The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress.

Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.

Srs2 binding to PCNA and its sumoylation contribute to RPA antagonism during the DNA damage response.

Activation of the DNA damage checkpoint upon genotoxin treatment induces a multitude of cellular changes, such as cell cycle arrest, to cope with genome stress. After prolonged genotoxin treatment, the checkpoint can be downregulated to allow cell cycle and growth resumption. In yeast, downregulation of the DNA damage checkpoint requires the Srs2 DNA helicase, which removes the ssDNA binding complex RPA and the associated Mec1 checkpoint kinase from DNA, thus dampening Mec1 activation. However, it is unclear whether the 'anti-checkpoint' role of Srs2 is temporally and spatially regulated to both allow timely checkpoint termination and to prevent superfluous RPA removal. Here we address this question by examining regulatory elements of Srs2, including its phosphorylation, sumoylation, and protein-interaction sites. Our genetic analyses and checkpoint level assessment suggest that the RPA countering role of Srs2 is promoted by Srs2 binding to PCNA, which is known to recruit Srs2 to subsets of ssDNA regions. RPA antagonism is further fostered by Srs2 sumoylation, which we found depends on the Srs2-PCNA interaction. Srs2 sumoylation is additionally reliant on Mec1 and peaks after Mec1 activity reaches maximal levels. Collectively, our data provide evidence for a two-step model wherein checkpoint downregulation is facilitated by PCNA-mediated Srs2 recruitment to ssDNA-RPA filaments and the subsequent Srs2 sumoylation stimulated upon Mec1 hyperactivation. We propose that this mechanism allows Mec1 hyperactivation to trigger checkpoint recovery.

Effects of micro-nano plastics on the environmental biogeochemical cycle of nitrogen: A comprehensive review.

Micro-nano plastics (MNPs; size <5 mm), ubiquitous and emerging pollutants, accumulated in the natural environment through various sources, and are likely to interact with nutrients, thereby influencing their biogeochemical cycle. Increasing scientific evidences reveal that MNPs can affect nitrogen (N) cycle processes by affecting biotopes and organisms in the environmental matrix and MNPs biofilms, thus plays a crucial role in nitrous oxide (N2O) and ammonia (NH3) emission. Yet, the mechanism and key processes behind this have not been systematically reviewed in natural environments. In this review, we systematically summarize the effects of MNPs on N transformation in terrestrial, aquatic, and atmospheric ecosystems. The effects of MNPs properties on N content, composition, and function of the microbial community, enzyme activity, gene abundance and plant N uptake in different environmental conditions has been briefly discussed. The review highlights the significant potential of MNPs to alter the properties of the environmental matrix, microbes and plant or animal physiology, resulting in changes in N uptake and metabolic efficiency in plants, thereby inhibiting organic nitrogen (ON) formation and reducing N bioavailability, or altering NH3 emissions from animal sources. The faster the decomposition of plastics, the more intense the perturbation of MNPs to organisms in the natural ecosystem. Findings of this provide a more comprehensive analysis and research directions to the environmentalists, policy makers, water resources planners & managers, biologists, and biotechnologists to do integrate approaches to reach the practical engineering solutions which will further diminish the long-term ecological and climatic risks.

Overexpression of soybean GmDHN9 gene enhances drought resistance of transgenic Arabidopsis.

Soybean is one of the important oil crops and a major source of protein and lipids. Drought can cause severe soybean yields. Dehydrin protein (DHN) is a subfamily of LEA proteins that play an important role in plant responses to abiotic stresses. In this study, the soybean GmDHN9 gene was cloned and induced under a variety of abiotic stresses. Results showed that the GmDHN9 gene response was more pronounced under drought induction. Subcellular localization results indicated that the protein was localized in the cytoplasm. The role of transgenic Arabidopsis plants in drought stress response was further studied. Under drought stress, the germination rate, root length, chlorophyll, proline, relative water content, and antioxidant enzyme content of transgenic Arabidopsis thaliana transgenic genes were higher than those of wild-type plants, and transgenic plants contained less O2-, H2O2 and MDA contents. In short, the GmDHN9 gene can regulate the homeostasis of ROS and enhance the drought resistance of plants.

Expanding Complex Morpholines Using Systematic Chemical Diversity.

