Elucidation of subfamily segregation and intramolecular coevolution of the olfactomedin-like proteins by comprehensive phylogenetic analysis and gene expression pattern assessment

AbstractThe categorization of genes by structural distinctions relevant to biological characteristics is very important for understanding of gene functions and predicting functional implications of uncharacterized genes. It was absolutely necessary to deploy an effective and efficient strategy to deal with the complexity of the large olfactomedin-like (OLF) gene family sharing sequence similarity but playing diversified roles in many important biological processes, as the simple highest-hit homology analysis gave incomprehensive results and led to inappropriate annotation for some uncharacterized OLF members. In light of evolutionary information that may facilitate the classification of the OLF family and proper association of novel OLF genes with characterized homologs, we performed phylogenetic analysis on all 116 OLF proteins currently available, including two novel members cloned by our group. The OLF family segregated into seven subfamilies and members with similar domain compositions or functional properties all fell into relevant subfamilies. Furthermore, our Northern blot analysis and previous studies revealed that the typical human OLF members in each subfamily exhibited tissue-specific expression patterns, which in turn supported the segregation of the OLF subfamilies with functional divergence. Interestingly, the phylogenetic tree topology for the OLF domains alone was almost identical with that of the full-length tree representing the unique phylogenetic feature of full-length OLF proteins and their particular domain compositions. Moreover, each of the major functional domains of OLF proteins kept the same phylogenetic feature in defining similar topology of the tree. It indicates that the OLF domain and the various domains in flanking non-OLF regions have coevolved and are likely to be functionally interdependent. Expanded by a plausible gene duplication and domain couplings scenario, the OLF family comprises seven evolutionarily and functionally distinct subfamilies, in which each member shares similar structural and functional characteristics including the composition of coevolved and interdependent domains. The phylogenetically classified and preliminarily assessed subfamily framework may greatly facilitate the studying on the OLF proteins. Furthermore, it also demonstrated a feasible and reliable strategy to categorize novel genes and predict the functional implications of uncharacterized proteins based on the comprehensive phylogenetic classification of the subfamilies and their relevance to preliminary functional characteristics

Ethyl 6-(4-fluoro­phen­yl)-4-hy­droxy-2-oxo-4-trifluoro­meth­yl-1,3-diazinane-5-carboxyl­ate monohydrate

The asymmetric unit of the title compound, C14H14F4N2O4·H2O, contains two crystallographically independent organic mol­ecules and two water mol­ecules. The two 1,3-diazinane rings adopt a half-chair conformation and the dihedral angles between their mean planes and those of the benzene rings are 75.65 (4)° and 49.41 (3)° in the two mol­ecules. The crystal structure is stabilized by inter­molecular O—H⋯O and N—H⋯O hydrogen bonds

Simultaneous and Direct Determination of Vancomycin and Cephalexin in Human Plasma by Using HPLC-DAD Coupled with Second-Order Calibration Algorithms

A simple, rapid, and sensitive method for the simultaneous determination of vancomycin and cephalexin in human plasma was developed by using HPLC-DAD with second-order calibration algorithms. Instead of a completely chromatographic separation, mathematical separation was performed by using two trilinear decomposition algorithms, that is, PARAFAC-alternative least squares (PARAFAC-ALSs) and self-weight-alternative-trilinear-decomposition- (SWATLD-) coupled high-performance liquid chromatography with DAD detection. The average recoveries attained from PARAFAC-ALS and SWATLD with the factor number of 4 (N = 4) were 101 ± 5% and 102 ± 4% for vancomycin, and 96 ± 3% and 97 ± 3% for cephalexininde in real human samples, respectively. The statistical comparison between PARAFAC-ALS and SWATLD is demonstrated to be similar. The results indicated that the combination of HPLC-DAD detection with second-order calibration algorithms is a powerful tool to quantify the analytes of interest from overlapped chromatographic profiles for complex analysis of drugs in plasma

Baseline elevated Lp-PLA2 is associated with increased risk for re-stenosis after stent placement

