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High-throughput sequencing for B cell receptor (BCR) repertoire provides useful insights for the adaptive immune system. With the continuous development of the BCR-seq technology, many efforts have been made to develop methods for analyzing the ever-increasing BCR repertoire data. In this review, we comprehensively outline different BCR repertoire library preparation protocols and summarize three major steps of BCR-seq data analysis

Carthamus tinctorius L. 1753 (Asteraceae), also called safflower, is a cash crop with both edible and medical properties. We analyzed and reported the safflower mitogenome based on combined short and long reads obtained from Illumina and Pacbio platforms, respectively. This safflower mitogenome mainly contained two circular chromosomes, with a total length of 321,872 bp, and encoded 55 unique genes, including 34 protein-coding genes (PCGs), 3 rRNA genes, and 18 tRNA genes. The total length of repeat sequences greater than 30 bp was 24,953 bp, accounting for 7.75% of the whole mitogenome. Furthermore, we characterized the RNA editing sites of protein-coding genes located in the safflower mitogenome, and the total number of RNA editing sites was 504. Then, we revealed partial sequence transfer events between plastid and mitochondria, in which one plastid-derived gene (psaB) remained intact in the mitogenome. Despite extensive arrangement events among the three mitogenomes of C. tinctorius, Arctium lappa, and Saussurea costus, the constructed phylogenetic tree based on mitogenome PCGs showed that C. tinctorius has a closer relationship with three Cardueae species, A. lappa, A. tomentosum, and S. costus, which is similar to the phylogeny constructed from the PCGs of plastid genomes. This mitogenome not only enriches the genetic information of safflower but also will be useful in the phylogeny and evolution study of the Asteraceae.

Understanding the molecular mechanisms of seed germination and seedling growth is vital for mining functional genes for the improvement of plant drought in a desert. Tamarix hispida is extremely resistant to drought and soil salinity perennial shrubs or trees. This study was the first to investigate the protein abundance profile of the transition process during the processes of T. hispida seed germination and seedling growth using label-free proteomics approaches. Our data suggested that asynchronous regulation of transcriptomics and proteomics occurs upon short-term seed germination and seedling growth of T. hispida. Enrichment analysis revealed that the main differentially abundant proteins had significant enrichment in stimulus response, biosynthesis, and metabolism. Two delta-1-pyrroline-5-carboxylate synthetases (P5CS), one Ycf3-interacting protein (Y3IP), one low-temperature-induced 65 kDa protein-like molecule, and four peroxidases (PRX) were involved in both water deprivation and hyperosmotic salinity responses. Through a comparative analysis of transcriptomics and proteomics, we found that proteomics may be better at studying short-term developmental processes. Our results support the existence of several mechanisms that enhance tolerance to salinity and drought stress during seedling growth in T. hispida.

Insomnia is an anabatic epidemiology, while the mechanism is extremely complicated; it remains one of the major scientific challenges in life sciences. Because of the advantage of having a similar genetic background and circadian rhythm as those of humans, the Drosophila melanogaster model organism is hugely popular in sleep-related drug screening studies. Seven-day-old virgin D. melanogaster was used to establish the sleep deprivation model by repeated light stimulation at night. Using PySolo activity monitoring system and Drosophila activity as indices, the effective fractions of Zhi-Zi-Hou-Po decoction (ZZHPD) for insomnia were screened; the content of monoamine neurotransmitters dopamine (DA), 5-hydroxyindole-3-acetic acid (5-HIAA), Homovanillic acid (HVA), and 5-hydroxytryptamine (5-HT) in the brain of D. melanogaster were determined by high-performance liquid chromatography-electro-chemical detection. The herb-compound-target-disease target network were further constructed through network pharmacology to identify the potential targets and pathways of ZZHPD in the intervention of insomnia. Finally, the molecular docking method was used for evaluating the binding characteristics of important compounds from ZZHPD with related targets. The results showed that a certain dose of ZZHPD and its petroleum ether, dichloromethane, ethyl acetate, and n-butanol fractions could improve sleep. The dichloromethane fraction from ZZHPD extracts showed the best anti-insomnia effect among all extracts. It can also reduce the content of DA and HVA in the brain of D. melanogaster and increase 5-HT and 5-HIAA levels. The network pharmacology showed that the main active ingredients in ZZHPD included magnolol, honokiol, hesperidin, and so forth. According to the screening conditions, there were 71 targets and the result of KEGG enrichment analysis revealed that 73 pathways were associated with insomnia, which were primarily involved in inflammatory response, central neurotransmitter regulation, and apoptosis to relieve insomnia. The molecular docking results clarified that naringenin and apigenin have an intimate relationship with GABAA receptor, histamine H1, orexin receptor type 2, and interleukin-6. The mechanism of relieving insomnia is the result of the interaction of multi-components, multi-targets, and multi-pathways, which provides a certain theoretical basis for the treatment of insomnia and related diseases as well as clinical research.

Somatosensory stimulation can effectively induce plasticity in the motor cortex representation of the stimulated body part. Specific interactions have been reported between different representations within the primary motor cortex. However, studies evaluating somatosensory stimulation-induced plasticity between different representations within the primary motor cortex are sparse. The purpose of this study was to investigate the effect of somatosensory stimulation on the modulation of plasticity between different representations within the primary motor cortex. Twelve healthy volunteers received both electroacupuncture (EA) and sham EA at the TE5 acupoint (located on the forearm). Plasticity changes in different representations, including the map volume, map area, and centre of gravity (COG) were evaluated by transcranial magnetic stimulation (TMS) before and after the intervention. EA significantly increased the map volume of the forearm and hand representations compared to those of sham EA and significantly reduced the map volume of the face representation compared to that before EA. No significant change was found in the map volume of the upper arm and leg representations after EA, and likewise, no significant changes in map area and COG were observed. These results suggest that EA functions as a form of somatosensory stimulation to effectively induce plasticity between different representations within the primary motor cortex, which may be related to the extensive horizontal intrinsic connectivity between different representations. The cortical plasticity induced by somatosensory stimulation might be purposefully used to modulate human cortical function.

Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.

Objective This study aimed to assess the effect and mechanism of i-type lysozyme on cutaneous wound healing animal model and Multiple cell models both in vivo and in vitro. Methods Therefore, to evaluate its regenerative efficacy on wound healing process, we daily applied i-type lysozyme on murine full-thickness excisional wounds. After sacrifice on indicated days, skin tissues around surgical defects were harvested and assessed for re-epithelialization, granulation tissue formation, neovascularization and remodeling. To elucidate the underlying mechanisms, i-type lysozyme was analyzed for its tissue regenerative potency on the proliferation, invasion, migration and tube formation against keratinocytes, fibroblasts and endothelial cells. Antioxidant and antimicrobial experiments were also conducted to elucidate protective ability of i-type lysozyme to wound bed. Results It displayed excellent bi-directional regulation in wound repair, with significant acceleration of epidermal and dermal regeneration as well as the efficient attenuation of excessive collagen deposition and fibrosis in the surgical lesion. I-type lysozyme treatment augmented the proliferation and migration of HaCaT, NIH 3T3 and HUVECs, enhanced the invasion of HaCaT and HUVECs as well as accelerated tube formation of HUVECs. Additionally, it significantly recovered the proliferation of H2O2-damaged cells, whereas represented no microbicidal effect under effective concentration of wound healing. Conclusion Our findings demonstrate the bi-directional regulation of i-type lysozyme in wound healing process through promoting tissue regeneration while hampering scar formation, implying that it is a promising therapeutic agent for wound repair.

Background Nitrogen, as a constituent of amino acids and nucleic acids, is an essential macronutrient for all living organisms. The nitrogen-fixation clade (NFC) is a clade, consisting of Fabales, Fagales, Cucurbitales, and Rosales, where all nodulating plants have been originated. The plant-specific RWP-RK family of transcription factors are involved in nitrate responses and play specific roles in nodule inception. In the present study, by investigation of RWP-RKs at genome-wide level and comparative coexpression networks, the roles of RWP-RKs involved in nitrate response and nodulation were analyzed to reveal evolution of RWP-RKs and a relationship between nitrogen signaling and nodulation.Results Here, we systematically investigated 292 RWP-RKs from 26 species of legumes and non-legumes of NFC by whole-genomic analysis and characterized their evolutionary relationships, protein motifs, and gene structures. We compared RWP-RK networks from Arabidopsis thaliana under N-starvation and N-supplementation conditions, as well as transcriptome atlases from Phaseolus vulgaris and Glycine max. This revealed that N starvation, which is essential for nodulation, alters the connectivity of RWP-RKs to other genes, including symbiosis-related genes. Meanwhile, appropriately low concentrations of nitrates stimulate nodulation by regulating RWP-RK expression in P. vulgaris.Conclusions Our comparative evolutionary analysis of RWP-RKs between A. thaliana and legumes revealed the evolutionary features and the relationship between the nitrate signaling pathway in a model organism and nodulation in legumes.

Radix aconiti lateralis (Fuzi) is widely used in China as a traditional Chinese medicine for the treatment of asthenia, pain and inflammation. However, its toxic alkaloids often lead to adverse reactions. Currently, most of the toxicity studies on Fuzi are focused on the heart and nervous system, and more comprehensive toxicity studies are needed. In this study, based on the previous reports of Fuzi hepatotoxicity, serum pharmacochemistry and network toxicology were used to screen the potential toxic components of Heishunpian(HSP), a processed product of Fuzi, and to explore the possible mechanism of HSP-induced hepatotoxicity. The results obtained are expressed based on the toxicological evidence chain (TEC). It was found that 22 potential toxic components screened can affect Th17 cell differentiation, Jak-STAT signaling pathway, glutathione metabolism, and other related pathways by regulating AKT1, IL2, F2, GSR, EGFR and other related targets, which induces oxidative stress, metabolic disorders, cell apoptosis, immune response, and excessive release of inflammatory factors, eventually inducing liver damage in rats. This is the first study on HSP-induced hepatotoxicity based on the TEC concept, providing references for further studies on the toxicity mechanism of Fuzi.

As a Traditional Chinese Medicine (TCM), Shuangxia Decoction (SXD) has been used to treat insomnia in oriental countries for more than thousands of years and it presents remarkable clinical effects. However, its active pharmacological fraction and the mechanism of sedative-hypnotic effects have not been explored. In this paper, we investigated active pharmacological fraction and revealed the detailed mechanisms underlying the sedative-hypnotic effects of SXD. It showed that SXD water extract compared to ethanol extract possessed better sedative effects on locomotion activity in normal mice and increased sleep duration in subhypnotic dose of sodium pentobarbital-treated mice. SXD alleviated p-chlorophenylalanine (PCPA) -induced insomnia by increasing the content of 5-HT in cortex [F (4, 55) = 12.67], decreasing the content of dopamine (DA) and norepinephrine (NE). Furthermore, SXD enhanced the expression of 5-HT