NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions.

Up to 80% of the human genome produces "dark matter" RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice. These napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we show that a structured napRNA regulates myoblast differentiation and a napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Our approach establishes a paradigm for discovering various classes of ncRNAs with regulatory functions.

The Atlas of the Inferior Mesenteric Artery and Vein under Maximum-Intensity Projection and Three-Dimensional Reconstruction View.

(1) Background: Understanding vascular patterns is crucial for minimizing bleeding and operating time in colorectal surgeries. This study aimed to develop an anatomical atlas of the inferior mesenteric artery (IMA) and vein (IMV). (2) Methods: A total of 521 patients with left-sided colorectal cancer were included. IMA and IMV patterns were identified using maximum-intensity projection (MIP) and three-dimensional (3D) reconstruction techniques. The accuracy of these techniques was assessed by comparing them with surgical videos. We compared the amount of bleeding and operating time for IMA ligation across different IMA types. (3) Results: Most patients (45.7%) were classified as type I IMA, followed by type II (20.7%), type III (22.6%), and type IV (3.5%). Newly identified type V and type VI patterns were found in 6.5% and 1% of patients, respectively. Of the IMVs, 49.9% drained into the superior mesenteric vein (SMV), 38.4% drained into the splenic vein (SPV), 9.4% drained into the SMV-SPV junction, and only 2.3% drained into the first jejunal vein (J1V). Above the root of the left colic artery (LCA), 13.1% of IMVs had no branches, 50.1% had one, 30.1% had two, and 6.7% had three or more branches. Two patients had two main IMV branches, and ten had IMVs at the edge of the mesocolon with small branches. At the IMA root, 37.2% of LCAs overlapped with the IMV, with 34.0% being lateral, 16.9% distal, 8.7% medial, and both the marginal type of IMV and the persistent descending mesocolon (PDM) type represented 1.4%. MIP had an accuracy of 98.43%, and 3D reconstruction had an accuracy of 100%. Blood loss and operating time were significantly higher in the complex group compared to the simple group for IMA ligation (p < 0.001). (4) Conclusions: A comprehensive anatomical atlas of the IMA and IMV was provided. Complex IMA patterns were associated with increased bleeding and operating time.

RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators.

A kink-turn (K-turn) is a three-dimensional RNA structure that exists in all three primary phylogenetic domains. In this study, we developed the RIP-PEN-seq method to identify the full-length sequences of RNAs bound by the K-turn binding protein 15.5K and discovered a previously uncharacterized class of RNAs with backward K-turn motifs (bktRNAs) in humans and mice. All bktRNAs share two consensus sequence motifs at their fixed terminal position and have complex folding properties, expression and evolution patterns. We found that a highly conserved bktRNA1 guides the methyltransferase fibrillarin to install RNA methylation of U12 small nuclear RNA in humans. Depletion of bktRNA1 causes global splicing dysregulation of U12-type introns by impairing the recruitment of ZCRB1 to the minor spliceosome. Most bktRNAs regulate the splicing of local introns by interacting with the 15.5K protein. Taken together, our findings characterize a class of small RNAs and uncover another layer of gene expression regulation that involves crosstalk among bktRNAs, RNA splicing and RNA methylation.

Healthy Adult Left and Right Ventricular Torsion and Torsion Rates With MR-Feature Tracking.

