Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing.

Tn5 transposon tagments double-stranded DNA and RNA/DNA hybrids to generate nucleic acids that are ready to be amplified for high-throughput sequencing. The nucleic acid substrates for the Tn5 transposon must be explored to increase the applications of Tn5. Here, we found that the Tn5 transposon can transpose oligos into the 5' end of single-stranded DNA longer than 140 nucleotides. Based on this property of Tn5, we developed a tagmentation-based and ligation-enabled single-stranded DNA sequencing method called TABLE-seq. Through a series of reaction temperature, time, and enzyme concentration tests, we applied TABLE-seq to strand-specific RNA sequencing, starting with as little as 30 pg of total RNA. Moreover, compared with traditional dUTP-based strand-specific RNA sequencing, this method detects more genes, has a higher strand specificity, and shows more evenly distributed reads across genes. Together, our results provide insights into the properties of Tn5 transposons and expand the applications of Tn5 in cutting-edge sequencing techniques.

FUS reads histone H3K36me3 to regulate alternative polyadenylation.

Complex organisms generate differential gene expression through the same set of DNA sequences in distinct cells. The communication between chromatin and RNA regulates cellular behavior in tissues. However, little is known about how chromatin, especially histone modifications, regulates RNA polyadenylation. In this study, we found that FUS was recruited to chromatin by H3K36me3 at gene bodies. The H3K36me3 recognition of FUS was mediated by the proline residues in the ZNF domain. After these proline residues were mutated or H3K36me3 was abolished, FUS dissociated from chromatin and bound more to RNA, resulting in an increase in polyadenylation sites far from stop codons genome-wide. A proline mutation corresponding to a mutation in amyotrophic lateral sclerosis contributed to the hyperactivation of mitochondria and hyperdifferentiation in mouse embryonic stem cells. These findings reveal that FUS is an H3K36me3 reader protein that links chromatin-mediated alternative polyadenylation to human disease.

Potential value of CT-based comprehensive nomogram in predicting occult lymph node metastasis of esophageal squamous cell paralaryngeal nerves: a two-center study.

PURPOSE: The aim of this study is to construct a combined model that integrates radiomics, clinical risk factors and machine learning algorithms to predict para-laryngeal lymph node metastasis in esophageal squamous cell carcinoma. METHODS: A retrospective study included 361 patients with esophageal squamous cell carcinoma from 2 centers. Radiomics features were extracted from the computed tomography scans. Logistic regression, k nearest neighbor, multilayer perceptron, light Gradient Boosting Machine, support vector machine, random forest algorithms were used to construct radiomics models. The receiver operating characteristic curve and The Hosmer-Lemeshow test were employed to select the better-performing model. Clinical risk factors were identified through univariate logistic regression analysis and multivariate logistic regression analysis and utilized to develop a clinical model. A combined model was then created by merging radiomics and clinical risk factors. The performance of the models was evaluated using ROC curve analysis, and the clinical value of the models was assessed using decision curve analysis. RESULTS: A total of 1024 radiomics features were extracted. Among the radiomics models, the KNN model demonstrated the optimal diagnostic capabilities and accuracy, with an area under the curve (AUC) of 0.84 in the training cohort and 0.62 in the internal test cohort. Furthermore, the combined model exhibited an AUC of 0.97 in the training cohort and 0.86 in the internal test cohort. CONCLUSION: A clinical-radiomics integrated nomogram can predict occult para-laryngeal lymph node metastasis in esophageal squamous cell carcinoma and provide guidance for personalized treatment.

Effect of transglutaminase crosslinking combined with lactic fermentation on the potential allergenicity and conformational structure of soy protein.

