SMARCC2 silencing suppresses oncogenic activation through modulation of chromatin accessibility in breast cancer.

SWI/SNF chromatin remodeling complexes play a key role in gene transcription as epigenetic regulators and are typically considered to act as tumor suppressors in cancers. Compared to other cancer-related components of the SWI/SNF complex, research on SMARCC2, a component of the initial BAF core, has been relatively limited. This study aimed to elucidate the role of SMARCC2 in breast cancer by employing various in vitro and in vivo methods including cell proliferation assays, mammosphere formation, and xenograft models, complemented by RNA-seq, ATAC-seq, and ChIP analyses. The results showed that SMARCC2 silencing surprisingly led to the suppression of breast tumorigenesis, indicating a pro-tumorigenic function for SMARCC2 in breast cancer, which contrasts with the roles of other SWI/SNF subunits. In addition, SMARCC2 depletion reduces cancer stem cell features of breast cancer cells. Mechanistic study showed that SMARCC2 silencing downregulated the oncogenic Ras-PI3K signaling pathway, likely by directly regulating the chromatin accessibility of the enhancers of the key genes such as PIK3CB. Together, these results expand our understanding of the SWI/SNF complex's role in cancer development and identify SMARCC2 as a promising new target for breast cancer therapies.

Remediation of uranium-contaminated alkaline soil by rational application of phosphorus fertilizers: Effect and mechanism.

In alkaline soil, abundant carbonates will mobilize uranium (U) and increase its ecotoxicity, which is a serious threat to crop growth. However, the knowledge of U remediation in alkaline soils remains very limited. In this study, U-contaminated alkaline soil (tillage layer) was collected from the Ili mining area of Xinjiang, the soil remediation was carried out by using phosphorus (P) fertilizers of different solubility (including KH2PO4, Ca(H2PO4)2, CaHPO4, and Ca3(PO4)2), and the pathways and mechanisms of U passivation in the alkaline soil were revealed. The results showed that water-soluble P fertilizers, KH2PO4 and Ca(H2PO4)2, were highly effective at immobilizing U, and significantly reduced the bioavailability of soil U. The exchangeable U was reduced by 70.5 ± 0.1% (KH2PO4) and 68.2 ± 1.9% (Ca(H2PO4)2), which was converted into the Fe-Mn oxide-bound and residual phases. Pot experiments showed that soil remediation by KH2PO4 significantly promoted crop growth, especially for roots, and reduced U uptake in crops by 94.5 ± 1.0%. The immobilization of U by KH2PO4 could be attributed to the release of phosphate anions, which react with the uranyl ion (UO22+) forming a stable mineral of meta-ankoleite and enhancing the binding of UO22+ to the soil Fe-Mn oxides. In addition, KH2PO4 dissolution produces acidity and P fertilizer, which can reduce soil alkalinity and improve crop growth. The findings in this work demonstrate that a rational application of P fertilizer can effectively, conveniently, and cheaply remediate U contamination and improve crop yield and safety on alkaline farmland.

TCOF1 coordinates oncogenic activation and rRNA production and promotes tumorigenesis in HCC.

Treacle ribosome biogenesis factor 1 (TCOF1) is a nucleolar factor that regulates ribosomal DNA (rDNA) transcription in the nucleolus. TCOF1 has been previously reported to be implicated in Treacher Collins-Franceschetti syndrome (TCS), a congenital disorder of craniofacial development. Except TCS, TCOF1 has not been reported to be involved in other diseases so far. Here, we show that TCOF1 expression is aberrantly elevated in human hepatocellular carcinoma (HCC) and correlates with HCC progression and poor outcome. In vitro and in vivo studies reveal oncogenic roles of TCOF1 in HCC. Mechanistically, TCOF1 regulates KRAS-activated genes and epithelial-mesenchymal transition (EMT) genes in HCC and is required for the increased ribosomal RNA (rRNA) production, a hallmark of cancer. Interestingly, our analysis reveals an inverse correlation between TCOF1 expression and tumor infiltration of antitumor immune cells, suggesting that TCOF1 may also have an important impact on antitumor immune responses in HCC. Together, our findings support a model in which TCOF1 coordinates oncogenic activation and rRNA production to promote HCC tumorigenesis. The inverse correlation between TCOF1 expression and the infiltration of antitumor immune cells opens a new avenue to understanding the promoting role of TCOF in HCC tumorigenesis.

