Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems.

Phages (viruses of bacteria and archaea) are a ubiquitous top-down control on microbial communities by selectively infecting and killing cells. As obligate parasites, phages are inherently linked to processes that impact their hosts' distribution and physiology, but phages can also be impacted by external, environmental factors, such as UV radiation degrading their virions. To better understand these complex links of phages to their hosts and the environment, we leverage the unique ecological context of the Isthmus of Panama, which narrowly disconnects the productive Tropical Eastern Pacific (EP) and nutrient-poor Tropical Western Atlantic (WA) provinces.

Synthesizing evidence for the external cycling of NO in high- to low-NO atmospheres.

External cycling regenerating nitrogen oxides (NO ≡ NO + NO) from their oxidative reservoir, NO, is proposed to reshape the temporal-spatial distribution of NO and consequently hydroxyl radical (OH), the most important oxidant in the atmosphere. Here we verify the in situ external cycling of NO in various environments with nitrous acid (HONO) as an intermediate based on synthesized field evidence collected onboard aircraft platform at daytime. External cycling helps to reconcile stubborn underestimation on observed ratios of HONO/NO and NO/NO by current chemical model schemes and rationalize atypical diurnal concentration profiles of HONO and NO lacking noontime valleys specially observed in low-NO atmospheres.

Phylogenetic diversity and functional potential of large and cell-associated viruses in the Bay of Bengal.

The BoB, the world's largest bay, is of significant economic importance to surrounding countries, particularly Bangladesh, which heavily relies on its coastal resources. Concurrently, the BoB holds substantial ecological relevance due to the region's high vulnerability to climate change-induced impacts. Yet, our understanding of the BoB's microbiome in relation to marine food web and biogeochemical cycling remains limited.

Characterization of prophages in bacterial genomes from the honey bee ( gut microbiome.

The gut of the European honey bee ( possesses a relatively simple bacterial community, but little is known about its community of prophages (temperate bacteriophages integrated into the bacterial genome). Although prophages may eventually begin replicating and kill their bacterial hosts, they can also sometimes be beneficial for their hosts by conferring protection from other phage infections or encoding genes in metabolic pathways and for toxins. In this study, we explored prophages in 17 species of core bacteria in the honey bee gut and two honey bee pathogens.

An Inversion Framework for Optimizing Non-Methane VOC Emissions Using Remote Sensing and Airborne Observations in Northeast Asia During the KORUS-AQ Field Campaign.

We aim to reduce uncertainties in CHO and other volatile organic carbon (VOC) emissions through assimilation of remote sensing data. We first update a three-dimensional (3D) chemical transport model, GEOS-Chem with the KORUSv5 anthropogenic emission inventory and inclusion of chemistry for aromatics and CH, leading to modest improvements in simulation of CHO (normalized mean bias (NMB): -0.57 to -0.

Extended DNA-binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks.

Elevated DNA replication stress causes instability of the DNA replication fork and increased DNA mutations, which underlies tumorigenesis. The DNA replication stress regulator silencing-defective 2 (SDE2) is known to bind to TIMELESS (TIM), a protein of the fork protection complex, and enhances its stability, thereby supporting replisome activity at DNA replication forks. However, the DNA-binding activity of SDE2 is not well defined.

Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages.

Recent research has underscored the immense diversity and key biogeochemical roles of large DNA viruses in the ocean. Although they are important constituents of marine ecosystems, it is sometimes difficult to detect these viruses due to their large size and complex genomes. This is true for "jumbo" bacteriophages, which have genome sizes >200 kbp and large capsids reaching up to 0.

Boundary layer versus free tropospheric submicron particle formation: A case study from NASA DC-8 observations in the Asian continental outflow during the KORUS-AQ campaign.

In this study, we contrasted major secondary inorganic species and processes responsible for submicron particle formation (SPF) events in the boundary layer (BL) and free troposphere (FT) over the Korean Peninsula during Korea-United States Air Quality (KORUS-AQ) campaign (May-June, 2016) using aircraft observations. The number concentration of ultrafine particles with diameters between 3 nm and 10 nm (N) during the entire KORUS-AQ period reached a peak (7,606 ± 12,003 cm ) at below 1 km altitude, implying that the particle formation around the Korean Peninsula primarily occurred in the daytime BL. During the BL SPF case (7 May, 2016), the SPF over Seoul metropolitan area was more attributable to oxidation of NO rather than SO-to-sulfate conversion.

