Conserved allosteric perturbation of the GTPase domains by region 1 of Ras hypervariable regions.

Ras proteins are important intracellular signaling hubs that can interact with numerous downstream effectors and upstream regulators through their GTPase domains (G-domains) anchored to plasma membranes by the C-terminal hypervariable regions (HVRs). The biological functions of Ras were proposed to be regulated at multiple levels including the intramolecular G-domain-HVR interactions, of which the exact mechanism and specificity are still controversial. Here, we demonstrate that the HVRs, instead of having direct contacts, can weakly perturb the G-domains via an allosteric interaction that is restricted to a ∼20 Å range and highly conserved in the tested Ras isoforms (HRas and KRas4B) and nucleotide-bound states. The origin of this allosteric perturbation has been localized to a short segment (residues 167-171) coinciding with region 1 of HVRs, which exhibits moderate to weak α-helical propensities. A charge-reversal mutation (E168K) of KRas4B in region 1, previously described in the Catalog of Somatic Mutations in Cancer database, was found to induce similar chemical shift perturbations as truncation of the HVR does. Further membrane paramagnetic relaxation enhancement (mPRE) data show that this region 1 mutation alters the membrane orientations of KRas4B and moderately increases the relative population of the signaling-compatible state.

Fragment-Guided Genome Mining of Octacyclic Cyclophane Alkaloids from Fungi.

Nature uses compact but functionalized biosynthetic fragments as building blocks to generate complex natural products. To leverage this strategy for the discovery of natural products with new scaffolds, we performed genome mining to identify biosynthetic gene clusters (BGCs) in fungi that embed genes that can synthesize targeted fragments. The three-enzyme pathway that biosynthesizes the strained dityrosine cyclophane in the herquline A pathway was used to identify a large number of potential BGCs that may use the cyclophane as a fragment. Characterization of a conserved BGC from fungal strains led to the isolation of octacyclin A, an octacyclic natural product with an unprecedented structure, including two hetero-[3.3.1]bicycles and a combination of fused, bridged, and macrocyclic rings. Biosynthetic steps leading to octacyclin A were fully elucidated using pathway reconstitution and enzymatic assays, unveiling intriguing chemical logic and new enzymatic reactions in building the octacyclic core. Our work demonstrates the potential utility of fragment-guided genome mining in expanding natural product chemical space.

Performance of two semi-analytical algorithms in deriving water inherent optical properties in the Southern Ocean.

Remotely sensed inherent optical properties (IOPs) are key proxies for synoptic mapping of primary production and carbon export in the global ocean. However, the IOPs inversion algorithms are scarcely evaluated in the Southern Ocean (SO) because of limited field observations. In this study, the performance of two widely used semi-analytical algorithms (SAAs), i.e., the quasi-analytical algorithm (QAA) and the generalized IOP model (GIOP), were evaluated using a compiled in situ bio-optical dataset in SO, as well as measurements from the Visible Infrared Imaging Radiometer Suite (VIIRS). Evaluations with in situ data show that QAA and GIOP have comparable performance in retrieving the total absorption coefficient (a(λ)), absorption coefficients of phytoplankton (aph(λ)), and that of detritus and colored dissolved organic matter (adg(λ)). Overall, it was found that remotely sensed a(λ) and aph(λ) by both SAAs agreed well with field measurements, with the mean absolute percentage difference (MAPD) of derived a(λ) and aph(λ) in the blue-green bands being ∼20% and ∼40%, respectively. However, derived adg(λ) by both SAAs were higher than the measured values at the lower end (adg(443) < ∼0.01 m-1), but lower at the higher end (adg(443) > ∼0.02 m-1), with MAPD of ∼60%. Results of this effort suggest confident products of a(λ) and aph(λ) from VIIRS in SO, but more dedicated efforts on the measurements and evaluation of adg(λ) in SO would be desired.

Modified endoscopic retrograde appendicitis therapy vs. laparoscopic appendectomy for uncomplicated acute appendicitis in children.