Interallelic interaction and gene regulation in budding yeast.

InDrosophila, homologous chromosome pairing leads to "transvection," in which the enhancer of a gene can regulate the allelic transcription intrans.Interallelic interactions were also observed in vegetative diploid budding yeast, but their functional significance is unknown. Here, we show that aGAL1reporter can interact with its homologous allele and affect its expression. By ectopically inserting two allelic reporters, one driven by wild-typeGAL1promoter (WTGAL1pr) and the other by a mutant promoter with delayed response to galactose induction, we found that the two reporters physically associate, and the WTGAL1prtriggers synchronized firing of the defective promoter and accelerates its activation without affecting its steady-state expression level. This interaction and the transregulatory effect disappear when the same reporters are located at nonallelic sites. We further demonstrated that the activator Gal4 is essential for the interallelic interaction, and the transregulation requires fully activated WTGAL1prtranscription. The mechanism of this phenomenon was further discussed. Taken together, our data revealed the existence of interallelic gene regulation in yeast, which serves as a starting point for understanding long-distance gene regulation in this genetically tractable system.

Fabricating biogenic Fe(III) flocs from municipal sewage sludge using NAFO processes: Characterization and arsenic removal ability.

This study involved fabricating biogenic Fe(III) flocs enriched from municipal sludge using microbial nitrate-dependent anaerobic Fe(II)-oxidizing (NAFO) processes. The research focused on bacterial community compositions and physicochemical properties of the biogenic Fe(III) flocs and their ability to adsorb arsenic (As). High-throughput sequencing analysis showed that significant microbial succession occurs in the raw sludge after the NAFO processes. The predominant bacterial communities in the biogenic Fe(III) flocs included Rhodanobacter, Parvibaculum, Gemmatimonas and Segetibacter genera. Microscopic and spectroscopic analyses included scanning electron microscopy - energy disperse spectroscopy (SEM-EDS), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy. These tests indicated that biogenic Fe(III) flocs were a mixture of NAFO bacteria and nanosized, poorly crystalline Fe(III) oxide particles. Batch experiments showed that after 120 min of reaction time, more than 95% of As(III) and As(V) (at an initial concentrations of 0.25 mg/L) were effectively removed with 120 ppm biogenic Fe(III) flocs. In addition, biogenic Fe(III) flocs removed As more effectively than abiotic Fe(III) flocs. These findings indicated that biogenic Fe(III) flocs produced from municipal sludge using NAFO processes performed well in removing As.

Uranium Bioreduction and Biomineralization.

Following the development of nuclear science and technology, uranium contamination has been an ever increasing concern worldwide because of its potential for migration from the waste repositories and long-term contaminated environments. Physical and chemical techniques for uranium pollution are expensive and challenging. An alternative to these technologies is microbially mediated uranium bioremediation in contaminated water and soil environments due to its reduced cost and environmental friendliness. To date, four basic mechanisms of uranium bioremediation-uranium bioreduction, biosorption, biomineralization, and bioaccumulation-have been established, of which uranium bioreduction and biomineralization have been studied extensively. The objective of this review is to provide an understanding of recent developments in these two fields in relation to relevant microorganisms, mechanisms, influential factors, and obstacles.

Decoupling of divergent gene regulation by sequence-specific DNA binding factors.

Divergent gene pairs (DGPs) are abundant in eukaryotic genomes. Since two genes in a DGP potentially share the same regulatory sequence, one might expect that they should be co-regulated. However, an inspection of yeast DGPs containing cell-cycle or stress response genes revealed that most DGPs are differentially-regulated. The mechanism underlying DGP differential regulation is not understood. Here, we showed that co- versus differential regulation cannot be explained by genetic features including promoter length, binding site orientation, TATA elements, nucleosome distribution, or presence of non-coding RNAs. Using time-lapse fluorescence microscopy, we carried out an in-depth study of a differentially regulated DGP, PFK26-MOB1. We found that their differential regulation is mainly achieved through two DNA-binding factors, Tbf1 and Mcm1. Similar to 'enhancer-blocking insulators' in higher eukaryotes, these factors shield the proximal promoter from the action of more distant transcription regulators. We confirmed the blockage function of Tbf1 using synthetic promoters. We further presented evidence that the blockage mechanism is widely used among genome-wide DGPs. Besides elucidating the DGP regulatory mechanism, our work revealed a novel class of insulators in yeast.

