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Viruses subvert macromolecular pathways in infected host cells to aid in viral gene amplification or to counteract innate immune responses. Roles for host-encoded, noncoding RNAs, including microRNAs, have been found to provide pro- and anti-viral functions. Recently, circular RNAs (circRNAs), that are generated by a nuclear back-splicing mechanism of pre-mRNAs, have been implicated to have roles in DNA virus-infected cells. This study examines the circular RNA landscape in uninfected and hepatitis C virus (HCV)-infected liver cells. Results showed that the abundances of distinct classes of circRNAs were up-regulated or down-regulated in infected cells. Identified circRNAs displayed pro-viral effects. One particular up-regulated circRNA, circPSD3, displayed a very pronounced effect on viral RNA abundances in both hepatitis C virus- and Dengue virus-infected cells. Though circPSD3 has been shown to bind factor eIF4A3 that modulates the cellular nonsense-mediated decay (NMD) pathway, circPSD3 regulates RNA amplification in a pro-viral manner at a post-translational step, while eIF4A3 exhibits the anti-viral property of the NMD pathway. Findings from the global analyses of the circular RNA landscape argue that pro-, and likely, anti-viral functions are executed by circRNAs that modulate viral gene expression as well as host pathways. Because of their long half-lives, circRNAs likely play hitherto unknown, important roles in viral pathogenesis.

Abstract Background The mitosis-to-meiosis switch during spermatogenesis requires dynamic changes in gene expression. However, the regulation of meiotic transcriptional and post-transcriptional machinery during this transition remains elusive. Results We report that methyltransferase-like protein 16 (METTL16), an N6-methyladenosine (m6A) writer, is required for mitosis-to-meiosis transition during spermatogenesis. Germline conditional knockout of Mettl16 in male mice impairs spermatogonial differentiation and meiosis initiation. Mechanistically, METTL16 interacts with splicing factors to regulate the alternative splicing of meiosis-related genes such as Stag3. Ribosome profiling reveals that the translation efficiency of many meiotic genes is dysregulated in METTL16-deficient testes. m6A-sequencing shows that ablation of METTL16 causes upregulation of the m6A-enriched transcripts and downregulation of the m6A-depleted transcripts, similar to Meioc and/or Ythdc2 mutants. Further in vivo and in vitro experiments demonstrate that the methyltransferase activity site (PP185-186AA) of METTL16 is necessary for spermatogenesis. Conclusions Our findings support a molecular model wherein the m6A writer METTL16-mediated alternative splicing and translation efficiency regulation are required to control the mitosis-to-meiosis germ cell fate decision in mice, with implications for understanding meiosis-related male fertility disorders.

Background and Objective Chronic kidney disease (CKD) is a major public health issue, and accurate prediction of the progression of kidney failure is critical for clinical decision-making and helps improve patient outcomes. As such, we aimed to develop and externally validate a machine-learned model to predict the progression of CKD using common laboratory variables, demographic characteristics, and an electronic health records database. Methods We developed a predictive model using longitudinal clinical data from a single center for Chinese CKD patients. The cohort included 987 patients who were followed up for more than 24 months. Fifty-three laboratory features were considered for inclusion in the model. The primary outcome in our study was an estimated glomerular filtration rate ≤15 mL/min/1.73 m2 or kidney failure. Machine learning algorithms were applied to the modeling dataset (n = 296), and an external dataset (n = 71) was used for model validation. We assessed model discrimination via area under the curve (AUC) values, accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1 score. Results Over a median follow-up period of 3.75 years, 148 patients experienced kidney failure. The optimal model was based on stacking different classifier algorithms with six laboratory features, including 24-h urine protein, potassium, glucose, urea, prealbumin and total protein. The model had considerable predictive power, with AUC values of 0.896 and 0.771 in the validation and external datasets, respectively. This model also accurately predicted the progression of renal function in patients over different follow-up periods after their initial assessment. Conclusions A prediction model that leverages routinely collected laboratory features in the Chinese population can accurately identify patients with CKD at high risk of progressing to kidney failure. An online version of the model can be easily and quickly applied in clinical management and treatment.

Abstract Chromosomal instability (CIN) is closely associated to the early detection of several clinical tumours. In this study, the authors first established a novel prognostic model of melanoma using the hub genes of CIN, based on the datasets of The cancer genome atlas‐skin cutaneous melanoma (TCGA‐SKCM) and GSE65904 cohorts. Based on the risk scores of our model, the disease‐specific survival (DSS) prognosis was worse in the high‐risk group. Combining risk score, stage, age, ulceration, and clark factors, a Nomogram was generated to predict 1, 3, 5‐year survival rates, which indicated a good clinical validity. Our finding also showed a correlation between high/low risk and tumour infiltration levels of ‘activated CD8 T cells’ and ‘effector memory CD8 T cells’. Moreover, the authors first performed a CIN‐based tumour clustering analysis using TCGA‐SKCM cases, and identified two melanoma clusters, which exhibit the distinct DSS prognosis and the tumour‐infiltrating levels of CD8 T cells. Taken together, a promising CIN‐related prognostic signature and clustering for melanoma cases were first established in our study.

Abstract Acute myeloid leukemia is the most common acute leukemia in adults, the barrier of refractory and drug resistance has yet to be conquered in the clinical. Abnormal gene expression and epigenetic changes play an important role in pathogenesis and treatment. A super-enhancer is an epigenetic modifier that promotes pro-tumor genes and drug resistance by activating oncogene transcription. Multi-omics integrative analysis identifies the super-enhancer-associated gene CAPG and its high expression level was correlated with poor prognosis in AML. CAPG is a cytoskeleton protein but has an unclear function in AML. Here we show the molecular function of CAPG in regulating NF-κB signaling pathway by proteomic and epigenomic analysis. Knockdown of Capg in the AML murine model resulted in exhausted AML cells and prolonged survival of AML mice. In conclusion, SEs-associated gene CAPG can contributes to AML progression through NF-κB.

