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Main conclusion: A member of the rice GT61 clade B is capable of transferring both 2-O-xylosyl and 2-O-arabinosyl residues onto xylan and another member specifically catalyses addition of 2-O-xylosyl residue onto xylan. Grass xylan is substituted predominantly with 3-O-arabinofuranose (Araf) as well as with some minor side chains, such as 2-O-Araf and 2-O-(methyl)glucuronic acid [(Me)GlcA]. 3-O-Arabinosylation of grass xylan has been shown to be catalysed by grass-expanded clade A members of the glycosyltransferase family 61. However, glycosyltransferases mediating 2-O-arabinosylation of grass xylan remain elusive. Here, we performed biochemical studies of two rice GT61 clade B members and found that one of them was capable of transferring both xylosyl (Xyl) and Araf residues from UDP-Xyl and UDP-Araf, respectively, onto xylooligomer acceptors, whereas the other specifically catalysed Xyl transfer onto xylooligomers, indicating that the former is a xylan xylosyl/arabinosyl transferase (named OsXXAT1 herein) and the latter is a xylan xylosyltransferase (named OsXYXT2). Structural analysis of the OsXXAT1- and OsXYXT2-catalysed reaction products revealed that the Xyl and Araf residues were transferred onto O-2 positions of xylooligomers. Furthermore, we demonstrated that OsXXAT1 and OsXYXT2 were able to substitute acetylated xylooligomers, but only OsXXAT1 could xylosylate GlcA-substituted xylooligomers. OsXXAT1 and OsXYXT2 were predicted to adopt a GT-B fold structure and molecular docking revealed candidate amino acid residues at the predicted active site involved in binding of the nucleotide sugar donor and the xylohexaose acceptor substrates. Together, our results establish that OsXXAT1 is a xylan 2-O-xylosyl/2-O-arabinosyl transferase and OsXYXT2 is a xylan 2-O-xylosyltransferase, which expands our knowledge of roles of the GT61 family in grass xylan synthesis. [ABSTRACT FROM AUTHOR]

A highly active MnO2 catalyst with mixed crystal forms for the catalytic combustion of ethyl acetate was successfully prepared. The characterization results showed that increasing the hydrothermal temperature promotes the transformation of MnO2 from α phase to β phase, and the microscopic morphology gradually evolves from stacked granular to rod-like structure, thereby obtaining biphasic mesoporous MnO2. In particular, the lattice fringes of α and β phases observed in HRTEM further proved that MnO2 possesses a dual-phase structure. XPS verified that MnO2–180°C has the highest Oads/Olatt (0.45) and Mn3+/Mn4+ (0.90) ratio, and as oxygen vacancies appear together with the formation of Mn3+ ions. The MnO2–180°C catalyst displayed the best performance that T99 (the temperature needed for 99% conversion) is as low as 170°C even though under the high space velocity of 68 000 mL g–1 h–1. Furthermore, the catalytic activity remained unchanged after 24 h of continuous reaction, demonstrating excellent low-temperature catalytic performance and good stability. [ABSTRACT FROM AUTHOR]

Purpose Forkhead box (FOX) family proteins regulate transcription and DNA repair and are involved in cell growth, differentiation, embryogenesis, and lifespan. The transcription factor FOXE1 is a member of the FOX family. The relationship between the expression level of FOXE1 and colorectal cancer (CRC) prognosis remains controversial. It is vital to verify the relationship between FOXE1 expression and the prognosis of patients with CRC. Methods We constructed a tissue microarray containing 879 primary colorectal cancer tissues and 203 normal mucosa samples. The tumor and normal mucosa tissues were stained with FOXE1 by immunohistochemistry, and the staining results were divided into two groups: high expression group and low expression group. Chi-square test was performed for the classification variable of the difference between FOXE1 expression levels and clinicopathological parameters. The survival curve was calculated according to the Kaplan–Meier method and the logarithmic rank test. The Cox proportional risk regression model was used for multivariate analysis of prognostic factors in patients with CRC.Results The expression level of FOXE1 in colorectal cancer was higher than that in the normal mucosa adjacent to cancer, although the difference was not significant. However, the expression of FOXE1 was correlated with tumor size, T stage, N stage, M stage, and pTNM stage. Univariate and multivariate analyses suggested that FOXE1 could be used as an independent prognostic factor in patients with CRC. Conclusions FOXE1 may be a potential independent prognostic factor for colorectal cancer patients. [ABSTRACT FROM AUTHOR]

