System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection.

The compendium of RNA-binding proteins (RBPs) has been greatly expanded by the development of RNA-interactome capture (RIC). However, it remained unknown if the complement of RBPs changes in response to environmental perturbations and whether these rearrangements are important. To answer these questions, we developed "comparative RIC" and applied it to cells challenged with an RNA virus called sindbis (SINV). Over 200 RBPs display differential interaction with RNA upon SINV infection. These alterations are mainly driven by the loss of cellular mRNAs and the emergence of viral RNA. RBPs stimulated by the infection redistribute to viral replication factories and regulate the capacity of the virus to infect. For example, ablation of XRN1 causes cells to be refractory to SINV, while GEMIN5 moonlights as a regulator of SINV gene expression. In summary, RNA availability controls RBP localization and function in SINV-infected cells.

Structural and spectroscopic characterization of RufO indicates a new biological role in rufomycin biosynthesis.

Rufomycins constitute a class of cyclic heptapeptides isolated from actinomycetes. They are secondary metabolites that show promising treatment against Mycobacterium tuberculosis infections by inhibiting a novel drug target. Several nonproteinogenic amino acids are integrated into rufomycins, including a conserved 3-nitro-tyrosine. RufO, a cytochrome P450 (CYP)-like enzyme, was proposed to catalyze the formation of 3-nitro-tyrosine in the presence of O2 and NO. To define its biological function, the interaction between RufO and the proposed substrate tyrosine is investigated using various spectroscopic methods that are sensitive to the structural change of a heme center. However, a low- to high-spin state transition and a dramatic increase in the redox potential that are commonly found in CYPs upon ligand binding have not been observed. Furthermore, a 1.89-Å crystal structure of RufO shows that the enzyme has flexible surface regions, a wide-open substrate access tunnel, and the heme center is largely exposed to solvent. Comparison with a closely related nitrating CYP reveals a spacious and hydrophobic distal pocket in RufO, which is incapable of stabilizing a free amino acid. Molecular docking validates the experimental data and proposes a possible substrate. Collectively, our results disfavor tyrosine as the substrate of RufO and point to the possibility that the nitration occurs during or after the assembly of the peptides. This study indicates a new function of the unique nitrating enzyme and provides insights into the biosynthesis of nonribosomal peptides.

Analysis of human health effects under ozone exposure in the oasis area of Hetao Plain.

This article, based on OMI data products, utilizes spatial distribution, ozone-sensitive control areas, Pearson correlation methods, and the Ben-MAP model to study the changes in ozone column concentration from 2018 to 2022, along with the influencing factors and the health of populations exposed to ozone. The findings suggest a spatial variation in the ozone column concentration within the study area, with an increasing trend observed from west to east and from south to north. Over time, the ozone column concentration exhibits an initial increase followed by a subsequent decrease, with the peak concentration observed in 2019 at 37.45 DU and the nadir recorded in 2022 at 33.10 DU. The monthly mean distribution exhibits an inverted V-shaped pattern during the warm season from April to September, with a peak in July (46.71 DU) and a trough in April (35.29 DU). The Hetao Plain Oasis area is primarily a NOx control area in sensitive control areas. The concentrations of O3 and precursor HCHO exhibited significant positive correlations with vegetation index and air temperature, while showing significant negative correlations with wind speed and air pressure. The precursor NO2, in contrast, exhibited a significant negative correlation with both the vegetation index and relative humidity. Based on the ground-based monitoring sites and analysis of human health benefits, the study area witnessed 1944.45 deaths attributed to warm season O3 exposure in 2018, with a subsequent reduction in premature deaths by 149.7, 588.2, and 231.75 for the years 2019 to 2021 respectively when compared to the baseline year. In 2021, the observed decrease in warm-season O3 concentration within that region compared to 2018 resulted in a significant reduction, leading to the prevention of 126 premature deaths.

Analysis of variation characteristics, transport paths, and influencing factors of atmospheric NO2 pollution in Western Europe.