OBJECTIVES: Modified endoscopic retrograde appendicitis therapy (mERAT) has been proposed as an alternative to laparoscopic appendectomy for the treatment of appendicitis. However, data from children in large samples are lacking. The aim of this article is to evaluate the efficacy between mERAT and laparoscopic appendectomy (LA) in children with uncomplicated appendicitis. METHOD: We retrospectively analyzed 594 patients with suspected uncomplicated appendicitis from October 2018 to May 2021. A pool of 294 consecutive patients who met the inclusion criteria were ultimately enrolled in this study (228 and 66 patients in mERAT and LA, respectively). Given the differences in baseline clinical data (gender, age), the regression equation including differences in clinical baseline, grouping factor, and white blood cell count was established to address the influence of potential confounding factors. RESULT: The initial success rate of mERAT management was 96.9%, and the recurrence rate was 6.9% in the mERAT group and 1.7% in the LA group within 1 year, which was no significant difference. But the mERAT group had a lower rate of adverse events. Finally, those results indicated that the treatment modalities, LA or mERAT, had no significant effect on initial success rate (P = 0.99) or recurrence rate (P = 0.17) within 1 year, but a significant effect on the adverse events rate during hospitalization (P = 0.01) in the multivariate regression analysis. CONCLUSION: Among children with uncomplicated appendicitis, an initial mERAT management strategy had a success rate of 96.9%, which was similar to the LA group at 1 year. This follow-up supports the feasibility of mERAT alone as an alternative to surgery for uncomplicated appendicitis.

Two pairs of 2-pyrone enantiomers and a benzophenone analogue from the endophytic fungus Penicillium egyptiacum.

Four new 2-pyrone derivatives, two pairs of enantiomers, (±)-egypyrone A [(±)-1] and (±)-egypyrone B [(±)-2], together with a new benzophenone analogue, orbiophenone B (3), were isolated from the endophytic fungus Penicillium egyptiacum. The enantiomeric mixtures (±)-1 and (±)-2 were separated through chiral HPLC, respectively. Their structures were elucidated by extensive analysis of spectroscopic data and the absolute configuration was determined by comparing the optical rotation of structurally similar molecule. Subsequently, the cytotoxic activities of (±)-1, (±)-2, and 3 against the U87 cell line were tested and no activity was observed at a concentration of 10 µM.

Biosynthesis of AS2077715 and Funiculosin: Pathway Reconstitution and Identification of Enzymes that Form the All-cis Cyclopentanetetraol Moiety.

The complete biosynthetic pathways of the potent antifungals AS2077715 (1) and funiculosin (2) are reconstituted and characterized. A five-enzyme cascade, including a multifunctional flavin-dependent monooxygenease and a repurposed O-methyltransferase, is involved to perform the dearomatization, stereoselective ring contraction, and redox transformations to morph a hydroxyphenyl-containing precursor into the unusual all-cis cyclopentanetetraol moiety.

Genome Mining from Agriculturally Relevant Fungi Led to a d-Glucose Esterified Polyketide with a Terpene-like Core Structure.

Comparison of biosynthetic gene clusters (BGCs) found in devastating plant pathogens and biocontrol fungi revealed an uncharacterized and conserved polyketide BGC. Genome mining identified the associated metabolite to be treconorin, which has a terpene-like, trans-fused 5,7-bicyclic core that is proposed to derive from a (4 + 3) cycloaddition. The core is esterified with d-glucose, which derives from the glycosidic cleavage of a trehalose ester precursor. This glycomodification strategy is different from the commonly observed glycosylation of natural products.

Silencing lncRNA Snhg6 mitigates bleomycin-induced pulmonary fibrosis in mice via miR-26a-5p/TGF-ß1-smads axis.