The morpholine heterocycle is a structural unit found in many bioactive compounds and FDA-approved drugs, but the generation of more complex C-functionalized morpholine derivatives remains considerably underexplored. Using systematic chemical diversity (SCD), a concept that guides the expansion of saturated drug-like scaffolds through regiochemical and stereochemical variation, we describe the synthesis of a collection of methyl-substituted morpholine acetic acid esters starting from enantiomerically pure amino acids and amino alcohols. In total, 24 diverse substituted morpholines were produced that vary systematically in regiochemistry and stereochemistry (relative and absolute). These diverse C-substituted morpholines can be directly applied in fragment screening or incorporated as building blocks in medicinal chemistry and library synthesis.

Chemical components with antibacterial properties found in sanchen powder from traditional Tibetan medicine.

ETHNOPHARMACOLOGICAL RELEVANCE: Sanchen powder is a traditional Tibetan medicine comprising Bambusae Concretio Silicea, Carthami Flos, and Bovis Calculus Artifactus. Bambusae Concretio Silicea is the dried mass of secreted fluid in the stalks of Gramineae plants such as Bambusa textilis McClure or Schizostachyum chinense Rendle. Carthami Flos is the dried flower of Carthamus tinctorius L. in the Compositae plant. Bovis Calculus Artifactus is made from ox bile powder, cholic acid, hyodeoxycholic acid, taurine, bilirubin, cholesterol, and trace elements. Research has evidenced the antibacterial efficacy of Sanchen powder, albeit its active constituents for this effect are yet to be established. AIM OF THE STUDY: To investigate effective compounds, potential targets, and molecular mechanism of Sanchen powder for its antibacterial properties by using network pharmacology combined with in vitro validation, with the aims of observing the action of effective compounds in Sanchen powder and exploring new therapeutic strategies for antibacterial. MATERIALS AND METHODS: In this study, UPLC-Q-TOF-MS was utilized to identify the chemical composition in Sanchen powder and its blood-borne chemical ingredients post-oral intake. A network pharmacology analysis was used to establish the chemical compound in the blood following oral administration-target-disease network. The study aimed to identify antibacterial active ingredients, which were then subjected to molecular docking and pharmacodynamic experiments to verify their efficacy. RESULTS: The findings demonstrate that following oral administration, the blood contains seven key components of Sanchen powder, including bilirubin, glycochenodeoxycholic acid, glycocholic acid, taurocholic acid, phenylalanine, safflomin A, and tryptophan. Additionally, the network pharmacology and molecular docking study results indicate the potential antibacterial effects of bilirubin, glycocholic acid, and glycochenodeoxycholic acid. In vitro antibacterial experiments revealed that bilirubin, glycocholic acid, and glycochenodeoxycholic acid could restrict the growth of the Staphylococcus aureus cell membrane at a certain concentration. Moreover, they exhibited antibacterial effects on Staphylococcus aureus, Pseudomonas aeruginosa, Staphylococcus epidermidis, and Escherichia coli. CONCLUSIONS: Bilirubin, glycocholic acid, and glycochenodeoxycholic acid could be effective therapeutic ingredients for the antibacterial effects of Sanchen powder. These results offer a foundation for further clinical application and research on the antibacterial effect of Sanchen powder, a Traditional Tibetan Medicine.

The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress.

Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.

Exploiting the Carboxylate-Binding Pocket of ß-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library.

ß-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important ß-lactam class of antibiotics. The OXA-48 and NDM-1 ß-lactamases cause resistance to the last-resort ß-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel ß-lactamase inhibitors. We exploited the ß-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all ß-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-ß-lactam pharmacophores for the development of ß-lactamase inhibitors for enzymes of different structural and mechanistic classes.

ATXN3 promotes proliferation, stemness and motility of clear cell renal cell carcinoma cells by regulating S100A8 ubiquitination.

