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To control the ongoing coronavirus disease-2019 (COVID-19) pandemic, CoronaVac (Sinovac), an inactivated vaccine, has been granted emergency use authorization by many countries. However, the underlying mechanisms of the inactivated COVID-19 vaccine-induced immune response remain unclear, and little is known about its features compared to (Severe acute respiratory syndrome coronavirus 2) SARS-CoV-2 infection. Here, we implemented single-cell RNA sequencing (scRNA-seq) to profile longitudinally collected PBMCs (peripheral blood mononuclear cells) in six individuals immunized with CoronaVac and compared these to the profiles of COVID-19 infected patients from a Single Cell Consortium. Both inactivated vaccines and SARS-CoV-2 infection altered the proportion of different immune cell types, caused B cell activation and differentiation, and induced the expression of genes associated with antibody production in the plasma. The inactivated vaccine and SARS-COV-2 infection also caused alterations in peripheral immune activity such as interferon response, inflammatory cytokine expression, innate immune cell apoptosis and migration, effector T cell exhaustion and cytotoxicity, however, the magnitude of change was greater in COVID-19 patients, especially those with severe disease, than in immunized individuals. Further analyses revealed a distinct peripheral immune cell phenotype associated with CoronaVac immunization (HLA class II upregulation and IL21R upregulation in naïve B cells) versus SARS-CoV-2 infection (HLA class II downregulation and IL21R downregulation in naïve B cells from severe disease individuals). There were also differences in the expression of important genes associated with proinflammatory cytokines and thrombosis. In conclusion, this study provides a single-cell atlas of the systemic immune response to CoronaVac immunization and revealed distinct immune responses between inactivated vaccines and SARS-CoV-2 infection.

Although previous studies have reported the use of metabolomics for infectious diseases, little is known about the potential function of plasma metabolites in children infected with mycoplasma pneumoniae (MP). Here, a combination of liquid chromatography-quadrupole time-of-flight mass spectrometry and random forest-based classification model was used to provide a broader range of applications in MP diagnosis. In the training cohort, plasma from 63 MP pneumonia children (MPPs), 37 healthy controls (HC), and 29 infectious disease controls (IDC) were collected. After multivariate analyses, 357 metabolites were identified to be differentially expressed among MPP, HC, and IDC groups, and 3 metabolites (568.5661, 459.3493, and 1004.3684) had high diagnostic values. In an independent cohort with 57 blinded subjects, samples were successfully classified into different groups, demonstrating the reliability of these biomarkers for distinguishing MPPs from controls. A metabolomic signature analysis identified major classes of glycerophospholipids, sphingolipids, and fatty acyls were increased in MPPs. These markedly altered metabolites are mainly involved in glycerophospholipid and sphingolipid metabolism. As the ubiquitous building blocks of eukaryotic cell membranes, dysregulated lipid metabolism indicates damage of the cellular membrane and the activation of immunity in MPPs. Moreover, lipid metabolites, differentially expressed between severe and mild MPPs, were correlated with the markers of extrapulmonary complications, suggesting that they may be involved in MPP disease severity. These findings may offer new insights into biomarker selection and the pathogenesis of MPP in children.

Several observational studies have reported associations between low levels of fat-soluble vitamins (A, D and E) and the incidence of pneumonia. Whether infection affects or negatively regulates serum vitamin levels remains controversial. Our aims were to develop and validate a simple-pretreatment and fast method to determine the serum levels of selected fat-soluble vitamins, namely vitamin A (retinol), vitamin D (25-OH-D

Mesenchymal stem cells (MSCs) are known for their multilineage differentiation potential with immune-modulatory properties. The molecular underpinnings of differentiation remain largely undefined. In this study, we investigated the cellular and molecular features of chemically induced osteogenesis from MSC isolated from human adipose tissue (human adipose MSCs, hAMSCs) using single-cell RNA-sequencing (scRNA-seq). We found that a near complete differentiation of osteogenic clusters from hAMSCs under a directional induction. Both groups of cells are heterogeneous, and some of the hAMSCs cells are intrinsically prepared for osteogenesis, while variant OS clusters seems in cooperation with a due division of the general function. We identified a set of genes related to cell stress response highly expressed during the differentiation. We also characterized a series of transitional transcriptional waves throughout the process from hAMSCs to osteoblast and specified the unique gene networks and epigenetic status as key markers of osteogenesis.

Inorganic pyrophosphatases (PPases) catalyze the hydrolysis of pyrophosphate to phosphates. PPases play essential roles in growth and development, and are found in all kingdoms of life. Human possess two PPases, PPA1 and PPA2. PPA1 is present in all tissues, acting largely as a housekeeping enzyme. Besides pyrophosphate hydrolysis, PPA1 can also directly dephosphorylate phosphorylated c-Jun N-terminal kinases 1 (JNK1). Upregulated expression of PPA1 has been linked to many human malignant tumors. PPA1 knockdown induces apoptosis and decreases proliferation. PPA1 is emerging as a potential prognostic biomarker and target for anti-cancer drug development. In spite of the biological and physiopathological importance of PPA1, there is no detailed study on the structure and catalytic mechanisms of mammalian origin PPases. Here we report the crystal structure of human PPA1 at a resolution of 2.4 Å. We also carried out modeling studies of PPA1 in complex with JNK1 derived phosphor-peptides. The monomeric protein fold of PPA1 is similar to those found in other family I PPases. PPA1 forms a dimeric structure that should be conserved in animal and fungal PPases. Analysis of the PPA1 structure and comparison with available structures of PPases from lower organisms suggest that PPA1 has a largely pre-organized and relatively rigid active site for pyrophosphate hydrolysis. Results from the modeling study indicate the active site of PPA1 has the potential to accommodate double-phosphorylated peptides from JNK1. In short, results from the study provides new insights into the mechanisms of human PPA1 and basis for structure-based anti-cancer drug developments using PPA1 as the target.

