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Objective To clarify the structural and functional characteristics of the gut microbiota in individuals with qi stagnation constitution (QSC) and identify the potential biomarkers related to QSC. Methods This cross-sectional study involved individuals with QSC and balanced constitution (BC) confirmed by TCM clinicians. The clinical features were recorded, and fecal samples were collected for 16S rDNA sequencing. The structure of the fecal-associated microbiome (FAM) was described by the alpha-diversity indexes, beta-distances, and relative abundances of dominant taxa. The differences in FAM distribution were analyzed by the Wilcoxon rank-sum test, MetagenomeSeq, and LEfSe analysis. The 16S rDNA gene sequences were assigned to the KEGG dataset to predict the functional information of bacterial metabolic pathways by using PICRUSt. Differences in functional pathways between groups were assessed with the Wilcoxon rank-sum test. The ROC curve based on specific operational taxonomic units (OTUs) was constructed, and the AUC was calculated. Results Twenty-two individuals with BC and 8 with QSC were recruited. Significant differences between the two groups were found in body mass index, health status, and low-density lipoprotein, etc. There was no significant difference in the alpha-diversity index. PCoA showed no evident clustering of bacterial communities according to constitutions. Bacteroidaceae, Lachnospiraceae, Ruminococcaceae, and Prevotellaceae were the four common bacteria with high abundances. Notably, MetagenomeSeq, LEfSe analysis, and the Wilcoxon rank-sum test identified significantly different distributions of 66, 42, and 36 OTUs, respectively. Predictive function analysis showed that 13 metabolic pathways were significantly differentially distributed, including those related to fatty acid synthesis. Five specific OTUs were selected as potential biomarkers of a QSC, and the AUC was 0.94. Conclusion Individuals with QSC have unique FAM structure and related functional characteristics. Five specific OTUs were identified to serve as potentially effective biomarkers related to QSC.

Background: To investigate the microRNA (miRNA)-gene interactions underlying leukocyte functions and characteristics, especially the potential serum biomarkers, implicated in the traditional Chinese medicine (TCM)-defined Pi-qi-deficiency syndrome (PQDS) and Pi-wei damp-heat syndrome (PDHS) resulting from chronic atrophic gastritis (CAG). Methods: Using RNA/miRNA-sequencing approach, we identified the syndrome-specific miRNAs and genes in leukocytes or serums, and further analyzed their functions and pathways to decode their potential roles in contributing to the characteristics and functions of leukocytes. Especially, we validated the syndrome (Zheng)-specific miRNA-gene interactions to explorer their roles for the characteristic and functional changes of leukocytes. Also, we evaluated the possibility of location of syndrome-specific miRNAs into plasma exosomes, and analyzed their validated targets to reveal their potential roles in the body.Results: Compared with healthy control population, we found that despite being the TCM-defined syndromes resulting from the same disease of CAG, the Zheng-specific genes and miRNAs were not same. The PDHS-specific leukocyte genes were mainly involved in defense and immune responses, and enriched in neutrophil degranulation and nucleotide-binding-oligomerisation-domains (NOD)-like receptor signaling pathways, as well as several synapses-related pathways. The expression upregulation of PDHS-specific genes enriched in the neutrophil degranulation pathway, indicated the enhanced leukocyte degranulation activation in the PDHS. The PQDS-specific genes in leukocytes were implicated in inflammatory response, extracellular matrix (ECM) organization and collagen catabolism. They could be enriched in mitogen-activated protein kinase (MAPK) signaling, IL17 signaling and helper T (Th) cell differentiation pathways, especially the pathways associated with cell-to-cell adhesion/junction and communication such as ECM-receptor interaction, cell adhesion molecules (CAM) and ECM organization, probably directly contributing to the characteristics and functions of leukocytes in the PQDS. Also, the experimentally-supported miRNA-gene interactions, concerned with the targets of COL4A2 (collagen, type IV, alpha 2), COL26A1 (collagen, type XXVI, alpha 1), SPP1 (secreted phosphoprotein 1) and PROCR (endothelial protein C receptor), were specifically implicated in the regulation of pathways related to cell-to-cell adhesion/junction and communication, suggesting the potential roles of the PQDS-specific miRNA-gene interactions for the characteristic and functional changes of leukocytes in the PQDS. Interestingly, the PQDS-specific miRNAs in the serums and the corresponding leukocytes, seemed to have the common roles in contributing to the characteristics and functions of leukocytes in the TCM-defined PQDS of CAG. Importantly, the hsa-miR-122-5p could be a potential biomarker candidate for the TCM-defined PQDS, capable of being contained and carried in plasma exosomes and especially much higher expression in both the leukocytes and corresponding serums in the CAG patients with PQDS rather than PDHS. Conclusions: These results may provide new insights into the characteristic and functional changes of leukocytes in the two TCM syndromes, PDHS and PQDS, especially the miRNA-mediated gene regulation underlying leukocyte characteristics and functions, with potential leukocyte and serum biomarkers for future application in integrative medicine.Trial registration: ClinicalTrials.gov, NCT02915393. Registered on September 17, 2016.