BACKGROUND: Food allergies are a growing concern worldwide, with soy proteins being important allergens that are widely used in various food products. This study investigated the potential of transglutaminase (TGase) and lactic acid bacteria (LAB) treatments to modify the allergenicity and structural properties of soy protein isolate (SPI), aiming to develop safer soy-based food products. RESULTS: Treatment with TGase, LAB or their combination significantly reduced the antibody reactivity of ß-conglycinin and the immunoglobulin E (IgE) binding capacity of soy protein, indicating a decrease in allergenicity. TGase treatment led to the formation of high-molecular-weight aggregates, suggesting protein crosslinking, while LAB treatment resulted in partial protein hydrolysis. These structural changes were confirmed by Fourier transform infrared spectroscopy, which showed a decrease in ß-sheet content and an increase in random coil and ß-turn contents. In addition, changes in intrinsic fluorescence and ultraviolet spectroscopy were also observed. The alterations in protein interaction and the reduction in free sulfhydryl groups highlighted the extensive structural modifications induced by these treatments. CONCLUSION: The synergistic application of TGase and LAB treatments effectively reduced the allergenicity of SPI through significant structural modifications. This approach not only diminished antibody reactivity of ß-conglycinin and IgE binding capacity of soy protein but also altered the protein's primary, secondary and tertiary structures, suggesting a comprehensive alteration of SPI's allergenic potential. These findings provide a promising strategy for mitigating food allergy concerns and lay the foundation for future research on food-processing techniques aimed at allergen reduction. © 2024 Society of Chemical Industry.

Emission and optical characteristics of brown carbon in size-segregated particles from three types of Chinese ships.

Brown carbon (BrC) is one of the important light absorption substances that have high light absorption ability under short wavelength light. However, limit studies have focused on the BrC emission from ships. In this study, size-segregated particulate matters (PM) were collected from three different types of ships, light absorption characteristics and size distribution of methanol-soluble BrC and water-soluble BrC in PM from ship exhausts were investigated. Results showed that four-stroke low-power diesel fishing boat (4-LDF) had the highest mass concentrations of methanol-soluble organic carbon (MSOC) and water-soluble organic carbon (WSOC), followed by 2-stroke high-power heavy-fuel-oil vessel (2-HHV), and four-stroke high-power marine-diesel vessel (4-HMV). While 2-HHV had obviously higher light absorption coefficients of methanol-soluble BrC (Abs365,M) and water-soluble BrC (Abs365,W) in unit weight of PM than the other two types of ships. The tested ships presented comparable or higher absorption efficiency of BrC in water extracts (MAE365,W) compared with other BrC emission sources. Majority of BrC was concentrated in fine particles, and the particle size distributions of both Abs365,M and Abs365,W showed bimodal patterns, peaking at 0.43-0.65 µm and 4.7-5.8 µm, respectively. However, different particle size distributions were found for MAE365,M between diesel and heavy fuel oil ships. Besides, different wavelength dependence in particles with different size were also detected. Ship exhaust could be confirmed as a non-ignorable BrC emission source, and complex influencing factor could affect the light absorption characteristics of ship emissions. Particle size should also be considered when light absorption ability of BrC was evaluated.

Stable Two-dimensional Nanoconfined Ionic Liquids with Highly Efficient Ionic Conductivity.

Amid the burgeoning environmental concerns, electrochemical energy storage is of great demand, inspiring the rapid development of electrolytes. Quasi-liquid solid electrolytes (QLSEs) demonstrate exciting properties that combine high ionic conductivity and safety. Herein, a QLSE system is constructed by confining ionic liquids (ILs) into 2D materials-based membranes, which creates a subtle platform for the investigation of the nanoconfined ion transport process. The highest ionic conductivity increment of 506% can be observed when ILs are under nanoconfinement. Correlation of experimental results and simulation evidently prove the diffusion behaviors of ILs are remarkably accelerated when confined in nanochannels, ascribing from the promoted dissociation of ILs. Concurrently, nanoconfined ILs demonstrate a highly ordered distribution, lower interplay, and higher free volume compared against bulk systems. This work reveals and analyzes the phenomenon of ionic conductivity elevation in nanoconfined ILs, and offers inspiring opportunities to fabricate the highly stable and efficient QLSEs based on layered nanomaterials for energy storage applications.

Acetic Acid Mediated Regioselective [3 + 3] Cycloaddition of Substituted Cyclopropane-1,1-dicarbonitriles with 1,4-Dithiane-2,5-diol.