Climate change and air pollution are one of the global environmental problems. It is significant to grasp the air pollution situation of Western Europe in recent 10 years for its or the global pollution control. Based on the OMI tropospheric nitrogen dioxide (NO2) column density data, the spatial and temporal distribution characteristics, variation trend, transmission path, and influencing factors of NO2 in 15 countries in Western Europe from 2011 to 2022 are discussed in this paper. Meanwhile, the annual average spatial and temporal distribution in 2023 is predicted by the random forest (RF) model. The results showed that (1) the 12-year spatial distribution map showed an increasing trend from southwest to northeast, with the border area of the Netherlands and Germany and Milan as two high-value areas, and the overall trend over time was that the high-concentration area gradually shrank, the low-concentration area gradually expanded, and the annual average concentration gradually decreased. (2) The inter-month trend presents a "U" shape, with the mean NO2 pollution ranking in winter > autumn > spring > summer. (3) Natural factors are one of the reasons affecting NO2; for instance, NO2 pollution has a strong positive correlation with the lifted index, relative humidity, and wind speed and a moderately strong negative correlation with precipitable water and air temperature. (4) Exogenous atmospheric transport is another important factor affecting the change of NO2 pollution in Western Europe. The HYSPLIT model is used to analyze the backward trajectory of Milan, Italy, and Nijmegen, Netherlands, in the four seasons of 2022. Both are mainly influenced by westerly airflows, and therefore, the transport effect in the atmosphere brings air pollutants from westerly regions in the atmosphere.

Surprising Hydrophobic Polymer Surface with a High Content of Hydrophilic Polar Groups.

The wetting property of a solid surface has been a hotspot for centuries, and many studies suggest that the hydrophobicity is highly related to the polar components. However, the underlying mechanism of polar moieties on the hydrophobicity remains unclear. Here, we tailor the surface polar moieties of epoxy resin (EP) by ozone modification and assess their wetting properties. Our results show that, for the modified EP with more (60.54%) polar moieties, the polar effect on hydrophobicity cannot be empirically observed. To reveal the underlying mechanism, the absorption parameters, including equilibrium distance, adsorption radius, and effective adsorption sites for water on EP before and after ozone treatment, are calculated on the basis of molecular simulations. After ozone modification, the equilibrium distance (from 1.95 to 1.70 Å), adsorption radius (from 3.80 to 4.50 Å), and effective adsorption sites (from 1 to 2) change slightly and the EP surface remains hydrophobic, although the polar groups significantly increase. Therefore, it is concluded that the wetting properties of solid surfaces are dominated by the equilibrium distance, adsorption radius, and effective adsorption sites for water on solids, and the nonlinear relationship between polar groups and hydrophilicity is clarified.

TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.

Eukaryotic transcriptomes are complex, involving thousands of overlapping transcripts. The interleaved nature of the transcriptomes limits our ability to identify regulatory regions, and in some cases can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptomes, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5' and 3' ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identified thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-Seq, we accurately defined boundaries of lowly expressed unannotated and read-through transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explored transcription regulation among overlapping units and investigated their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription units. Our work shows that, by paring the 5' and 3' end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitate accurate assignment of promoters to genes and easily identify transcriptionally fused genes.

The RNA exosome shapes the expression of key protein-coding genes.

The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify ∼2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3' end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.

The application of small organic π-conjugated discotic derivatives in photoacoustic imaging and photothermal conversion.

Near-infrared absorbing dyes are catching people's attention as they are committed to find materials with greater photoacoustic (PA) and photothermal (PT) effect. In this study, a new series of organic π-conjugated discotic derivatives synthesized via [2 + 2] click chemistry were introduced. The PA intensity and PT conversion effect of the derivatives were monitored. It was found that the π-conjugated discotic derivatives had a proper absorption peak and PA intensity by introducing the click regents. Furthermore, the PA intensity remained relatively high, while B12 molecules were embedded in hydrophobic phospholipid bilayer of liposomes (B12⊂L). The application in biological therapy for tumors become possible as the toxicity of B12⊂L was low. What's more, when B12 molecules embedded in poly (N-isopropylacrylamide)-block-poly (2-nitrobenzyl methacrylate) (PNIPAM-b-PNBM) thermosensitive micelles were irradiated by laser, the molecules could take the place of direct temperature stimulus. This work affords us a way to solve the problem in which direct temperature stimulus is inapplicable.