Objective To explore the structural and functional characteristics of the fecal-associated microbiome (FAM) in a traditional Chinese medicine (TCM) qi-deficiency constitution (QDC) by comparing with balanced constitution (BC) and screen the related biomarkers. Methods In this cross-sectional study, the TCM constitutions of subjects were determined based on published the Classification and Determination of constitution in TCM and further confirmed by a TCM clinician. Clinical characteristics were recorded, and fecal samples were collected for 16S rDNA sequencing using the Illumina Miseq platform. The FAM structure was described using alpha-diversity indexes, beta-diversity indexes, and the relative abundances of the dominant taxa. Differences in the FAM distribution and function were analyzed with a Wilcoxon rank-sum test, MetagenomeSeq, and LEfSe analysis, after which a receiver operating characteristic curve based on the specific operational taxonomic units (OTUs) was constructed to calculate the area under the curve. Results Our study population was composed of 22 BCs and 9 QDCs. There were no significant differences between the two groups in the distribution of clinical characteristics or alpha-diversity indexes, except for the sweets preference and blood glucose level. In principal coordinate analysis and partial least squares discriminant analysis, the bacterial communities in the BC group samples and QDC group samples clustered separately. Notably, there were 214 OTUs significantly distributed between groups in the MetagenomeSeq analysis, 200 OTUs identified by the Wilcoxon rank-sum test, and 6 OTUs found by the LEfSe analysis. Predicted function analysis revealed that six metabolic pathways were distinctly distributed between the two groups. The area under the curve for the receiver operating characteristic curve based on the four specific OTUs was 0.88. Conclusion Unique FAM structural and related functional characteristics are displayed in individuals with a QDC, and four specific OTUs could be used as QDC biomarkers to assist in clinical diagnosis.

The apextrin C-terminal (ApeC) domain is a class of newly discovered protein domains with an origin dating back to prokaryotes. ApeC-containing proteins (ACPs) have been found in various marine and aquatic invertebrates, but their functions and the underlying mechanisms are largely unknown. Early studies suggested that amphioxus ACP1 and ACP2 bind to bacterial cell walls and have a role in immunity. Here we identified another two amphioxus ACPs (ACP3 and ACP5), which belong to the same phylogenetic clade with ACP1/2, but show distinct expression patterns and sequence divergence (40-50% sequence identities). Both ACP3 and ACP5 were mainly expressed in the intestine and hepatic cecum, and could be up-regulated after bacterial challenge. Both prokaryotic-expressed recombinant ACP3 and ACP5 could bind with several species of bacteria and yeasts, showing agglutinating activity but no microbicidal activity. ELISA assays suggested that their ApeC domains could interact with peptidoglycan (PGN), but not with lipoteichoic acid (LTA), lipopolysaccharides (LPS) and zymosan A. Furthermore, they can only bind to Lys-type PGN from Staphylococcus aureus, but not to DAP-type PGN from Bacillus subtilis and not to moieties of PGN such as MDPs, NAMs and NAGs. This recognition spectrum is different from that of ACP1/2. We also found that when expressed in mammalian cells, ACP3 could interact with TRAF6 via a conserved non-ApeC region, which inhibited the ubiquitination of TRAF6 and hence suppressed downstream NF-κB activation. This work helped define a novel subfamily of ACPs, which have conserved structures, and have related yet diversified molecular functions. Its members have dual roles, with ApeC as a lectin and a conserved unknown region as a signal transduction regulator. These findings expand our understanding of the ACP functions and may guide future research on the role of ACPs in different animal clades.

Objective: To identify potential serum protein candidates involved in linking the traditional Chinese medicine (TCM)-defined qi deficiency constitution (QDC) to Pi-qi-deficiency syndrome (PQDS) of chronic superficial gastritis (CSG). Methods: Using participants with the TCM-defined balanced constitution as a control population, label-free quantitative proteomics was adopted to identify differentially expressed proteins (DEPs) in serum samples from two case populations: case population 1 (participants with QDC) and case population 2 (patients with PQDS of CSG). The DEPs discovered in both case populations were analyzed to identify common DEPs as potential candidates for proteins involved in the link between QDC and PQDS. Based on Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and Gene Ontology (GO) enrichment analysis and analysis of protein–protein interaction networks, we evaluated the possible functions of these potential serum candidates. Results: We discovered 24 and 28 proteins that were differentially expressed in case populations 1 and 2, respectively, compared with the control population. Hierarchical clustering analysis showed that the expression profile of DEPs of individuals from the same population clustered well, while those from different populations were segregated. Furthermore, GO analysis revealed the 10 DEPs that were common to both case populations to be mainly associated with negative regulation of cellular metabolic and immune system processes while KEGG analysis indicated these proteins to be associated with complement and coagulation cascades and peroxisome proliferator-activated receptor signaling. Notably, serum levels of C4b-binding protein beta chain, glycosylphosphatidylinositol-specific phospholipase D1 and MS-F1 light chain variable region proteins were notably higher in the two case populations compared with the control, particularly in the case of CSG with PQDS. Conclusion: The results presented here provide new insights into the molecular mechanisms underlying development of PQDS of CSG from QDC, and suggest candidate serum biomarkers for future application in integrative medicine. Keywords: Qi deficiency constitution, Pi-qi-deficiency syndrome, Chronic superficial gastritis, Serum biomarker

