Adeno-associated virus type 2 in US children with acute severe hepatitis.

As of August 2022, clusters of acute severe hepatitis of unknown aetiology in children have been reported from 35 countries, including the USA1,2. Previous studies have found human adenoviruses (HAdVs) in the blood from patients in Europe and the USA3-7, although it is unclear whether this virus is causative. Here we used PCR testing, viral enrichment-based sequencing and agnostic metagenomic sequencing to analyse samples from 16 HAdV-positive cases from 1 October 2021 to 22 May 2022, in parallel with 113 controls. In blood from 14 cases, adeno-associated virus type 2 (AAV2) sequences were detected in 93% (13 of 14), compared to 4 (3.5%) of 113 controls (P < 0.001) and to 0 of 30 patients with hepatitis of defined aetiology (P < 0.001). In controls, HAdV type 41 was detected in blood from 9 (39.1%) of the 23 patients with acute gastroenteritis (without hepatitis), including 8 of 9 patients with positive stool HAdV testing, but co-infection with AAV2 was observed in only 3 (13.0%) of these 23 patients versus 93% of cases (P < 0.001). Co-infections by Epstein-Barr virus, human herpesvirus 6 and/or enterovirus A71 were also detected in 12 (85.7%) of 14 cases, with higher herpesvirus detection in cases versus controls (P < 0.001). Our findings suggest that the severity of the disease is related to co-infections involving AAV2 and one or more helper viruses.

A Streptomyces species from the ginseng rhizosphere exhibits biocontrol potential.

Plants and their associated microbes live in complicated, changeable, and unpredictable environments. They usually interact with each other in many ways through multidimensional, multiscale, and multilevel coupling manners, leading to challenges in the coexistence of randomness and determinism or continuity and discreteness. Gaining a deeper understanding of these diverse interaction mechanisms can facilitate the development of data-mining theories and methods for complex systems, coupled modeling for systems with different spatiotemporal scales and functional properties, or even a universal theory of information and information interactions. In this study, we use a "closed-loop" model to present a plant-microbe interaction system and describe the probable functions of microbial natural products. Specifically, we report a rhizosphere species, Streptomyces ginsengnesis G7, which produces polyketide lydicamycins and other active metabolites. Interestingly, these distinct molecules have the potential to function both as antibiotics and as herbicides for crop protection. Detailed laboratory experiments conducted in Arabidopsis (Arabidopsis thaliana), combined with a comprehensive bioinformatics analysis, allow us to rationalize a model for this specific plant-microbe interaction process. Our work reveals the benefits of exploring otherwise neglected resources for the identification of potential functional molecules and provides a reference to better understand the system biology of complex ecosystems.

Interpretable online network dictionary learning for inferring long-range chromatin interactions.

Dictionary learning (DL), implemented via matrix factorization (MF), is commonly used in computational biology to tackle ubiquitous clustering problems. The method is favored due to its conceptual simplicity and relatively low computational complexity. However, DL algorithms produce results that lack interpretability in terms of real biological data. Additionally, they are not optimized for graph-structured data and hence often fail to handle them in a scalable manner. In order to address these limitations, we propose a novel DL algorithm called online convex network dictionary learning (online cvxNDL). Unlike classical DL algorithms, online cvxNDL is implemented via MF and designed to handle extremely large datasets by virtue of its online nature. Importantly, it enables the interpretation of dictionary elements, which serve as cluster representatives, through convex combinations of real measurements. Moreover, the algorithm can be applied to data with a network structure by incorporating specialized subnetwork sampling techniques. To demonstrate the utility of our approach, we apply cvxNDL on 3D-genome RNAPII ChIA-Drop data with the goal of identifying important long-range interaction patterns (long-range dictionary elements). ChIA-Drop probes higher-order interactions, and produces data in the form of hypergraphs whose nodes represent genomic fragments. The hyperedges represent observed physical contacts. Our hypergraph model analysis has the objective of creating an interpretable dictionary of long-range interaction patterns that accurately represent global chromatin physical contact maps. Through the use of dictionary information, one can also associate the contact maps with RNA transcripts and infer cellular functions. To accomplish the task at hand, we focus on RNAPII-enriched ChIA-Drop data from Drosophila Melanogaster S2 cell lines. Our results offer two key insights. First, we demonstrate that online cvxNDL retains the accuracy of classical DL (MF) methods while simultaneously ensuring unique interpretability and scalability. Second, we identify distinct collections of proximal and distal interaction patterns involving chromatin elements shared by related processes across different chromosomes, as well as patterns unique to specific chromosomes. To associate the dictionary elements with biological properties of the corresponding chromatin regions, we employ Gene Ontology (GO) enrichment analysis and perform multiple RNA coexpression studies.

Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads.

BACKGROUND: Pathogenic infections pose a significant threat to global health, affecting millions of people every year and presenting substantial challenges to healthcare systems worldwide. Efficient and timely testing plays a critical role in disease control and transmission prevention. Group testing is a well-established method for reducing the number of tests needed to screen large populations when the disease prevalence is low. However, it does not fully utilize the quantitative information provided by qPCR methods, nor is it able to accommodate a wide range of pathogen loads. RESULTS: To address these issues, we introduce a novel adaptive semi-quantitative group testing (SQGT) scheme to efficiently screen populations via two-stage qPCR testing. The SQGT method quantizes cycle threshold (Ct) values into multiple bins, leveraging the information from the first stage of screening to improve the detection sensitivity. Dynamic Ct threshold adjustments mitigate dilution effects and enhance test accuracy. Comparisons with traditional binary outcome GT methods show that SQGT reduces the number of tests by 24% on the only complete real-world qPCR group testing dataset from Israel, while maintaining a negligible false negative rate. CONCLUSION: In conclusion, our adaptive SQGT approach, utilizing qPCR data and dynamic threshold adjustments, offers a promising solution for efficient population screening. With a reduction in the number of tests and minimal false negatives, SQGT holds potential to enhance disease control and testing strategies on a global scale.

Emergence of Novel Norovirus GII.4 Variant.

We detected a novel GII.4 variant with an amino acid insertion at the start of epitope A in viral protein 1 of noroviruses from the United States, Gabon, South Africa, and the United Kingdom collected during 2017-2022. Early identification of GII.4 variants is crucial for assessing pandemic potential and informing vaccine development.

Cholic acid exposure during late pregnancy causes placental dysfunction and fetal growth restriction by reactive oxygen species-mediated activation of placental GCN2/eIF2α pathway.

Epidemiological studies suggest that fetal growth restriction (FGR) caused by gestational cholestasis is associated with elevated serum cholic acid (CA). Here, we explore the mechanism by which CA induces FGR. Pregnant mice except controls were orally administered with CA daily from gestational day 13 (GD13) to GD17. Results found that CA exposure decreased fetal weight and crown-rump length, and increased the incidence of FGR in a dose-dependent manner. Furthermore, CA caused placental glucocorticoid (GC) barrier dysfunction via down-regulating the protein but not the mRNA level of placental 11ß-Hydroxysteroid dehydrogenase-2 (11ß-HSD2). Additionally, CA activated placental GCN2/eIF2α pathway. GCN2iB, an inhibitor of GCN2, significantly inhibited CA-induced down-regulation of 11ß-HSD2 protein. We further found that CA caused excessive reactive oxygen species (ROS) production and oxidative stress in mouse placentas and human trophoblasts. NAC significantly rescued CA-induced placental barrier dysfunction by inhibiting activation of GCN2/eIF2α pathway and subsequent down-regulation of 11ß-HSD2 protein in placental trophoblasts. Importantly, NAC rescued CA-induced FGR in mice. Overall, our results suggest that CA exposure during late pregnancy induces placental GC barrier dysfunction and subsequent FGR may be via ROS-mediated placental GCN2/eIF2α activation. This study provides valuable insight for understanding the mechanism of cholestasis-induced placental dysfunction and subsequent FGR.