PSI showed higher tolerance to Sb(V) than PSII due to stimulation of cyclic electron flow around PSI.

The knowledge of the effects of Sb(V) on the physiological characteristics of cyanobacteria was still limited. In the present study, responses of photosystem I and II (PSI and PSII), cyclic electron flow (CEF), and interphotosystem electron transport of Microcystis aeruginosa to 5-100 mg/l Sb(V) were synchronously measured using the Dual-PAM-100. 5 mg/l Sb (V) significantly inhibited PSII activity, but had no significant effects on PSI activity. At higher concentrations of Sb(V), the quantum yield and electron transport of PSI were less affected compared to PSII. The ratio of Y(II)/Y(I) significantly decreased with increasing Sb(V) concentration. It decreased from 0.7 for control to 0.4 for 100 mg/l Sb(V)-treated cells, indicating that the change of the distribution of quantum yields between two photosystems and more serious inhibition of PSII under stress of Sb(V) compared to PSI. CEF was activated associated with the inhibition of linear electron flow after exposure to Sb(V). The contribution of Y(CEF) to the quantum yield and activity of PSI increased with increasing Sb(V) concentrations. The cyclic electron transport rate made a significant contribution to electron transport rate of PSI, especially at high Sb(V) concentration (100 mg/l) and high illumination (above 555 µmol photons/m(2)/s). The stimulation of CEF was essential for the higher tolerance of PSI than PSII to Sb(V).

Acetylation regulates Jun protein turnover in Drosophila.

C-Jun is a major transcription factor belonging to the activating protein 1 (AP-1) family. Phosphorylation has been shown to be critical for c-Jun activation and stability. Here, we report that Jra, the Drosophila Jun protein, is acetylated in vivo. We demonstrate that the acetylation of Jra leads to its rapid degradation in response to osmotic stress. Intriguingly, we also found that Jra phosphorylation antagonized its acetylation, indicating the opposite roles of acetylation and phosphorylation in Jra degradation process under osmotic stress. Our results provide new insights into how c-Jun proteins are precisely regulated by the interplay of different posttranslational modifications.

Herbicidal effects of harmaline from Peganum harmala on photosynthesis of Chlorella pyrenoidosa: probed by chlorophyll fluorescence and thermoluminescence.

The herbicidal effects of harmaline extracted from Peganum harmala seed on cell growth and photosynthesis of green algae Chlorella pyrenoidosa were investigated using chlorophyll a fluorescence and thermoluminescence techniques. Exposure to harmaline inhibited cell growth, pigments contents and oxygen evolution of C. pyrenoidosa. Oxygen evolution was more sensitive to harmaline toxicity than cell growth or the whole photosystem II (PSII) activity, maybe it was the first target site of harmaline. The JIP-test parameters showed that harmaline inhibited the donor side of PSII. Harmaline decreased photochemical efficiency and electron transport flow of PSII but increased the energy dissipation. The charge recombination was also affected by harmaline. Amplitude of the fast phase decreased and the slow phase increased at the highest level of harmaline. Electron transfer from QA(-) to QB was inhibited and backward electron transport flow from QA(-) to oxygen evolution complex was enhanced at 10 µg mL(-1) harmaline. Exposure to 10 µg mL(-1) harmaline caused appearance of C band in thermoluminescence. Exposure to 5 µg mL(-1) harmaline inhibited the formation of proton gradient. The highest concentration of harmaline treatment inhibited S3QB(-) charge recombination but promoted formation of QA(-)YD(+) charge pairs. P. harmala harmaline may be a promising herbicide because of its inhibition of cell growth, pigments synthesis, oxygen evolution and PSII activities.

Macronutrient and PFOS bioavailability manipulated by aeration-driven rhizospheric organic nanocapsular assembly.