Background SAPHO syndrome is a rare disease characterized by inflammatory lesions on skin and bones. Diversified manifestation and inadequate understanding of etiology has limited its diagnosis and treatment. The co-occurrence of other immune-mediated diseases strongly suggests an involvement of autoimmunity in SAPHO syndrome. However, the role of the largest population of circulating immune cells, neutrophils, is still not well explored. In this study, we performed RNA sequencing to profile the mRNA expression of neutrophils purified from peripheral blood of SAPHO patients to identify key genes associated with SAPHO syndrome, trying to find new functional molecules or biomarkers for this rare disease. Results A total of 442 differentially expressed genes were identified (p 2), in which 294 genes were upregulated and 148 genes were downregulated. Five differentially expressed genes of interest were verified by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), among which S100A12 was upregulated and positively related to high-sensitivity C-reactive protein (hsCRP), while the downregulated gene MYADM was positively related to osteocalcin. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differentially expressed genes were enriched in “systemic lupus erythematosus” and “ECM-receptor interaction”. Gene ontology (GO) enrichment showed that differentially expressed genes may participate in biological processes such as “cell migration” and “cell adhesion”. Conclusions In conclusion, this study provides a first insight into transcriptome characteristics of SAPHO syndrome, indicating an over-active neutrophil recruitment in patients and possibly suggesting molecular candidates for further study on diagnosis and pathology of this disease. Electronic supplementary material The online version of this article (10.1186/s13023-019-1169-3) contains supplementary material, which is available to authorized users.

Objective: Propionibacterium acnes (P. acnes) plays an important role in the development of acne, an inflammatory skin disease with a high-incidence. In this study, we used high-throughput RNA sequencing (RNA-seq) to reveal the anti-inflammatory mechanism of baicalin on P. acnes-induced acne in rabbits. Methods: The Kligman method was used to induce acne in the ears of New Zealand rabbits. The effect of baicalin on the acne model was evaluated by the number of acne lesions and hematoxylin and eosin (H&E) staining of acne tissues. Enzyme-linked immunoabsorbent assay was used to measure the protein expression levels of tumor necrosis factor α (TNFA), interleukin-1 β (IL1B), IL6, and IL8 in the serum of rabbits. RNA-seq was performed to investigate the mechanism of anti-inflammatory activities of baicalin on acne. Immunohistochemical analysis and Western blot were used to validate the expression levels of related proteins in acne tissues. Results: Baicalin treatment significantly reduced the number of acne lesions and lesions of the ear as well as levels of serum inflammatory cytokines. RNA-seq data showed that baicalin treatment globally suppressed inflammation, especially the TNF signaling pathway and Staphylococcus aureus infection pathway, in the rabbit acne model. Conclusion: Baicalin effectively ameliorates P. acnes-induced acne in rabbits by suppressing the inflammatory response in rabbits. Keywords: Acne, Baicalin, P. acnes, TNF signaling pathway, Complement pathway

Domestication of a transposon (a DNA sequence that can change its position in a genome) to give rise to the RAG1–RAG2 recombinase (RAG) and V(D)J recombination, which produces the diverse repertoire of antibodies and T cell receptors, was a pivotal event in the evolution of the adaptive immune system of jawed vertebrates. The evolutionary adaptations that transformed the ancestral RAG transposase into a RAG recombinase with appropriately regulated DNA cleavage and transposition activities are not understood. Here, beginning with cryo-electron microscopy structures of the amphioxus ProtoRAG transposase (an evolutionary relative of RAG), we identify amino acid residues and domains the acquisition or loss of which underpins the propensity of RAG for coupled cleavage, its preference for asymmetric DNA substrates and its inability to perform transposition in cells. In particular, we identify two adaptations specific to jawed-vertebrates—arginine 848 in RAG1 and an acidic region in RAG2—that together suppress RAG-mediated transposition more than 1,000-fold. Our findings reveal a two-tiered mechanism for the suppression of RAG-mediated transposition, illuminate the evolution of V(D)J recombination and provide insight into the principles that govern the molecular domestication of transposons. Identification of the changes that converted a transposase to a recombinase sheds light on the evolution of the vertebrate adaptive immune system.

Synovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) syndrome is known as a rare disease characterized by inflammatory lesions on bones and skin. Polymorphism of clinical manifestation and lack of molecular biomarkers have both limited its diagnosis. Our study performed RNA sequencing (RNA-seq) and integrative bioinformatics analysis of long noncoding RNA (lncRNA)-messenger RNA (mRNA) profile in patients with SAPHO syndrome and healthy controls. A total of 4,419 differentially expressed (DE) mRNAs and 2,713 lncRNAs were identified (p < 0.05, fold change > 2) and a coexpression network was constructed to further investigate their regulatory interactions. The DE lncRNAs were predicted to interact with mRNAs in both cis and trans manners. Functional prediction found that the lncRNA-targeted genes may function in SAPHO syndrome by participating in biological process such as adipocytokine signaling pathway, ErbB signaling pathway, FoxO signaling pathway, as well as production and function of miRNAs. The expression levels of three pairs of coexpressed lncRNA-mRNAs were validated by qRT-PCR, and their relative expression levels were consistent with the RNA-seq data. The deregulated RNAs GAS7 and lnc-CLLU1.1-1:2 may serve as potential diagnostic biomarkers, and the combined receiver operating characteristic (ROC) curve of the two showed more reliable diagnostic ability with an AUC value of 0.871 in distinguishing SAPHO patients from healthy controls. In conclusion, this study provides a first insight into long noncoding RNA transcriptome profile changes associated with SAPHO syndrome and inspiration for further investigation on clinical biomarkers and molecular regulators of this inadequately understood clinical entity.