A robust method for simultaneous determination of eight B vitamins in human serum by liquid chromatography tandem mass spectrometry.

The level of vitamin B group in human serum is an important index of human health. Among B vitamins, cyanocobalamin in serum is unstable and its content is extremely low. Rapid and simultaneous detection of multiple B vitamins including cyanocobalamin is a challenge. Herein, we have developed a rapid and stable method that can realize the determination of thiamine, riboflavin, nicotinamide, pantothenic acid, pyridoxic acid, biotin, 5-methyltetrahydrofolate, and cyanocobalamin simultaneously in 6 min. The method was established based on protein precipitation with methanol and then chromatographic separation was achieved using Waters acquity ultra-high-performance liquid chromatography high strength silica T3 column, which was stable and sensitive especially for cyanocobalamin. Limit of quantification, precision, trueness, and matrix effect were validated according to the European Medicines Agency and United States Food and Drug guidelines and Clinical and Laboratory Standards Institute guidelines on bioanalytical method. The limit of quantification for thiamine, riboflavin, nicotinamide, pantothenic acid, pyridoxic acid, biotin, 5-methyltetrahydrofolate, and cyanocobalamin was 0.4, 0.4, 0.8, 2.0, 0.4, 0.1, 0.4, and 0.04 ng/mL separately, respectively. Intra- and interday precisions were 1.1%-12.4% and 2.0%-13.5%, respectively. The relative errors were between 0.3% and 13.3%, and the matrix effects were between 2.6% and 10.4%.

Cross-cultural experiences and self-development: a psychobiographical study of Bruce Lee.

A common challenge people face in today's cross-cultural world is how to solve a series of adaptation problems caused by cultural conflict. Exploring Bruce Lee's successful cross-cultural experiences through psychobiography offers some inspiration and thoughts. How did Bruce Lee successfully integrate martial arts, symbolising the Eastern culture, with films representing the Western culture, finally propelling kung fu films onto the international stage? Numerous publicly available materials about Bruce Lee were collected for this study, and the research data were evaluated using thematic analysis. Bruce Lee's success benefitted from reconstructing cultural environment information and exercising his initiative to shape a new cultural environment. His life experiences reflect individual cognition behaviour and social and cultural environments as two aspects of a dynamic circulation system and show that the two have reached internal and spiralling harmony through mutual integration. In the context of the Oriental collectivism culture's family narrative, Chinese adults' personality development features the unique theme of 'inheritance and innovation'. Dealing with the relationship between self-actualisation and familism is another important and challenging task in developing the Chinese personality.

Detoxification of tetracycline and synthetic dyes by a newly characterized Lentinula edodes laccase, and safety assessment using proteomic analysis.

Fungal laccase has strong ability in detoxification of many environmental contaminants. A putative laccase gene, LeLac12, from Lentinula edodes was screened by secretome approach. LeLac12 was heterogeneously expressed and purified to characterize its enzymatic properties to evaluate its potential use in bioremediation. This study showed that the extracellular fungal laccase from L. edodes could effectively degrade tetracycline (TET) and the synthetic dye Acid Green 25 (AG). The growth inhibition of Escherichia coli and Bacillus subtilis by TET revealed that the antimicrobial activity was significantly reduced after treatment with the laccase-HBT system. 16 transformation products of TET were identified by UPLC-MS-TOF during the laccase-HBT oxidation process. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that LeLac12 could completely mineralize ring-cleavage products. LeLac12 completely catalyzed 50 mg/L TET within 4 h by adding AG (200 mg/L), while the degradation of AG was above 96% even in the co-contamination system. Proteomic analysis revealed that central carbon metabolism, energy metabolism, and DNA replication/repair were affected by TET treatment and the latter system could contribute to the formation of multidrug-resistant strains. The results demonstrate that LeLac12 is an efficient and environmentally method for the removal of antibiotics and dyes in the complex polluted wastewater.

Inhibition of DCUN1D1 attenuates periodontitis by suppressing NF-κB signaling.