Idiopathic pulmonary fibrosis (IPF) is an interstitial pulmonary disease with slow onset and high mortality. Epithelial-mesenchymal transition (EMT) is a significant condition for tissue fibrosis, and lncRNA-Snhg6 (small nucleolar RNA host gene 6) is related to EMT in some cancer cells, but its role in pulmonary fibrosis remains obscure. Here, we found that TGF-ß1 and Snhg6 were up-regulated in lung tissues of BLM-induced lung fibrosis mouse, and Snhg6 expression was significantly increased in primary lung fibroblasts after BLM treatment. Snhg6 knockdown notably alleviated the pulmonary dysfunction, and the increase of fibrosis area and collagen deposition induced by BLM. MiR-26a-5p was downregulated in BLM-induced fibrotic lung tissues, and it was negatively regulated by Snhg6. Silencing Snhg6 markedly alleviated the TGF-ß1-induced increase in fibrotic marker expression, cell proliferation, migration and differentiation, as well as the nuclear transport of p-Smad2/3 by modulating miR-26a-5p expression in mouse lung fibroblasts. Moreover, overexpressing Snhg6-induced collagen accumulation and fibroblast activation in fibroblasts, which was reversed by treatment with miR-26a-5p mimic or oxymatrine (an inhibitor of TGF-ß1-Smads pathway). Interestingly, silencing Snhg6 in vivo mitigated BLM-driven pulmonary fibrosis by regulating the miR-26a-5p/TGF-ß1-Smads axis. Our data revealed that Snhg6 contributed to the process of BLM-driven lung fibrosis in mouse by modulating the miR-26a-5p/TGF-ß1-Smads axis, suggesting that Snhg6 might be a therapeutic target for lung fibrosis.

[Application of ultrasound-guided endoscopic retrograde appendicitis therapy in children with appendix-related chronic abdominal pain]. / è¶ å£°å¼•å¯¼å† é•œä¸‹é€†è¡Œé˜‘å°¾ç‚Žæ²»ç–—æœ¯åœ¨é˜‘å°¾ç›¸å ³æ ¢æ€§è ¹ç—›æ‚£å„¿ä¸­çš„åº”ç”¨ä»·å€¼.

OBJECTIVES: To study the clinical efficacy of ultrasound-guided endoscopic retrograde appendicitis therapy in children with appendix-related chronic abdominal pain. METHODS: A retrospective analysis was performed on the medical data of 30 children with the chief complaint of chronic abdominal pain who were admitted from August 2019 to May 2021. All the children were found to have inflammation of the appendix or intracavitary stool and fecalith by ultrasound and underwent ultrasound-guided endoscopic retrograde appendicitis therapy. The medical data for analysis included clinical manifestations, endoscopic findings, white blood cell count, neutrophil percentage, length of hospital stay, and cure rate. RESULTS: Among the 30 children with chronic abdominal pain, there were 13 boys (43%) and 17 girls (57%), with a mean age of (9±3) years (range 3-15 years) at diagnosis. The median duration of the disease was 12 months, and the median length of hospital stay was 3 days. The children had a median white blood cell count of 6.7×109/L and a neutrophil percentage of 50%±13%. Fecalith and a large amount of feces were flushed out of the appendix cavity for 21 children (70%) during surgery. The follow-up rate was 97% (29/30), and the median follow-up time was 11 months (range 5-26 months). Of the 29 children, abdominal pain completely disappeared in 27 children (93%). CONCLUSIONS: Ultrasound-guided endoscopic retrograde appendicitis therapy is effective in children with chronic abdominal pain caused by feces or fecalith in the appendix cavity.

Identification of diatom taxonomy by a combination of region-based full convolutional network, online hard example mining, and shape priors of diatoms.

Diatom test is one of the commonly used diagnostic methods for drowning in forensic pathology, which provides supportive evidence for drowning. However, in forensic practice, it is time-consuming and laborious for forensic experts to classify and count diatoms, whereas artificial intelligence (AI) is superior to human experts in processing data and carrying out classification tasks. Some AI techniques have focused on searching diatoms and classifying diatoms. But, they either could not classify diatoms correctly or were time-consuming. Conventional detection deep network has been used to overcome these problems but failed to detect the occluded diatoms and the diatoms similar to the background heavily, which could lead to false positives or false negatives. In order to figure out the problems above, an improved region-based full convolutional network (R-FCN) with online hard example mining and the shape prior of diatoms was proposed. The online hard example mining (OHEM) was coupled with the R-FCN to boost the capacity of detecting the occluded diatoms and the diatoms similar to the background heavily and the priors of the shape of the common diatoms were explored and introduced to the anchor generation strategy of the region proposal network in the R-FCN to locate the diatoms precisely. The results showed that the proposed approach significantly outperforms several state-of-the-art methods and could detect the diatom precisely without missing the occluded diatoms and the diatoms similar to the background heavily. From the study, we could conclude that (1) the proposed model can locate the position and identify the genera of common diatoms more accurately; (2) this method can reduce the false positives or false negatives in forensic practice; and (3) it is a time-saving method and can be introduced.

