UV damage induces production of mitochondrial DNA fragments with specific length profiles.

UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Photodamage and other bulky lesions occurring in nuclear genomes can be repaired through nucleotide excision repair (NER), where incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current evidence suggests that the only way to eliminate bulky mtDNA damage is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with antidamage antibodies and sequenced (XR-seq) to produce high-resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in regular intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. The mechanisms producing these fragments are unclear, but we hypothesize that they result from a previously uncharacterized DNA degradation pathway or repair mechanism in mitochondria.

Correlative geochemical imaging of Desmophyllum dianthus reveals biomineralisation strategy as a key coral vital effect.

The chemical and isotopic composition of stony coral skeletons form an important archive of past climate. However, these reconstructions are largely based on empirical relationships often complicated by "vital effects" arising from uncertain physiological processes of the coral holobiont. The skeletons of deep-sea corals, such as Desmophyllum dianthus, are characterised by micron-scale or larger geochemical heterogeneity associated with: (1) centres of calcification (COCs) where nucleation of new skeleton begins, and (2) fibres that thicken the skeleton. These features are difficult to sample cleanly using traditional techniques, resulting in uncertainty surrounding both the causes of geochemical differences and their influence on environmental signals. Here we combine optical, and in-situ chemical and isotopic, imaging tools across a range of spatial resolutions (~ 100 nm to 10 s of µm) in a correlative multimodal imaging (CMI) approach to isolate the microstructural geochemistry of each component. This reveals COCs are characterised by higher organic content, Mg, Li and Sr and lower U, B and δ11B compared to fibres, reflecting the contrasting biomineralisation mechanisms employed to construct each feature. CMI is rarely applied in Environmental/Earth Sciences, but here we illustrate the power of this approach to unpick the "vital effects" in D. dianthus, and by extension, other scleractinian corals.

Arctic and Antarctic forcing of ocean interior warming during the last deglaciation.

Subsurface water masses formed at high latitudes impact the latitudinal distribution of heat in the ocean. Yet uncertainty surrounding the timing of low-latitude warming during the last deglaciation (18-10 ka) means that controls on sub-surface temperature rise remain unclear. Here we present seawater temperature records on a precise common age-scale from East Equatorial Pacific (EEP), Equatorial Atlantic, and Southern Ocean intermediate waters using new Li/Mg records from cold water corals. We find coeval warming in the tropical EEP and Atlantic during Heinrich Stadial 1 (+ 6 °C) that closely resemble warming recorded in Antarctic ice cores, with more modest warming of the Southern Ocean (+ 3 °C). The magnitude and depth of low-latitude ocean warming implies that downward accumulation of heat following Atlantic Meridional Overturning Circulation (AMOC) slowdown played a key role in heating the ocean interior, with heat advection from southern-sourced intermediate waters playing an additional role.

Enhanced subglacial discharge from Antarctica during meltwater pulse 1A.

Subglacial discharge from the Antarctic Ice Sheet (AIS) likely played a crucial role in the loss of the ice sheet and the subsequent rise in sea level during the last deglaciation. However, no direct proxy is currently available to document subglacial discharge from the AIS, which leaves significant gaps in our understanding of the complex interactions between subglacial discharge and ice-sheet stability. Here we present deep-sea coral 234U/238U records from the Drake Passage in the Southern Ocean to track subglacial discharge from the AIS. Our findings reveal distinctively higher seawater 234U/238U values from 15,400 to 14,000 years ago, corresponding to the period of the highest iceberg-rafted debris flux and the occurrence of the meltwater pulse 1A event. This correlation suggests a causal link between enhanced subglacial discharge, synchronous retreat of the AIS, and the rapid rise in sea levels. The enhanced subglacial discharge and subsequent AIS retreat appear to have been preconditioned by a stronger and warmer Circumpolar Deep Water, thus underscoring the critical role of oceanic heat in driving major ice-sheet retreat.

UV damage induces production of mitochondrial DNA fragments with specific length profiles.

UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). In eukaryotic cells, photodamage and other bulky lesions occurring in nuclear genomes (nucDNAs) can be repaired through nucleotide excision repair (NER), where dual incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current views hold that the only way to eliminate bulky DNA damage in mtDNAs is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with anti-damage antibodies and sequenced (XR-seq) to produce high resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in 2-nt (S. cerevisiae) or 4-nt (A. thaliana) intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. We hypothesize that these fragments may reflect the outcome of a previously uncharacterized mechanism of NER-like repair in mitochondria or a programmed mtDNA degradation pathway.

