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Abstract. The hydroxyl (OH), hydroperoxy (HO2), and organic peroxy (RO2)radicals play important roles in atmospheric chemistry. In the presence ofnitrogen oxides (NOx), reactions between OH and volatile organiccompounds (VOCs) can initiate a radical propagation cycle that leads to theproduction of ozone and secondary organic aerosols. Previous measurements ofthese radicals under low-NOx conditions in forested environmentscharacterized by emissions of biogenic VOCs, including isoprene andmonoterpenes, have shown discrepancies with modeled concentrations. During the summer of 2016, OH, HO2, and RO2 radical concentrationswere measured as part of the Program for Research on Oxidants:Photochemistry, Emissions, and Transport – Atmospheric Measurements ofOxidants in Summer (PROPHET-AMOS) campaign in a midlatitude deciduousbroadleaf forest. Measurements of OH and HO2 were made by laser-inducedfluorescence–fluorescence assay by gas expansion (LIF-FAGE) techniques,and total peroxy radical (XO2) mixing ratios were measured by the Ethane CHemical AMPlifier (ECHAMP) instrument. Supporting measurements ofphotolysis frequencies, VOCs, NOx, O3, and meteorological datawere used to constrain a zero-dimensional box model utilizing either theRegional Atmospheric Chemical Mechanism (RACM2) or the Master ChemicalMechanism (MCM). Model simulations tested the influence of HOxregeneration reactions within the isoprene oxidation scheme from the LeuvenIsoprene Mechanism (LIM1). On average, the LIM1 models overestimated daytimemaximum measurements by approximately 40 % for OH, 65 % for HO2,and more than a factor of 2 for XO2. Modeled XO2 mixing ratioswere also significantly higher than measured at night. Addition of RO2 + RO2 accretion reactions for terpene-derived RO2 radicals tothe model can partially explain the discrepancy between measurements andmodeled peroxy radical concentrations at night but cannot explain thedaytime discrepancies when OH reactivity is dominated by isoprene. Themodels also overestimated measured concentrations of isoprene-derivedhydroxyhydroperoxides (ISOPOOH) by a factor of 10 during the daytime,consistent with the model overestimation of peroxy radical concentrations.Constraining the model to the measured concentration of peroxy radicalsimproves the agreement with the measured ISOPOOH concentrations, suggestingthat the measured radical concentrations are more consistent with themeasured ISOPOOH concentrations. These results suggest that the models maybe missing an important daytime radical sink and could be overestimating therate of ozone and secondary product formation in this forest.

 

Accelerated climate warming is causing significant reductions in the volume of Arctic glaciers, such that previously ice‐capped bare ground is uncovered, harboring soil development. Monitoring the thermal and hydrologic characteristics of soils, which strongly affect microbial activity, is important to understand the evolution of emerging terrestrial landscapes. We instrumented two sites on the forefield of a retreating Svalbard glacier, representing sediment ages of approximately 5 and 60 years since exposure. Our instrumentation included an ERT array complemented by adjacent point sensor measurements of subsurface temperature and water content. Sediments were sampled at each location and at two more additional sites (120 and 2000 years old) along a chronosequence aligned with the direction of glacial retreat. Analysis suggests older sediments have a lower bulk density and contain fewer large minerals, which we interpret to be indicative of sediment reworking over time. Two months of monitoring data recorded during summer 2021 indicate that the 60‐year‐old sediments are stratified showing more spatially consistent changes in electrical resistivity, whereas the younger sediments show a more irregular structure, with consequences on heat and moisture conductibility. Furthermore, our sensors reveal that young sediments have a higher moisture content, but a lower moisture content variability.

 

Leader cells direct collective migration through sensing cues in their microenvironment to determine migration direction. The mechanism by which leader cells sense the mechanical cue of organized matrix architecture culminating in a mechanical response is not well defined. In this study, we investigated the effect of organized collagen matrix fibers on leader cell mechanics and demonstrate that leader cells protrude along aligned fibers resulting in an elongated phenotype of the entire cluster. Further, leader cells show increased mechanical interactions with their nearby matrix compared to follower cells, as evidenced by increased traction forces, increased and larger focal adhesions, and increased expression of integrin-α2. Together our results demonstrate changes in mechanical matrix cues drives changes in leader cell mechanoresponse that is required for directional collective migration. Our findings provide new insights into two fundamental components of carcinogenesis, namely invasion and metastasis.

 

Abstract Uracil DNA-glycosylase (UNG) is a DNA repair enzyme that removes the highly mutagenic uracil lesion from DNA using a base flipping mechanism. Although this enzyme has evolved to remove uracil from diverse sequence contexts, UNG excision efficiency depends on DNA sequence. To provide the molecular basis for rationalizing UNG substrate preferences, we used time-resolved fluorescence spectroscopy, NMR imino proton exchange measurements, and molecular dynamics simulations to measure UNG specificity constants ( k cat / K M ) and DNA flexibilities for DNA substrates containing central AUT, TUA, AUA, and TUT motifs. Our study shows that UNG efficiency is dictated by the intrinsic deformability around the lesion, establishes a direct relationship between substrate flexibility modes and UNG efficiency, and shows that bases immediately adjacent to the uracil are allosterically coupled and have the greatest impact on substrate flexibility and UNG activity. The finding that substrate flexibility controls UNG efficiency is likely significant for other repair enzymes and has major implications for the understanding of mutation hotspot genesis, molecular evolution, and base editing. 

