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Long non-coding RNA (lncRNA) play vital regulatory roles in various biological processes. Intestine is one of the most sensitive organs to environmental and homeostatic disruptions for fish. However, systematic profiles of lncRNAs in the intestine of teleost in responses to pathogen infections is still limited. Turbot (Scophthalmus maximus L.), an important commercial fish species in China, has been suffering with Vibrio anguillarum infection, resulted in dramatic economic loss. Hereinto, the intestinal tissues of turbot were sampled at 0 h, 2 h, 12 h, and 48 h following V. anguillarum infection. The histopathological analysis revealed that the pathological trauma was mainly present in intestinal tunica mucosal epithelium. After high-throughput sequencing and bioinformatic analysis, a total of 9722 lncRNAs and 21,194 mRNAs were obtained, and the average length and exon number of lncRNAs were both less than those of mRNAs. Among which, a set of 158 lncRNAs and 226 mRNAs were differentially expressed (DE-lncRNAs and DEGs) in turbot intestine at three time points, related to many immune-related genes such as complement, interleukin, chemokine, lysosome, and macrophage, indicating their potential critical roles in immune responses. In addition, 2803 and 1803 GO terms were enriched for DEGs and co-expressed target genes of DE-lncRNAs, respectively. Moreover, 127 and 50 KEGG pathways including cell adhesion molecules (CAMs), phagosome, JAK-STAT signaling pathway, cytokine-cytokine receptor interaction, and intestinal immune network for IgA production, were enriched for DEGs and co-expressed target genes of DE-lncRNAs, respectively. Finally, qRT-PCR was conducted to confirm the reliability of sequencing data. The present study will set the foundation for the future exploration of lncRNA functions in teleost in response to bacterial infection.

Turbot (Scophthalmus maximus) is an important cold-water economic fish. However, the production and development of turbot industry has been constantly hindered by the frequent occurrence of some diseases. Lacking full-length transcriptome for turbot limits immune gene discoveries and gene structures analysis. Therefore, we generated a full-length transcriptome using mixed immune-related tissues of turbot with PacBio Sequel platform. In this study, a total of 31.7 Gb high quality data were generated with the average subreads length of 2618 bp. According to the presence of 5' and 3' primers as well as poly (A) tails, FL (Full-length) and NFL (Non-full-length) isoforms were obtained. Meanwhile, we identified 32,003 non-redundant transcripts, 76.02% of which was novel isoforms of known genes. In addition, 12,176 alternative splicing (AS) events, 6614 polyadenylation (APA) events, 1905 transcription factors, and 2703 lncRNAs were identified. This work is a comprehensive report on the full-length transcriptome of immune-related tissues of turbot, and it also provides valuable molecular resources for future research on the adaptation mechanisms and functional genomics of turbot.

Chemokines are a superfamily of structurally related cytokines, which exert essential roles in guiding cell migration in development, homeostasis, and immunity. CC and CXC chemokines are the two major subfamilies in teleost species. In this study, a total of seventeen CC and CXC chemokines, with inclusion of twelve CC and five CXC chemokines, were systematically identified from the turbot genome, making turbot the teleost harboring the least number of CC and CXC chemokines among all teleost species ever reported. Phylogeny, synteny, and genomic organization analyses were performed to annotate these genes, and multiple chemokine genes were identified in the turbot genome, due to the tandem duplications (CCL19 and CCL20), the whole genome duplications (CCL20, CCL25, and CXCL12), and the teleost-specific members (CCL34-36, CCL44, and CXCL18). In addition, chemokines were ubiquitously expressed in nine examined healthy tissues, with high expression levels observed in liver, gill, and spleen. Moreover, most chemokines were significantly differentially expressed in gill and spleen after Aeromonas salmonicida infection, and exhibited tissue-specific and time-dependent manner. Finally, protein-protein interaction network (PPI) analysis indicated that turbot chemokines interacted with a few immune-related genes such as interleukins, cathepsins, stats, and TLRs. These results should be valuable for comparative immunological studies and provide insights for further functional characterization of chemokines in teleost.