The mechanisms underlying the osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) remain unclear. In the present study, we aimed to identify the key biological processes during osteogenic differentiation. To this end, we downloaded three microarray data sets from the Gene Expression Omnibus (GEO) database: GSE12266, GSE18043 and GSE37558. Differentially expressed genes (DEGs) were screened using the limma package, and enrichment analysis was performed. Protein‐protein interaction network (PPI) analysis and visualization analysis were performed with STRING and Cytoscape. A total of 240 DEGs were identified, including 147 up‐regulated genes and 93 down‐regulated genes. Functional enrichment and pathways of the present DEGs include extracellular matrix organization, ossification, cell division, spindle and microtubule. Functional enrichment analysis of 10 hub genes showed that these genes are mainly enriched in microtubule‐related biological changes, that is sister chromatid segregation, microtubule cytoskeleton organization involved in mitosis, and spindle microtubule. Moreover, immunofluorescence and Western blotting revealed dramatic quantitative and morphological changes in the microtubules during the osteogenic differentiation of human adipose‐derived stem cells. In summary, the present results provide novel insights into the microtubule‐ and cytoskeleton‐related biological process changes, identifying candidates for the further study of osteogenic differentiation of the mesenchymal stem cells.

SummeryCoronaVac (Sinovac), an inactivated vaccine for SARS-CoV-2, has been widely used for immunization. However, analysis of the underlying molecular mechanisms driving CoronaVac-induced immunity is still limited. Here, we applied a systems biology approach to understand the mechanisms behind the adaptive immune response to CoronaVac in a cohort of 50 volunteers immunized with 2 doses of CoronaVac. Vaccination with CoronaVac led to an integrated immune response that included several effector arms of the adaptive immune system including specific IgM/IgG, humoral response and other immune response, as well as the innate immune system as shown by complement activation. Metabolites associated with immunity were also identified implicating the role of metabolites in the humoral response, complement activation and other immune response. Networks associated with the TCA cycle and amino acids metabolic pathways, such as phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and glycine, serine and threonine metabolism were tightly coupled with immunity. Critically, we constructed a multifactorial response network (MRN) to analyze the underlying interactions and compared the signatures affected by CoronaVac immunization and SARS-CoV-2 infection to further identify immune signatures and related metabolic pathways altered by CoronaVac immunization. These results suggest that protective immunity against SARS-CoV-2 can be achieved via multiple mechanisms and highlights the utility of a systems biology approach in defining molecular correlates of protection to vaccination.

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with heterogeneous clinical manifestations and the pathogenesis of SLE is still unclear. Various omics results have been reported for SLE, but the molecular hallmarks of SLE, especially in patients with different disease activity, using an integrated multi-omics approach have not been fully investigated. Here, we collected blood samples from 10 healthy controls (HCs) and 40 SLE patients with different clinical activity including inactive (IA), low activity (LA), and high activity (HA). Using an integrative analysis of proteomic, metabolomic and lipidomic profiles, we report the multi-omics landscape for SLE. The molecular changes suggest that both the complement system and the inflammatory response were activated in SLEs and were associated with disease activity. Additionally, activation of the immunoglobulin mediated immune response were observed in the LA stage of the disease, however this immune response was suppressed slightly in the HA stage. Finally, an imbalance in lipid metabolism, especially in sphingolipid metabolism, accompanied with dysregulated apolipoproteins were observed to contribute to the disease activity of SLE. The multi-omics data presented in this study and the characterization of peripheral blood from SLE patients may thus help provide important clues regarding the pathogenesis of SLE.

Although previous studies have reported the use of metabolomics for infectious diseases, little is known about the potential function of plasma metabolites in children infected with

Polymyxin B, a last line antibiotic for extensively drug resistant gram-negative bacteria, therapeutic drug monitoring (TDM) is recommended to minimize its nephrotoxicity and improve efficacy. In the present study, we developed a novel quantification method of polymyxin B in dried blood spots (DBS) using liquid chromatography coupled with mass spectrometry (LC-MS/MS), which was performed on a Shimadzu Prominence HPLC system coupled with a 4500 triple quadrupole mass spectrometer. An aliquot of 50 μL whole blood sample was spotted on Whatman 903® paper cards. Each DBS sample was cut off into a 6 mm diameter disc and extracted by acetonitrile in water (30% in volume, containing 6% formic acid, v/v). Both intra and inter-batch accuracy was in the range of 92.6%-111.0% for polymyxin B1 and 91.5%-111.5% for polymyxin B2. The precision was in the range of 5.2%-12.2% for polymyxin B1 and 4.9%-13.1% for polymyxin B2. The matrix effects for polymyxin B1 and polymyxin B2 at low, medium and high concentrations were ranged from 102.2%-107.9% and 99.8%-106.2%, respectively. The extraction recoveries were85.4%. Stability results showed that DBS cards can be transported at room temperature within 2 days and was stable in sealed plastic bags for 38 days at -70 °C. Bland-Altman analysis demonstrated that concentrations of polymyxin B measured in DBS and plasma methods were in moderate agreement with 95.1% samples within the 95% confidence interval of limits of agreement. The DBS method was successfully applied in clinic for TDM of polymyxin B, which can be an alternative approach in clinic.

