Lipidomic changes during different growth stages of Nitzschia closterium f. minutissima

Ultra Performance Liquid Chromatography-Electrospray ionization-Quadrupole-Time of Flight Mass Spectrometry (UPLC-ESI-Q-TOF–MS) is a powerful lipidomic tool. In this study, we developed a UPLC/Q-TOF–MS based method to investigate the lipid metabolomic changes in different growth phases of Nitzschia closterium f. minutissima. The data classification and biomarker selection were carried out by using multivariate statistical analysis, including principal components analysis (PCA), projection to latent structures with discriminant analysis (PLS-DA), and orthogonal projection to latent structures with discriminant analysis (OPLS-DA). We discovered that the intercellular lipid metabolites were significantly different among exponential, early stationary and late stationary phases. Thirty-one lipid molecules were selected and identified as putative biomarkers, including free fatty acid, Harderoporphyrin, phosphatidylglycerol, 1,2-diacyglycerl-3-O-4′-(N,N-trimethy)-homoserine, triacylglycerol, cholesterol, sulfoquinovosyldiacylglycerol, lyso-sulfoquinovosyldiacylglycerol, monogalactosyldiacylglycerol, digalactosyldiacylglycerol and lyso-digalactosyldiacylglycerol. These lipids have been shown previously to function in energy storage, membrane stability and photosynthesis efficiency during the growth of diatoms. Further analysis on the putative biomarkers demonstrated that nitrate starvation played critical role in the transition from exponential phase to stationary phase in N. closterium. This study is the first one to explore the lipidomic changes of microalgae in different growth phases, which promotes better understanding of their physiology and ecology.     

A synthesis of methane emissions from 71 northern,temperate, and subtropical wetlands

Wetlands are the largest natural source of atmospheric methane. Here, we assess controls on methane flux using a database of approximately 19 000 instantaneous measurements from 71 wetland sites located across subtropical, temperate, and northern high latitude regions. Our analyses confirm general controls on wetland methane emissions from soil temperature, water table, and vegetation, but also show that these relationships are modified depending on wetland type (bog, fen, or swamp), region (subarctic to temperate), and disturbance. Fen methane flux was more sensitive to vegetation and less sensitive to temperature than bog or swamp fluxes. The optimal water table for methane flux was consistently below the peat surface in bogs, close to the peat surface in poor fens, and above the peat surface in rich fens. However, the largest flux in bogs occurred when dry 30‐day averaged antecedent conditions were followed by wet conditions, while in fens and swamps, the largest flux occurred when both 30‐day averaged antecedent and current conditions were wet. Drained wetlands exhibited distinct characteristics, e.g. the absence of large flux following wet and warm conditions, suggesting that the same functional relationships between methane flux and environmental conditions cannot be used across pristine and disturbed wetlands. Together, our results suggest that water table and temperature are dominant controls on methane flux in pristine bogs and swamps, while other processes, such as vascular transport in pristine fens, have the potential to partially override the effect of these controls in other wetland types. Because wetland types vary in methane emissions and have distinct controls, these ecosystems need to be considered separately to yield reliable estimates of global wetland methane release.     

Long‐term evaluation of field‐wide oriental beetle (Col., Scarabaeidae) mating disruption in blueberries using female‐mimic pheromone lures

The oriental beetle, Anomala orientalis (Waterhouse) (Col., Scarabaeidae), is the most important root‐feeding pest of blueberries and turfgrass in New Jersey, USA. Previous studies showed that mating disruption is a feasible option for oriental beetle management; however, assessing its efficiency can be challenging, and little is known on its long‐term effects. Accordingly, we conducted studies to investigate low‐dose pheromone lures equivalent to oriental beetle females (i.e. female mimics) as easy‐to‐use indicators of mating disruption success, determine the distance at which oriental beetle males respond to female‐mimic lures and assess the long‐term (3‐year) effects of mating disruption on oriental beetle populations in entire blueberry fields. Our studies showed that rubber septa baited with 0.3 μg of the oriental beetle sex pheromone (Z)‐7‐tetradecen‐2‐one attract similar numbers of males as compared with virgin females and can thus be used as a female mimic. The range of attraction of this lure was found to be also similar to virgin females and <30 m. In blueberries, mating disruption provided 87% inhibition of oriental beetle populations (trap shutdown) over a 3‐year period. Oriental beetle male captures in disrupted fields were threefold higher along the field edges than in the field interiors, indicating movement of males from nearby areas into the pheromone‐treated fields. In addition, mating disruption reduced male attraction to female‐mimic lures by 93% in all 3 years and reduced the number of larvae in sentinel potted plants in 1 of 2 years. These results show for the first time that mating disruption provides consistent long‐term field‐wide control of oriental beetle populations and that female‐mimic pheromone lures can be used as a new tool to assess oriental beetle mating disruption success.     