Ribosome biogenesis is a fundamental process in eukaryotic cells. NOTCHLESS (NLE) is involved in 60S ribosome biogenesis in yeast, but its role in Arabidopsis (A. thaliana) remains exclusive. Here, we found that Arabidopsis NLE (AtNLE) is highly conservative in phylogeny, which encoding a WD40-repeat protein. AtNLE is expressed in actively dividing tissues. AtNLE-GFP is localized in the nucleus. AtNLE physically interacts with the MIDAS domain of AtMDN1, a protein involved in the biogenesis of the 60S ribosomal subunit in Arabidopsis. The underexpressing mutant nle-2 shows short roots and reduced cell number in the root meristem. In addition, the null mutant nle-1 is embryo lethal, and defective embryos are arrested at the early globular stage. This work suggests that AtNLE interacts with AtMDN1, and AtNLE functions in root and embryo development.

Diabetes mellitus (DM) aggravates periodontitis, resulting in accelerated periodontal bone resorption. Disordered glucose metabolism in DM causes reactive oxygen species (ROS) overproduction resulting in compromised bone healing, which makes diabetic periodontal bone regeneration a major challenge. Inspired by the natural bone healing cascade, a mesoporous silica nanoparticle (MSN)-incorporated PDLLA (poly(dl-lactide))-PEG-PDLLA (PPP) thermosensitive hydrogel with stepwise cargo release is designed to emulate the mesenchymal stem cell “recruitment-osteogenesis” cascade for diabetic periodontal bone regeneration. During therapy, SDF-1 quickly escapes from the hydrogel due to diffusion for early rat bone marrow stem cell (rBMSC) recruitment. Simultaneously, slow degradation of the hydrogel starts to gradually expose the MSNs for sustained release of metformin, which can scavenge the overproduced ROS under high glucose conditions to reverse the inhibited osteogenesis of rBMSCs by reactivating the AMPK/β-catenin pathway, resulting in regulation of the diabetic microenvironment and facilitation of osteogenesis. In vitro experiments indicate that the hydrogel markedly restores the inhibited migration and osteogenic capacities of rBMSCs under high glucose conditions. In vivo results suggest that it can effectively recruit rBMSCs to the periodontal defect and significantly promote periodontal bone regeneration under type 2 DM. In conclusion, our work provides a novel therapeutic strategy of a bioinspired drug-delivery system emulating the natural bone healing cascade for diabetic periodontal bone regeneration.

Accurately segmenting building roofs from satellite images is crucial for evaluating the photovoltaic power generation potential of urban roofs and is a worthwhile research topic. In this study, we propose an attention-based full-scale fusion (AFSF) network to segment a roof mask from the given satellite images. By developing an attention-based residual ublock, the channel relationship of the feature maps can be modeled. By integrating attention mechanisms in multi-scale feature fusion, the model can learn different weights for features of different scales. We also design a ladder-like network to utilize weakly labeled data, thereby achieving pixel-level semantic segmentation tasks assisted by image-level classification tasks. In addition, we contribute a new roof segmentation dataset, which is based on satellite images and uses the roof as the segmentation target rather than the entire building to further promote the algorithm research of estimating roof area using satellite images. The experimental results on the new roof segmentation dataset, WHU dataset, and IAIL dataset demonstrate the effectiveness of the proposed network.

A knowledge graph is a structured semantic network designed to describe physical entities and relations in the world. A comprehensive and accurate knowledge graph is essential for tasks such as knowledge inference and recommendation systems, making link prediction a popular problem for knowledge graph completion. However, existing approaches struggle to model complex relations among entities, which severely hampers their ability to complete knowledge graphs effectively. To address this challenge, we propose a novel hierarchical multi-head attention network embedding framework, called RiQ-KGC, which integrates different-grained contextual information of knowledge graph triples and models quaternion rotation relations between entities. Furthermore, we propose a relation instantiation method for alleviating the difficulty of expressing complex relations between entities. To enhance the expressiveness of relation representation, the relation is integrated by Transformer to obtain multi-hop neighbor information, so that one relation can be embedded into different embeddings according to different entities. Experimental results on four datasets demonstrate that RiQ-KGC exhibits strong competitiveness compared to state-of-the-art models in link prediction, while the ablation experiments reveal that the proposed relation instantiation method achieves great performance.

As an important farmed fish, tilapia has poor tolerance to low-temperatures. At the same time, different tilapia strains have apparent differences in low-temperature tolerance. In this study, using the iTRAQ method, the phosphorylated proteomics of two tilapia strains (Oreochromis niloticus and Oreochromis aureus) with different tolerances to low-temperature stress were quantitatively and comparatively analyzed, to clarify the physiological mechanism of tilapia’s response to low-temperature stress. Through the GO and IPR analyses of differentially phosphorylated proteins, a number of similarities in physiological activities and regulatory effects were found between the two tilapias in response to low-temperature stress. Many differentially phosphorylated proteins are mainly involved in lipid metabolism, cell proliferation and apoptosis. However, the difference in endurance of low temperature of these two tilapias might be related to the differences in categories, expression and modification level of genetic products which were involved in the aforementioned physiological processes. And meanwhile, the enrichment results of KEGG showed the changes of multiple immune-related and growth-related phosphorylated proteins in the cytokine-cytokine receptor interaction pathway in O. aureus are more prominent. Furthermore, the significantly enriched pathway of carbohydrate digestion and absorption in O. niloticus may indicate that low-temperature stress exerts a more severe impact on energy metabolism. The relative results would help elucidating the molecular mechanism by which tilapia responds to low-temperature stress, and developing culture of tilapia species.