Background: Gastric cancer (GC) remains a global challenge due to its high morbidity and mortality rates especially in Asia as well as poor response to treatment. As a member of the adhesion protein family and transmembrane glycoprotein, EpCAM expressed excessively in cancer cells including GC cells. The database assay showed that EpCAM is excessively expressed and easily mutated in cancers, especially in early stage of GC. Methods: To explore the roles EpCAM plays in oncogenesis and progression of GC, the expression of EpCAM was deleted in GC cells with CRISPR/Cas9 method, and then the changes of cell proliferation, apoptosis, motility and motility associated microstructures in EpCAM-deleted GC cells (EpCAM-/-SGC7901) were detected to evaluate the rules EpCAM played. Results: The results showed that EpCAM deletion caused cell proliferation, motility and the development of motility-relevant microstructures inhibited significantly, apoptotic trend and contact inhibition enhanced in EpCAM-deleted GC cells. The results of western blot suggested that EpCAM modulates the expression of epithelial/endothelial mesenchymal transition (EMT) correlated genes. All results as above indicated that EpCAM plays important roles to enhance the oncogenesis, malignancy and progression as a GC enhancer. Conclusions: Combining our results and published data together, the interaction of EpCAM with other proteins was also discussed and concluded in the discussion. Our results support that EpCAM can be considered as a novel target for the diagnosis and therapy of GC in future. [ABSTRACT FROM AUTHOR]

Quantum communication network scales point-to-point quantum communication protocols to more than two detached parties, which would permit a wide variety of quantum communication applications. Here, we demonstrate a fully-connected quantum communication network, exploiting three pairs of Einstein—Podolsky—Rosen (EPR) entangled sideband modes, with high degree entanglement of 8.0 dB, 7.6 dB, and 7.2 dB. Each sideband modes from a squeezed field are spatially separated by demultiplexing operation, then recombining into new group according to network requirement. Each group of sideband modes are distributed to one of the parties via a single physical path, making sure each pair of parties build their own private communication links with high channel capacity better than any classical scheme. [ABSTRACT FROM AUTHOR]

Introduction: The association between diabetes mellitus (DM) and risk of osteoarthritis (OA) is inconsistent based on published observational studies. This study aimed to conduct a two-sample Mendelian randomization (MR) analysis to explore the causal link between glycated hemoglobin (HbA1c) level and OA risk. Methods: Genome-wide association studies (GWAS) summary statistics were obtained from the publicly available Integrative Epidemiology Unit (IEU) OpenGWAS database. A series of screening processes were performed to select qualified instrumental single-nucleotide polymorphisms (SNPs) strongly related to exposure. The inverse-variance-weighted method, weighted-median method, and MR–Egger method were performed to ensure robust and reliable results. The MR–Egger intercept test, Cochran's Q test, and the leave-one-out sensitivity analysis were utilized to assess the horizontal pleiotropy, heterogeneities, and stability of these genetic variants for OA. Odds ratio (OR) and 95% confidence interval (CI) were calculated. Results: MR analyses found a robust causal association of genetically determined HbA1c with knee OA (OR = 1.561; 95% CI 1.110–2.197; P = 0.011), but not with hip OA (OR = 1.073; 95% CI 0.674–1.710; P = 0.766) or overall OA (OR = 1.141; 95% CI 0.904–1.441; P = 0.804). Sensitivity analyses showed that there was a strong association between SNPs and HbA1c (F = 21.138), no evidence of heterogeneity (Q = 150.625, P = 0.402), and no potential SNPs affecting the causal link. Conclusion: Our MR study supported a causal effect of genetically increased HbA1c on knee OA risk. [ABSTRACT FROM AUTHOR]