Background Integrins play a prominent role in osteogenic differentiation by transmitting both mechanical and chemical signals. Integrin expression is closely associated with tensile stress, which has a positive effect on osteogenic differentiation. We investigated the relationship between integrin αVβ3 and tensile stress. Methods Human fibroblasts were treated with c (RGDyk) and lentivirus transduction to inhibit function of integrin αVβ3. Y-15, cytochalasin D and verteporfin were used to inhibit phosphorylation of FAK, polymerization of microfilament and function of nuclear YAP, respectively. Fibroblasts were exposed to a cyclic tensile stress of 10% at 0.5 Hz, once a day for 2 h each application. Fibroblasts were harvested on day 4 and 7 post-treatment. The expression of ALP, RUNX2, integrin αVβ3, β-actin, talin-1, FAK, vinculin, and nuclear YAP was detected by Western blot or qRT-PCR. The expression and distribution of integrin αVβ3, vinculin, microfilament and nuclear YAP. Results Cyclic tensile stress was found to promote expression of ALP and RUNX2. Inhibition of integrin αVβ3 activation downregulated the rearrangement of microfilament and the expression of ALP, RUNX2 and nuclear YAP. When the polymerization of microfilament was inhibited the expression of ALP, RUNX2 and nuclear YAP were decreased. The phosphorylation of FAK induced by cyclic tensile stress reduced by the inhibition of integrin αVβ3. The expression of ALP and RUNX2 was decreased by inhibition of phosphorylation of FAK and inhibition of nuclear YAP. Conclusions Cyclic tensile stress promotes osteogenesis of human fibroblasts via integrin αVβ3-microfilament axis. Phosphorylation of FAK and nuclear YAP participates in this process.

BACKGROUND Acute respiratory distress syndrome (ARDS) in infants is acute and progressive hypoxic respiratory failure caused by various extrapulmonary pathogenic factors besides cardiogenic factors. Diffuse alveolar injury and progression to pulmonary fibrosis are pathological features of ARDS. The present study sought to determine how puerarin influences the inflammatory response caused by pulmonary fibrosis in ARDS in infants. MATERIAL AND METHODS The human lung fibroblasts cell line HLF1 was treated with different concentrations of puerarin in different groups for various times. TGF-ß1 was overexpressed by TGF-ß1 (2 ng/mL) in routine experiments, and the treated cells and culture supernatant were collected for analysis in each step. Cell apoptosis was measured by flow cytometry, TUNEL assay, and detection of caspase 3 and Bcl-2. Cell proliferation was assessed by CCK-8 assay. Real-time PCR and Western blot assay were used to assess mRNA and protein levels of TGF-ß1 and Smad3, respectively. The related cytokines were assessed by ELISA. RESULTS Results showed that puerarin promoted the apoptosis and inhibited the proliferation of HLF1 cells. Caspase 3 was upregulated, whereas Bcl-2, TGF-ß1, and Smad3 were downregulated by puerarin. IL-1, IL-2, and IL-4, secreted by HLF1 cells, were reduced, but IL-10 showed the opposite trend. When TGF-ß1 was overexpressed, Smad3 was promoted, and IL-1, IL-2, and IL-4 was increased in HLF1 cells. Finally, overexpression of TGF-ß1 reversed the effect of puerarin in HLF1 cells. CONCLUSIONS Puerarin regulated the proliferation and apoptosis of pulmonary fibrosis cells, and affected the secretion of inflammatory cytokines. Thus, puerarin alleviated the inflammatory response resulting from pulmonary fibrosis by regulating the TGF-ß1/Smad3 pathway in infants with ARDS.

Polycystic ovary syndrome (PCOS) is one of the most complex and common reproductive and endocrinologic disorders in the child-bearing age of women. Recently, miR-222 were reported to be associated with the etiology of PCOS. However, the function of miR-222 during the pathogenesis of PCOS remains unclear. In the present study, we aimed to investigate the role of miR-222 in PCOS. Firstly, miR-222 expression was examined by quantitative real-time PCR (qRT-PCR) in PCOS. The effects of miR-222 on proliferation, apoptosis and cell cycle in KGN cells were analyzed by CCK-8 assay and flow cytometry analysis, respectively. In addition, bioinformatics analysis was used to predict the target genes of miR-222, and dual-luciferase reporter assay was applied to verified the interaction between miR-222 and p27 Kip1 in KGN cells. Moreover, the expressions of p27 Kip1 in KGN cells treated with miR-222 mimics or miR-222 inhibitor were evaluated by qRT-PCR and western blot assays. The results showed that the expression of miR-222 was remarkably upregulated in PCOS tissues compared with corresponding normal tissues. In the gain-of-function and loss-of-function assays, we revealed that miR-222 mimics significantly promoted cell proliferation, while miR-222 inhibitor induced cell apoptosis and cell cycle arrested. Furthermore, p27 Kip1 was identified as a target gene of miR-222, and could be negatively regulated by miR-222 mimics in KGN cells. In conclusion, our findings suggested that miR-222 may promote the progression of PCOS by targeting p27 Kip1.

Stroke is the third leading cause of disability-adjusted life years worldwide, and drugs available for its treatment are limited. This study aimed to explore high-confidence candidate genes associated with ischemic stroke (IS) through bioinformatics analysis and identify potential diagnostic biomarkers and gene-drug interactions. Weighted gene coexpression network analysis (WGCNA) and differentially expressed genes (DEGs) were integrated to identify overlapping genes. Then, high-confidence candidate genes were screened by least absolute shrinkage and selection operator (LASSO) regression. Receiver operating characteristic (ROC) curves were used to evaluate the diagnostic value of high-confidence candidate genes as biomarkers for IS. The NetworkAnalyst database was used to construct the TF-gene network and miRNA-TF regulatory network of the high-confidence candidate genes. The DGIdb database was used to identified gene-drug interactions. Through the comprehensive analysis of GSE58294 and GSE16561, 10 high-confidence candidate genes were identified by LASSO regression: ARG1, LY96, ABCA1, SLC22A4, CD163, TPM2, SLC25A42, ID3, FAM102A and CD79B. FAM102A had the highest diagnostic value, and the area under curve (AUC), sensitivity and specificity values were 0.974, 0.919 and 0.936, respectively. The HPA database demonstrated that 10 high-confidence candidate genes were expressed in the brain and blood in normal humans. Finally, DGIdb database analysis identified 8 gene-drug interactions. We identified IS-related diagnostic biomarkers and gene-drug interactions that potentially provide new insights into the diagnosis and treatment of IS.

