Balancing act of a leading strand DNA polymerase-specific domain and its exonuclease domain promotes genome-wide sister replication fork symmetry.

Pol2 is the leading-strand DNA polymerase in budding yeast. Here we describe an antagonism between its conserved POPS (Pol2 family-specific catalytic core peripheral subdomain) and exonuclease domain and the importance of this antagonism in genome replication. We show that multiple defects caused by POPS mutations, including impaired growth and DNA synthesis, genome instability, and reliance on other genome maintenance factors, were rescued by exonuclease inactivation. Single-molecule data revealed that the rescue stemmed from allowing sister replication forks to progress at equal rates. Our data suggest that balanced activity of Pol2's POPS and exonuclease domains is vital for genome replication and stability.

Molecular Basis for Control of Diverse Genome Stability Factors by the Multi-BRCT Scaffold Rtt107.

BRCT domains support myriad protein-protein interactions involved in genome maintenance. Although di-BRCT recognition of phospho-proteins is well known to support the genotoxic response, whether multi-BRCT domains can acquire distinct structures and functions is unclear. Here we present the tetra-BRCT structures from the conserved yeast protein Rtt107 in free and ligand-bound forms. The four BRCT repeats fold into a tetrahedral structure that recognizes unmodified ligands using a bi-partite mechanism, suggesting repeat origami enabling function acquisition. Functional studies show that Rtt107 binding of partner proteins of diverse activities promotes genome replication and stability in both distinct and concerted manners. A unified theme is that tetra- and di-BRCT domains of Rtt107 collaborate to recruit partner proteins to chromatin. Our work thus illustrates how a master regulator uses two types of BRCT domains to recognize distinct genome factors and direct them to chromatin for constitutive genome protection.

Occurrence, Spatial Distribution, and Bioaccumulation of Dissolved Synthetic Musks in Freshwaters across China.

Commercial chemicals, such as synthetic musks, are of global concern, but data on their occurrence and spatial distribution in aquatic environments of large scale are scarce. Two sampling campaigns were conducted in the present study to measure freely dissolved synthetic musks in freshwaters across China using passive samplers, along with biological coexposure at selected sites. Polycyclic musks (PCMs) dominated synthetic musks, with a detection frequency of 95%. Higher concentrations of PCMs were observed in densely populated Mid, East, and South China compared to less populated regions, indicating the significance of anthropogenic activities for synthetic musks in water. The concentration ratios of galaxolide (HHCB)/tonalide (AHTN) were significantly higher in low-latitude areas than in high-latitude areas from June to September, suggesting that solar radiation played an important role in the degradation of HHCB/AHTN. Significant correlations were found between dissolved concentrations of HHCB and AHTN and their lipid-normalized concentrations in coexposed fish and clam. The estimated hazard quotients for HHCB and AHTN in freshwater fish consumed by humans were less than 0.01 at all sampling sites except the Yangtze River Basin. These results help to understand the environmental fate and ecological risks of synthetic musks on a large geographical scale.

The Srs2 helicase dampens DNA damage checkpoint by recycling RPA from chromatin.

The DNA damage checkpoint induces many cellular changes to cope with genotoxic stress. However, persistent checkpoint signaling can be detrimental to growth partly due to blockage of cell cycle resumption. Checkpoint dampening is essential to counter such harmful effects, but its mechanisms remain to be understood. Here, we show that the DNA helicase Srs2 removes a key checkpoint sensor complex, RPA, from chromatin to down-regulate checkpoint signaling in budding yeast. The Srs2 and RPA antagonism is supported by their numerous suppressive genetic interactions. Importantly, moderate reduction of RPA binding to single-strand DNA (ssDNA) rescues hypercheckpoint signaling caused by the loss of Srs2 or its helicase activity. This rescue correlates with a reduction in the accumulated RPA and the associated checkpoint kinase on chromatin in srs2 mutants. Moreover, our data suggest that Srs2 regulation of RPA is separable from its roles in recombinational repair and critically contributes to genotoxin resistance. We conclude that dampening checkpoint by Srs2-mediated RPA recycling from chromatin aids cellular survival of genotoxic stress and has potential implications in other types of DNA transactions.