Dimeric guaianes from leaves of Xylopia vielana as snail inhibitors identified by high content screening.

The transcriptional repressor Snail trriggers epithelial-mesenchymal transition (EMT), the process allowing cancer cells with invasive and metastasis properties. In this study, we screened medicinal plants for the Snail inhibitory active components by high content screen (HCS) and found that the crude extract of Xylopia vielana leaves showed potential activity. Subsequently, bioassay-guided isolation of the extract of Xylopia vielana was performed to obtain twenty-four dimeric guaianes (1-24), including 16 new analogues (1-5, 8-11, 13-15, 17, 18, 21, and 22). Their structures were elucidated by the comprehensive application of multiple spectroscopic methods. Compounds 1, 11, 12, and 16 were initially identified as the active compounds. Wound healing assay, transwell migration assay and western blot experiments verified that compounds 1 and 12 inhibited the expression of Snail in a concentration-dependent manner, and compound 12 was verified as a potent tumor migration inhibitory agent. This work showed a practical strategy for the discovery of new Snail inhibitors from natural products and provided potential insights for dimeric guaianes as anticancer lead compounds specifically targeting Snail protein.

Energy Storage and Electrocaloric Cooling Performance of Advanced Dielectrics.

Dielectric capacitors are widely used in pulse power systems, electric vehicles, aerospace, and defense technology as they are crucial for electronic components. Compact, lightweight, and diversified designs of electronic components are prerequisites for dielectric capacitors. Additionally, wide temperature stability and high energy storage density are equally important for dielectric materials. Ferroelectric materials, as special (spontaneously polarized) dielectric materials, show great potential in the field of pulse power capacitors having high dielectric breakdown strength, high polarization, low-temperature dependence and high energy storage density. The first part of this review briefly introduces dielectric materials and their energy storage performance. The second part elaborates performance characteristics of various ferroelectric materials in energy storage and refrigeration based on electrocaloric effect and briefly shed light on advantages and disadvantages of various common ferroelectric materials. Especially, we summarize the polarization effects of underlying substrates (such as GaN and Si) on the performance characteristics of ferroelectric materials. Finally, the review will be concluded with an outlook, discussing current challenges in the field of dielectric materials and prospective opportunities to assess their future progress.

Self-Resistance in the Biosynthesis of Fungal Macrolides Involving Cycles of Extracellular Oxidative Activation and Intracellular Reductive Inactivation.

Self-resistance genes are employed by many microbial producers of bioactive natural products to avoid self-harm. Herein, we describe a unique strategy for self-resistance toward a macrolide antibiotic, A26771B (1), identified by elucidating its biosynthetic pathway in the fungus Penicillium egyptiacum. A highly reducing polyketide synthase and a trans-acting thioesterase generate the macrolide backbone, and a cytochrome P450 and an acyltransferase, respectively catalyze hydroxylation and succinylation to form the prodrug berkeleylactone E (2). Then, extracellular oxidative activation by a secreted flavin-dependent oxidase forms 1, while intracellular reductive inactivation by a short-chain reductase reforms 2, forming a redox cycle. Our work illustrates a unique redox-mediated resistance mechanism for fungal antibiotics and contributes to the understanding of antibiotic biosynthesis and resistance.

Highly Oxygenated Caryophyllene-Type Sesquiterpenes from a Plant-Associated Fungus, Pestalotiopsis hainanensis, and Their Biosynthetic Gene Cluster.

Seven new ß-caryophyllene derivatives, pestalotiphains A-G (1-7), along with six known analogues (8-13), were isolated from the plant-associated Pestalotiopsis hainanensis. Compound 1 represents the first example of a caryophyllene-adenine hybrid, and 2 contains a novel oxatricyclo[4.3.1.0] system. Their structures and absolute configurations were assigned by interpretation of a combination of spectroscopic data and electronic circular dichroism calculations. Compound 8 exhibited moderate inhibition of HL-60 and THP-1 cell lines (IC50, 6.2 and 2.0 µM, respectively). A candidate biosynthetic gene cluster responsible for these compounds was uncovered by bioinformatics analyses and confirmed by a biochemical approach.