Gynecologic malignancies, mainly including ovarian cancer, cervical cancer and endometrial cancer, are leading causes of death among women worldwide with high incidence and mortality rate. Recently, adoptive T cell therapy (ACT) using engineered T cells redirected by genes which encode for tumor-specific T cell receptors (TCRs) or chimeric antigen receptors (CARs) has demonstrated a delightful potency in B cell lymphoma treatment. Researches impelling ACT to be applied in treating solid tumors like gynecologic tumors are ongoing. This review summarizes the preclinical research and clinical application of engineered T cells therapy for gynecologic cancer in order to arouse new thoughts for remedies of this disease.

Human skin fibroblasts (HSFs) approximate the multidirectional differentiation potential of mesenchymal stem cells, so they are often used in differentiation, cell cultures, and injury repair. They are an important seed source in the field of bone tissue engineering. However, there are a few studies describing the mechanism of osteogenic differentiation of HSFs. Here, osteogenic induction medium was used to induce fibroblasts to differentiate into osteoblasts, and the role of the mechanical sensitive element PDLIM5 in microfilament-mediated osteogenic differentiation of human fibroblasts was evaluated. The depolymerization of microfilaments inhibited the expression of osteogenesis-related proteins and alkaline phosphatase activity of HSFs, while the polymerization of microfilaments enhanced the osteogenic differentiation of HSFs. The evaluation of potential protein molecules affecting changes in microfilaments showed that during the osteogenic differentiation of HSFs, the expression of PDLIM5 increased with increasing induction time, and decreased under the state of microfilament depolymerization. Lentivirus-mediated PDLIM5 knockdown by shRNA weakened the osteogenic differentiation ability of HSFs and inhibited the expression and morphological changes of microfilament protein. The inhibitory effect of knocking down PDLIM5 on HSF osteogenic differentiation was reversed by a microfilament stabilizer. Taken together, these data suggest that PDLIM5 can mediate the osteogenic differentiation of fibroblasts by affecting the formation and polymerization of microfilaments.

Human adipose-derived stem cells (hASCs) are ideal seed cells for tissue engineering due to their multidirectional differentiation potential. Microfilaments, microtubules, and intermediate filaments are responsible for supporting the intracellular space. Vimentin, a type III intermediate filament protein that is specifically expressed in cells of mesenchymal origin, can function as a scaffold and endow cells with tension and shear stress resistance. Actin stress fibers (ASF) act as an important physical device in stress signal transduction, providing stiffness for cells, and promoting osteogenesis. Through direct physical contact, cross-linkers, and spatial interactions, vimentin and actin networks exist as intersecting entities. Spatial interactions occur in the overlapping area of cytoskeleton subsystems, which could affect cell morphology, cell mechanics, and cell fate. However, how does the spatial organization between the cytoskeletal subsystems changed during osteogenesis, especially between vimentin and ASF, is still not understood, and its mechanism effect on cell fate remains unclear. In our study, WB experiment was used to detect the expression changes in Vimentin, ASF, and other proteins. Cells were reconstructed by three-dimensional scanning with fluorescence microscope, and the spatial thickness of vimentin and ASF cytoskeletons and the thickness of the overlapping area between them were calculated, respectively, so as to observe the spatial reorganization of vimentin and ASF in cells. Cytochalasin D (an inhibitor of actin polymerization) and vimentin upregulated/downregulated cells were used to verify the change in the spatial organization between vimentin and ASF and its influence on osteogenesis. Then, heat shock protein 27 (HSP27) was downregulated to illuminate the regulatory mechanisms of spatial organization between vimentin and ASF during osteogenesis. The amounts and the spatial positions of vimentin and actin stress fiber exhibited opposite trends during osteogenesis. Through controlling the anchor sites on the nucleus, intermediate filaments vimentin can reduce the spatial proportion of actin stress fibers, which can be regulated by HSP27. In addition, depolymerization of actin stress fibers lead to lower osteogenic differentiation ability, resulting in osteogenesis and lipogenesis existed simultaneously, that can be resisted by vimentin. Our data indicate that the spatial reorganization of vimentin and actin stress fibers is a key factor in the regulation of the differentiation state of hASCs. And their spatial overlapping area is detrimental to hASCs osteogenesis, providing a new perspective for further exploring the mechanism underlying hASCs osteogenesis.

Human Caprin-1 and Caprin-2 are prototypic members of the caprin (cytoplasmic activation/proliferation-associated protein) protein family. Vertebrate caprin proteins contain two highly conserved homologous regions (HR1 and HR2) and C-terminal RGG motifs. Drosophila caprin (dCaprin) shares HR1 and RGG motifs but lacks HR2. Caprin-1 and Caprin-2 have important and non-redundant functions. The detailed molecular mechanism s of their actions remain largely unknown. Previously, we determined the crystal structure of a ~120-residue fragment of Caprin-1 within the HR1 region. The structure has a noval all α-helical fold that self-associates to form a homodimer. In this study, the crystal structure of a corresponding fragment from Caprin-2 is reported. The Caprin-2 fragment has similar protein fold and dimeric structure as those of the Caprin-1 fragment. Structural comparison reveals that the molecular interactions mediating homodimerization of Caprin-1 and Caprin-2 are largely conserved in the two systems. Structural modelling study of the corresponding dCaprin fragment indicates that dCaprin may also adopt similar dimeric structure. Presence of a dimerization domain within HR1 may represent an evolutionarily conserved feature of the caprin protein family. Interestingly, while Caprin-1 and Caprin-2 adopt similar overall dimeric structures, the two structures have quite different molecular surface properties. In the Caprin-1 dimeric structure, some of the surface areas are known or suspected to function as binding sites for Carpin-1 interacting proteins. The different surface properties of the caprin dimeric structures may dictate their intermolecular interaction with specific protein partners.

