Selective Oligonucleotide and MRNA Pull-Down with Shielded Covalent Probes

Shielded covalent (SC) probes combine programmable base pairing, molecular conformation change, and activatable covalent crosslinking to achieve selective and durable capture of nucleic acid targets, including efficient discrimination of SNPs. Capture yields appear consistent with the thermodynamics of probe/target hybridization, allowing rational probe design. We will demonstrate RNA pull-down using surface-immobilized SC probes, exploiting covalent target capture to remove unwanted material using stringent washes, and then reversing the crosslinks to recover the targets. RNA pull-downs using SC probes will provide a powerful framework for exploring the in vivo binding partners of RNAs

Local Production and Developing Core Regions: Ceramic Characterization in the Lake Pátzcuaro Basin, Western Mexico

A core region is the first place for expected shifts in archaeological materials before, during, and after political changes like state emergence and imperial consolidation. Yet, studies of ceramic production have shown that there are sometimes limited or more subtle changes in the ceramic economy throughout such political fluctuations. This article synthesizes recent efforts to address political economic changes via geochemical characterization (neutron activation analysis; NAA) in the Lake Pátzcuaro Basin in western Mexico. This region was home to the Purépecha state and then empire (Tarascan; ca. AD 1350-1530), one of the most powerful kingdoms in the Americas before European arrival. The combined ceramic dataset from four sites in the region result in eight geochemical groups. Our analysis indicates that the region experienced long-term and relatively stable ceramic production that was not substantially altered by the emergence of the state and empire. In addition, we find evidence for (1) dispersed, localized production; (2) long-lived compositional ceramic recipes; and (3) a complex ceramic economy with differential community participation. We discuss why documenting local ceramic production and craft production more generally is important for the study of past political economies

Diesel particulate matter emission factors and air quality implications from in–service rail in Washington State, USA

AbstractWe sought to evaluate the air quality implications of rail traffic at two sites in Washington State. Our goals were to quantify the exposure to diesel particulate matter (DPM) and airborne coal dust from current trains for residents living near the rail lines and to measure the DPM and black carbon emission factors (EFs). We chose two sites in Washington State, one at a residence along the rail lines in the city of Seattle and one near the town of Lyle in the Columbia River Gorge (CRG). At each site, we made measurements of size–segregated particulate matter (PM1, PM2.5 and PM10), CO2 and meteorology, and used a motion–activated camera to capture video of each train for identification. We measured an average DPM EF of 0.94g/kg diesel fuel, with an uncertainty of 20%, based on PM1 and CO2 measurements from more than 450 diesel trains. We found no significant difference in the average DPM EFs measured at the two sites. Open coal trains have a significantly higher concentration of particles greater than 1μm diameter, likely coal dust. Measurements of black carbon (BC) at the CRG site show a strong correlation with PM1 and give an average BC/DPM ratio of 52% from diesel rail emissions. Our measurements of PM2.5 show that living close to the rail lines significantly increases PM2.5 exposure. For the one month of measurements at the Seattle site, the average PM2.5 concentration was 6.8μg/m3 higher near the rail lines compared to the average from several background locations. Because the excess PM2.5 exposure for residents living near the rail lines is likely to be linearly related to the diesel rail traffic density, a 50% increase in rail traffic may put these residents over the new U.S. National Ambient Air Quality Standards, an annual average of 12μg/m3

Association Between Early Hyperoxia Exposure After Resuscitation From Cardiac Arrest and Neurological Disability: Prospective Multicenter Protocol-Directed Cohort Study