Androgen-responsive lncRNA LINC00304 promotes cell cycle and proliferation via regulating CCNA1.

BACKGROUND: Long noncoding RNA (lncRNA) plays a vital role in the development of many diseases. The abnormal expression of lncRNA is closely related to the occurrence and development of different kinds of tumors including prostate cancer (PCa). METHODS: Differentially expressed lncRNA LINC00304 was identified using a publicly available gene expression data set (GSE38241) and quantitative polymerase chain reaction validation. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were used to predict the molecular function of LINC00304. A lncRNA microarray, bioinformatic analysis, and chromatin immunoprecipitation assay were carried out to verify the upstream androgen receptor (AR) signaling pathway. Subsequently, the function of LINC00304 was observed by a series of in vitro assays. RESULTS: We observed higher expression of LINC00304 in PCa cells and samples compared with normal prostate cells and tissues. Functional analysis of LINC00304 showed it was related to regulating cell cycle process, cellular developmental process, and focal adhesion. Further, we identified androgen-inhibited lncRNA, LINC00304 as a direct target of AR. A series of functional studies revealed that overexpression of LINC00304 could significantly promote cell proliferation and cell cycle progression in PCa cells. We also find that LINC00304 can significantly promote CCNA1 expression in PCa cells. CONCLUSIONS: Our results indicate that LINC00304 may represent a new diagnostic and therapeutic biomarker for PCa.

A novel androgen-reduced prostate-specific lncRNA, PSLNR, inhibits prostate-cancer progression in part by regulating the p53-dependent pathway.

BACKGROUND: Prostate cancer (PCa) is one of the most common cancers in males in China. Long noncoding RNAs (lncRNAs) reportedly play crucial roles in human cancer progression in many studies. However, the molecular mechanisms underlying PCa progression remain unclear. MATERIALS AND METHODS: We investigated the lncRNA transcriptome using publicly available RNA-sequencing data to identify prostate-specific lncRNAs. Then, the chromatin immunoprecipitation (ChIP) assay identified lncRNA with a direct binding to androgen receptor (AR), hereafter denoted as PSLNR. Quantitative real-time polymerase chain reaction analysis and Western blot analysis were performed to detect the expression of p53 signaling-related genes after overexpression PSLNR. The effects of overexpression of PSLNR on cell proliferation, cell cycle, and cell apoptosis were assessed by using CCK-8 and flow cytometric analysis. We then detected the expression of PSLNR in tissues. RESULT: We reported a novel androgen-reduced prostate-specific lncRNA, PSLNR, that inhibited PCa progression via the p53-dependent pathway. By analyzing the NOCODE data set, we reported that PSLNR was specifically expressed in the prostate, suggesting the potential of PSLNR as a biomarker for PCa treatment. The AR pathway was also confirmed to be an upstream regulation signaling pathway of PSLNR by transcriptionally regulating its expression in androgen-dependent PCa cells. PSLNR also significantly inhibited PCa proliferation by inducing cell apoptosis in a p53-dependent manner. Thus, PSLNR may be a candidate diagnosis and therapeutic target for PCa. CONCLUSIONS: Our study revealed for the first time a novel androgen-reduced prostate-specific lncRNA, PSLNR, which inhibited PCa progression via the p53-dependent pathway, suggesting that PSLNR may be a candidate diagnosis and therapeutic target for PCa.

Androgen-responsive circular RNA circSMARCA5 is up-regulated and promotes cell proliferation in prostate cancer.

Prostate cancer (PCa) is one of the most commonly diagnosed cancers in males worldwide. Circular RNA (circRNA) is a unique class of RNA transcribed by RNA polymerase II characterized by jointing 3' and 5' ends together via exon or intron circularization. However, the molecular functions of circRNAs in prostate cancer have rarely been explored. In present study, we found circ-SMARCA5 was up-regulated in prostate cancer samples compared to match normal tissues. We also observed circ-SMARCA5 expression was significantly induced after DHT treatment. Functional experiments showed circ-SMARCA5 acted as an oncogene in prostate cancer by promoting cell cycle and inhibiting cell apoptosis. We thought this study provided useful information for exploring circRNAs as potential therapeutic and prognostic targets for prostate cancer.