Background Diamond-Blackfan anemia (DBA), a congenital pure red cell aplasia (PRCA), is characterized by normochromic macrocytic anemia, reticulocytopenia, and nearly absent erythroid progenitors in the bone marrow. DBA10, a subset of DBA, is an autosomal dominant disease caused by a mutation in RPS26. So far, there are 30 disease-causing variants in RPS26 being reported, however, only three of them are small insert mutations. Case presentation Here we report a three-month Chinese boy who presents with anemia from postnatal day 2. He was suspected to have Diamond-Blackfan anemia, according to the clinical result. Thus, whole-exome sequencing was performed for precise diagnosis. Conclusion Here, a novel insert mutation c.96dupG in RPS26 was identified by whole-exome sequencing, which caused neonatal DBA in a Chinese boy. This is the first case report of a Chinese DBA10 patient who carries a small insertion in the RPS26 gene. These findings expand the mutation diversity of RPS26 and demonstrate the clinical presentations of the Chinese DBA10 patient. Electronic supplementary material The online version of this article (10.1186/s12881-019-0848-1) contains supplementary material, which is available to authorized users.

Landslides are one of the major geohazards threatening human society. The objective of this study was to conduct a landslide hazard susceptibility assessment for Ruijin, Jiangxi, China, and to provide technical support to the local government for implementing disaster reduction and prevention measures. Machine learning approaches, e.g., random forests (RFs) and support vector machines (SVMs) were employed and multiple geo-environmental factors such as land cover, NDVI, landform, rainfall, lithology, and proximity to faults, roads, and rivers, etc., were utilized to achieve our purposes. For categorical factors, three processing approaches were proposed: simple numerical labeling (SNL), weight assignment (WA)-based and frequency ratio (FR)-based. Then 19 geo-environmental factors were respectively converted into raster to constitute three 19-band datasets, i.e., DS1, DS2, and DS3 from three different processes. Then, 155 observed landslides that occurred in the past decades were vectorized, among which 70% were randomly selected to compose a training set (TS1) and the remaining 30% to form a validation set (VS1). A number of non-landslide (no-risk) samples distributed in the whole study area were identified in low slope (&lt, 1–3°) zones such as urban areas and croplands, and also added to the TS1 and VS1 in the same ratio. For comparison, we used the FR approach to identify the no-risk samples in both flat and non-flat areas, and merged them into the field-observed landslides to constitute another pair of training and validation sets (TS2 and VS2) using the same ratio of 7:3. The RF algorithm was applied to model the probability of the landslide occurrence using DS1, DS2, and DS3 as predictive variables and TS1 and TS2 for training to obtain the SNL-based, WA-based, and FR-based RF models, respectively. Verified against VS1 and VS2, the three models have similar overall accuracy (OA) and Kappa coefficient (KC), which are 89.61%, 91.47%, and 94.54%, and 0.7926, 0.8299, and 0.8908, respectively. All of them are much better than the three models obtained by SVM algorithm with OA of 81.79%, 82.86%, and 83%, and KC of 0.6337, 0.655, and 0.660. New case verification with the recent 26 landslide events of 2017–2020 revealed that the landslide susceptibility map from WA-based RF modeling was able to properly identify the high and very high susceptibility zones where 23 new landslides had occurred, and performed better than the SNL-based and FR-based RF modeling, though the latter has a slightly higher OA and KC. Hence, we concluded that all three RF models achieve reasonable risk prediction, but WA-based and FR-based RF modeling deserves a recommendation for application elsewhere. The results of this study may serve as reference for the local authorities in prevention and early warning of landslide hazards.

Caprin-1 plays roles in many important biological processes, including cellular proliferation, innate immune response, stress response and synaptic plasticity. Caprin-1 has been implicated in several human diseases, including osteosarcoma, breast cancer, viral infection, hearing loss and neurodegenerative disorders. The functions of Caprin-1 depend on its molecular-interaction network. Direct interactions have been established between Caprin-1 and the fragile X mental retardation protein (FMRP), Ras GAP-activating protein-binding protein 1 (G3BP1) and theJapanese encephalitis virus(JEV) core protein. Here, crystal structures of a fragment (residues 132–251) of Caprin-1, which adopts a novel all-α-helical fold and mediates homodimerization through a substantial interface, are reported. Homodimerization creates a large and highly negatively charged concave surface suggestive of a protein-binding groove. The FMRP-interacting sequence motif forms an integral α-helix in the dimeric Caprin-1 structure in such a way that the binding of FMRP would not disrupt the homodimerization of Caprin-1. Based on insights from the structures and existing biochemical data, the existence of an evolutionarily conserved ribonucleoprotein (RNP) complex consisting of Caprin-1, FMRP and G3BP1 is proposed. The JEV core protein may bind Caprin-1 at the negatively charged putative protein-binding groove and an adjacent E-rich sequence to hijack the RNP complex.

Vancomycin is a glycopeptide antibiotic widely used against Gram-positive bacteria such as methicillin-resistant Staphylococcus aureus and coagulase-negative Staphylococcus. Several studies have found that in adults, continuous infusions of vancomycin showed earlier attainment of desired target drug concentrations and reduced nephrotoxicity relative to intermittent infusion. In the pediatric population, there is no consensus on the best vancomycin infusion method. The present study developed and validated a simple and cost-effective UPLC method to determine serum vancomycin levels in pediatric patients and applied it to the therapeutic drug monitoring of vancomycin in children who were treated with either continuous infusion or intermittent infusion of vancomycin. The sample preparation procedure involves only protein precipitation and filtration, and the UPLC method takes 5 min/sample. The assay was linear from 5 mg/L to 100 mg/L (R2 = 0.999). The precision and accuracy were determined at 4 concentration levels. The intraday variability (%CV) ranged from 1.23% to 6.01% (n = 6), and the interday variability ranged from 3.02% to 9.75% (n = 18). The accuracies were good and ranged from 91.21% to 112.63%. Serum vancomycin was stable at room temperature for 12 h or for 3 freeze/thaw cycles, and the processed sample was stable in an autosampler within 15.5 h.

