Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs.

Enhancers and the enhancer RNAs (eRNAs) have been strongly implicated in regulations of transcriptions. Based the multi-omics data (ATAC-seq, ChIP-seq and RNA-seq) from public databases, Pig-eRNAdb is a dataset that comprehensively integrates enhancers and eRNAs for pigs using the machine learning strategy, which incorporates 82,399 enhancers and 37,803 eRNAs from 607 samples across 15 tissues of pigs. This user-friendly dataset covers a comprehensive depth of enhancers and eRNAs annotation for pigs. The coordinates of enhancers and the expression patterns of eRNAs are downloadable. Besides, thousands of regulators on eRNAs, the target genes of eRNAs, the tissue-specific eRNAs, and the housekeeping eRNAs are also accessible as well as the sequence similarity of eRNAs with humans. Moreover, the tissue-specific eRNA-trait associations encompass 652 traits are also provided. It will crucially facilitate investigations on enhancers and eRNAs with Pig-eRNAdb as a reference dataset in pigs.

Selaginellin derivatives from Selaginella tamariscina and evaluation for anti-breast cancer activity.

A phytochemical investigation of Selaginella tamariscina led to the isolation of 17 selaginellin derivatives. Their inhibitory activities against breast cancer cells were screened, and preliminary structure-activity relationships were also established. Among them, dimeric selaginellin 17 showed potential activity against MDA-MB-231 cells with an IC50 value of 3.2 ± 0.1 µM, corresponding to 4-fold higher potency than the reference compound 5-FU (IC50 14.8 ± 0.2 µM). Mechanistic studies indicated that 17 could cause G2/M phase arrest in MDA-MB-231 cells and induce apoptosis accompanied by increased ROS levels.

Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies.

Retrocopies are gene duplicates arising from reverse transcription of mature mRNA transcripts and their insertion back into the genome. While long being regarded as processed pseudogenes, more and more functional retrocopies have been discovered. How the stripped-down retrocopies recover expression capability and become functional paralogs continually intrigues evolutionary biologists. Here, we investigated the function and evolution of retrocopies in the context of 3D genome organization. By mapping retrocopy-parent pairs onto sequencing-based and imaging-based chromatin contact maps in human and mouse cell lines and onto Hi-C interaction maps in 5 other mammals, we found that retrocopies and their parental genes show a higher-than-expected interchromosomal colocalization frequency. The spatial interactions between retrocopies and parental genes occur frequently at loci in active subcompartments and near nuclear speckles. Accordingly, colocalized retrocopies are more actively transcribed and translated and are more evolutionarily conserved than noncolocalized ones. The active transcription of colocalized retrocopies may result from their permissive epigenetic environment and shared regulatory elements with parental genes. Population genetic analysis of retroposed gene copy number variants in human populations revealed that retrocopy insertions are not entirely random in regard to interchromosomal interactions and that colocalized retroposed gene copy number variants are more likely to reach high frequencies, suggesting that both insertion bias and natural selection contribute to the colocalization of retrocopy-parent pairs. Further dissection implies that reduced selection efficacy, rather than positive selection, contributes to the elevated allele frequency of colocalized retroposed gene copy number variants. Overall, our results hint a role of interchromosomal colocalization in the "resurrection" of initially neutral retrocopies.

A pharmacovigilance study of etoposide in the FDA adverse event reporting system (FAERS) database, what does the real world say?

