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"Zhao, Lin-lin"
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Mapping the epigenetic modifications of DNA and RNA
Over 17 and 160 types of chemical modifications have been identified in DNA and RNA, respectively. The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics. Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study. Here, we review the recent technological advances in this rapidly evolving field. We focus on high-throughput detection methods and biological findings for these modifications, and discuss questions to be addressed as well. We also summarize third-generation sequencing methods, which enable long-read and single-molecule sequencing of DNA and RNA modification.
Journal Article
Contextual Region-Based Convolutional Neural Network with Multilayer Fusion for SAR Ship Detection
Synthetic aperture radar (SAR) ship detection has been playing an increasingly essential role in marine monitoring in recent years. The lack of detailed information about ships in wide swath SAR imagery poses difficulty for traditional methods in exploring effective features for ship discrimination. Being capable of feature representation, deep neural networks have achieved dramatic progress in object detection recently. However, most of them suffer from the missing detection of small-sized targets, which means that few of them are able to be employed directly in SAR ship detection tasks. This paper discloses an elaborately designed deep hierarchical network, namely a contextual region-based convolutional neural network with multilayer fusion, for SAR ship detection, which is composed of a region proposal network (RPN) with high network resolution and an object detection network with contextual features. Instead of using low-resolution feature maps from a single layer for proposal generation in a RPN, the proposed method employs an intermediate layer combined with a downscaled shallow layer and an up-sampled deep layer to produce region proposals. In the object detection network, the region proposals are projected onto multiple layers with region of interest (ROI) pooling to extract the corresponding ROI features and contextual features around the ROI. After normalization and rescaling, they are subsequently concatenated into an integrated feature vector for final outputs. The proposed framework fuses the deep semantic and shallow high-resolution features, improving the detection performance for small-sized ships. The additional contextual features provide complementary information for classification and help to rule out false alarms. Experiments based on the Sentinel-1 dataset, which contains twenty-seven SAR images with 7986 labeled ships, verify that the proposed method achieves an excellent performance in SAR ship detection.
Journal Article
The Effects of Dietary Nutrition on Sleep and Sleep Disorders
Sleep disorder significantly affects the life quality of a large number of people but is still an underrecognized disease. Dietary nutrition is believed to play a significant impact on sleeping wellness. Many nutritional supplements have been used trying to benefit sleep wellness. However, the relationship between nutritional components and sleep is complicated. Nutritional factors vary dramatically with different diet patterns and depend significantly on the digestive and metabiotic functions of each individual. Moreover, nutrition can profoundly affect the hormones and inflammation status which directly or indirectly contribute to insomnia. In this review, we summarized the role of major nutritional factors, carbohydrates, lipids, amino acids, and vitamins on sleep and sleep disorders and discussed the potential mechanisms.
Journal Article
Chromosome-level genome assembly and single-cell analysis unveil molecular mechanisms of arm regeneration in the ophiuroid Ophiura sarsii vadicola
Background
Ophiuroids, belonging to Ophiuroidea in Echinodermata, possess remarkable regenerative capacities in their arms, relying on cellular recruitment and de-differentiation. However, limited high-quality genomic resources have hindered the investigation of the underlying molecular mechanisms of ophiuroid regeneration.
Results
Here, we report a chromosome-level genome of
Ophiura sarsii vadicola
, 259.28 Mbp in length with a scaffold N50 length of 66.91 Mbp. We then perform bulk and single-cell RNA sequencing analysis to investigate gene expression and cellular dynamics during arm regeneration. We identify five distinct cellular clusters involved in the arm regeneration and infer the dynamic transformations from sensory stimulation to injury response, wound healing, and tissue regeneration. We find that progenitor cells derived from connective tissue cells differentiate into muscle, cartilage, endothelial, and epithelial cells. Pseudotime analysis indicates that muscle differentiation occurs early in the regeneration process.
Conclusions
Our genomic resource and single-cell atlas shed light on the mechanisms of organ regeneration in ophiuroids.
Journal Article
Chemical Antioxidant Quality Markers of Chrysanthemum morifolium Using a Spectrum-Effect Approach
Traditionally, the quality evaluation of Chrysanthemum morifolium (CM) cv. (Juhua) attributes its habitats and processing methods, however, this strategy of neglecting bioactive ingredients usually results in deviation of quality evaluation. This study aims to explore the quality marker (Q-marker) based on spectrum-effect relationship and quality control strategy of CMs. The chromatographic fingerprint of 30 flower head samples of CMs from five different habitats including Hang-baiju, Gongju, Huaiju, Taiju and Boju were constructed by high performance liquid chromatography and analyzed through chemometrics methods such as similarity analysis (SA), cluster analysis (CA) and principal component analysis (PCA). The common peaks were quantified by external standard method and relative correction factor method. The in-vitro radical scavenging capacity assays of DPPH·, ·OH and ABTS were carried out. The Q-marker was explored by the correlation analysis between the contents of common peaks and in-vitro radical scavenging capacity, and then used to evaluate the quality of 30 flower head samples of CMs. A total of eight common peaks were appointed in 30 flower head samples of CMs, and their similarities ranged from 0.640 to 0.956. CA results showed that 30 flower head samples of CMs could be divided into five categories with reference to the Euclidean distance of 5. PCA results showed that common peaks played a major role in differential contribution of CMs. The quantification of common peaks hinted that their contents possessed significant variation whether for different accessions or the same accessions of CMs. The correlation analysis showed that chlorogenic acid, 3,5- O -dicaffeoylquinic acid, unknown peak 1, 4,5- O -dicaffeoylquinic acid and kaempferol-3- O -rutinoside could be used as the Q-markers for the quality evaluation of 30 flower head samples of commercially available CMs. The analysis strategy that combines chromatographic fingerprint analysis, multiple ingredients quantification, in-vitro chemical anti-oxidant activity evaluation and spectrum-effect relationship analysis clarified the therapeutic material basis and discovered the Q-markers, which possibly offers a more comprehensive quality assessment of CMs.