Previous studies have demonstrated a potential role of STAT4 polymorphisms in increased juvenile idiopathic arthritis (JIA) risk in Caucasian populations; however, their role remains unclear in Han Chinese populations. We aimed to investigate single nucleotide polymorphisms (SNPs) of STAT4 and their role in JIA in Han Chinese populations.This study included 205 JIA cases and 267 healthy controls. MassArray high-throughput DNA analyser and mass spectrometry were used to analyse 16 STAT4 SNP sites. The relationship between these SNPs and JIA risk was calculated using multiple logistic regressions.The G allele of rs11893432 was associated with an increased risk of JIA (odds ratio [OR]: 1.73; 95% confidence interval [CI]: 1.03-2.88; p=0.037). This relationship was observed in oligoarticular JIA (OR: 2.75; 95% CI: 1.29-5.83; p=0.026), and not in polyarticular JIA or systemic JIA. The GG motif was significantly correlated with oligoarticular JIA risk,compared to the CC+CG motif (OR: 1.88; 95% CI: 1.06-3.32; p=0.034). The C allele of rs1018981 and the A allele of rs10931481 were associated with a greater risk of polyarticular JIA (C allele: [OR: 7.82; 95% CI: 1.06-57.74; p=0.044]; A allele: [OR: 2.86; 95% CI: 1.23, 6.65; p=0.039).The G allele of rs11893432 was significantly associated with JIA risk, particularly oligoarticular JIA, in Han Chinese populations. SNPs at rs1018981 and rs10931481 were correlated with higher risk of polyarticular JIA.

Fbxo7 and PI31 contain a conserved FP domain that mediates the homo-/hetero-dimerization of the proteins. The PI31 FP domain may also interact with the F-box motif in Fbxo7. The FP domain-mediated protein-protein interactions are important for the functions of Fbxo7 and PI31. The crystal structures of the Fbxo7 and PI31 FP domains were determined previously, showing that a C-terminal helix in the Fbxo7 FP domain was not present in the PI31 FP domain. Here, we determine the crystal structure of the PI31 FP domain using a longer protein construct. The structure is comparable to the Fbxo7 FP domain (including the C-terminal helix), indicating that the two FP domains share the same global fold. However, the FP domains also harbor their own characteristic structural features, mainly in the longest loop (which has a largely fixed conformation due to extensive hydrogen bonding and hydrophobic interactions) and the C-terminal end regions. The crystal structures also reveal fundamental differences in the modes of protein-protein interactions mediated by the two FP domains: the PI31 FP domain utilizes either an α interface or β interface for homodimeric interaction, whereas the Fbxo7 FP domain utilizes an αβ interface. We perform modeling studies to show that the domain-specific structural features may dictate specific modes of inter-domain interactions. We propose that a heterodimeric interaction would be mediated by an αβ interface consisting of the α-helical and β-sheet surfaces of the Fbxo7 and PI31 FP domains, respectively. We also discuss the structural/functional significance of various modes of FP domain-mediated protein-protein interactions.

TAX1BP1 is a pleiotropic multi-domain protein involved in many important biological processes such as signal transduction, cell growth and apoptosis, transcriptional coactivation, membrane trafficking, neurotransmission and autophagy. The N-terminus of TAX1BP1 contains a SKICH domain implicated in autophagy. SKICH domains are also present in four other proteins including NDP52, CALCOCO1, SKIP and PIPP. The SKICH domains of SKIP and PIPP mediate plasma membrane localisation. The functions of the SKICH domains of NDP52 and CALCOCO1 are not known. Here we report the crystal structure of the TAX1BP1 SKICH domain, which has an Ig-like fold similar to the NDP52 SKICH domain. Extensive pairwise and clustered aromatic π-stacking interactions are present in the TAX1BP1 SKICH domain. The aromatic residues mediating these interactions can be classified into four groups with varying degrees of conservation among different protein families. The interactions mediated by highly conserved residues are found in the interior and one outward face of the Ig-like β-barrel, representing common structural features of the SKICH domains. Three TAX1BP1-specific pairwise interactions locate in the loop regions, each augmented by a proline-aromatic interaction. The three proline-aromatic clusters are linked together by more generic hydrophobic interactions, forming a unique hydrophobic surface at one end of the TAX1BP1 SKICH domain. The structures and homologous models of SKICH domains from different proteins reveal substantial differences in electrostatic surface properties of the domains. Together with existing biochemical data, results from the structural study suggest that an intact SKICH domain is required for the autophagy function of TAX1BP1.

TAX1BP1 is a highly conserved, pleiotropic protein that plays many essential functions in human cells, including negative regulation of inflammatory and antimicrobial responses mediated by NF-κB and IRF3 signaling, inhibition of apoptosis, transcriptional coactivation and autophagyetc.TAX1BP1 contains a SKICH domain at the N-terminus, three coiled-coil domains in the middle and two ubiquitin-binding zinc-finger motifs at the C-terminus. The SKICH domain and the linker sequence between the SKICH domain and the coiled-coil region mediate interaction with ubiquitin-like proteins of the LC3/GABARAP family, which are autophagosome markers. For structure determination of the SKICH domain of TAX1BP1, a protein construct (amino acids 15–148) corresponding to the SKICH domain plus the linker region was expressed, purified and crystallized. A native diffraction data set has been collected to 1.9 Å resolution. A molecular-replacement solution has been found by using the structure of the SKICH domain of NDP52, a paralog of TAX1BP1.