MYC-dependent downregulation of telomerase by FLT3 inhibitors is required for their therapeutic efficacy on acute myeloid leukemia.

The somatic mutation of FLT3 occurs in 30% of acute myeloid leukemia (AML), with the majority of mutations exhibiting internal tandem duplication (ITD). On the other hand, the induction of telomerase reverse transcriptase (hTERT) and the activation of telomerase is a key step in AML development. Here, we sought to determine whether FLT3ITD regulates hTERT expression in AML cells and whether hTERT expression affects FLT3 inhibitors' therapeutic efficacy on AML. FLT3ITD-harboring AML cell lines and primary cells treated with the FLT3 inhibitor PKC412 displayed a rapid decline in the levels of hTERT mRNA and telomerase activity. Moreover, PKC412 inhibited hTERT gene transcription in a c-MYC-dependent manner. The ectopic expression of hTERT significantly attenuated the apoptotic effect of PKC412 on AML cells. Mechanistically, hTERT enhanced the activity of FLT3 downstream effectors or alternative RTK signaling, thereby enhancing AKT phosphorylation, in AML cells treated with PKC412. Collectively, PKC412 downregulates hTERT expression and telomerase activity in a MYC-dependent manner and this effect is required for its optimal anti-AML efficacy, while hTERT over-expression confers AML cells resistance to a targeted therapeutic agent PKC412. These findings suggest that the functional interplay between FLT3ITD and hTERT contributes to the AML pathogenesis and interferes with the efficacy of FLT3ITD-targeted therapy.

Correction to: MYC-dependent downregulation of telomerase by FLT3 inhibitors is required for their therapeutic efficacy on acute myeloid leukemia.

The original version of this article contained a mistake. The name of Magnus Björkhom should have been Magnus Björkholm.

Fe-Catalyzed Aerobic Oxidative C-CN Bond Cleavage of Arylacetonitriles Leading to Various Esters.

Fe-catalyzed aerobic oxidative esterifications of arylacetonitriles with alcohols, tri alkoxsilanes, silicate esters, or borate esters have been developed. The acyl groups which were in situ generated via chemoselective C(CO)-CN bond cleavage were directly used as electrophiles, leading to corresponding aryl esters in good to excellent yields under molecular oxygen when attacked by alcohols or alcohol surrogates. Dioxygen serves as both oxidant and reactant in this protocol. The reaction has a very broad substrate scope. Cheap starting materials as well as environmentally benign and inexpensive iron catalyst and ideal oxidant O2 feature this transformation and make it a practical and sustainable protocol to afford esters.

Effect of 1-octyl-3-methylimidazolium chloride on cell replication and membrane permeability of Escherichia coli DH5α.

Ionic liquids (ILs) have elicited attention due to their unique properties. ILs may pose environmental risks to aquatic ecosystems once released into water during generation and application. Therefore, the toxic and antimicrobial properties of ILs should be analysed. This study aims to evaluate the cytotoxicity of 1-octyl-3-methylimidazolium chloride ([C8mim] [Cl]) on Escherichia coli DH5α by MTT (3-[4,5-dimethylthiazol-2yl]-2,5 diphenyl tetrazolium bromide) assay, and to determine the effect of [C8mim] [Cl] on the replication and membrane permeability of E. coli DH5α. The results showed that [C8mim] [Cl] decreased cell viability and inhibited bacterial cell replication. [C8mim] [Cl] increased protein and nucleic acid contents in the extracellular fluid, damaged the cell membrane, and increased membrane permeability. The increase of cell membrane permeability induced by [C8mim] [Cl] could be the cause of decreased cell viability and replication.

Expression of Serum Anti-BP180/230 Antibodies in Bullous Pemphigoid Patients Combined with Nervous System Diseases and Relevant Factor Analysis.