An acetic acid mediated regioselective [3 + 3] cycloaddition of substituted cyclopropane-1,1-dicarbonitriles with in situ generated mercaptoacetaldehyde was developed for the synthesis of highly stereoselective tetrahydrothiopyranols. This transformation created two new bonds in a single operation for generating complexity in tetrahydrothiopyrans. This method is characterized by cheap and readily available starting materials, simple operation, and mild reaction conditions.

Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals.

Cell-based biosensors have great potential to detect various toxic and pathogenic contaminants in aqueous environments. However, frequently they cannot meet practical requirements due to insufficient sensing performance. To address this issue, we investigated a modular, cascaded signal amplifying methodology. We first tuned intracellular sensory receptor densities to increase sensitivity, and then engineered multi-layered transcriptional amplifiers to sequentially boost output expression level. We demonstrated these strategies by engineering ultrasensitive bacterial sensors for arsenic and mercury, and improved detection limit and output up to 5,000-fold and 750-fold, respectively. Coupled by leakage regulation approaches, we developed an encapsulated microbial sensor cell array for low-cost, portable and precise field monitoring, where the analyte can be readily quantified via displaying an easy-to-interpret volume bar-like pattern. The ultrasensitive signal amplifying methodology along with the background regulation and the sensing platform will be widely applicable to many other cell-based sensors, paving the way for their real-world applications.

Superhydrophilic and Photothermal Fe-TCPP Nanofibrous Membrane for Efficient Oil-in-Water Nanoemulsion Separation.

Separation and purification of surfactant-stabilized oil-in-water nanoemulsions is a great environmental challenge. Membrane-based separation strategies are more effective over conventional methods in the treatment of nanoemulsion waste water. In this paper, we construct a superhydrophilic membrane by coating a thin photothermal-responsive iron tetrakis(4-carboxyphenyl)porphyrin (Fe-TCPP) nanofibrous metal organic framework (MOF) selective layer on a macroporous polyethersulfone membrane. The as-prepared membrane exhibits high separation performance of oil-in-water nanoemulsions with permeance of 46.4 L·m-2·h-1·bar-1 and separation efficiency of 99%. It also demonstrates nice anti-oil/ionic-fouling property, good recyclability, and desirable stability. The high separation performance is accredited to the superhydrophilicity, highly charged surface, and nanometer pore sizes of the Fe-TCPP nanofibrous membrane. Due to the unique photothermal property of Fe-TCPP nanofibers, the permeance can be enhanced more than 50% by visible light without deteriorating the rejection. This photo-stimuli MOF-based thin-layer membrane offers great potential for the generation of point-of-use water treatment devices.

Piperidine-Mediated [3 + 3] Cyclization of 2-Amino-4H-chromen-4-ones and 2-Benzylidenemalononitriles: To Access 2-Aminochromeno[2,3-b]pyridine Derivatives.

Piperidine-mediated [3 + 3] cyclization of 2-amino-4H-chromen-4-ones and substituted 2-benzylidenemalononitriles was developed for the synthesis of 2-amino-4-aryl-5H-chromeno[2,3-b]pyridin-5-one derivatives. This novel transformation provides a highly efficient and facile route to functionalized 5H-chromeno[2,3-b]pyridines from readily available substrates under mild reaction conditions.

Frictional Drag Effect between Massless and Massive Fermions in Single-Layer/Bilayer Graphene Heterostructures.

