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Assessments of the climate impacts of energy technologies and other emissions sources can depend strongly on the equivalency metric used to compare short- and long-lived greenhouse gas emissions. However, the consequences of metric design choices are not fully understood, and in practice, a single metric, the global warming potential (GWP), is used almost universally. Many metrics have been proposed and evaluated in recent decades, but questions still remain about which ones perform better and why. Here, we develop new insights on how the design of equivalency metrics can impact the outcomes of climate policies. We distill the equivalency metric problem into a few key design choices that determine the metric values and shapes seen across a wide range of different proposed metrics. We examine outcomes under a hypothetical 1.5 or 2^∘C policy target and discuss extensions to other policies. Across policy contexts, the choice of time parameters is particularly important. Metrics that emphasize the immediate impacts of short-lived gases such as methane can reduce rates of climate change but may require more rapid technology changes. Differences in outcomes across metrics are more pronounced when fossil fuels, with or without carbon capture and storage, play a larger role in energy transitions. By identifying a small set of consequential design decisions, these insights can help make metric choices and energy transitions more deliberate and effective at mitigating climate change.

 

Vase-shaped microfossils (VSMs) are found globally in middle Neoproterozoic (800–730 Ma) marine strata and represent the earliest evidence for testate (shell-forming) amoebozoans. VSM tests are hypothesized to have been originally organic in life but are most commonly preserved as secondary mineralized casts and molds. A few reports, however, suggest possible organic preservation. Here, we test the hypothesis that VSMs from shales of the lower Walcott Member of the Chuar Group, Grand Canyon, Arizona, contain original organic material, as reported by B. Bloeser in her pioneering studies of Chuar VSMs. We identified VSMs from two thin section samples of Walcott Member black shales in transmitted light microscopy and used scanning electron microscopy to image VSMs. Carbonaceous material is found within the internal cavity of all VSM tests from both samples and is interpreted as bitumen mobilized from Walcott shales likely during the Cretaceous. Energy dispersive X-ray spectroscopy (EDS) and wavelength dispersive X-ray spectroscopy (WDS) reveal that VSM test walls contain mostly carbon, iron, and sulfur, while silica is present only in the surrounding matrix. Raman spectroscopy was used to compare the thermal maturity of carbonaceous material within the samples and indicated the presence of pyrite and jarosite within fossil material. X-ray absorption spectroscopy revealed the presence of reduced organic sulfur species within the carbonaceous test walls, the carbonaceous material found within test cavities, and in the sedimentary matrix, suggesting that organic matter sulfurization occurred within the Walcott shales. Our suite of spectroscopic analyses reveals that Walcott VSM test walls are organic and sometimes secondarily pyritized (with the pyrite variably oxidized to jarosite). Both preservation modes can occur at a millimeter spatial scale within sample material, and at times even within a single specimen. We propose that sulfurization within the Walcott Shales promoted organic preservation, and furthermore, the ratio of iron to labile VSM organic material controlled the extent of pyrite replacement. Based on our evidence, we conclude that the VSMs are preserved with original organic test material, and speculate that organic VSMs may often go unrecognized, given their light-colored, translucent appearance in transmitted light. 

Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.

 

Plant DNA isolation and purification is a time-consuming and laborious process relative to epithelial and viral DNA sample preparation due to the cell wall. The lysis of plant cells to free intracellular DNA normally requires high temperatures, chemical surfactants, and mechanical separation of plant tissue prior to a DNA purification step. Traditional DNA purification methods also do not aid themselves towards fieldwork due to the numerous chemical and bulky equipment requirements.

In this study, intact plant tissue was coated by hydrophobic magnetic ionic liquids (MILs) and ionic liquids (ILs) and allowed to incubate under static conditions or dispersed in a suspension buffer to facilitate cell disruption and DNA extraction. The DNA-enriched MIL or IL was successfully integrated into the qPCR buffer without inhibiting the reaction. The two aforementioned advantages of ILs and MILs allow plant DNA sample preparation to occur in one minute or less without the aid of elevated temperatures or chemical surfactants that typically inhibit enzymatic amplification methods. MIL or IL-coated plant tissue could be successfully integrated into a qPCR assay without the need for custom enzymes or manual DNA isolation/purification steps that are required for conventional methods.