OBJECTIVE: To explore the anti-BP230/180 and anti-BP180 antibodies in patients with bullous pemphigoid (BP) combined with neurological diseases, and to analyse the relevant factors. STUDY DESIGN: Analytical study. Place and Duration of the Study: Neurology Department, Cangzhou People's Hospital, Cangzhou, from April 2019 to June 2022. METHODOLOGY: Eighty BP patients were chosen based on associated neurological diseases, they were split into single (n=42) and combined groups (n=38). Expression of anti-BP180/230 antibodies was compared between the two groups. Associations with neurological diseases were analysed and the factors affecting the expression of anti-BP180/230 antibodies were explored. RESULTS: Out of 80 patients, 61 were positive for anti-BP180 antibodies and 58 were positive for anti-BP230 antibodies. The proportion of patients with positive anti-BP230/180 antibodies in the single group was considerably lower than in the combined group (p<0.05). Presence of both nervous system diseases and BP was found to be associated with the presence of anti-BP230/180 antibodies (p<0.001). Univariate analysis showed statistically significant association with age (<70 years, total IgE (>100 IU/ml), and EOS count >0.5 x 109/L (p<0.05). Logistic analysis demonstrated that age, total IgE and EOS count were independent risk factors affecting the expression of anti-BP180 and anti-BP23 antibodies (p<0.05). CONCLUSION: Serum anti-BP230/180 antibodies expression is abnormally high in BP patients having nervous system diseases. Combined nervous system diseases, age, total IgE and EOS count are independent risk factors affecting expression of anti-BP180/230 antibodies. KEY WORDS: Anti-BP180 antibody, Anti-BP230 antibody, Bullous pemphigoid, Nervous system diseases.

Engagement-free and Contactless Bed Occupancy and Vital Signs Monitoring.

This paper presents the design and evaluation of an engagement-free and contactless vital signs and occupancy monitoring system called BedDot. While many existing works demonstrated contactless vital signs estimation, they do not address the practical challenge of environment noises, online bed occupancy detection and data quality assessment in the realworld environment. This work presents a robust signal quality assessment algorithm consisting of three parts: bed occupancy detection, movement detection, and heartbeat detection, to identify high-quality data. It also presents a series of innovative vital signs estimation algorithms that leverage the advanced signal processing and Bayesian theorem for contactless heart rate (HR), respiration rate (RR), and inter-beat interval (IBI) estimation. The experimental results demonstrate that BedDot achieves over 99% accuracy for bed occupancy detection, and MAE of 1.38 BPM, 1.54 BPM, and 24.84 ms for HR, RR, and IBI estimation, respectively, compared with an FDA-approved device. The BedDot system has been extensively tested with data collected from 75 subjects for more than 80 hours under different conditions, demonstrating its generalizability across different people and environments.

Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation.

Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Chromatin organization has been shown to play a role in the faster response of primed cells. However, the contribution of post-transcriptional regulation is not yet explored. Here we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose. We find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. Our work shows that gene-specific differences in intrinsic nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that primed cells present altered levels of RNA degradation machinery and that both nuclear and cytoplasmic mRNA decay modulate transcriptional memory. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.

The tumor suppressive role of miRNA-370 by targeting FoxM1 in acute myeloid leukemia.

BACKGROUND: Recent evidence has accumulated that MicroRNA (miRNA) dysregulation occurs in the majority of human malignancies including acute myeloid leukemia (AML) and may contribute to onco-/leukemo-genesis. METHODS: The expression levels of miR-370 and FoxM1 were assessed in 48 newly diagnosed AML patients, 40 AML patients in 1st complete remission (CR) and 21 healthy controls. Quantitative real-time PCR, western blots, colony formation assay, and ß-Galactosidase ( SA-ß-Gal) staining were used to characterize the changes induced by overexpression or inhibition of miR-370 or FoxM1. RESULTS: We found that the down-regulation of miR-370 expression was a frequent event in both leukemia cell lines and primary leukemic cells from patients with de novo AML. Lower levels of miR-370 expression were found in 37 of 48 leukemic samples from AML patients compared to those in bone marrow cells derived from healthy adult individuals. Ectopic expression of miR-370 in HL60 and K562 cells led to cell growth arrest and senescence. In contrast, depletion of miR-370 expression using RNA interference enhanced the proliferation of those leukemic cells. Mechanistically, miR-370 targets the transcription factor FoxM1, a well established oncogenic factor promoting cell cycle progression. Moreover, when HL60 and K562 cells were treated with 5-aza-2'-deoxycytidine, a DNA methylation inhibitor, miR-370 expression was up-regulated, which indicates epigenetic silencing of miR-370 in leukemic cells. CONCLUSIONS: Taken together, miR-370 may function as a tumor suppressor by targeting FoxM1, and the epigenetic silence of miR-370 thus leads to derepression of FoxM1 expression and consequently contributes to AML development and progression.

