Predicting Co-Author Relationship in Medical Co-Authorship Networks

Research collaborations are encouraged because a synergistic effect yielding good results often appears. However, creating and organizing a strong research group is a difficult task. One of the greatest concerns of an individual researcher is locating potential collaborators whose expertise complement his best. In this paper, we propose a method that makes link predictions in co-authorship networks, where topological features between authors such as Adamic/Adar, Common Neighbors, Jaccard''s Coefficient, Preferential Attachment, Katz_β, and PropFlow may be good indicators of their future collaborations. Firstly, these topological features were systematically extracted from the network. Then, supervised models were used to learn the best weights associated with different topological features in deciding co-author relationships. Finally, we tested our models on the co-authorship networks in the research field of Coronary Artery Disease and obtained encouraging accuracy (the precision, recall, F1 score and AUC were, respectively, 0.696, 0.677, 0.671 and 0.742 for Logistic Regression, and respectively, 0.697, 0.678, 0.671 and 0.743 for SVM). This suggests that our models could be used to build and manage strong research groups.     

Naa10p and IKKα interaction regulates EMT in oral squamous cell carcinoma via TGF‐β1/Smad pathway

Epithelial‐mesenchymal transition (EMT) has been contributed to increase migration and invasion of cancer cells. However, the correlate of Naa10p and IKKα with EMT in oral squamous cell carcinoma (OSCC) is not yet fully understood. In our present study, we found N‐α‐acetyltransferase 10 protein (Naa10p) and IκB kinase α (IKKα) were abnormally abundant in oral squamous cell carcinoma (OSCC). Bioinformatic results indicate that the expression of Naa10p and IKKα is correlated with TGF‐β1/Smad and EMT‐related molecules. The Transwell migration, invasion, qRT‐PCR and Western blot assay indicated that Naa10p repressed OSCC cell migration, invasion and EMT, whereas IKKα promoted TGF‐β1–mediated OSCC cell migration, invasion and EMT. Mechanistically, Naa10p inhibited IKKα activation of Smad3 through the interaction with IKKα directly in OSCC cells after TGF‐β1 stimulation. Notably, knockdown of Naa10p reversed the IKKα‐induced change in the migration, invasion and EMT‐related molecules in OSCC cells after TGF‐β1 stimulation. These findings suggest that Naa10p interacted with IKKα mediates EMT in OSCC cells through TGF‐β1/Smad, a novel pathway for preventing OSCC.     

Mouse DNA polymerase kappa has a functional role in the repair of DNA strand breaks

The Y-family of DNA polymerases support of translesion DNA synthesis (TLS) associated with stalled DNA replication by DNA damage. Recently, a number of studies suggest that some specialized TLS polymerases also support other aspects of DNA metabolism beyond TLS in vivo. Here we show that mouse polymerase kappa (Polκ) could accumulate at laser-induced sites of damage in vivo resembling polymerases eta and iota. The recruitment was mediated through Polκ C-terminus which contains the PCNA-interacting peptide, ubiquitin zinc finger motif 2 and nuclear localization signal. Interestingly, this recruitment was significantly reduced in MSH2-deficient LoVo cells and Rad18-depleted cells. We further observed that Polκ-deficient mouse embryo fibroblasts were abnormally sensitive to H₂O₂ treatment and displayed defects in both single-strand break repair and double-strand break repair. We speculate that Polκ may have an important role in strand break repair following oxidative stress in vivo.     

The effect of cold, acid and ethanol shocks on synthesis of membrane fatty acid, freeze-drying survival and malolactic activity of Oenococcus oeni

The effects of stress shocks on the freeze-drying viability, malolactic activity and membrane fatty acid composition of the Oenococcus oeni SD-2a cells were studied. O. oeni SD-2a cells after 2 h of stress exposure exhibited better freeze-drying viability and malolactic fermentation ability. A decrease in unsaturated fatty acids/saturated fatty acids (UFA/SFA) ratio and in the C18:1 relative concentration, and an increase in cyclopropane fatty acids (CFA) content mainly due to the increase in C19cyc11 relative concentration were observed in all stress shocked cells. There was a significant negative correlation between C19cyc11 and C18:lcis11, C16:0 in all stress shocks. The freeze-drying viability exhibited a significant positive correlation with the levels of C19cyc11 in cold and acid shocks. The only significant positive correlation between the ability of O. oeni SD-2a to conduct malic acid degradation and membrane composition existed with C14:0 in ethanol shocks. In general, freeze-drying viabilities were maximum for cells with low UFA/SFA ratio and high CFA levels, and, consequently, with low membrane fluidity. Moreover, CFA formation played a major role in protecting stress shocked cells from lyophilization. However, changes observed in membrane fatty acid composition are not enough to explain the greater freeze-drying viability of cells shocked at 8% ethanol. Thus, other mechanisms could be responsible for this increase in the bacterial resistance to lyophilization.     

