A highly sensitive, long-time stable Ag/AgCl ultra-micro sensor for in situ monitoring chloride ions inside the crevice using SECM.

Tracking the variation of Cl- timely within the crevice is of great significance for comprehending the dynamic mechanism of crevice corrosion. The reported chloride ion selective electrodes are difficult to realize the long-time Cl- detection inside the confined crevice, due to their millimeter size or a relative limited lifespan. For this purpose, an Ag/AgCl ultra-micro sensor (UMS) with a radius of 12.5 µm was fabricated and optimized using laser drawing and electrodeposition techniques. Results show the AgCl film's structure is significantly impacted by the deposited current density, and further affects the linear response, life span and stability of Ag/AgCl UMS. The UMS prepared at current density of 0.1 mA/cm2 for 2 h shows a rapid response (several seconds), excellent stability and reproducibility, strong acid/alkali tolerance, sufficient linearity (R2 > 0.99), and long lifespan (86 days). Moreover, combined with the potentiometric mode of scanning electrochemical microscope (SECM), the Ag/AgCl UMS was successfully applied to monitor the in-situ radial Cl- concentration in micro-regions inside a 100 µm gap of stainless steel. The findings demonstrated that there was obvious radial difference in Cl- concentration inside the crevice, where the fastest rise in Cl- concentration was at the opening. The proposed method which combines the UMS with SECM has attractive practical applications for microzone Cl- monitoring in real time inside crevice. It may further promote the study of other localized corrosion mechanism and the development of microzone ions detection method.

Multifunctional modified polyvinyl alcohol: A powerful biomaterial for enhancing bioreactor performance in nitrate, Mn(II) and Cd(II) removal.

The co-existence of multiple pollutants in wastewater such as nitrate and heavy metal, is of high concern due to the potential environmental impact. In this study, a novel biomaterial PPy@Fe3O4/PVA was synthesized as a multifunctional bacteria immobilized carrier, to enhance simultaneous denitrification, Cd(II) and Mn(II) removal efficiency in bioreactor environments. The morphology and main components of the PPy@Fe3O4/PVA material were characterized by SEM and XRD. Using PPy@Fe3O4/PVA as a carrier, the maximum removal efficiencies for nitrate (0.207 mg L-1·h-1), Mn(II) (90.98%) and Cd(II) (98.78%) were increased by 27.05%, 30.27%, and 16.48%, respectively, compared to in the absence of PPy@Fe3O4/PVA. Regeneration experiments were performed, demonstrating the excellent stability and reusability of the PPy@Fe3O4/PVA material. Furthermore, effects of key factors were investigated on the performance of the PPy@Fe3O4/PVA bioreactor in simultaneous denitrification, Mn(II) and Cd(II) removal. Experimental results indicate that the highest nitrate, Mn(II) and Cd(II) removal efficiencies were obtained under the conditions of HRT of 10 h, initial Mn(II) concentration of 40 mg/L and initial Cd(II) concentration of 10 mg/L. Gas chromatography analysis indicated that N2 was the mainly final gaseous product. Moreover, the bioreactor community diversity was markedly influenced by the initial concentration of Cd(II) and Pseudomonas sp. H117 played a primary role in the process of simultaneous denitrification, Mn(II) and Cd(II) removal.

CTHRC1 promotes M2-like macrophage recruitment and myometrial invasion in endometrial carcinoma by integrin-Akt signaling pathway.

The infiltration of tumor-associated macrophages (TAMs) is associated with tumor progression and poor prognosis in endometrial cancer (EC). Collagen triple helix repeat containing 1 (CTHRC1), a secreted ECM protein, has been reported to have important roles in promoting cancer invasion and metastasis, but the functional role of CTHRC1 and its association with TAMs in EC remain unclear. Here we report that, in EC patients, CTHRC1 expression was up-regulated in endometrial cancer tissues compared with normal endometrium (P < 0.0001), and is positively correlated with tumor grade and depth of myometrial invasion (P = 0.024 and P = 0.0002, respectively). Meanwhile, CTHRC1 expression was positively correlated with an increased number of infiltrating TAMs, especially M2-like TAMs (P = 0.003, P = 0.001). In the tumor microenvironment of EC, CTHRC1 not only promoted myometrial invasion by interacting with Integrin ß3-Akt signaling pathway, but also promoted infiltration of M2-like TAMs by upregulating Fractalkine chemokine receptor (CX3CR1) expression in macrophages. Changing levels of recombinant CTHRC1 protein (rCTHRC1) promoted tumor migration and invasion via enhancing macrophage recruitment in vitro. In summary, our findings eventually provided a novel role for CTHRC1 in remodeling the tumor immune microenvironment to promote tumor metastasis in EC patients.