To meet the ever-increasing demand for next-generation lithography machines, the actuator plays an important role in the achievement of high acceleration of the wafer stage. However, the voice coil motor, which is widely used in high-precision positioning systems, is reaching its physical limits. To tackle this problem, a novel way to design the actuator using the magnetoresistance effect is argued due to the high force densities. However, the strong nonlinearity limits its application in the nan-positioning system. In particular, the hysteresis is coupled with eddy effects and displacement, which lead to a rate-dependent and displacement-dependent hysteresis effect in the reluctance actuator. In this paper, a Hammerstein structure is used to model the rate-dependent reluctance actuator. At the same time, the displacement-dependent of the model is regarded as the interference with the system. Additionally, a control strategy combining inverse model compensation and the disturbance observer-based discrete sliding mode control was proposed, which can effectively suppress the hysteresis effect. It is worthy pointing out that the nonlinear system is transformed into a linear system with inversion bias and disturbance by the inverse model compensation. What is more, the sliding mode controller based on the disturbance observer is designed to deal with the unmodeled dynamics, displacement disturbances, and model identification errors in linear systems. Thus, the tracking performance and robustness to external disturbances of the system are improved. The simulation results show that it is superior to the PI controller combined with an inverse compensator and even to the discrete sliding mode controller connected with inverse compensator, confirming the effectiveness of the novel control method in alleviating hysteresis.

The immersed boundary–lattice Boltzmann (IB-LB) coupling scheme is known as an efficient scheme for fluid–structure interactions (FSIs). However, the conventional IB-LB schemes suffer from instability because they involve a high-Reynolds-number flow or a larger stiffness structure. An averagely weighted iteration approach is presented to improve the stability restriction in this paper. This new approach, which improves the stability by mitigating the high-frequency fluctuations, is implemented by iteratively calculating the external force, and averagely weighting the force obtained at every iterative step. Five cases are simulated to verify the accuracy and effectiveness of the present approach. Under the premise of maintaining the accuracy of the conventional IB-LB method, the implementation of the present approach can significantly enhance the numerical stability. Compared with the conventional IB-LB method, the present approach can significantly expand the material parameter range for simulation; in particular, this approach qualitatively improves the upper limit of the bending rigidity coefficient by approximately 8000 times. To use the outstanding stability of the present approach, the IB inertia force can be directly incorporated into the simulation. In addition, under the low-viscosity condition, the present approach can effectively simulate the large-deformation FSI problem.

Ophiocordyceps sinensis exhibits more than 5 months of vegetative growth in Thitarodes xiaojinensis hemocoel. The peculiar development process of O. sinensis has been elucidated through morphological observation and omics technology; however, little information has been reported regarding the changes that occur in the host T. xiaojinensis. The RNA sequencing data showed that when O. sinensis blastospores were in the proliferative stage, the greatest change in the infected larval fat body was the selectively upregulated immune recognition and antimicrobial peptide genes. When O. sinensis blastospores were in the stationary stage, the immune pathways of T. xiaojinensis reverted to normal levels, which coincides with the successful settlement of O. sinensis. Pathway enrichment analysis showed a higher expression of genes involved in energy metabolism pathway in this stage. Metabolomic analyses revealed a reduction of amino acids and lipids in hemolymph, but an upregulation of lipids in the fat body of the host larvae after O. sinensis infection. We present the first transcriptome integrated with the metabolome study of T. xiaojinensis infected by O. sinensis. It will improve our understanding of the interaction mechanisms between the host and entomopathogenic fungi, and facilitate future functional studies of genes and pathways involved in these interactions.

Bidirectional DNA replication complexes initiated from the same origin remain colocalized in a factory configuration for part or all their lifetimes. However, there is little evidence that sister replisomes are functionally interdependent, and the consequence of factory replication is unknown. Here, we investigated the functional relationship between sister replisomes in Escherichia coli, which naturally exhibits both factory and solitary configurations in the same replication cycle. Using an inducible transcription factor roadblocking system, we found that blocking one replisome caused a significant decrease in overall progression and velocity of the sister replisome. Remarkably, progression was impaired only if the block occurred while sister replisomes were still in a factory configuration – blocking one fork had no significant effect on the other replisome when sister replisomes were physically separate. Disruption of factory replication also led to increased fork stalling and requirement of fork restart mechanisms. These results suggest that physical association between sister replisomes is important for establishing an efficient and uninterrupted replication program. We discuss the implications of our findings on mechanisms of replication factory structure and function, and cellular strategies of replicating problematic DNA such as highly transcribed segments.

It is very challenging to visualize implantable medical devices made of biodegradable polymers in deep tissues. Herein, we designed a novel macromolecular contrast agent with ultrahigh radiopacity (iodinate content > 50%) via polymerizing an iodinated trimethylene carbonate monomer into the two ends of poly(ethylene glycol) (PEG). A set of thermosensitive and biodegradable polyester-PEG-polyester triblock copolymers with varied polyester compositions synthesized by us, which were soluble in water at room temperature and could spontaneously form hydrogels at body temperature, were selected as the demonstration materials. The addition of macromolecular contrast agent did not obviously compromise the injectability and thermogelation properties of polymeric hydrogels, but conferred them with excellent X-ray opacity, enabling visualization of the hydrogels at clinically relevant depths through X-ray fluoroscopy or Micro-CT. In a mouse model, the 3D morphology of the radiopaque hydrogels after injection into different target sites was visible using Micro-CT imaging, and their injection volume could be accurately obtained. Furthermore, the subcutaneous degradation process of a radiopaque hydrogel could be non-invasively monitored in a real-time and quantitative manner. In particular, the corrected degradation curve based on Micro-CT imaging well matched with the degradation profile of virgin polymer hydrogel determined by the gravimetric method. These findings indicate that the macromolecular contrast agent has good universality for the construction of various radiopaque polymer hydrogels, and can nondestructively trace and quantify their degradation in vivo. Meanwhile, the present methodology developed by us affords a platform technology for deep tissue imaging of polymeric materials.