BACKGROUND: Lipoprotein associated phospholipase A2 (Lp-PLA2) is a novel biomarker for cardiovascular risk prediction. Whether increased Lp-PLA2 level is associated with re-stenosis after stent-placement is unclear. METHODS: Totally 326 participants eligible for stent-placement were enrolled and divided into two groups according to baseline Lp-PLA2 levels (named normal and elevated groups). Baseline characteristics and clinical outcomes were compared between normal and elevated groups. The relationships between Lp-PLA2 and other risk factors with re-stenosis were evaluated. RESULTS: Only the between-group difference of Lp-PLA2 was significant (123.2 ± 33.6 ng/mL vs 336.8 ± 85.4 ng/mL, P < 0.001) while other demographic and clinical characteristics between these two groups were comparable. Approximately 55.1% and 58.5% of participants in normal and elevated groups presented with acute coronary syndrome, and the percentage of tri-vessels stenoses was significantly higher in elevated group (40.8% vs 32.1%, P = 0.016). Nearly 96.0% and 94.0% of participants in normal and elevated Lp-PLA2 groups were placed with drug-eluting stents, and the others were with bare-metal stents. After 1 year’s follow-up, the incidence of clinical end-points was comparable (13.3% vs 15.4%, P = 0.172). Nevertheless, the incidence of re-stenosis was marginally higher in elevated Lp-PLA2 group (8.5% versus 4.6%, P = 0.047). With multivariate analysis, after adjustment for other risk factors, Lp-PLA2 remained an independent predictor for re-stenosis with a hazard ratio of 1.140. No synergistic effect between Lp-PLA2 and other risk factors for re-stenosis was found. CONCLUSION: Increased Lp-PLA2 level is associated with an increased risk of re-stenosis. Lp-PLA2 assessment may be useful in predicting subjects who are at increased risk for re-stenosis

Ethyl 6-[4-(dimethyl­amino)phen­yl]-4-hydr­oxy-2-oxo-4-(trifluoro­methyl)­hexa­hydro­pyrimidine-5-carboxyl­ate

The title compound, C16H20F3N3O4, was prepared by reaction of 4-(dimethyl­amino)benzaldehyde, ethyl 4,4,4-trifluoro-3-oxo­butanoate and urea. In the title mol­ecule, the pyrimidine ring adopts a half-chair conformation and there is an intra­molecular hydrogen bond (O—H⋯O). The crystal structure is stabilized by two types inter­molecular hydrogen bonds (N—H⋯O and N—H⋯N)

Evaluation of LOXL1 polymorphisms in exfoliation syndrome in a Chinese population

Purpose: To evaluate the association profiles of the lysyl oxidase-like 1 (LOXL1) gene polymorphisms with exfoliation syndrome in a Chinese population. Methods: Fifty unrelated patients with exfoliation syndrome and 125 control subjects were included. Genotypes of the three single nucleotide polymorphisms (SNPs) of LOXL1 (rs1048661, rs3825942, and rs2165241) were analyzed by direct sequencing, and a case-control association study was performed. Results: The three SNPs were significantly associated with exfoliation syndrome (XFS) and exfoliation glaucoma (XFG) individually. After controlling for rs3825942 and rs2165241, the association between rs1048661 and XFS/XFG remained significant (p=3.6x10(-7)). At this SNP, the T allele and TT genotype conferred a 7.59-(95% confidence interval [CI]: 3.87-14.89, p=6.95x10(-11)) and 8.69-(95% CI: 4.15-18.20, p&lt;1.00x10(-7)) fold increased risk to the disease. The alleles of T at rs1048661 and C at rs2165241 were found to be risk alleles in Chinese subjects, which were opposite to Caucasian individuals. The haplotypes T-G, defined by SNPs rs1048661 and rs3825942, and T-C by SNPs rs1048661 and rs2165241, were also significantly associated with the disorder. However when the genotypic or allelic frequencies of the three SNPs were compared between XFS and XFG, no significant difference was detected. Conclusions: LOXL1 is a susceptibility gene of XFS/XFG in the Chinese population, and the association is mainly attributed to SNP rs1048661. The risk alleles of rs1048661 and rs2165241 in Chinese subjects were found to be opposite to that of Caucasians. The genotypic and allelic distributions of these SNPs are similar between XFS and XFG.Biochemistry &amp; Molecular BiologyOphthalmologySCI(E)30ARTICLE250-522349-23571

Quality of reporting of systematic reviews published in “evidence-based” Chinese journals