Determination of malignancy in thyroid nodules remains a major diagnostic challenge. Here we report the feasibility and clinical utility of developing an AI-defined protein-based biomarker panel for diagnostic classification of thyroid nodules: based initially on formalin-fixed paraffin-embedded (FFPE), and further refined for fine-needle aspiration (FNA) tissue specimens of minute amounts which pose technical challenges for other methods. We first developed a neural network model of 19 protein biomarkers based on the proteomes of 1724 FFPE thyroid tissue samples from a retrospective cohort. This classifier achieved over 91% accuracy in the discovery set for classifying malignant thyroid nodules. The classifier was externally validated by blinded analyses in a retrospective cohort of 288 nodules (89% accuracy; FFPE) and a prospective cohort of 294 FNA biopsies (85% accuracy) from twelve independent clinical centers. This study shows that integrating high-throughput proteomics and AI technology in multi-center retrospective and prospective clinical cohorts facilitates precise disease diagnosis which is otherwise difficult to achieve by other methods. [ABSTRACT FROM AUTHOR]

The spatial structure of geochemical patterns is influenced by various geological processes, one of which may be mineralization. Thus, analysis of spatial geochemical patterns facilitates understanding of regional metallogenic mechanisms and recognition of geochemical anomalies related to mineralization. Convolutional neural networks (CNNs) used in previous studies to extract spatial features require regular data (e.g., raster maps) as input. Due to the complex and diverse geological environment, geochemical samples are inevitably irregularly distributed and even partially missing in many spaces, leading to the inapplicability of CNN-based methods for geochemical anomaly identification. Also, interpolation from samples to regular grids often introduces uncertainties. To address these problems, this study innovatively transformed geochemical sampled point data into graphs and introduced graph learning to extract the geochemical patterns. Correspondingly, a novel framework of geochemical identification named GAUGE (recognition of Geochemical Anomalies Using Graph lEarning) is proposed. To assess the performance of the proposed method, this study recognized anomalies related to Au deposits in the Longyan area, the Wuyishan polymetallic metallogenic belt, China. For a set of regularly distributed samples, GAUGE achieved an accuracy similar to that of a traditional convolution autoencoder. More importantly, GAUGE achieved an area under the curve of 0.833, outperforming one-class support vector machine, isolation forest, autoencoder, and deep autoencoder network for a set of irregularly distributed samples by 10.6, 5.2, 4.8, and 2.5%, respectively. By introducing graph learning into geochemical anomaly recognition, this study provides a new perspective of extracting both spatial structure and compositional relationships of multivariate geochemical patterns, which can be applied directly to irregularly distributed samples in irregularly shaped regions without the need for interpolation. Such an improvement greatly enhances the applicability of machine learning methods in geochemical anomaly recognition, providing support for mineral resources evaluation and exploration. [ABSTRACT FROM AUTHOR]

Objectives: Ovarian cancer is one of the most fatal gynecological malignancies. It is emergently needed to select a novel molecular fragment as a targeting element for the future development of molecular imaging diagnosis and targeting chemotherapy to ovarian cancer. Results: After five rounds of biopanning, a total of 44 positive phage clones were selected from final phage displayed peptide library. Nine consensus sequences were found based on the assay of sequencing results, then one clone of each consensus group was characterized and identified further by immunofluorescence assay. The result showed the phage clone R20 presents best targeting capacity. Then we synthesized peptide (OSP2) clone R20 displayed, it was characterized with high specificity and sensitivity binding to human ovarian cancer by a tissue chip assay. The target of OSP2 was predicted and docked as human carbonic anhydrase XII (CA12), an important protein usually deregulated in cancer. Conclusions: Taken together, OSP2 and its target indicate a novel investigation way in future to develop novel agent or drug delivery formulation for molecular imaging diagnosis and targeting chemotherapy of ovarian cancer. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "The high expression of FOXE1 in colorectal cancer predicts a promising prognosis: a retrospective study." The correction states that there was an error in Table 1 of the original article, and provides the corrected version of the table. The corrected table shows the relationship between FOXE1 expression and various clinicopathological parameters. The correction also mentions that there was no significant correlation between sex, age, location, and overall survival in the univariate survival analysis of clinicopathological parameters. The publisher remains neutral regarding jurisdictional claims and institutional affiliations. [Extracted from the article]