BACKGROUND: Studies examining the association between hyperoxia exposure after resuscitation from cardiac arrest and clinical outcomes have reported conflicting results. Our objective was to test the hypothesis that early postresuscitation hyperoxia is associated with poor neurological outcome. METHODS: This was a multicenter prospective cohort study. We included adult patients with cardiac arrest who were mechanically ventilated and received targeted temperature management after return of spontaneous circulation. We excluded patients with cardiac arrest caused by trauma or sepsis. Per protocol, partial pressure of arterial oxygen (Pao2) was measured at 1 and 6 hours after return of spontaneous circulation. Hyperoxia was defined as a Pao2 >300 mm Hg during the initial 6 hours after return of spontaneous circulation. The primary outcome was poor neurological function at hospital discharge, defined as a modified Rankin Scale score >3. Multivariable generalized linear regression with a log link was used to test the association between Pao2 and poor neurological outcome. To assess whether there was an association between other supranormal Pao2 levels and poor neurological outcome, we used other Pao2 cut points to define hyperoxia (ie, 100, 150, 200, 250, 350, 400 mm Hg). RESULTS: Of the 280 patients included, 105 (38%) had exposure to hyperoxia. Poor neurological function at hospital discharge occurred in 70% of patients in the entire cohort and in 77% versus 65% among patients with versus without exposure to hyperoxia respectively (absolute risk difference, 12%; 95% confidence interval, 1-23). Hyperoxia was independently associated with poor neurological function (relative risk, 1.23; 95% confidence interval, 1.11-1.35). On multivariable analysis, a 1-hour-longer duration of hyperoxia exposure was associated with a 3% increase in risk of poor neurological outcome (relative risk, 1.03; 95% confidence interval, 1.02-1.05). We found that the association with poor neurological outcome began at ≥300 mm Hg. CONCLUSIONS: Early hyperoxia exposure after resuscitation from cardiac arrest was independently associated with poor neurological function at hospital discharge

Fruit Quality And Consumption By Songbirds During Autumn Migration

Seasonal fruits are an important food resource for small songbirds during autumn migration in southern New England. Therefore, conservation and management of important stopover sites used by migrating birds requires knowledge about nutritional requirements of songbirds and nutritional composition of commonly consumed fruits. We measured nutrient composition and energy density of nine common fruits on Block Island, Rhode Island, and conducted a field experiment to estimate consumption rates of three of these fruits by birds during autumn migration. Most common fruits on Block Island contained primarily carbohydrates (41.3–91.2% dry weight), and little protein (2.6–8.6%) and fat (0.9–3.7%), although three contained more fat: Myrica pennsylvanica (50.3%), Viburnum dentatum (41.3%), and Parthenocissus quinquefolia (23.6%). Bird consumption of high-fat, high-energy V. dentatum fruit and high-carbohydrate, low-energy Phytolacca americana fruit was greater than consumption of Aronia melanocarpa, a high-carbohydrate, low-energy fruit. We estimated that migratory birds on Block Island must eat up to four times their body mass in fruit wet weight each day to satisfy their energy requirements when eating low-energy fruits such as P. americana, and they cannot satisfy their protein requirements when eating only certain high-energy fruits such as V. dentatum. Our results suggest that many migratory birds must eat both fruits and insects to meet their dietary needs. Thus, shrubland habitat at important migratory stopover sites such as Block Island should be managed so that it contains a variety of preferred fruit-bearing shrubs and an adequate abundance of insects

A Culture of Fire: Identifying Community Risk Perceptions Surrounding Prescribed Burning in the Flint Hills, Kansas

In the Flint Hills region of eastern Kansas, there is a long tradition of spring prescribed burns. However, air quality concerns in downwind communities have sparked conversation regarding the environmental and social impacts of these burns. This study aimed to identify the risk perceptions associated with prescribed burns using two theoretical frameworks: the social amplification of risk framework and the protective action decision model. In April 2022, we conducted 18 in-depth, semi-structured interviews with Flint Hills community members from different social stations. Participants identified several benefits of prescribed burns: cattle production gains, invasive species management, prairie ecological health maintenance, and wildfire prevention. Some participants viewed prescribed burning as a protective response. However, risk perceptions differed between rural and urban participants: rural community members were primarily concerned with prescribed fires that went out of control, while those in downwind cities were primarily concerned with smoke exposure. Participants sometimes used protective actions to mitigate their risks, but also explained the complexities of changing burn practices that are integral to the local culture, economies, and greater society. Additionally, formal communication of health and safety risks from prescribed burns is not uniform across Kansas counties. We therefore recommend systematic county and statewide communication of burn practices and protective behaviors. Understanding community perceptions of the risks and effects of prescribed burns, and any protective actions taken, can inform how professional communicators approach burning in similar agricultural and ranching communities