Background SAPHO syndrome is a group of symptoms consisting of synovitis, acne, pustulosis, hyperostosis and osteosis. There is no specific laboratory index assist in the diagnosis of SAPHO because of its highly heterogeneous clinical manifestations. Pathogenic microorganisms had been identified in biopsies of some SAPHO cases and particular gene mutations were also linked to the occurrence of SAPHO. It is largely unknown whether intestinal microbiome plays a role in pathogenesis of SAPHO. To explore the intestinal microbiome structure of SAPHO syndrome, fecal samples from 17 SAPHO patients and 14 healthy controls (HC) were collected for 16S rDNA sequencing. Results Our results showed that there was no significant difference in alpha indexes and beta diversity between SAPHO and HC samples, while there were 14 operational taxonomic units (OTUs) in the Wilcoxon rank-sum test and 42 OTUs in the MetagenomeSeq analysis showed significant difference in distribution between the SAPHO and HC groups, 3 of which in Firmicutes were also observed in the random forest analysis and used to construct a receiver operating characteristic curve to evaluate the diagnostic value, the area under the curve was 0.86. Conclusion Fecal-associated microbiome in the SAPHO samples was characterized by the alteration in abundance of some nondominant species, and the 3 selected OTUs in Firmicutes could serve as candidate biomarkers for SAPHO syndrome diagnosis.

Neutrophils are a major member of the innate immune system and play pivotal roles in host defense against pathogens and pathologic inflammatory reactions. Neutrophils can be recruited to inflammation sites via the guidance of cytokines and chemokines. Overwhelming infiltration of neutrophils can lead to indiscriminate tissue damage, such as in rheumatoid arthritis (RA). Neutrophils isolated from peritoneal exudate respond to a defined chemoattractant, N-formyl-Met-Leu-Phe (fMLP), in vitro in Transwell or Zigmond chamber assays. The air pouch experiment can be used to evaluate the chemotaxis of neutrophils towards lipopolysaccharide (LPS) in vivo. The adjuvant-induced arthritis (AA) mouse model is frequently used in RA research, and immunohistochemical staining of joint sections with anti-myeloperoxidase (MPO) or anti-neutrophil elastase (NE) antibodies is a well-established method to measure neutrophil infiltration. These methods can be used to discover promising therapies targeting neutrophil migration.

Objects. To investigate the lncRNA-mediated trans- and cis-regulation of genes expression underlying leukocyte functions and characteristics, especially the leukocyte-related biomarkers implicated in the linkage between traditional Chinese medicine- (TCM-) defined qi-deficiency constitution (QDC) and Pi-qi-deficiency syndrome (PQDS) of chronic superficial gastritis (CSG). Methods. We adopted RNA-sequencing approach to identify differential lncRNAs and genes in leukocytes, clustered expression profiles, and analyzed biological functions and pathways of differential genes to decode their potential roles in contributing to characteristics and functions of leukocytes. In addition, interaction networks were created to detail the interactions between differential genes. In particular, we explored differential lncRNAs-mediated regulation of differential genes and predicted the subcellular location of lncRNAs to reveal their potential roles. Results. Compared with TCM-defined balanced constitution (BC), 183 and 93 genes as well as 749 and 651 lncRNAs were differentially expressed (P<0.05 and |log2 (fold change)| ≥1) in leukocytes of individuals from case populations 1 (QDC) and 2 (PQDS), respectively. Of them, 12 genes and 111 lncRNAs were common to each case population. Several networks were created to detail the interactions among case-specific genes, especially case-specific lncRNAs-mediated regulation of case-specific genes. Also, interaction networks were created for the common lncRNAs and genes. HCL analyses showed that differential genes and lncRNAs, especially the common genes and lncRNAs, kept similar expression patterns in both case populations. Furthermore, function enrichment analyses just indicated the common biological processes, namely, extracellular matrix organization and cell adhesion via plasma membrane adhesion molecules. In addition, most common genes underwent very tight and complex regulation of many trans- and cis-acting lncRNAs. In particular, of them, ADAMTSL5, COL26A1, COL27A1, MSH5, and LOC390937 could be regulated by multiple case-specific and common lncRNAs, including the means that directs binding of the common lncRNAs to their coded proteins. The common changes in the extracellular matrix and integral components of plasma membrane related to cell-cell adhesion/junction and communication may implicate the linkage between QDC and PQDS, contributing to alterations in characteristics and functions of leukocytes. Conclusions. These results may provide new insights into the characteristic and functional changes of leukocytes in QDC and PQDS, especially the mechanism underlying the linkage of QDC to PQDS, with potential leukocytes biomarkers for future application in integrative medicine.