The respiratory rate (RR) serves as a critical physiological parameter in the context of both diagnostic and prognostic evaluations. Due to the challenges of direct measurement, RR is still predominantly measured through the traditional manual counting-breaths method in clinic practice. Numerous algorithms and machine learning models have been developed to predict RR using physiological signals, such as electrocardiogram (ECG) or/and photoplethysmogram (PPG) signals. Yet, the accuracy of these existing methods on available datasets remains limited, and their prediction on new data is also unsatisfactory for actual clinical applications. In this paper, we proposed an enhanced Transformer model with inception blocks for predicting RR based on both ECG and PPG signals. To evaluate the generalization capability on new data, our model was trained and tested using subject-level ten-fold cross-validation using data from both BIDMC and CapnoBase datasets. On the test set, our model achieved superior performance over five popular deep-learning-based methods with mean absolute error (1.2) decreased by 36.5% and correlation coefficient (0.85) increased by 84.8% compared to the best results of these models. In addition, we also proposed a new pipeline to preprocess ECG and PPG signals to improve model performance. We believe that the development of the TransRR model is expected to further expedite the clinical implementation of automatic RR estimation.

The influence of landscape structure on species communities is intimately connected to the spatial scales at which measurements are made. If we do not measure landscape structure at its most impactful scale, otherwise known as the “scale of effect”, we might fail to detect crucial community–landscape relationships. In our study, we focused on the “scale of effect” as it pertains to the relationship between urban bird diversity and landscape structure. We investigated eight types of landscape structure variables alongside elevation attributes across 16 spatial scales around 28 sampling sites in Kunming, Yunnan Province, China. Our objective was to identify the most influential scale at which the environmental variables under investigation affect the taxonomic and functional diversity of bird species. We utilized PLSR and VIP scores to overcome challenges posed by multicollinearity among predictors. We found that the influence of landscape characteristics on bird species richness and functional dispersion index (FDis) was scale-dependent. Notably, the influence of the area of open water on FDis is most pronounced at smaller scales, while at larger scales, open water dispersion becomes more essential. Additionally, in a highly fragmented urban matrix, the importance of forest connectivity may exceed that of patch size at medium scales. However, the significance of forest coverage increases with scale, which underscores the importance of preservation efforts at larger scales to prevent forest fragmentation. We also noted a considerable impact from landscape-level subdivision across almost all scales. These findings highlight the importance of shifting urban conservation planning towards a multi-scale approach, which would allow for the identification of priority intervention scales.

Long-term high stocking density often brings negative effects such as decreased body weight, decreased immunity, and increased mortality to cultured fish, while the effects of short-term stocking are relatively less studied. In this experiment, we characterized spatial and temporal gene expression in black porgy (Acanthopagrus schlegelii) liver by establishing two stocking density groups—high (H: 26.5 kg/m3) and low (L: 2.95 kg/m3)—and conducting transcriptome sequencing before collecting liver samples at two time points: 6 h (AL and AH) and 60 d (CL and CH) into the culture trial. There were 648 and 550 differentially expressed genes (DEGs) in the AL-vs-AH and CL-vs-CH groups, respectively. The DEGs in the AL-vs-AH group were significantly enriched in steroid biosynthesis, terpenoid backbone biosynthesis, the PPAR signaling pathway, proteasome, aminoacyl-tRNA biosynthesis, and ribosome biogenesis in eukaryotes. The DEGs in the CL-vs-CH group were more significantly enriched in lipid metabolism-related pathways, such as the PPAR signaling pathway, fatty acid metabolism, and cholesterol metabolism. In addition, immune-related pathways such as the phagosome and complement and coagulation cascades were also enriched in the CL-vs-CH group. The expression changes concerning the DEGs in each group were further analyzed. The DEGs related to steroid synthesis, protein synthesis, and the degradation pathways were down-regulated, but immune-related genes were generally up-regulated in the AH group. The DEGs related to lipid synthesis were significantly up-regulated in the CH group, but the DEGs related to lipid consumption and utilization were down-regulated. The expression of immune-related DEGs was also negatively affected in the CH group. These results suggest that acute and chronic crowding stress affects lipid metabolism and immune regulation in the liver of black porgy. Acute stress particularly affected hepatic protein metabolism, while chronic stress showed more effects on hepatic lipid metabolism. The results of this study provide a theoretical basis for understanding the effects of high stocking densities upon black porgy and may also provide a reference for crowding stress regulation studies in other fish species.

Zhang et al. design ginsenoside structural analogues and demonstrate that their combination shows more potent immunomodulatory activities than individual ginsenosides used alone at the same dosages. They predict that these analogues act on the joint target NLRP3 and consequently suggest that structural analogues hit a shared target to achieve cumulative bioactivity.

It is important to further enhance the performance of green and efficient non-homogeneous catalysts for advanced oxidation process of Peroxymonosulfate (PMS-AOP) for green treatment of industrial wastewater. In this paper, nitrogen–sulfur co-doped MOFs-derived carbon material (CoSN@C) was prepared by one-pot synthesis followed by carbonization, and its morphological structure was characterized by XRD and SEM. After pyrolysis, the CoSN@C still maintained the dodecahedral morphology and structure of ZIF-67. The synergistic effects of S and N significantly elevated the activation of PMS. The results show that the CoSN@C + PMS system can effectively activate PMS to degrade Rhodamine B (RhB), with a rate constant (1.85 min−1) four times higher than that of the CoN@C + PMS system (0.44 min−1). The optimal catalytic process parameters of material dosage, PMS concentration, temperature, pH, and other parameters were also investigated for the activation of PMS to remove Rhodamine B. The cyclic experiment shows that the CoSN@C has excellent recyclability and the degradation rate of RhB still reached 88.9% after four cycles. Radical capture experiments and EPR tests showed that the CoSN@C + PMS system generated a large amount of SO4·− and ·OH radicals adsorbed on the catalyst surface and a certain amount of singlet oxygen, and the free radical pathway and non-radical pathway worked together to degrade RhB efficiently and rapidly. While non-radical pathway with singlet oxygen as main reactive oxygen species played a key role in the CoN@C + PMS system. This work provides a new idea for the rational design of non-homogeneous catalysts for PMS-AOP system.