The emergence of two-dimensional layered materials offers an excellent opportunity for the fabrication of double-layer electron systems that are in close proximity but electronically isolated. In this work, heterostructures consisting of one single-layer graphene (SLG) and one bilayer graphene (BLG) separated by an ultrathin hBN layer are successfully fabricated, enabling the experimental investigation of the interlayer frictional drag effect between massless and massive fermions. With varying carrier densities, a giant positive peak of drag response emerges at the double neutrality point, around which nonmonotonic temperature dependent behaviors of drag resistance are further observed. These observations can be attributed to the anticorrelations in the distributions of e-h puddles between layers. More importantly, as the system shifts toward the strong coupling regime, the carrier density dependence of drag resistance Rdrag shows a crossover from 1/n3 to 1/n2 for the density matched cases, which is a unique characteristic predicted for massless-massive fermion systems. Consequently, a generalized carrier dependent expression (1/(|nS| + |nB|)2) is obtained for the strong coupling regime, where nS and nB are the carrier densities of SLG and BLG, respectively. Our study provides insight into the electronic frictional effects between massless and massive fermions and thus will promote the investigations of interlayer interactions in hybrid structures hosting different types of carriers.

Comprehensive Profiling of Diverse Genetic Reporters with Application to Whole-Cell and Cell-Free Biosensors.

Whole-cell and cell-free transcription-translation biosensors have recently become favorable alternatives to conventional detection methods, as they are cost-effective, environmental friendly, and easy to use. Importantly, the biological responses from the biosensors need to be converted into a physicochemical signal for easy detection, and a variety of genetic reporters have been employed for this purpose. Reporter gene selection is vital to a sensor performance and application success. However, it was largely based on trial and error with very few systematic side-by-side investigations reported. To address this bottleneck, here we compared eight reporters from three reporter categories, i.e., fluorescent (gfpmut3, deGFP, mCherry, mScarlet-I), colorimetric (lacZ), and bioluminescent (luxCDABE from Aliivibrio fischeri and Photorhabdus luminescens, NanoLuc) reporters, under the control of two representative biosensors for mercury- and quorum-sensing molecules. Both whole-cell and cell-free formats were investigated to assess key sensing features including limit of detection (LOD), input and output dynamic ranges, response time, and output visibility. For both whole-cell biosensors, the lowest detectable concentration of analytes and the fastest responses were achieved with NanoLuc. Notably, we developed, to date, the most sensitive whole-cell mercury biosensor using NanoLuc as reporter, with an LOD ≤ 50.0 fM HgCl2 30 min postinduction. For cell-free biosensors, overall, NanoLuc and deGFP led to shorter response time and lower LOD than the others. This comprehensive profile of diverse reporters in a single setting provides a new important benchmark for reporter selection, aiding the rapid development of whole-cell and cell-free biosensors for various applications in the environment and health.

5'-AMP-activated protein kinase-activating transcription factor 1 cascade modulates human monocyte-derived macrophages to atheroprotective functions in response to heme or metformin.

OBJECTIVE: Intraplaque hemorrhage (IPH) is an important driver of the progression of atherosclerotic plaques. Recently, we characterized Mhem as a novel macrophage phenotype that limits the atherogenicity of IPH. Mhem are directed by activating transcription factor 1 (ATF1), which is activated by phosphorylation. A better understanding of the counteratherogenic ATF1-Mhem pathway may facilitate antiatherosclerotic therapies. APPROACH AND RESULTS: We tested the hypothesis that heme in pathologically relevant concentrations activates the ATF1-Mhem pathway via 5'-AMP-activated protein kinase (AMPK) in primary human monocyte-derived macrophages and mouse bone marrow macrophages. We found that heme (10 µmol/L) activates AMPK, and downstream ATF1-mediated coinduction of heme oxygenase and liver X receptor that characterize Mhem. Heme increased macrophage phospho-AMPK, phospho-ATF1, and its target genes, and these effects were inhibited by the AMPK antagonist dorsomorphin, or by AMPK-knockdown with small inhibitory ribonucleic acid. The AMPK-activating oral hypoglycemic agent metformin also induced and phosphorylated ATF1 at a clinically relevant concentration (10 µmol/L). Functional effects of heme and metformin were inhibited by AMPK-knockdown and included suppression of macrophage oxidative stress; increased cholesterol export; protection from foam-cell formation; and suppression of macrophage inflammatory activation (human leukocyte antigen type DR expression). CONCLUSIONS: Our data indicate that heme activates the ATF1 pathway in human macrophages via AMPK, and that a similar response occurs after treatment of cells with metformin. Our results suggest an in vitro mechanism that may explain the clinical evidence that metformin has vascular protective effects beyond its role in treating hyperglycemia.

