Increased anaerobic conditions promote the denitrifying nitrogen removal potential and limit anammox substrate acquisition within paddy irrigation and drainage units.

Microbial nitrogen (N) removal is crucial for purifying surface water quality in paddy irrigation and drainage units (IDUs). However, the spatiotemporal microbial N removal potential characteristics within these IDUs and the effects of changing anaerobic conditions on this potential remain insufficiently studied. In this study, we investigated the microbial N removal potential of conventional rice-wheat rotation and anaerobically enhanced rice-crayfish rotation IDUs using field measurements, isotope tracing techniques, and quantitative PCR. Our findings reveal that paddy fields were identified as hotspots for anammox activity, contributing to 76.0 %-97.4 % of the total anammox N removal potential in the IDU, while denitrification processes in ditches accounted for 43.5 %-77.4 % of the IDU's denitrification potential. During the rice transplanting period, the anammox N removal potential peaked, representing 35.8 % and 71.8 % of the total anammox N removal potential of the paddy fields in rice-wheat and rice-crayfish IDUs, respectively. An increase in anaerobic conditions diminished the anammox N removal potential while amplifying denitrification capabilities. The N removal potential in paddy fields decreased with increasing depth, contrasting with the relative stability in ditches. Spatiotemporal fluctuations in N removal potentials within these units are influenced by Fe2+ concentration, carbon and N content, WFPS, and pH levels. This study provides a scientific basis for improving nitrogen removal and water quality treatment in IDUs.

E3 ligase DECREASED GRAIN SIZE 1 promotes degradation of a G-protein subunit and positively regulates grain size in rice.

Grain size is one of the most important traits determining crop yield. However, the mechanism controlling grain size remains unclear. Here, we confirmed the E3 ligase activity of DECREASED GRAIN SIZE 1 (DGS1) in positive regulation of grain size in rice (Oryza sativa) suggested in a previous study. Rice G-protein subunit gamma 2 (RGG2), which negatively regulates grain size, was identified as an interacting protein of DGS1. Biochemical analysis suggested that DGS1 specifically interacts with canonical Gγ subunits (rice G-protein subunit gamma 1 [RGG1] and rice G-protein subunit gamma 2 [RGG2]) rather than non-canonical Gγ subunits (DENSE AND ERECT PANICLE 1 [DEP1], rice G-protein gamma subunit type C 2 [GCC2], GRAIN SIZE 3 [GS3]). We also identified the necessary domains for interaction between DGS1 and RGG2. As an E3 ligase, DGS1 ubiquitinated and degraded RGG2 via a proteasome pathway in several experiments. DGS1 also ubiquitinated RGG2 by its K140, K145 and S147 residues. Thus, this work identified a substrate of the E3 ligase DGS1 and elucidated the post transcriptional regulatory mechanism of the G-protein signalling pathway in the control of grain size.

FLOURY ENDOSPERM24, a heat shock protein 101 (HSP101), is required for starch biosynthesis and endosperm development in rice.

Endosperm is the main storage organ in cereal grain and determines grain yield and quality. The molecular mechanisms of heat shock proteins in regulating starch biosynthesis and endosperm development remain obscure. Here, we report a rice floury endosperm mutant flo24 that develops abnormal starch grains in the central starchy endosperm cells. Map-based cloning and complementation test showed that FLO24 encodes a heat shock protein HSP101, which is localized in plastids. The mutated protein FLO24T296I dramatically lost its ability to hydrolyze ATP and to rescue the thermotolerance defects of the yeast hsp104 mutant. The flo24 mutant develops more severe floury endosperm when grown under high-temperature conditions than normal conditions. And the FLO24 protein was dramatically induced at high temperature. FLO24 physically interacts with several key enzymes required for starch biosynthesis, including AGPL1, AGPL3 and PHO1. Combined biochemical and genetic evidence suggests that FLO24 acts cooperatively with HSP70cp-2 to regulate starch biosynthesis and endosperm development in rice. Our results reveal that FLO24 acts as an important regulator of endosperm development, which might function in maintaining the activities of enzymes involved in starch biosynthesis in rice.