Making low GI of the Chinese steamed bread (CSB) with acceptable eating quality is a challenge. A CSB prepared from wheat flour partially substituted by lotus root powder (LRP) showed good prospects. RVA profile and texture profile were determined to evaluate the texture, while animal test were used to confirm the bio-functional attributes. The addition of LRP effectively changed the RVA profile of lotus-wheat incorporated flour (LWIF). CSB prepared from 30% LWIF showed acceptable eating quality with higher springiness, cohesiveness, and recovery while lower hardness. After 12 weeks of 30% LWIF administrating, the fast blood glucose of diabetic rat decreased from 17.6 to 5.8 mmol/L together with the reduction of serum TC, TG and LDL-C. The hepatic histopathological examination and serum levels changes of SOD, CAT and FFA confirmed LWIF could effectively protect the liver of the diabetic rats from damage caused by oxidative stress. [ABSTRACT FROM AUTHOR]

The polyphenol distribution in fresh waxy corns of different color varieties and their functional activities, which may be useful for treating various chronic diseases, were investigated. The in vitro antioxidant activity, and hypoglycemic and hypocholesterolemic effects of the free and bound corn phenolics were determined to evaluate the edible value of fresh waxy corn. The colored varieties contained more phenols than the common varieties (white and/or yellow). The total free phenolic acid content of the six varieties was 6637.73 µg/g DW (dry weight), which was slightly higher (P > 0.05) than that of the total bound form (6276.65 µg/g DW). The total free flavonoid content was 5850.09 µg/g DW, which was higher (P < 0.05) than that of the total bound form (4874.51µg/g DW). No bound anthocyanin was detected in the methanol extracts of the tested varieties. For all the varieties, free polyphenols contributed 86−100 % and 70−78 % of the 2, 2-diphenyl-1-picrylhydrazyl (DPPH) and hydroxyl radical scavenging abilities, respectively, and 100 % of the ferric reducing capacity. The free phenolics in fresh waxy corn showed better (P < 0.05) hypoglycemic effect than the bound form in terms of inhibition of α-amylase activity, whereas the bound phenolics of most varieties showed higher α-glucosidase inhibitory activity than the free forms. The free phenolics showed better (P < 0.05) glycocholesterol binding than the bound form for all varieties. The bound polyphenols showed better sodium cholate and taurocholate binding than the free form for most varieties. In conclusion, the difference between free and bound polyphenol content and functional activities indicates that fresh waxy corn can be potentially used for the development of functional food. [ABSTRACT FROM AUTHOR]

Plants generate a plethora of secondary compounds (toxins) that potently influence the breadth of the breeding niches of animals, including Drosophila. Capsaicin is an alkaloid irritant from hot chili peppers, and can act as a deterrent to affect animal behaviors, such as egg laying choice. However, the mechanism underlying this ovipositional avoidance remains unknown. Here, we report that Drosophila females exhibit a robust ovipositional aversion to capsaicin. First, we found that females were robustly repelled from laying eggs on capsaicin-containing sites. Second, genetic manipulations show that the ovipositional aversion to capsaicin is mediated by activation of nociceptive neurons expressing the painless gene. Finally, we found that capsaicin compromised the health and lifespan of flies through intestinal dysplasia and oxidative innate immunity. Overall, our study suggests that egg-laying sensation converts capsaicin into an aversive behavior for female Drosophila, mirroring an adaptation to facilitate the survival and fitness of both parents and offspring. [ABSTRACT FROM AUTHOR]