Selective Nucleic Acid Capture with Shielded Covalent Probes

Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible, and not all desired targets bound). These difficulties are fundamental, stemming from reliance on base pairing to provide both selectivity and affinity. Shielded covalent (SC) probes eliminate the longstanding trade-off between selectivity and durable target capture, achieving selectivity via programmable base pairing and molecular conformation change, and durable target capture via activatable covalent cross-linking. In pure and mixed samples, SC probes covalently capture complementary DNA or RNA oligo targets and reject two-nucleotide mismatched targets with near-quantitative yields at room temperature, achieving discrimination ratios of 2–3 orders of magnitude. Semiquantitative studies with full-length mRNA targets demonstrate selective covalent capture comparable to that for RNA oligo targets. Single-nucleotide DNA or RNA mismatches, including nearly isoenergetic RNA wobble pairs, can be efficiently rejected with discrimination ratios of 1–2 orders of magnitude. Covalent capture yields appear consistent with the thermodynamics of probe/target hybridization, facilitating rational probe design. If desired, cross-links can be reversed to release the target after capture. In contrast to existing probe chemistries, SC probes achieve the high sequence selectivity of a structured probe, yet durably retain their targets even under denaturing conditions. This previously incompatible combination of properties suggests diverse applications based on selective and stable binding of nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent washes in vitro or in situ, or by enzymes in vivo)

Constraining uncertainties in particle-wall deposition correction during SOA formation in chamber experiments

The effect of vapor-wall deposition on secondary organic aerosol (SOA) formation has gained significant attention; however, uncertainties in experimentally derived SOA mass yields due to uncertainties in particle-wall deposition remain. Different approaches have been used to correct for particle-wall deposition in SOA formation studies, each having its own set of assumptions in determining the particle-wall loss rate. In volatile and intermediate-volatility organic compound (VOC and IVOC) systems in which SOA formation is governed by kinetically limited growth, the effect of vapor-wall deposition on SOA mass yields can be constrained by using high surface area concentrations of seed aerosol to promote the condensation of SOA-forming vapors onto seed aerosol instead of the chamber walls. However, under such high seed aerosol levels, the presence of significant coagulation may complicate the particle-wall deposition correction. Here, we present a model framework that accounts for coagulation in chamber studies in which high seed aerosol surface area concentrations are used. For the α-pinene ozonolysis system, we find that after accounting for coagulation, SOA mass yields remain approximately constant when high seed aerosol surface area concentrations ( ≥  8000 µm^2 cm^(−3)) are used, consistent with our prior study (Nah et al., 2016) showing that α-pinene ozonolysis SOA formation is governed by quasi-equilibrium growth. In addition, we systematically assess the uncertainties in the calculated SOA mass concentrations and yields between four different particle-wall loss correction methods over the series of α-pinene ozonolysis experiments. At low seed aerosol surface area concentrations (< 3000 µm^2 cm^(−3)), the SOA mass yields at peak SOA growth obtained from the particle-wall loss correction methods agree within 14 %. However, at high seed aerosol surface area concentrations ( ≥  8000 µm^2 cm^(−3)), the SOA mass yields at peak SOA growth obtained from different particle-wall loss correction methods can differ by as much as 58 %. These differences arise from assumptions made in the particle-wall loss correction regarding the first-order particle-wall loss rate. This study highlights the importance of accounting for particle-wall deposition accurately during SOA formation chamber experiments and assessing the uncertainties associated with the application of the particle-wall deposition correction method when comparing and using SOA mass yields measured in different studies

Improved estimates of preindustrial biomass burning reduce the magnitude of aerosol climate forcing in the Southern Hemisphere.

Fire plays a pivotal role in shaping terrestrial ecosystems and the chemical composition of the atmosphere and thus influences Earth's climate. The trend and magnitude of fire activity over the past few centuries are controversial, which hinders understanding of preindustrial to present-day aerosol radiative forcing. Here, we present evidence from records of 14 Antarctic ice cores and 1 central Andean ice core, suggesting that historical fire activity in the Southern Hemisphere (SH) exceeded present-day levels. To understand this observation, we use a global fire model to show that overall SH fire emissions could have declined by 30% over the 20th century, possibly because of the rapid expansion of land use for agriculture and animal production in middle to high latitudes. Radiative forcing calculations suggest that the decreasing trend in SH fire emissions over the past century largely compensates for the cooling effect of increasing aerosols from fossil fuel and biofuel sources