Visible-light-driven alkene dicarboxylation with formate and CO2 under mild conditions.

Low-cost formate salt was used as the reductant and part of the carboxyl source in a visible-light-driven dicarboxylation of diverse alkenes, including simple styrenes. The highly competing hydrocarboxylation side reaction was successfully overridden. Good yields of products were obtained under mild reaction conditions at ambient temperature and pressure of CO2. The dual role of formate salt may stimulate the discovery of a range of new transformations under mild and friendly conditions.

Osteocytes support bone metastasis of melanoma cells by CXCL5.

Bone metastasis is a common complication of certain cancers such as melanoma. The spreading of cancer cells into the bone is supported by changes in the bone marrow environment. The specific role of osteocytes in this process is yet to be defined. By RNA-seq and chemokines screening we show that osteocytes release the chemokine CXCL5 when they are exposed to melanoma cells. Osteocytes-mediated CXCL5 secretion enhanced the migratory and invasive behaviour of melanoma cells. When the expression of the CXCL5 receptor, CXCR2, was down-regulated in melanoma cells in vitro, we observed a significant decrease in melanoma cell migration in response to osteocytes. Furthermore, melanoma cells with down-regulated CXCR2 expression showed less bone metastasis and less bone loss in the bone metastasis model in vivo. Furthermore, when simultaneously down-regulating CXCL5 in osteocytes and CXCR2 in melanoma cells, melanoma progression was abrogated in vivo. In summary, these data suggest a significant role of osteocytes in bone metastasis of melanoma, which is mediated through the CXCL5-CXCR2 pathway.

Expression of HIF1α in intestinal epithelium restricts arthritis inflammation by inhibiting RIPK3-induced cell death machinery.

OBJECTIVES: To investigate the mechanism by which intestinal epithelial cell (IEC) death induces arthritis. METHODS: IEC death was assessed by staining for necroptosis and apoptosis markers and fluorescence in situ hybridisation at different time points during collagen-induced arthritis (CIA). During the development of CIA, messenger RNA (mRNA) sequencing was performed, followed by Gene Ontology enrichment analysis of differentially expressed genes. Mice deficient for hypoxia-inducible factor 1α (Hif1a) in IECs (Hif1a ∆IEC) were generated and induced for arthritis. mRNA sequencing, chromatin immunoprecipitated (ChIP) DNA sequencing and ChIP-qualitative PCR were performed on IECs from Hif1a ∆IEC mice and littermate controls. Effects of HIF1α stabilisation by inhibition of prolyl hydroxylase domain-containing enzymes and treatment with the inhibitor of receptor-interacting protein kinase-3 (RIPK3) were tested in intestinal organoids and in CIA. RESULTS: IEC underwent apoptotic and necroptotic cell death at the onset of arthritis, leading to impaired gut barrier function. HIF1α was identified as one of the most upregulated genes in IECs during the onset of arthritis. Deletion of Hif1a in IEC enhanced IEC necroptosis, triggered intestinal inflammation and exacerbated arthritis. HIF1α was found to be a key transcriptional repressor for the necroptosis-inducing factor RIPK3. Enhanced RIPK3 expression, indicating necroptosis, was also found in the intestinal epithelium of patients with new-onset rheumatoid arthritis. Therapeutic stabilisation of HIF1α as well as small-molecule-based RIPK3 inhibition rescued intestinal necroptosis in vitro and in vivo and suppressed the development of arthritis. CONCLUSION: Our results identify IEC necroptosis as a critical link between the gut and the development of arthritis.

Expanding Olefin-Linked Covalent Organic Frameworks toward Selective Photocatalytic Oxidation of Organic Sulfides.