Life on the edge-a changing genetic landscape within an iconic American pika metapopulation over the last half century.

Declines and extirpations of American pika (Ochotona princeps) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipitation regimes. Here, we report on a decline in available genetic resources for an iconic American pika metapopulation, located at the southwestern edge of the species distribution in the Bodie Hills of eastern California, USA. Composed of highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas around the end of the 19th century from nearby natural talus outcrops. Genetic data extracted from both contemporary samples and archived natural history collections allowed us to track population and patch-level genetic diversity for Bodie pikas across three distinct sampling points during the last half- century (1948-1949, 1988-1991, 2013-2015). Reductions in within-population allelic diversity and expected heterozygosity were observed across the full time period. More extensive sampling of extant patches during the 1988-1991 and 2013-2015 periods revealed an increase in population structure and a reduction in effective population size. Furthermore, census records from the last 51 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (Nevada, USA) provide further support of the increasing isolation and genetic coalescence occurring in this region. This study highlights the importance of museum samples and long-term monitoring in contextualizing our understanding of population viability.

Reaction-Induced Metal-Metal Oxide Interactions in Pd-In2 O3 /ZrO2 Catalysts Drive Selective and Stable CO2 Hydrogenation to Methanol.

Ternary Pd-In2 O3 /ZrO2 catalysts exhibit technological potential for CO2 -based methanol synthesis, but developing scalable systems and comprehending complex dynamic behaviors of the active phase, promoter, and carrier are key for achieving high productivity. Here, we show that the structure of Pd-In2 O3 /ZrO2 systems prepared by wet impregnation evolves under CO2 hydrogenation conditions into a selective and stable architecture, independent of the order of addition of Pd and In phases on the zirconia carrier. Detailed operando characterization and simulations reveal a rapid restructuring driven by the metal-metal oxide interaction energetics. The proximity of InPdx alloy particles decorated by InOx layers in the resulting architecture prevents performance losses associated with Pd sintering. The findings highlight the crucial role of reaction-induced restructuring in complex CO2 hydrogenation catalysts and offer insights into the optimal integration of acid-base and redox functions for practical implementation.

Direct Observation of Ni Nanoparticle Growth in Carbon-Supported Nickel under Carbon Dioxide Hydrogenation Atmosphere.

Understanding nanoparticle growth is crucial to increase the lifetime of supported metal catalysts. In this study, we employ in situ gas-phase transmission electron microscopy to visualize the movement and growth of ensembles of tens of nickel nanoparticles supported on carbon for CO2 hydrogenation at atmospheric pressure (H2:CO2 = 4:1) and relevant temperature (450 °C) in real time. We observe two modes of particle movement with an order of magnitude difference in velocity: fast, intermittent movement (vmax = 0.7 nm s-1) and slow, gradual movement (vaverage = 0.05 nm s-1). We visualize the two distinct particle growth mechanisms: diffusion and coalescence, and Ostwald ripening. The diffusion and coalescence mechanism dominates at small interparticle distances, whereas Ostwald ripening is driven by differences in particle size. Strikingly, we demonstrate an interplay between the two mechanisms, where first coalescence takes place, followed by fast Ostwald ripening due to the increased difference in particle size. Our direct visualization of the complex nanoparticle growth mechanisms highlights the relevance of studying nanoparticle growth in supported nanoparticle ensembles under reaction conditions and contributes to the fundamental understanding of the stability in supported metal catalysts.

Wildfire facilitates upslope advance in a shade-intolerant but not a shade-tolerant conifer.

Wildfires may facilitate climate tracking of forest species moving upslope or north in latitude. For subalpine tree species, for which higher elevation habitat is limited, accelerated replacement by lower elevation montane tree species following fire may hasten extinction risk. We used a dataset of postfire tree regeneration spanning a broad geographic range to ask whether the fire facilitated upslope movement of montane tree species at the montane-to-subalpine ecotone. We sampled tree seedling occurrence in 248 plots across a fire severity gradient (unburned to >90% basal area mortality) and spanning ~500 km of latitude in Mediterranean-type subalpine forest in California, USA. We used logistic regression to quantify differences in postfire regeneration between resident subalpine species and the seedling-only range (interpreted as climate-induced range extension) of montane species. We tested our assumption of increasing climatic suitability for montane species in subalpine forest using the predicted difference in habitat suitability at study plots between 1990 and 2030. We found that postfire regeneration of resident subalpine species was uncorrelated or weakly positively correlated with fire severity. Regeneration of montane species, however, was roughly four times greater in unburned relative to burned subalpine forest. Although our overall results contrast with theoretical predictions of disturbance-facilitated range shifts, we found opposing postfire regeneration responses for montane species with distinct regeneration niches. Recruitment of shade-tolerant red fir declined with fire severity and recruitment of shade-intolerant Jeffrey pine increased with fire severity. Predicted climatic suitability increased by 5% for red fir and 34% for Jeffrey pine. Differing postfire responses in newly climatically available habitats indicate that wildfire disturbance may only facilitate range extensions for species whose preferred regeneration conditions align with increased light and/or other postfire landscape characteristics.