Several studies have revealed that urban rivers with relatively complete habitat structures can support a high level of biodiversity in urban areas. However, few studies have analyzed the impact of the plan, design, and management of multi-scale urban riverside green space on bird communities by assessing several aspects of diversity (e.g., taxonomic and functional). In this study, we explored bird community variation (taxonomic and functional) among three rivers (28 sampling sites) with different levels of human disturbance along the urban development gradient in Kunming, Yunnan Province, China, during an annual cycle. This study related bird species richness and functional diversity to environmental variables at three spatial scales: landscape metrics at two different landscape scales (500 and 100 m radius) and vegetation structure at patch scales (20 m radius). Using partial least squares regression (PLSR) and multiple linear regression, we found that bird species richness and functional diversity were strongly related to various landscape- and patch-level variables. Multiple linear regression models revealed that, compared with the richness influenced by explanatory variables on three spatial scales (500, 100, and 20 m), the functional diversity was significantly influenced by explanatory variables on the 100 and 20 m scales. Tree cover at the 20 m scale had significantly positive impacts on bird species richness and functional diversity. Forest land in the 100 m scale had a significantly positive effect on bird species richness and functional diversity, while construction land in the two landscape scales (the 500- and 100 m scales) had a significantly negative effect on species richness. Accordingly, we suggest that urban riverside green space should be planned and managed at multiple scales.

Abstract Background Asthma is one of the main intractable diseases recognized by the international medical community. The current widely used bronchodilators for asthma—β2-adrenal receptor agonists—have limited therapeutic effects, necessitating the development of novel antiasthma drugs with increased efficacy and fewer adverse effects. In this study, we investigated the relaxant effects and underlying mechanism of an ethyl acetate extract from dandelion (EAED) on mouse airway smooth muscle. Methods The effects of EAED on agonist-induced precontraction in mouse airway smooth muscle were evaluated with force measurement. Mouse lung slices were used to study the effects of EAED on bronchial smooth muscle. The intracellular Ca2+ concentration was measured using a calcium imaging system. L-type voltage-dependent calcium channel (VDLCC) and non-selective cationic channel (NSCC) currents were measured by patch-clamp. The lung functions of healthy and asthmatic mouse groups were assessed via the forced oscillation technique. Results EAED inhibits acetylcholine-induced sustained contractions of whole airway smooth muscle by inhibiting VDLCCs, NSCCs, and some unknown channels, reduces the agonist-induced increase in the cytosolic free Ca2+ concentration in airway smooth muscle cells, blocks VDLCC and NSCC currents, and relieves the respiratory resistance of healthy and asthmatic mice. Conclusions EAED may have potential beneficial effects on mitigating asthma attacks.

A judgment method of the final setting time of mass concrete based on strain monitoring and the selection criterion of the starting point of effective deformation are proposed, and the safety of the concrete structure is evaluated based on this. Firstly, the strain monitoring theory of mass concrete is analyzed to clarify the temperature effect component and monitoring mechanism of an early strain of concrete. Then, taking the mass concrete plate of an engineering project as the research object combined with the mechanical analysis, the early strain monitoring data are segmented, and the relationship between the strain response and the temperature in different stages is fitted based on robust regression, so as to explore the correlation between strain and temperature in each stage and better explain the setting process of the concrete structure. Finally, taking the final setting time as the starting point of the effective strain, the safety of the concrete structure is further evaluated. The results show that there is a clear linear relationship between the strain response and temperature, and a high negative correlation between strain and temperature after the final setting. The time point when the frequency modulus corresponding to the strain enters a steady change and decreases with the increase of temperature is taken as the final setting time, which conforms to the concrete condensation mechanism and the temperature effect of early strain monitoring.

Androgen receptor (AR) signaling is essential for maintaining spermatogenesis and male fertility. However, the molecular mechanisms by which AR acts between male germ cells and somatic cells during spermatogenesis have not begun to be revealed until recently. With the advances obtained from the use of transgenic mice lacking AR in Sertoli cells (SCARKO) and single-cell transcriptomic sequencing (scRNA-seq), the cell specific targets of AR action as well as the genes and signaling pathways that are regulated by AR are being identified. In this study, we collected scRNA-seq data from wild-type (WT) and SCARKO mice testes at p20 and identified four somatic cell populations and two male germ cell populations. Further analysis identified that the distribution of Sertoli cells was completely different and uncovered the cellular heterogeneity and transcriptional changes between WT and SCARKO Sertoli cells. In addition, several differentially expressed genes (DEGs) in SCARKO Sertoli cells, many of which have been previously implicated in cell cycle, apoptosis and male infertility, have also been identified. Together, our research explores a novel perspective on the changes in the transcription level of various cell types between WT and SCARKO mice testes, providing new insights for the investigations of the molecular and cellular processes regulated by AR signaling in Sertoli cells.

Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I–VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.

Secondary structure plays an important role in determining the function of noncoding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA secondary structure. Unfortunately, even though new methods have been proposed over the past 40 years, the performance of computational prediction methods has stagnated in the last decade. Recently, with the increasing availability of RNA structure data, new methods based on machine learning (ML) technologies, especially deep learning, have alleviated the issue. In this review, we provide a comprehensive overview of RNA secondary structure prediction methods based on ML technologies and a tabularized summary of the most important methods in this field. The current pending challenges in the field of RNA secondary structure prediction and future trends are also discussed.

N6-methyladenosine (m6A) RNA modification is the most common internal mRNA modification in mammals and has been reported to play a key role in gene expression regulation. In this study, we detected a high level of m6A methylation of the PLOD2 3′-untranslated regions (3′UTR) in renal cell carcinoma (RCC). Furthermore, we found that the high expression level of PLOD2 was a prognostic indicator for patients with RCC. A dm6ACRISPR demethylation system was performed to accurately and specifically demethylate 3′UTR of PLOD2 and caused an inactivation of PLOD2 expression. Furthermore, we also performed many in vitro experiments to confirm that PLOD2 exerted tumor promoter effects by promoting tumor proliferation and migration. In conclusion, PLOD2 mRNA demethylated by dCas13b-ALKBH5 might provide a new light on the treatment for RCC.