In vertebrates, PIAS genes encode versatile cellular regulators, with functions extremely complex and redundant. Here we try to understand their functions from an evolutionary perspective. we evaluate the sequences, expression and molecular functions of amphioxus PIAS genes and compare them with their vertebrate counterparts. Phylogenetic analysis suggests a single PIAS gene in ancestral chordates, which has been duplicated into four families (PIAS1-4) in vertebrates by 2R-WGD but remained single in a basal chordate (amphioxus). Amphioxus PIAS encodes two variants with and without a Serine/Threonine-rich tail, which are retained in human PIAS1-3 but lost in PIAS4. We show that amphioxus PIAS binds C-terminus of NF-κB Rel and blocks the DNA binding activity. In humans, such function is retained in PIAS1, altered in PIAS4, and lost in PIAS2-3. Instead, PIAS3 has evolved new ability to inhibit Rel by binding RHD and promoting SUMOylation. We show that amphioxus PIAS also inhibits NF-κB by binding with upstream signalling adaptor TICAM-like and MyD88. Finally, we verify that human PIAS1, 3 and 4, but not 2, were capable of these newly-discovered functions. Our study offers insight into the sub- and neo-functionalization of PIAS genes and suggests a conserved ancient role for chordate PIAS in NF-κB signalling.

Objective Neutrophils play an important role in the pathogenesis of rheumatoid arthritis (RA). In this study, we used the adjuvant-induced arthritis murine model to evaluate the efficacy of celastrol on neutrophil-mediated inflammation in RA. Methods Freund's complete adjuvant-induced arthritis was used as the murine model of RA. Celastrol was intraperitoneally administrated daily after onset of the disease. The joint diameter and inflammatory score were evaluated daily during the treatment period. Myeloperoxidase (MPO) and neutrophil elastase (NE) activities were evaluated by immunohistochemical analyses. Quantitative PCR and enzyme-linked immunoabsorbent assay were used to quantify the expression of cytokines. The expression of apoptosis-related proteins Bcl-2, Bax and caspase-3 were evaluated by western blot. Results Celastrol suppressed inflammation in joints of arthritic mice and diminished the expression of MPO and NE in the joint tissue. Celastrol significantly inhibited the expression of TNFα and IL-6 induced by LPS in neutrophils in a dose-dependent manner in vitro . Moreover, celastrol induced apoptosis of LPS-stimulated neutrophils by increasing the expression of Bax and cleaved caspase-3 while decreasing Bcl-2 expression. Conclusion Our findings show that celastrol significantly alleviates murine arthritis by modulating the inflammatory activities of neutrophils. These results indicate that celastrol could serve as an alternative or adjunct modality for the treatment of RA.

Bioactive compounds from medicinal plants with anti-inflammatory and immunosuppressive effects have been emerging as important sources of drugs for the treatment of inflammatory disorders. Triptolide, a diterpene triepoxide, is a pharmacologically active compound isolated from Tripterygium wilfordii Hook F (TwHF) that is used as a remedy for inflammatory and autoimmune diseases. As the most promising bioactive compound obtained from TwHF, triptolide has attracted considerable interest recently, especially for its potent anti-inflammatory and immunosuppressive activities. Over the past few years, an increasing number of studies have been published emphasizing the value of triptolide in the treatment of diverse inflammatory disorders. Here, we systematically review the mechanism of action and the therapeutic properties of triptolide in various inflammatory diseases according to different systematic organs, including lupus nephritis, inflammatory bowel disease, asthma, and rheumatoid arthritis with pubmed and Embase. Based on this review, potential research strategies might contribute to the clinical application of triptolide in the future.

Rheumatoid arthritis (RA) is a prototypical autoimmune disorder mainly characterized by joint inflammation and cartilage destruction. Neutrophils actively take part in the initiation and progression of RA. Neutrophils express inflammatory mediators, including cytokines and chemokines. Aberrant formation of neutrophil extracellular traps (NETs) has been demonstrated in the pathogenesis of RA. Thus, neutrophils are regarded as important therapeutic targets in RA treatment. Quercetin is one of the major flavonoids found in fruits and vegetables. Previous studies have demonstrated that quercetin is a potential agent for the treatment of RA. However, the underlying antiarthritic mechanism of quercetin has not been investigated clearly. In this study, we analyzed the therapeutic mechanism of quercetin for RA. Our results showed that quercetin ameliorates inflammation in RA mice by inhibiting neutrophil activities. Quercetin inhibited neutrophil infiltration and reduced the plasma levels of inflammatory cytokines. Quercetin promoted the apoptosis of activated neutrophils. In addition, quercetin inhibited NET formation by suppressing autophagy. These findings suggest that quercetin may be an alternative agent for the treatment of RA by inhibiting neutrophil activities.

