Facile synthesis of magnetic metal organic frameworks for the enrichment of low‐abundance peptides for MALDI‐TOF MS analysis

In this work, core‐shell magnetic metal organic framework (MOF) microspheres were successfully synthesized by coating magnetite particles with mercaptoacetic acid and subsequent reactions with ethanol solutions of Cu(OAc)₂ and benzene‐1,3,5‐tricarboxylic acid (designated as H₃btc) alternately. The resulting Fe₃O₄@[Cu₃(btc)₂] possess strong magnetic responsiveness. We applied the novel nanocomposites in the enrichment of low‐concentration standard peptides, peptides in MYO and BSA tryptic digests and in human urine in combination with MALDI‐TOF MS analysis for the first time. In addition, the Cu₃(btc)₂ MOF shells exhibit strong affinity to peptides, thus providing a rapid and convenient approach to the concentration of low‐abundance peptides. Notably, peptides at an extremely low concentration of 10 pM could be detected by MALDI‐TOF MS after enrichment with the magnetic MOF composites. In brief, the facile synthesis and efficient enrichment process of the Fe₃O₄@[Cu₃(btc)₂] microspheres make them promising candidates for the isolation of peptides in even complex biological environments.     

Ecological risk assessment of heavy metals (Zn,Cr, Pb,As and Cu) in sediments of Dohezar River,North of Iran,Tonekabon city

Sediments of the Dohezar River in Tonekabon contain high levels of heavy metals and therefore, they were chemically analyzed to determine concentrations of these elements. In fact, this research intended to evaluate the ecological risks of the heavy metals As, Pb, Cr, Zn, and Cu in the river sediments. Contamination indices such as enrichment factor and contamination factor, potential ecological risk index for each heavy metal (Ei), and potential ecological risk index (RI) were evaluated. Considering the average concentrations of the heavy metals at all of the Stations, the maximum average for the elements was zinc and the minimum was copper. Therefore, the averages of changes in the concentrations of the elements are Zn > Cr > Pb > As > Cu. Considering calculation of the enrichment factors for the heavy metals according to the EF classification table, the maximum number of Stations (43.02%) with respect to contamination with As were in class 4(moderately severe enrichment). With respect to enrichment of Pb, Zn, Cr, and copper, the rest of the stations with 83.72, 77.91, 86.05, and 69.77%, respectively, were in class 2 (minor enrichment). Considering the high concentrations of the studied elements in the sediments of the region compared to the background value, and based on calculations related to contamination factor, arsenic with the average of 11.9 exceeded the most from the standard limit. It was followed by Pb with 2.2, zinc with 2, Cr with 1.8, and Cu with1.6 (copper exceeding the least from the standard limit). With respect to Ei (the potential ecological risk index for each heavy metal), arsenic was the element with the highest environmental risk. Moreover, with respect to RI (potential ecological risk index), most Stations were in the low-grade range (low environmental risk). This research used statistical studies on correlation coefficients and cluster analysis to find the origin of the heavy metals in the sediments of the region. The low correlation between the heavy metals in the soil can indicate they probably did not have the same source. Moreover, these elements have different geochemical behaviors due to their low correlation. Finally, the kriging method was employed to extract interpolation maps of the spatial distribution for each of the heavy metals.     

Growth and nitrogen accretion of dinitrogen-fixing Alnus glutinosa (L.) Gaertn. under elevated carbon dioxide

Short-term studies of tree growth at elevated CO₂ suggest that forest productivity may increase as atmospheric CO₂ concentrations rise, although low soil N availability may limit the magnitude of this response. There have been few studies of growth and N₂ fixation by symbiotic N₂-fixing woody species under elevated CO₂ and the N inputs these plants could provide to forest ecosystems in the future. We investigated the effect of twice ambient CO₂ on growth, tissue N accretion, and N₂ fixation of nodulated Alnus glutinosa (L.) Gaertn. grown under low soil N conditions for 160 d. Root, nodule, stem, and leaf dry weight (DW) and N accretion increased significantly in response to elevated CO₂. Whole-plant biomass and N accretion increased 54% and 40%, respectively. Delta-¹⁵N analysis of leaf tissue indicated that plants from both treatments derived similar proportions of their total N from symbiotic fixation suggesting that elevated CO₂ grown plants fixed approximately 40% more N than did ambient CO₂ grown plants. Leaves from both CO₂ treatments showed similar relative declines in leaf N content prior to autumnal leaf abscission, but total N in leaf litter increased 24% in elevated compared to ambient CO₂ grown plants. These results suggest that with rising atmospheric CO₂ N₂-fixing woody species will accumulate greater amounts of biomass N through N₂ fixation and may enhance soil N levels by increased litter N inputs.     