How anthropogenic factors influence the dissolved oxygen in surface water over three decades in eastern China?

The aquatic environment, linked to the sustainable development of human existence and ecological environment, is influenced comprehensively by anthropogenic and natural activities. In light of the continuously low concentration of dissolved oxygen (DO) in surface water in plain river networks and the phenomenon of delay in the improvement of surface water quality, this research aims to introduce a method that may be utilized in identifying the critical driving forces of DO in surface water and their lagging characteristics, which will contribute to the assessment and adjustment of water quality drivers and/or policies. The research analyzes a typical small watershed in a river network region of the Yangtze River Delta plain as the study area, collecting 35-year (1986-2020) data on several water quality parameters, decades of anthropogenic activities, and two natural factors. The time series methods of vector autoregressive model, Granger causality tests, forecast error variance decompositions, and impulse response functions (hereinafter referred to as VAR+), which are rarely applied in related research, were employed in this study and proved helpful for screening out pivotal drivers and capturing the lagging responses of DO level to driving forces at each lagged time. Results show that there exists a fluctuating drop in DO level in surface water from 1986 to 2008 and a steady climb from 2008 to 2020, with the lowest DO level being present in 2008. The impulsive perturbations of phosphate fertilizer consumption (PFC), motor vessel number, and precipitation minimally increase DO concentration, while the impulsive perturbation of gross domestic product (GDP) causes the sharpest drop in DO level. With these perturbations, the driving force of PFC persists for approximately seven years, and the driving forces of water temperature, permanent population, and GDP persist for only five years. Future research could be conducted with spatial hysteresis, selection of lag order and variable quantity within the model, as well as intermediate variables between drivers and DO level for exploring driving pathways and mechanisms.

Rethinking personal carbon trading (PCT) mechanism: A comprehensive review.

The implementation of Personal Carbon Trading (PCT) holds promise in facilitating a noteworthy contribution towards the attainment of emissions reduction predicated on consumption patterns and consequently motivating lifestyle modifications. As individual consumption behaviors usually lead to continuous changes in carbon emissions, it is crucial to rethink PCT from a systematic perspective. This review employed a bibliometric analysis of 1423 papers related to PCT, highlighting the key themes of carbon emissions from energy consumption, climate change, and public opinion on policies in the context of PCT. Most of the existing PCT researches focus on theoretical assumptions and public attitudes, while the quantification of carbon emissions and simulation of PCT require further investigation. Furthermore, the concept of Tan Pu Hui is seldom addressed in PCT studies and case analyses. Moreover, there are limited PCT schemes worldwide that can be directly implemented in practice, leading to a scarcity of large-scale, high-participation case studies. To address these gaps, this review proposes a framework to clarify how PCT can stimulate individual emission reductions on the consumption side, comprising two phases, from motivation to behavior and behavior to target. Future endeavors should prioritize the enhancement of the systematic study of the theoretical foundation of PCT, encompassing carbon emissions accounting and policy design, the incorporation of cutting-edge technology, and the reinforcement of integrated policy practice. This review serves as a valuable reference for future research endeavors and policymaking efforts.

Sumoylation of the DNA polymerase ε by the Smc5/6 complex contributes to DNA replication.

DNA polymerase epsilon (Pol ε) is critical for genome duplication, but little is known about how post-translational modification regulates its function. Here we report that the Pol ε catalytic subunit Pol2 in yeast is sumoylated at a single lysine within a catalytic domain insertion uniquely possessed by Pol2 family members. We found that Pol2 sumoylation occurs specifically in S phase and is increased under conditions of replication fork blockade. Analyses of the genetic requirements of this modification indicate that Pol2 sumoylation is associated with replication fork progression and dependent on the Smc5/6 SUMO ligase known to promote DNA synthesis. Consistently, the pol2 sumoylation mutant phenotype suggests impaired replication progression and increased levels of gross chromosomal rearrangements. Our findings thus indicate a direct role for SUMO in Pol2-mediated DNA synthesis and a molecular basis for Smc5/6-mediated regulation of genome stability.