BACKGROUND: The number of systematic reviews (SRs)/meta-analyses (MAs) has increased dramatically in China over the past decades. However, evaluation of quality of reporting of systematic reviews published has not been undertaken. The objective of this study is to evaluate the quality of reporting of SRs/MAs assessing efficacy and/or harms of clinical interventions published in “evidence-based” Chinese journals. METHODS: Web-based database searches were conducted for the Chinese Journal of Evidence-based Medicine, the Journal of Evidence-Based Medicine, the Chinese Journal of Evidence Based Pediatrics, and the Chinese Journal of Evidence-Based Cardiovascular Medicine. SRs/MAs assessing efficacy and/or harms of clinical interventions were included. The cut-off was December 31st 2011. The PRISMA statement was applied to assess the quality of reporting. Each item was assessed as follows: ‘Yes’ for total compliance, scored ‘1’; ‘partial’ for partial compliance, scored ‘0.5’; and ‘No’ for non-compliance, scored ‘0’. The review was considered to have major flaws if it received a total score of ≤15.0, minor flaws if it received a total score of 15.5 to 21.0, and minimal flaws if it received a total score 21.5 to 27.0. Odds ratios were used for binary variables, and the mean difference was used for continuous variables. Analyses were performed using RevMan 5.0 software. RESULTS: Overall, 487 SRs/MAs were identified and assessed. The included reviews had medium quality with minor flaws based on PRISMA total scores (range: 8.5–26.0; mean: 19.6 ± 3.3). The stratified analysis showed that SRs/MAs with more than 3 authors, from a university, hospital + university cooperation, multiple affiliations (≥2), and funding have significantly higher quality of reporting of SRs/MAs; 58% of the included reviews were considered to have minor flaws (total score of 15.6 to 21.0). Only 9.6% of reviews were considered to have major flaws. Specific areas needing improvement in reporting include the abstract, protocol and registration, and characteristics of the search. CONCLUSIONS: The reporting of SRs published in “evidence-based” Chinese journals is poor and needs to be improved in order for reviews to be useful. SR authors should use the PRISMA checklist to ensure complete and accurate accounts of their SRs

Shikonin Prolongs Allograft Survival via Induction of CD4+FoxP3+ Regulatory T Cells

A transplanted organ is usually rejected without any major immunosuppressive treatment because of vigorous alloimmune responsiveness. However, continuous global immunosuppression may cause severe side effects, including nephrotoxicity, tumors, and infections. Therefore, it is necessary to seek novel immunosuppressive agents, especially natural ingredients that may provide sufficient efficacy in immunosuppression with minimal side effects. Shikonin is a bioactive naphthoquinone pigment, an ingredient originally extracted from the root of Lithospermum erythrorhizon. Previous studies have shown that shikonin regulates immunity and exerts anti-inflammatory effects. In particular, it can ameliorate arthritis in animal models. However, it is unclear whether shikonin inhibits alloimmunity or allograft rejection. In this study and for the first time, we demonstrated that shikonin significantly prolonged the survival of skin allografts in wild-type mice. Shikonin increased the frequencies of CD4+Foxp3+ regulatory T cells (Tregs) post-transplantation and induced CD4+Foxp3+ Tregs in vitro as well. Importantly, depleting the Tregs abrogated the extension of skin allograft survival induced by shikonin. It also decreased the frequencies of CD8+CD44highCD62Llow effector T cells and CD11c+CD80+/CD11c+CD86+ mature DCs after transplantation. Moreover, we found that shikonin inhibited the proliferation of T cells in vitro and suppressed their mTOR signaling. It also reduced the gene expression of pro-inflammatory cytokines, including IFNγ, IL-6, TNFα, and IL-17A, while increasing the gene expression of anti-inflammatory mediators IL-10, TGF-β1, and indoleamine-2, 3-dioxygenase (IDO) in skin allografts. Further, shikonin downregulated IDO protein expression in skin allografts and DCs in vitro. Taken together, shikonin inhibits allograft rejection via upregulating CD4+Foxp3+ Tregs. Thus, shikonin is a novel immunosuppressant that could be potentially used in clinical transplantation

Effects of tumor metabolic microenvironment on regulatory T cells

Recent studies have shown that on one hand, tumors need to obtain a sufficient energy supply, and on the other hand they must evade the body’s immune surveillance. Because of their metabolic reprogramming characteristics, tumors can modify the physicochemical properties of the microenvironment, which in turn affects the biological characteristics of the cells infiltrating them. Regulatory T cells (Tregs) are a subset of T cells that regulate immune responses in the body. They exist in large quantities in the tumor microenvironment and exert immunosuppressive effects. The main effect of tumor microenvironment on Tregs is to promote their differentiation, proliferation, secretion of immunosuppressive factors, and chemotactic recruitment to play a role in immunosuppression in tumor tissues. This review focuses on cell metabolism reprogramming and the most significant features of the tumor microenvironment relative to the functional effects on Tregs, highlighting our understanding of the mechanisms of tumor immune evasion and providing new directions for tumor immunotherapy