The limited amount of equipment, chemicals, and time required to disrupt plant cells while simultaneously extracting DNA using MILs makes the described procedure ideal for fieldwork and lab work in low resource environments.

 

Pure molybdenum disulfide (MoS₂) solid lubricant coatings could attain densities comparable to doped films (and the associated benefits to wear rate and environmental stability) through manipulation of the microstructure via deposition parameters. Unfortunately, pure films can exhibit highly variable microstructures and mechanical properties due to processes that are not controlled during deposition (i.e., batch-to-batch variation). This work focuses on developing a relationship between density, hardness, friction, and wear for pure sputtered MoS₂coatings. Results show that dense films (ρ = 4.5 g/cm³) exhibit a 100 × lower wear rate compared to porous coatings (ρ = 3.04–3.55 g/cm³). The tribological performance of high density pure MoS₂coatings is shown to surpass that of established composite coatings, achieving a wear rate 2 × (k = 5.74 × 10^–8mm³/Nm) lower than composite MoS₂/Sb₂O₃/Au in inert environments.

 

Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resulted in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future. 

We address the problem of optimally identifying all kilonovae detected via gravitational-wave emission in the upcoming LIGO/Virgo/KAGRA observing run, O4, which is expected to be sensitive to a factor of ∼7 more binary neutron star (BNS) alerts than previously. Electromagnetic follow-up of all but the brightest of these new events will require >1 m telescopes, for which limited time is available. We present an optimized observing strategy for the DECam during O4. We base our study on simulations of gravitational-wave events expected for O4 and wide-prior kilonova simulations. We derive the detectabilities of events for realistic observing conditions. We optimize our strategy for confirming a kilonova while minimizing telescope time. For a wide range of kilonova parameters, corresponding to a fainter kilonova compared to GW170817/AT 2017gfo, we find that, with this optimal strategy, the discovery probability for electromagnetic counterparts with the DECam is ∼80% at the nominal BNS gravitational-wave detection limit for O4 (190 Mpc), which corresponds to an ∼30% improvement compared to the strategy adopted during the previous observing run. For more distant events (∼330 Mpc), we reach an ∼60% probability of detection, a factor of ∼2 increase. For a brighter kilonova model dominated by the blue component that reproduces the observations of GW170817/AT 2017gfo, we find that we can reach ∼90% probability of detection out to 330 Mpc, representing an increase of ∼20%, while also reducing the total telescope time required to follow up events by ∼20%.

 

Multiple gram-negative bacteria encode type III secretion systems (T3SS) that allow them to inject effector proteins directly into host cells to facilitate colonization. To be secreted, effector proteins must be at least partially unfolded to pass through the narrow needle-like channel (diameter <2 nm) of the T3SS. Fusion of effector proteins to tightly packed proteins—such as GFP, ubiquitin, or dihydrofolate reductase (DHFR)—impairs secretion and results in obstruction of the T3SS. Prior observation that unfolding can become rate-limiting for secretion has led to the model that T3SS effector proteins have low thermodynamic stability, facilitating their secretion. Here, we first show that the unfolding free energy ( Δ G unfold 0 ) of two Salmonella effector proteins, SptP and SopE2, are 6.9 and 6.0 kcal/mol, respectively, typical for globular proteins and similar to published Δ G unfold 0 for GFP, ubiquitin, and DHFR. Next, we mechanically unfolded individual SptP and SopE2 molecules by atomic force microscopy (AFM)-based force spectroscopy. SptP and SopE2 unfolded at low force ( F unfold ≤ 17 pN at 100 nm/s), making them among the most mechanically labile proteins studied to date by AFM. Moreover, their mechanical compliance is large, as measured by the distance to the transition state (Δ x ‡ = 1.6 and 1.5 nm for SptP and SopE2, respectively). In contrast, prior measurements of GFP, ubiquitin, and DHFR show them to be mechanically robust ( F unfold > 80 pN) and brittle (Δ x ‡ < 0.4 nm). These results suggest that effector protein unfolding by T3SS is a mechanical process and that mechanical lability facilitates efficient effector protein secretion.