Application of Hi-throat/Hi-volume SPE technique in analyzing occurrence, influencing factors and human health risk of organophosphate esters (OPEs) in drinking water of China.

Organophosphate esters (OPEs) are typical industrial additives widely applied in various industrial and household products, but they may pollute drinking water. In the present study, the occurrence of OPEs in drinking water was analyzed. For this purpose, 25 drinking water samples were collected from households in 25 cities in China. The concentrations of OPEs were accurately determined according to a high-throughput organic analysis testing combined with high-volume solid phase extraction (Hi-throat/Hi-volume SPE) technique. Through this technique, nine OPEs were detected, with spiked recoveries from 77% to 101%, and their total concentrations (ΣOPEs) ranging from 46.8 to 251 (average 126) ng L-1. The detection frequencies of the selected OPEs determined via Hi-throat/Hi-volume SPE were 88.0%-100%, which are much higher than those previously reported. The limit of detections of the OPEs was low at < 0.01 ng L-1, which could be mainly attributed to the high volume of accumulated drinking water (>20 L). OPEs in drinking water presented a decreasing trend from cities in coastal provinces to inland cities of China. Redundancy analysis showed that the concentrations of OPEs in drinking water were significantly influenced by economic-demographic influencing factors. The non-carcinogenic and lifetime carcinogenic risks (non-CR and CR) of the analyzed OPEs in drinking water were negligible for urban residents in China.

Sources apportionment and carcinogenic risk of polycyclic aromatic hydrocarbons in gas phase of urban Shanghai: Based on high volume solid phase extraction (Hi-volume SPE).

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants, posing potentially serious threats to human health. This study analyzed compositional characteristics, sources, and carcinogenic risks of PAHs in the atmospheric gas phase at an urban site in Shanghai, East China. Seventy-four gas phase samples were collected during the warm months of May-October 2018 using a high-volume solid phase extraction (Hi-volume SPE) technique. The total concentration of sixteen priority PAHs (ΣPAHs) was in the range of 5.54-182.05 ng m-3 (average 34.47 ng m-3) and the total of seven carcinogenic PAHs (ΣCPAHs) was in range of 0.03-1.49 ng m-3 (average 0.48 ng m-3), accounting for 1.47% of ΣPAHs and indicating low carcinogenic potential. Redundancy analyses indicated positive correlations between ΣPAHs and air quality, and ΣCPAHs and average high temperature, and a negative correlation between ΣPAHs and wind speed. Four possible sources, namely petroleum and petrogenic sources, traffic emissions, coal combustion, and mixed gasoline and coal combustion sources, were identified by positive matrix factorization (PMF), accounting for 62.84%, 19.31%, 10.15%, and 7.69% of ΣPAHs, respectively. The overall lifetime lung cancer risk (LLCR) through inhalation of PAHs was estimated to be at a low risk level of 1.61 × 10-5. The LLCR based on PMF apportionment decreased in the order of mixed gasoline and coal combustion sources (47.07%) > traffic emissions (35.10%) > petroleum and petrogenic sources (11.06%) > coal combustion (6.74%). This study demonstrates the effectiveness of Hi-volume SPE in collecting and analyzing atmospheric gas phase PAHs.

Developmental regulation of the Tetrahymena thermophila origin recognition complex.