Ultrafine-grained tungsten (UFG W) produced by severe plastic deformation technology has many potential applications due to its high strength and ductility. To reveal the mechanism for the high ductility of UFG W, the deformation and failure behaviors of coarse-grained tungsten (CG W) and UFG W have been compared based on a three-dimensional crystal plastic finite element method (CPFEM) simulation. Cohesive element method has been utilized to model the behavior of grain boundaries (GBs). Both plastic deformation in grain interiors and grain boundary opening have been observed in different periods of deformation in UFG W. It is concluded that the high GB density and elongated microstructure in the UFG W suppress crack propagation, decrease the stress concentration and impurity concentration on GBs, therefore enhance the ductility of the material. [ABSTRACT FROM AUTHOR]

Aims: Evidence indicates that curcumin seems to improve outcomes in non-alcoholic fatty liver disease (NAFLD). A meta-analysis was performed to evaluate the effects of curcumin inNAFLD. Methods: We searched PubMed, EMBASE, and the Cochrane Library from inception through March 2018 to identify randomized controlled trials (RCTs) evaluating the role of curcumin inNAFLD. The mean difference (MD) and 95% confidence interval (CI) were calculated. Results: Four RCTs with a total of 229 NAFLD patients were included. Curcumin was more likely to lower LDL-C, triglycerides, FBS, HOMA-IR, weight and AST levels compared with placebo, and the difference was statistically significant [MD = − 27.02, 95% CI (− 52.30, − 1.74); MD = − 33.20, 95% CI (− 42.30, − 24.09); MD = − 5.63, 95% CI (− 10.36, − 0.90); MD = − 0.53, 95% CI (− 1.00, − 0.05); MD = − 2.27, 95% CI (− 3.11, − 1.44); MD = − 7.43, 95% CI (− 11.31, − 3.54), respectively]. However, the beneficial effect of curcumin did not achieve statistical significance in lowering total cholesterol, HDL-C, HbA1c, ALT or insulin levels [MD = − 30.47,95% CI (− 60.89. − 0.06); MD = − 0.98, 95% CI (− 2.88, 0.92); MD = − 0.41, 95% CI (− 1.41, 0.59); MD = − 6.02, 95% CI (− 15.61, 3.57); MD = − 0.92, 95% CI (− 2.33, 0.49)]. Conclusions: Curcumin is effective in lowering LDL-C, triglycerides, FBS, HOMA-IR, weight, and AST levels in NAFLD patients, and it is well tolerated. Further RCTs are required to confirm our findings. [ABSTRACT FROM AUTHOR]

To analyze the anti-tumor mechanism of Baicalin in human colon cancer. The MTT assay and colony formation assay demonstrated that Baicalin treatment inhibits the proliferation of DLD1 and HCT-116 cells. The apoptosis rates were induced upon Baicalin treatment and which was determined by FACS. The qPCR and western blot analysis showed that Baicalin promotes expression of DKK1 (Dickkopf), an important antagonist of Wnt signaling pathway, thereby reduces the expression of its downstream protein β-catenin and c-Myc. Reduction of DKK1 expression by siRNA attenuates β-catenin and c-Myc expression. microRNA-217 (miR-217) is decreased upon Baicalin treatment. Moreover, DKK1 is identified as the direct downstream target gene of miR-217 through the dual-luciferase reporter assay. miR-217/DKK1-mediated inhibition of Wnt signaling pathway participate in apoptosis induced by Baicalin. [ABSTRACT FROM AUTHOR]

In colorectal cancer (CRC), despite the complex inducing and regulating mechanism in necrosis progress, the prognostic value of tumor necrosis has been reported. It is generally recognized that necrosis is associated with many process involving severe hypoxia, inflammatory responses and angiogenesis, all of which contribute to promote tumor growth and poor prognosis. In addition to local hypoxia, regulation by RIP kinase and the conversion from apoptosis to necrosis can result in necrosis also. Recent studies showed necrosis can be a histopathologic characteristic for special molecular phenotype of CRC. A novel and attractive complementary treatment, tumor necrosis therapy, using radiolabelled compounds avid for necrosis has emerged. However, the complicated regulatory mechanisms of tumor necrosis were rarely reported in CRC, and we collected and reviewed these effect and relevance in CRC. [ABSTRACT FROM AUTHOR]