Introduction: Etoposide is a broad-spectrum antitumor drug that has been extensively studied in clinical trials. However, limited information is available regarding its real-world adverse reactions. Therefore, this study aimed to assess and evaluate etoposide-related adverse events in a real-world setting by using data mining method on the U.S. Food and Drug Administration Adverse Event Reporting System (FAERS) database. Methods: Through the analysis of 16,134,686 reports in the FAERS database, a total of 9,892 reports of etoposide-related adverse drug events (ADEs) were identified. To determine the significance of these ADEs, various disproportionality analysis algorithms were applied, including the reporting odds ratio (ROR), the proportional reporting ratio (PRR), the Bayesian confidence propagation neural network (BCPNN), and the multi-item gamma Poisson shrinker (MGPS) algorithms. Results: As a result, 478 significant disproportionality preferred terms (PTs) that were identified by all four algorithms were retained. These PTs included commonly reported adverse events such as thrombocytopenia, leukopenia, anemia, stomatitis, and pneumonitis, which align with those documented in the drug's instructions and previous clinical trials. However, our analysis also uncovered unexpected and significant ADEs, including thrombotic microangiopathy, ototoxicity, second primary malignancy, nephropathy toxic, and ovarian failure. Furthermore, we examined the time-to-onset (TTO) of these ADEs using the Weibull distribution test and found that the median TTO for etoposide-associated ADEs was 10 days (interquartile range [IQR] 2-32 days). The majority of cases occurred within the first month (73.8%) after etoposide administration. Additionally, our analysis revealed specific high-risk signals for males, such as pneumonia and cardiac infarction, while females showed signals for drug resistance and ototoxicity. Discussion: These findings provide valuable insight into the occurrence of ADEs following etoposide initiation, which can potentially support clinical monitoring and risk identification efforts.

Deciphering Cellular Heterogeneity and Communication Patterns in Porcine Antral Follicles by Single-Cell RNA Sequencing.

The antral follicle stage is a critical period in mammalian oocyte maturation, marked by complex interactions between oocyte development and neighboring granulosa cells. Understanding the heterogeneity and communication patterns of granulosa cells within antral follicles is crucial for deciphering their roles in follicle development and oocyte maturation. Here, we employed single-cell RNA-sequencing to explore the molecular and cellular characteristics of porcine antral follicles. Our analysis revealed distinct subpopulations within mural and cumulus granulosa cells, indicating diverse cellular states and functions within the follicles. Functional enrichment analysis unveiled the involvement of specific subpopulations in steroid biosynthesis, cumulus expansion, and cellular communication. Moreover, comparing mature and less mature follicles highlighted differences in cell distribution and functions, indicating developmental-specific variations. Our findings shed light on the intricate cellular heterogeneity and communication network within porcine antral follicles, providing valuable insights into the regulation of follicle development and oocyte maturation in pigs. These results hold promise for improving pig reproductive efficiency and advancing human reproductive medicine.

Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs.

The molecular mechanisms controlling the transition from meiotic arrest to meiotic resumption in mammalian oocytes have not been fully elucidated. Single-cell omics technology provides a new opportunity to decipher the early molecular events of oocyte growth in mammals. Here we focused on analyzing oocytes that were collected from antral follicles in different diameters of porcine pubertal ovaries, and used single-cell M&T-seq technology to analyze the nuclear DNA methylome and cytoplasmic transcriptome in parallel for 62 oocytes. 10× Genomics single-cell transcriptomic analyses were also performed to explore the bi-directional cell-cell communications within antral follicles. A new pipeline, methyConcerto, was developed to specifically and comprehensively characterize the methylation profile and allele-specific methylation events for a single-cell methylome. We characterized the gene expressions and DNA methylations of individual oocyte in porcine antral follicle, and both active and inactive gene's bodies displayed high methylation levels, thereby enabled defining two distinct types of oocytes. Although the methylation levels of Type II were higher than that of Type I, Type II contained nearly two times more of cytoplasmic transcripts than Type I. Moreover, the imprinting methylation patterns of Type II were more dramatically divergent than Type I, and the gene expressions and DNA methylations of Type II were more similar with that of MII oocytes. The crosstalk between granulosa cells and Type II oocytes was active, and these observations revealed that Type II was more poised for maturation. We further confirmed Insulin Receptor Substrate-1 in insulin signaling pathway is a key regulator on maturation by in vitro maturation experiments. Our study provides new insights into the regulatory mechanisms between meiotic arrest and meiotic resumption in mammalian oocytes. We also provide a new analytical package for future single-cell methylomics study.

CRISPR/Cas9 for hepatitis B virus infection treatment.