BACKGROUND: The clinical value of myocardial torsion quantification in prognostic assessment and risk stratification of various cardiovascular diseases is gradually being recognized. However, normal values of left and right ventricular (LV and RV) torsion and torsion rates (TRs) have not been fully determined, and their correlation with age and gender has not been well studied. PURPOSE: To establish normal ranges of biventricular torsion, peak systolic and diastolic TRs using magnetic resonance feature tracking (MR-FT) technique based on a large sample of healthy adults, and further investigate their relationship with age and gender. STUDY TYPE: Retrospective. POPULATION: 566 Healthy adults (312 males, aged 43 ± 10 years; 254 females, aged 43 ± 11 years). FIELD STRENGTH/SEQUENCE: 1.5T/gradient echo. ASSESSMENT: Biventricular torsion, peak systolic, and diastolic TRs. STATISTICAL TESTS: Shapiro-Wilk test, Student's t-test, Mann-Whitney-U test, linear regression, intraclass correlation coefficient, Bland-Altman analysis. Differences were regarded as statistically significant at P < 0.05. RESULTS: Women demonstrated greater magnitudes of left ventricle (LV) torsion (1.23 ± 0.44 vs. 1.00 ± 0.42°/cm), peak systolic TR (9.69 ± 3.70 vs. 8.27 ± 3.73°/cm*sec), peak diastolic TR (-7.78 ± 2.82 vs. -6.06 ± 2.44°/cm*sec), and RV torsion (2.20 ± 1.23 vs. 1.65 ± 1.11°/cm*sec), peak systolic TR (16.07 ± 8.18 vs. 12.62 ± 7.08°/cm*sec), peak diastolic TR (-15.39 ± 6.53 vs. -11.70 ± 6.03°/cm*sec). For both genders, the magnitudes of LV and RV torsion, peak systolic, and diastolic TRs increased linearly with age. All the measurements of biventricular torsion, peak systolic and diastolic TRs achieved good to excellent intraobserver and interobserver reproducibility, with all intraclass correlation coefficients >0.70. DATA CONCLUSION: The present study systematically provided age- and sex-stratified reference values for LV and RV torsion and TRs using MR-FT technique. Women and aging are associated with greater magnitudes of biventricular torsion, peak systolic, and diastolic TRs. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY: Stage 2.

[Protein expression, purification and mouse antiserum preparation of monkeypox virus A23R].

Objective To express the monkeypox virus (MPXV) A23R protein in Escherichia coli and purify by Ni-NTA affinity column, and to prepare mouse antiserum against MPXV A23R. Methods The recombinant plasmid pET-28a-MPXV-A23R was constructed and transformed into Escherichia coli BL21 to induce the expression of A23R protein. After optimizing the conditions of expression, A23R protein was highly expressed. Recombinant A23R protein was purified by Ni-NTA affinity column and identified by Western blot analysis. The purified protein was used to immunize mice for preparing the A23R polyclonal antibody, and the antibody titer was detected by ELISA. Results The expression of A23R recombinant protein reached the peak under the induced conditions of 0.6 mmol/L isopropyl-ß-D-thiogalactoside (IPTG), 37 DegreesCelsius and 20 hours. The purity of the protein was about 96.07% and was identified by Western blot analysis. The mice were immunized with recombinant protein, and the titer of antibody reached 1:102 400 at the 6th week after immunization. Conclusion MPXV A23R is expressed highly and purified with a high purity and its antiserum from mouse is obtained with a high titre.

One-step integrated coronary-carotid-cerebral computed tomography angiography to evaluate cardiovascular and cerebrovascular atherosclerosis.