Apextrin C-terminal (ApeC) is a novel protein domain with unknown functions, although early studies suggest that some ApeC-containing proteins (ACPs) bind to carbohydrates and have a role in development and immunity. Here we investigated the taxonomic distribution, sequence diversification and origin of ACPs in Metazoa. Most ACPs are present in invertebrates from aquatic or moist environments, including cnidarians, mollusks, echinoderms, cephalochordates, flatworms, water bears, nematodes and annelids. However, ACPs are absent in vertebrates and in most arthropod lineages (e.g. insects and crustaceans) except arachnids. ACPs apparently undergo rapid turnover and diversification, hence no orthologs could be found between (sub)phyla. ApeC can function either as a standalone domain or as a partner domain. It has been found to pair up with over ten different domain types in different ACPs. The partner domains are related to immunity, extracellular matrix, protein-protein and protein-carbohydrate interactions. Notably, the domain pair with the widest taxonomic distribution is MACPF/perforin-ApeC, which represent a classic group of ACPs called apextrins. ApeC also frequently pairs up with itself to form dual-ApeC modules in different phyla. Notably, in parasite flatworms, dual-ApeCs are present in 70% of ACPs and all inherited from a common ancestor. The broad distribution of MACPF-ApeC and dual-ApeC suggest their conserved yet unknown functions. We also discovered distant ApeC homologs in bacteria, hence tracing the origin of ApeC back to prokaryotes. Our findings show that ApeC has an ancient origin and is able to function alone or in complex domain architectures, though it is less prevalent than other versatile domains such as immunoglobulin domains and C-type lectin domains. This work provides a foundation for further functional study of this novel domain type.

Ethnopharmacological relevance Fructus gardenia is widely used for treatment of stroke and infectious diseases in Chinese medicine. Geniposide is the key bioactive compound related to the pharmacodynamic actions of gardenia on ischemic stroke. The molecular mechanism by which geniposide improves the ischemic brain injury was observed in the study. Aim of the study Recent studies showed that geniposide had protective activities against the inflammatory response in ischemic stroke. However, the molecular mechanism of geniposide anti-inflammatory role has not yet been fully elucidated. In this study, we investigated the effect of geniposide on the expression of P2Y14 receptor and downstream signaling pathway in brain microvascular endothelial cells (BMECs). Materials and methods An in vitro model of cerebral ischemia in BMECs was established by oxygen-glucose-deprivation (OGD). To further confirm the specific effect of geniposide on P2Y14 receptor and downstream signaling pathways, we set up a UDP-glucose (an agonist of the P2Y14 receptor) stimulated model. After administration of geniposide, the expression of P2Y14 receptor, phosphorylation of RAF-1, mitogen activated protein kinase kinase1/2 (MEK1/2), extracellular signal-regulated kinase 1/2 (ERK1/2), level of interleukin-8 (IL-8), interleukin-1β (IL-1β), monocyte chemotactic protein 1 (MCP-1) in BMECs were determined. Results The mRNA and protein expression of P2Y14 in the rat BMECs were up-regulated in OGD-induced injury. After administration of Geniposide, the expression of P2Y14 receptor was significantly down-regulated, the phosphorylation of RAF-1, MEK1/2, ERK1/2 were suppressed. Similar data were obtained in UDP-glc stimulated model. We also observed that geniposide markedly declined the production of IL-8, IL-1β and MCP-1 in OGD-induced BMECs. Conclusion Geniposide exerted anti-inflammatory effects by interfering with the expression of P2Y14 receptor, which subsequently inhibits the downstream ERK1/2 signaling pathways and the release of the pro-inflammatory cytokines IL-8, MCP-1, IL-1β. Therefore, this study provides the evidence for gardenia's clinical application in cerebral ischemia.

Introduction Susceptibility to lipid metabolic dysfunction are more frequent in individuals with dampness-heat (DH) constitution, which might be caused by the changes in the gut microbiome. This study is to explore the structural and functional characteristics of the fecal-associated microbiome (FAM) in DH constitution and screen FAM-related biomarkers of DH constitution. Methods Fecal samples were collected. The FAM structure was described with alpha/beta diversity indexes and relative abundances of dominant taxa; the distribution/functional differences of the FAM between DH and balanced constitutions were analyzed by Wilcoxon rank-sum test, MetagenomeSeq and LEfSe analysis, and the specific OTUs were screened to construct ROC curve. Results There was a significant difference between the groups in the sweet preference, ACE and Chao1 indexes. In PCoA and PLS-DA, the bacterial communities in the balanced samples and DH samples clustered separately. Notably, there were 115 differentially distributed OTUs between groups identified in the MetagenomeSeq analysis and 213 OTUs identified with the Wilcoxon rank-sum test. Predicted functions showed that 12 metabolic pathways were differentially distributed between groups, including the pathway related to glycerolipid metabolism. The AUC of ROC curve based on the 4 screened specific OTUs was 0.91, and the relative abundance of these 4 OTUs could result in changes in lipid metabolism. Conclusion Unique FAM structural characteristics were identified in DH constitution, which might involve in changes in lipid metabolism and susceptibility to lipid metabolic dysfunction. The 4 screened specific OTUs could be used as potential biomarkers of DH constitution to assist clinical diagnosis.