Competition between reverse water gas shift reaction and methanol synthesis from CO2: influence of copper particle size.

Converting CO2 into value-added chemicals and fuels, such as methanol, is a promising approach to limit the environmental impact of human activities. Conventional methanol synthesis catalysts have shown limited efficiency and poor stability in a CO2/H2 mixture. To design improved catalysts, crucial for the effective utilization of CO2, an in-depth understanding of the active sites and reaction mechanism is desired. The catalytic performance of a series of carbon-supported Cu catalysts, with Cu particle sizes in the range of 5 to 20 nm, was evaluated under industrially relevant temperature and pressure, i.e. 260 °C and 40 bar(g). The CO2 hydrogenation reaction exhibited clear particle size effects up to 13 nm particles, with small nanoparticles having the lower activity, but higher methanol selectivity. MeOH and CO formation showed a different size-dependence. The TOFCO increased from 1.9 × 10-3 s-1 to 9.4 × 10-3 s-1 with Cu size increasing from 5 nm to 20 nm, while the TOFMeOH was size-independent (8.4 × 10-4 s-1 on average). The apparent activation energies for MeOH and CO formation were size-independent with values of 63 ± 7 kJ mol-1 and 118 ± 6 kJ mol-1, respectively. Hence the size dependence was ascribed to a decrease in the fraction of active sites suitable for CO formation with decreasing particle size. Theoretical models and DFT calculations showed that the origin of the particle size effect is most likely related to the differences in formate coverage for different Cu facets whose abundancy depends on particle size. Hence, the CO2 hydrogenation reaction is intrinsically sensitive to the Cu particle size.

Stylasterid corals build aragonite skeletons in undersaturated water despite low pH at the site of calcification.

Anthropogenic carbon emissions are causing seawater pH to decline, yet the impact on marine calcifiers is uncertain. Scleractinian corals and coralline algae strongly elevate the pH of their calcifying fluid (CF) to promote calcification. Other organisms adopt less energetically demanding calcification approaches but restrict their habitat. Stylasterid corals occur widely (extending well below the carbonate saturation horizon) and precipitate both aragonite and high-Mg calcite, however, their mode of biocalcification and resilience to ocean acidification are unknown. Here we measure skeletal boron isotopes (δ11B), B/Ca, and U/Ca to provide the first assessment of pH and rate of seawater flushing of stylasterid CF. Remarkably, both aragonitic and high-Mg calcitic stylasterids have low δ11B values implying little modification of internal pH. Collectively, our results suggest stylasterids have low seawater exchange rates into the calcifying space or rely on organic molecule templating to facilitate calcification. Thus, despite occupying similar niches to Scleractinia, Stylasteridae exhibit highly contrasting biocalcification, calling into question their resilience to ocean acidification.

Manganese Oxide as a Promoter for Copper Catalysts in CO2 and CO Hydrogenation.

In this work, we discuss the role of manganese oxide as a promoter in Cu catalysts supported on graphitic carbon during hydrogenation of CO2 and CO. MnOx is a selectivity modifier in an H2/CO2 feed and is a highly effective activity promoter in an H2/CO feed. Interestingly, the presence of MnOx suppresses the methanol formation from CO2 (TOF of 0.7 ⋅ 10-3 s-1 at 533 K and 40 bar) and enhances the low-temperature reverse water-gas shift reaction (TOF of 5.7 ⋅ 10-3 s-1) with a selectivity to CO of 87 %C. Using time-resolved XAS at high temperatures and pressures, we find significant absorption of CO2 to the MnO, which is reversed if CO2 is removed from the feed. This work reveals fundamental differences in the promoting effect of MnOx and ZnOx and contributes to a better understanding of the role of reducible oxide promoters in Cu-based hydrogenation catalysts.

Microfabrication Enables Quantification of Interfacial Activity in Thermal Catalysis.