The development of a negative selection system for the isolation of plant temperature-sensitive auxin auxotrophs

Summary A protocol has been developed for the negative selection of plant auxotrophs using the nucleoside analogues BUdR and FUdR. The protocol was optimised using nitrogen-starved protoplast-derived cells of Nicotiana plumbaginifolia to simulate auxotrophy. The present results represent a significant improvement over previous reports in that: 1) The background of colonies escaping BUdR/FUdR kill is low and reproducible. 2) The protocol was improved to the point where background survival was 0.03% for non-starved cultures and 0.09% for auxin-starved cultures. 3) It was shown that UV irradiation decreases BUdR sensitivity of dividing cells and that this is overcome by increased exposure to BUdR. 4) Application of the method to auxin-starved haploid protoplast-derived cell suspensions resulted, for the first time, in the selection of temperature-sensitive (ts) auxin auxotrophs. 5) It could be demonstrated, for the first time, that the method in practice enriches for auxotrophs, in this case by a factor of 10 for auxin auxotrophs and at least 60 for ts auxin auxotrophs.Abbreviations BUdR 5-bromodeoxyuridine - FUdR 5-fluoro-deoxyuridine - MNNG N-methyl-N-nitro-N-nitrosoguanidine - NAA 1-naphthaleneacetic acid - BAP 6-benzylamino-purine - CFE colony forming efficiency - PE plating efficiency - ts temperature sensitive     

Designed synthesis of fluorous‐functionalized magnetic mesoporous microspheres for specific enrichment of phosphopeptides with fluorous derivatization

In this work, for the first time, perfluorinated magnetic mesoporous microspheres were designed and synthesized for the highly specific enrichment of fluorous‐derivatized phosphopeptides through the unique fluorine–fluorine interactions. The perfluorinated magnetic mesoporous microspheres were prepared through a surfactant‐mediated one‐pot approach and successfully applied to the selective extraction of fluorous‐derivatized phosphopeptides from β‐casein tryptic digest, protein mixtures, and human serum. Thanks to the hydrophilic silanol groups exposed on the surface, perfluorinated groups modified in the pore channels and the magnetic cores, the flourous‐functionalized magnetic microspheres exhibited excellent dispersibility, specificity toward fluorous‐derivatized phosphopeptides while facilitated separation procedures. The novel composites achieved a high selectivity of 1:1000 toward nonphosphorylated peptides and proved to be practicable in the enrichment of endogenous phosphopeptides in the human serum sample.     

Design and synthesis of magnetic binary metal oxides nanocomposites through dopamine chemistry for highly selective enrichment of phosphopeptides

In this work, for the first time, magnetic binary metal oxides nanocomposites which integrated Zr and Ti into one entity on an atomic scale on polydopamine coated magnetic graphene (magG/PD/(Zr‐Ti)O₄) was designed and synthesized, and applied to the enrichment of phosphopeptides. The newly prepared magG/PD/(Zr‐Ti)O₄ composites gathered the advantages of large surface area, superparamagnetism, biocompatibility and the enhanced affinity properties to phosphopeptides. MagG/PD/ZrO₂, magG/PD/TiO₂, as well as the simple physical mixture of them were introduced to compare with magG/PD/(Zr‐Ti)O₄ composites. High sensitivity (1 pg/μL or 4.0 × 10^–11 M) and selectivity (weight ratio of β‐casein and BSA reached up to 1:8000) toward phosphopeptides were also presented for magG/PD/(Zr‐Ti)O₄ composites. Additionally, mouse brain tissue was chose as the real samples to further investigate the phosphopeptides enrichment ability of this new material.     

基于ceRNA网络识别登革热诊断标志物

通过比较登革热患者和健康人群转录组数据,识别差异基因,构建失调ceRNA网络,筛选关键基因富集分析,解析潜在生物学功能,助力登革热诊断标志物的研究。从GEO数据库下载登革热外周血芯片数据,识别差异基因并进行富集分析。结合miRNA-mRNA互作数据,利用超几何算法和皮尔森相关性计算方法识别登革热失调ceRNA互作对,使用Cytoscape软件可视化ceRNA网络与模块挖掘,对网络模块进行功能富集及外部数据验证表达模式。筛选出251个差异基因,发现其富集在细胞周期等生物学通路中。经外部数据验证,网络模块基因的表达趋势与训练集数据大致相同,表明模块基因在登革热疾病中的潜在诊断效能。本研究可为确定有效的疾病诊断分子标志物提供思路。     

Large quantity cryopreservation of bovine testicular cells and its effect on enrichment of type A spermatogonia

Cryopreservation has become an integral component of any cell transplantation technique helping to overcome the issues associated with known spatial and temporal barriers between donor and recipient. The aim of this study was to develop a protocol for large quantity cryopreservation of bovine testicular germ cells. The impact of 3 different packaging methods (5 ml semen straw, 20 ml freezing bag and 1.5 ml cryovial) and varying cell densities (3 × 10⁶, 9 × 10⁶, or 18 × 10⁶ cells/ml) on the survival of testis germ cells was examined. Cells processed in 5 ml semen straws had a significantly higher viability (70.7 ± 1.2%, P < 0.05) compared to those cells in 20 ml freezing bags (46.7 ± 0.1%) or 1.5 ml cryovials (46.3 ± 2.2%). For 5 ml straws, a 20 min cooling prior to cryopreservation resulted in a higher post thaw viability (73.2 ± 0.6%) than a 10 min cooling (56.0 ± 2.2%), while the density of the cell suspension did not impact on post thaw viability. Thus cryopreservation of testicular germ cells in 5 ml straws at a density between 3 × 10⁶ and 18 × 10⁶ cells/ml in liquid nitrogen vapour for 20 min cooling appears to be a simple and practical way to preserve cells. Subsequent testing of frozen/thawed cells exhibited viable cultures and retained the ability to proliferate. The freezing protocol does not preferentially preserve type A spermatogonia. However, the cell surface properties of somatic cells appear to be affected by the freezing procedure and therefore the frozen/thawed cells are less suitable for enriching type A spermatogonia by differential plating.