Regional geoengineering, by reflecting sunlight over a very limited spatial domain, might be considered as a means to target specific regional impacts of climate change. One of the obvious concerns raised by such approaches is the extent to which the resulting effects would be detectable well beyond the targeted region (e.g. in neighbouring countries). A few studies have explored this question for targeted regions that are still comparatively large. We consider idealized simulations with increased ocean albedo over relatively small domains; the Gulf of Mexico (0.23% of Earth's surface) and over the Australian Great Barrier Reef (0.07%), both with negligible global radiative forcing. Applied over these very small domains, the only statistically significant non-local changes we find are some limited reduction on summer precipitation in Florida in the Gulf of Mexico case (adjacent to the targeted region). The lack of transboundary effects suggests that governance needs for such targeted interventions are quite distinct from those for more global sunlight reflection.

 

Repetitive elements (REs) are integral to the composition, structure, and function of eukaryotic genomes, yet remain understudied in most taxonomic groups. We investigated REs across 601 insect species and report wide variation in RE dynamics across groups. Analysis of associations between REs and protein-coding genes revealed dynamic evolution at the interface between REs and coding regions across insects, including notably elevated RE–gene associations in lineages with abundant long interspersed nuclear elements (LINEs). We leveraged this large, empirical data set to quantify impacts of long-read technology on RE detection and investigate fundamental challenges to RE annotation in diverse groups. In long-read assemblies, we detected ∼36% more REs than short-read assemblies, with long terminal repeats (LTRs) showing 162% increased detection, whereas DNA transposons and LINEs showed less respective technology-related bias. In most insect lineages, 25%–85% of repetitive sequences were “unclassified” following automated annotation, compared with only ∼13% inDrosophilaspecies. Although the diversity of available insect genomes has rapidly expanded, we show the rate of community contributions to RE databases has not kept pace, preventing efficient annotation and high-resolution study of REs in most groups. We highlight the tremendous opportunity and need for the biodiversity genomics field to embrace REs and suggest collective steps for making progress toward this goal.

 

Abstract Low nitrogen use efficiency (NUE) is ubiquitous in agricultural systems, with mounting global scale consequences for both atmospheric aspects of climate and downstream ecosystems. Since NUE-related soil characteristics such as water holding capacity and organic matter are likely to vary at small scales (< 1 ha), understanding the influence of soil characteristics on NUE at the subfield scale (< 32 ha) could increase fertilizer NUE. Here, we quantify NUE in four conventionally managed dryland winter-wheat fields in Montana following multiple years of sub-field scale variation in experimental N fertilizer applications. To inform farmer decisions that incorporates NUE, we developed a generalizable model to predict subfield scale NUE by comparing six candidate models, using ecological and biogeochemical data gathered from open-source data repositories and from normal farm operations, including yield and protein monitoring data. While NUE varied across fields and years, efficiency was highest in areas of fields with low N availability from both fertilizer and estimated mineralization of soil organic N (SON). At low levels of applied N, distinct responses among fields suggest distinct capacities to supply non-fertilizer plant-available N, suggesting that mineralization supplies more available N in locations with higher total N, reducing efficiency for any applied rate. Comparing modelling approaches, a random forest regression model of NUE provided predictions with the least error relative to observed NUE. Subfield scale predictive models of NUE can help to optimize efficiency in agronomic systems, maximizing both economic net return and NUE, which provides a valuable approach for optimization of nitrogen fertilizer use. 

Uracil is a common DNA lesion which is recognized and removed by uracil DNA-glycosylase (UDG) as a part of the base excision repair pathway. Excision proceeds by base flipping, and UDG efficiency is thought to depend on the ease of deformability of the bases neighboring the lesion. We used molecular dynamics simulations to assess the flexibility of a large library of dsDNA strands, containing all tetranucleotide motifs with U:A, U:G, T:A or C:G base pairs. Our study demonstrates that uracil damaged DNA largely follows trends in flexibility of undamaged DNA. Measured bending persistence lengths, groove widths, step parameters and base flipping propensities demonstrate that uracil increases the flexibility of DNA, and that U:G base paired strands are more flexible than U:A strands. Certain sequence contexts are more deformable than others, with a key role for the 3’ base next to uracil. Flexibilities are large when this base is an A or G, and repressed for a C or T. A 5’ T adjacent to the uracil strongly promotes flexibility, but other 5’ bases are less influential. DNA bending is correlated to step deformations and base flipping, and bending aids flipping. Our study implies that the link between substrate flexibility and UDG efficiency is widely valid, helps explain why UDG prefers to bind U:G base paired strands, and suggests that the DNA bending angle of the UDG-substrate complex is optimal for base flipping. 

Pulsar timing arrays (PTAs) are Galactic-scale gravitational wave (GW) detectors consisting of precisely timed pulsars distributed across the sky. Within the decade, PTAs are expected to detect nanohertz GWs emitted by close-separation supermassive black hole binaries (SMBHBs), thereby opening up the low-frequency end of the GW spectrum for science. Individual SMBHBs which power active galactic nuclei are also promising multi-messenger sources; they may be identified via theoretically predicted electromagnetic (EM) signatures and be followed up by PTAs for GW observations. In this work, we study the detection and parameter estimation prospects of a PTA which targets EM-selected SMBHBs. Adopting a simulated Galactic millisecond pulsar population, we envisage three different pulsar timing campaigns which observe three mock sources at different sky locations. We find that an all-sky PTA which times the best pulsars is an optimal and feasible approach to observe EM-selected SMBHBs and measure their source parameters to high precision (i.e., comparable to or better than conventional EM measurements). We discuss the implications of our findings in the context of future PTA experiments with the planned Deep Synoptic Array-2000 and the multi-messenger studies of SMBHBs such as the well-known binary candidate OJ 287.