The Tetrahymena thermophila DNA replication machinery faces unique demands due to the compartmentalization of two functionally distinct nuclei within a single cytoplasm, and complex developmental program. Here we present evidence for programmed changes in ORC and MCM abundance that are not consistent with conventional models for DNA replication. As a starting point, we show that ORC dosage is critical during the vegetative cell cycle and development. A moderate reduction in Orc1p induces genome instability in the diploid micronucleus, aberrant division of the polyploid macronucleus, and failure to generate a robust intra-S phase checkpoint response. In contrast to yeast ORC2 mutants, replication initiation is unaffected; instead, replication forks elongation is perturbed, as Mcm6p levels decline in parallel with Orc1p. Experimentally induced down-regulation of ORC and MCMs also impairs endoreplication and gene amplification, consistent with essential roles during development. Unexpectedly Orc1p and Mcm6p levels fluctuate dramatically in developing wild type conjugants, increasing for early cycles of conventional micronuclear DNA replication and macronuclear anlagen replication (endoreplication phase I, rDNA gene amplification). This increase does not reflect the DNA replication load, as much less DNA is synthesized during this developmental window compared to vegetative S phase. Furthermore, although Orc1p levels transiently increase prior to endoreplication phase II, Orc1p and Mcm6p levels decline when the replication load increases and unconventional DNA replication intermediates are produced. We propose that replication initiation is re-programmed to meet different requirements or challenges during the successive stages of Tetrahymena development.

Checkpoint Activation of an Unconventional DNA Replication Program in Tetrahymena.

The intra-S phase checkpoint kinase of metazoa and yeast, ATR/MEC1, protects chromosomes from DNA damage and replication stress by phosphorylating subunits of the replicative helicase, MCM2-7. Here we describe an unprecedented ATR-dependent pathway in Tetrahymena thermophila in which the essential pre-replicative complex proteins, Orc1p, Orc2p and Mcm6p are degraded in hydroxyurea-treated S phase cells. Chromosomes undergo global changes during HU-arrest, including phosphorylation of histone H2A.X, deacetylation of histone H3, and an apparent diminution in DNA content that can be blocked by the deacetylase inhibitor sodium butyrate. Most remarkably, the cell cycle rapidly resumes upon hydroxyurea removal, and the entire genome is replicated prior to replenishment of ORC and MCMs. While stalled replication forks are elongated under these conditions, DNA fiber imaging revealed that most replicating molecules are produced by new initiation events. Furthermore, the sole origin in the ribosomal DNA minichromosome is inactive and replication appears to initiate near the rRNA promoter. The collective data raise the possibility that replication initiation occurs by an ORC-independent mechanism during the recovery from HU-induced replication stress.

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.

Replication fork regression and its regulation.

One major challenge during genome duplication is the stalling of DNA replication forks by various forms of template blockages. As these barriers can lead to incomplete replication, multiple mechanisms have to act concertedly to correct and rescue stalled replication forks. Among these mechanisms, replication fork regression entails simultaneous annealing of nascent and template strands, which leads to regression of replication forks and formation of four-way DNA junctions. In principle, this process can lead to either positive outcomes, such as DNA repair and replication resumption, or less desirable outcomes, such as misalignment between nascent and template DNA and DNA cleavage. While our understanding of replication fork regression and its various possible outcomes is still at an early stage, recent studies using combinational approaches in multiple organisms have begun to identify the enzymes that catalyze this DNA transaction and how these enzymes are regulated, as well as the specific manners by which fork regression can influence replication. This review summarizes these recent progresses. In keeping with the theme of this series of reviews, we focus on studies in yeast and compare to findings in higher eukaryotes. It is anticipated that these findings will form the basis for future endeavors to further elucidate replication fork remodeling and its implications for genome maintenance.

Environmental Risk Implications of Metals in Sludges from Waste Water Treatment Plants: The Discovery of Vast Stores of Metal-Containing Nanoparticles.