We are sorry for the inconvenience. These authors contributed equally: Yaoting Sun, Sathiyamoorthy Selvarajan, Zelin Zang, Wei Liu, Yi Zhu, Hao Zhang Correction to: I Cell Discovery i (2022) 8:85 https://doi.org/10.1038/s41421-022-00442-x published online 06 September 2022 In this article, the authors have found an error in Data Availability section, the iProX ID is incorrect. [Extracted from the article]

In this work, a core-shell molecularly imprinted polymer (MIP) was synthesized through sol-gel coating procedure by using silica beads, emodin, 3-aminopropyltriethoxysilane, tetraethoxysilane and tetrahydrofuran as supporting matrix, template, functional monomer, cross-linker and solvent, respectively. The selective recognition property for emodin and its analogues (physcion and aloe emodin) of the resultant MIP was evaluated in a chromatographic column for high-performance liquid chromatography (HPLC). The retention time and imprinted factor of MIP column for emodin, physcion and aloe emodin were 5.11, 0.63, 0.69 min and 4.69, 0.75, 1.38, respectively. It showed that the MIP beads had a good binding ability for emodin. Finally, one-step separation of emodin from alcohol extract of Rheum palmatum L. at semi-preparative scale was achieved and 380 mg of emodin was collected in 5 days. The product was characterized by mass spectrometry and HPLC and its purity was 95 %. [ABSTRACT FROM AUTHOR]

High-intensity focused ultrasound (HIFU) is an innovative, noninvasive, extracorporeal technique that induces coagulative necrosis of tumor tissue by thermal effects and cavitation. In published studies, HIFU has usually been used as an alternative to surgery, with or without other treatment modalities, to achieve curative tumor ablation or palliative tumor cytoreduction. Neoadjuvant HIFU treatment for primary inoperable malignant fibrous histiocytoma has never been reported, and neoadjuvant radiotherapy, chemoradiation, or chemotherapy is routinely under consideration. This is the first case in which HIFU ablation contributed as a neoadjuvant therapy to facilitate function-sparing resection, not as a replacement for surgery. It suggests that HIFU ablation may have some unique major advantages for treating inoperable huge soft-tissue sarcomas as a neoadjuvant local treatment modality, especially for patients for whom neoadjuvant chemotherapy or radiotherapy is not indicated. [ABSTRACT FROM AUTHOR]

The use of molecularly imprinted polymers (MIPs) prepared by ring-opening metathesis polymerization (ROMP) for bisphenol A (BPA) was reported in this article. The resulting MIPs have high imprinting and adsorption capacities, and can be used for separation and determination of BPA in environmental water samples. The successful application of ROMP in the molecular imprinting field is described here. For the first time, two cross-linkers (dicyclopentadiene and 2,5-norbornadiene) and two Grubbs catalysts (first and second generation) were investigated to compare their effects on the binding performance of MIPs. The ROMP technique is able to create the imprinted polymers within 1 h under mild conditions. Furthermore, it can provide MIPs with obvious imprinting effects towards the template, very fast template rebinding kinetics, high binding capacity and appreciable selectivity over structurally related compounds. The adsorption process for MIPs in this study can be completed within 45 min, which is much faster than that of bulk MIPs synthesized by traditional free-radical polymerization. The resulting imprinting polymer was evaluated for its use as a sorbent support in an off-line solid-phase extraction approach to recover BPA from diluted aqueous samples. The optimized extraction protocol resulted in a reliable MISPE method suitable for selective extraction and preconcentration of BPA from tap water, human urine and liquid milk samples. This article demonstrates the practical feasibility of the MIPs prepared via ROMP as solid-phase extraction materials. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Although changes in lipid profile have been documented in gastrointestinal cancers, the specific relationship between serum lipid levels and lymph node (N) stages in gastric cancer remains uncertain. Preoperative serum lipid concentrations were retrospectively examined in 501 patients who underwent curative resection for primary gastric cancer. Univariate and multivariate analyses were carried out to investigate the association of serum lipid levels with nodal stages. The serum high-density lipoprotein cholesterol (HDL-C) levels in gastric cancer patients correlated well with N stages. Cases with low HDL-C (<40 mg/dl) presented more advanced pN2–3 disease (57.6%, 83/144) than those with normal HDL-C (36.4%, 130/357; P<0.05). The observed elevation of the TC/HDL-C ratio for patients with pN2–3 disease was statistically significant when compared with that for patients with pN0–1 disease (mean values 3.57 vs. 3.31, P < 0.05). By receiver operating characteristic analysis, the combination of serum HDL-C concentration and TC/HDL-C ratio led to a sensitivity of 70.0% and a specificity of 51.0% in predicting stage pN2–3. A logistic regression model revealed that both low HDL-C (<40 mg/dl) and high TC/HDL-C ratio (≥3.32) had an independent association with advanced pN2–3 stages. When patients’ lipid levels were stratified by means of histological differentiation, the significant correlation of serum HDL-C levels with nodal stages was only detected in differentiated gastric cancer. For gastric cancer patients, preoperative low serum HDL-C concentration or high TC/HDL-C ratio might be a potential biomarker of advanced pN2–3 stages, especially for those with the histologically differentiated type. [ABSTRACT FROM AUTHOR]