Nuclear factor kappa-B (NF-κB) signaling-mediated inflammation contributes greatly to the pathogenesis of periodontitis. Neddylation, a ubiquitin-like posttranslational modification, is known to regulate NF-κB signaling. DCUN1D1 (defective in cullin neddylation 1 domain containing 1) is a critical factor in neddylation and has been shown to regulate NF-κB activation. However, the previse roles of DCUN1D1 in periodontitis are not fully elucidated. To explore the roles of DCUN1D1 in periodontitis, the expression of DCUN1D1 was measured in gingival tissues of patients with periodontitis. We inhibited DCUN1D1 by siRNA knocking down or using inhibitor in gingival fibroblasts and the lipopolysaccharides (LPS)-induced expression of IL-6 and TNF-α, and activation of NF-κB were measured. The expression of DCUN1D1 was increased in gingival tissues of patients with periodontitis. Knocking down or inhibiting DCUN1D1 suppressed LPS-induced production of IL-6 and TNF-α, decreased NF-κB activity, and inhibited LPS-induced activation of NF-κB. Inhibiting DCUN1D1 ameliorates periodontitis by suppressing NF-κB signaling.

In Situ Polymerization-Mediated Antigen Presentation.

Activating antigen-presenting cells is essential to generate adaptive immunity, while the efficacy of conventional activation strategies remains unsatisfactory due to suboptimal antigen-specific priming. Here, in situ polymerization-mediated antigen presentation (IPAP) is described, in which antigen-loaded nanovaccines are spontaneously formed and efficiently anchored onto the surface of dendritic cells in vivo through co-deposition with dopamine. The resulting chemically bound nanovaccines can promote antigen presentation by elevating macropinocytosis-based cell uptake and reducing lysosome-related antigen degradation. IPAP is able to prolong the duration of antigen reservation in the injection site and enhance subsequent accumulation in the draining lymph nodes, thereby eliciting robust antigen-specific cellular and humoral immune responses. IPAP is also applicable for different antigens and capable of circumventing the disadvantages of complicated preparation and purification. By implementation with ovalbumin, IPAP induces a significant protective immunity against ovalbumin-overexpressing tumor cell challenge in a prophylactic murine model. The use of the SARS-CoV-2 Spike protein S1 subunit also remarkably increases the production of S1-specific immunoglobulin G in mice. IPAP offers a unique strategy for stimulating antigen-presenting cells to boost antigen-specific adaptive responses and proposes a facile yet versatile method for immunization against various diseases.

Safety, tolerability, and pharmacokinetics of ibrexafungerp in healthy Chinese subjects: a randomized, double-blind, placebo-controlled phase 1 trial.

Ibrexafungerp (code name in China: HS-10366) is a first-in-class and orally active triterpenoid antifungal agent with broad antifungal activity against Candida spp., Aspergillus spp., and other fungal pathogens. It was approved by the U.S. Food and Drug Administration for the treatment of vulvovaginal candidiasis. The study aimed to evaluate the safety, tolerability, and pharmacokinetic (PK) characteristics of oral ibrexafungerp in healthy Chinese adults. A single-center, randomized, double-blind, placebo-controlled single ascending dose (SAD, n = 42), and multiple ascending dose (MAD, n = 28) study was conducted in healthy Chinese subjects from March to October 2022. There were three cohorts in the SAD stage (300, 600, and 1,500 mg) and two cohorts in the MAD stage [450 mg once daily (QD) for 7 days; a loading dose of 750 mg twice daily (BID) for the first 2 days followed by a maintenance dose of 750 mg QD for consecutive 5 days]. Eligible participants in each cohort were randomly assigned in a 6:1 ratio to receive either ibrexafungerp or placebo orally. The primary objectives were to evaluate the safety and tolerability. The secondary objective was to evaluate PK parameters, including Cmax, AUC, and t1/2. A total of 70 healthy Chinese subjects were enrolled in the study. The mean (SD) age was 29.0 (6.32), and 55.7% were male. All treatment-emergent adverse events (TEAEs) were mild or moderate. There were no serious adverse events, and no subjects were discontinued from the study due to TEAEs. All TEAEs were recovered or resolved. The most common TEAEs were diarrhea, abdominal pain, and nausea. In the SAD stage, Cmax, and AUC increased in an approximately dose-proportional manner in the dose range of 300-1,500 mg. The mean t1/2 was within 18.29-21.30 hours. In the MAD stage, an accumulation of exposure (Cmax and AUC) was observed following multiple doses. This phase 1 study demonstrates a favorable safety, tolerability, and PK profile of ibrexafungerp in healthy Chinese subjects.