Hepatitis B virus (HBV) infection remains a global health challenge. Despite the availability of effective preventive vaccines, millions of people are at risk of cirrhosis and hepatocellular carcinoma. Current drug therapies inhibit viral replication, slow the progression of liver fibrosis and reduce infectivity, but they rarely remove the covalently sealed circular DNA (cccDNA) of the virus that causes HBV persistence. Alternative treatment strategies, including those based on CRISPR/cas9 knockout virus gene, can effectively inhibit HBV replication, so it has a good prospect. During chronic infection, some virus gene knockouts based on CRISPR/cas9 may even lead to cccDNA inactivation. This paper reviews the progress of different HBV CRISPR/cas9, vectors for delivering to the liver, and the current situation of preclinical and clinical research.

From 1D to 2D: Controllable Preparation of 2D Ni-MOFs for Supercapacitors.

Controllable modulation strategies between one-dimensional (1D) and two-dimensional (2D) structures have been rarely reported for metal-organic frameworks (MOFs). Here, 1D, 1D/2D, and 2D Ni-MOFs can be facilely prepared by adjusting the ratio of Ni2+ and the pyromellitic acid linker. A low-dimensional structure can shorten the transmission distance, while MOFs with a high Ni2+ content can supply rich active sites for oxidation-reduction reactions. The 2D structure Ni-MOF with an optimized Ni2+/pyromellitic acid ratio presents a good performance of 1036 F g-1 at a current density of 1 A g-1 with a comparable rate performance of 62% at 20 A g-1. The study may offer a facile design to control the structure of MOFs for employing in electrochemical energy storage.

Study on detection of CNVs using human whole genome bisulfite sequencing data.

It has been reported that the aberrant DNA methylation may result in copy number variations (CNVs), and the CNVs may alter the levels of DNA methylation. Whole genome bisulfite sequencing (WGBS) is able to generate the sequencing data of DNAs, and shows the potential ability to detect CNVs. However, the evaluations and performances on the detections of CNVs using WGBS data is still unclear. In this study, five software with different strategies for CNV detections, e.g., BreakDancer, cn.mops, CNVnator, DELLY and Pindel, were selected to explore and benchmark the performances of CNV detections with WGBS data. Based on the real (2.62 billion reads) and simulated (12.35 billion reads) WGBS data of humans, we calculated the number, precision, recall, relative ability, memory usage, and running time of CNV detections by 150 times, and tried to figure out the optimal strategy for CNV detections with WGBS data. Based on the real WGBS data, Pindel detected the most deletions and duplications, CNVnator detected the deletions with the highest precision, cn.mops detected the duplications with the highest precision, Pindel detected the deletions with the highest recall, and cn.mops detected the duplications with the highest recall. Based on the simulated WGBS data, BreakDancer detected the most deletions, and cn.mops detected the most duplications. The CNVnator showed the highest precision and recall for both deletions and duplications. In real and simulated WGBS data, the ability of CNVnator to detect CNVs was likely to overtake that in the whole genome sequencing data. Additionally, DELLY and BreakDancer displayed the lowest peak of memory usage and the lest CPU runtime, while CNVnator expressed the highest peak of memory usage and the most CPU runtime. Taken together, CNVnator and cn.mops showed the excellent performances of CNV detections with WGBS data. These results suggested that it was feasible to detect CNVs using WGBS data, and provided the useful information to further investigate both CNVs and DNA methylation using WGBS data alone.

Intravaginal delivery for CRISPR-Cas9 technology: For example, the treatment of HPV infection.

The increasing incidence of sexually transmitted diseases in women, including human papillomavirus (HPV) infection, has led to the need to develop user-friendly potential prevention methods. At present, although there are several therapeutic parts, none of them has a preventive effect, but they are only limited to providing patients with symptom relief. Researchers have now recognized the need to find effective local preventive agents. One of the potential undiscovered local fungicides is the vaginal delivery of CRISPR/Cas9. CRISPR/Cas9 delivery involves silencing gene expression in a sequence-specific manner in the pathogenic agent, thus showing microbicidal activity. However, vaginal mucosal barrier and physiological changes (such as pH value and variable epithelial thickness in the menstrual cycle) are the main obstacles to effective delivery and cell uptake of CRISPR/Cas9. To enhance the vaginal delivery of CRISPR/Cas9, so far, nano-carrier systems such as lipid delivery systems, macromolecular systems, polymer nanoparticles, aptamers, and cell-penetrating peptides have been extensively studied. In this paper, various nano-carriers and their prospects in the preclinical stage are described, as well as the future significance of CRISPR/Cas9 vaginal delivery based on nano-carriers.