PURPOSE: This study aims to develop a low-radiation dose, one-step integrated coronary-carotid-cerebral computed tomography angiography (ICCC-CTA) technique to analyze the relationship between cardiovascular and cerebrovascular atherosclerosis and evaluate the risk factors of plaque to provide an early-stage treatment to patients and reduce vascular events. METHODS: A total of 300 consecutive asymptomatic patients with cardiovascular risk factors who underwent ICCC-CTA were enrolled in this prospective study. The association between coronary and carotid-cerebrovascular atherosclerosis was assessed. The primary cardiovascular risk factors for various plaque types in cardiovascular or cerebrovascular disease were evaluated using multivariate analysis. RESULTS: Among 300 patients, 189 (63%) had plaques in their coronary and cerebral arteries. The presence of calcified and mixed plaques in the carotid-cerebral and coronary arteries was strongly correlated (χ2 = 20.71, P = 0.001; χ2 = 8.96, P = 0.003, respectively). Multivariate logistic regression analysis revealed that abnormal blood glucose [OR = 1.44, 95% CI 0.12-0.62, P = 0.01] and abnormal total cholesterol [OR = 1.28, 95% CI 0.07-0.46, P = 0.01] are risk factors in all the models in the coronary artery, non-calcified plaque group. Abnormal blood glucose [OR = 1.43, 95% CI 0.11-0.61, P = 0.01] and abnormal systolic blood pressure [OR = 1.02, 95% CI 0.01-0.04, P = 0.02] are risk factors in all the models in the coronary artery calcified plaque group. Abnormal blood glucose level [OR = 1.44, 95% CI = 0.12-0.62, P = 0.01] was only a risk factor in the non-calcified plaque carotid-cerebral artery group. CONCLUSIONS: We confirm that elevated blood glucose and total cholesterol levels are associated with coronary and carotid-cerebrovascular plaques using the novel one-step low dose cerebral-carotid-cardiac CTA technique. These findings will provide insights for further studies focusing on developing low-radiation dose one-step ICCC-CTA to screen cardiovascular/cerebrovascular plaques in general population with cardiovascular risk factors. ADVANCES IN KNOWLEDGE: We developed a low-radiation dose, one-step ICCC-CTA technique to detect cardiovascular and cerebrovascular atherosclerosis. We evaluated the risk factors for plaque burden for the early treatment and reduction of vascular events. These findings supported the development of low-radiation dose one-step ICCC-CTA to screen for cardiovascular/cerebrovascular disease in general population with cardiovascular risk factors.

A Novel Homodimer Peptide-Drug Conjugate Improves the Efficacy of HER2-Positive Breast Cancer Therapy.

Tumor-targeting peptide-drug conjugates (PDCs) have become a focus of research in recent years. However, due to the instability of peptides and their short in vivo effective half-life, they have limited clinical application. Herein, we propose a new DOX PDC based on a homodimer HER-2-targeting peptide and acid-sensitive hydrazone bond, which could enhance the anti-tumor effect of DOX and reduce systemic toxicities. The PDC could accurately deliver DOX into HER2-positive SKBR-3 cells, with it showing 2.9 times higher cellular uptake than free DOX and enhanced cytotoxicity with respect to IC50 of 140 nM (vs. 410 nM for free DOX). In vitro assays showed that the PDC had high cellular internalization efficiency and cytotoxicity. In vivo anti-tumor experiments indicated that the PDC could significantly inhibit the growth of HER2-positive breast cancer xenografts in mice and reduce the side effects of DOX. In summary, we constructed a novel PDC molecule targeting HER2-positive tumors, which may overcome some deficiencies of DOX in breast cancer therapy.

Highly Robust {In2}-Organic Framework for Efficiently Catalyzing CO2 Cycloaddition and Knoevenagel Condensation.

To improve the catalytic performance of metal-organic frameworks (MOFs), creating higher defects is now considered as the most effective strategy, which can not only optimize the Lewis acidity of metal ions but also create more pore space to enhance diffusion and mass transfer in the channels. Herein, the exquisite combination of scarcely reported [In2(CO2)5(H2O)2(DMF)2] clusters and 2,6-bis(2,4-dicarboxylphenyl)-4-(4-carboxylphenyl)pyridine (H5BDCP) under solvothermal conditions generated a highly robust nanoporous framework of {[In2(BDCP)(DMF)2(H2O)2](NO3)}n (NUC-65) with nanocaged voids (14.1 Å) and rectangular nanochannels (15.94 Å × 11.77 Å) along the a axis. It is worth mentioning that an In(1) ion displays extremely low tetra-coordination modes after the thermal removal of its associated four solvent molecules of H2O and DMF. Activated {[In2(BDCP)](Br)}n (NUC-65Br), as a defective material because of its extremely unsaturated metal centers, could be generated by bromine ion exchange, solvent exchange, and vacuum drying. Catalytic experiments proved that the conversion of epichlorohydrin with 1 atm CO2 into 4-(chloromethyl)-1,3-dioxolan-2-one catalyzed by 0.11 mol % NUC-65Br could reach 99% at 65 °C within 24 h. Moreover, with the aid of 5 mol % cocatalyst n-Bu4NBr, heterogeneous NUC-65Br owns excellent universal catalytic performance in most epoxides under mild conditions. In addition, NUC-65Br, as a heterogeneous catalyst, exhibits higher activity and better selectivity for Knoevenagel condensation of aldehydes and malononitrile. Hence, this work offers a fresh insight into the design of structure defect cationic metal-organic frameworks, which can be better applied to various fields because of their promoted performance.