Ubiquitous presence of the extremely persistent pollutants, per- and polyfluoroalkyl substances, is drawing ever-increasing concerns for their high eco-environmental risks which, however, are insufficiently considered based on the assembly characteristics of those amphiphilic molecules in environment. This study investigated the re-organization and self-assembly of perfluorooctane sulfonate (PFOS) and macronutrient molecules from rhizospheric organic (RhO) matter induced with a common operation of aeration. Atomic force microscopy (AFM) with infrared spectroscopy (IR)-mapping clearly showed that, after aeration and stabilization, RhO nanocapsules (∼ 1000 nm or smaller) with a core of PFOS-protein complexes coated by "lipid-carbohydrate" layers were observed whereas the capsule structure with a lipid core surrounded by "protein-carbohydrate-protein" multilayers was obtained in the absence of PFOS. It is aeration that exerted the disassociation of pristine RhO components, after which the environmental concentration PFOS restructured the self-assembly structure in a conspicuous "disorder-to-order" transition. AFM IR-mapping analysis of faeces combined with quantification of component uptake denoted the decreased ingestion and utilization of both PFOS and proteins compared with lipids and carbohydrates when Daphnia magna were fed with RhO nanocapsules. RhO nanocapsules acted as double-edged swords via simultaneously impeding the bioaccessibility of hazardous PFOS molecules and macronutrient proteins; and the latter might be more significant, which caused a malnutrition status within merely 48 h. Elucidating the assembly structure of natural organic matter and environmental concentration PFOS, the finding of this work could be a crucial supplementation to the high-dose-dependent eco-effect investigations on PFOS.

Microbial antagonistic mechanisms of Hg(II) and Se(IV) in efficient wastewater treatment using granular sludge.

The antagonistic effects of mercury (Hg) and selenium (Se) have been extensively studied in higher animals and plants. In this study, the microbial antagonistic effects of Hg and Se were utilized for wastewater treatment. We developed and optimized a new granular sludge approach to efficiently remove Hg(II) and Se(IV) from wastewater. Under anaerobic-oxic-anaerobic (AOA) conditions, the removal rates of Hg(II) and Se(IV) reached up to 99.91±0.07 % and 97.7 ± 0.8 %, respectively. The wastewater Hg(II) was mostly (97.43±0.01 %) converted to an inert mineral called tiemannite (HgSe) in the sludge, and no methylmercury (MeHg) was detected. The HgSe in sludge is less toxic, with almost no risk of secondary release, and it can be recovered with high purity. An inhibition experiment of mercury reduction and the high expression of the mer operon indicated that most Hg(II) (∼71 %) was first reduced to Hg0, and then Hg0 reacted with Se0 to synthesize HgSe. Metagenomic results showed that the final sludge (day 182) was dominated by two unclassified bacteria in the orders Rhodospirillales (27.7 %) and Xanthomonadales (6.3 %). Their metagenome-assembled genomes (MAGs) were recovered, suggesting that both of them can reduce Hg(II) and Se(IV). Metatranscriptomic analyses indicate that they can independently and cooperatively synthesize HgSe. In summary, granular sludge under AOA conditions is an efficient method for removing and recovering Hg from wastewater. The microbial transformation of Hg2+to Hg0 to HgSe may occur widely in both engineering and natural ecosystems.

Efficient and synergistic treatment of selenium (IV)-contaminated wastewater and mercury (II)-contaminated soil by anaerobic granular sludge: Performance and mechanisms.

Wastewater containing selenium (Se) and soil contaminated by mercury (Hg) are two environmental problems, but they are rarely considered for synergistic treatment. In this work, anaerobic granular sludge (AnGS) was used to address both of the aforementioned issues simultaneously. The performance and mechanisms of Se(IV) removal from wastewater and Hg(II) immobilization in soil were investigated using various technologies. The results of the reactor operation indicated that the AnGS efficiently removed Se from wastewater, with a removal rate of 99.94 ± 0.05%. The microbial communities in the AnGS could rapidly reduce Se(IV) to Se0 nanoparticles (SeNPs). However, the AnGS lost the ability to reduce Se(IV) once the Se0 content reached the saturation value of 5.68 g Se/L. The excess sludge of Se0-rich AnGS was applied to remediate soil contaminated with Hg(II). The Se0-rich AnGS largely decreased the percentage of soil Hg in the mobile, extractable phase, with up to 99.1 ± 0.3% immobilization. Soil Hg(II) and Hg0 can react with Se (-II) and Se0, respectively, to form HgSe. The formation of inert HgSe was an important pathway for immobilizing Hg. Subsequently, the pot experiments indicated that soil remediation using Se0-rich AnGS significantly decreased the Hg content in pea plants. Especially, the content of Hg decreased from 555 ± 100 to 24 ± 3 µg/kg in roots after remediation. In summary, AnGS is an efficient and cost-effective material for synergistically treating Se-contaminated wastewater and Hg-contaminated soil.