Lancelet (amphioxus) represents the most basally divergent extant chordate (cephalochordates) that diverged from the other two chordate lineages (urochordates and vertebrates) more than half a billion years ago. As it occupies a key position in evolution, it is considered as one of the best proxies for understanding the chordate ancestral state. Thus, the construction of a database with multiple lancelet genomes and gene annotation data, including protein domains, is urgently needed to investigate the loss and gain of domains in orthologues among species, especially ancient domain types (non-vertebrate-specific domains) and novel domain combination, which is helpful for providing new insight into the chordate ancestral state and vertebrate evolution. Here, we present an integrated genome database for lancelet, LanceletDB, which provides reference haploid genome sequence and annotation data for lancelet (Branchiostoma belcheri), including gene models and annotation, protein domain types, gene expression pattern in embryogenesis, different expression sequence tag sets and alternative polyadenylation (APA) sites profiled by the sequencing APA sites method. Especially, LanceletDB allows comparison of domain types and combination in orthologues among type species so as to decode the ancient domain types and novel domain combination during evolution. We also integrated the released diploid lancelet genome annotation data (Branchiostoma floridae) to expand LanceletDB and extend its usefulness. These data are available through the search and analysis page, basic local alignment search tool page and genome browser to provide an integrated display.

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by cellular infiltration into the joints and cartilage destruction. Neutrophils play a crucial role in the pathogenesis of RA. Triptolide (TP) is a bioactive compound derived from Tripterygium wilfordii Hook F, which has been used in folk medicine as a treatment for a variety of inflammatory disorders, including RA, for many centuries. Previous studies have shown that TP possesses anti-arthritic activity. However, the anti-arthritic mechanism of TP remains to be fully defined. In the present study, we used the adjuvant-induced arthritis (AA) murine model of RA to investigate the impact of TP on RA and neutrophil function. TP alleviated AA by reducing neutrophil recruitment and suppressing the expression of interleukin-6 and tumour necrosis factor-α in vivo. TP also suppressed the expression of pro-inflammatory cytokines in neutrophils, promoted neutrophil apoptosis and inhibited the migration, NETosis and autophagy of neutrophils in vitro. Based on our findings, TP effectively ameliorates RA by down-regulating neutrophil inflammatory functions, indicating that TP represents a potential therapeutic agent for RA.

Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3'-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3'-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.

Animals exploit different germ-line-encoded proteins with various domain structures to detect the signature molecules of pathogenic microbes. These molecules are known as pathogen-associated molecular patterns (PAMPs), and the host proteins that react with PAMPs are called pattern recognition proteins (PRPs). Here, we present a novel type of protein domain structure capable of binding to bacterial peptidoglycan (PGN) and the minimal PGN motif muramyl dipeptide (MDP). This domain is designated as apextrin C-terminal domain (ApeC), and its presence was confirmed in several invertebrate phyla and subphyla. Two apextrin-like proteins (ALP1 and ALP2) were identified in a basal chordate, the Japanese amphioxus Branchiostoma japonicum (bj). bjALP1 is a mucosal effector secreted into the gut lumen to agglutinate the Gram-positive bacterium Staphylococcus aureus via PGN binding. Neutralization of secreted bjALP1 by anti-bjALP1 monoclonal antibodies caused serious damage to the gut epithelium and rapid death of the animals after bacterial infection. bjALP2 is an intracellular PGN sensor that binds to TNF receptor-associated factor 6 (TRAF6) and prevents TRAF6 from self-ubiquitination and hence from NF-κB activation. MDP was found to compete with TRAF6 for bjALP2, which released TRAF6 to activate the NF-κB pathway. BjALP1 and bjALP2 therefore play distinct and complementary functions in amphioxus gut mucosal immunity. In conclusion, discovery of the ApeC domain and the functional analyses of amphioxus ALP1 and ALP2 allowed us to define a previously undocumented type of PRP that is represented across different animal phyla.

The genomic annotation of amphioxus genome reveals an extraordinary complexity and diversity of immune effector genes in amphioxus. Transcriptomic analysis combined with qRT-PCR has suggested a dynamic and sequential profile of these immune effectors in response to bacterial infection. Further functional analyses on these major effectors and others provide us with an understanding of how these immune effectors evolved and function in response to bacterial challenge. This chapter introduces functional characterizations of galectin, C-type lectins, peptidoglycan recognition proteins, gram-negative bacteria–binding proteins, chitin-binding proteins, apextrin-like proteins, bactericidal/permeability-increasing protein, lysozymes, intelectin, transferrin, and a tachylectin-related homolog.

Tandem 3′ untranslated regions (UTRs), produced by alternative polyadenylation (APA) in the terminal exon of a gene, could have critical roles in regulating gene networks. Here we profiled tandem poly(A) events on a genome-wide scale during the embryonic development of zebrafish (Danio rerio) using a recently developed SAPAS method. We showed that 43% of the expressed protein-coding genes have tandem 3′ UTRs. The average 3′ UTR length follows a V-shaped dynamic pattern during early embryogenesis, in which the 3′ UTRs are first shortened at zygotic genome activation, and then quickly lengthened during gastrulation. Over 4000 genes are found to switch tandem APA sites, and the distinct functional roles of these genes are indicated by Gene Ontology analysis. Three families of cis-elements, including miR-430 seed, U-rich element, and canonical poly(A) signal, are enriched in 3′ UTR-shortened/lengthened genes in a stage-specific manner, suggesting temporal regulation coordinated by APA and trans-acting factors. Our results highlight the regulatory role of tandem 3′ UTR control in early embryogenesis and suggest that APA may represent a new epigenetic paradigm of physiological regulations.

Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%–5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.