Fabrication of Z-scheme Cd0.85Zn0.15S/Co9S8dual-functional photocatalyst for effective hydrogen evolution and organic pollutant degradation.

A Z-scheme Cd0.85Zn0.15S/Co9S8(CZS-CS) photocatalyst was reasonably fabricated by a simple solvothermal method for the effective visible-light-driven H2evolution and organic pollutants degradation. The precise construction of the CZS-CS composites provided an efficient heterogeneous contact interface and abundant reaction sites for the proposed photocatalytic reaction. The homogeneous Co9S8nanocrystals were uniformly wrapped on the surface of Cd0.85Zn0.15S nanorods, forming an intimate-contact interface, markedly contributed to the light collection and effectively inhibited the charge-carrier recombination. The optimized CZS-CS-15 composites exhibited a special H2production rate reaching 19.15 mmol·h-1·g-1, roughly 1915 and 4.5 times of pure Co9S8and Cd0.85Zn0.15S samples and 85% of tetracycline (TC) molecule within 15 min was degraded. Furthermore, trapping experiments confirmed that h+was the main active species for TC photodegradation. Moreover, the obtained photocatalysts manifested stability without apparent activity declines during the proposed reactions. Finally, the Z-scheme photocatalytic mechanism was verified to illustrate the characteristics of efficient charge transfer and high redox ability. This study provided a rational and learnable strategy for designing dual-functional Z-scheme heterojunction photocatalysts.

Effectiveness of inactivated COVID-19 vaccines against mild disease, pneumonia, and severe disease among persons infected with SARS-CoV-2 Omicron variant: real-world study in Jilin Province, China.

It is critical to determine the real-world performance of vaccines against coronavirus disease 2019 (COVID-19) so that appropriate treatments and policies can be implemented. There was a rapid wave of infections by the Omicron variant in Jilin Province (China) during spring 2022. We examined the effectiveness of inactivated vaccines against Omicron using real-world data from this epidemic. This retrospective case-case study of vaccine effectiveness (VE) examined infected patients who were quarantined and treated from April 16 to June 8, 2022 and responded to an electronic questionnaire. Data were analyzed by univariable and multivariable analyses. A total of 2968 cases with SARS-CoV-2 infections (asymptomatic: 1061, mild disease: 1763, pneumonia: 126, severe disease: 18) were enrolled in the study. Multivariable regression indicated that the risk for pneumonia or severe disease was greater in those who were older or had underlying diseases, but was less in those who received COVID-19 vaccines. Relative to no vaccination, VE against the composite of pneumonia and severe disease was significant for those who received 2 doses (60.1%, 95%CI: 40.0%, 73.5%) or 3 doses (68.1%, 95%CI: 44.6%, 81.7%), and VE was similar in the subgroups of males and females. However, VE against the composite of all three classes of symptomatic diseases was not significant overall, nor after stratification by sex. There was no statistical difference in the VE of vaccines from different manufacturers. The inactivated COVID-19 vaccines protected patients against pneumonia and severe disease from Omicron infection, and booster vaccination enhanced this effect.

ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes.