Isolation, Structure Elucidation, and Absolute Configuration of Syncarpic Acid-Conjugated Terpenoids from Rhodomyrtus tomentosa.

Three new syncarpic acid-conjugated sesquiterpenoids, tomentodiones E-G (1-3), and six new syncarpic acid-conjugated monoterpenoids, tomentodiones H-M (4-9), were isolated from the leaves of Rhodomyrtus tomentosa. Compounds 1-3 represent the first examples of ß-calacorene-based meroterpenoids. Their structures and absolute configurations were determined by a combination of NMR and ECD spectroscopy and X-ray diffraction analysis. On the basis of ECD data analysis for isolated and synthesized compounds, an empirical rule was proposed to determine the absolute configuration at C-7' of syncarpic acid-conjugated terpenoids. Additionally, a study of the reversal effect of multidrug resistance in doxorubicin-resistant human breast cancer cells showed that the noncytotoxic (+)-4 exerted the strongest potentiation effect of doxorubicin susceptibility, with an enhancement of 16.5-fold at a concentration of 30 µM.

The lncRNA XIST exhibits oncogenic properties via regulation of miR-449a and Bcl-2 in human non-small cell lung cancer.

Long non-coding RNAs (lncRNAs) are associated with the occurrence, development and prognoses of non-small cell lung cancer (NSCLC). In the present study, we investigated the functional mechanisms of the lncRNA XIST in two human NSCLC cell lines, A549 and NCI-H1299. In all the 5 NSCLC cell lines (NL9980, NCI-H1299, NCI-H460, SPC-A-1 and A549) tested, the expression levels of XIST were significantly elevated, as compared with those in normal human bronchial epithelial cell line BEAS-2B. In A549 and NCI-H1299 cells, knockdown of XIST by siRNA significantly inhibited the cell proliferation, migration and invasion, and promoted cell apoptosis. Furthermore, XIST knockdown elevated the expression of E-cadherin, and suppressed the expression of Bcl-2. Moreover, knockdown of XIST significantly suppressed the tumor growth in NSCLC A549 xenograft mouse model. Bioinformatic analysis and luciferase reporter assays revealed that XIST was negatively regulated by miR-449a. We further identified reciprocal repression between XIST and miR-449a, which eventually influenced the expression of Bcl-2: XIST functioned as a miRNA sponge of miR-449a, which was a negative regulator of Bcl-2. These data show that expression of the lncRNA XIST is associated with an increased growth rate and metastatic potential in NSCLC A549 and NCI-H1299 cells partially through miR-449a, and suggest that XIST may be a potential prognostic factor and therapeutic target for patients with NSCLC.

KDM1A triggers androgen-induced miRNA transcription via H3K4me2 demethylation and DNA oxidation.

BACKGROUND: Androgen receptor (AR) is a ligand dependent transcription factor that regulates the transcription of target genes. AR activity is closely involved in the maintenance and progression of prostate cancer. After the binding with androgen, AR moves into nucleus and binds to DNA sequence containing androgen response elements (ARE). Flavin-dependent monoamine oxidase KDM1A is necessary for AR driven transcription while the mechanism remains unclear. METHODS: The association between androgen-dependent transcription and oxidation was tested through pharmaceutical inhibitions and siRNA knockdown of DNA oxidation repair components in prostate cancer cells. The recruitment of involved proteins and the histone methylation dynamics on ARE region was explored by chromatin immunoprecipitation (ChIP). RESULTS: Oxidation inhibition reduced AR dependent expression of KLK3, TMPRSS2, hsa-miR-125b2, and hsa-miR-133b. And such reduction could be restored by H2 O2 treatment. KDM1A recruitment and H3K4me2 demethylation on ARE regions, which produce H2 O2 , are associated with AR targets transcription. AR targets transcription and coupled oxidation recruit 8-oxoguanine-DNA glycosylase (OGG1) and the nuclease APEX1 to ARE regions. Such recruitment depends on KDM1A, and is necessary for AR targets transcription. CONCLUSION: Our work underlined the importance of histone demethylation and DNA oxidation/repairing machinery in androgen-dependent transcription. The present finds have implications for research into new druggable targets for prostate cancer relying on the cascade of AR activity regulation.