This study established a simple and rapid method for simultaneous determination of short-chain chlorinated paraffins (SCCPs) and medium-chain chlorinated paraffins (MCCPs) in human serum by high performance liquid chromatography coupled with electron spray ionization quadrupole time-of-flight mass spectrometry (HPLC-ESI-Q-TOF/MS). A simple pretreatment procedure of protein precipitation by acetonitrile coupled with liquid-liquid extraction by n-hexane was employed for extraction and purification. The purified samples were separated by a PFP chromatographic column. This method could effectively eliminate the matrix effect by lipids and other matrix substances in serum samples with less time and solvent consuming. 76 congener groups of SCCPs and MCCPs with C10-C17 and Cl5-Cl13 were quantified by their [M-H]− ions. Method detection limit (MDL) were 1.0–8.0 ng mL−1 for ∑SCCPs and ∑MCCPs. Recoveries were 98.4 ± 4.42%, 98.8 ± 3.96% and 90.7 ± 2.79% for SCCPs and 93.1 ± 6.67%, 108 ± 1.21% and 90.8 ± 3.78% for MCCPs at spiking concentrations of 20, 50 and 200 ng·mL−1, respectively. The relative standard deviations (RSDs) of intra- and inter-day variations were 1.41% and 9.84% for SCCPs, and 4.23% and 6.26% for MCCPs. The suitability of the developed method was demonstrated through the application to analysis of SCCPs and MCCPs in human serum samples.

Aim Methylation abnormalities in T lymphocytes have been reported to correlate with systemic lupus erythematosus (SLE). Previous studies identified hypomethylation in the promoter of several genes linked to SLE. Long interspersed nucleotide element-1 (LINE-1) constitutes 17–25% of the human genome, and LINE-1 hypomethylation has been reported in SLE. Limited information is available regarding LINE-1 methylation in juvenile SLE (JSLE). Method Methylation levels of LINE-1 in peripheral blood mononuclear cells (PBMCs) from 59 JSLE and 47 control samples were examined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Total homocysteine (tHcy) concentrations in plasma were measured by immunoassay. Results Significant hypomethylation of LINE-1 was observed in PBMCs from JSLE patients (60.93% in cases compared with 62.88% in controls, P = 0.001). Significant LINE-1 hypomethylation was observed in active SLE compared to controls (60.66% vs. 62.88%, P = 0.001). According to other clinical parameters, a significant correlation was found between LINE-1 methylation levels and the Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2000) of the cases (r = −0.285, P = 0.032). The risk of JSLE increased with decreasing levels of LINE-1 methylation, with an odds ratio of 14.5 (95% CI: 2.8–75.6, P = 0.002). Cases had significantly higher plasma concentrations of tHcy than controls (15.11 vs. 11.02 μmol/L, P = 0.028); the correlation between LINE-1 methylation levels and tHcy was significant (r = −0.4, P = 0.013). Correlations between methylation levels of LINE-1 and complement component 3 were significant (r = 0.317, P = 0.044; r = 0.387, P = 0.031, in total JSLE and active JSLE, respectively). Conclusion Hypomethylation of LINE-1 is associated with risk of JSLE, and LINE-1 methylation levels were related to disease activity and clinical manifestations. The correlation between tHcy levels and LINE-1 methylation was significant.

The objective of this study was to determine how the clinical presentation of systemic lupus erythematosus in pediatric varied with the age of onset of the disease. We reviewed the charts of a total of 88 Chinese pediatric patients (pSLE) diagnosed and admitted first time to our hospitals between 2005 and 2008. Patients were divided into 3 groups, depending on the age at diagnosis: preschool (1-6 years), school age (7-11 years), and adolescent groups (12-18 years). Among the three groups, we compared the sex ratio, disease duration at diagnosis, symptoms at the onset of the disease, clinical manifestations, laboratory examinations, SLEDAI (Systemic Lupus Erythematosus Disease Activity Index) 2000, and SLICC/ACR SDI (Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index for Systemic Lupus Erythematosus). Most pediatric patients were in the adolescent group (47.7%), while the disease duration at diagnosis was shortest in preschool-age patients (0.65 ± 0.5 months). The most common symptoms at the onset of pSLE were fever, rash, arthritis, and seizures. Hematologic system and neuropsychiatric system were damaged commonly. The preschool-age patients had the shortest disease duration at diagnosis, the highest incidence of neuropsychiatric system involvement, and the poorest prognosis of all the age groups, especially the boys. Patients in adolescence had the peak incidence of pediatric SLE and high disease activity, begins to acquire some of the adult characteristics. School-age is a transition stage between other stages.

Background Major depressive disorder (MDD) is associated with dysfunction of the emotional circuitry in the brain. Psychotherapy and antidepressant treatment both aid in modulating this dysfunction, albeit probably through different mechanisms. A plausible “top-down” emotional regulation mechanism for psychotherapy has been described in previous studies, but the underlying findings are still contradictory. Methods A total of 23 MDD patients and 20 healthy controls were enrolled. The early neural effects within 5 weeks of guided imagery—a psychotherapeutic method for treating depression—were assessed through resting-state functional magnetic resonance imaging using the regional homogeneity analytical method. Results At baseline, regional homogeneity was reduced in cortical regions and increased in limbic areas in the pre-treatment scans of MDD patients as compared to controls. After 5 weeks of guided imagery therapy, regional homogeneity in the ventromedial prefrontal cortex and the anterior cingulate gyrus both increased. Higher pre-treatment regional homogeneity in the dorsal anterior cingulate gyrus was positively correlated with an improved response to guided imagery therapy. Conclusion The changes in regional homogeneity induced by guided imagery therapy demonstrate that this method of psychotherapy takes effect through a “top-down” mechanism. Future studies comparing various psychotherapeutic methodologies across multiple time points in the treatment course should yield more valuable insights on this topic.