Non-coding RNAs (ncRNAs) are emerging as key regulators of various biological processes. Although thousands of ncRNAs have been discovered, the transcriptional mechanisms and networks of the majority of ncRNAs have not been fully investigated. In this study, we updated ChIPBase to version 3.0 (https://rnasysu.com/chipbase3/) to provide the most comprehensive transcriptional regulation atlas of ncRNAs and protein-coding genes (PCGs). ChIPBase has identified ∼151 187 000 regulatory relationships between ∼171 600 genes and ∼3000 regulators by analyzing ∼55 000 ChIP-seq datasets, which represent a 30-fold expansion. Moreover, we de novo identified ∼29 000 motif matrices of transcription factors. In addition, we constructed a novel 'Enhancer' module to predict ∼1 837 200 regulation regions functioning as poised, active or super enhancers under ∼1300 conditions. Importantly, we constructed exhaustive coexpression maps between regulators and their target genes by integrating expression profiles of ∼65 000 normal and ∼15 000 tumor samples. We built a 'Disease' module to obtain an atlas of the disease-associated variations in the regulation regions of genes. We also constructed an 'EpiInter' module to explore potential interactions between epitranscriptome and epigenome. Finally, we designed 'Network' module to provide extensive and gene-centred regulatory networks. ChIPBase will serve as a useful resource to facilitate integrative explorations and expand our understanding of transcriptional regulation.

Single-base resolution mapping of 2'-O-methylation sites by an exoribonuclease-enriched chemical method.

2'-O-methylation (Nm) is one of the most abundant RNA epigenetic modifications and plays a vital role in the post-transcriptional regulation of gene expression. Current Nm mapping approaches are normally limited to highly abundant RNAs and have significant technical hurdles in mRNAs or relatively rare non-coding RNAs (ncRNAs). Here, we developed a new method for enriching Nm sites by using RNA exoribonuclease and periodate oxidation reactivity to eliminate 2'-hydroxylated (2'-OH) nucleosides, coupled with sequencing (Nm-REP-seq). We revealed several novel classes of Nm-containing ncRNAs as well as mRNAs in humans, mice, and drosophila. We found that some novel Nm sites are present at fixed positions in different tRNAs and are potential substrates of fibrillarin (FBL) methyltransferase mediated by snoRNAs. Importantly, we discovered, for the first time, that Nm located at the 3'-end of various types of ncRNAs and fragments derived from them. Our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation.

Research on sensing characteristics of third-order runway series symmetric microring resonator based on hybrid plasma waveguide and metal insulator metal.

In this paper, a high-sensitivity refractive index sensor based on a hybrid plasma waveguide and metal-insulator-metal waveguide combined third-order runway series mosaic microring resonator is proposed. In this structure, a GaAs waveguide ring surrounds a gold waveguide ring in the middle, and the innermost layer is a disk made of gold material. The outer groove waveguide is composed of GaAs-air-alloy, and the inner groove waveguide is made of the Gold-Air-Gold material disc. By filling different substances in the groove, the change of refractive index will affect the optical signal strength of the output spectrum. The finite element method simulates the transmission spectrum and electric field distribution of the sensor structure. The amplitude coupling coefficient and attenuation factor affecting the resonator's performance are analyzed, and the structural parameters of the slot waveguide are optimized. The numerical simulation results show that the sensor quality factor of this structure is 1.54 × 104 , the sensitivity is 1.2 × 103 nm/RIU which is about 1.5 times higher than that of the Si ring with the same structure, the detection limit can reach 8.1892 × 10-7 RIU, and the free spectral range can reach 109 nm. Compared with the traditional microring structure, this microring has higher design freedom and free spectral range and is more suitable for producing biosensors with high sensitivity, low detection limit, and multi-parameter measurement.

Fluorine-Functionalized NbO-Type {Cu2}-Organic Framework: Enhanced Catalytic Performance on the Cycloaddition Reaction of CO2 with Epoxides and Deacetalization-Knoevenagel Condensation.