Adeno-associated virus serotype 2 mediated transduction and coexpression of the human apoAI and SR-BI gene in HepG2 cells.

Cholesterol efflux is the first step in the reverse cholesterol transport (RCT) pathway, removing excess cholesterol from tissues, including the arterial wall, thus preventing the development of atherosclerosis. Adeno-associated virus (rAAV) has demonstrated significant promise as a DNA-delivery vector to treat serious human diseases. In this study, we constructed recombinant adeno-associated viruses coexpressing apoAI and SR-BI successfully, the double gene mRNA and protein were both strongly expressed in transduced HepG2 cells. A novel safe and efficient method of promoting the reverse cholesterol transport (RCT) may be established. These results may provide a new method for gene therapy of Arteriosclerosis.

[Quantifying the amplitude of microvolt T wave alternans with sparse principal component analysis].

T wave alternans in ECG is an important prediction factor for a sudden death. It is crucial in clinic to quantify the amplitude of T wave alternans. However, T wave alternans are highly non-stationary, which makes accurate quantification very difficult. In this study, we proposed a new method to improve the amplitude quantification. We identified T wave alternans by principal component analysis (PCA) with statistical test, and processed the principal components with T wave alternans further by imposing sparse constraint. We evaluated and compared our method against other 4 popular solutions on an international benchmark database. The results including rank correlation coefficient and relative error indicate that this sparse principal component (SPC) based method is better than others.

Using TIF-Seq2 to investigate association between 5´ and 3´mRNA ends.

The development of high-throughput technologies has revealed pervasive transcription in all genomes that have been investigated so far. This has uncovered a highly interleaved transcriptome organization involving thousands of overlapping coding and non-coding RNA isoforms that challenge our traditional definitions of genes and functional regions of the genome. In this chapter, we discuss the application of an improved Transcript Isoform Sequencing approach (TIF-Seq2) able to concurrently determine the start and end sites of individual RNA molecules. We exemplify its use for the investigation of the human transcriptome and show how it is especially well suited to discriminate between overlapping molecules and accurately define their boundaries.

Deep learning algorithms for brain disease detection with magnetic induction tomography.

PURPOSE: In order to improve the reconstruction accuracy of magnetic induction tomography (MIT) and achieve fast imaging especially in the detection of cerebral hemorrhage, artificial intelligence algorithms are proposed to improve the accuracy of MIT inverse problem. METHODS: According to the standard geometric data of human head, a three-dimensional (3D) head model containing four layer tissues is established for brain image reconstruction of MIT. Four deep learning (DL) networks, including restricted Boltzmann machine (RBM), deep belief network (DBN), stacked autoencoder (SAE), and denoising autoencoder (DAE), are used to solve the nonlinear reconstruction problem of MIT, and the reconstruction results of DL networks and back-projection algorithm are compared. Finally, in order to verify the practical value of DL algorithms, the phantom experiment is carried out with MIT detection system. RESULTS: Using the nonlinear data learning ability of DL algorithms, the rapid and high-precision imaging of cerebral hemorrhage can be realized. Compared with the back-projection algorithm, the DL improves the artifact and the accuracy of the reconstruction image. The location and volume of bleeding can be reconstructed and the prediction time reaches 20 ms. Moreover, the anti-noise performance of the networks can reach 20 dB. CONCLUSIONS: The DL can effectively improve the reconstruction accuracy and prediction speed of the image when it is applied to the reconstruction of cerebral hemorrhage in MIT. This feasibility study MIT to be a potential technology for brain diseases to fully meet the needs of accurate, rapid, and low-cost clinical diagnosis and continuous monitoring.