Variability and Time of Day Dependence of Ozone Photochemistry in Western Wildfire Plumes.

Understanding the efficiency and variability of photochemical ozone (O) production from western wildfire plumes is important to accurately estimate their influence on North American air quality. A set of photochemical measurements were made from the NOAA Twin Otter research aircraft as a part of the Fire Influence on Regional to Global Environments and Air Quality (FIREX-AQ) experiment. We use a zero-dimensional (0-D) box model to investigate the chemistry driving O production in modeled plumes.

The role of a suburban forest in controlling vertical trace gas and OH reactivity distributions - a case study for the Seoul metropolitan area.

We present trace gas vertical profiles observed by instruments on the NASA DC-8 and at a ground site during the Korea-US air quality study (KORUS) field campaign in May to June 2016. We focus on the region near the Seoul metropolitan area and its surroundings where both anthropogenic and natural emission sources play an important role in local photochemistry. Integrating ground and airborne observations is the major research goal of many atmospheric chemistry field campaigns.

Widespread endogenization of giant viruses shapes genomes of green algae.

Endogenous viral elements (EVEs)-viruses that have integrated their genomes into those of their hosts-are prevalent in eukaryotes and have an important role in genome evolution. The vast majority of EVEs that have been identified to date are small genomic regions comprising a few genes, but recent evidence suggests that some large double-stranded DNA viruses may also endogenize into the genome of the host. Nucleocytoplasmic large DNA viruses (NCLDVs) have recently become of great interest owing to their large genomes and complex evolutionary origins, but it is not yet known whether they are a prominent component of eukaryotic EVEs.

Unbiased Screens Show CD8 T Cells of COVID-19 Patients Recognize Shared Epitopes in SARS-CoV-2 that Largely Reside outside the Spike Protein.

Developing effective strategies to prevent or treat coronavirus disease 2019 (COVID-19) requires understanding the natural immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We used an unbiased, genome-wide screening technology to determine the precise peptide sequences in SARS-CoV-2 that are recognized by the memory CD8 T cells of COVID-19 patients. In total, we identified 3-8 epitopes for each of the 6 most prevalent human leukocyte antigen (HLA) types.

SDE2 integrates into the TIMELESS-TIPIN complex to protect stalled replication forks.

Protecting replication fork integrity during DNA replication is essential for maintaining genome stability. Here, we report that SDE2, a PCNA-associated protein, plays a key role in maintaining active replication and counteracting replication stress by regulating the replication fork protection complex (FPC). SDE2 directly interacts with the FPC component TIMELESS (TIM) and enhances its stability, thereby aiding TIM localization to replication forks and the coordination of replisome progression.

Anthropogenic control over wintertime oxidation of atmospheric pollutants.

During winter in the mid-latitudes, photochemical oxidation is significantly slower than in summer and the main radical oxidants driving formation of secondary pollutants, such as fine particulate matter and ozone, remain uncertain, owing to a lack of observations in this season. Using airborne observations, we quantify the contribution of various oxidants on a regional basis during winter, enabling improved chemical descriptions of wintertime air pollution transformations. We show that 25-60% of NO is converted to NO via multiphase reactions between gas-phase nitrogen oxide reservoirs and aerosol particles, with ~93% reacting in the marine boundary layer to form >2.

A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase.

Bacteriophages play critical roles in the biosphere, but their vast genomic diversity has obscured their evolutionary origins, and phylogenetic analyses have traditionally been hindered by their lack of universal phylogenetic marker genes. In this study we mine metagenomic data and identify a clade of Caudovirales that encodes the β and β' subunits of multi-subunit RNA polymerase (RNAP), a high-resolution phylogenetic marker which enables detailed evolutionary analyses. Our RNAP phylogeny revealed that the Caudovirales RNAP forms a clade distinct from cellular homologs, suggesting an ancient acquisition of this enzyme.