The high catalytic activity of metal-organic frameworks (MOFs) can be realized by increasing their effective active sites, which prompts us to perform the functionalization on selected linkers by introducing a strong Lewis basic group of fluorine. Herein, the exquisite combination of paddle-wheel [Cu2(CO2)4(H2O)] clusters and meticulously designed fluorine-funtionalized tetratopic 2',3'-difluoro-[p-terphenyl]-3,3″,5,5″-tetracarboxylic acid (F-H4ptta) engenders one peculiar nanocaged {Cu2}-organic framework of {[Cu2(F-ptta)(H2O)2]·5DMF·2H2O}n (NUC-54), which features two types of nanocaged voids (9.8 Å × 17.2 Å and 10.1 Å × 12.4 Å) shaped by 12 paddle-wheel [Cu2(COO)4H2O)2] secondary building units, leaving a calculated solvent-accessible void volume of 60.6%. Because of the introduction of plentifully Lewis base sites of fluorine groups, activated NUC-54a exhibits excellent catalytic performance on the cycloaddition reaction of CO2 with various epoxides under mild conditions. Moreover, to expand the catalytic scope, the deacetalization-Knoevenagel condensation reactions of benzaldehyde dimethyl acetal and malononitrile were performed using the heterogenous catalyst of NUC-54a. Also, NUC-54a features high recyclability and catalytic stability with excellent catalytic performance in subsequent catalytic tests. Therefore, this work not only puts forward a new solution for developing high-efficiency heterogeneous catalysts, but also enriches the functionalization strategies for nanoporous MOFs.

CREB1 contributes colorectal cancer cell plasticity by regulating lncRNA CCAT1 and NF-κB pathways.

The CREB1 gene encodes an exceptionally pleiotropic transcription factor that frequently dysregulated in human cancers. CREB1 can regulate tumor cell status of proliferation and/or migration; however, the molecular basis for this switch involvement in cell plasticity has not fully been understood yet. Here, we first show that knocking out CREB1 triggers a remarkable effect of epithelial-mesenchymal transition (EMT) and leads to the occurrence of inhibited proliferation and enhanced motility in HCT116 colorectal cancer cells. By monitoring 45 cellular signaling pathway activities, we find that multiple growth-related pathways decline significantly while inflammatory pathways including NF-κB are largely upregulated in comparing between the CREB1 wild-type and knocked out cells. Mechanistically, cells with CREB1 knocked out show downregulation of MYC as a result of impaired CREB1-dependent transcription of the oncogenic lncRNA CCAT1. Interestingly, the unbalanced competition between the coactivator CBP/p300 for CREB1 and p65 leads to the activation of the NF-κB pathway in cells with CREB1 disrupted, which induces an obvious EMT phenotype of the cancer cells. Taken together, these studies identify previously unknown mechanisms of CREB1 in CRC cell plasticity via regulating lncRNA CCAT1 and NF-κB pathways, providing a critical insight into a combined strategy for CREB1-targeted tumor therapies.

Nanoporous {Y2}-Organic Frameworks for Excellent Catalytic Performance on the Cycloaddition Reaction of Epoxides with CO2 and Deacetalization-Knoevenagel Condensation.

Stable metal-organic frameworks containing periodically arranged nanosized pores and active Lewis acid-base active sites are considered as ideal candidates for efficient heterogeneous catalysis. Herein, the exquisite combination of [Y2(CO2)7(H2O)2] cluster (abbreviated as {Y2}) and multifunctional linker of 2,4,6-tri(2,4-dicarboxyphenyl)pyridine (H6TDP) led to a nanoporous framework of {[Y2(TDP)(H2O)2]·5H2O·4DMF}n (NUC-53, NUC = North University of China), which is a rarely reported binuclear three-dimensional (3D) framework with hierarchical tetragonal-microporous (0.78 nm) and octagonal-nanoporous (1.75 nm) channels. The inner walls of these channels are aligned by {Y2} clusters and plentifully coexisted Lewis acid-base sites of YIII ions and Npyridine atoms. Furthermore, NUC-53 has a quite large void volume of ∼65.2%, which is significantly higher than most documented 3D rare-earth-based MOFs. The performed catalytic experiments exhibited that activated NUC-53 showed a high catalytic activity on the cycloaddition reactions of CO2 with styrene oxide under mild conditions with excellent turnover number (TON: 1980) and turnover frequency (TOF: 495 h-1). Moreover, the deacetalization-Knoevenagel condensation reactions of benzaldehyde dimethyl acetal and malononitrile could be efficiently prompted by the heterogeneous catalyst of NUC-53. These findings not only pave the way for the construction of nanoporous MOF based on rare-earth clusters with a variety of catalytic activities but also provide some new insights into the catalytic mechanism.

Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs.

RNA polymerase III (Pol III) transcribes hundreds of non-coding RNA genes (ncRNAs), which involve in a variety of cellular processes. However, the expression, functions, regulatory networks and evolution of these Pol III-transcribed ncRNAs are still largely unknown. In this study, we developed a novel resource, Pol3Base (http://rna.sysu.edu.cn/pol3base/), to decode the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. The current release of Pol3Base includes thousands of regulatory relationships between ∼79 000 ncRNAs and transcription factors by mining 56 ChIP-seq datasets. By integrating CLIP-seq datasets, we deciphered the interactions of these ncRNAs with >240 RNA binding proteins. Moreover, Pol3Base contains ∼9700 RNA modifications located within thousands of Pol III-transcribed ncRNAs. Importantly, we characterized expression profiles of ncRNAs in >70 tissues and 28 different tumor types. In addition, by comparing these ncRNAs from human and mouse, we revealed about 4000 evolutionary conserved ncRNAs. We also identified ∼11 403 tRNA-derived small RNAs (tsRNAs) in 32 different tumor types. Finally, by analyzing somatic mutation data, we investigated the mutation map of these ncRNAs to help uncover their potential roles in diverse diseases. This resource will help expand our understanding of potential functions and regulatory networks of Pol III-transcribed ncRNAs.

Investigation on the catalytic behavior of a novel thulium-organic framework with a planar tetranuclear {Tm4} cluster as the active center for chemical CO2 fixation.

Herein, the exquisite combination of coplanar [Tm4(CO2)10(µ3-OH)2(µ2-HCO2)(OH2)2] clusters ({Tm4}) and structure-oriented functional BDCP5- leads to the highly robust nanoporous {Tm4}-organic framework {(Me2NH2)[Tm4(BDCP)2(µ3-OH)2(µ2-HCO2)(H2O)2]·7DMF·5H2O}n (NUC-37, H5BDCP = 2,6-bis(2,4-dicarboxylphenyl)-4-(4-carboxylphenyl)pyridine). To the best of our knowledge, NUC-37 is the first anionic {Ln4}-based three-dimensional framework with embedded hierarchical microporous and nanoporous channels, among which each larger one is shaped by six rows of coplanar {Tm4} clusters and characterized by plentiful coexisting Lewis acid-base sites on the inner wall including open TmIII sites, Npyridine atoms, µ3-OH and µ2-HCO2. Catalytic experimental studies exhibit that NUC-37 possesses highly selective catalytic activity on the cycloaddition of epoxides with CO2 as well as high recyclability under gentle conditions, which should be ascribed to its nanoscale channels, rich bifunctional active sites, and stable physicochemical properties. This work offers an effective means for synthesizing productive cluster-based Ln-MOF catalysts by employing structure-oriented ligands and controlling the solvothermal reaction conditions.

Nitrogen Kinetic Isotope Effects of Nitrification by the Complete Ammonia Oxidizer Nitrospira inopinata.