Infectious hypodermal and haematopoietic necrosis virus (IHHNV) is the smallest known virus in shrimp, which causes runt-deformity syndrome (RDS) and leads to huge economic loss every year in penaeid shrimp farming. Previous studies have shown that the juvenile Penaeus vannamei is more susceptible to IHHNV infection than the adults, but the mechanism is still unclear. In order to investigate the mechanism of pathogenic differences in IHHNV infection of P. vannamei at different developmental stages, the juvenile and adult P. vannamei were studied by transcriptome high-throughput sequencing to analyze their response to IHHNV infection. GO and KEGG enrichment were analyzed to search for differentially expressed genes (DEGs) related to immunity, growth and metabolism. The results showed that many immune-related genes of the juvenile and adult P. vannamei responded differently to IHHNV infection. For the adult P. vannamei, the expression of most immune-related genes was significantly up-regulated, which means that a cellular defense response was triggered after IHHNV infection. However, most immune-related genes in juvenile P. vannamei were inhibited, indicating that the immune system of juvenile the P. vannamei is imperfect and makes it to be more susceptible to IHHNV. Similarly, the growth-related genes of P. vannamei were changed during IHHNV infection. For the juvenile P. vannamei, the growth-related genes were significantly down-regulated, which resulted in a growth hormone disorder and prevented the juvenile P. vannamei from growth. In the adult P. vannamei, most molting-related genes were significantly up-regulated, indicating that IHHNV infection leads the adult P. vannamei to early molting to eliminate pathogen in the body. Metabolic process data showed that energy metabolism pathway was affected when P. vannamei infected with IHHNV. The adult P. vannamei infected with IHHNV can cause energetically costly and lead to the disturbance of the metabolism, activate complex immune systems to resist the invasion of pathogens. The results of this study clarified the response mechanism of P. vannamei at different developmental stages to IHHNV infection, which can provide new insights to IHHNV effective control and a reference for the study of sensitive period of different shrimp virus to host infection.

Late Devonian–Early Carboniferous spores recovered from the depths of 2140 m to 2031.3 m in the CSDP-2 Borehole in the southern Yellow Sea are systematically documented to characterize palynological associations for the stratigraphic correlation. The taxonomic study identifies 96 species belonging to 48 genera, including a re-examination of 33 previously described and indeterminate species. Three palynological associations are established for the Wutong Formation in the CSDP-2 Borehole. In ascending order, these are the late Famennian Aneurospora asthenolabrata–Geminospora lemurata (AL) Association from the proposed Guanshan Member, the latest Famennian Cymbosporites circinatus–Asperispora acuta (CA) Association from the lower part of the proposed Leigutai Member, and the Tournaisian Auroraspora macra–Lophozonotriletes involutus (MI) Association of the upper part of the latter member. The AL and CA associations are correlated with the palynological assemblages in the Guanshan Member, and those in the lower to middle parts of the Leigutai Member of the Wutong Formation that outcrops in the suburbs of Nanjing and southern Jiangsu. The MI Association is similar to those derived from the uppermost beds of the subsurface Wutong Formation and is dated as early Tournaisian.

Intercropping cereals and legumes is practiced widely in the world for improving yields and economic benefits. Shorter legume crops in intercropping are shaded by taller cereals, substantially reducing legume growth and yield. Reducing shade in intercropping by shortening the plant height of cereals by seedling defoliation has been proposed as a practical approach to increase crop yields and land productivity. A two-year field experiment was conducted to investigate the effect of defoliation of cereal crops at seedling stage on the growth and yield of peanut (Arachis hypogaea L.) intercropped with corn (Zea mays L.) or millet (Setaria italica L.). In comparison with non-defoliation controls, defoliation reduced final plant height by 29 cm on average for corn and 18 cm for millet. Photosynthetically active radiation on peanut in intercropping systems with corn or millet intercropping was respectively 27.0% and 22.8% higher than those in controls, significantly improving the light environment of intercropped peanut. Net photosynthetic rates of peanut were on average 25.5% higher in corn and peanut intercropping and 19.6% higher in millet and peanut intercropping than those in non-defoliation controls. Total biomass of intercropped peanut increased owing to increased root growth. Across two years, yield of peanut intercropped with corn was 27.7% and with millet 32.8% higher than those of controls. Defoliation of cereal crops did not affect corn yield but significantly decreased millet yield by 24.5%. Our results suggest that applying seedling defoliation in intercropped corn could increase peanut yield without compromising corn yield in an intercropping system.