Olefin-linked covalent organic frameworks (COFs) have exhibited great potential in visible-light photocatalysis. In principle, expanding fully conjugated COFs can facilitate light absorption and charge transfer, leading to improved photocatalysis. Herein, three olefin-linked COFs with the same topology are synthesized by combining 2,4,6-trimethyl-1,3,5-triazine (TMT) with 1,3,5-triformylbenzene (TFB), 1,3,5-tris(4-formylphenyl)benzene (TFPB), and 1,3,5-tris(4-formylphenylethynyl)benzene (TFPEB), namely, TMT-TFB-COF, TMT-TFPB-COF, and TMT-TFPEB-COF, respectively. From TMT-TFB-COF to TMT-TFPB-COF, expanding phenyl rings provides only limited expansion for π-conjugation due to the steric effect of structural twisting. However, from TMT-TFPB-COF to TMT-TFPEB-COF, the insertion of acetylenes eliminates the steric effect and provides more delocalized π-electrons. As such, TMT-TFPEB-COF exhibits the best optoelectronic properties among these three olefin-linked COFs. Consequently, the photocatalytic performance of TMT-TFPEB-COF is much better than those of TMT-TFB-COF and TMT-TFPB-COF on the oxidation of organic sulfides into sulfoxides with oxygen. The desirable reusability and substrate compatibility of the TMT-TFPEB-COF photocatalyst are further confirmed. The selective formation of organic sulfoxides over TMT-TFPEB-COF under blue light irradiation proceeds via both electron- and energy-transfer pathways. This work highlights a rational design of expanding the π-conjugation of fully conjugated COFs toward selective visible-light photocatalysis.

Single-use flexible ureteroscope provides an alternative treatment for upper urinary calculi: A systematic review and meta-analysis.

OBJECTIVE: This study aimed to evaluate the efficacy and safety of single-use flexible ureteroscope and reusable flexible ureteroscope for upper urinary calculi. METHODS: We conducted a meta-analysis that had a comprehensive search in PubMed, Embase, Cochrane Library, Web of Science, and WanFang databases from 2000/01/01 to 2023/06/01 for available randomized controlled trials. "Ureteroscopes," "Flexible Ureteroscope," "Single-use," and "Upper Urinary Calculi" were used as the major keywords for the search. Review Manager 5.0 and STATA 12.0 were used for calculation and statistical analysis. RESULTS: A total of 9 randomized controlled trials comprising 1293 participants were included in our meta-analysis. Single use-FURS had better results in stone-free rate (relative risk: 1.08, 95% confidence interval: [1.02, 1.15], P = .02) and postoperative infection (relative risk: 0.41, 95% confidence interval: [0.23, 0.72], P = .002). Operative time, hemoglobin decline, postoperative serum creatinine, postoperative hospital stay, and overall complication after surgery showed no significant differences between the 2 procedures (P > .05). CONCLUSION: Single-use flexible ureteroscope provides a valuable alternative to reusable flexible ureteroscope in upper urinary calculi with its better visual field performance and manipulation, opening a new technological revolution for kidney stone treatment.

WEAK SEED DORMANCY 1, an aminotransferase protein, regulates seed dormancy in rice through the GA and ABA pathways.

Seed dormancy is a critical trait that enhances plant survival by preventing seed germination at the wrong time or under unsuitable conditions. Lack of seed dormancy in rice can lead to pre-harvest sprouting on mother plants leading to reduced yield and seed quality. Although some genes have been identified, knowledge of regulation of seed dormancy is limited. Here, we characterized a weak seed dormancy mutant named weak seed dormancy 1 (wsd1) that showed a higher seed germination percentage than the wild-type following the harvest ripeness. We cloned the WSD1 encoding an aminotransferase protein using a MutMap approach. WSD1 was stably expressed after imbibition and its protein was localized in the endoplasm reticulum. A widely targeted metabolomics assay and amino acid analysis showed that WSD1 had a role in regulating homeostasis of amino acids. PAC treatment and RNA-seq analysis showed that WSD1 regulates seed dormancy by involvement in the GA biosynthesis pathway. GA1 content and expression of GA biosynthesis-related genes were increased in the wsd1 mutant compared with the wild-type. The wsd1 mutant had reduced sensitivity to ABA. Our overall results indicated that WSD1 regulates seed dormancy by balancing the ABA and GA pathways.

Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato.