Analysis of nitrogen isotope fractionation effects is useful for tracing biogeochemical nitrogen cycle processes. Nitrification can cause large nitrogen isotope effects through the enzymatic oxidation of ammonia (NH3) via nitrite (NO2-) to nitrate (NO3-) (15εNH4+→NO2- and 15εNO2-→NO3-). The isotope effects of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and of nitrite-oxidizing bacteria (NOB) have been analyzed previously. Here, we studied the nitrogen isotope effects of the complete ammonia oxidizer (comammox) Nitrospira inopinata that oxidizes NH3 to NO3-. At high ammonium (NH4+) availability (1 mM) and pH between 6.5 and 8.5, its 15εNH4+→NO2- ranged from -33.1 to -27.1‰ based on substrate consumption (residual substrate isotopic composition) and -35.5 to -31.2‰ based on product formation (cumulative product isotopic composition), while the 15εNO2-→NO3- ranged from 6.5 to 11.1‰ based on substrate consumption. These values resemble isotope effects of AOB and AOA and of NOB in the genus Nitrospira, suggesting the absence of fundamental mechanistic differences between key enzymes for ammonia and nitrite oxidation in comammox and canonical nitrifiers. However, ambient pH and initial NH4+ concentrations influenced the isotope effects in N. inopinata. The 15εNH4+→NO2- based on product formation was smaller at pH 6.5 (-31.2‰) compared to pH 7.5 (-35.5‰) and pH 8.5 (-34.9‰), while 15εNO2-→NO3- was smaller at pH 8.5 (6.5‰) compared to pH 7.5 (8.8‰) and pH 6.5 (11.1‰). Isotopic fractionation via 15εNH4+→NO2- and 15εNO2-→NO3- was smaller at 0.1 mM NH4+ compared to 0.5 to 1.0 mM NH4+. Environmental factors, such as pH and NH4+ availability, therefore need to be considered when using isotope effects in 15N isotope fractionation models of nitrification. IMPORTANCE Nitrification is an important nitrogen cycle process in terrestrial and aquatic environments. The discovery of comammox has changed the view that canonical AOA, AOB, and NOB are the only chemolithoautotrophic organisms catalyzing nitrification. However, the contribution of comammox to nitrification in environmental and technical systems is far from being completely understood. This study revealed that, despite a phylogenetically distinct enzymatic repertoire for ammonia oxidation, nitrogen isotope effects of 15εNH4+→NO2- and 15εNO2-→NO3- in comammox do not differ significantly from those of canonical nitrifiers. Thus, nitrogen isotope effects are not suitable indicators to decipher the contribution of comammox to nitrification in environmental samples. Moreover, this is the first systematic study showing that the ambient pH and NH4+ concentration influence the isotope effects of nitrifiers. Hence, these key parameters should be considered in comparative analyses of isotope effects of nitrifiers across different growth conditions and environmental samples.

Overexpression of Stat3 increases circulating cfDNA in breast cancer.

PURPOSE: Current studies on circulating cell-free DNA (cfDNA) have been focusing on its potential as biomarkers in liquid biopsy by detecting its content or genetic and epigenetic changes for the evaluation of tumor burden and therapeutic efficacy. However, the regulatory mechanism of cfDNA release remains unclear. Stat3 has been documented as an oncogene for the development and metastasis of breast cancer cells. In this study, we investigated whether Stat3 affects the release of cfDNA into blood and its association with the number of circulating tumor cells (CTCs). METHODS: The cfDNA level in plasma of patients with breast cancer and healthy volunteers were determined by quantitative real-time PCR. Three mouse breast cancer models with different Stat3 expression were generated and used to established three breast cancer orthotopic animal models to examine the effect of Stat3 on cfDNA release in vivo. Stat3 mediated Epithelial-mesenchymal phenotype transition of CTCs was determined by immunofluorescence assay and Western blot assay. RESULTS: The data showed that Stat3 increased circulating cfDNA, which is correlated with the increased volume of primary tumors and number of CTCs, accompanied with the dynamic EMT changes regulated by Snail induction. Furthermore, the high level of total circulating cfDNA and Stat3-cfDNA in patients with breast cancer were detected by quantitative real-time PCR using GAPDH and Stat3 primers. CONCLUSION: Our results suggested that Stat3 increases the circulating cfDNA and CTCs in breast cancer.