Synthesis of the Ni2P-Co Mott-Schottky Junction as an Electrocatalyst to Boost Sulfur Conversion Kinetics and Application in Separator Modification in Li-S Batteries.

To overcome the shuttling effect and sluggish conversion kinetics of polysulfides, a large number of catalysts have been designed for lithium-sulfur (Li-S) batteries. Herein, a Mott-Schottky junction catalyst composed of Co nanoparticles and Ni2P was designed to improve polysulfide kinetics. Our investigations reveal the rearrangement of charges at the Schottky junction interface and the construction of the built-in electric field are crucial for lowering the activation energy of the dissolved Li2Sn reduction and Li2S nucleation reaction. Furthermore, a series of experimental and electrochemical tests were performed to demonstrate that the Schottky catalytic effect enhanced the synergistic catalytic effect. With a Ni2P-Co@CNT catalyst, the battery exhibits an initial specific capacity of 874 mAh g-1 at a rate of 4.0 C, and the decay rate per cycle is 0.049% in 700 cycles. Meanwhile, the battery shows 0.118% decay rate per cycle at 0.5 C in 100 cycles at a high sulfur loading of 10 mg cm-2. The Schottky heterojunction structure proposed here has been shown to have a good catalytic effect on the reduction of Li2Sn and nucleation of Li2S, which provides a profound guidance for efficient and rational catalyst design.

Expression Profile of Housekeeping Genes and Tissue-Specific Genes in Multiple Tissues of Pigs.

Pigs have become an ideal model system for human disease research and development and an important farm animal that provides a valuable source of nutrition. To profile the all-sided gene expression and their biological functions across multiple tissues, we conducted a comprehensive analysis of gene expression on a large scale around the side of housekeeping genes (HKGs), tissue specific genes (TSGs), and the co-expressed genes in 14 various tissues. In this study, we identified 2351 HKGs and 3018 TSGs across tissues, among which 4 HKGs (COX1, UBB, OAZ1/NPFF) exhibited low variation and high expression levels, and 31 particular TSGs (e.g., PDC, FKBP6, STAT2, and COL1A1) were exclusively expressed in several tissues, including endocrine brain, ovaries, livers, backfat, jejunum, kidneys, lungs, and longissimus dorsi muscles. We also obtained 17 modules with 230 hub genes (HUBGs) by weighted gene co-expression network analysis. On the other hand, HKGs functions were enriched in the signaling pathways of the ribosome, spliceosome, thermogenesis, oxidative phosphorylation, and nucleocytoplasmic transport, which have been highly suggested to involve in the basic biological tissue activities. While TSGs were highly enriched in the signaling pathways that were involved in specific physiological processes, such as the ovarian steroidogenesis pathway in ovaries and the renin-angiotensin system pathway in kidneys. Collectively, these stable, specifical, and co-expressed genes provided useful information for the investigation of the molecular mechanism for an understanding of the genetic and biological processes of complex traits in pigs.

The primordial differentiation of tumor-specific memory CD8+ T cells as bona fide responders to PD-1/PD-L1 blockade in draining lymph nodes.

Blocking PD-1/PD-L1 signaling transforms cancer therapy and is assumed to unleash exhausted tumor-reactive CD8+ T cells in the tumor microenvironment (TME). However, recent studies have also indicated that the systemic tumor-reactive CD8+ T cells may respond to PD-1/PD-L1 immunotherapy. These discrepancies highlight the importance of further defining tumor-specific CD8+ T cell responders to PD-1/PD-L1 blockade. Here, using multiple preclinical tumor models, we revealed that a subset of tumor-specific CD8+ cells in the tumor draining lymph nodes (TdLNs) was not functionally exhausted but exhibited canonical memory characteristics. TdLN-derived tumor-specific memory (TTSM) cells established memory-associated epigenetic program early during tumorigenesis. More importantly, TdLN-TTSM cells exhibited superior anti-tumor therapeutic efficacy after adoptive transfer and were characterized as bona fide responders to PD-1/PD-L1 blockade. These findings highlight that TdLN-TTSM cells could be harnessed to potentiate anti-tumor immunotherapy.