The PLATZ (plant AT protein and zinc-binding protein) transcription factor family is involved in the regulation of plant growth and development and plant stress response. In this study, 24 SlPLATZs were identified from the cultivated tomato genome and classified into four groups based on the similarity of conserved patterns among members of the same subfamily. Fragment duplication was an important way to expand the SlPLATZ gene family in tomatoes, and the sequential order of tomato PLATZ genes in the evolution of monocotyledonous and dicotyledonous plants and the roles they played were hypothesized. Expression profiles based on quantitative real-time reverse transcription PCR showed that SlPLATZ was involved in the growth of different tissues in tomatoes. SlPLATZ21 acts mainly in the leaves. SlPLATZ9, SlPLATZ21, and SlPLATZ23 were primarily involved in the red ripening, expanding, and mature green periods of fruit, respectively. In addition, SlPLATZ1 was found to play an important role in salt stress. This study will lay the foundation for the analysis of the biological functions of SlPLATZ genes and will also provide a theoretical basis for the selection and breeding of new tomato varieties and germplasm innovation.

Enhancing rice production sustainability and resilience via reactivating small water bodies for irrigation and drainage.

Rice farming threatens freshwater resources, while also being increasingly vulnerable to drought due to climate change. Rice farming needs to become more sustainable and resilient to climate change by improving irrigation drainage systems. Small water bodies, used to store drainage water and supply irrigation in traditional rice farming systems have gradually been abandoned in recent decades. This has resulted in a higher water footprint (WF) associated with rice farming due to increased freshwater usage and wastewater release, also leaving rice production more vulnerable to extreme weather events. Here, we propose how protecting and reactivating small water bodies for rice irrigation and drainage can decrease rice production WF in China by 30%, save 9% of China's freshwater consumption, increase irrigation self-sufficiency from 3% to 31%, and alleviate yield loss in dry years by 2-3%. These findings show that redesigning rice irrigation drainage systems can help meet water scarcity challenges posed by climate change.

Genome-wide identification and expression analyses of phenylalanine ammonia-lyase gene family members from tomato (Solanum lycopersicum) reveal their role in root-knot nematode infection.

Phenylalanine ammonia-lyase (PAL) is a key enzyme and rate-limiting enzyme of phenylpropanoid metabolism, which is a very important pathway in plants, and the secondary products it produces play an important role in plant growth and development, disease resistance, and stress resistance responses. However, PALs still lack systematic characterization in tomato. Based on a bioinformatics methods, PAL family genes were identified and characterized from tomato. qRT-PCR was used to study the expression of PAL genes in cultivated tomato after root-knot nematode infection. In this study, 14 and 11 PAL genes were identified in cultivated and wild tomatoes, and phylogenetic analysis classified them into three subfamilies, with different subfamilies of PAL proteins evolving in different directions in monocotyledonous and dicotyledonous plants. The extensive presence of stress, growth, hormone, and light response elements in the promoter sequences of SlPAL (Solanum lycopersicum) and SpenPAL (Solanum pennellii) genes suggests that this family has a critical role in abiotic stress. Collinearity indicates that members of the tomato and Arabidopsis PAL genes family are from the same ancestor, and the SlPAL10 gene is directly homologous to monocotyledonous rice and maize, suggesting that the SlPAL10 gene was present before monocotyledonous differentiation. Two co-expressed gene modules containing PAL genes were screened by WGCNA, and the core genes in the network were mined and functionally annotated by calculating the connectivity of genes within the modules. In addition, the expression of some genes changed significantly after root-knot nematode infection, with up-regulation of 4 genes and down-regulation of 3 genes. This result provides a data reference for the study of PAL family gene functions in tomato, and also provides a potential application for the subsequent selection of PAL genes in tomato for root-knot nematode resistance.

Benzothiadiazole covalent organic framework photocatalysis with an electron transfer mediator for selective aerobic sulfoxidation.