Focused energy delivery (FED) is a technique that can precisely bring energy to the specific region, which arouses wide attention in precision electronic warfare (PREW). This paper first proposes a joint optimization model with respect to the locations of the array and the transmitted signals to improve the performance of FED. As the problem is nonconvex and NP-hard, particle swarm optimization (PSO) is adopted to solve the locations of the array, while designing the transmitted signals under a feasible array is considered as a unimodular quadratic program (UQP) subproblem to calculate the fitness criterion of PSO. In the PSO-UQP framework established, two methods are presented for the UQP subproblem, which are more efficient and more accurate respectively than previous works. Furthermore, a threshold value is set in the framework to determine which method to adopt to take full advantages of the methods above. Meanwhile, we obtain the maximum localization error that FED can tolerate, which is significant for implementing FED in practice. Simulation results are provided to demonstrate the effectiveness of the joint optimization algorithm, and the correctness of the maximum localization error derived.

Graphical abstract, Introduction The SARS-CoV-2 pandemic has endangered global health, the world economy, and societal values. Despite intensive measures taken around the world, morbidity and mortality remain high as many countries face new waves of infection and the spread of new variants. Worryingly, more and more variants are now being identified, such as 501Y.V1 (B.1.1.7) in the UK, 501Y.V2 (B.1.351) in South Africa, 501Y.V3 in Manaus, Brazil, and B.1.617/B.1.618 in India, which could lead to a severe epidemic rebound. Moreover, some variants have a stronger immune escape ability. To control the new SARS-CoV-2 variant, we may need to develop and redesign new vaccines repeatedly. So it is important to investigate how our immune system combats and responds to SARS-CoV-2 infection to develop safe and effective medical interventions. Objectives In this study, we performed a longitudinal and proteome-wide analysis of antibodies in the COVID-19 patients to revealed some immune processes of COVID-19 patients against SARS-CoV-2 and found some dominant epitopes of a potential vaccine. Methods Microarray assay, Antibody depletion assays, Neutralization assay. Results We profiled a B-cell linear epitope landscape of SARS-CoV-2 and identified the epitopes specifically recognized by either IgM, IgG, or IgA. We found that epitopes more frequently recognized by IgM are enriched in non-structural proteins. We further identified epitopes with different immune responses in severe and mild patients. Moreover, we identified 12 dominant epitopes eliciting antibodies in most COVID-19 patients and identified five key amino acids of epitopes. Furthermore, we found epitope S-82 and S-15 are perfect immunogenic peptides and should be considered in vaccine design. Conclusion This data provide useful information and rich resources for improving our understanding of viral infection and developing a novel vaccine/neutralizing antibodies for the treatment of SARS-CoV-2.

The class A scavenger receptors play important roles in innate immunity and are distributed on plasma membrane of macrophages and other cell types. Notably, the class A scavenger receptor 4 (SCARA4) contains a typical C-type (calcium-dependent) lectin domain, which belongs to the collectin family of pattern recognition receptors and is involved in the immune response against infection. Here, one turbot SCARA4 gene was identified with a 2,292 bp open reading frame (ORF) encoding 763 amino acid residues. Multiple sequence analysis and phylogenetic analysis confirmed that SmSCARA4 gene was more close to that of P. olivaceus. Gene structure and syntenic analysis showed conserved exon/intron organization pattern and syntenic pattern across selected vertebrate species. Tissue distribution analysis showed SmSCARA4 was expressed in all the tested healthy tissues with the relative high expression levels in skin, gill and spleen. Following both E. tarda and V. anguillarum challenge in vivo, SmSCARA4 was significantly repressed in gill and intestine. Remarkably, SmSCARA4 showed the strongest binding ability to LPS and strongest upregulation in turbot head kidney macrophages in response to LPS. Knockdown and overexpression of SmSCARA4 revealed its interactions with the two pro-inflammatory cytokines, TNF-α and IL-1β. Finally, repression of SmSCARA4 via combined treatment of LPS and overexpression of SmSCARA4 construct in turbot head kidney macrophages further indicated an inhibitory role of SmSCARA4 in LPS-stimulated inflammation. Taken together, turbot SmSCARA4 plays an important role in turbot immunity, especially in the mucosa-related systems; SmSCARA4 possesses strong binding specificity to LPS, and exerts protective roles in response to LPS infection by reducing the release of pro-inflammatory cytokines. The mechanisms of inhibitory role of SmSCARA4 in LPS-elicited inflammation await further investigation.

