challenge of integrating human elements into decadal prediction systems. We then suggest approaches for overcoming these challenges and gaps, highlighting the important role of co-production of tools and scenarios, to build trust and ensure uptake with end users of decadal prediction systems. We also highlight opportunities for combining narratives and quantitative predictions to better incorporate the human dimension in future efforts to light the grey zone of decadal-scale prediction.

Description: Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

Description: Eutrophication in marine waters is traditionally assessed by checking if nutrients, algal biomass and oxygen are below/above a given threshold. However, increased biomass, nutrient concentrations and oxygen demand do not lead to undesirable environmental effects if the flow of carbon/energy from primary producers toward high trophic levels is consistently preserved. Consequently, traditional indicators might provide a misleading assessment of the eutrophication risk. To avoid this, we propose to evaluate eutrophication by using a new index based on plankton trophic fluxes instead of biogeochemical concentrations. A preliminary, model-based, assessment suggests that this approach might give a substantially different picture of the eutrophication status of our seas, with potential consequences on marine ecosystem management. Given the difficulties to measure trophic fluxes in the field, the use of numerical simulations is recommended although the uncertainty associated with biogeochemical models inevitably affects the reliability of the index. However, given the effort currently in place to develop refined numerical tools describing the marine environment (Ocean Digital Twins), a reliable, model-based, eutrophication index could be operational in the near future.