Covalent organic frameworks (COFs) are promising visible light photocatalysts for aerobic oxidation reactions. However, COFs usually suffer from the assault of reactive oxygen species, leading to hindered electron transfer. This scenario could be addressed by integrating a mediator to promote photocatalysis. Starting with 4,4'-(benzo-2,1,3-thiadiazole-4,7-diyl)dianiline (BTD) and 2,4,6-triformylphloroglucinol (Tp), TpBTD-COF is developed as a photocatalyst for aerobic sulfoxidation. Adding an electron transfer mediator 2,2,6,6-tetramethylpiperidine-1­oxyl (TEMPO), the conversions are radically accelerated, over 2.5 times of that without TEMPO. Moreover, the robustness of TpBTD-COF is preserved by TEMPO. Remarkably, TpBTD-COF could endure multiple cycles of sulfoxidation, even with higher conversions than the fresh one. TpBTD-COF photocatalysis with TEMPO implements diverse aerobic sulfoxidation by an electron transfer pathway. This work highlights that benzothiadiazole COFs are an avenue for tailor-made photocatalytic transformations.

Design and Synthesis of a Triazine-Based sp2 Carbon-Conjugated Covalent Organic Framework for Blue Light Photocatalysis.

Fully conjugated covalent organic frameworks (COFs) can exhibit great potential in semiconductor photocatalysis. But their syntheses remain elusive due to the low reversibility of vinylene linkage. Herein, by tuning the amount of base and temperature, a novel triazine-based sp2  carbon-conjugated COF (TA-sp2 c-COF) is successfully constructed over Cs2 CO3 . Besides, the influence of modulating factors on the chemical and optoelectronic properties of TA-sp2 c-COF is thoroughly investigated. TA-sp2 c-COF adopts an eclipsed AA stacking structure with uniform micropores (1.4 nm). The blue light photocatalysis of the highly crystalline TA-sp2 c-COF is established for the selective oxidative coupling of amines with oxygen, and the predominant role of superoxide is identified in forming imines. This work foretells that meticulous modulation of reaction conditions is the key to constructing sp2  carbon-conjugated COFs toward solar photocatalysis.

Role of the TPX2/NCOA5 axis in regulating proliferation, migration, invasion and angiogenesis of breast cancer cells.

Breast cancer is a common malignant tumor in women. Increasing evidence has demonstrated that nuclear receptor coactivator 5 (NCOA5) and targeting protein for xenopus kinesin-like protein 2 (TPX2) serve vital roles in the progression of breast cancer. However, to the best of our knowledge, the molecular mechanisms underlying the involvement of TPX2/NCOA5 in the development of breast cancer are not fully understood at present. In the present study, the expression levels of NCOA5 and TPX2 were compared between paired non-tumor and tumor tissues of patients with breast cancer using the TNMplot tool. Expression differences of NCOA5 and TPX2 in human breast epithelial cell lines (MCF10A and MCF12A) and human breast cancer cell lines (MCF7 and T47D) were assessed via reverse transcription-quantitative PCR and western blotting. Additionally, proliferation, migration and invasion of breast cancer cells were determined via Cell Counting Kit-8, would healing and transwell assays. In vitro angiogenesis was determined using a tube formation assay. Furthermore, TPX2 was identified as a high-confidence NCOA5 interactor based on BioPlex network data sets. A co-immunoprecipitation assay was adopted to confirm the interaction between TPX2 and NCOA5. The present study revealed that TPX2 and NCOA5 were highly expressed in breast cancer cells. TPX2 interacted with NCOA5 and there was a positive association between TPX2 and NCOA5 expression. NOCA5 knockdown repressed the proliferation, migration, invasion and in vitro angiogenesis of breast cancer cells. In addition, TPX2 knockdown suppressed the proliferation, migration and invasion of breast cancer cells, and inhibited in vitro angiogenesis, and all of these effects were reversed following NCOA5 overexpression. In conclusion, NCOA5 was a downstream target of TPX2 in enhancing proliferation, migration, invasion and angiogenesis of breast cancer cells.

Selective oxidation of amines powered with green light and oxygen over an anthraquinone covalent organic framework.