Preparation of a Klebsiella pneumoniae conjugate nanovaccine using glycol-engineered Escherichia coli.

BACKGROUND: Engineered strains of Escherichia coli have been used to produce bioconjugate vaccines using Protein Glycan Coupling Technology (PGCT). Nanovaccines have also entered the vaccine development arena with advances in nanotechnology and have been significantly developed, but chassis cells for conjugate nanovaccines have not been reported. RESULTS: To facilitate nanovaccine preparation, a generic recombinant protein (SpyCather4573) was used as the acceptor protein for O-linked glycosyltransferase PglL, and a glycol-engineered Escherichia coli strain with these two key components (SC4573 and PglL) integrated in its genome was developed in this study. The targeted glycoproteins with antigenic polysaccharides produced by our bacterial chassis can be spontaneously bound to proteinous nanocarriers with surface exposed SpyTag in vitro to form conjugate nanovaccines. To improve the yields of the targeted glycoprotein, a series of gene cluster deletion experiments was carried out, and the results showed that the deletion of the yfdGHI gene cluster increased the expression of glycoproteins. Using the updated system, to the best of our knowledge, we report for the first time the successful preparation of an effective Klebsiella pneumoniae O1 conjugate nanovaccine (KPO1-VLP), with antibody titers between 4 and 5 (Log10) after triple immunization and up to 100% protection against virulent strain challenge. CONCLUSIONS: Our results define a convenient and reliable framework for bacterial glycoprotein vaccine preparation that is flexible and versatile, and the genomic stability of the engineered chassis cells promises a wide range of applications for biosynthetic glycobiology research.

Insights into the Superior Bioavailability of Biogenic Sulfur from the View of Its Unique Properties: The Key Role of Trace Organic Substances.

Elemental sulfur (S0) is widely utilized in environmental pollution control, while its low bioavailability has become a bottleneck for S0-based biotechnologies. Biogenic sulfur (bio-S0) has been demonstrated to have superior bioavailability, while little is known about its mechanisms thus far. This study investigated the bioavailability and relevant properties of bio-S0 based on the denitrifying activity of Thiobacillus denitrificans with chemical sulfur (chem-S0) as the control. It was found that the conversion rate and removal efficiency of nitrate in the bio-S0 system were 2.23 and 2.04 times those of the chem-S0 system. Bio-S0 was not pure orthorhombic sulfur [S: 96.88 ± 0.25% (w/w)]. Trace organic substances detected on the bio-S0 surface were revealed to contribute to its hydrophilicity, resulting in better dispersibility in the aqueous liquid. In addition, the adhesion force of T. denitrificans on bio-S0 was 1.54 times that of chem-S0, endowing a higher bacterial adhesion efficiency on the sulfur particle. The weaker intermolecular binding force due to the low crystallinity of bio-S0 led to enhanced cellular uptake by attached bacteria. The mechanisms for the superior bioavailability of bio-S0 were further proposed. This study provides a comprehensive view of the superior bioavailability of bio-S0 and is beneficial to developing high-quality sulfur resources.

White and green striate leaves 1, predicted to encode a 16S rRNA processing protein, plays a critical role in the processing of chloroplast ribosomes in maize (Zea mays L.).