Recently, receptor interacting protein (RIP)-1 has been recognized as an intracellular sensor at the crossroads of apoptosis, necroptosis, and cell survival. To reveal when this crucial molecule originated and how its function in integrating stress signals evolved, in this study we report on two RIP1 homologs in Chinese amphioxus (Branchiostoma belcheri tsingtauense), designated B. belcheri tsingtauense RIP1a and B. belcheri tsingtauense RIP1b. Phylogenetic analysis indicates that they are generated by domain recombination and lineage-specific duplication. Similar to human RIP1, both B. belcheri tsingtauense RIP1a and B. belcheri tsingtauense RIP1b activate NF-κB in a kinase activity-independent manner and induce apoptosis through the Fas-associated death domain protein-caspase cascade. Moreover, we found that the natural point mutation of Q to I in the RIP homotypic interaction motif of B. belcheri tsingtauense RIP1a provides negative feedback for amphioxus RIP1-mediated signaling. Thus, our study not only suggests that RIP1 has emerged as a molecular switch in triggering cell death or survival in a basal chordate, but also adds new insights into the regulation mechanisms of RIP1-related signaling, providing a novel perspective on human diseases mediated by RIP1.

Both amphioxus and the sea urchin encode a complex innate immune gene repertoire in their genomes, but the composition and mechanisms of their innate immune systems, as well as the fundamental differences between two systems, remain largely unexplored. In this study, we dissect the mucosal immune complexity of amphioxus into different evolutionary-functional modes and regulatory patterns by integrating information from phylogenetic inferences, genome-wide digital expression profiles, time course expression dynamics, and functional analyses. With these rich data, we reconstruct several major immune subsystems in amphioxus and analyze their regulation during mucosal infection. These include the TNF/IL-1R network, TLR and NLR networks, complement system, apoptosis network, oxidative pathways, and other effector genes (e.g., peptidoglycan recognition proteins, Gram-negative binding proteins, and chitin-binding proteins). We show that beneath the superficial similarity to that of the sea urchin, the amphioxus innate system, despite preserving critical invertebrate components, is more similar to that of the vertebrates in terms of composition, expression regulation, and functional strategies. For example, major effectors in amphioxus gut mucous tissue are the well-developed complement and oxidative-burst systems, and the signaling network in amphioxus seems to emphasize signal transduction/modulation more than initiation. In conclusion, we suggest that the innate immune systems of amphioxus and the sea urchin are strategically different, possibly representing two successful cases among many expanded immune systems that arose at the age of the Cambrian explosion. We further suggest that the vertebrate innate immune system should be derived from one of these expanded systems, most likely from the same one that was shared by amphioxus.

Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308,034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin-Benson-Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production.

Alternative polyadenylation (APA) has been found to be involved in tumorigenesis, development, and cell differentiation, as well as in the activation of several subsets of immune cells in vitro. Whether APA takes place in immune responses in vivo is largely unknown. We profiled the variation in tandem 3′ untranslated regions (UTRs) in pathogen-challenged zebrafish and identified hundreds of APA genes with ∼10% being immune response genes. The detected immune response APA genes were enriched in TLR signaling, apoptosis, and JAK-STAT signaling pathways. A greater number of microRNA target sites and AU-rich elements were found in the extended 3′ UTRs than in the common 3′ UTRs of these APA genes. Further analysis suggested that microRNA and AU-rich element–mediated posttranscriptional regulation plays an important role in modulating the expression of APA genes. These results indicate that APA is extensively involved in immune responses in vivo, and it may be a potential new paradigm for immune regulation.

Proteins fused to the elastin-like polypeptide (ELP) tag can be selectively separated from crude cell extract without chromatography. To avoid the interference of the ELP tag on properties of the target protein, it is necessary to remove the ELP tag from target protein by protease digestion. Therefore, an additional chromatographic purification step is required to remove the proteases, and this is time- and labor-consuming. Here we demonstrate the utility of the ELP-tagged proteases for cleavage of ELP fusion proteins, allowing one-step removal of the cleaved ELP tag and ELP-tagged proteases without chromatography.

Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution., The lancelet, or amphioxus, is an extant basal chordate that diverged from other chordate lineages about 550 million years ago. Here the authors sequence and assemble the diploid genome of a male adult of the Chinese lancelet, B. belcheri, and highlight genomic features that may have played an important role in the origin and evolution of vertebrates.

In this article, we describe a high-throughput cloning method, seamless enzyme-free cloning (SEFC), which allows one-step assembly of DNA fragments in vivo via homologous recombination in Escherichia coli. In the method, the desired open reading frame (ORF) is amplified by use of ORF-specific primers with flanking sequences identical to the two ends of a linearized vector. The polymerase chain reaction (PCR) product and the linearized vector are then cotransformed into E. coli cells, where the ORF is incorporated into the vector in vivo. SEFC is a simple, reliable, and inexpensive method of cloning in which PCR fragments are fused into expression vectors without unwanted amino acids or extra in vitro manipulations apart from the single PCR amplification step. Using this method, we successfully cloned human liver complete ORFs into the yeast AD and DB vectors and generated a clone resource of 4964 AD-ORFs and 4676 DB-ORFs in 3months. This approach will be useful for daily DNA cloning and for creating proteome-scale clone resources.