Wavefront-coded phase measuring deflectometry for the all-focused measurement.

Phase measuring deflectometry is a powerful measuring method for complex optical surfaces, which captures the reflected fringe images encoded on the screen under the premise of focusing the measured specular surface. Due to the limited depth of field of the camera, the captured images and the measured surface cannot be focused at the same time. To solve the position-angle uncertainty issue, in this Letter, the wavefront coding technology is used to modulate the imaging wavefront of the deflectometry, thereby making the measuring system insensitive to the defocus and other low-order aberration including astigmatism, field curvature, and so on. To obtain the accurate phase, the captured fringe images are deconvoluted using the modulated point spread function to reduce the phase error. Demonstrated with a highly curved spherical surface, the measurement accuracy can be improved by four times. Experiments demonstrate that the proposed method can successfully reconstruct the complex surfaces defocusing the captured images, which can greatly release the focusing requirement and improve measurement accuracy.

Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.

Whole genome bisulfite sequencing (WGBS) is an essential technique for methylome studies. Although a series of tools have been developed to overcome the mapping challenges caused by bisulfite treatment, the latest available tools have not been evaluated on the performance of reads mapping as well as on biological insights in multiple mammals. Herein, based on the real and simulated WGBS data of 14.77 billion reads, we undertook 936 mappings to benchmark and evaluate 14 wildly utilized alignment algorithms from reads mapping to biological interpretation in humans, cattle and pigs: Bwa-meth, BSBolt, BSMAP, Walt, Abismal, Batmeth2, Hisat_3n, Hisat_3n_repeat, Bismark-bwt2-e2e, Bismark-his2, BSSeeker2-bwt, BSSeeker2-soap2, BSSeeker2-bwt2-e2e and BSSeeker2-bwt2-local. Specifically, Bwa-meth, BSBolt, BSMAP, Bismark-bwt2-e2e and Walt exhibited higher uniquely mapped reads, mapped precision, recall and F1 score than other nine alignment algorithms, and the influences of distinct alignment algorithms on the methylomes varied considerably at the numbers and methylation levels of CpG sites, the calling of differentially methylated CpGs (DMCs) and regions (DMRs). Moreover, we reported that BSMAP showed the highest accuracy at the detection of CpG coordinates and methylation levels, the calling of DMCs, DMRs, DMR-related genes and signaling pathways. These results suggested that careful selection of algorithms to profile the genome-wide DNA methylation is required, and our works provided investigators with useful information on the choice of alignment algorithms to effectively improve the DNA methylation detection accuracy in mammals.

One-Dimensional Co-Carbonate Hydroxide@Ni-MOFs Composite with Super Uniform Core-Shell Heterostructure for Ultrahigh Rate Performance Supercapacitor Electrode.

The insufficient contact between two phases in the heterostructure weakens the coupling interaction effect, which makes it difficult to effectively improve the electrochemical performance. Herein, a Co-carbonate hydroxide@ Ni-metal organic frameworks (Co-CH@Ni-MOFs) composite with super uniform core-shell heterostructure is fabricated by adopting 1D Co-CH nanowires as structuredirecting agents to induce the coating of Ni-MOFs. Both experimental and theoretical calculation results demonstrate that the heterostructure plays a vital role in the high performance of the as-prepared materials. On the one hand, the construction of super uniform core-shell heterostructure can create a large number of interfacial active sites and take advantages of the electrochemical characteristics of each component. On the other hand, the heterostructure can increase the adsorption energy of OH- ions and promote the electrochemical activity for improving the reversible redox reaction kinetics. Based on the aforementioned advantages, the as-fabricated Co-CH@Ni-MOFs electrode exhibits a high specific capacity of 173.1 mAh g-1 (1246 F g-1 ) at 1 A g-1 , an ultrahigh rate capability of 70.3% at 150 A g-1 and excellent cycling stability with 90.1% capacity retention after 10 000 cycles at 10 A g-1 . This study may offer a versatile design for fabricating a MOFs-based heterostructure as energy storage electrodes.

PAL-SLAM: a feature-based SLAM system for a panoramic annular lens.