Ribosomes play a crucial role in protein biosynthesis and are linked to plant growth and development. The RimM protein has been shown to be involved in the maturation of 30S ribosomal subunits, but its exact function in plants is still unknown. In this study, we discovered a maize mutant with white and green striate leaves (wgsl1) and reduced chlorophyll content. Genetic analysis showed that the wgsl1 mutation was recessive and controlled by a single nuclear gene. Map-based cloning of ZmWGSL1 identified a base substitution (G to A) that generated a missense mutation within the Zm00001d039036 gene in the wgsl1 mutant. Zm00001d039036 encodes a 16S rRNA processing protein containing the RimM motif. Further analysis of transcriptomic data showed that the transcript levels of many ribosomal proteins involved in the small and big ribosomal subunits were dramatically up-regulated in the wgsl1 mutant. Moreover, the level of ribosomal multimers was decreased. This suggests that ZmWGSL1 plays a crucial role in the maturation of the ribosome, leading to abnormal plant growth and development. In addition, subcellular localization results indicate that WGSL1 is localized in chloroplasts. Therefore, we suggest that WGSL1 is a nuclear-encoded protein, is transported to the chloroplast to drive functions, and affects the processing of ribosomes in the chloroplast. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01407-y.

Deep learning network for fusing optical and infrared images in a complex imaging environment by using the modified U-Net.

The fusion of optical and infrared images is a critical task in the field of image processing. However, it is challenging to achieve optimal results when fusing images from complex environments. In this paper, we propose a deep learning network model comprising an encoding network and a decoding network based on the modified U-Net network to fuse low-quality images from complex imaging environments. As both encoding and decoding networks use similar convolutional modules, they can share similar layer structures to improve the overall fusion performance. Furthermore, an attention mechanism module is integrated into the decoding network to identify and capture the crucial features of the fused images. It can assist the deep learning network to extract more relevant image features and thus get more accurate fusion. The proposed model has been compared with some existing methods to prove its performance in view of subjective and objective evaluations.

The influence of iris -ciliary angle (ICA) on the vault after implantation of V4c implantable collamer lens: a chain mediation model of ICL haptic related factors.

BACKGROUND: This study aims to identify the relationship between iris -ciliary angle (ICA) and the vault. Additionally, we also seek to investigate the chain mediating effects of the ICL haptic related factors on this relationship. METHODS: The participants were categorized into three groups according to the ICA value as follows: low ICA group (< 35°); moderate ICA group (35°-70°); high ICA group (> 70°). We compared the preoperative ocular characteristics and postoperative examinations among the three groups. Multiple variable stepwise regression was performed to establish the vault prediction formula. The Process V4.0 in SPSS and Hayes's PROCESS model 6 was conducted to further elucidate the mediating effects of the final tip point of ICL haptic and the ICL arc-lens arc on the relationship between the ICA and vault. RESULTS: There was a significant difference in the positions of the ICL haptic among three ICA groups. The regression vault equation was Vault = 679.42-7.26*TCA + 192.30*ACD-196.37*CLR + 73.21* STS(horizontal).A significant negative correlation was found between the ICA and vault (P < 0.01).The chain mediation model revealed that the final tip point of ICL haptic and the ICL arc-Lens arc were sequential mediators between ICA and vault (effect = -1.63, 95% CI = -2.72--0.73). CONCLUSION: The ICA was associated with vault via the mediation effect of the final tip point of the ICL haptic and the ICL arc -lens arc. Assessment of ICL haptic related parameters adds significant information to interpret the vault after surgery.

A Nomogram Model for Predicting Prognosis in Spontaneous Intracerebral Hemorrhage Patients.