A myriad of heterogeneous catalysts comprises multiple phases that need to be precisely structured to exert their maximal contribution to performance through electronic and structural interactions at their peripheries. In view of the nanometric, tridimensional, and anisotropic nature of these materials, a quantification of the interface and the impact of catalytic sites located there on the global performance is a highly challenging task. Consequently, the true origin of catalysis often remains subject of debate even for widely studied materials. Herein, an integrated strategy based on microfabricated catalysts and a custom-designed reactor is introduced for determining interfacial contributions upon catalytic activity assessment under process-relevant conditions, which can be easily implemented in the common catalysis research infrastructure and will accelerate the rational design of multicomponent heterogeneous catalysts for diverse applications. The method is validated by studying the high-pressure continuous-flow hydrogenation of CO and CO2 over Cu-ZnO catalysts, revealing linear correlations between the methanol formation rate and the interface between the metal and the oxide. Characterization of fresh and used materials points to the model catalyst preparation as the current challenge of the methodology that can be addressed through further development of nanotechnological tools.

Noncanonical outcomes of break-induced replication produce complex, extremely long-tract gene conversion events in yeast.

Long-tract gene conversions (LTGC) can result from the repair of collapsed replication forks, and several mechanisms have been proposed to explain how the repair process produces this outcome. We studied LTGC events produced from repair collapsed forks at yeast fragile site FS2. Our analysis included chromosome sizing by contour-clamped homogeneous electric field electrophoresis, next-generation whole-genome sequencing, and Sanger sequencing across repair event junctions. We compared the sequence and structure of LTGC events in our cells to the expected qualities of LTGC events generated by proposed mechanisms. Our evidence indicates that some LTGC events arise from half-crossover during BIR, some LTGC events arise from gap repair, and some LTGC events can be explained by either gap repair or "late" template switch during BIR. Also based on our data, we propose that models of collapsed replication forks be revised to show not a one-end double-strand break (DSB), but rather a two-end DSB in which the ends are separated in time and subject to gap repair.

Highly Potent SARS-CoV-2 Neutralization by Intravenous Immunoglobulins manufactured from Post-COVID-19 and COVID-19-Vaccinated Plasma Donations.

From September 2020, some immunoglobulin lots from US plasma contained neutralizing antibodies against the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Paralleled by the increasing numbers of post-coronavirus disease 2019 (COVID-19) donors, immunoglobulin lot antibody positivity increased to 93% by January 2021, at a mean titer of approximately 30 IU/mL. The correlation predicted that anti-SARS-CoV-2 potency would reach 345 IU/mL by July 2021. In addition to post-COVID-19 donors, the rapidly increasing number of plasma donors vaccinated against COVID-19 resulted in a mean antibody titer of >600 IU/mL in July 2021 immunoglobulin lots, with SARS-CoV-2 antibody titers for several lots even higher than those of earlier produced hyperimmune globulin products.

Methanol Synthesis by Hydrogenation of Hybrid CO2 -CO Feeds.

The impact of carbon monoxide on CO2 -to-methanol catalysts has been scarcely investigated, although CO will comprise up to half of the carbon feedstock, depending on the origin of CO2 and process configuration. In this study, copper-based systems and ZnO-ZrO2 are assessed in cycling experiments with hybrid CO2 -CO feeds and their CO sensitivity is compared to In2 O3 -based materials. All catalysts are found to be promoted upon CO addition. Copper-based systems are intrinsically more active in CO hydrogenation and profit from exploiting this carbon source for methanol production, whereas CO induces surplus formation of oxygen vacancies (i. e., the catalytic sites) on ZnO-ZrO2 , as in In2 O3 -based systems. Mild-to-moderate deactivation occurs upon re-exposure to CO2 -rich streams, owing to water-induced sintering for all catalysts except ZnO-ZrO2 , which responds reversibly to feed variations, likely owing to its more hydrophobic nature and the atomic mixing of its metal components. Catalytic systems are categorized for operation in hybrid CO2 -CO feeds, emphasizing the significance of catalyst and process design to foster advances in CO2 utilization technologies.

Nanostructure of nickel-promoted indium oxide catalysts drives selectivity in CO2 hydrogenation.

Metal promotion in heterogeneous catalysis requires nanoscale-precision architectures to attain maximized and durable benefits. Herein, we unravel the complex interplay between nanostructure and product selectivity of nickel-promoted In2O3 in CO2 hydrogenation to methanol through in-depth characterization, theoretical simulations, and kinetic analyses. Up to 10 wt.% nickel, InNi3 patches are formed on the oxide surface, which cannot activate CO2 but boost methanol production supplying neutral hydrogen species. Since protons and hydrides generated on In2O3 drive methanol synthesis rather than the reverse water-gas shift but radicals foster both reactions, nickel-lean catalysts featuring nanometric alloy layers provide a favorable balance between charged and neutral hydrogen species. For nickel contents >10 wt.%, extended InNi3 structures favor CO production and metallic nickel additionally present produces some methane. This study marks a step ahead towards green methanol synthesis and uncovers chemistry aspects of nickel that shall spark inspiration for other catalytic applications.