PRASA: an integrated web server that analyzes protein interaction types.

This work presents the Protein Association Analyzer (PRASA) (http://zoro.ee.ncku.edu.tw/prasa/) that predicts protein interactions as well as interaction types. Protein interactions are essential to most biological functions. The existence of diverse interaction types, such as physically contacted or functionally related interactions, makes protein interactions complex. Different interaction types are distinct and should not be confused. However, most existing tools focus on a specific interaction type or mix different interaction types. This work collected 7234058 associations with experimentally verified interaction types from five databases and compiled individual probabilistic models for different interaction types. The PRASA result page shows predicted associations and their related references by interaction type. Experimental results demonstrate the performance difference when distinguishing between different interaction types. The PRASA provides a centralized and organized platform for easy browsing, downloading and comparing of interaction types, which helps reveal insights into the complex roles that proteins play in organisms.

YGA: identifying distinct biological features between yeast gene sets.

The advance of high-throughput experimental technologies generates many gene sets with different biological meanings, where many important insights can only be extracted by identifying the biological (regulatory/functional) features that are distinct between different gene sets (e.g. essential vs. non-essential genes, TATA box-containing vs. TATA box-less genes, induced vs. repressed genes under certain biological conditions). Although many servers have been developed to identify enriched features in a gene set, most of them were designed to analyze one gene set at a time but cannot compare two gene sets. Moreover, the features used in existing servers were mainly focused on functional annotations (GO terms), pathways, transcription factor binding sites (TFBSs) and/or protein-protein interactions (PPIs). In yeast, various important regulatory features, including promoter bendability, nucleosome occupancy, 5'-UTR length, and TF-gene regulation evidence, are available but have not been used in any enrichment analysis servers. This motivates us to develop the Yeast Genes Analyzer (YGA), a web server that simultaneously analyzes various biological (regulatory/functional) features of two gene sets and performs statistical tests to identify the distinct features between them. Many well-studied gene sets such as essential, stress-response, TATA box-containing and cell cycle genes were pre-compiled in YGA for users, if they have only one gene set, to compare with. In comparison with the existing enrichment analysis servers, YGA tests more comprehensive regulatory features (e.g. promoter bendability, nucleosome occupancy, 5'-UTR length, experimental evidence of TF-gene binding and TF-gene regulation) and functional features (e.g. PPI, GO terms, pathways and functional groups of genes, including essential/non-essential genes, stress-induced/-repressed genes, TATA box-containing/-less genes, occupied/depleted proximal-nucleosome genes and cell cycle genes). Furthermore, YGA uses various statistical tests to provide objective comparison measures. The two major contributions of YGA, comprehensive features and statistical comparison, help to mine important information that cannot be obtained from other servers. The sophisticated analysis tools of YGA can identify distinct biological features between two gene sets, which help biologists to form new hypotheses about the underlying biological mechanisms responsible for the observed difference between these two gene sets. YGA can be accessed from the following web pages: http://cosbi.ee.ncku.edu.tw/yga/ and http://yga.ee.ncku.edu.tw/.

AH-DB: collecting protein structure pairs before and after binding.

This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological functions. For example, copper-zinc superoxide dismutase (SOD1), which destroys free superoxide radicals in the body, undergoes a large conformational transition from an 'open' state (apo structure) to a 'closed' state (holo structure). Many studies have utilized collections of apo-holo structure pairs to investigate the conformational transitions and critical residues. However, the collection process is usually complicated, varies from study to study and produces a small-scale data set. AH-DB is designed to provide an easy and unified way to prepare such data, which is generated by identifying/mapping molecules in different Protein Data Bank (PDB) entries. Conformational transitions are identified based on a refined alignment scheme to overcome the challenge that many structures in the PDB database are only protein fragments and not complete proteins. There are 746,314 apo-holo pairs in AH-DB, which is about 30 times those in the second largest collection of similar data. AH-DB provides sophisticated interfaces for searching apo-holo structure pairs and exploring conformational transitions from apo structures to the corresponding holo structures.