OBJECTIVES: Intracranial hemorrhage is the second most common stroke subtype following ischemic stroke and usually induces high mortality and disability. Here, we conducted a retrospective study to establish a nomogram clinical prediction model. METHODS: First, the baseline data of patients who presented to our hospital in 2015-2021 were collected and compared (789 patients for the training cohort and 378 patients for the validation cohort). Second, univariate and binary logistic analyses were performed to screen out alternative indicators. Finally, a clinical prediction model by nomogram was established that included such indicators to estimate the prognosis of intracranial hemorrhage patients. RESULTS: Univariate logistic analysis was used to screen several possible impact factors, including hypertension, hematoma volume, Glasgow Coma Scale (GCS) score, intracranial hemorrhage (ICH) score, irregular shape, uneven density, intraventricular hemorrhage (IVH) relation, fibrinogen, D-dimer, low density lipoprotein (LDL), high-density lipoprotein (HDL), creatinine, total protein, hemoglobin (HB), white blood cell (WBC), neutrophil blood cell (NBC), lymphocyte blood cell (LBC), the neutrophil lymphocyte ratio (NLR), surgery, deep venous thrombosis (DVT) or pulmonary embolism (PE) rate, hospital day, and hypertension control. Further binary logistic analysis revealed that ICH score (p = 0.036), GCS score (p = 0.000), irregular shape (p = 0.000), uneven density (p = 0.002), IVH relation (p = 0.014), surgery (p = 0.000) were independent indicators to construct a nomogram clinical prediction model. The C statistic was 0.840. CONCLUSIONS: ICH score, GCS score, irregular shape, uneven density, IVH relation, surgery are easily available indicators to assist neurologists in formulating the most appropriate therapy for every intracranial hemorrhage patient. Further large prospective clinical trials are needed to obtain more integrated and reliable conclusions.

Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing.

DNA is a promising next-generation data storage medium, but challenges remain with synthesis costs and recording latency. Here, we describe a prototype of a DNA data storage system that uses an extended molecular alphabet combining natural and chemically modified nucleotides. Our results show that MspA nanopores can discriminate different combinations and ordered sequences of natural and chemically modified nucleotides in custom-designed oligomers. We further demonstrate single-molecule sequencing of the extended alphabet using a neural network architecture that classifies raw current signals generated by Oxford Nanopore sequencers with an average accuracy exceeding 60% (39× larger than random guessing). Molecular dynamics simulations show that the majority of modified nucleotides lead to only minor perturbations of the DNA double helix. Overall, the extended molecular alphabet may potentially offer a nearly 2-fold increase in storage density and potentially the same order of reduction in the recording latency, thereby enabling new implementations of molecular recorders.

Hsa_circ_0081069 facilitates tongue squamous cell carcinoma progression by modulating MAP2K4 expression via miR-634.

It has been demonstrated that circular RNA (circRNA) is involved in the progression of tongue squamous cell carcinoma (TSCC). The aim of this study was to investigate the intrinsic mechanism of circ_0081069 in TSCC progression. The expression levels of circ_00081069, miR-634, and mitogen-activated protein kinase kinase 4 (MAP2K4) in TSCC tissues and cells were detected by quantitative real-time PCR (qRT-PCR). Cell counting kit 8 assay, Edu assay, and flow cytometry assay were used to detect cell proliferation and cell cycle distribution. Transwell assay was used to detect cell migration and invasion abilities. Western blot analysis was performed to detect the protein expression. Dual-luciferase reporter assay was used to detect the targeting relationships of circ_0081069, miR-634 and MAP2K4. Immunohistochemical staining was used to measure MAP2K4-positive cells in tissues. The effect of circ_0081069 silencing on tumor formation in TSCC in vivo was explored by xenograft tumor assay. Circ_0081069 was highly expressed in TSCC tissues and cells. Silencing of circ_0081069 inhibited cell proliferation, cell cycle progress, cell migration and invasion in vitro, as well as hindered tumor growth in vivo. Mechanistically, circ_0081069 targeted miR-634 to negatively regulate miR-634 expression, and inhibition of miR-634 was able to weaken the inhibitory effect of circ_0081069 knockdown on proliferation, migration, and invasion of TSCC cells. MiR-634 targeted MAP2K4 and negatively regulated MAP2K4 expression, and overexpression of miR-634 inhibited TSCC cell proliferation, migration, and invasion, while co-overexpression of MAP2K4 was able to reverse the effects of miR-634 in TSCC cells. Circ_0081069 is involved in the regulation of proliferation, cycle progress, migration, and invasion of TSCC cells through the miR-634/MAP2K4 axis and has the potential to serve as a diagnostic biomarker and therapeutic target.