Fine structure of sensory apparatus on the head of Cixiopsis punctatus.

The external morphology of the heads of adult male and female Cixiopsis punctatus (Matsumura) (Hemiptera: Fulgoromorpha: Tropiduchidae) was studied using scanning electron microscopy. Eleven types of sensilla or sensory organs were identified: trichoid sensilla on the pedicel, scape, maxillae, and labium; campaniform sensilla on the antennal pedicel, antennal scape, maxillae, and labium; plate organs on the antennal pedicel; coeloconic sensilla in Bourgoin's organ and styloconic sensilla on the expanded flagellar base; Evans' organ and button-like sensilla on the maxillary plates; basiconic sensilla, peg sensilla, and coin-shaped sensilla on the labium. Styloconic sensilla on the expanded flagellar base and peg sensilla located between the dorsal sensory field and the opening of the maxillae and mandibles were first reported in Tropiduchidae. The external morphology, distribution, and abundance of sensilla located on antennae, maxillae, and labium in C. punctatus were illustrated.

One-step hydrothermal growth of porous nickel manganese layered double hydroxide nanosheet film towards efficient visible-light modulation.

Electrochromic smart windows have attracted great attention due to their dynamic regulation of the solar spectrum. NiO and MnO2 are typical anodic coloration materials and widely investigated as complementary electrodes with WO3. However, NiO and MnO2 films often cannot be bleached to complete transparency, resulting in low transmittances and low optical modulations in the short-wavelength visible region. Herein, we report a porous nickel manganese layered double hydroxide (NiMn-LDH) nanosheet film directly grown on fluorine-doped tin oxide (FTO) glass using a one-step hydrothermal method, which demonstrates a high transmittance of 80.1% at 550 nm (without deduction of FTO glass). Induced by the double-redox couples of Ni2+/Ni3+ and Mn3+/Mn4+ associated synergistic electrochromic effect, the as-grown NiMn-LDH film electrode exhibits a large optical modulation of 68.5% at 550 nm, and a large solar irradiation modulation of 59.0% in the visible region of 400-800 nm. After annealing at 450 °C for 2 h, the NiMn-LDH film can be transformed into Ni6MnO8 film with a reduced optical modulation of 30.0% at 550 nm. Furthermore, the NiMn-LDH film electrode delivers an areal capacitance of 30.8 mF cm-2 at a current density of 0.1 mA cm-2. These results suggest that the as-prepared NiMn-LDH film electrode is a promising candidate for both electrochromic and energy storage applications.

Preoperative Classification of Peripheral Nerve Sheath Tumors on MRI Using Radiomics.

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft-tissue tumors prevalent in neurofibromatosis type 1 (NF1) patients, posing a significant risk of metastasis and recurrence. Current magnetic resonance imaging (MRI) imaging lacks decisiveness in distinguishing benign peripheral nerve sheath tumors (BPNSTs) and MPNSTs, necessitating invasive biopsies. This study aims to develop a radiomics model using quantitative imaging features and machine learning to distinguish MPNSTs from BPNSTs. Clinical data and MRIs from MPNST and BPNST patients (2000-2019) were collected at a tertiary sarcoma referral center. Lesions were manually and semi-automatically segmented on MRI scans, and radiomics features were extracted using the Workflow for Optimal Radiomics Classification (WORC) algorithm, employing automated machine learning. The evaluation was conducted using a 100× random-split cross-validation. A total of 35 MPNSTs and 74 BPNSTs were included. The T1-weighted (T1w) MRI radiomics model outperformed others with an area under the curve (AUC) of 0.71. The incorporation of additional MRI scans did not enhance performance. Combining T1w MRI with clinical features achieved an AUC of 0.74. Experienced radiologists achieved AUCs of 0.75 and 0.66, respectively. Radiomics based on T1w MRI scans and clinical features show some ability to distinguish MPNSTs from BPNSTs, potentially aiding in the management of these tumors.