The open-reading frame PF0895 in the genome of the hyperthermophilic archaeon, Pyrococcus furiosus, encodes a 206-residue protein (MR 23,152). The structure of the recombinant protein was solved by single isomorphous replacement with anomalous scattering (SIRAS) using a mercury derivative. It has been refined to 1.70 Å with a crystallographic R and Rfree values of 19.7% and 22.3%, respectively. The PF0895 structure is similar to those of the ATP binding cassettes observed in the ABC transporter family. However, bioinformatics and molecular analyses indicate that PF0895 is not part of the expected five-gene operon that encodes a typical prokaryotic solute-binding ABC transporter. Rather, transcriptional profiling data show that PF0895 is part of a novel four-gene operon (PF0895–PF0896–PF0897–PF0897.1) where only PF0895 has homologs in other organisms. Interestingly, from genome analysis, P. furiosus itself contains a second version of this complex, encoded by PF1090–PF1093. From the structural studies we can only conclude that one of the subunits of this novel membrane complex, PF0895, and its homolog PF1090, likely bind a purine nucleotide. PF0895 is therefore predicted to be part of a membrane-bound multiprotein complex unrelated to ABC transporters that is so far unique to P. furiosus. It appears to play a role in the stress response, as its expression is down regulated when the organism is subjected to cold-shock, where cells are transferred from 95°C, near the optimal growth temperature, to 72°C, near the minimal growth temperature. The related PF1090-containing operon is unaffected by cold-shock and is independently regulated. [ABSTRACT FROM AUTHOR]

Proteins derived from the coding regions of Pyrococcus furiosus are targets for three-dimensional X-ray and NMR structure determination by the Southeast Collaboratory for Structural Genomics (SECSG). Of the 2200 open reading frames (ORFs) in this organism, 220 protein targets were cloned and expressed in a high-throughput (HT) recombinant system for crystallographic studies. However, only 96 of the expressed proteins could be crystallized and, of these, only 15 have led to structures. To address this issue, SECSG has recently developed a two-tier approach to protein production and crystallization. In this approach, tier-1 efforts are focused on producing protein for new Pfu(italics?) targets using a high-throughput approach. Tier-2 protein production efforts support tier-1 activities by (1) producing additional protein for further crystallization trials, (2) producing modified protein (further purification, methylation, tag removal, selenium labeling, etc) as required and (3) serving as a salvaging pathway for failed tier-1 proteins. In a recent study using this two-tiered approach, nine structures were determined from a set of 50 Pfu proteins, which failed to produce crystals suitable for X-ray diffraction analysis. These results validate this approach and suggest that it has application to other HT crystal structure determination applications. [ABSTRACT FROM AUTHOR]