Rapid amplification and cloning of Tn5 flanking fragments by inverse PCR

A simple approach is described to efficiently amplify DNA sequences flanking transposon Tn5 insertions. The method involves: (i) digestion with a restriction enzyme that cuts within Tn5; (ii) self-ligation under conditions favouring the production of monomeric circles; (iii) four parallel PCR reactions using primers designed to amplify left or right flanking sequences, and to distinguish target amplicons from non-specific products. This reveals the number of Tn5 insertions and the size of flanking genomic restriction fragments, without Southern blot analysis. The amplified product contains restriction sites that facilitate cohesive-end cloning. This rapid method is demonstrated using Tn5 and Tn5-Mob tagged DNA sequences involved in albicidin biosynthesis in Xanthomonas albilineans. It is generally applicable for efficient recovery of DNA sequences flanking transposon Tn5 derivatives in insertional mutagenesis studies.     

Intratumoral heterogeneity determines discordant results of diagnostic tests for human epidermal growth factor receptor (HER) 2 in gastric cancer specimens

Accurate assessment of human epidermal growth factor receptor (HER) 2 is essential for efficient selection of patients who may benefit from therapies targeting this surface receptor (e.g., trastuzumab). Intratumoral heterogeneity of HER2 expression may potentially contribute to inaccurate assessment of HER2 status. To clarify intratumoral heterogeneity of HER2 expression and its potential clinical impact on assessment of HER2 status, we analyzed 148 endoscopic biopsy specimens and 117 excisional tumor specimens collected from 148 patients with primary gastric cancer. Specifically, we assessed HER2 protein overexpression and gene amplification using, respectively, immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). There were 28 IHC-positive cases and 25 FISH-positive cases among these 148 patients. Heterogeneous HER2 protein expression was demonstrated in 23 of 29 (79.3%) IHC-positive cases, while gene expression heterogeneity was found in 11 of 25 (44.0%) FISH-positive cases. Intratumoral heterogeneity was the main reason of discordant results between IHC and FISH or between endoscopic biopsy and excisional tumor specimens. The clinical significance and impact of intratumoral HER2 expression heterogeneity on treatment outcome in gastric cancer require further studies.     

Reverse micelle-based chemiluminescence system for quinine sulphate.

A new chemiluminescence (CL) method is proposed for the determination of quinine sulphate, which is based on the dichloromethane solvent extraction of the ion-pair complex of tetrachloroaurate (III) with quinine sulphate, and luminol CL detection in a reversed micellar medium formed by the cation surfactant cetyltrimethylammonium bromide in a dichloromethane-cyclohexane (3:7, v/v)-water (0.35 mol/L Na2CO3 buffer solution, pH 11.5). The ion-pair complex of tetrachloroaurate (III) with quinine sulphate produced an analytical CL signal when it entered the reversed micellar water pool. In optimum conditions, CL intensities are proportional to the concentrations of the studied drug over the range 0.015-10 microg/mL, with a detection limit of 1.5 ng/mL. The relative standard deviation (RSD) is 1.38% for 2.5 microg/mL quinine sulphate (n=11). The method has been applied to the determination of the studied drug in biological fluids, with satisfactory results.     

ELISA检测抗-HIV室内质控血清的制备和应用

为了提高抗-HIV的检测质量,进行室内质控以鉴别诊断试剂的质量和控制操作误差,试制了抗-HIV室内质控血清,收集抗-HIV诊断试剂盒中阳性对照血清,采用不同品牌、不同批号的诊断试剂检测后,稀释、分装成低值弱阳性,即为室内质控血清,将质控血清放不同温度下保存,考核其稳定性和精密性,并应用于两厂家各3批试剂的检测,结果试制的室内质控血清在-20℃条件下存放5个月,在4℃条件下存放29天稳定性良好,检测结果稳定,该质控血清适宜作抗-HIV检测室内质控使用。     

TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis

Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in combination with highly frequent HLA alleles to predict potential shared neoantigens across tumor patients, which would facilitate the discovery of putative targets for neoantigen-based cancer immunotherapy. TSNAdb is freely available at http://biopharm.zju.edu.cn/tsnadb.