Background: Clear cell renal cell carcinoma (ccRCC) is a dominant subtype of kidney cancer with a dismal outcome at advanced stages. Ataxin 3 (ATXN3) has been proven to play a cancer-promoting role in several tumors and is upregulated in the patients with renal cell carcinoma. Thus, the objective of this research is to examine the biological roles and underlying mechanisms of ATXN3 in ccRCC. Methods: Bioinformatics analysis was carried out to analyze ATXN3 expression in ccRCC tissues and patient survival. Gain- and loss-of-function assays were applied to explore the effect of ATXN3 on ccRCC cell malignant behavior in vitro. The effect of ATXN3 on the NF-κB pathway was assessed by Western blot and immunofluorescence staining. The binding between ATXN3 and S100A8 and the effect of ATXN3 on S100A8 ubiquitination were verified using coimmunoprecipitation. Results: ATXN3 was upregulated in ccRCC tissues and correlated with adverse patient outcome. ATXN3 overexpression facilitated the proliferation, stemness, invasion and migratory capacity of ccRCC cells, whereas silencing had the opposite effect. ATXN3 enhanced the activity of the NF-κB pathway. Silencing ATXN3 facilitated S100A8 ubiquitination. Rescue experiments demonstrated that S100A8 downregulation reversed the promoting effect of ATXN3 on malignant behavior and NF-κB pathway activation in ccRCC cells. Conclusion: ATXN3 exerts a cancer-promoting effect in ccRCC by regulating S100A8 ubiquitination. Therefore, targeting the ATXN3/S100A8/NF-κB axis may provide a novel underlying therapeutic strategy for ccRCC.

CRISPR-Hybrid: A CRISPR-Mediated Intracellular Directed Evolution Platform for RNA Aptamers.

Recent advances in gene editing and precise regulation of gene expression based on CRISPR technologies have provided powerful tools for the understanding and manipulation of gene functions. Fusing RNA aptamers to the sgRNA of CRISPR can recruit cognate RNA-binding protein (RBP) effectors to target genomic sites, and the expression of sgRNA containing different RNA aptamers permit simultaneous multiplexed and multifunctional gene regulations. Here, we report an intracellular directed evolution platform for RNA aptamers against intracellularly expressed RBPs. We optimized a bacterial CRISPR-hybrid system coupled with FACS, and identified novel high affinity RNA aptamers orthogonal to existing aptamer-RBP pairs. Application of orthogonal aptamer-RBP pairs in multiplexed CRISPR allowed effective simultaneous transcriptional activation and repression of endogenous genes in mammalian cells.

The FLIP-FIGNL1 complex regulates the dissociation of RAD51/DMC1 in homologous recombination and replication fork restart.

Recruitment of RAD51 and/or DMC1 recombinases to single-strand DNA is indispensable for homology search and strand invasion in homologous recombination (HR) and for protection of nascent DNA strands at stalled replication forks. Thereafter RAD51/DMC1 dissociate, actively or passively, from these joint molecules upon DNA repair or releasing from replication stress. However, the mechanism that regulates RAD51/DMC1 dissociation and its physiological importance remain elusive. Here, we show that a FLIP-FIGNL1 complex regulates RAD51 and DMC1 dissociation to promote meiotic recombination and replication fork restart in mammals. Mice lacking FLIP are embryonic lethal, while germline-specific deletion of FLIP leads to infertility in both males and females. FLIP-null meiocytes are arrested at a zygotene-like stage with massive RAD51 and DMC1 foci, which frequently co-localize with SHOC1 and TEX11. Furthermore, FLIP interacts with FIGNL1. Depletion of FLIP or FIGNL1 in cell lines destabilizes each other and impairs RAD51 dissociation. Thus, the active dissociation of RAD51/DMC1 by the FLIP-FIGNL1 complex is a crucial step required for HR and replication fork restart, and represents a conserved mechanism in somatic cells and germ cells.

Two-dimensional MN4 materials as effective multifunctional electrocatalysts for the hydrogen-evolution, oxygen-evolution, and oxygen-reduction reactions.

Two-dimensional (2D) materials confining single atoms (SAs) for catalysis, such as graphene confining metal single atoms (M-N-C), integrate both aspects of 2D materials and single-atom catalysts (SACs). Significant advantages have been established in this new category of catalysts, which have seen rapid development in recent years. Recent studies have suggested a new class of novel 2D materials with a chemical formula of MN4 naturally holding a uniformly distributed M-N4 moiety. We investigated MN4 monolayers as multifunctional catalysts for the hydrogen-evolution reaction (HER), oxygen-evolution reaction (OER), and oxygen-reduction reaction (ORR). Among them, the IrN4 monolayer demonstrated high catalytic activity towards these three reactions. The CoN4 monolayer was predicted to be an excellent bifunctional catalyst for the OER and ORR. A uniformly distributed and short-distanced M-N4 moiety on the MN4 monolayer made reactions between the intermediates during the OER and ORR possible, facilitating the release of O2 and H2O, respectively. In addition, the M atom of the MN4 monolayer having electronic states located at the Fermi level was active for catalyzing the HER. More importantly, changes in the Gibbs free energy of the two key intermediates of adsorption (ΔGOH* and ΔGOOH*) correlated closely with the Bader charge on the M atom (BM).