BackgroundOverarching conceptualizations propose that the complex social-emotional effects of oxytocin (OXT) in humans are partly mediated by interactions with other neurotransmitter systems. Recent animal models suggest that the anxiolytic effects of OXT are critically mediated by the serotonin (5-HT) system, yet direct evidence in humans is lacking.MethodsTo determine the role of 5-HT in OXT-induced attenuation of amygdala threat reactivity and sensitization/ desensitization, we conducted a parallel-group randomized placebo-controlled double-blind experiment during which n = 121 healthy subjects underwent a transient decrease in 5-HT signaling via acute tryptophan depletion (ATD, TRYP-) or the corresponding placebo-control protocols before the administration of intranasal OXT or placebo intranasal spray, respectively. Mean and repetition-dependent changes in threat-specific amygdala reactivity towards threatening stimuli (angry faces) as assessed by fMRI served as the primary outcome.ResultsNo treatment main or interaction effects on amygdala threat reactivity were observed, yet OXT switched bilateral amygdala threat sensitization to desensitization and this effect was significantly attenuated during decreased central 5-HT signaling via pretreatment with TRYP-.ConclusionsThe present findings provide the first evidence for a role of OXT in threat-specific amygdala desensitization in humans and suggest that these effects are critically mediated by the 5-HT system. OXT may have a therapeutic potential to facilitate amygdala desensitization and adjunct up-regulation of 5-HT neurotransmission may facilitate OXT’s anxiolytic potential.The trial was preregistered on clinicaltrials.gov (https://clinicaltrials.gov/ct2/show/NCT03426176, ID NCT03426176)

In this paper, we generalize the usual multiplicative ∊ -indicator I ∊ and additive ∊ -indicator I ∊ + to the forms with L p -norm, i.e. I ∊ p -indicator and I ∊ + p -indicator, and investigate their properties under different p. From the analysis, we find that both I ∊ p -indicator and I ∊ + p -indicator have a good performance on measuring the population convergence and diversity, especially when p is set to be infinity. In order to show their differences more intuitively, we implement a series of comparative experiments by the proposed I ∊ p -indicator and I ∊ + p -indicator based evolutionary algorithm. The experimental results confirm that all these ∊ -indicators have good performances, particulary as p is set to be infinity. We also compare the proposed indicator-based evolutionary algorithm with five existing algorithms. The experimental results demonstrate that our algorithm is effective. In addition, considering that the usual IGD metric is not accurate in measuring the convergence of a population, we adopt the measure based on I ∊ + p -indicator and propose a more effective performance metric, which is denoted as IGD ∊ + .

To mitigate the deficiency of the conventional steel frames, a novel steel frame system using rocking truss (SFWRT) and self-centering energy dissipative devices (SCED) was developed. The SCED consists of structural members, pre-tension tendons, abutting element and friction dissipation devices, which exhibits excellent self-centering and energy dissipation capacity. This new structural system is analyzed using Incremental Dynamic Analysis method (IDA). A scaled earthquake acceleration response spectrum from a specified ground motion was used in this analysis. It is found that the formation of the plastic hinges of the structural components includes four stages: emergence, developing, degradation and completely bearing capacity loss. A comparative study is also made to investigate the development of these plastic hinges under different ground motions in both traditional steel frame and SFWRT. The results for evaluating the lateral collapse resistance capacity indicate that the rocking truss can significantly decrease the structural dynamic response and improve the seismic performance of buildings. The collapse probability curves of the steel frame and SFWRT based on three limit states are compared. It is found that the rocking truss is helpful to reduce the collapse probability under earthquakes. The damage of the steel frame as well as the expected loss of the main structure after an earthquake can be significantly reduced with the help of rocking truss, which would also reduce the repair cost and improve the structural resilience under earthquakes significantly.