Signature of quantum interference effect in inter-layer Coulomb drag in graphene-based electronic double-layer systems.

The distinguishing feature of a quantum system is interference arising from the wave mechanical nature of particles which is clearly central to macroscopic electronic properties. Here, we report the signature of quantum interference effect in inter-layer transport process. Via systematic magneto-drag experiments on graphene-based electronic double-layer systems, we observe low-field correction to the Coulomb-scattering-dominated inter-layer drag resistance in a wide range of temperature and carrier density, with its characteristics sensitive to the band topology of graphene layers. These observations can be attributed to a new type of quantum interference between drag processes, with the interference pathway comprising different carrier diffusion paths in the two constituent conductors. The emergence of such effect relies on the formation of superimposing planar diffusion paths, among which the impurity potentials from intermediate insulating spacer play an essential role. Our findings establish an ideal platform where the interplay between quantum interference and many-body interaction is essential.

SMYD5 catalyzes histone H3 lysine 36 trimethylation at promoters.

Histone marks, carriers of epigenetic information, regulate gene expression. In mammalian cells, H3K36me3 is mainly catalyzed by SETD2 at gene body regions. Here, we find that in addition to gene body regions, H3K36me3 is enriched at promoters in primary cells. Through screening, we identify SMYD5, which is recruited to chromatin by RNA polymerase II, as a methyltransferase catalyzing H3K36me3 at promoters. The enzymatic activity of SMYD5 is dependent on its C-terminal glutamic acid-rich domain. Overexpression of full-length Smyd5, but not the C-terminal domain-truncated Smyd5, restores H3K36me3 at promoters in Smyd5 knockout cells. Furthermore, elevated Smyd5 expression contributes to tumorigenesis in liver hepatocellular carcinoma. Together, our findings identify SMYD5 as the H3K36me3 methyltransferase at promoters that regulates gene expression, providing insights into the localization and function of H3K36me3.

Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors.

In type II CRISPR systems, the guide RNA (gRNA) comprises a CRISPR RNA (crRNA) and a hybridized trans-acting CRISPR RNA (tracrRNA), both being essential in guided DNA targeting functions. Although tracrRNAs are diverse in sequence and structure across type II CRISPR systems, the programmability of crRNA-tracrRNA hybridization for Cas9 is not fully understood. Here, we reveal the programmability of crRNA-tracrRNA hybridization for Streptococcus pyogenes Cas9, and in doing so, redefine the capabilities of Cas9 proteins and the sources of crRNAs, providing new biosensing applications for type II CRISPR systems. By reprogramming the crRNA-tracrRNA hybridized sequence, we show that engineered crRNA-tracrRNA interactions can not only enable the design of orthogonal cellular computing devices but also facilitate the hijacking of endogenous small RNAs/mRNAs as crRNAs. We subsequently describe how these re-engineered gRNA pairings can be implemented as RNA sensors, capable of monitoring the transcriptional activity of various environment-responsive genomic genes, or detecting SARS-CoV-2 RNA in vitro, as an Atypical gRNA-activated Transcription Halting Alarm (AGATHA) biosensor.

Programming living sensors for environment, health and biomanufacturing.

Synthetic biology offers new tools and capabilities of engineering cells with desired functions for example as new biosensing platforms leveraging engineered microbes. In the last two decades, bacterial cells have been programmed to sense and respond to various input cues for versatile purposes including environmental monitoring, disease diagnosis and adaptive biomanufacturing. Despite demonstrated proof-of-concept success in the laboratory, the real-world applications of microbial sensors have been restricted due to certain technical and societal limitations. Yet, most limitations can be addressed by new technological developments in synthetic biology such as circuit design, biocontainment and machine learning. Here, we summarize the latest advances in synthetic biology and discuss how they could accelerate the development, enhance the performance and address the present limitations of microbial sensors to facilitate their use in the field. We view that programmable living sensors are promising sensing platforms to achieve sustainable, affordable and easy-to-use on-site detection in diverse settings.