Nanoparticle (NP) assessment in sludge materials, although of growing importance in eco- and biotoxicity studies, is commonly overlooked and, at best, understudied. In the present study, sewage sludge samples from across the mega-city of Shanghai, China were investigated for the first time using a sequential extraction method coupled with single particle inductively coupled plasma mass spectrometry (SP-ICP-MS) to quantify the abundance of metal-containing NPs in the extraction fractions and transmission electron microscopy to specifically identify the nanophases present. In general, most sludges observed showed high concentrations of Cr, Cu, Cd, Ni, Zn, and Pb, exceeding the maximum permitted values in the national application standard of acid soil in China. NPs in these sludges contribute little to the volume and mass but account for about half of the total particle number. Based on electron microscopy techniques, various NPs were further identified, including Ti-, Fe-, Zn-, Sn-, and Pb-containing NPs. All NPs, ignored by traditional metal risk evaluation methods, were observed at a concentration of 107 -1011 particles/g within the bioavailable fraction of metals. These results indicate the underestimate or misestimation in evaluating the environmental risks of metals based on traditional sequential extraction methods. A new approach for the environmental risk assessment of metals, including NPs, is urgently needed.

Organic Contaminants in Chinese Sewage Sludge: A Meta-Analysis of the Literature of the Past 30 Years.

The production of sewage sludge is increasing in China but with unsafe disposal practices, causing potential risk to human health and the environment. Using literature from the past 30 years (N = 159), we conducted a meta-analysis of organic contaminants (OCs) in Chinese sludge. Most data were available from developed and populated regions, and no data were found for Tibet. Since 1987, 35 classes of chemicals consisting of 749 individual compounds and 1 mixture have been analyzed, in which antibiotics and polycyclic aromatic hydrocarbons (PAHs) were the most targeted analytes. For 13 classes of principal OCs (defined as chemicals detected in over five studies) in sludge, the median (expressed in nanograms per gram dry weight) was the highest for phthalate esters (27 900), followed by alkylphenol polyethoxylates (12 000), synthetic musks (5800), antibiotics (4240), PAHs (3490), ultraviolet stabilizers (670), bisphenol analogs (160), organochlorine pesticides (110), polybrominated diphenyl ethers (100), pharmaceuticals (84), hormones (69), perfluorinated compounds (21), and polychlorinated biphenyls (15). Concentrations of PAHs in sludges collected between 1998 and 2012 showed a decreasing trend. Study findings suggest the need for a Chinese national sewage sludge survey to identify and regulate toxic OCs, ideally employing both targeted as well as nontargeted screening approaches.

New insight into the effects of Ca(II) on cake layer structure in submerged membrane bioreactors.

The effects of Ca(II) on the structure of the cake layer in submerged membrane bioreactors (SMBRs) were investigated in this study. Three parallel laboratory-scale SMBRs were operated with synthetic municipal wastewater with three Ca(II) levels (82, 208 and 410 mg l(-1)). As the Ca(II) concentration increased, the sludge floc size increased and the molecular weight of the soluble microbial products (SMP) in the bulk liquid decreased. These observations were attributed to the neutralization and bridging function of Ca(II). Furthermore, Ca(II) addition did not change the thickness of the cake layer, but inhibited the deposition of other elements, such as Al, Si, Mg, and Fe. As a result of Ca(II) addition, the cake layer became less compact and more porous. The interspaces among the flocs in the cake layer helped to reduce the membrane fouling potential.

Effects of low-concentration Cr(VI) on the performance and the membrane fouling of a submerged membrane bioreactor in the treatment of municipal wastewater.

The effects of low-concentration Cr(VI) (0.4 mg l(-1)) on the performance of a submerged membrane bioreactor (SMBR) in the treatment of municipal wastewater, as well as membrane fouling were investigated. Compared with the SMBR for control municipal wastewater, the SMBR for Cr(VI)-containing municipal wastewater had a higher concentration of soluble microbial products (SMP) with lower molecular weights, and smaller sludge particle sizes. Furthermore, low-concentration Cr(VI) induced membrane fouling, especially irreversible membrane pore blocking, which markedly shortened the service life of the membrane.

Comprehensive risk assessment of heavy metals in lake sediment from public parks in Shanghai.