Journal Article
Semen microbiota in normal and leukocytospermic males
Large numbers of microbes can be present in seminal fluid, and there are differences in the semen microbiota between normal and abnormal semen samples. To evaluate the semen microbiota in patients with leukocytospermia, 87 seminal fluid samples, including 33 samples with a normal seminal leukocyte count and 54 samples with leukocytospermia, were obtained for a cross-sectional analysis. Twenty samples with a normal seminal leukocyte count had normal sperm parameters (Control group), and 13 samples with a normal seminal leukocyte count were from asthenozoospermia patients (Ast group). However, 32 samples with leukocytospermia were from asthenozoospermia patients (LA group), and only 22 samples with leukocytospermia had normal sperm parameters (Leu group). The 16S ribosomal RNA (rRNA) gene sequencing method was used to sequence the microbiota in the seminal fluid, and multiple bioinformatics methods were utilized to analyze the data. Finally, the results showed that the worse sperm parameters were observed in the leukocytospermia-related groups. Semen microbiota analysis found that there was increased alpha diversity in the leukocytospermia-related groups. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the primary phyla in the seminal fluid. Two microbiota profiles, namely, Lactobacillus-enriched and Streptococcus-enriched groups, were identified in this study. The majority of the samples in the groups with a normal seminal leukocyte count could be categorized as Lactobacillus-enriched, whereas the majority of the leukocytospermia samples could be categorized as Streptococcus-enriched. Our study indicated that males with leukocytospermia have worse sperm parameters and a different semen microbiota composition compared to males with a normal seminal leukocyte count.
Journal Article
Targeted protein degradation: mechanisms, strategies and application
Traditional drug discovery mainly focuses on direct regulation of protein activity. The development and application of protein activity modulators, particularly inhibitors, has been the mainstream in drug development. In recent years, PROteolysis TArgeting Chimeras (PROTAC) technology has emerged as one of the most promising approaches to remove specific disease-associated proteins by exploiting cells’ own destruction machinery. In addition to PROTAC, many different targeted protein degradation (TPD) strategies including, but not limited to, molecular glue, Lysosome-Targeting Chimaera (LYTAC), and Antibody-based PROTAC (AbTAC), are emerging. These technologies have not only greatly expanded the scope of TPD, but also provided fresh insights into drug discovery. Here, we summarize recent advances of major TPD technologies, discuss their potential applications, and hope to provide a prime for both biologists and chemists who are interested in this vibrant field.
Journal Article
Autophagy-mediated degradation of integumentary tapetum is critical for embryo pattern formation
Autophagy modulates the degradation and recycling of intracellular materials and contributes to male gametophyte development and male fertility in plants. However, whether autophagy participates in seed development remains largely unknown. Here, we demonstrate that autophagy is crucial for timely programmed cell death (PCD) in the integumentary tapetum, the counterpart of anther tapetum, influencing embryo pattern formation and seed viability. Inhibition of autophagy resulted in delayed PCD of the integumentary tapetum and defects in embryo patterning. Cell-type-specific restoration of autophagic activities revealed that the integumentary tapetum plays a non-autonomous role in embryo patterning. Furthermore, high-throughput, comprehensive lipidomic analyzes uncovered an unexpected seed-developmental-stage-dependent role of autophagy in seed lipid metabolism: it contributes to triacylglycerol degradation before fertilization and to triacylglycerol biosynthesis after fertilization. This study highlights the critical role of autophagy in regulating timely integumentary tapetum PCD and reveals its significance in seed lipid metabolism and viability.
A seed consists of an embryo, endosperm, and seed coat. Here the authors show that autophagy plays a crucial role in regulating timely programmed cell death in the innermost seed coat, thereby influencing embryo pattern formation and seed viability.
Journal Article
Application of Berberine on Treating Type 2 Diabetes Mellitus
Traditional Chinese medicine (TCM) performs a good clinical practice and is showing a bright future in the treatment of diabetes mellitus (DM). TCM treatment has certain advantages of less toxicity and/or side effects, and herbs could provide multiple therapeutic effects. Berberine (BBR) is a classical natural medicine. In this review, we summarize the application of BBR in the treatment of DM from two aspects. First, modern pharmacological effects of BBR on glucose metabolism are summarized, such as improving insulin resistance, promoting insulin secretion, inhibiting gluconeogenesis in liver, stimulating glycolysis in peripheral tissue cells, modulating gut microbiota, reducing intestinal absorption of glucose, and regulating lipid metabolism. BBR is used to treat diabetic nephropathy (DPN), diabetic neuropathy (DN), and diabetic cardiomyopathy due to its antioxidant and anti-inflammatory activities. Second, the clinical application of BBR is reviewed, such as listing some clinical trials on the effectiveness and safety of BBR, explaining applicable stage and syndrome, the reasonable dose and dose formulation, and the toxicity and/or side effects. This review provides scientific evidence about BBR, as well as introducing some traditional Chinese medical theory and clinical experience, in order to guide clinician to use BBR more suitably and reasonably.
Journal Article