iTRAQ‐based quantitative proteomic analysis reveals new metabolic pathways of wheat seedling growth under hydrogen peroxide stress

As an abundant ROS, hydrogen peroxide (H₂O₂) plays pivotal roles in plant growth and development. In this work, we conducted for the first time an iTRAQ‐based quantitative proteomic analysis of wheat seedling growth under different exogenous H₂O₂ treatments. The growth of seedlings and roots was significantly restrained by increased H₂O₂ concentration stress. Malondialdehyde, soluble sugar, and proline contents as well as peroxidase activity increased with increasing H₂O₂ levels. A total of 3 425 proteins were identified by iTRAQ, of which 157 showed differential expression and 44 were newly identified H₂O₂‐responsive proteins. H₂O₂‐responsive proteins were mainly involved in stress/defense/detoxification, signal transduction, and carbohydrate metabolism. It is clear that up‐regulated expression of signal transduction and stress/defence/detoxification‐related proteins under H₂O₂ stress, such as plasma membrane intrinsic protein 1, fasciclin‐like arabinogalactan protein, and superoxide dismutase, could contribute to H₂O₂ tolerance of wheat seedlings. Increased gluconeogenesis (phosphoenol‐pyruvate carboxykinase) and decreased pyruvate kinase proteins are potentially related to the higher H₂O₂ tolerance of wheat seedlings. A metabolic pathway of wheat seedling growth under H₂O₂ stress is presented.     

Activation of Smurf E3 Ligase Promoted by Smoothened Regulates Hedgehog Signaling through Targeting Patched Turnover

Hedgehog signaling plays conserved roles in controlling embryonic development; its dysregulation has been implicated in many human diseases including cancers. Hedgehog signaling has an unusual reception system consisting of two transmembrane proteins, Patched receptor and Smoothened signal transducer. Although activation of Smoothened and its downstream signal transduction have been intensively studied, less is known about how Patched receptor is regulated, and particularly how this regulation contributes to appropriate Hedgehog signal transduction. Here we identified a novel role of Smurf E3 ligase in regulating Hedgehog signaling by controlling Patched ubiquitination and turnover. Moreover, we showed that Smurf-mediated Patched ubiquitination depends on Smo activity in wing discs. Mechanistically, we found that Smo interacts with Smurf and promotes it to mediate Patched ubiquitination by targeting the K1261 site in Ptc. The further mathematic modeling analysis reveals that a bidirectional control of activation of Smo involving Smurf and Patched is important for signal-receiving cells to precisely interpret external signals, thereby maintaining Hedgehog signaling reliability. Finally, our data revealed an evolutionarily conserved role of Smurf proteins in controlling Hh signaling by targeting Ptc during development.     

The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers

The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.     

内陆干旱区典型旱生植物蒸腾耗水量模拟研究

内陆干旱区植物耗水量是生态恢复和水资源管理的重要依据。参照甘肃省民勤县青土湖附近气象条件、干旱区典型植物生理特征以及土壤水力特征参数,采用Tardieu-Davies模型（气孔导度模型）,计算在适宜和极限生态地下水埋深下7种典型植物生长季蒸腾耗水量,并与国内外研究成果对比,得出以下结论：适宜、极限生态地下水埋深下,7种植物生长季内平均蒸腾量分别为793、602 mm。不同植物蒸腾量差异大,适宜生态地下水位埋深下水生植物芦苇（Phragmites australis）、河岸带植被柽柳（Tamarix chinensis）蒸腾量最大,分别为1292、1147 mm;耐旱性强的荒漠植被梭梭（Haloxylon ammodendron）蒸腾量最小,为279 mm;其它植被盐节木（Halocnemum strobilaceum）（940 mm）、罗布麻（Poacynum hendersonii）（913 mm）、白刺（Nitraria tangutorum）（534 mm）、胡杨（Populus euphratica）（448 mm）蒸腾量依次减小。由适宜生态地下水埋深降低至极限生态地下水埋深时,植物蒸腾量平均减少24%。耐旱性强的梭梭、白刺减幅大,分别为53、35%;耐旱性弱的芦苇、柽柳减幅小,分别为19、13%。