Simultaneous localization and mapping (SLAM) is widely used in autonomous driving and intelligent robot positioning and navigation. In order to overcome the defects of traditional visual SLAM in rapid motion and bidirectional loop detection, we present a feature-based PAL-SLAM system for a panoramic-annular-lens (PAL) camera in this paper. We use a mask to extract and match features in the annular effective area of the images. A PAL-camera model, based on precise calibration, is used to transform the matched features onto a unit vector for subsequent processing, and a prominent inlier-checking metric is designed as an epipolar constraint in the initialization. After testing on large-scale indoor and outdoor PAL image dataset sequences, comprising of more than 12,000 images, the accuracy of PAL-SLAM is measured as typically below 1 cm. This result holds consistent in conditions when the camera rotates rapidly, or the Global Navigation Satellite System (GNSS) signals are blocked. PAL-SLAM can also detect unidirectional and bidirectional loop closures. Hence it can be used as a supplement or alternative to expensive commercial navigation systems, especially in urban environments where there are many signal obstructions such as buildings and bridges.

Nanosheet-assembled NiCo-LDH hollow spheres as high-performance electrodes for supercapacitors.

Layered double hydroxides (LDHs) have been considered as favorable pseudocapacitive electrode materials for supercapacitors due to their tunable layered structure/compositions and low cost. Here, we report the NiCo-LDH hollow spheres prepared with Co-glycerate as the sacrificial template and cobalt source. The hollow spheres are assembled with frizzy NiCo-LDH nanosheets, where the hollow structure can inhibit agglomeration of the LDH nanosheets to expose more active sites and shorten the diffusion path of electrolyte ions. The prepared NiCo-LDH hollow spheres show a high specific capacitance of 1962 F g-1 at 1 A g-1 and good capacitance retention rate of 66.4 % at 30 A g-1. The asymmetric supercapacitors fabricated using NiCo-LDH hollow spheres as positive electrode yields a large energy density 62.9 Wh kg-1 at the power density of 0.8 kW kg-1. This research may develop a facile synthesis way to prepare LDH hollow spheres for supercapacitors.

Genome-Wide Histone H3K27 Acetylation Profiling Identified Genes Correlated With Prognosis in Papillary Thyroid Carcinoma.

Thyroid carcinoma (TC) is the most common endocrine malignancy, and papillary TC (PTC) is the most frequent subtype of TC, accounting for 85-90% of all the cases. Aberrant histone acetylation contributes to carcinogenesis by inducing the dysregulation of certain cancer-related genes. However, the histone acetylation landscape in PTC remains elusive. Here, we interrogated the epigenomes of PTC and benign thyroid nodule (BTN) tissues by applying H3K27ac chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) along with RNA-sequencing. By comparing the epigenomic features between PTC and BTN, we detected changes in H3K27ac levels at active regulatory regions, identified PTC-specific super-enhancer-associated genes involving immune-response and cancer-related pathways, and uncovered several genes that associated with disease-free survival of PTC. In summary, our data provided a genome-wide landscape of histone modification in PTC and demonstrated the role of enhancers in transcriptional regulations associated with prognosis of PTC.

MXenes induced formation of Ni-MOF microbelts for high-performance supercapacitors.

For the sake of developing new energy storage devices for satisfying the energy needs of the modern society, we herein report an innovative MXene-induced strategy to synthesize Ti3C2Tx MXenes/Ni based metal-organic framework composites (Ti3C2Tx/Ni-MOFs) for high-performance supercapacitors. The two-dimensional (2D) MXenes with oxygen-containing groups on the surface can be used as structure-directing agents to tune the Ni-MOFs into 2D microbelts. The presence of MXenes cannot only improve conductivity of the composite but also provide additional electric double layer capacitance and faradaic pseudocapacitance. The 2D Ni-MOF microbelts can offer rich activity sites for the faradaic redox reactions and shorten the ion transport path. Taking advantages of synergistic effects of Ni-MOF microbelts and Ti3C2Tx MXenes, the prepared Ti3C2Tx/Ni-MOFs electrode shows a good electrochemical performance with 1124 F g-1 at the current density of 1 A g -1 and 62% rate capability at 20 A g -1. This work can offer a new insight to design 2D MOF belts as high-performance electrode materials for supercapacitors.