Clay fractions in the non-calcareous surface sediments from the eastern Pacific were analyzed for clay minerals, REE and 143Nd/144Nd. Montmorillonite/illite ratio (M/I ratio), total REE contents (ΣREE), LREE/HREE ratio and cerium anomaly (δCe) may effectively indicate the genesis of clay minerals. Clay fractions with M/I ratio <1, δCe >0.85, ΣREE <400 μg/g, LREE/HREE ratio ≈4, and REE patterns similar to those of pelagic sediments are terrigenous and autogenetic mixed clay fractions and contain more autogenetic montmorillonite. Clay fractions with M/I ratio >1, δCe=0.86 to 1.5, ΣREE=200 to 350 μg/g, LREE/HREE ratio ≈6 and REE distribution patterns similar to that of China loess are identified as terrigenous clay fraction. The 143Nd/144Nd ratios or ɛNd values of clay fractions inherit the features of terrigenous sources of clay minerals. Clay fractions are divided into 4 types according to ɛNd values. Terrigenous clay minerals of type I with the ɛNd values of ™8 to ™6 originate mainly from North American fluvial deposits. Those of type II with the ε Nd values of ™9 to ™7 are mainly from the East Asia and North American fluvial deposits. Those of type III with ε Nd values of ™6 to ™3 could come from the central and eastern Pacific volcanic islands. Those of type IV with ε Nd values of ™13 to ™12 may be from East Asia eolian. The terrigenous and autogenetic mixed clay fractions show patchy distributions, indicating that there are volcanic or hot-spot activities in the eastern Pacific plate, while the terrigenous clay fractions cover a large part of the study area, proving that the terrigenous clay minerals are dominant in the eastern Pacific. [ABSTRACT FROM AUTHOR]

Fiftysix samples of nannofossil ooze were collected from Core PC5794 in the northern equatorial Pacific at 5 cm intervals. With the methods of mass spectrometer (VG354) and ICP, the Nd isotopic compositions (εNd(t)), Mn contents and Mg/Sr ratios of carbonate phase have been analyzed. CaCO3 contents of bulk sediments were obtained by dissolution of 0.5 mol/L HCl. Based on these data, the high-resolution εNd(t) profile of seawater in early Miocene with core depth(or time) have been established. The values of εNd(t) range from -6.2 to -2.97 and 4 fluctuation cycles existed during 24.06-22.02 Ma. 4 low εNd(t) values (about-6.4) correspond to high CaCO3 contents, which implicates that there were 4 cold epochs or 4 times of Antarctic Bottom Water activity. They occurred at the time of 24.06 Ma, 23.85 Ma, 22.88 Ma and 22.26 Ma, respectively. High εNd(t) values correspond to the high Mn contents and high values of Mg/Sr ratio, which indicates the existence of 4 intense hydrothermal activity periods during 24.06-22 Ma, the durations of them are 4.05-23.98 Ma, 23.69-23.15 Ma, 22.74-22.37 Ma and 22.06-22.02 Ma, respectively. [ABSTRACT FROM AUTHOR]

We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines. [ABSTRACT FROM AUTHOR]

Studies a floating dust weather occurrence over the Qingdao region in China. Atmospheric dust concentration; Source and formation mechanism; Elemental comparison of the air-borne floating dust; Satellite photos of the cloud.

A correction to the article "Fast native-SAD phasing for routine macromolecular structure determination," by Vincent Olieric, Lirong Chen, and Hua Zhang that was published online on December 15, 2014 is presented.

ReDuNing injection (RDN) is a patented traditional Chinese medicine, and the components of it were proven to have antiviral and important anti-inflammatory activities. Several reports showed that RDN had potential effects in the treatment of influenza and pneumonia. Though there were several experimental reports about RDN, the experimental results were not enough and complete due to that it was difficult to predict and verify the effect of RDN for a large number of human diseases. Here we employed multiscale model by integrating molecular docking, network pharmacology and the clinical symptoms information of diseases and explored the interaction mechanism of RDN on human diseases. Meanwhile, we analyzed the relation among the drug molecules, target proteins, biological pathways, human diseases and the clinical symptoms about it. Then we predicted potential active ingredients of RDN, the potential target proteins, the key pathways and related diseases. These attempts may offer several new insights to understand the pharmacological properties of RDN and provide benefit for its new clinical applications and research. [ABSTRACT FROM AUTHOR]