Background: The supplementation of betaine, an osmoprotective compatible solute, in the cultivation media has been widely used to protect bacterial cells. To explore the effects of betaine addition on industrial fermentation, Escherichia coli THRD, an l-threonine producer, was used to examine the production of l-threonine with betaine supplementation and the underlying mechanism through which betaine functions was investigated. Results: Betaine supplementation in the medium of E. coli THRD significantly improved l-threonine fermentation parameters. The transcription of zwf and corresponding enzyme activity of glucose-6-phosphate dehydrogenase were significantly promoted by betaine addition, which contributed to an enhanced expression of zwf that provided more nicotinamide adenine dinucleotide phosphate (NADPH) for l-threonine synthesis. In addition, as a result of the betaine addition, the betaine-stimulated expression of enhanced green fluorescent protein (eGFP) under the zwf promoter within a plasmid-based cassette proved to be a transcription-level response of zwf. Finally, the promoter of the phosphoenolpyruvate carboxylase gene ppc in THRD was replaced with that of zwf, while l-threonine fermentation of the new strain was promoted by betaine addition. Conclusions: We reveal a novel mode of betaine that facilitates the microbial production of useful compounds. Betaine supplementation upregulates the expression of zwf and increases the NADPH synthesis, which may be beneficial for the cell growth and thereby promote the production of l-threonine. This finding might be useful for the production of NADPH-dependent amino acids and derivatives in E. coli THRD or other E. coli strains.How to cite: Li Y, Zhang D, Cai N, et al. Betaine supplementation improved l-threonine fermentation of Escherichia coli THRD by upregulating zwf (glucose-6-phosphate dehydrogenase) expression. Electron J Biotechnol 2019;39. https://doi.org/10.1016/j.ejbt.2019.03.004. Keywords: Betaine, Escherichia coli THRD, Escherichia coli, Industrial fermentation, l-Threonine producer, l-Threonine, NADPH, Osmoprotective compatible solute, Pentose phosphate pathway, zwf

Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.

BackgroundCD4+ T cells play multiple roles in controlling tumor growth and increasing IFN-γ+ T-helper 1 cell population could promote cell-mediated anti-tumor immune response. We have previously showed that low-dose DNA demethylating agent decitabine therapy promotes CD3+ T-cell proliferation and cytotoxicity; however, direct regulation of purified CD4+ T cells and the underlying mechanisms remain unclear.MethodsThe effects of low-dose decitabine on sorted CD4+ T cells were detected both in vitro and in vivo. The activation, proliferation, intracellular cytokine production and cytolysis activity of CD4+ T cells were analyzed by FACS and DELFIA time-resolved fluorescence assays. In vivo ubiquitination assay was performed to assess protein degradation. Moreover, phosphor-p65 and IκBα levels were detected in sorted CD4+ T cells from solid tumor patients with decitabine-based therapy.ResultsLow-dose decitabine treatment promoted the proliferation and activation of sorted CD4+ T cells, with increased frequency of IFN-γ+ Th1 subset and enhanced cytolytic activity in vitro and in vivo. NF-κB inhibitor, BAY 11-7082, suppressed decitabine-induced CD4+ T cell proliferation and IFN-γ production. In terms of mechanism, low-dose decitabine augmented the expression of E3 ligase β-TrCP, promoted the ubiquitination and degradation of IκBα and resulted in NF-κB activation. Notably, we observed that in vitro low-dose decitabine treatment induced NF-κB activation in CD4+ T cells from patients with a response to decitabine-primed chemotherapy rather than those without a response.ConclusionThese data suggest that low-dose decitabine potentiates CD4+ T cell anti-tumor immunity through enhancing IκBα degradation and therefore NF-κB activation and IFN-γ production.

Optogenetic systems have been increasingly investigated in the field of biomedicine. Previous studies had found the inhibitory effect of the light-inducible genetic circuits on cancer cell growth. In our study, we applied an AND logic gates to the light-inducible genetic circuits to inhibit the cancer cells more specifically. The circuit would only be activated in the presence of both the human telomerase reverse transcriptase (hTERT) and the human uroplakin II (hUPII) promoter. The activated logic gate led to the expression of the p53 or E-cadherin protein, which could inhibit the biological function of tumor cells. In addition, we split the dCas9 protein to reduce the size of the synthetic circuit compared to the full-length dCas9. This light-inducible system provides a potential therapeutic strategy for future bladder cancer.

Myeloid cells, including monocytes/macrophages, primarily rely on glucose and lipid metabolism to provide the energy and metabolites needed for their functions and survival. AMP-activated protein kinase (AMPK, its gene is PRKA for human, Prka for rodent) is a key metabolic sensor that regulates many metabolic pathways. We studied recruitment and viability of Prkaa1-deficient myeloid cells in mice and the phenotype of these mice in the context of cardio-metabolic diseases. We found that the deficiency of Prkaa1 in myeloid cells downregulated genes for glucose and lipid metabolism, compromised glucose and lipid metabolism of macrophages, and suppressed their recruitment to adipose, liver and arterial vessel walls. The viability of macrophages in the above tissues/organs was also decreased. These cellular alterations resulted in decreases in body weight, insulin resistance, and lipid accumulation in liver of mice fed with a high fat diet, and reduced the size of atherosclerotic lesions of mice fed with a Western diet. Our results indicate that AMPKα1/PRKAA1-regulated metabolism supports monocyte recruitment and macrophage viability, contributing to the development of diet-induced metabolic disorders including diabetes and atherosclerosis.