Active anaerobic methane oxidation in the groundwater table fluctuation zone of rice paddies.

Rice paddies are globally important sources of methane emissions and also active regions for methane consumption. However, the impact of fluctuating groundwater levels on methane cycling has received limited attention. In this study, we delved into the activity and microbial mechanisms underlying anaerobic oxidation of methane (AOM) in paddy fields. A comprehensive approach was employed, including 13C stable isotope assays, inhibition experiments, real-time quantitative reverse transcription PCR, metagenomic sequencing, and binning technology. Geochemical profiles revealed the abundant coexistence of both methane and electron acceptors in the groundwater table fluctuation (GTF) zone, at a depth of 40-60 cm. Notably, the GTF zone exhibited the highest rate of AOM, potentially linked to the reduction of iron oxides and nitrate. Within this zone, Candidatus Methanoperedens (belonging to the ANME-2d group) dominated the Archaea population, accounting for a remarkable 85.4 %. Furthermore, our results from inhibition experiments, RT-qPCR, and metagenome-assembled genome (MAG) analysis highlighted the active role of Ca. Methanoperedens GTF50 in the GTF zone. This microorganism could independently mediate AOM process through the intriguing "reverse methanogenesis" pathway. Considering the similarity in geochemical conditions across different paddy fields, it is likely that Ca. Methanoperedens-mediated AOM is prevalent in the GTF zones.

Deterioration of single-use biodegradable plastics in high-humidity air and freshwaters over one year: Significant disparities in surface physicochemical characteristics and degradation rates.

More single-use plastics are accumulating in the environment, and likewise biodegradable plastics (BPs), which are being vigorously promoted, cannot escape the fate. Currently, studies on the actual degradation of BPs in open-air and freshwaters are underrepresented despite they are potentially headmost leakage and contamination sites for disposable BPs. Herein, we compared the degradation behavior of six BP materials and non-degradable polypropylene (PP) plastics over a 1-year in situ suspension in the high-humidity air, a eutrophic river, and an oligotrophic lake. Moreover, a 3-months laboratory incubation was performed to detect the release of dissolved organic carbon (DOC) from BPs. In both air and freshwaters, poly(p-dioxanone) (PPDO) degraded significantly while PP and polylactic acid (PLA) showed no signs of degradation. The average degradation rates of three poly(butylene adipate-co-terephthalate) (PBAT)-based films varied: 100% in river, 55% in lake, and 10% in air. In addition to PLA, surface chemical groups, hydrophilicity, and thermal stability of BPs changed, and microplastics were found on their surfaces. Correspondingly, BPs with faster degradation rates released relatively higher amounts of DOC. Environmental microbial and chemical characteristics may contribute to differences in BP degradation besides polymer specificity. Altogether, our results indicate the need for appropriate monitoring of BPs.

Polysaccharide preferred minority-dominant community assembly and exoenzyme enrichment in transparent exopolymer particles: Implication for global carbon cycle in water.

The ubiquitous transparent exopolymer particles (TEPs) are an important organic carbon pool and an ideal microhabitat for bacteria in aquatic environments. They play a crucial role in the global carbon cycle. Organic matter transformation and carbon turnover in TEPs strongly depend on the assembly of their associated bacterial communities and enzyme activity. However, the mechanisms of bacterial community assembly and their potential effects on the organic carbon cycle in TEPs are still unclear. In this study, we comparatively explored the community assembly of TEP-associated bacteria and bacterioplankton from surface freshwater using metagenomics. It was found that the bacterial community assembly in TEPs followed a minority-dominant rule and was governed by homogeneous selection. Pseudomonadota and Actinomycetota, which are responsible for polysaccharide degradation, serve as taxon-specific biomarkers among the abundant and diverse bacteria in TEPs. The network of TEP-associated bacteria displayed stronger robustness than that of bacterioplankton. Bin 76 (majorly Acinetobacter) was the overwhelmingly dominant taxa in TEPs, whereas there was no clearly dominant taxa in TEP-free water. Exoenzyme analysis showed that 64 out of 71 identified polysaccharide hydrolases were markedly linked with the dominant bin 76 in TEPs, while no such linkage was observed for bacterioplankton. Generally, Acinetobacter, which is capable of utilizing polysaccharides, is preferred to be assembled in TEPs together with high polysaccharide hydrolase activity. This may significantly accelerate the turnover of organic carbon in the giant global TEP pool. These findings are important for a deep understanding of the carbon cycle in water.