Assessment of NO observations during DISCOVER-AQ and KORUS-AQ field campaigns.

NASA's Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality (DISCOVER-AQ, conducted in 2011-2014) campaign in the United States and the joint NASA and National Institute of Environmental Research (NIER) Korea-United States Air Quality Study (KORUS-AQ, conducted in 2016) in South Korea were two field study programs that provided comprehensive, integrated datasets of airborne and surface observations of atmospheric constituents, including nitrogen dioxide (NO), with the goal of improving the interpretation of spaceborne remote sensing data. Various types of NO measurements were made, including in situ concentrations and column amounts of NO using ground- and aircraft-based instruments, while NO column amounts were being derived from the Ozone Monitoring Instrument (OMI) on the Aura satellite. This study takes advantage of these unique datasets by first evaluating in situ data taken from two different instruments on the same aircraft platform, comparing coincidently sampled profile-integrated columns from aircraft spirals with remotely sensed column observations from ground-based Pandora spectrometers, intercomparing column observations from the ground (Pandora), aircraft (in situ vertical spirals), and space (OMI), and evaluating NO simulations from coarse Global Modeling Initiative (GMI) and high-resolution regional models.

HONO Emissions from Western U.S. Wildfires Provide Dominant Radical Source in Fresh Wildfire Smoke.

Wildfires are an important source of nitrous acid (HONO), a photolabile radical precursor, yet in situ measurements and quantification of primary HONO emissions from open wildfires have been scarce. We present airborne observations of HONO within wildfire plumes sampled during the Western Wildfire Experiment for Cloud chemistry, Aerosol absorption and Nitrogen (WE-CAN) campaign. ΔHONO/ΔCO close to the fire locations ranged from 0.

Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses.

The discovery of eukaryotic giant viruses has transformed our understanding of the limits of viral complexity, but the extent of their encoded metabolic diversity remains unclear. Here we generate 501 metagenome-assembled genomes of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from environments around the globe, and analyze their encoded functional capacity. We report a remarkable diversity of metabolic genes in widespread giant viruses, including many involved in nutrient uptake, light harvesting, and nitrogen metabolism.

Taehwa Research Forest: A receptor site for severe domestic pollution events in Korea during 2016.

During the May-June 2016 International Cooperative Air Quality Field Study in Korea (KORUS-AQ), light synoptic meteorological forcing facilitated Seoul metropolitan pollution outflow to reach the remote Taehwa Research Forest (TRF) site and cause regulatory exceedances of ozone on 24 days. Two of these severe pollution events are thoroughly examined. The first, occurring on 17 May 2016, tracks transboundary pollution transport exiting eastern China and the Yellow Sea, traversing the Seoul Metropolitan Area (SMA), and then reaching TRF in the afternoon hours with severely polluted conditions.

Proteolytic control of genome integrity at the replication fork.

Faithful duplication of the genome is critical for the survival of an organism and prevention of malignant transformation. Accurate replication of a large amount of genetic information in a timely manner is one of the most challenging cellular processes and is often perturbed by intrinsic and extrinsic barriers to DNA replication fork progression, a phenomenon referred to as DNA replication stress. Elevated DNA replication stress is a primary source of genomic instability and one of the key hallmarks of cancer.

Conditional degradation of SDE2 by the Arg/N-End rule pathway regulates stress response at replication forks.

Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generates Lys-SDE2Ct, the C-terminal SDE2 fragment bearing an N-terminal Lys residue.

Modeling NHNO Over the San Joaquin Valley During the 2013 DISCOVER-AQ Campaign.

The San Joaquin Valley (SJV) of California experiences high concentrations of particulate matter NHNO during episodes of meteorological stagnation in winter. A rich data set of observations related to NHNO formation was acquired during multiple periods of elevated NHNO during the Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality (DISCOVER-AQ) field campaign in SJV in January and February 2013. Here NHNO is simulated during the SJV DISCOVER-AQ study period with the Community Multiscale Air Quality (CMAQ) model, diagnostic model evaluation is performed using the DISCOVER-AQ data set, and integrated reaction rate analysis is used to quantify HNO production rates.