The vasa gene is essential for germ cell development and gametogenesis both in vertebrates and in invertebrates. In the present study, vasa (Rcvasa) cDNA was cloned from cobia (Rachycentron canadum) using the RACE amplification method. We found that the full-length cDNA sequence of Rcvasa comprises 2571 bp, containing a 5′-UTR of 145 bp, a 3′-UTR of 341 bp, and an open reading frame (ORF) of 2085 bp, encoding a protein of 694 aa. The deduced amino acid sequence contains 8 conserved motifs of the DEAD-box protein family, 7 RGG repeats, and 10 RG repeats in the N-terminal region. Comparisons of the deduced amino acid sequence with those of other teleosts revealed the highest percentage identity (86.0%) with Seriola quinqueradiata. By using semiquantitative RT-PCR, Rcvasa appeared to be specifically expressed in the testis and ovary, among 13 tissues analyzed. In addition, annual changes in Rcvasa expression levels were examined in the gonads by quantitative real-time PCR (qRT-PCR). The expression of Rcvasa in the testis first increased significantly at 120 dph (stage II–III), then stabilized as the testis developed from 185 dph (stage III) to 360 dph (stage V). During the development of the ovary (stage I to II), the expression of Rcvasa first increased and reached the highest level at 210 dph (stage II), then decreased. Furthermore, the results of chromogenic in situ hybridization (CISH) revealed that Rcvasa mRNA was mainly expressed in germ cells and barely detected in somatic cells. In the testis, Rcvasa mRNA signal was concentrated in the periphery of spermatogonia, primary spermatocytes, and secondary spermatocytes and was significantly weaker in spermatids and spermatozoa. In the ovary, Rcvasa mRNA signal was uniformly distributed in the perinuclear cytoplasm and was intense in early primary oocytes (stage I and II). These findings could provide a reference for understanding the regulatory mechanisms of vasa expression during the development of germ cells in cobia.

Quantifying cell-type proportions and their corresponding gene expression profiles in tissue samples would enhance understanding of the contributions of individual cell types to the physiological states of the tissue. Current approaches that address tissue heterogeneity have drawbacks. Experimental techniques, such as fluorescence-activated cell sorting, and single cell RNA sequencing are expensive. Computational approaches that use expression data from heterogeneous samples are promising, but most of the current methods estimate either cell-type proportions or cell-type-specific expression profiles by requiring the other as input. Although such partial deconvolution methods have been successfully applied to tumor samples, the additional input required may be unavailable. We introduce a novel complete deconvolution method, CDSeq, that uses only RNA-Seq data from bulk tissue samples to simultaneously estimate both cell-type proportions and cell-type-specific expression profiles. Using several synthetic and real experimental datasets with known cell-type composition and cell-type-specific expression profiles, we compared CDSeq's complete deconvolution performance with seven other established deconvolution methods. Complete deconvolution using CDSeq represents a substantial technical advance over partial deconvolution approaches and will be useful for studying cell mixtures in tissue samples. CDSeq is available at GitHub repository (MATLAB and Octave code): https://github.com/kkang7/CDSeq.

Summary: Yin Yang 1 (YY1) regulates early embryogenesis and adult tissue formation. However, the role of YY1 in stem cell regulation remains unclear. YY1 has a Polycomb group (PcG) protein-dependent role in mammalian cells. The PcG-independent functions of YY1 are also reported, although their underlying mechanism is still undefined. This paper reports the role of YY1 and BAF complex in the OCT4-mediated pluripotency network in mouse embryonic stem cells (mESCs). The interaction between YY1 and BAF complex promotes mESC proliferation and pluripotency. Knockdown of Yy1 or Smarca4, the core component of the BAF complex, downregulates pluripotency markers and upregulates several differentiation markers. Moreover, YY1 enriches at both promoter and super-enhancer regions to stimulate transcription. Thus, this study elucidates the role of YY1 in regulating pluripotency through its interaction with OCT4 and the BAF complex and the role of BAF complex in integrating YY1 into the core pluripotency network. : In this article, Junjun Ding and colleagues show the role of YY1 in regulating embryonic stem cells through its interaction with OCT4 and the BAF complex to activate transcription, promote ESC proliferation, and maintain pluripotency, and the role of BAF complex in integrating YY1 into the core pluripotency network. Keywords: YY1, polycomb, the BAF complex, super-enhancer, pluripotency, Oct4, interactome, cell cycle

Systems metabolic engineering is a multidisciplinary area that integrates systems biology, synthetic biology and evolutionary engineering. It is an efficient approach for strain improvement and process optimization, and has been successfully applied in the microbial production of various chemicals including amino acids. In this review, systems metabolic engineering strategies including pathway-focused approaches, systems biology-based approaches, evolutionary approaches and their applications in two major amino acid producing microorganisms: Corynebacterium glutamicum and Escherichia coli, are summarized.

The rapid development of synthetic biology has conferred almost perfect modification on single cells, and provided methodological support for synthesizing microbial consortia, which have a much wider application potential than synthetic single cells. Co-cultivating multiple cell populations with rational strategies based on interacting relationships within natural microbial consortia provides theoretical as well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding of natural microbial consortia. According to their composition complexity, synthetic microbial consortia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc.

Acquired therapeutic resistance by tumors is a substantial impediment to reducing the morbidity and mortality that are attributable to human malignancies. The mechanisms responsible for the dramatic shift between chemosensitivity and chemoresistance in colorectal carcinoma have not been defined. Here, we report that LRP16 selectively interacts and activates double-stranded RNA-dependent kinase (PKR), and also acts as scaffolds to assist the formation of a ternary complex of PKR and IKKβ, prolonging the polymers of ADP-ribose (PAR)-dependent nuclear factor kappa B (NF-κB) transactivation caused by DNA-damaging agents and confers acquired chemoresistance. We also identified a small molecule, MRS2578, which strikingly abrogated the binding of LRP16 to PKR and IKKβ, converting LRP16 into a death molecule and forestalling colon tumorigenesis. Inclusion of MRS2578 with etoposide, versus each drug alone, exhibited synergistic antitumor cytotoxicity in xenografts. Our combinatorial approach introduces a strategy to enhance the efficacy of genotoxicity therapies for the treatment of tumors.