Eliminating Resistance-Capacitance Coupling Shielding for Depicting the Defect Landscape in Perovskite Solar Cells by Capacitance Spectroscopy.

Capacitance spectroscopy techniques have been widely utilized to evaluate the defect properties in perovskites, which contribute to the efficiency and operation stability development for perovskite solar cells (PSCs). Yet the interplay between the charge transporting layer (CTL) and the perovskite on the capacitance spectroscopy results is still unclear. Here, they show that a pseudo-trap-state capacitance signal is generated in thermal admittance spectroscopy (TAS) due to the enhanced resistance capacitance (RC) coupling caused by the carrier freeze-out of the CTL in PSCs, which could be discerned from the actual defect-induced trap state capacitance signal by tuning the series resistance of PSCs. By eliminating the RC coupling shielding effect on the defect-induced capacitance spectroscopy, it is obtain the actual defect density which is 4-folds lower than the pseudo-trap density, and the spatial distribution of defects in PSCs which reveals that the commonly adopted interface passivators can passivate the defects about 60 nm away from the decorated surface. It is further revealed that phenethylammonium ions (PEA+) possess a better passivation capability over octylammonium ions (OA+) due to the deeper passivation depth for PEA+ on the surface defects in perovskite films.

Excess Ca(2+) does not alleviate but increases the toxicity of Hg(2+) to photosystem II in Synechocystis sp. (Cyanophyta).

This study demonstrated that excess Ca(2+) increased the toxicity of Hg(2+) to PSII of cyanobacterium Synechocystis sp. using fast rise chlorophyll fluorescence test. Excess Ca(2+) increased the inhibitory effect of Hg(2+) on O2 evolution. Exposure to Hg(2+) caused increase in functional antenna size (ABS/RC), trapping rate of reaction center (TR0/RC), dissipated energy flux per reaction center (DI0/RC) and maximum quantum yield of non-photochemical deexcitation ( [Formula: see text] ), indicating that some reaction centers were transformed to dissipation sinks under Hg(2+) stress. Hg(2+) stress slowed down electron transport on both donor side and acceptor side and caused accumulation of P680(+). Excess Ca(2+) intensified all the Hg(2+) toxic effects on PSII function and led to dysfunction of PSII. The number of reaction centers that were transformed into dissipation sinks increased with increasing Ca(2+) concentration.

Simultaneous analysis of photosystem responses of Microcystis aeruginoga under chromium stress.

Chromium (Cr) is a toxic metal that poses a great threat to aquatic ecosystems. Information is limited on coinstantaneous responses of photosystems I (PSI) and II (PSII) to Cr(VI) stress due to lack of instruments that can simultaneously measure PSI and PSII activities. In the present study, responses of quantum yields of energy conversion and electron transport rates of PSI and PSII in Microcystis aeruginosa cells to Cr(VI) stress were simultaneously analyzed by a DUAL-PAM-100 system. Quantum yield of cyclic electron flow (CEF) under Cr(VI) stress and its physiological role in alleviating toxicity of Cr(VI) were also analyzed. At 5 mg L(-1) Cr(VI), quantum yield and electron transport rate of PSII decreased significantly, and light-induced non-photochemical fluorescence quenching lost. Cr(VI) also inhibited efficiency of PSII to use energy under high light more than of PSI. PSII showed lower maximal electron transport rate and light adaptability than PSI. Electron transport rate of PSI was higher and decreased less than that of PSII, implying less sensitivity of PSI to high light and Cr(VI). Energy dissipation through non-light-induced non-photochemical fluorescence quenching increased with increasing Cr(VI) concentration. CEF was stimulated under Cr(VI) treatment and made a significant contribution to quantum yield and electron transport of PSI, which was essential for protection of PSI from stresses of Cr(VI) and high light.