Bioorthogonal surface-enhanced Raman scattering flower-like nanoprobe with embedded standards for accurate cancer cell imaging.

Developing precise and effective strategies for cancer identification and imaging is attractive due to their importance for early cancer detection, prognosis, and subsequent treatment. Herein, we reported a novel bioorthogonal surface-enhanced Raman scattering (SERS) nanoprobe for accurate cancer cell imaging. A novel core-molecule-shell nanoflower (Au@4-MBN@Au) with rich electromagnetic hot spots and enhanced Raman scattering was first synthesized by optimizing the embedded concentrations of 4-mercaptobenzonitrile (4-MBN). Then, Au@4-MBN@Au was further modified with FA-PEG-SH molecules to acquire the bioorthogonal SERS nanoprobe Au@4-MBN@Au-PEG-FA. The SERS nanoprobe illustrated a robust and stable nitrile stretching vibration Raman signal (2223 cm-1) in the cellular silent region, ensuring high sensitivity and ultra-accuracy SERS imaging of cancer cells. Furthermore, cell imaging results demonstrated Au@4-MBN@Au-PEG-FA could recognize FR-positive HeLa cells with high selectivity due to the high affinity between folate receptor and folic acid. More notably, Au@4-MBN@Au-PEG-FA has been applied to identify FR-positive Hela cells from co-cultured cancer cells with similar morphology by SERS imaging for the first time. With improved signal-to-background ratio, high selectivity, and excellent stability, we anticipate the SERS nanoprobe Au@4-MBN@Au-PEG-FA could be applied for FR-related cancer theranostics and clinical detection in the future.

H2A.Z deposition by SWR1C involves multiple ATP-dependent steps.

Histone variant H2A.Z is a conserved feature of nucleosomes flanking protein-coding genes. Deposition of H2A.Z requires ATP-dependent replacement of nucleosomal H2A by a chromatin remodeler related to the multi-subunit enzyme, yeast SWR1C. How these enzymes use ATP to promote this nucleosome editing reaction remains unclear. Here we use single-molecule and ensemble methodologies to identify three ATP-dependent phases in the H2A.Z deposition reaction. Real-time analysis of single nucleosome remodeling events reveals an initial priming step that occurs after ATP addition that involves a combination of both transient DNA unwrapping from the nucleosome and histone octamer deformations. Priming is followed by rapid loss of histone H2A, which is subsequently released from the H2A.Z nucleosomal product. Surprisingly, rates of both priming and the release of the H2A/H2B dimer are sensitive to ATP concentration. This complex reaction pathway provides multiple opportunities to regulate timely and accurate deposition of H2A.Z at key genomic locations.

Internal Standard Assisted Surface-Enhanced Raman Scattering Nanoprobe with 4-NTP as Recognition Unit for Ratiometric Imaging Hydrogen Sulfide in Living Cells.

Hydrogen sulfide (H2S), as the third endogenous gasotransmitter, is closely associated with various physiological and pathological processes, whereas many aspects of its functions remain unclear. Effective tools for the accurate detection of H2S in living organisms are urgently needed. We herein reported an internal standard assisted surface-enhanced Raman scattering (SERS) nanoprobe for ratiometric detection of H2S in vitro and in living cells based on the reduction of nitros with H2S. This nanoprobe consists of an internal standard (4-mercaptobenzonitrile, MPBN) embedded core-molecule-shell Au nanoflower (Au@MPBN@Au) as the high plasmonic active SERS substrate and the 4-nitrothiophenol (4-NTP) molecule immobilized on the surface as the H2S recognition unit. With the addition of H2S, the nitros peak (1329 cm-1) decreased. Meanwhile, three obvious new peaks appeared at 1139, 1387, and 1433 cm-1, which were related to the vibration of the dimerized product 4,4'-dimercaptoazobisbenzene (DMAB) of 4-aminothiophenol (4-ATP). However, the peak intensity at 2223 cm-1 derived from MPBN was not influenced by the outer environment. Thus, the H2S level was able to be determined based on the ratio of two peak intensities (I1139/I2223) with a detection limit as low as 0.24 µM. Notably, we have proved that SERS nanoprobe Au@MPBN@Au@4-NTP could ratiometrically image both the endogenous and exogenous H2S in living cells. We anticipate that Au@MPBN@Au@4-NTP could be applied for the study of H2S-related physiological function in the future.