Experience-dependent plasticity shapes postnatal development of neural circuits, but the mechanisms that refine dendritic arbors, remodel spines, and impair synaptic activity are poorly understood. Mature brain-derived neurotrophic factor (BDNF) modulates neuronal morphology and synaptic plasticity, including long-term potentiation (LTP) via TrkB activation. BDNF is initially translated as proBDNF, which binds p75NTR. In vitro, recombinant proBDNF modulates neuronal structure and alters hippocampal long-term plasticity, but the actions of endogenously expressed proBDNF are unclear. Therefore, we generated a cleavage-resistant probdnf knockin mouse. Our results demonstrate that proBDNF negatively regulates hippocampal dendritic complexity and spine density through p75NTR. Hippocampal slices from probdnf mice exhibit depressed synaptic transmission, impaired LTP, and enhanced long-term depression (LTD) in area CA1. These results suggest that proBDNF acts in vivo as a biologically active factor that regulates hippocampal structure, synaptic transmission, and plasticity, effects that are distinct from those of mature BDNF.

Wetlands play an important role in the feeding, breeding, and lives of birds. However, available habitats for bird species are changing due to intensifying human activity, especially in the context of China’s mass urbanization. Urban sprawl has taken over the wetlands along the lakes in the past decades, which places tremendous pressure on wetland ecosystems and, therefore, on bird communities. However, the ways urban land cover pattern along the urban-rural gradient affects bird communities is still unclear. To investigate the influence of land cover pattern on the α and β diversity of birds in the urban-rural gradient we chose 31 sites distributed within the wetlands around the Dianchi Lake in Yunnan, China. We calculated the species richness to indicate α diversity and used the Morisita−Horn index to indicate β diversity. Meanwhile, we assessed the land cover pattern of each site by measuring the proportion of emergent plants, floating plants, submerged plants, ponds, forests, lawns, roads, agricultural lands and built lands in a quadrat of 1 square kilometer. Simple linear regressions, model selection, and an averaging approach based on corrected Akaike information criterion (AICc) were used to test the effects of land cover pattern on bird diversity. Using one-way ANOVA and Tukey’s HSD (honestly significant difference) test, we compared the difference between α and β diversity, respectively, along the urban-rural gradient. Based on our analyses, urban and suburban wetland birds were significantly homogeneous. The community structure in rural wetlands, however, was significantly different from that of the suburban and urban areas. According to our research, the land cover patterns that influenced bird species richness were the built lands acreage, submerged plants acreage, ponds acreage, and the edge density of emergent plants. Meanwhile, of these variables, the built lands acreage, ponds acreage and edge density of emergent plants were significantly different in urban, suburban, and rural wetlands. Therefore, to maintain high biodiversity in wetlands affected by urbanization, we must pay more attention to the land cover patterns.

Abstract Background A "bidirectional gene pair" is defined as two adjacent genes which are located on opposite strands of DNA with transcription start sites (TSSs) not more than 1000 base pairs apart and the intergenic region between two TSSs is commonly designated as a putative "bidirectional promoter". Individual examples of bidirectional gene pairs have been reported for years, as well as a few genome-wide analyses have been studied in mammalian and human genomes. However, no genome-wide analysis of bidirectional genes for plants has been done. Furthermore, the exact mechanism of this gene organization is still less understood. Results We conducted comprehensive analysis of bidirectional gene pairs through the whole Arabidopsis thaliana genome and identified 2471 bidirectional gene pairs. The analysis shows that bidirectional genes are often coexpressed and tend to be involved in the same biological function. Furthermore, bidirectional gene pairs associated with similar functions seem to have stronger expression correlation. We pay more attention to the regulatory analysis on the intergenic regions between bidirectional genes. Using a hierarchical stochastic language model (HSL) (which is developed by ourselves), we can identify intergenic regions enriched of regulatory elements which are essential for the initiation of transcription. Finally, we picked 27 functionally associated bidirectional gene pairs with their intergenic regions enriched of regulatory elements and hypothesized them to be regulated by bidirectional promoters, some of which have the same orthologs in ancient organisms. More than half of these bidirectional gene pairs are further supported by sharing similar functional categories as these of handful experimental verified bidirectional genes. Conclusion Bidirectional gene pairs are concluded also prevalent in plant genome. Promoter analyses of the intergenic regions between bidirectional genes could be a new way to study the bidirectional gene structure, which may provide a important clue for further analysis. Such a method could be applied to other genomes.

Abstract Background Alternative splicing (AS) is an important regulatory mechanism for gene expression and protein diversity in eukaryotes. Previous studies have demonstrated that it can be causative for, or specific to splicing-related diseases. Understanding the regulation of AS will be helpful for diagnostic efforts and drug discoveries on those splicing-related diseases. As a novel exon-centric microarray platform, exon array enables a comprehensive analysis of AS by investigating the expression of known and predicted exons. Identifying of AS events from exon array has raised much attention, however, new and powerful algorithms for exon array data analysis are still absent till now. Results Here, we considered identifying of AS events in the framework of variable selection and developed a regression method for AS detection (REMAS). Firstly, features of alternatively spliced exons were scaled by reasonably defined variables. Secondly, we designed a hierarchical model which can represent gene structure and transcriptional influence to exons, and the lasso type penalties were introduced in calculation because of huge variable size. Thirdly, an iterative two-step algorithm was developed to select alternatively spliced genes and exons. To avoid negative effects introduced by small sample size, we ranked genes as parameters indicating their AS capabilities in an iterative manner. After that, both simulation and real data evaluation showed that REMAS could efficiently identify potential AS events, some of which had been validated by RT-PCR or supported by literature evidence. Conclusion As a new lasso regression algorithm based on hierarchical model, REMAS has been demonstrated as a reliable and effective method to identify AS events from exon array data.