Longitudinal analysis of SARS-CoV-2 antibodies in 8000 U.S. first-time convalescent plasma donations.

BACKGROUND: Coronavirus disease 2019 (COVID-19) convalescent individuals carry antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that, through a plasma donation, can be used as a potential therapeutic either in direct transfusion or for the manufacture of hyperimmune globulin (HIG). The success of such interventions depends on the antibody potency in such plasma donations, but little information on the collection of potent units is currently available. STUDY DESIGN AND METHODS: A total of 8749 plasma units, collected from April until September 2020 from first-time U.S. COVID-19 convalescent plasma donors, were characterized for SARS-CoV-2 immunoglobulin G (IgG) antibodies by Abbott chemiluminescent microparticle immunoassay (CMIA). The period between COVID-19 onset until donation and donor age, ethnicity, sex, and COVID-19 severity were evaluated against the obtained signal (index S/C). RESULTS: A marked decrease in mean index S/C was seen over the plasma collection period surveyed, which was significantly correlated to decreases in mean plasma donor age (p < .0001; R2 = .726) and percentage of donations obtained from COVID-19 convalescent patients who had been hospitalized (p = .001; R2 = .4426). The highest titer plasma units were obtained soon after convalescence from COVID-19 patients who required hospitalization, from advanced age donors, and from Black/African/Hispanic American versus White/Caucasian ethnicities, whereas there was no effect of donor sex on the values obtained with the Abbott CMIA. CONCLUSION: Since the onset of the pandemic, the average SARS-CoV-2 IgG values of first-time U.S. COVID-19 convalescent plasma donations have significantly dropped, mainly due to donations from progressively younger aged donors who tend to experience less severe COVID-19.

Effects of postfire climate and seed availability on postfire conifer regeneration.

Large, severe fires are becoming more frequent in many forest types across the western United States and have resulted in tree mortality across tens of thousands of hectares. Conifer regeneration in these areas is limited because seeds must travel long distances to reach the interior of large burned patches and establishment is jeopardized by increasingly hot and dry conditions. To better inform postfire management in low elevation forests of California, USA, we collected 5-yr postfire recovery data from 1,234 study plots in 19 wildfires that burned from 2004-2012 and 18 yrs of seed production data from 216 seed fall traps (1999-2017). We used these data in conjunction with spatially extensive climate, topography, forest composition, and burn severity surfaces to construct taxon-specific, spatially explicit models of conifer regeneration that incorporate climate conditions and seed availability during postfire recovery windows. We found that after accounting for other predictors both postfire and historical precipitation were strong predictors of regeneration, suggesting that both direct effects of postfire moisture conditions and biological inertia from historical climate may play a role in regeneration. Alternatively, postfire regeneration may simply be driven by postfire climate and apparent relationships with historical climate could be spurious. The estimated sensitivity of regeneration to postfire seed availability was strongest in firs and all conifers combined and weaker in pines. Seed production exhibited high temporal variability with seed production varying by over two orders of magnitude among years. Our models indicate that during droughts postfire conifer regeneration declines most substantially in low-to-moderate elevation forests. These findings enhance our mechanistic understanding of forecasted and historically documented shifts in the distribution of trees.

Rapid shifts in circulation and biogeochemistry of the Southern Ocean during deglacial carbon cycle events.

The Southern Ocean plays a crucial role in regulating atmospheric CO2 on centennial to millennial time scales. However, observations of sufficient resolution to explore this have been lacking. Here, we report high-resolution, multiproxy records based on precisely dated deep-sea corals from the Southern Ocean. Paired deep (∆14C and δ11B) and surface (δ15N) proxy data point to enhanced upwelling coupled with reduced efficiency of the biological pump at 14.6 and 11.7 thousand years (ka) ago, which would have facilitated rapid carbon release to the atmosphere. Transient periods of unusually well-ventilated waters in the deep Southern Ocean occurred at 16.3 and 12.8 ka ago. Contemporaneous atmospheric carbon records indicate that these Southern Ocean ventilation events are also important in releasing respired carbon from the deep ocean to the atmosphere. Our results thus highlight two distinct modes of Southern Ocean circulation and biogeochemistry associated with centennial-scale atmospheric CO2 jumps during the last deglaciation.