Automatic Gray Image Coloring Method Based on Convolutional Network.

Image coloring is a time-consuming and laborious work. For a work, color collocation is an important factor to determine its quality. Therefore, automatic image coloring is a topic with great research significance and application value. With the development of computer hardware, deep learning technology has achieved satisfactory results in the field of automatic coloring. According to the source of color information, this paper can divide automatic coloring methods into three types: image coloring based on prior knowledge, image coloring based on reference pictures, and interactive coloring. The coloring method can meet the needs of most users, but there are disadvantages such as users cannot get the multiple objects in a picture of different reference graph coloring. Aiming at this problem, based on the instance of color image segmentation and image fusion technology, the use of deep learning is proposed to implement regional mixed color more and master the method. It can be divided into foreground color based on reference picture and background color based on prior knowledge. In order to identify multiple objects and background areas in the image and fuse the final coloring results together, a method of image coloring based on CNN is proposed in this paper. Firstly, CNN is used to extract their semantic information, respectively. According to the extractive semantic information, the color of the designated area of the reference image is transferred to the designated area of the grayscale image. During the transformation, images combined with semantic information are input into CNN model to obtain the content feature map of grayscale image and the style feature map of reference image. Then, a random noise map is iterated to make the noise map approach the content feature map as a whole and the specific target region approach the designated area of the style feature map. Experimental results show that the proposed method has good effect on image coloring and has great advantages in network volume and coloring effect.

Regular diet is non-inferior to restricted diet after polypectomy with decreased hospitalization length of stay and cost: a randomized-controlled trial.

Background: There are no data comparing a regular diet with a restricted diet after endoscopic polypectomy in patients with colorectal polyps. The current guidelines also did not provide the detailed information of dietary patterns after polypectomy. In this study, we aimed to evaluate the safety and efficacy of different diets on post-polypectomy outcomes. Methods: A total of 302 patients with colorectal polyps who underwent polypectomy were prospectively enrolled between March 2019 and December 2019 in Nanfang Hospital (Guangzhou, China). Enrolled patients were then randomly assigned to a regular diet group or a restricted diet group after polypectomy. The study is a non-inferior design and the primary end point was the post-operative adverse events (AE) rate. Secondary end points included length of stay (LOS) and hospitalization cost. Results: Among all the included patients, 148 patients received a restricted diet and 154 patients received a regular diet after polypectomy. A total of 376 polyps were removed, with 183 polyps in the restricted diet group and 193 polyps in the regular diet group. Shorter LOS (4.0 ± 1.4 vs 4.8 ± 1.7, P < 0.001) and lower hospitalization costs (7,701.63 ± 2,579.07 vs 8,656.05 ± 3,138.53, P = 0.001) were observed in the regular diet group. In particular, there was no significant difference in 3-day AE rates between the restricted diet and the regular diet group (1.35% [2/148] vs 2.60% [4/154], P = 0.685). Subgroup analysis looking at the number of polyps removed in each patient and different treatment modalities also showed similar findings. Conclusion: Regular diet should be recommended after polypectomy for polyps <20 mm as it can shorten LOS and save hospitalization costs.

Pharmacokinetic Evaluation of Red Raspberry (Poly)phenols from Two Doses and Association with Metabolic Indices in Adults with Prediabetes and Insulin Resistance.

This study aimed to investigate pharmacokinetic variables of two doses of red raspberry (RR) (poly)phenols and their association with metabolic indices in adults with prediabetes and insulin resistance (preDM-IR) compared to metabolically healthy adults (reference). Thirty-two adults (preDM-IR, n = 21; reference, n = 11) consumed three meals containing 0 g (control), 125 g, or 250 g of frozen RR on three separate days in random order. Plasma (poly)phenolic metabolites and metabolic indices were characterized over a 0-8 h period and again at 24 h. Twenty-four metabolites were significantly increased by RR interventions in all subjects (p < 0.05). Individuals with preDM-IR compared to reference had a lower capacity to generate several metabolites, including 4'-hydroxy-3'-methoxycinnamic acid and hydroxymethoxycinnamic acid isomer, both negatively correlated with postprandial insulin concentrations (p < 0.05). The results suggest that RR (poly)phenols are metabolized in a dose-related manner, and further research is required to understand their role in insulin management.