The exploration of emerging photocatalysts like covalent organic frameworks (COFs) is an essential but challenging endeavor to find sustainable solutions for selective organic transformations. Anthraquinones are envisaged to construct COFs for visible light photocatalysis because their derivatives are employed industrially as oxidation catalysts or organic dyes. Herein, an anthraquinone COF, TpAQ-COF, is successfully constructed with 1,3,5-triformylphloroglucinol (Tp) and 2,6-diaminoanthraquinone (AQ). Then, the selective oxidation of amines over TpAQ-COF is implemented. Amines can be effectively converted into corresponding imines over TpAQ-COF powered with green light and oxygen, during which superoxide radical anion is discerned as the pivotal reactive oxygen species. This work suggests that COFs could inherit the advantages of molecular building blocks for selective reactions powered with broad visible light.

Thermodynamically consistent master equation based on subsystem eigenstates.

Master equations under appropriate assumptions are efficient tools for the study of open quantum systems. For many-body systems, subsystems of which locally couple to thermal baths and weakly interact with each other, the local approach provides a more convenient description than the global approach. However, these local master equations are believed to generate inconsistencies with the laws of thermodynamics when intersubsystem interactions exist. Here we develop an alternative local master equation by virtue of similar approximations used in deriving the traditional Gorini-Kossakowski-Lindblad-Sudarshan master equation. In particular, we stick to using eigenstates of each subsystem to construct quantum jump operators, and the secular approximation is also employed to modify the intersubsystem interactions. Our results show that violations of thermodynamic laws will be avoided after correcting intersubsystem interactions. Finally, we study a two-qubit heat transfer model and this further shows the validity of our modified master equation.

The transcriptional regulatory network of hormones and genes under salt stress in tomato plants (Solanum lycopersicum L.).

Salt stress has become one of the main limiting factors affecting the normal growth and development of tomatoes as well as fruit quality and yields. To further reveal the regulatory relationships between tomato hormones under salt stress, the interaction between hormones and TF and the genome-wide gene interaction network were analyzed and constructed. After salt treatment, the levels of ABA, SA, and JA were significantly increased, the levels of GA were decreased, and IAA and tZ showed a trend of first increasing and then decreasing. The expression patterns of hormone biosynthesis and signal transduction related genes were analyzed based on RNA-seq analysis, the co-expression network of hormones and genome-wide co-expression networks were constructed using weighted gene co-expression network analysis (WGCNA). The expression patterns of specific transcription factors under salt stress were also systematically analyzed and identified 20 hormone-related candidate genes associated with salt stress. In conclusion, we first revealed the relationship between hormones and genes in tomatoes under salt stress based on hormone and transcriptome expression profiles and constructed a gene regulatory network. A transcriptional regulation model of tomato consisted of six types of hormones was also proposed. Our study provided valuable insights into the molecular mechanisms regulating salt tolerance in tomatoes.

Potential to mitigate nitrogen emissions from paddy runoff: A microbiological perspective.

Ditches and ponds are the basic units of agroecosystems that serve irrigation and drainage and also perform the natural ecological function of reducing nitrogen (N) emissions. To better enhance the design and advance management strategies in the paddy field ecosystem to minimize N emission, the N cycling microorganism in the paddy field ecosystem including interconnected fields with rice-wheat rotation, ditches, and ponds in central China was investigated by metagenomic techniques. Our results showed that ditches and ponds may be N removal hotspots by microorganisms in the rice and wheat seasons respectively. Given seasonal variation, the abundance of N-related microorganisms was high during the rice season. However, the Shannon and Simpson indices were lower and the microbial co-occurrence network was destabilized, which could make microbes in the rice season fragile and sensitive. Phytoplankton as key environmental factors affecting the N cycling microbial could promote more stable microbial communities through maintaining a good mutualistic symbiosis. While high algae concentration significantly promotes the abundance of norB than nosZ (P < 0.05), which may result in more N2O production. To trade off N removal and N2O emission, the algae concentration needs to be controlled. Our findings provide a systematic profile of N-related microorganisms in the paddy field ecosystem, and it would benefit in developing effective strategies for limiting N pollution in agriculture.