−1 programmed ribosomal frameshifting (PRF) is utilized by many viruses to synthesize their enzymatic (Pol) and structural (Gag) proteins at a defined ratio. For efficient −1 PRF, two cis-acting elements are required: a heptanucleotide frameshift site and a downstream stimulator such as a pseudoknot. We have analyzed the gag-pol junction sequences from 4254 HIV-1 strains. Approximately ninety-five percent of the sequences can form four pseudoknots PK1–PK4 (∼97% contain PK1, PK3, and PK4), covering ∼72 nt including the frameshift site. Some pseudoknots are mutually excluded due to sequence overlap. PK1 and PK3 arrange tandemly. Their stems form a quasi-continuous helix of ∼22 bp. We propose a novel mechanism for possible roles of these pseudoknots. Multiple alternative structures may exist at the gag-pol junction. In most strains, the PK1–PK3 tandem pseudoknots may dominate the structurally heterogeneous pool of RNA due to their greater overall stability. The tandem pseudoknots may function as a breaking system to slow down the ribosome. The ribosome unwinds PK1 and stem 1 of PK3 before it can reach the frameshift site. Then, PK4 can form rapidly because the intact stem 2 of PK3 makes up a large part of the stem 1 of PK4. The newly formed PK4 jams the entrance of the mRNA tunnel. The process then proceeds as in a typical case of −1 PRF. This mechanism incorporates several exquisite new features while still being consistent with the current paradigm of pseudoknot-dependent −1 PRF.

Paediatric systemic lupus erythematosus (pSLE) refers to childhood-onset systemic lupus erythematosus. pSLE has its own unique characteristics, and its pathogenesis is unclear. To study the relationship between microRNAs (miRNAs) and pSLE, we selected three pSLE patients who were newly diagnosed and had not yet been treated, and two controls were also included. We collected their peripheral blood mononuclear cells to perform Agilent human miRNA (8 × 15 k) 12.0 analysis. To verify the results, we next selected 12 other pSLE patients who had different disease activities and 3 healthy controls and conducted real-time PCR. The results showed high expression of miRNA-516a-3p, miRNA-629 and miRNA-525-5p in pSLE patients with active disease; these levels were normal in patients without active disease. Increased expression levels of these three miRNAs were positively correlated with the score obtained from the systemic lupus erythematosus disease activity index scoring system (SLEDAI) 2000 and C-reactive protein (CRP) levels. Furthermore, the target genes of these three miRNAs were important to the pathogenesis of pSLE. Therefore, these three miRNAs might be specific to pSLE and may be used as novel biomarkers of pSLE to diagnose and monitor the disease.

Catenin-β-like protein 1 (CTNNBL1) is a highly conserved protein with multiple functions, one of which is to act as an interaction partner of the antibody-diversification enzyme activation-induced cytidine deaminase (AID) for its nuclear import and subnuclear trafficking. Here, the crystal structure of full-length human CTNNBL1 is reported. The protein contains six armadillo (ARM) repeats that pack into a superhelical ARM domain. This ARM domain is unique within the ARM protein family owing to the presence of several unusual structural features. Moreover, CTNNBL1 contains significant and novel non-ARM structures flanking both ends of the central ARM domain. A strong continuous hydrophobic core runs through the whole structure, indicating that the ARM and non-ARM structures fold together to form an integral structure. This structure defines a highly restrictive and discriminatory protein-binding groove that is not observed in other ARM proteins. The presence of a cluster of histidine residues in the groove implies a pH-sensitive histidine-mediated mechanism that may regulate protein binding activity. The many unique structural features of CTNNBL1 establish it as a distinct member of the ARM protein family. The structure provides critical insights into the molecular interactions between CTNNBL1 and its protein partners, especially AID.

Background Psychotherapy has demonstrated comparable efficacy to antidepressant medication in the treatment of major depressive disorder. Metabolic alterations in the MDD state and in response to treatment have been detected by functional imaging methods, but the underlying white matter microstructural changes remain unknown. The goal of this study is to apply diffusion tensor imaging techniques to investigate psychotherapy-specific responses in the white matter. Methods Twenty-one of forty-five outpatients diagnosed with major depression underwent diffusion tensor imaging before and after a four-week course of guided imagery psychotherapy. We compared fractional anisotropy in depressed patients (n = 21) with healthy controls (n = 22), and before-after treatment, using whole brain voxel-wise analysis. Results Post-treatment, depressed subjects showed a significant reduction in the 17-item Hamilton Depression Rating Scale. As compared to healthy controls, depressed subjects demonstrated significantly increased fractional anisotropy in the right thalamus. Psychopathological changes did not recover post-treatment, but a novel region of increased fractional anisotropy was discovered in the frontal lobe. Conclusions At an early stage of psychotherapy, higher fractional anisotropy was detected in the frontal emotional regulation-associated region. This finding reveals that psychotherapy may induce white matter changes in the frontal lobe. This remodeling of frontal connections within mood regulation networks positively contributes to the “top-down” mechanism of psychotherapy.

A high performance liquid chromatographic (HPLC) method with programmed wavelength ultraviolet (UV) detection was established to simultaneously determine tryptophan (Trp) and its key metabolites kynurenine (Kyn) and 5-hydroxytryptamine (5-HT). A BDS-Hypersil-C8 column (150 mm x 4.6 mm, 5 microm) was used for the analysis at 25 degrees C. The separation was carried out with the mobile phase consisting of 10 mmol/L sodium acetate-acetic acid (pH 4. 5) and acetonitrile (94: 6, v/v) using theophylline as internal standard (IS) at a flow rate of 0.6 mL/min. The eluates were monitored by the programmed wavelength UV detection at 360 nm for Kyn and IS, 220 nm for 5-HT and 302 nm for Trp. The mean recoveries were in the range of 87% to 113%. The linearities were from 3.97 to 400 micromol/L for Trp, 0.421 to 20.2 micromol/L for Kyn and 4.36 to 980.5 nmol/L for 5-HT. The detection limits were 0.134 micromol/L for Trp, 0.016 micromol/L for Kyn and 2.03 nmol/L for 5-HT. Fifteen plasma samples of patients with depression and fifteen plasma samples of healthy controls were tested, and the results demonstrated that the metabolism of Trp in the plasma from the depression group was significantly different from that of the control group.