Rapid urbanization has caused potential pollution of heavy metal in Shanghai. A comprehensive pollution study of heavy metals (Cd, Cu, Pb, and Zn) in 35 lake surface sediments from city parks in the four different urbanized areas of Shanghai was conducted. Intensive human activities caused moderate enrichment of the four metals in highly urbanized areas, especially Cd with the significant enrichment in the central urban core area. However, the levels of the four metals in all the sediments were lower than the corresponding consensus-based Probable Effect Concentration, indicating adverse effects not to occur frequently. The integrated pollution assessments of multiple heavy metals also suggested low ecological risk and 15-29 percent probability of toxicity in most of sediments. The metal speciation analysis showed that Cd, Cu, Pb, and Zn were dominated by the non-residual fractions and thus they have high mobility and bioavailability, indicating significant anthropogenic sources. According to the Risk Assessment Code, Cd had the highest bioavailable fraction and represented high or very high risk, followed by Zn with medium or high risks in most of samples, while no or low risk was found for Cu and Pb at most sites because they were dominated by reducible and residual fractions. Correlation analysis showed that chemical fractions of heavy metals were prone to transform among each other if environmental conditions changed. Therefore, in view of anthropogenic inputs and speciation distribution, heavy metals with very high bioavailability at very low total levels and those with low bioavailability at very high total levels should not be ignored.

Potential gap in understanding cyanoHABs: Light-dependent morphological variations in colonial cyanobacterium Microcystis.

Colony formation is a crucial characteristic of Microcystis, a cyanobacterium known for causing cyanobacterial harmful algal blooms (cyanoHABs). It has been observed that as Microcystis colonies grow larger, they often become less densely packed, which correlates with a decrease in light penetration. The objective of this study was to investigate the effects of light limitation on the morphological variations in Microcystis, particularly in relation to the crowded cellular environment. The results indicated that when there was sufficient light (transmittance = 100 %) to support a growth rate of 0.11±0.01 day-1, a significant increase in colony size was found, from 466±15 µm to 1030±111 µm. However, under light limitation (transmittance = 50 % - 1 %) where the growth rate was lower than 0, there was no significant improvement in colony size. Microcystis in the light limitation groups exhibited a loose cell arrangement and even the presence of holes or pores within the colony, confirming the negative correlation between colony size and cell arrangement. This pattern is driven by regional differences in growth within the colony, as internal cells have a significantly lower frequency of division compared to peripheral cells, due to intra-colony self-shading (ICSS). The research demonstrates that Microcystis can adjust its cell arrangement to avoid excessive self-shading, which has implications for predicting and controlling cyanoHABs. These findings also contribute to the understanding of cyanobacterial variations and can potentially inform future research on the diverse phycosphere.

Assessing neonicotinoid accumulation and ecological risks in the aquatic environment of Yangtze River Basin, China.

Neonicotinoids (NNIs) constitute commonly used pesticides across various regions, however, the lack of research and data on its long-term effects and threshold levels within specific ecosystems have left an important knowledge gap. This study aimed to comprehensively examine NNI concentrations and their potential impacts on human health and aquatic organisms in the region of the Yangtze River Basin (YRB). The study employed datasets on seven commonly applied NNIs across 244 surface water samples collected from 12 distinct geographic sites within the YRB. The relative potency factor was used to evaluate human exposure risks, while the species sensitivity distribution could estimate acute and chronic hazardous concentrations for 5% of species (HC5) for NNIs impacting aquatic organisms. Analysis revealed varying NNI concentrations across the sampled sites, with thiacloprid recording the lowest concentration at 0.1 ng L-1, and dinotefuran recording a high concentration of 408 ng L-1. The observation indicated NNI concentration declined at sampling sites downstream of the YRB. Infants were identified as the most vulnerable to NNI exposure, with an estimated daily intake of 40.8 ng kg-1 bw d-1. The acute HC5 was determined at 946 ng L-1 and a chronic HC5 at 338 ng L-1, to NNI hazards. These findings highlight the urgent need for a more comprehensive understanding of the ecological implications and hazards posed by NNIs within the YRB. Variations in NNI concentrations across sites, potential risks to human health, and increased vulnerability of aquatic organisms from this study underscore the necessity for further research and concerted efforts to mitigate these ecological threats in the region.